item: #1 of 702 id: cord-102145-bi8jyz6r author: Wilson, Audrey E title: Spatial heterogeneity in resources alters selective dynamics in Drosophila melanogaster date: 2020-09-05 words: 5932 flesch: 33 summary: Across the six mutation types, there was no consistent overall pattern in purging rate between the NT, UCT, and SCT environmental treatments. We found that allele purging dynamics depended on spatial environment, however the patterns of purging rates between the environments differed across distinct deleterious mutations. keywords: environments; males; mating; mutant; mutations; purging; selection; treatment cache: cord-102145-bi8jyz6r.txt plain text: cord-102145-bi8jyz6r.txt item: #2 of 702 id: cord-102151-26lumewy author: Cox, Robert M. title: Therapeutic Targeting of Measles Virus Polymerase with ERDRP-0519 Suppresses All RNA Synthesis Activity date: 2020-09-24 words: 1800 flesch: 30 summary: In addition to its direct anti-MeV impact, the 30 insight gained in this study can therefore serve as a blueprint for indication spectrum expansion through Morbilliviruses belong to the paramyxovirus family of highly contagious respiratory RNA viruses Several cryo-electron microscopy-based reconstructions of mononegavirus polymerase proteins 100 have been reported, including structural models of PIV-5 and RSV L polymerases that are closely 101 related to MeV L (31, 32). This study informs selection of ERDRP-0519 as clinical candidate for measles therapy and identifies a previously unrecognized druggable site in mononegavirus L polymerase proteins that can silence all synthesis of viral RNA. keywords: compound; erdrp-0519; mev; mononegavirus; polymerase; rna cache: cord-102151-26lumewy.txt plain text: cord-102151-26lumewy.txt item: #3 of 702 id: cord-102156-v98vrely author: Harda, Zofia title: Loss of mu and delta opioid receptors on neurons expressing dopamine receptor D1 has no effect on reward sensitivity date: 2020-03-20 words: 7677 flesch: 48 summary: The complete loss of mu opioid receptors abolishes the rewarding effects of morphine in mice (Matthes et al., 1996) , and the reintroduction of mu receptor expression to direct pathway medium spiny neurons of the striatum is sufficient to restore morphine-conditioned place preference (Cui et al., 2014) . It has also been reported that the selective deletion of mu opioid receptors in forebrain GABAergic neurons (including those in the striatum) spares opioid-conditioned place preference but affects motivation to self-administer heroin or obtain palatable food (Charbogne et al., 2017) . keywords: cell; current; delta; effects; fig; mice; neurons; opioid; receptors; reward cache: cord-102156-v98vrely.txt plain text: cord-102156-v98vrely.txt item: #4 of 702 id: cord-102158-5xg40s4o author: Coulibali, Zonlehoua title: Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada date: 2020-03-12 words: 3321 flesch: 35 summary: Agricultural and Forest Meteorology Yield levels of potato crops: Recent achievements and future 722 prospects Prediction of soil nitrogen supply in potato fields using soil temperature and water 727 content information SA. Computers and 673 Electronics in Agriculture Site-specific multilevel 675 modeling of potato response to nitrogen fertilization Effects of soil compaction on potato growth and its 678 removal by cultivation Differentiation of potato ecosystems on 680 the basis of relationships among physical, chemical and biological soil parameters Agronomic practices An analysis of the response of sugar beet and potatoes to 685 fertilizer nitrogen and mineral soil mineral nitrogen Potato response to crop sequence and 688 nitrogen fertilization following sod breakup in a Gleyed Humo-Ferric Podzol Responses of potato (Solanum tuberosum L.) to 691 green manure cover crops and nitrogen fertilization rates Soil mineralizable nitrogen 694 and soil nitrogen supply under two-year potato rotations Italian ryegrass 697 management effects on nitrogen supply to a subsequent potato crop Effect of straw and fertilizer nitrogen management for 700 spring barley on soil nitrogen supply to a subsequent potato crop A model of the development and bulking of potatoes 703 (Solanum Tuberosum L.) keywords: crop; data; fertilization; fertilizer; models; nitrogen; optimal; potato; response; soil; tuber; yield cache: cord-102158-5xg40s4o.txt plain text: cord-102158-5xg40s4o.txt item: #5 of 702 id: cord-102178-ju826pao author: Carey, Clayton M. title: Conflicts with diarrheal pathogens trigger rapid evolution of an intestinal signaling axis date: 2020-03-30 words: 5271 flesch: 40 summary: GC-C expressing organoids that ruptured during the experiment were excluded from analysis. In order to regulate intestinal water levels GC-C must interact with endogenous guanylin and uroguanylin peptides 8 . keywords: bats; buffer; figure; human; ligand; min; organoids; peptides; sta; uroguanylin cache: cord-102178-ju826pao.txt plain text: cord-102178-ju826pao.txt item: #6 of 702 id: cord-102184-8u73adnk author: Li, Jinzhi title: Visual input into the Drosophila melanogaster mushroom body date: 2020-05-02 words: 8719 flesch: 47 summary: We have a thorough understanding of how olfactory Kenyon cells integrate input from the 470 antennal lobe: most Kenyon cells receive, on average, input from seven projection neurons and the projection neurons connecting to the same Kenyon cell share no apparent common features (Caron et al., 2013; One to three-day-old flies were used when mapping the connectivity rate between input neurons 570 and α/βp Kenyon cells. keywords: accessory calyx; bp kenyon; dorsal accessory; figure; gal4; input; kenyon cells; lines; neurons; photo cache: cord-102184-8u73adnk.txt plain text: cord-102184-8u73adnk.txt item: #7 of 702 id: cord-102189-wo9gg7nx author: Mathew, Nimitha R. title: Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses date: 2020-08-24 words: 10555 flesch: 49 summary: Bmem cells (cluster C5) were ~50/50 IgM+/class switched, while all GC clusters´ cells were dominated by IgG2b/c. IgA isotype was highly enriched both in Bmem as well as in PB in all organs, suggesting a potential preferential recruitment of these cells into the effector arm ( Fig. 1H and Fig S1C) . It is interesting to ponder the potential function(s) of early arriving Bmem cells in the lung. keywords: affinity; analysis; bcr; bmem; cells; clonal; clones; clusters; data; et al; fig; infection; memory; mice; mln; mutation; organs; single; specific; spleen cache: cord-102189-wo9gg7nx.txt plain text: cord-102189-wo9gg7nx.txt item: #8 of 702 id: cord-102199-mc6zruyx author: Toksvang, Linea Natalie title: Hepatotoxicity during 6-thioguanine treatment in inflammatory bowel disease and childhood acute lymphoblastic leukaemia: a systematic review date: 2019-01-30 words: 2384 flesch: 15 summary: Pediatr Blood Cancer 6-Thioguanine: A new old drug to procure remission in inflammatory bowel disease High variation of tioguanine absorption in patients with chronic active Crohn's disease 6-thioguanine can cause serious liver injury in inflammatory bowel disease patients 6-Thioguanine associated nodular regenerative hyperplasia in patients with inflammatory bowel disease may induce portal hypertension Treatment of inflammatory bowel disease with 6-thioguanine (6-TG): Retrospective case series from a tertiary care center Efficacy of 6-thioguanine in patients with Crohn's disease intolerant to azathioprine Biotransformation of 6-thioguanine in inflammatory bowel disease patients: A comparison of oral and intravenous administration of 6-thioguanine Lower 6-thioguanine (6-TG) levels may be as effective as higher 6-TG levels in IBD patients treated with thioguanine 6-Thioguanine in children with acute lymphoblastic leukaemia: Influence of food on parent drug pharmacokinetics and 6-thioguanine nucleotide concentrations 6-Thioguanine as an alternative therapy in inflammatory bowel disease-experience in a London district general hospital Splitting a therapeutic dose of thioguanine may avoid liver toxicity and be an efficacious treatment for severe inflammatory bowel disease: a 2-center observational cohort study Efficacy and safety of 6-thioguanine in the management of inflammatory bowel disease To evaluate the efficacy and safety of 6-thioguanine therapy in patients with inflammatory bowel disease-a London DGH experience A systematic survey evaluating 6-thioguanine-related hepatotoxicity in patients with inflammatory bowel disease Toxicity and efficacy of intensive chemotherapy for children with acute lymphoblastic leukemia (ALL) after first bone marrow or extramedullary relapse The Prevalence of Nodular Regenerative Hyperplasia in Inflammatory Bowel Disease Patients Treated with Thioguanine Is Not Associated with Clinically Significant Liver Disease Thioguanine in inflammatory bowel disease: Long-term efficacy and safety. Pediatr Blood Cancer Psychosomatic complications during treatment for ulcerative colitis Long-term follow-up of children with 6-thioguanine-related chronic hepatoxicity following treatment for acute lymphoblastic leukaemia Variceal hemorrhage in a patient with ulcerative colitis treated with 6-thioguanine Acute sinusoidal obstruction syndrome after 6-thioguanine therapy for Crohn's disease Thioguanine treatment-related sinusoidal obstruction syndrome in 2 children MRI Patterns in a Case of 6-Thioguanine-Related Hepatic Sinusoidal Obstruction Syndrome Safe 6-thioguanine therapy of a TPMT deficient Crohn's disease patient by using therapeutic drug monitoring Veno-occlusive disease of the liver associated with thiopurines in a child with acute lymphoblastic leukemia Pharmacokinetics of 6-thioguanine and 6-mercaptopurine combination maintenance therapy of childhood ALL: Hypothesis and case report The case of colitis ulcerosa -Diagnostic and therapeutic difficulties Hepatotoxicity associated with 6-thioguanine therapy for Crohn's disease Liver venoocclusive disease (VOD) in a patient given 6-thioguanine for crohn's disease Early nodular hyperplasia of the liver occurring with inflammatory bowel diseases in association with thioguanine therapy Safety of Tioguanine During Pregnancy in Inflammatory Bowel Disease Thioguanine-induced symptomatic thrombocytopenia On the limitation of 6-tioguaninenucleotide monitoring during tioguanine treatment Thioguanine use in inflammatory bowel disease: 13 year experience in a tertiary centre Toxicity of 6-thioguanine: no hepatotoxicity in a series of IBD patients treated with longterm, low dose 6-thioguanine. keywords: 6tg; acute; bowel; disease; hepatotoxicity; patients; thioguanine cache: cord-102199-mc6zruyx.txt plain text: cord-102199-mc6zruyx.txt item: #9 of 702 id: cord-102206-mb0qcd0b author: Seymour, Elif title: Configurable Digital Virus Counter on Robust Universal DNA Chips date: 2020-10-22 words: 5918 flesch: 48 summary: As we improved SP-IRIS to develop it as a robust POC diagnostic platform, we focused on optimizing virus capture efficiency of antibody microarray chips, one of the most important factors that affect assay sensitivity in solid-phase immunoassays. Antibody spots were ~150 μm in diameter. keywords: antibody; cartridge; chip; detection; dna; ebov; iris; spots; surface; virus cache: cord-102206-mb0qcd0b.txt plain text: cord-102206-mb0qcd0b.txt item: #10 of 702 id: cord-102219-d3gkfo7s author: Perzel Mandell, Kira A. title: Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex date: 2019-10-30 words: 5039 flesch: 41 summary: Previously, many studies of brain DNA methylation have used the Illumina Infinium® HumanMethylation450 BeadChip (450k) and more recent Infinium MethylationEPIC (850k) microarray technologies. This corresponds to 30x coverage of the human genome as extra reads were generated to account for the addition of PhiX. Data Processing: The raw WGBS data was processed using FastQC to control for quality of reads 12 , Trim Galore to trim reads and remove adapter content 13 , Arioc for alignment to the GRCh38.p12 genome (obtained from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.27_GRCh38.p12/GC A_000001405.27_GRCh38.p12_assembly_structure/Primary_Assembly/assembled_chromoso mes/) 14 , duplicate alignments were removed with SAMBLASTER 15 , and the Bismark methylation extractor to extract methylation data from the sequencing data 16 . keywords: age; brain; cpgs; data; development; dmrs; dnam; gene; methylation; sex; sites cache: cord-102219-d3gkfo7s.txt plain text: cord-102219-d3gkfo7s.txt item: #11 of 702 id: cord-102226-aioqogaw author: Chiu, Elliott S. title: Presence of endogenous viral elements negatively correlates with FeLV susceptibility in puma and domestic cat cells date: 2020-06-24 words: 4160 flesch: 41 summary: We demonstrated that puma fibroblasts are more permissive to FeLV than domestic cat cells, and domestic cat FeLV restriction was highly related to enFeLV LTR copy number. Here, we evaluate FeLV infection of puma (P. concolor) and domestic cat cells in vitro and in 79 situ to examine the susceptibility of endemic and novel hosts to FeLV infection with respect to 80 enFeLV to provide further evaluation of this relationship. keywords: antigen; cat; cats; cells; copy; enfelv; felv; ltr; puma; virus cache: cord-102226-aioqogaw.txt plain text: cord-102226-aioqogaw.txt item: #12 of 702 id: cord-102231-cquxqbc2 author: Martinez, Xavier title: FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments date: 2020-08-28 words: 3468 flesch: 40 summary: To illustrate the sharing of such visual experiences, we have prepared four typical datasets depicted in Figure 2 and Figure 3 ): a simple structural view, a collection of small molecules binding to a viral protein, an MD trajectory and a bioinformatics sample with conservation as well as mutation data. key: cord-102231-cquxqbc2 authors: Martinez, Xavier; Baaden, Marc title: FAIR sharing of molecular visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.27.270140 sha: doc_id: 102231 cord_uid: cquxqbc2 Motivated by the current Covid-19 pandemic that has spurred a substantial flow of structural data we describe how molecular visualization experiences can be used to make these datasets accessible to a broad audience. keywords: covid-19; data; example; experiences; figure; sharing; software; visualization cache: cord-102231-cquxqbc2.txt plain text: cord-102231-cquxqbc2.txt item: #13 of 702 id: cord-102257-da4zn49x author: Almodaresi, Fatemeh title: Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index date: 2020-08-12 words: 13689 flesch: 51 summary: The process of finding the segment on the reference that is most similar to the query read, and therefore most likely to be the source of the fragment from which the read was drawn, is known as read mapping or read alignment. The main goal in read alignment is to find alignments of contiguous sub-string of the underlying reference that yields a minimum edit distance (or maximum alignment score) between the read and the reference sequence at the alignment position. keywords: abundance; alignment; bowtie2; cpm; debga; end; index; mems; mode; puffaligner; read; reference; samples; score; sequence; star; tools cache: cord-102257-da4zn49x.txt plain text: cord-102257-da4zn49x.txt item: #14 of 702 id: cord-102270-rfhtlodc author: Azhar, Mohd. title: Rapid, field-deployable nucleobase detection and identification using FnCas9 date: 2020-04-21 words: 3978 flesch: 40 summary: Although FELUDA results can be precisely determined by agarose or capillary electrophoresis, we envisioned fluorescence or chemiluminescence as alternate end-point readouts to expand the scope of devices that can suit FELUDA based detection. In recent times, CRISPR based detection of nucleic acids has provided an economical and quicker alternative to sequencing-based platforms which are often difficult to implement in the field. keywords: cleavage; crispr; detection; dna; feluda; figure; fncas9; pam; reaction; sca cache: cord-102270-rfhtlodc.txt plain text: cord-102270-rfhtlodc.txt item: #15 of 702 id: cord-102279-ena1usqv author: Long, Rory K. M. title: Super Resolution Microscopy and Deep Learning Identify Zika Virus Reorganization of the Endoplasmic Reticulum date: 2020-06-23 words: 3688 flesch: 45 summary: Graphs show quantification of volume percent of NS4B, NS2B and dsRNA ER regions relative to total ER, CER or PER. 3D voxel-based visu-137 alization and quantification showed that the density of ER tubular structures in the dsRNA-positive 138 ER is higher, for both the ERmoxGFP or Sec61β-GFP ER reporters, than in the dsRNA-negative CER 139 regions of ZIKV-infected cells or the CER of mock-infected cells ( Figure 3B ). keywords: cells; cer; dsrna; ermoxgfp; figure; mock; ns2b; ns4b; zikv cache: cord-102279-ena1usqv.txt plain text: cord-102279-ena1usqv.txt item: #16 of 702 id: cord-102321-csdezu6y author: Booeshaghi, A. Sina title: Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)* date: 2020-10-14 words: 1276 flesch: 55 summary: b) Changes in ACE2 expression as determined by the fraction of ACE2 positive cells. Angiotensin-converting enzyme 2 (ACE2 ) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target UCSC Genome Browser enters 20th year An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications Analyse des infiniment petits Moutard Decrease in ACE2 mRNA expression in aged mouse lung. keywords: ace2; cell; expression cache: cord-102321-csdezu6y.txt plain text: cord-102321-csdezu6y.txt item: #17 of 702 id: cord-102324-tu804znm author: Le Sage, Valerie title: Pre-existing immunity provides a barrier to airborne transmission of influenza viruses date: 2020-06-15 words: 4365 flesch: 32 summary: As demonstrated in Figure 1 , ferrets are naturally susceptible to human H1N1pdm09 and H3N2 influenza virus infections. The primary correlate of protection against influenza virus infections has been mapped to antibodies against of the two antigenic determinants on the surface of the virus particle, glycoproteins hemagglutinin (HA) and neuraminidase (NA) (26) . keywords: exposure; ferrets; fig; h1n1pdm09; h3n2; immunity; infection; influenza; transmission; virus cache: cord-102324-tu804znm.txt plain text: cord-102324-tu804znm.txt item: #18 of 702 id: cord-102336-ex3zlq38 author: De Wijngaert, Brent title: Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date: 2020-04-14 words: 2286 flesch: 52 summary: Much of our understanding of mitochondrial DNA transcription comes from studies of yeast (S. cerevisiae) and human mtRNAPs (2, 3, 5) . Insights into transcription: structure and function of singlesubunit DNA-dependent RNA polymerases Maintenance and Expression of Mammalian Mitochondrial DNA Structural basis of mitochondrial transcription Mechanism of bacterial transcription initiation: RNA polymerase -promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis Mechanism of transcription initiation by the yeast mitochondrial RNA polymerase Structural Basis of Mitochondrial Transcription Initiation The thumb subdomain of yeast mitochondrial RNA polymerase is involved in processivity, transcript fidelity and mitochondrial transcription factor binding Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase Mutations in the yeast mitochondrial RNA polymerase specificity factor, Mtf1, verify an essential role in promoter utilization Structure of a transcribing T7 RNA polymerase initiation complex Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism Movies S1 -S3 Movie S1. keywords: dna; fig; mtf1; rna; transcription cache: cord-102336-ex3zlq38.txt plain text: cord-102336-ex3zlq38.txt item: #19 of 702 id: cord-102350-e1vc2q4j author: Yoon, Hye-Jin title: Signature of N-terminal domain (NTD) structural re-orientation in NPC1 for proper alignment of cholesterol transport: Molecular dynamics study with mutation date: 2020-06-09 words: 4979 flesch: 42 summary: Right after the cholesterol transfer from NPC2 to NTD, the alignment of cholesterol in NTD must be directed more or less to NPC2 cholesterol leaving region. [23] The mutational study, both theoretically and experimentally, may provide opportunities to gain insight into the mechanism of NPC1 cholesterol transfer process directly or indirectly. keywords: cholesterol; domain; npc1; npc2; ntd; protein; simulation; structure; transport cache: cord-102350-e1vc2q4j.txt plain text: cord-102350-e1vc2q4j.txt item: #20 of 702 id: cord-102356-knvfbuzv author: Knyazev, Sergey title: Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction date: 2020-10-08 words: 5749 flesch: 45 summary: We show that CliqueSNV can accurately assemble viral haplotypes with frequencies as low as 0.1% and maintains consistent performance across short and long bases sequencing platforms. In contrast to other haplotyping methods, CliqueSNV infers viral haplotypes by detection of clusters of statistically linked SNVs rather than through assembly of overlapping reads used with methods such as Savage (24) . keywords: cliquesnv; datasets; frequencies; frequency; haplotype; number; populations; reads; sequencing; variants cache: cord-102356-knvfbuzv.txt plain text: cord-102356-knvfbuzv.txt item: #21 of 702 id: cord-102358-kf04tra6 author: Sheffield, Lakbira title: Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila date: 2020-09-21 words: 3919 flesch: 39 summary: Rather, our data suggest that impaired tolerance in aged flies 208 could be due to differential regulation of the genes that are uniquely expressed in infected 209 young flies, uniquely expressed in infected aged flies or a combination of both. Additionally, we show that aged flies mount 111 a more robust transcriptional response to FHV than young flies, including the regulation of 112 innate immunity genes; response, which is different from the response of flies undergoing 113 aging. keywords: age; aging; drosophila; fhv; figure; flies; genes; infection cache: cord-102358-kf04tra6.txt plain text: cord-102358-kf04tra6.txt item: #22 of 702 id: cord-102364-t5bt2eb4 author: Yao, Dehui title: Human H-ferritin presenting RBM of spike glycoprotein as potential vaccine of SARS-CoV-2 date: 2020-06-08 words: 1870 flesch: 48 summary: After blocking with 5% BSA, ACE2 protein (concentration 0.5 μg/ml) was allowed to bind to the surface coated proteins for 2 h at 37C, followed by washing with washing buffer three times. We chose a short polypeptide sequence (72 amino acid) of spike glycoprotein RBM (S-RBM) based on latest 3-D cryo-EM studies of spike glycoprotein-ACE2 complex [8, 9] . keywords: ace2; cov-2; hftn; rbm; receptor; sars cache: cord-102364-t5bt2eb4.txt plain text: cord-102364-t5bt2eb4.txt item: #23 of 702 id: cord-102366-2alcsd1p author: Cheek, Martin title: Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, Critically Endangered species from Ebo, Cameroon date: 2020-10-07 words: 9039 flesch: 55 summary: Documented extinctions of plant species are increasing, e.g. Oxygyne triandra Schltr. of Southwest Region, Cameroon is now known to be globally extinct (Cheek et al., 2018c) . Two new African species of Salacia (Salacioideae, Celastraceae) Revision and new species of the African genus Mischogyne (Annonaceae) The plants of Bali Ngemba Forest Reserve, Cameroon. keywords: area; cameroon; cheek; ebo; et al; flowers; forest; gabon; gabunensis; genus; libreville; plants; pseudohydrosme; species cache: cord-102366-2alcsd1p.txt plain text: cord-102366-2alcsd1p.txt item: #24 of 702 id: cord-102367-l1u094bp author: López, María S. title: Dengue arbovirus affecting temperate Argentina province for more than a decade 2009-2020 date: 2020-08-11 words: 2633 flesch: 45 summary: The aim of this work is to perform a description of spatio-temporal fluctuations of dengue (DENV) cases from 2009 to the present in Santa Fe province. The data presented in this work provide a detailed description of dengue virus transmission for Santa Fe province by department. keywords: argentina; cases; dengue; denv; province; santa cache: cord-102367-l1u094bp.txt plain text: cord-102367-l1u094bp.txt item: #25 of 702 id: cord-102370-5uy8dq18 author: Marano, Jeffrey M. title: Rolling Circle Amplification is a high fidelity and efficient alternative to plasmid preparation for the rescue of infectious clones date: 2020-06-23 words: 4120 flesch: 48 summary: However, the titer of RCA product transfection was significantly higher than the plasmid titer in HEK293T cells (p=0.0027). 1 µl of RCA product was then used as the template for a subsequent 10 µl RCA reaction. keywords: cdna; cells; dna; mutations; plasmid; rca; rescue; transfection; virus cache: cord-102370-5uy8dq18.txt plain text: cord-102370-5uy8dq18.txt item: #26 of 702 id: cord-102376-wk70iipl author: Tausch, Simon H. title: PathoLive – Real-time pathogen identification from metagenomic Illumina datasets date: 2020-04-14 words: 6957 flesch: 41 summary: The time needed to produce results from the intermediary sequencing data was lower than 25 minutes for all output cycles. We analyzed a human serum sample from Sudan that was confirmed via PCR to contain Crimean-Congo hemorrhagic Fever Virus (CCHFV) but only shows a small amount of related reads in the corresponding Illumina sequencing data (45 out of 1,178,054 reads were reported by Andrusch et al. in 2018 (Andrusch, et al., 2018 to unambiguously belong to CCHFV). keywords: analysis; data; et al; ngs; pathogen; patholive; reads; results; sample; score; sequence; sequencing; species; time cache: cord-102376-wk70iipl.txt plain text: cord-102376-wk70iipl.txt item: #27 of 702 id: cord-102377-n57hoty4 author: Egli, Adrian title: High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters date: 2020-04-04 words: 1066 flesch: 44 summary: We combined geographical and epidemiological data with whole genome sequencing of influenza viruses at the scale of urban quarters and statistical blocks, the smallest geographic subdivisions within a city. Urban quarters with higher socioeconomic 215 scores showed a median seroprotection rate of 26.1%, whereas those with lower socioeconomic 216 scores showed a median seroprotection rate of 14.6% (p=0.05). keywords: figure; influenza; population; quarters cache: cord-102377-n57hoty4.txt plain text: cord-102377-n57hoty4.txt item: #28 of 702 id: cord-102383-m5ahicqb author: Romano, Alessandra title: Energy dynamics for systemic configurations of virus-host co-evolution date: 2020-05-15 words: 3778 flesch: 26 summary: Virus and host cell dynamics are strictly connected, and convey in virion assembly to ensure virus spread in the body. Virus and host cell dynamics are strictly connected, generating a complex dynamics that conveys in virion assembly to ensure virus spread in the body. keywords: cell; dynamics; energy; flows; host; interaction; stock; system; virus cache: cord-102383-m5ahicqb.txt plain text: cord-102383-m5ahicqb.txt item: #29 of 702 id: cord-102406-9gnbe3n1 author: González-Arias, Fabio title: Scalable Analysis of Authentic Viral Envelopes on FRONTERA date: 2020-07-06 words: 4168 flesch: 33 summary: Due to the size and chemical complexity of authentic viral envelopes, MD simulations can include millions -even hundreds of millions -of particles, particularly when the physiological solvent environment of the system is taken into account. A framework for deploying largescale analysis of MD simulation trajectories on Frontera is presented. keywords: analysis; envelope; frontera; lipid; membrane; minimization; model; parallel; simulation; viruses; vmd cache: cord-102406-9gnbe3n1.txt plain text: cord-102406-9gnbe3n1.txt item: #30 of 702 id: cord-102412-cnlvyey4 author: Tekman, Mehmet title: A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date: 2020-08-28 words: 6425 flesch: 46 summary: The rst wave of software utilities to deal with the analysis of single cell datasets were statistical packages, aimed at tackling the issue of dropout events during sequencing, which would manifest as a high prevalence of zero-entries in over 80% of the featurecount matrix. The continuing rise in single cell technologies has led to previously unprecedented levels of analysis into cell heterogeneity within tissue samples, providing new insights into developmental and differentiation pathways for a wide range of disciplines. keywords: 10x; analysis; cell; data; datasets; erent; galaxy; processing; scrna; seq; sequencing; tools; training; user; work cache: cord-102412-cnlvyey4.txt plain text: cord-102412-cnlvyey4.txt item: #31 of 702 id: cord-102444-n4vdxdhp author: Rhea, Elizabeth M. title: The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation date: 2020-07-15 words: 10260 flesch: 52 summary: WGA also had no effect on Raybiotech S1 transport ( Figure 11 , panel C). Figure 4 shows that the amount of I-S1 (Raybiotech) increased with time in the parenchymal (m = 0.187  0.016 L/gmin, r2 = 0.952, n = 9, p<0.0001) and capillary (m = 0.027  0.006 L/g-min, r2 = 0.757, n = 9, p = 0.0023) fractions, whereas it remained constant for luminal binding (r2 = 0.145) with a mean of 1.75  0.50 L/g. Wheatgerm agglutinin (WGA) is a plant lectin that facilitates uptake of many glycoproteins, including those of viruses, and crosses the BBB by the mechanism of adsorptive transcytosis 18, 37, 38Here, we used 2-way ANOVAs followed by multiple comparisons test to compare effects on WGA treatment on the two sources of S1 proteins (n = 7 for each vehicletreated group, n = 8 for WGA-treated Raybiotech group, n = 6 for WGA-treated Amsbio group). keywords: ace2; alb; bbb; blood; brain; figure; min; panel; raybiotech; serum; spleen; tissues; transport; uptake; wga cache: cord-102444-n4vdxdhp.txt plain text: cord-102444-n4vdxdhp.txt item: #32 of 702 id: cord-102449-6foh1uvn author: Bosker, Hans Rutger title: Beat gestures influence which speech sounds you hear date: 2020-07-13 words: 7607 flesch: 40 summary: Nevertheless, whether non-facial visual cues, such as beat gestures, also aid in lexical stress perception, and might even do so in the presence of auditory cues to lexical stressas in everyday conversationsis unknown. Conversely, if the audiovisual speaker produced a beat gesture on the second syllable (in orange), participants were biased to perceive the initial syllable as Multimodal Language Processing in Human Communication Speaking: From Intention to Articulation Language as a multimodal phenomenon: implications for language learning, processing and evolution The neurobiology of language beyond single-word processing Why We Should Study Multimodal Language Knowledgebased and signal-based cues are weighted flexibly during spoken language comprehension What do we mean by prediction in language comprehension? Prediction during language comprehension: Benefits, costs, and ERP components Using Language Integration of Word Meaning and World Knowledge in Language Comprehension Electrophysiology reveals semantic memory use in language comprehension Hearing lips and seeing voices Audiovisual Speech Perception and the McGurk Effect The McGurk Effect: Auditory Visual Speech Perception's Piltdown Man Forty Years After Hearing Lips and Seeing Voices: the McGurk Effect Revisited How visual cues to speech rate influence speech perception The supramodal brain: implications for auditory perception Visible Action as Utterance Fifteen ways of looking at a pointing gesture keywords: beat; duration; experiment; gesture; participants; perception; speech; stress; syllable; vowel cache: cord-102449-6foh1uvn.txt plain text: cord-102449-6foh1uvn.txt item: #33 of 702 id: cord-102451-pcuzylva author: Swoger, Maxx title: Vimentin intermediate filaments mediate cell shape on visco-elastic substrates date: 2020-09-08 words: 3912 flesch: 42 summary: The adhesive forces are expected to be smaller than the frictional slippage regime in vimentin expressing cells, resulting in increased retrograde flow and reduced cell spreading. 2 , we find that unlike substrate stiffness, small changes in substrate viscoelasticity has profound effects on how vimentin impacts cell spreading. keywords: adhesion; cell; fig; filaments; gels; spreading; stress; substrates; type; vimentin cache: cord-102451-pcuzylva.txt plain text: cord-102451-pcuzylva.txt item: #34 of 702 id: cord-102454-fqwks0rb author: Liao, Yan Shin J. title: Acid exposure impairs mucus secretion and disrupts mucus transport in neonatal piglet airways date: 2019-06-13 words: 6001 flesch: 44 summary: Several lines of evidence suggest that airway mucus is abnormal in early CF disease (5, 6) . Our previous data suggested that neonatal piglets challenged with intra-airway acid exhibit airway obstruction (22) , suggesting defects in mucus secretion, production and/or transport. keywords: aceturate; acid; airway; diminazene; figure; muc5b; mucus; piglets; secretion; submucosal; transport cache: cord-102454-fqwks0rb.txt plain text: cord-102454-fqwks0rb.txt item: #35 of 702 id: cord-102458-7sssm3zk author: Milanez-Almeida, Pedro title: Blood gene expression-based prediction of lethality after respiratory infection by influenza A virus in mice date: 2020-10-27 words: 4637 flesch: 29 summary: Briefly, to be considered for inclusion in the signature of lethality, on days 1 to 3 after infection genes had to be differentially expressed (DE) , in comparison to PBS-treated animals, in the lungs of lethally infected mice but not DE in the lungs of non-lethally infected animals (see Fig. 1 and Methods for more details) (13, 22, 23) . By day four, however, DE of all 9 positive control of infection genes could be detected in the blood of animals infected with 1 LD50 PR8 (Fig. S5c) , likely reflecting the spread of PR8 in the lungs and evolving host immunity. keywords: blood; data; genes; iav; infection; influenza; lethal; lethality; mice; model cache: cord-102458-7sssm3zk.txt plain text: cord-102458-7sssm3zk.txt item: #36 of 702 id: cord-102463-d440jsek author: Eguchi, Raphael R. title: IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation date: 2020-08-10 words: 5165 flesch: 39 summary: eLife Critical assessment of methods of protein structure prediction (CASP)-Round XIII RosettaBackrub-a web server for flexible backbone protein structure modeling and design Evaluation of protein engineering and process optimization approaches to enhance antibody drug manufacturability Predictive tools for stabilization of therapeutic proteins Post-translational Modifications of Recombinant Proteins: Significance for Biopharmaceuticals General strategy for the generation of human antibody variable domains with increased aggregation resistance We thank Sergey Ovchinnikov for helpful discourse during early phases of this project, and for contributing initial code that became part of the torsion-reconstruction loss function. To address this fundamental challenge in modeling protein structure, we explore the use of deep neural networks to infer a continuous structural space in which we can smoothly interpolate between different backbone conformations. keywords: backbone; design; distance; figure; generative; model; protein; space; structures; training; vae cache: cord-102463-d440jsek.txt plain text: cord-102463-d440jsek.txt item: #37 of 702 id: cord-102481-obig3mu1 author: Alić, Ivan title: “Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain” date: 2020-01-31 words: 10739 flesch: 45 summary: These data corroborate the notion that subtle genotypic variation in BACE2 levels may play an important role in affecting the age of dementia onset in both DS and non-DS individuals. Our data in Fig.1 suggest that anti-amyloidogenic activity of BACE2 is gene-dose dependent, and its level varies between individuals, with SNP allelic differences in BACE2 gene correlating with age of dementia onset. keywords: activity; alzheimer; amyloid; app; aβx-34; bace2; dementia; disease; dupapp; fig; ipsc; isogenic; lines; organoids; pathology; peptide; samples; secretase; supplementary; t21 cache: cord-102481-obig3mu1.txt plain text: cord-102481-obig3mu1.txt item: #38 of 702 id: cord-102486-llmfgavd author: Sprenger, Kayla G. title: Optimizing immunization protocols to elicit broadly neutralizing antibodies date: 2020-01-06 words: 9126 flesch: 45 summary: During AM, B cells proliferate, and upon induction of the activation-induced cytidine deaminase (AID) gene, mutations are introduced into the BCR at a high rate via a process known as somatic hypermutation. B cells with BCRs that bind to the Ag with higher affinity are more likely to internalize Ag. keywords: ags; binding; bnab; breadth; cells; conserved; fig; frustration; immunization; residues cache: cord-102486-llmfgavd.txt plain text: cord-102486-llmfgavd.txt item: #39 of 702 id: cord-102498-km03fnc4 author: Kinaneh, Safa title: Identification, Localization and Expression of NHE Isoforms in the Alveolar Epithelial Cells date: 2020-09-03 words: 1811 flesch: 50 summary: We 172 performed western blot to evaluate NHE8 protein expression in lungs, one (CHF-1w) 173 and four (CHF-4w) weeks following ACF procedure, as compared to sham operated 174 rats. Western blotting to isolated 227 basolateral membranes of AEC was negative for NHE8 expression (Fig. 2D) . keywords: alveolar; expression; nhe8; rats cache: cord-102498-km03fnc4.txt plain text: cord-102498-km03fnc4.txt item: #40 of 702 id: cord-102502-hroxg2u1 author: Megremis, Spyridon title: Microbial and autoantibody immunogenic repertoires in TIF1γ autoantibody positive dermatomyositis date: 2020-03-26 words: 8452 flesch: 39 summary: Overall, we demonstrate that plasma from anti-TIF1 DM patients contain a higher number of microbial epitopes per species and against a wider microbial repertoire. Ig repertoire sequence overlap determined that only 0.65% of DM epitope set were present in healthy controls (fold-change (FC) values of >=5x to 546x abundance vs HC individuals) while 6.44% of healthy epitope set was retained in the DM group (FC values of >=5.3x to 1240x vs DM) (Fig. S1F ). keywords: autoantibodies; dermatomyositis; enrichment; epitope; figure; microbial; ngs; number; p20; patients; proteins; species; trim; viral; viruses cache: cord-102502-hroxg2u1.txt plain text: cord-102502-hroxg2u1.txt item: #41 of 702 id: cord-102504-d840uu3e author: Hass, Kenneth N. title: Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection (IMPACT) System for Rapid Viral DNA Sensing date: 2020-03-20 words: 4437 flesch: 49 summary: 27, 28 One of the main advantages of the IMPACT chip compared to traditional CRISPR assays is its ability to limit the background caused by dye-quencher probes, which is typically seen in CRISPR detection in the liquid state and needs to be designed around to lower the detection limit. Therefore, we used 3 hrs incubation to prepare the IMPACT chip for solid phase CRISPR detection. keywords: channel; chip; crispr; detection; dna; fluorescence; probe; reporter; surface; target cache: cord-102504-d840uu3e.txt plain text: cord-102504-d840uu3e.txt item: #42 of 702 id: cord-102505-g37ti2jj author: Schaworonkow, Natalie title: EEG-triggered TMS reveals stronger brain state-dependent modulation of motor evoked potentials at weaker stimulation intensities date: 2018-01-22 words: 4666 flesch: 37 summary: Objective We further characterize the effect of µ-rhythm phase on the MEP input-output (IO) curve by measuring the degree of excitability modulation across a range of stimulation intensities. Results MEP amplitude is modulated by µ-phase across a wide range of stimulation intensities, with larger MEPs at the surface negative peak. keywords: brain; eeg; intensities; intensity; max; mep; participants; peak; phase; stimulation; trials cache: cord-102505-g37ti2jj.txt plain text: cord-102505-g37ti2jj.txt item: #43 of 702 id: cord-102511-7zgd45fl author: Khodakov, Dmitriy title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 words: 4292 flesch: 39 summary: There are patents pending on the Donut PCR chip and Donut PCR instrument presented in this work. key: cord-102511-7zgd45fl authors: Khodakov, Dmitriy; Li, Jiaming; Zhang, Jinny X.; Zhang, David Yu title: Donut PCR: a rapid, portable, multiplexed, and quantitative DNA detection platform with single-nucleotide specificity date: 2020-05-05 journal: bioRxiv DOI: 10.1101/2020.04.24.058453 sha: doc_id: 102511 cord_uid: 7zgd45fl Current platforms for molecular analysis of DNA markers are either limited in multiplexing (qPCR, isothermal amplification), turnaround time (microarrays, NGS), quantitation accuracy (isothermal amplification, microarray, nanopore sequencing), or specificity against single-nucleotide differences (microarrays, nanopore sequencing). keywords: amplification; chamber; chip; dna; donut; fig; human; instrument; pcr; platform; reaction; snp cache: cord-102511-7zgd45fl.txt plain text: cord-102511-7zgd45fl.txt item: #44 of 702 id: cord-102530-wetqqt2i author: Brandell, Ellen E. title: The rise of disease ecology date: 2020-07-17 words: 2709 flesch: 32 summary: As with 295 emergent topics, our topic detection was sensitive to detecting changes in frequency over time, have remained prominent foci of disease ecology, whereas an increase in a priori selected topics such as emerging infectious diseases, climate change, and effects of biodiversity loss 341 emphasize how this expanding field has grown to meet global health crises and priorities. At the same time, infrastructure has developed around disease ecology, such as a 48 specialized National Science Foundation and National Institutes of Health funding program and 49 conference series (Scheiner & Rosenthal 2004) , which have helped to direct research effort and 50 create networks amongst researchers. keywords: articles; disease; ecology; gender; literature; research; topic; women cache: cord-102530-wetqqt2i.txt plain text: cord-102530-wetqqt2i.txt item: #45 of 702 id: cord-102551-8igfuaw2 author: Boonyaratanakornkit, Jim title: Protective Antibodies Against Human Parainfluenza Virus Type 3 (HPIV3) Infection date: 2020-10-30 words: 8154 flesch: 43 summary: In the circulating peripheral blood of healthy individuals, the frequency of HPIV3 neutralizing B cells was only 2% of HPIV3 preFspecific B cells. preF-binding B cells sorted from tonsils produced HPIV3 neutralizing antibodies, as compared to 5% from the spleen and 2% from peripheral blood (Fig. 3b) . keywords: antibodies; antibody; binding; buffer; cells; e12; fab; fig; hpiv3; human; infection; monoclonal; pi3; pref; rsv; thermo; virus cache: cord-102551-8igfuaw2.txt plain text: cord-102551-8igfuaw2.txt item: #46 of 702 id: cord-102555-vnmc9ii8 author: Araki, Takuma title: Sphingobium sp. SYK-6 syringate O-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR date: 2020-07-28 words: 2174 flesch: 31 summary: In this study, we clarified the regulatory system of SA catabolism in SYK-6 by 117 identifying and characterizing an IclR-type transcriptional regulator, DesX, which 118 regulates desA transcription. pSDA1_F pSDA1_R pSDA2_F pSDA2a_F pSDA2b_F pSDA2c_F pSDA2_R pSDA3_F pSDA3_R pSDA4_F pSDA4_R p16bdX_F p16bdX_R desAp1_F desAp1_R desAp2_F desAp2_R desAp3_F desAp3_R desAp4_F desAp4_R desAp5_F desAp5_R desAp6_F desAp7_F desAp7_R desAp8_F desAp8_R GCGCAGAACCTTACCAACGT AGCCATGCAGCACCTGTCA GCCTTCGCCTTCCTCAACTA CACCGGAACCCACTGCTT GCTCTCCGACACGATGATCA ACGTACTGCTTCGCCTTGTTG TTTCGAGCATTATTCGCATTTC TCCGCAGGCGAATATTCCT CCGGTGGAACGGGAAGA CCACGCCACGTTGTTCAC GACATGCTGTGGCAGATGTG CGCATCTGCCGCTCATAC CAGAAGGTGGACTCGTCGT AGGATATCGAGCGTGCG TGACGTACGACAATGCGGAA TGACGCCTCCATCATTCTCG ATGATCCGCGTCTTCTCGTC ATGAGTCACTCGCCTTCCA TCAGCACCGGCATTCACTT GCATCGATGAGGGCATCCAT CCGACGAGGTTGAACTGGTT TCATAATCCGCCCAGGGAC GACGTCACCATGGGAAGCTTGACACGATCTACCTGCGCA CCTGCAGGATATCTGGATCCTCCTCGTGGGACTGGTCAT Carbon balance in terrestrial detritus Lignins: natural polymers from oxidative coupling of 518 4-hydroxyphenyl-propanoids Lignin biosynthesis Lignin biosynthesis and structure A field of dreams: Lignin valorization into chemicals, materials, fuels, 523 and health-care products Opportunities and challenges 525 in biological lignin valorization Genetic and biochemical investigations on bacterial catabolic 527 pathways for lignin-derived aromatic compounds Bacterial 529 catabolism of lignin-derived aromatics: new findings in a recent decade: update on bacterial lignin 530 catabolism Engineered microbial production of 2-pyrone-4,6-dicarboxylic acid from 533 lignin residues for use as an industrial platform chemical Glucose-free cis,cis-muconic acid production via new metabolic designs corresponding to the 536 heterogeneity of lignin Development of the production of 2-pyrone-4,6-dicarboxylic acid from 539 lignin extracts, which are industrially formed as by-products, as raw materials The protocatechuate 4,5-cleavage pathway: overview and new findings Genetic and biochemical 613 characterization of a 2-pyrone-4,6-dicarboxylic acid hydrolase involved in the protocatechuate 614 4,5-cleavage pathway of Sphingomonas paucimobilis SYK-6 Identification of three alcohol dehydrogenase genes involved in the 617 stereospecific catabolism of arylglycerol-β-aryl ether by Sphingobium sp. strain SYK-6 DdvK, a novel major facilitator 620 superfamily transporter essential for 5,5'-dehydrodivanillate uptake by Sphingobium sp A rapid and sensitive method for the quantitation of microgram quantities of 623 protein utilizing the principle of protein-dye binding Cloning and expression of Pseudomonas paucimobilis SYK-6 genes involved in the degradation of 626 vanillate and protocatechuate in P. putida Use of bacteriophage T7 RNA polymerase to direct selective 628 high-level expression of cloned genes Improved M13 phage cloning vectors and host strains: 630 nucleotide sequences of the M13mp18 and pUC19 vectors ZAP: a bacteriophage λ expression vector with 632 in vivo excision properties Small mobilizable 634 multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection 635 of defined deletions in the chromosome of Corynebacterium glutamicum Improved 637 broad-host-range RK2 vectors useful for high and low regulated gene expression levels in 638 gram-negative bacteria D666-D675. keywords: desa; desx; fig; lignin; study; syk-6; transcriptional; type cache: cord-102555-vnmc9ii8.txt plain text: cord-102555-vnmc9ii8.txt item: #47 of 702 id: cord-102565-egtbzhg7 author: Richards, Gareth title: Assortative Mating, Autistic Traits, Empathizing, and Systemizing date: 2020-10-28 words: 5449 flesch: 27 summary: With excellent attention to detail, and the ability to remain focussed on repetitive tasks, autistic people often have an aptitude for working in Science, Technology, Engineering, and Mathematics (STEM) industries (Baron- Cohen et al., 1997 These findings may therefore be informative regarding why autism is associated with interest and aptitude for STEM (Baron- Cohen et al., 1997 Baron-Cohen, Wheelwright, Skinner, et al., 2001; Ruzich et al., 2015; Wei et al., 2013) , and why children in geographical regions enriched with STEM industry are at elevated likelihood of developing the condition (Roelfsema et al., 2012) . keywords: autism; autistic; couple; et al; mating; scores; systemizing; traits cache: cord-102565-egtbzhg7.txt plain text: cord-102565-egtbzhg7.txt item: #48 of 702 id: cord-102570-lpwwlrqm author: Fenn, Gareth D. title: Crystallization and structure of ebselen bound to cysteine 141 of human inositol monophosphatase (IMPase) date: 2020-08-18 words: 3435 flesch: 54 summary: Here we present the crystallization and first structure of human IMPase covalently complexed with ebselen, a 1.47Å crystal structure (PDB entry 6ZK0). Structures of IMPase have been published with a variety of ligands, including a structure of human IMPase with the lithium mimetic L-690,330 keywords: cys141; ebselen; impase; inositol; site; structure cache: cord-102570-lpwwlrqm.txt plain text: cord-102570-lpwwlrqm.txt item: #49 of 702 id: cord-102588-vpu5w9wh author: Le, Trang T. title: treeheatr: an R package for interpretable decision tree visualizations date: 2020-07-10 words: 2391 flesch: 45 summary: The simplicity of decision tree models allows for clear visualizations that can be incorporated with rich additional information such as the feature space. The state-of-the-art Python's dtreeviz produces decision trees with detailed histograms at inner nodes but still draw pie chart of different classes at leaf nodes. keywords: decision; heatmap; leaf; node; tree; treeheatr cache: cord-102588-vpu5w9wh.txt plain text: cord-102588-vpu5w9wh.txt item: #50 of 702 id: cord-102595-3lbrfsrh author: Adam, Kirsten C.S. title: Steady-state visually evoked potentials and feature-based attention: Pre-registered null results and a focused review of methodological considerations date: 2020-10-13 words: 9079 flesch: 42 summary: To further understand the lack of SSVEP attention effect, we performed additional non-pre-430 registered control analyses. We likewise found null attention effects when 573 analyzing only accurate trials ( Figure S11) . keywords: attend; attention; color; cue; effect; feature; frequency; participants; ssvep; target; task; trial cache: cord-102595-3lbrfsrh.txt plain text: cord-102595-3lbrfsrh.txt item: #51 of 702 id: cord-102608-1ilforzm author: Litviňuková, Monika title: Cells and gene expression programs in the adult human heart date: 2020-04-10 words: 4162 flesch: 27 summary: Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. keywords: adult; cardiac; cells; differences; disease; expression; figure; genes; heart; muscle; right; table; ventricular cache: cord-102608-1ilforzm.txt plain text: cord-102608-1ilforzm.txt item: #52 of 702 id: cord-102612-xx5l8r9e author: Kodani, Andrew title: Zika virus alters centrosome organization to suppress the innate immune response date: 2020-09-15 words: 4919 flesch: 38 summary: As ZIKV infection causes CEP63 to overaccumulate at centrosomes, we determined whether ZIKV NS3 interacts with CEP63. Immunoprecipitation of endogenous CEP63 in ZIKV-infected cells revealed that CEP63 interacts with ZIKV NS3 (Figure 3B ). To confirm the interaction of ZIKV NS3 with CEP63, we transfected cells with Myc-tagged Brazilian ZIKV NS3 and found that Myc-NS3 co-precipitated with endogenous CEP63, but not CP110, another centrosomal protein that misaccumulates at the centrosome upon ZIKV infection ( Figure 3C ). keywords: cells; centrin; centrosome; cep63; dtx4; figure; infection; mib1; ns3; tbk1; zikv cache: cord-102612-xx5l8r9e.txt plain text: cord-102612-xx5l8r9e.txt item: #53 of 702 id: cord-102613-hly07ne3 author: Danko, David title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date: 2020-05-04 words: 6556 flesch: 51 summary: Samples show distinct microbial signatures which may be used to accurately predict properties of their city of origin including population, proximity to the coast, and taxonomic profile. compared to an average of 6.01M 194 reads per sample. keywords: amr; cities; city; distance; figure; genes; number; reads; samples; species; supp; taxa; taxonomic cache: cord-102613-hly07ne3.txt plain text: cord-102613-hly07ne3.txt item: #54 of 702 id: cord-102631-a8fsr6ys author: Zeng, Zipeng title: Generation of kidney ureteric bud and collecting duct organoids that recapitulate kidney branching morphogenesis date: 2020-04-28 words: 7103 flesch: 52 summary: After centrifugation, supernatant was carefully removed and UB cells were resuspended in appropriate amount of mUBCM (Y27632 was supplemented at 10µM final concentration for the first 24 hours) by pipetting up and down gently for less than 10 times. 200μg/ml G-418 (Invitrogen, Cat. # 10131027) was applied to select for UB cells that have been successfully infected. keywords: cells; culture; data; day; fig; gfp; human; kidney; medium; organoid; wnt11 cache: cord-102631-a8fsr6ys.txt plain text: cord-102631-a8fsr6ys.txt item: #55 of 702 id: cord-102632-yazl9usb author: Lobet, Guillaume title: QuoVidi: a open-source web application for the organisation of large scale biological treasure hunts date: 2020-07-01 words: 4497 flesch: 60 summary: Students living in an urban area were potentially at a disadvantage compared to students in the countryside. This is why we created a second module in the interface, the photo quiz, which allowed students to learn from photos contributed by other students, without having to submit their own photos. keywords: activity; animal; learning; pictures; platform; quests; students; web cache: cord-102632-yazl9usb.txt plain text: cord-102632-yazl9usb.txt item: #56 of 702 id: cord-102634-0n42h72w author: Willforss, Jakob title: OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons date: 2020-10-22 words: 5790 flesch: 39 summary: Data analysis was performed by JW and VS. OmicLoupe is implemented using R (v3.6.3) and RShiny (v1.4.0.2), using packages providing interactive visualizations: Plotly (v4.9.2.1), DT (v0.13) and packages for data visualization: ggplot2 (v3.3.0), GGally (v1.5.0), UpSetR (v1.4.0, [10] ) and dplyr (v0.8.5) for data processing. keywords: comparisons; data; datasets; features; figure; hours; omicloupe; samples; software; study cache: cord-102634-0n42h72w.txt plain text: cord-102634-0n42h72w.txt item: #57 of 702 id: cord-102661-lh7992rl author: Valentine, Charles C. title: Direct Quantification of in vivo Mutagenesis and Carcinogenesis Using Duplex Sequencing date: 2020-11-03 words: 9841 flesch: 42 summary: Errors in DNA replication as a basis of malignant changes Overview of biological mechanisms of human carcinogens Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice Overview of genotoxic carcinogens and non-genotoxic carcinogens Guidlines for Testing of Chemicals: OECD Test Guideline 488 -Transgenic Rodent Somatic and Germ Cell Gene Mutation Assays, adopted 26 Genotoxicity and Carcinogenicity Testing of Pharmaceuticals Mutation as a toxicological endpoint for regulatory decision-making A compendium of mutational signatures of environmental agents Detection of ultra-rare mutations by next-generation sequencing Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations Highthroughput sequencing in mutation detection: A new generation of genotoxicity tests? Next-generation genotoxicology: using modern sequencing technologies to assess somatic mutagenesis and cancer risk Validation of transgenic mice harboring the human prototype c-Haras gene as a bioassay model for rapid carcinogenicity testing Analysis of spontaneous and induced mutations in transgenic mice using a lambda ZAP/lacl shuttle vector Detailed review of transgenic rodent mutation assays Detecting ultralow-frequency mutations by Duplex Sequencing Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing Chemically induced mutations in a MutaMouse reporter gene inform mechanisms underlying Mapping the binding site of aflatoxin B1 in DNA: systematic analysis of the reactivity of aflatoxin B1 with guanines in different DNA sequences Mechanism of the inhibition of mutagenicity of a benzo ENU) increased brain mutations in prenatal and neonatal mice but not in the adults Efficient repair of O6-ethylguanine, but not O4 -ethylthymine or O2-ethylthymine, is dependent upon O6-alkylguanine-DNA alkyltransferase and nucleotide excision repair activities in human cells Efficient rescue of integrated shuttle vectors from transgenic mice: a model for studying mutations in vivo Other transgenic mutation assays: A new transgenic mouse mutagenesis test system using Spi-and 6-thioguanine selections The use of shuttle vectors for mutation analysis in transgenic mice and rats Mutational signatures are jointly shaped by DNA damage and repair Mutational spectra of aflatoxin B 1 in a mouse model of cancer establish biomarkers of exposure for human hepatocellular carcinoma Short title: Mutational spectra of aflatoxin B 1 in mice Transgenic mouse mutation assay systems can play an important role in regulatory mutagenicity testing in vivo for the detection of site-of-contact mutagens Detailed review paper on transgenic rodent mutation assays, series on testing and assessment whole-genome sequencing of organoid cultures The genome as a record of environmental exposure Tissue-specific mutation accumulation in human adult stem cells during life Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing Optimizing drug discovery by Investigative Toxicology: To illustrate the impact of TGR selection on mutant recovery, we plotted the functional class of all cII mutations identified by Duplex Sequencing of either genomic DNA obtained directly from mouse samples (Fig. 3A) or from a pool of 3,510 individual mutant plaques that were isolated post-selection (Fig. 3B) . keywords: assays; base; cii; dna; duplex; error; frequency; genomic; human; mouse; mutagenesis; mutant; mutations; nucleotide; rash2; samples; sequencing; tissue; urethane cache: cord-102661-lh7992rl.txt plain text: cord-102661-lh7992rl.txt item: #58 of 702 id: cord-102668-1yc38ok1 author: Siddiqui, Shoib S. title: Acidosis, Zinc and HMGB1 in Sepsis: A Common Connection Involving Sialoglycan Recognition date: 2020-07-15 words: 5404 flesch: 40 summary: So Far Targeting HMGB1 in the treatment of sepsis HMGB1, a potent proinflammatory cytokine in sepsis High mobility group 1 protein (HMG-1) stimulates proinflammatory cytokine synthesis in human monocytes Elevated serum levels of S100A8/A9 and HMGB1 at hospital admission are correlated with inferior clinical outcomes in COVID-19 patients Erythrocyte sialoglycoproteins engage Siglec-9 on neutrophils to suppress activation Selectin-mucin interactions as a probable molecular explanation for the association of Trousseau syndrome with mucinous adenocarcinomas Sepsis and Septic Shock Damage-Associated Molecular Patterns in Inflammatory Diseases DAMP-sensing receptors in sterile inflammation and inflammatory diseases Complexity of danger: the diverse nature of damage-associated molecular patterns High HMGB1 level is associated with poor outcome of septicemic melioidosis HMG-1 as a late mediator of endotoxin lethality in mice HMGB1 signals through toll-like receptor (TLR) 4 and TLR2 A critical cysteine is required for HMGB1 binding to Tolllike receptor 4 and activation of macrophage cytokine release HMGB1 and RAGE in inflammation and cancer CD24 and Siglec-10 selectively repress tissue damage-induced immune responses CD52 glycan binds the proinflammatory B box of HMGB1 to engage the Siglec-10 receptor and suppress human T cell function Occurrence of sialic acids in healthy humans and different disorders HMG-box domain stimulation of RAG1/2 cleavage activity is metal ion dependent The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies Specific Sialoforms Required for the Immune Suppressive Activity of Human Soluble CD52 A sialylated glycan microarray reveals novel interactions of modified sialic acids with proteins and viruses Human xeno-autoantibodies against a non-human sialic acid serve as novel serum biomarkers and immunotherapeutics in cancer Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays Heparan sulfate is essential for high mobility group protein 1 (HMGB1) signaling by the receptor for advanced glycation end products (RAGE) Design of anti-inflammatory heparan sulfate to protect against acetaminophen-induced acute liver failure A new group of chromatin-associated proteins with a high content of acidic and basic amino acids Emerging roles for HMGB1 protein in immunity, inflammation, and cancer HMGB1 in health and disease HMGB1 interacts with many apparently unrelated proteins by recognizing short amino acid sequences HMGB1 as biomarker and drug target The evolution of High Mobility Group Box (HMGB) chromatin proteins in multicellular animals Release of chromatin protein HMGB1 by necrotic cells triggers inflammation Tolerance, danger, and the extended family Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion The many faces of HMGB1: molecular structurefunctional activity in inflammation, apoptosis, and chemotaxis Therapeutic potential of HMGB1-targeting agents in sepsis Reversing established sepsis with antagonists of endogenous high-mobility group box 1 Identification of CD163 as an antiinflammatory receptor for HMGB1-haptoglobin complexes C1q and HMGB1 reciprocally regulate human macrophage polarization Tumor-infiltrating DCs suppress nucleic acid-mediated innate immune responses through interactions between the receptor TIM-3 and the alarmin HMGB1 T cell regulation mediated by interaction of soluble CD52 with the inhibitory receptor Siglec-10 Mutually exclusive redox forms of HMGB1 promote cell recruitment or proinflammatory cytokine release Regulation of Posttranslational Modifications of HMGB1 During Immune Responses High-mobility group box 1 protein orchestrates responses to tissue damage via inflammation, innate and adaptive immunity, and tissue repair CD52 inhibits Toll-like receptor activation of NF-κB and triggers apoptosis to suppress inflammation Alpha-1-acid glycoprotein Hernàndez Pando R. Alpha-1-acid glycoprotein, its local production and immunopathological participation in experimental pulmonary tuberculosis Detailed structural features of glycan chains derived from alpha1-acid glycoproteins of several different animals: the presence of hypersialylated, O-acetylated sialic acids but not disialyl residues Generation of monoclonal antibodies against highly conserved antigens Mechanistic insights into the protective impact of zinc on sepsis Persistent low serum zinc is associated with recurrent sepsis in critically ill patients -A pilot study Low zinc and selenium concentrations in sepsis are associated with oxidative damage and inflammation Zinc dyshomeostasis during polymicrobial sepsis in mice involves zinc transporter Zip14 and can be overcome by zinc supplementation Interleukin-6 regulates the zinc transporter Zip14 in liver and contributes to the hypozincemia of the acute-phase response The effect of physicochemical factors on the self-association of HMGB1: Thus, physiological blood pH limits interaction of HMGB1 with leukocyte receptors, suggesting natural inhibitor(s) of HMGB1 interaction in blood. keywords: acid; binding; blood; buffer; hmgb1; plasma; proinflammatory; sepsis; sialic; zinc cache: cord-102668-1yc38ok1.txt plain text: cord-102668-1yc38ok1.txt item: #59 of 702 id: cord-102691-pij32hbi author: Klein, Steffen title: Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies date: 2020-08-14 words: 8242 flesch: 46 summary: The essential function of the small hydrophobic proteins SP-B and SP-C to trigger adsorption of pulmonary surfactant lamellar bodies Identification of LBM180, a lamellar body limiting membrane protein of alveolar type II cells, as the ABC transporter protein ABCA3 ABCA3-mediated choline-phospholipids uptake into intracellular vesicles in A549 cells Structure of pulmonary surfactant membranes and films: The role of proteins and lipidprotein interactions Lamellar body ultrastructure revisited: high-pressure freezing and cryo-electron microscopy of vitreous sections Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography Focused-ion-beam thinning of frozenhydrated biological specimens for cryo-electron microscopy Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision Correlated cryofluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity Fluorescence-Based Detection of Membrane Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy Correlative cryo-electron microscopy reveals the structure of TNTs in neuronal cells Correlative cryo-light microscopy and cryo-electron tomography: from cellular territories to molecular landscapes High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers Correlated fluorescence microscopy and cryo-electron tomography of virusinfected or transfected mammalian cells Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy A selective autophagy pathway for phase separated endocytic protein deposits A continuous tumor-cell line from a human lung carcinoma with properties of type II alveolar epithelial cells Mind the gap: Micro-expansion joints drastically decrease the bending of FIB-milled cryolamellae Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments Long Term Culture of the A549 Cancer Cell Line Promotes Multilamellar Body Formation and Differentiation towards an Alveolar Type II Pneumocyte Phenotype PIE-scope, integrated cryocorrelative light and FIB/SEM microscopy Removal of subsurface fluorescence in cryoimaging using deconvolution Aberration-corrected cryoimmersion light microscopy Towards correlative super-resolution fluorescence and electron cryo-microscopy Polarized light microscopy reveals physiological and drug-induced changes in surfactant membrane assembly in alveolar type II pneumocytes Liquid-crystalline phase transitions in lipid droplets are related to cellular states and specific organelle association The surfactant lipid transporter ABCA3 is N-terminally cleaved inside LAMP3-positive vesicles Rab38 targets to lamellar bodies and normalizes their sizes in lung alveolar type II epithelial cells The structure of rat liver vault at 3.5 angstrom resolution Globally optimal stitching of tiled 3D microscopic image acquisitions Fiji: an open-source platform for biological-image analysis Automated electron microscope tomography using robust prediction of specimen movements Automated tilt series alignment and tomographic reconstruction in IMOD eC-CLEM: flexible multidimensional registration software for correlative microscopies We would like to thank Dr. Surafel Mulugeta for kindly providing the plasmid hABCA3-eGFP and to Prof. Dr. Hans-Georg Kräusslich for providing the HSAEpC cells. The fact that primary human lung cells showed less compact packing of lamellar membranes than ABCA3 overexpressing A549 cells indicates that LBs membrane spacing is variable and the LB maturation might be dependent on ABCA3 levels and its regulation in a primary or immortalized cell line. keywords: a549; abca3; cells; correlation; cryo; egfp; electron; fig; fluorescent; lamella; lbs; map; membrane; milling; organelles; signal; tem cache: cord-102691-pij32hbi.txt plain text: cord-102691-pij32hbi.txt item: #60 of 702 id: cord-102704-wfuzk2dp author: Meza, Diana K. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 words: 3185 flesch: 26 summary: Fields Virology Rabies in New Mexico 464 cavern bats Serological investigation of rabies virus neutralizing antibodies in bats captured in 469 the eastern Brazilian Amazon One Health, emerging infectious diseases and 472 wildlife: two decades of progress? This was 321 unsurprising, since virus neutralization tests are biologically dynamic systems that can be influenced 322 by many factors (e.g. variability in the humidity of the incubator, technical manipulation, light 323 condition of the microscope, variability in GFP expression in the cells) keywords: antibodies; dilution; model; neutralization; pmrffit; rabies; serum; test; virus cache: cord-102704-wfuzk2dp.txt plain text: cord-102704-wfuzk2dp.txt item: #61 of 702 id: cord-102705-mcit0luk author: Gupta, Chitrak title: Mind reading of the proteins: Deep-learning to forecast molecular dynamics date: 2020-07-29 words: 6366 flesch: 48 summary: Due to the recent success of Recurrent Neural Networks (RNN) for modeling time series data [4] , we conducted an exploratory study with RNNs to model the two new dynamically evolving MD trajectory data. Surprisingly, we find that the equilibrium MD time series is more challenging to learn, despite the non-Gaussian distribution atoms associated to the non-equilibrium MD. keywords: data; dynamics; equilibrium; fig; lead; learning; model; protein; series; sets; simulations; time cache: cord-102705-mcit0luk.txt plain text: cord-102705-mcit0luk.txt item: #62 of 702 id: cord-102720-ka95resa author: Aguilar, César title: Convergent evolution of Streptomyces protease inhibitors involving a tRNA-mediated condensation-minus NRPS date: 2020-10-27 words: 6478 flesch: 31 summary: Since this prediction suggests common structural features with previously described SPAs, such as leupeptin Kondo et al. 1969) , thiolstatin (Murao et al. 1985; Kamiyama et al. 1994) , bacithrocins (Kamiyama et al. 1994 ) and acetyl-leu-arginal Kondo et al. 1969) , it was hypothesized that livipeptin could have protease inhibitory activity. Amongst SPAs, the most widely used is the acetyl-leu/phe-arginal metabolite leupeptin, which was discovered by Umezawa and co-workers 4 more than fifty years ago Kondo et al. 1969 ). keywords: activity; bgc; coli; et al; figure; gene; leupeptin; lividans; livipeptin; protease; streptomyces; synthesis; transferase cache: cord-102720-ka95resa.txt plain text: cord-102720-ka95resa.txt item: #63 of 702 id: cord-102725-k0xhbssu author: Norwood, Jordan N. title: Intranasal Administration of Functionalized Soot Particles Disrupts Olfactory Sensory Neuron Progenitor Cells in the Neuroepithelium date: 2020-08-19 words: 4740 flesch: 44 summary: We do not know the mechanism by which oxygen functionalized soot preferentially damages GBCs. It could be that oxygen functionalized soot is more 20 prone to accumulating in the nasal epithelium (Fig. 2) (2003) DNA damage in nasal and brain tissues of canines exposed to air pollutants is associated with evidence of chronic brain inflammation and neurodegeneration. keywords: carbon; cells; et al; exposure; groups; neurons; olfactory; oxygen; particles; rearing; soot; treatment cache: cord-102725-k0xhbssu.txt plain text: cord-102725-k0xhbssu.txt item: #64 of 702 id: cord-102729-b1q7gbd6 author: Mickael, Alexandra title: Asip (Agouti-signaling protein) aggression gene regulate auditory processing genes in mice date: 2020-06-12 words: 4437 flesch: 45 summary: These observation indicates that hearing could regulating aggression behavior. We examined whether aggression behavior could be caused by social stress. keywords: aggression; analysis; asip; behavior; cells; genes; hearing; melanocortin; mice; model; receptors; role; startle cache: cord-102729-b1q7gbd6.txt plain text: cord-102729-b1q7gbd6.txt item: #65 of 702 id: cord-102734-ltuqoa2b author: Tsai, Hsiang-Yu title: Antagonistic Effects of Intraspecific Cooperation and Interspecific Competition on Thermal Performance date: 2020-05-04 words: 3937 flesch: 29 summary: We then quantified beetle breeding performance in the presence of interspecific competitors, mainly blowflies (Putman 1978; Putman 1983; Scott 1994; Sun et al. 2014) , to determine the beetle's realized TPC. When climate reshuffles competitors: a call for experimental macroecology Animal Aggregations, a Study in General Sociology Contrasting forms of competition set elevational range limits of species Ecological Niches: Linking Classical and Contemporary Approaches A chemically triggered transition from conflict to cooperation in burying beetles Influence of body temperature on food assimilation and locomotor performance in white-striped grass lizards, Takydromus wolteri (Lacertidae) Principles of Thermal Ecology: Temperature, Energy and Life Climatic predictors of temperature performance curve parameters in ectotherms imply complex responses to climate change The thermal mismatch hypothesis explains host susceptibility to an emerging infectious disease Hutchinson's duality: the once and future niche Inverse density dependence and the Allee effect Global buffering of temperatures under forest canopies Systematic variation in the temperature dependence of physiological and ecological traits Impacts of climate warming on terrestrial ectotherms across latitude Global metabolic impacts of recent climate warming Larval growth rates of the blowfly, Calliphora vicina, over a range of temperatures The role of temperature variability on insect performance and population dynamics in a warming world Direct and indirect effects of interspecific competition in a highly partitioned guild of reef fishes Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical birds Rapid adjustment of bird community compositions to local climatic variations and its functional consequences Crossing regimes of temperature dependence in animal movement Multiple stressors in a changing world: the need for an improved perspective on physiological responses to the dynamic marine environment The Hot-blooded Insects: Strategies and Mechanisms of Thermoregulation The evolution of thermal performance can constrain dispersal during range shifting Body temperature distributions of active diurnal lizards in three deserts: skewed up or skewed down? Integrating thermal physiology and ecology of ectotherms: a discussion of approaches Using field data to estimate the realized thermal niche of aquatic vertebrates Concluding remarks Mechanistic niche modelling: combining physiological and spatial data to predict species' ranges Heat accumulation and development rate of massed maggots of the sheep blowfly, Lucilia cuprina (Diptera: Calliphoridae) Resolving the paradox of environmental quality and sociality: the ecological causes and consequences of cooperative breeding in two lineages of birds Ecological transitions in grouping benefits explain the paradox of environmental quality and sociality Decoupling of behavioural and physiological thermal performance curves in ectothermic animals: a critical adaptive trait Latitudinal patterns of phenology and age-specific thermal performance across six Coenagrion damselfly species Mechanisms underpinning climatic impacts on natural populations: altered species interactions are more important than direct effects A summer carrion study of the baby pig Sus scrofa Linnaeus Ökologische untersuchungen an Necrophorus F. Zeitschrift für Morphologie und Ökologie der Tiere The role of carrion-frequenting arthropods in the decay process Carrion and Dung: the Decomposition of Animal Wastes Rates of projected climate change dramatically exceed past rates of climatic niche evolution among vertebrate species Quantifying the abundance of co-occurring conifers along Inland Northwest (USA) climate gradients Antimicrobial strategies in burying beetles breeding on carrion Field experiments on interspecific competition Competition with flies promotes communal breeding in the burying beetle, Nicrophorus tomentosus The ecology and behavior of burying beetles The ecology of cooperative breeding behaviour Can we predict ectotherm responses to climate change using thermal performance curves and body temperatures? keywords: beetles; breeding; climate; interspecific; performance; species; temperature; tpc; tpcs cache: cord-102734-ltuqoa2b.txt plain text: cord-102734-ltuqoa2b.txt item: #66 of 702 id: cord-102749-tgka0pl0 author: Tovo, Anna title: Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju date: 2020-05-01 words: 7847 flesch: 39 summary: Tested against mock microbial communities, of different level of complexity, generated in other studies (27, 45) and available online, the proposed updated version of Kaiju, Core-Kaiju, outperformed popular 16S rRNA and shotgun methods for taxonomic classification in the estimation of both the total biodiversity and taxa relative abundance distribution. Having a trustable tool for the detection of microbial biodiversity, as measured by the number of genera and their abundances, could have a fundamental impact in our knowledge of human microbial communities and could therefore lay the foundations for the identification of the main ecological properties modulating the healthy or ill status of an individual, which, in turn, could be of great help in preventing and treating diseases on the basis of the observed patterns. keywords: 16s; classification; communities; community; core; genera; kaiju; methods; microbial; number; sequencing; shotgun; taxa; taxonomic cache: cord-102749-tgka0pl0.txt plain text: cord-102749-tgka0pl0.txt item: #67 of 702 id: cord-102763-tc1z0nm9 author: Zhang, Yuan title: IgY antibodies against Ebola virus possess post-exposure protection and excellent thermostability date: 2020-05-21 words: 1770 flesch: 37 summary: Although several Ebola virus therapeutic antibodies have been reported in recent years, however, due to the poor thermal stability of mammalian antibody, their application in tropical endemic areas has been limited. The New England 452 journal of medicine New treatments for Ebola virus disease Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against 458 Antibody 461 therapeutics for Ebola virus disease. keywords: antibody; ebola; ebov; igy; virus cache: cord-102763-tc1z0nm9.txt plain text: cord-102763-tc1z0nm9.txt item: #68 of 702 id: cord-102766-n6mpdhyu author: Alam, Md. Nafis Ul title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date: 2020-06-25 words: 3202 flesch: 47 summary: It has been 90 demonstrated that RNA-Seq data can be a very promising avenue for improving knowledge on 91 RNA viruses when leveraged by tactful algorithms Viral metagenomics Third generation sequencing: technology and its potential impact on 602 evolutionary biodiversity research Virus taxonomy: the database of the International Committee on 606 Nucleic Acids Research Accelerated Profile HMM Searches BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-610 seq Data Bridger: a new framework for de novo transcriptome assembly using 612 RNA-seq data Shannon: An Information-Optimal de Novo RNA-Seq Assembler rnaSPAdes: a de novo transcriptome assembler and 616 its application to RNA-Seq data IDBA-tran: a more robust de novo de Bruijn graph assembler for 621 transcriptomes with uneven expression levels SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq 623 reads De novo assembly and analysis of RNA-seq data Full-length transcriptome assembly from RNA-Seq data without a 627 reference genome Oases: robust de novo RNA-seq assembly across the dynamic range 629 of expression levels S1 Fig. keywords: data; feature; genomes; learning; machine; models; rna; sequence; viruses cache: cord-102766-n6mpdhyu.txt plain text: cord-102766-n6mpdhyu.txt item: #69 of 702 id: cord-102770-t4zgph9k author: McComb, Scott title: Fine Molecular Tuning of Chimeric Antigen Receptors through Hinge Length Optimization date: 2020-10-30 words: 5573 flesch: 44 summary: After 24 h of T cell stimulation with beads, T cells were transduced with sdCAR-GFP lentiviral vectors (multiplicity of infection = 10) by spinfection. Briefly, lentivirus was added to T cells (1×10 6 cells/ml) and the mixture was centrifuged at 850 × g for 2 h at 32°C. keywords: antigen; car; cars; cells; egfr; fig; hinge; human; sdcar; signaling; target; targeting; tumour cache: cord-102770-t4zgph9k.txt plain text: cord-102770-t4zgph9k.txt item: #70 of 702 id: cord-102778-b1ul7zug author: Serrao, Juliet.M. title: Alfaxalone activates Human Pregnane-X Receptors with greater efficacy than Allopregnanolone: an in-vitro study with implications for neuroprotection during anesthesia date: 2020-09-06 words: 2103 flesch: 23 summary: This report is reassuring but the results of the study reported herein suggest that alfaxalone anesthesia may also be accompanied by positive effects on neuronal function mediated by PXR activation, protecting neurons from the adverse effects of surgical stress and other comorbidities commonly found in patients presenting for surgery [37] This was due to the inability to dissolve alfaxalone in water using 0.1% DMSO at concentrations higher than 50,000 nM. This result suggests that sedation and anesthesia achieved using alfaxalone may be accompanied by the effects caused by interaction of allopregnanolone with brain PXR such as stimulating the production of BDNF keywords: activation; alfaxalone; allopregnanolone; brain; pxr cache: cord-102778-b1ul7zug.txt plain text: cord-102778-b1ul7zug.txt item: #71 of 702 id: cord-102808-c7ajfvt5 author: Sundqvist, Martina title: Barbadin selectively modulates FPR2-mediated neutrophil functions independent of receptor endocytosis date: 2020-05-01 words: 5751 flesch: 27 summary: In summary, we show that Barbadin, similarly to latrunculin A, not only potentiates the ROS production induced by the different FPR2 agonists, but also resensitizes FPR2 signaling when added to FPR2 desensitized neutrophils. Collectively, these results suggest that Barbadin primes neutrophils in their response to FPR2 agonists, and the increased NADPH-oxidase activation is regulated independently of FPR2 internalization and FPR2-induced -arrestin recruitment. keywords: actin; agonist; ap2; barbadin; effect; fig; fpr2; neutrophils; production; receptor; ros cache: cord-102808-c7ajfvt5.txt plain text: cord-102808-c7ajfvt5.txt item: #72 of 702 id: cord-102809-06izdji8 author: Siddiqui, Nabil A. title: Radiolabelled Bacterial Metallophores as Targeted PET Imaging Contrast Agents for Accurate Identification of Bacteria and Outer Membrane Vesicles in vivo date: 2020-08-06 words: 5661 flesch: 35 summary: This was followed by a single i.v. administration of E. coli Nissle (5 x 10 6 cfu) 3 days before probe PET probe administration. Furthermore, when we administered 64 Cu-YbT in mice infected with live and heat-killed (90°C for 30 min) UTI89, we observed signals only from muscles harbouring live bacteria (Fig. 2d) . keywords: bacteria; coli; fig; imaging; metal; mice; omvs; pet; probe; vivo; ybt cache: cord-102809-06izdji8.txt plain text: cord-102809-06izdji8.txt item: #73 of 702 id: cord-102811-jlr4vb4u author: Baumeister, Sebastian E title: Physical activity and risk of Alzheimer’s disease: a two-sample Mendelian randomization study date: 2019-10-29 words: 2198 flesch: 32 summary: key: cord-102811-jlr4vb4u authors: Baumeister, Sebastian E; Karch, André; Bahls, Martin; Teumer, Alexander; Leitzmann, Michael F; Baurecht, Hansjörg title: Physical activity and risk of Alzheimer’s disease: a two-sample Mendelian randomization study date: 2019-10-29 journal: bioRxiv DOI: 10.1101/819821 sha: doc_id: 102811 cord_uid: jlr4vb4u Introduction Evidence from observational studies for the effect of physical activity on the risk of Alzheimer’s disease (AD) is inconclusive. Furthermore, the latter studies also have indicated that a decline in physical activity levels occurs during the subclinical or prodromal phase of dementia and that previous observational studies might have overestimated dementia risk associated with insufficient levels of physical activity as many studies were based on short follow-up times and thus may have been subject to reverse causation caused by decline in physical activity prior to the diagnosis of dementia [13] . keywords: activity; risk; studies; study cache: cord-102811-jlr4vb4u.txt plain text: cord-102811-jlr4vb4u.txt item: #74 of 702 id: cord-102823-zult69f2 author: Nguyen, Thin title: GraphDTA: Predicting drug–target binding affinity with graph neural networks date: 2020-10-02 words: 4966 flesch: 53 summary: New drugs cost US $2.6 billion to develop Drug repositioning: identifying and developing new uses for existing drugs Pharmacogenetics in drug discovery and development: a translational perspective Overcoming drug development bottlenecks with repurposing: old drugs learn new tricks A SARS-CoV-2-human protein-protein interaction map reveals drug targets and potential drug-repurposing. Large-scale comparison of machine learning methods for drug target prediction on ChEMBL Graph convolutional neural networks for predicting drug-target interactions Chemi-Net: A molecular graph convolutional network for accurate drug property prediction Convolutional neural network based on SMILES representation of compounds for detecting chemical motif Molecular graph convolutions: moving beyond fingerprints Graph convolutional networks for computational drug development and discovery Large-scale learnable graph convolutional networks Interpretable drug target prediction using deep neural representation SMILES, a chemical language and information system. keywords: affinity; drug; gcn; graph; layer; model; neural; prediction; protein; target cache: cord-102823-zult69f2.txt plain text: cord-102823-zult69f2.txt item: #75 of 702 id: cord-102835-71ome9h8 author: Levinson, Maxwell Adam title: FAIRSCAPE: A Framework for FAIR and Reproducible Biomedical Analytics date: 2020-08-15 words: 4772 flesch: 42 summary: An OpenAPI description of the interface is here: https://app.swaggerhub.com/apis/FAIRSCAPE/Evidence-Graph/0.1 The Search Service allows users to search for object metadata containing strings of interest. We used FAIRSCAPE services to analyze ten years of neonatal ICU vital signs data from over 6,000 babies with over 100 different highly comparative time series analysis (HCTSA) methods taken from the literature (Fulcher et al. 2013; keywords: computations; evidence; fairscape; framework; graph; metadata; object; pid; service; software; use; user cache: cord-102835-71ome9h8.txt plain text: cord-102835-71ome9h8.txt item: #76 of 702 id: cord-102842-51n5mnjb author: Węglarz-Tomczak, Ewelina title: Ebselen as a highly active inhibitor of PLProCoV2 date: 2020-05-17 words: 3336 flesch: 50 summary: PL Pro from SARS-CoV-1 (PL Pro SARS) and PL Pro CoV2 are closely related, with 82.9% sequence identity, and relatively distant from PL Pro from MERS (32.9% identity). in [8, 26] that showed PL Pro SARS has a catalytic triad composed of Cys112-His273-Asp287. keywords: coronavirus; cov-2; cov2; ebselen; pro; protease; sars cache: cord-102842-51n5mnjb.txt plain text: cord-102842-51n5mnjb.txt item: #77 of 702 id: cord-102866-40s64455 author: Bhadra, Sanchita title: One enzyme reverse transcription qPCR using Taq DNA polymerase date: 2020-05-30 words: 2867 flesch: 43 summary: We report optimized buffer and salt compositions that promote the reverse transcriptase activity of Taq DNA polymerase, and thereby allow it to be used as the sole enzyme in TaqMan RT-qPCR reactions. The buffer was supplemented with 0.4 mM deoxyribonucleotides (dNTP), 402 nM each of forward and reverse PCR primer pairs, 102 nM of the TaqMan probe, and 2.5 units of Taq DNA polymerase from indicated commercial vendors. keywords: dna; polymerase; qpcr; rna; taq cache: cord-102866-40s64455.txt plain text: cord-102866-40s64455.txt item: #78 of 702 id: cord-102868-wnsgjdcp author: Love, R. Rebecca title: Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms date: 2020-05-28 words: 2651 flesch: 37 summary: The procedures for filtering and calling molecular inversion genotypes were the same 320 for both OA and GT-seq platforms. key: cord-102868-wnsgjdcp authors: Love, R. Rebecca; Pombi, Marco; Guelbeogo, Moussa W.; Campbell, Nathan R.; Stephens, Melissa T.; Dabire, Roch K.; Costantini, Carlo; della Torre, Alessandra; Besansky, Nora J. title: Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.25.114793 sha: doc_id: 102868 cord_uid: wnsgjdcp Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. keywords: anopheles; gambiae; inversion; molecular; snps; tag; tags cache: cord-102868-wnsgjdcp.txt plain text: cord-102868-wnsgjdcp.txt item: #79 of 702 id: cord-102886-oo7q05ml author: Gomes, Fabio M. title: “Proliferation of DBLOX Peroxidase-Expressing Oenocytes Maintains Innate Immune Memory in Primed Mosquitoes” date: 2020-09-10 words: 1965 flesch: 37 summary: It is not clear whether individual immune cells maintain the training response, or if there are specific memory keeper cell populations that orchestrate a persistent re-training of effector immune cells. The transient systemic release of PGE 2 establishes a long-lasting release of hemocyte differentiation factor (HDF) which, in turn, induces an increase in the proportion of circulating granulocytes, a hallmark of immune priming (7, 8) . keywords: dblox; fig; hdf; oenocytes; priming; response cache: cord-102886-oo7q05ml.txt plain text: cord-102886-oo7q05ml.txt item: #80 of 702 id: cord-102891-0z397ppn author: Wren, Brandi title: Social contact behaviors are associated with infection status for whipworm (Trichuris sp.) in wild vervet monkeys (Chlorocebus pygerythrus) date: 2020-10-07 words: 2330 flesch: 28 summary: Of six parasites detected, one (Trichuris sp.) was associated with social grooming behaviors, but more specifically with direct physical contact with others. We are also grateful 481 to Katie Dean, Claire Detrich, Ruby Malzoni, Liz Sperling Moses for assistance in the laboratory Grooming systems of insects: structure, mechanics Pollen transport and deposition by bumble bees in Erythronium: 489 influences of floral nectar and bee grooming Grooming patterns in the primitively eusocial wasp 491 Polistes dominulus A video-tracking method to identify and understand circadian patterns in 493 Drosophila grooming Hoxb8 is required for normal grooming behaviour in 496 mice Self-grooming by rodents in social and sexual 498 contexts Costs and 500 constraints of anti-parasitic grooming in adult and juvenile 501 rodents Neurobiology of rodent self-grooming and its value for translational 504 neuroscience Relationship of bill morphology to grooming 506 behaviour in birds Comparative analysis of time spent grooming by 508 birds in relation to parasite load Of great tits and fleas: sleep baby 510 sleep Do grooming behaviours affect 512 visual properties of feathers in male domestic canaries, Serinus 513 canaria? keywords: grooming; group; monkeys; parasite; time; trichuris cache: cord-102891-0z397ppn.txt plain text: cord-102891-0z397ppn.txt item: #81 of 702 id: cord-102892-nt1zoktv author: Sweeney, Blake A. title: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date: 2020-09-11 words: 3368 flesch: 40 summary: 150 Comprehensive 2D structure template library 151 We compiled a library of 3,632 templates aggregating RNA 2D structure layouts from different 152 sources (Table 1) While the majority of the 3,632 templates were integrated from the existing sources (Table 1) , 164 103 templates have been manually curated specifically for this project, as described below (also 165 see Supplementary Table 1) . As new 2D structure templates are 318 introduced, the pipeline can be extended to cover new RNA types, including structured viral 319 RNAs. keywords: diagrams; models; r2dt; rna; sequence; structure; templates cache: cord-102892-nt1zoktv.txt plain text: cord-102892-nt1zoktv.txt item: #82 of 702 id: cord-102898-eyyd7ent author: Rizvi, Vaseef A. title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 words: 3049 flesch: 36 summary: Together, our study sheds light on distinct mechanisms that modulate JEV translation with likely consequences for viral pathogenesis. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . keywords: codon; jev; protein; region; ribosome; site; start; translation; trna; usage; virus cache: cord-102898-eyyd7ent.txt plain text: cord-102898-eyyd7ent.txt item: #83 of 702 id: cord-102905-rlee32x7 author: Leis, Jonathan title: Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date: 2020-05-04 words: 5784 flesch: 41 summary: Additionally, we designed and synthesized novel prazole analogs that act in the nanomolar range to block virus release, a major step forward in creating a VBI that can be brought to the clinic. In HIV, ESCRT proteins are recruited to virus budding complexes through an interaction between the L-domain (PTAPP motifs) in virus structural proteins (3) (4) (5) (6) (7) with cellular protein Tsg101 (Tumor susceptibility gene 101), a homolog of the E2 ubiquitin conjugating enzyme and a member of the ESCRT-I complex (6, (8) (9) (10) (11) . keywords: budding; cells; compounds; escrt; ilaprazole; particles; prazole; protein; release; tenatoprazole; tsg101; virus cache: cord-102905-rlee32x7.txt plain text: cord-102905-rlee32x7.txt item: #84 of 702 id: cord-102908-sr7j8z9c author: Mersmann, Sophia F. title: Learning to count: determining the stoichiometry of bio-molecular complexes using fluorescence microscopy and statistical modelling date: 2020-07-24 words: 5246 flesch: 35 summary: Figure 5A displays the mean number of bound antibody at increasing 9C12 concentrations; AdV-9C12 stoichiometries range from 29 to 115 across the titration of antibody. However, using stoichiometric estimates to calibrate fluorescent data revealed population heterogeneity with a small proportion of virus particles binding ∼200 antibody molecules. keywords: adv; antibody; binding; complexes; figure; molecules; particles; virus cache: cord-102908-sr7j8z9c.txt plain text: cord-102908-sr7j8z9c.txt item: #85 of 702 id: cord-102916-t2lcd300 author: Cai, Guoshuai title: SCANNER: A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data date: 2020-07-14 words: 1488 flesch: 37 summary: Also, it is equipped with multiple data interfaces for easy data sharing and currently provide a database for studying the smoking effect on single cell gene expression in lung. In recent years, single cell RNA sequencing (scRNA-seq) methods have been efficiently enabling the transcriptome profiling of each single cell (Kolodziejczyk, et al., 2015) . keywords: cell; data; scanner cache: cord-102916-t2lcd300.txt plain text: cord-102916-t2lcd300.txt item: #86 of 702 id: cord-102918-bkyk7or9 author: Burns, C. Sean title: Methodological Issues with Search in MEDLINE: A Longitudinal Query Analysis date: 2020-05-22 words: 1415 flesch: 31 summary: We devised twenty-nine sets of search queries comprised of five queries per set to search against the five MEDLINE database platforms. We found that search results vary considerably depending on MEDLINE platform, both within sets and across time. keywords: medline; query; reviews; search; systematic cache: cord-102918-bkyk7or9.txt plain text: cord-102918-bkyk7or9.txt item: #87 of 702 id: cord-102920-z5q3wo7v author: Sang, Eric R. title: Integrate Structural Analysis, Isoform Diversity, and Interferon-Inductive Propensity of ACE2 to Refine SARS-CoV2 Susceptibility Prediction in Vertebrates date: 2020-06-28 words: 6466 flesch: 39 summary: Our current results demonstrate several previously unstudied immunogenetic properties of animal ACE2 genes and imply some domestic animals, including dogs, pigs and cattle/goats, may obtain some immunogenetic diversity to confront SARS-CoV2 infection and face less COVID-19 risk than may have been previously thought. Data show that animal ACE2 gene promoters are evolutionally different in containing IFN-or virus-stimulated response elements (ISRE, PRDI, IFRs, and/or STAT1/3 factors) and cis-elements responsive to pro-inflammatory mediators. keywords: ace2; animal; cov2; fig; genes; human; ifn; isoforms; rbd; sars; species; susceptibility cache: cord-102920-z5q3wo7v.txt plain text: cord-102920-z5q3wo7v.txt item: #88 of 702 id: cord-102931-vxkbctiz author: Mao, Kai title: Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date: 2020-06-06 words: 8685 flesch: 37 summary: If the unique strand transcriptional architecture of the Caenorhabditis mitochondrial genome is linked with production of dsRNA from the mitochondria, and if the release of mitochondrial RNA into the cytosol in mitochondrial mutants is the trigger for the formation of EOL-1 foci, we would expect a suppression of EOL-1 focus formation by shutting down mitochondrial RNA biogenesis. Therefore, the formation EOL-1 foci required the biogenesis of mitochondrial RNA. keywords: antiviral; caenorhabditis; drh-1; elegans; et al; figure; genes; hsp-6(mg585; interference; mutant; mutations; pathway; response; rnai; silencing; transgene cache: cord-102931-vxkbctiz.txt plain text: cord-102931-vxkbctiz.txt item: #89 of 702 id: cord-102935-cx3elpb8 author: Hassani-Pak, Keywan title: KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species date: 2020-04-24 words: 2175 flesch: 45 summary: Evidence View is a ranked list of query related 121 evidence terms and enrichment scores along with linked genes. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. keywords: evidence; gene; information; knetminer; knowledge; search cache: cord-102935-cx3elpb8.txt plain text: cord-102935-cx3elpb8.txt item: #90 of 702 id: cord-102958-q8jamg07 author: Hahka, Taija M. title: Resiniferatoxin (RTX) ameliorates acute respiratory distress syndrome (ARDS) in a rodent model of lung injury date: 2020-09-14 words: 3752 flesch: 38 summary: Combined with the results shown in the current model of ALI, the potential of RTX to rescue lung function and protect multiple organs from collateral damage due to lung injury triggered inflammation is very encouraging and warrants additional studies as a rescue therapy for patients with lung injuries or infections resulting in inflammatory -mediated pneumonia. Therefore, in the current study we hypothesized that ablation of lung afferent innervation (thoracic spinal) by application of an ultrapotent, selective afferent neurotoxin, resiniferatoxin (RTX) will modify the course of the pathology including lung edema and local pulmonary inflammation associated with progressive ALI. Committee of the University of Nebraska Medical Center and performed in accordance with the National Institutes of Health's Guide for Use and Care of Laboratory Animals and with ARRIVE guidelines. keywords: afferents; ali; bleomycin; ganglia; injection; injury; lung; rats; rtx; spinal cache: cord-102958-q8jamg07.txt plain text: cord-102958-q8jamg07.txt item: #91 of 702 id: cord-102964-zh737cjk author: Ferraro, Francesco title: Modulation of endothelial organelle size as an antithrombotic strategy date: 2020-05-17 words: 5560 flesch: 38 summary: Endothelial VWF is stored in cell-specific secretory granules, Weibel-Palade bodies (WPBs), uniquely rod-like exocytic organelles generated in a wide range of lengths (0.5 to 5.0 µm). Blue asterisks: platelet aggregation in malignant melanoma of mice and humans Sepsis and septic shock: endothelial molecular pathogenesis associated with vascular microthrombotic disease Multidrug resistance protein 1 (MRP1, ABCC1), a multitasking ATPbinding cassette (ABC) transporter KLF2 provokes a gene expression pattern that establishes functional quiescent differentiation of the endothelium DNA damage triggers Golgi dispersal via DNA-PK and GOLPH3 A two-tier Golgi-based control of organelle size underpins the functional plasticity of endothelial cells Weibel-Palade body size modulates the adhesive activity of its von Willebrand Factor cargo in cultured endothelial cells Prolonged shear stress and KLF2 suppress constitutive proinflammatory transcription through inhibition of ATF2 Image-based drug screen identifies HDAC inhibitors as novel Golgi disruptors synergizing with JQ1 Statins and the vascular endothelial inflammatory response Temperature-dependence of Weibel-Palade body exocytosis and cell surface dispersal of von Willebrand factor and its propolypeptide Contribution of platelet vs. endothelial VWF to platelet adhesion and hemostasis Cardiac glycoside toxicity: more than 200 years and counting Image-based siRNA screen to identify kinases regulating Weibel-Palade body size control using electroporation Tumor necrosis factor alphamediated reduction of KLF2 is due to inhibition of MEF2 by NF-kappaB and histone deacetylases Statin treatment before percutaneous cononary intervention Kruppel-like factor 2 (KLF2) regulates endothelial thrombotic function A GBF1-Dependent Mechanism for Environmentally Responsive Regulation of ER-Golgi Transport Organelle size control systems: from cell geometry to organelledirected medicine Weibel-Palade bodies at a glance The physiological function of von Willebrand's factor depends on its tubular storage in endothelial Weibel-Palade bodies Cardiac glycosides as novel cancer therapeutic agents Cellular stress induces erythrocyte assembly on intravascular von Willebrand factor strings and promotes microangiopathy Ultralarge von Willebrand factor fibers mediate luminal Staphylococcus aureus adhesion to an intact endothelial cell layer under shear stress Statins exert endothelial atheroprotective effects via the KLF2 transcription factor The role of von Willebrand factor in thrombus formation Interaction of von Willebrand factor with platelets and the vessel wall In vivo imaging analysis of the interaction between unusually large von Willebrand factor multimers and platelets on the surface of vascular wall Biochemistry and genetics of von Willebrand factor Kruppel-like factor 2 as a novel mediator of statin effects in endothelial cells G protein-coupled receptor kinase 2 moderates recruitment of THP-1 cells to the endothelium by limiting histamine-invoked Weibel-Palade body exocytosis Microtubules and the organization of the Golgi complex Identification and characterization of Cardiac Glycosides as senolytic compounds Pathophysiology of thrombotic thrombocytopenic purpura The shear stress-induced transcription factor KLF2 affects dynamics and angiopoietin-2 content of Weibel-Palade bodies Cell adhesion mechanisms in platelets Thrombosis in diabetes: a shear flow effect? Mechanoenzymatic cleavage of the ultralarge vascular protein von Willebrand factor Affects (no defined mechanism) Integrin beta-2 (ITGB2) and inhibits Integrin alpha-L (ITGAL) High affinity nerve growth factor receptor (NTRK1), Macrophage colony-stimulating factor 1 receptor (CSF1R), Platelet-derived growth factor receptor alpha (PDGFRA), Platelet-derived growth factor receptor beta (PDGFRB) keywords: cells; dna; drugbank; drugs; endothelial; et al; ferraro; inhibits; protein; receptor; size; vwf; wpb; wpbs cache: cord-102964-zh737cjk.txt plain text: cord-102964-zh737cjk.txt item: #92 of 702 id: cord-102967-dx0tg077 author: Mahajan, Lakshmi S. title: Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date: 2020-06-16 words: 2855 flesch: 51 summary: While PRO-seq is highly specific for nascent, biotin-labeled RNAs, it is also possible that DAV PRO-seq reads may have derived from the mature DAV RNA genome that contaminated the sample in small frequencies. Precision Run-On sequencing (PRO-seq) is a nuclear run-on based nascent RNA sequencing method, widely used to map eukaryotic RNA polymerases by using labeled nucleotide analogues. keywords: dav; genome; pro; rdrp; reads; rna; seq cache: cord-102967-dx0tg077.txt plain text: cord-102967-dx0tg077.txt item: #93 of 702 id: cord-102968-mhawyect author: Desirò, Daniel title: SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date: 2018-09-23 words: 4046 flesch: 50 summary: For example, long-range RNA-RNA interactions (LRIs) play an important role in the life cycle of RNA viruses. Conclusion We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. keywords: hepatitis; interactions; range; rna; sequence; sim; tool; virus cache: cord-102968-mhawyect.txt plain text: cord-102968-mhawyect.txt item: #94 of 702 id: cord-102976-cic1gxrk author: Patel, Roosheel S. title: Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells date: 2020-05-07 words: 7161 flesch: 33 summary: Given the improved resolution and novel cell populations identified by scRNA-Seq, we grouped annotated cell clusters into summary populations and provided reference ranges for their frequency in healthy horses (Fig. 7A) . We next performed an in-depth analysis of B cell clusters, as defined by their expression of MS4A1 (CD20), CD79A, MHC-II components (i.e. DRA), and/or immunoglobulin transcripts In humans, T-bet + B cells have been described as atypical memory B cells, appearing in the peripheral blood during chronic infection and/or inflammation (17, 34) . keywords: bet; cells; clusters; data; equine; expression; fig; flow; gene; horses; human; scrna; seq; species cache: cord-102976-cic1gxrk.txt plain text: cord-102976-cic1gxrk.txt item: #95 of 702 id: cord-102977-yci9kq6x author: Liu, Haiming title: GHSR-1a is not Required for Ghrelin’s Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia date: 2019-12-06 words: 4894 flesch: 46 summary: Given that there are no treatments for cancer cachexia and that several clinical trials targeting this pathway have failed to 191 meet their primary endpoints (Garcia et al., 2015 , Temel, Abernethy et al., 2016 , there is a pressing 192 need to improve our understanding of the mechanisms of action of ghrelin in this setting. Weight loss and survival rates are correlated with IL-6 levels in cancer patients (Garcia et al., 2005, 202 Moses, Maingay et al., 2009 , Scott, McMillan et al., 1996 . keywords: bat; cachexia; cancer; et al; ghrelin; inflammation; tissue; tumor; wat cache: cord-102977-yci9kq6x.txt plain text: cord-102977-yci9kq6x.txt item: #96 of 702 id: cord-103015-3dxwbmd2 author: Shengjuler, Djoshkun title: The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date: 2017-08-04 words: 7102 flesch: 59 summary: The outcome is a new structural class of PIP-367 binding proteins with the capacity for multivalent binding to any mono-, bis-or tris-phosphorylated PIP, but with a unique conformational state determined by the nature of the 369 bound PIP. This approach was validated by using the PLC-δ1 PH domain 115 as a positive control, which showed PI(4,5)P2 binding specificity, as expected ( Figure S1 ) keywords: binding; et al; figure; membrane; pi(4,5)p2; pi4p; pip; protein; residues; rna; structure cache: cord-103015-3dxwbmd2.txt plain text: cord-103015-3dxwbmd2.txt item: #97 of 702 id: cord-103029-nc5yf6x4 author: Wichmann, Stefan title: Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank date: 2020-09-25 words: 8666 flesch: 47 summary: Other properties required for functional protein sequences can be inferred from the evolutionary information contained in sequence alignments of protein families. Constructed OLG sequences are also indistinguishable from natural sequences in terms of amino acid identity and secondary structure, while the minimum nucleotide change required for overprinting an overlapping sequence can be as low as 1.8% of the sequence. keywords: acid; amino; code; fig; genes; olg; olgs; overlapping; protein; sequences; structure cache: cord-103029-nc5yf6x4.txt plain text: cord-103029-nc5yf6x4.txt item: #98 of 702 id: cord-103041-ymr3e60k author: Wu, Yue title: Homeostatic mechanisms regulate distinct aspects of cortical circuit dynamics date: 2019-10-02 words: 7962 flesch: 36 summary: bioRxiv Potentiation of cortical inhibition by visual deprivation Sensory experience inversely regulates feedforward and feedback excitation-inhibition ratio in rodent visual cortex Training and spontaneous reinforcement of neuronal assemblies by spike timing plasticity Rapid and active stabilization of visual cortical firing rates across light-dark transitions A synaptic organizing principle for cortical neuronal groups Triplets of spikes in a model of spike timing-dependent plasticity Cell-specific restoration of stimulus preference after monocular deprivation in the visual cortex Critical role of cdk5 and polo-like kinase 2 in homeostatic synaptic plasticity during elevated activity Arc/arg3.1 mediates homeostatic synaptic scaling of ampa receptors Rate, timing, and cooperativity jointly determine cortical synaptic plasticity Bidirectional synaptic mechanisms of ocular dominance plasticity in visual cortex Metaplasticity at ca1 synapses by homeostatic control of presynaptic release dynamics Synaptic scaling mediated by glial tnf-α Modeling the dynamic interaction of hebbian and homeostatic plasticity Too many cooks? Recovery of stimulus preference at the single cell level, as well as network correlation structure, has also been reported during repeated episodes of monocular deprivation in the binocular region of visual cortex, each followed by eye reopening (Rose et al., 2016) . keywords: correlations; excitatory; fig; firing; inhibitory; network; neurons; plasticity; rates; synaptic cache: cord-103041-ymr3e60k.txt plain text: cord-103041-ymr3e60k.txt item: #99 of 702 id: cord-103046-w8bm4p44 author: Suarez, David L. title: Lack of susceptibility of poultry to SARS-CoV-2 and MERS-CoV date: 2020-06-16 words: 566 flesch: 43 summary: key: cord-103046-w8bm4p44 authors: Suarez, David L.; Pantin-Jackwood, Mary J.; Swayne, David E.; Lee, Scott A.; DeBlois, Suzanne M.; Spackman, Erica title: Lack of susceptibility of poultry to SARS-CoV-2 and MERS-CoV date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.16.154658 sha: doc_id: 103046 cord_uid: w8bm4p44 Chickens, turkeys, ducks, quail and geese were challenged with SARS-CoV-2 or MERS-CoV. Science MERS-CoV: a global challenge Human Coronavirus Infections-Severe Acute 113 Middle East Respiratory Syndrome (MERS), and SARS-114 Reference Module in Biomedical Sciences Identification of MERS-CoV in dromedary camels Middle East 118 respiratory syndrome coronavirus infection in non-camelid domestic mammals. keywords: cov; mers cache: cord-103046-w8bm4p44.txt plain text: cord-103046-w8bm4p44.txt item: #100 of 702 id: cord-103055-071a5b0x author: Rathbun, LI title: PLK1- and PLK4-mediated asymmetric mitotic centrosome size and positioning in the early zebrafish embryo date: 2020-04-14 words: 3166 flesch: 46 summary: When measuring mitotic centrosome size in C. elegans and zebrafish embryos ( Figure 1D -E), a significant decrease in mitotic centrosome area was identified from one round of division to the next ( Figure 1F ). During this time in development, we found that zebrafish mitotic centrosomes are asymmetric in size and display a directionality, where the larger mitotic centrosome within a spindle is positioned towards the embryonic midline in a PLK1-and PLK4-dependent manner. keywords: cell; centrosome; embryos; figure; size; spindle; zebrafish cache: cord-103055-071a5b0x.txt plain text: cord-103055-071a5b0x.txt item: #101 of 702 id: cord-103071-6cgih8o9 author: Mead, Benjamin E. title: High-throughput organoid screening enables engineering of intestinal epithelial composition date: 2020-04-28 words: 12466 flesch: 43 summary: To screen for novel biological targets with established pharmacophores which may regulate Paneth cell differentiation in vitro and translate in vivo, we require a physiological model system and a scalable screening approach to reasonably scan annotated small molecule space (up to thousands of samples) and measure specific changes of a single cell type (Paneth cells), within a dynamic (differentiation) and heterogeneous (organoid) system. For instance, identification of biological targets and accompanying small molecules which enhance Paneth cell differentiation from ISCs. keywords: abundance; assay; cell; control; culture; day; differentiation; et al; fig; gene; iii; inhibition; kpt-330; lyz; media; organoids; paneth; plate; screen; signaling; stem; supp; treatment; xpo1 cache: cord-103071-6cgih8o9.txt plain text: cord-103071-6cgih8o9.txt item: #102 of 702 id: cord-103077-sh4w2mye author: Lu, Shuai title: Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction date: 2020-10-16 words: 3142 flesch: 48 summary: Note that these methods only considering sequential or spatial neighbors of target antibody residue. In this study, we design and implement a new structurebased paratope predictor leveraging sequential and spatial neighbors of target antibody residue. keywords: antibody; features; neighbors; paratope; prediction; residue; sequence; structure cache: cord-103077-sh4w2mye.txt plain text: cord-103077-sh4w2mye.txt item: #103 of 702 id: cord-103081-k7ev5qkn author: Janosevic, Danielle title: The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline date: 2020-05-30 words: 4512 flesch: 49 summary: In fact, four hours after LPS administration, 155 cluster-specific GO terms were indistinguishable among the majority of cell types with 156 enrichment in terms related to defense, immune and bacterium responses (Fig. 5b) . Single cell RNA sequencing revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. keywords: cell; cluster; expression; fig; hours; kidney; rna; sepsis; supplementary; time; timeline cache: cord-103081-k7ev5qkn.txt plain text: cord-103081-k7ev5qkn.txt item: #104 of 702 id: cord-103085-vf4qyvft author: Seitz, Christian title: Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase date: 2020-11-02 words: 9741 flesch: 42 summary: In this work, we define binding site contacts to be those protein-ligand contacts seen in crystal structures. Our work shows that glycans can have an inhibitory effect on influenza NA primary site binding. keywords: acid; association; binding; conformation; figure; glycans; glycosylation; influenza; ligand; neuraminidase; oseltamivir; protein; simulations; site; site binding; structure; virus cache: cord-103085-vf4qyvft.txt plain text: cord-103085-vf4qyvft.txt item: #105 of 702 id: cord-103105-iqjksoim author: Marinaik, Chandranaik B. title: Programming Multifaceted Pulmonary T-Cell Immunity by Combination Adjuvants date: 2020-07-10 words: 7422 flesch: 46 summary: ADJ promotes crosspresentation of antigen to CD8 T cells (21) and hence, ADJ-induced increase in the number of antigen-bearing cells in lungs likely enhances TCR signaling and CD103 expression on effector CD8 T cells. It is possible that the residual TCR signaling in ADJ+GLA mice is sufficient to induce CD103 or other mechanisms including IFN production by CD4 T cells might have contributed to CD103 expression on CD8 T cells (43) . keywords: adj; adj+gla; cd4; cd8; cells; fig; groups; lungs; memory; mice; specific cache: cord-103105-iqjksoim.txt plain text: cord-103105-iqjksoim.txt item: #106 of 702 id: cord-103108-vmze2mdx author: Vanheer, Lotte title: Revealing the Key Regulators of Cell Identity in the Human Adult Pancreas date: 2020-09-25 words: 7974 flesch: 29 summary: We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We next sought to identify pancreatic cell types ( Figure 1D ). keywords: acinar; adult; alpha; analysis; beta; cell; data; development; diabetes; endocrine; et al; exocrine; expression; figure; gene; human; identity; pancreas; regulon; tfs; type cache: cord-103108-vmze2mdx.txt plain text: cord-103108-vmze2mdx.txt item: #107 of 702 id: cord-103112-m6cg67lz author: Schloer, Sebastian title: Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine date: 2020-08-16 words: 1557 flesch: 35 summary: Fig. 1 , both drug treatments were well tolerated, and cell viability was unaffected over A key feature of the late endosomal compartment is the acidic pH. We, therefore, assessed 243 whether fluoxetine treatment impacted endolysosomal pH values in Calu-3 cells, utilizing a 244 quantitative ratiometric fluorescence microscopy assay 12,13 . Calu-3 cells grown on semipermeable supports were infected with SARS-CoV-2 isolate at 0.1 449 MOI for 48 h. Cells were treated 1 h p.i. keywords: cells; fluoxetine; host; sars cache: cord-103112-m6cg67lz.txt plain text: cord-103112-m6cg67lz.txt item: #108 of 702 id: cord-103135-nly9vojr author: Fletcher, Nicola F. title: A novel antiviral formulation inhibits a range of enveloped viruses date: 2020-03-30 words: 6474 flesch: 38 summary: We next determined whether topical application of ViroSAL can also suppress virus infection when virus was inoculated subcutaneously into a mosquito bite. We have identified a novel antiviral formulation that is of great interest for prevention and/or treatment of a broad range of enveloped viruses. keywords: acids; activity; cells; control; et al; infection; infectivity; minutes; mosquito; skin; virosal; virus; viruses cache: cord-103135-nly9vojr.txt plain text: cord-103135-nly9vojr.txt item: #109 of 702 id: cord-103150-e9q8e62v author: Mishra, Shreya title: Improving gene-network inference with graph-wavelets and making insights about ageing associated regulatory changes in lungs date: 2020-11-04 words: 8220 flesch: 50 summary: An integrative approach for causal gene identification and gene regulatory pathway inference Singlecell transcriptomics unveils gene regulatory network plasticity Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery Supervised, semi-supervised and unsupervised inference of gene regulatory networks Reverse engineering cellular networks Evaluating measures of association for single-cell transcriptomics Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data SCENIC: single-cell regulatory network inference and clustering SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression Noise in gene expression: origins, consequences, and control, Science Comparative assessment of differential network analysis methods Murine single-cell RNA-seq reveals cellidentity-and tissue-specific trajectories of aging Wisdom of crowds for robust gene network inference GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods Enhancing experimental signals in single-cell RNA-sequencing data using graph signal processing Comparative Analysis of Single-Cell RNA Sequencing Methods A gene regulatory network in mouse embryonic stem cells Recovering Gene Interactions from Single-Cell Data Using Data Diffusion An accurate and robust imputation method scImpute for single-cell RNA-seq data Single-cell RNA-seq denoising using a deep count autoencoder SAVER: gene expression recovery for singlecell RNA sequencing A random matrix theory approach to denoise single-cell data Missing value estimation methods for DNA microarrays Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Histamine stimulation of surfactant secretion from rat type II pneumocytes Aging impairs VEGF-mediated, androgen-dependent regulation of angiogenesis Dysfunction of pulmonary surfactant mediated by phospholipid oxidation is cholesterol-dependent Age-Dependent Changes in the Pulmonary Renin-Angiotensin System Are Associated With Severity of Lung Injury in a Model of Acute Lung Injury in Rats MAPK and JAK-STAT signaling pathways are involved in the oxidative stress-induced decrease in expression of surfactant protein genes Transcription factor Etv5 is essential for the maintenance of alveolar type II cells, Proceedings of the National Academy of Sciences of the United States of Targeted deletion of Jun/AP-1 in alveolar epithelial cells causes progressive emphysema and worsens cigarette smoke-induced lung inflammation Androgen receptor and androgen-dependent gene expression in lung The Metabolic Signature of Macrophage Responses Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 JAK-STAT pathway activation in COPD, The European Androgen hazards with COVID-19 The H1 histamine receptor regulates allergic lung responses Late Breaking Abstract -Evaluation of the JNK inhibitor, CC-90001, in a phase 1b pulmonary fibrosis trial Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532) For filtering in the Fourier domain, we used Chebyshev-filter for gene expression profile. keywords: at2; cells; data; denoising; expression; gene; graph; inference; lung; methods; network; noise; profiles; seq; wavelet cache: cord-103150-e9q8e62v.txt plain text: cord-103150-e9q8e62v.txt item: #110 of 702 id: cord-103157-xe5ccw9j author: Mayer, David title: Developing and Deploying a Scalable Computing Platform to Support MOOC Education in Clinical Data Science date: 2020-08-27 words: 4325 flesch: 48 summary: The Computing project hosts student computing using RStudio Server Pro (v1.2.5019-6) 20 and R (v3.6.3). In response to these challenges we sought to create a hosted computing platform that would both manage student access to restricted materials and accommodate the unique challenges posed by MOOCs. keywords: access; computing; course; data; google; management; platform; science; server; students; use cache: cord-103157-xe5ccw9j.txt plain text: cord-103157-xe5ccw9j.txt item: #111 of 702 id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 words: 8989 flesch: 40 summary: The rsT3D I S4 RNA profiles were more consistent among lineages than those of the M1 and L1 segments and were similar to those of rsT1L S4, with non-canonical RNA segments just slightly larger than the full-length segment and at ~0.15 kb detected in several passages (Fig. 4) . Non-canonical reovirus segments feature large deletions. keywords: cells; dvgs; fig; length; passage; products; recombination; reovirus; rna; rotavirus; rst1l; rst3d; segments; sequence; sites; viruses cache: cord-103163-0rreoh4o.txt plain text: cord-103163-0rreoh4o.txt item: #112 of 702 id: cord-103174-4m3ajc8a author: Okada, Megan title: Doxycycline has Distinct Apicoplast-Specific Mechanisms of Antimalarial Activity date: 2020-10-16 words: 2815 flesch: 30 summary: To test the apicoplast specificity of first-cycle DOX 98 activity, we next asked whether 200 µM IPP could rescue parasites from DOX concentrations >5 99 µM. We observed that IPP shifted the 48-hour EC50 value of DOX from 5 ± 1 to 12 ± 2 µM 100 (average ± SD of 5 independent assays, P = 0.001 by unpaired t-test) ( Figure 2C and Figure 2 -101 figure supplement 1), suggesting that first-cycle growth defects from 5-10 µM DOX reflect an 102 apicoplast-specific mechanism but that DOX concentrations >10 µM cause off-target defects 103 outside this organelle. 532 Indirect effects of the COVID-19 pandemic on malaria intervention 315 coverage, morbidity, and mortality in Africa: a geospatial modelling analysis Dis Tetracyclines specifically target the apicoplast of the malaria parasite 318 Plasmodium falciparum Antimalarial drug resistance in Africa: the calm before 321 the storm? Tetracyclines in malaria Pharmacokinetics of oral doxycycline during combination 326 treatment of severe falciparum malaria Multiple antibiotics exert delayed effects against the 329 Plasmodium falciparum apicoplast Chemical rescue of malaria parasites lacking an apicoplast 332 defines organelle function in blood-stage Plasmodium falciparum Macrolides rapidly inhibit red blood cell invasion by the human 335 malaria parasite, Plasmodium falciparum Protein trafficking to the plastid 338 of Plasmodium falciparum is via the secretory pathway A mevalonate bypass system facilitates elucidation of plastid biology 341 in malaria parasites Avidity of the tetracyclines for the cations of metals Chemical and biological dynamics of tetracyclines Structural basis of 348 gene regulation by the tetracycline inducible Tet repressor-operator system Fluxes in free and total zinc are essential for progression of 351 intraerythrocytic stages of Plasmodium falciparum Bioavailable iron and heme metabolism in 354 Plasmodium falciparum Iron chelation therapy for 356 malaria: a review The suf 359 iron-sulfur cluster synthesis pathway is required for apicoplast maintenance in malaria 360 parasites Intracellular labile iron Diketo acid inhibitor mechanism and HIV-1 integrase: implications 364 for metal binding in the active site of phosphotransferase enzymes Retroviral intasome 367 assembly and inhibition of DNA strand transfer Inhibitors of 370 nonhousekeeping functions of the apicoplast defy delayed death in Plasmodium falciparum Delayed Death by Plastid Inhibition in 373 Apicomplexan Parasites Disruption of Apicoplast Biogenesis by Chemical Stabilization 376 of an Imported Protein Evades the Delayed-Death Phenotype in Malaria Parasites Small molecule inhibition of apicomplexan FtsH1 disrupts 379 plastid biogenesis in human pathogens Targeting Drugs Using a Chemical Supplementation Assay in Cultured Human Malaria 382 Parasites Pharmacokinetics and tolerability of a single oral 600-mg 384 dose of doxycycline Serum levels of doxycycline in 387 normal subjects after a single oral dose Has doxycycline, in 390 combination with anti-malarial drugs, a role to play in intermittent preventive treatment of 391 Plasmodium falciparum malaria infection in pregnant women in Africa? keywords: activity; apicoplast; cycle; dox; iron; parasites cache: cord-103174-4m3ajc8a.txt plain text: cord-103174-4m3ajc8a.txt item: #113 of 702 id: cord-103176-hfd8ur9a author: Frost, H. Robert title: Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring date: 2020-02-19 words: 7408 flesch: 42 summary: Although single cell data provides unprecedented insights into the structure and function of complex tissues and cell populations, technical and biological limitations make statistical analysis challenging [17] . In addition to the challenges of increased noise and missing data, important biological differences exist between bulk tissue and single cell data. keywords: analysis; cell; data; gene; methods; scrna; seq; seq data; set; sets; vam; variance cache: cord-103176-hfd8ur9a.txt plain text: cord-103176-hfd8ur9a.txt item: #114 of 702 id: cord-103180-5hkoeca7 author: Furstenau, Tara N. title: Sample pooling methods for efficient pathogen screening: Practical implications date: 2020-07-16 words: 3802 flesch: 51 summary: 43 Group testing theory primarily focuses on minimizing the number of tests required 44 to identify positive samples and many nearly-optimal strategies for sample pooling have 45 been described. 25 Due to practical concerns, Dorfman's group testing approach was never applied to 26 syphilis screening because the large number of negative samples had a tendency to 27 dilute the antigen in positive samples below the level of detection keywords: number; pooling; positive; samples; testing; tests cache: cord-103180-5hkoeca7.txt plain text: cord-103180-5hkoeca7.txt item: #115 of 702 id: cord-103181-my4n0vye author: Valle-Casuso, José Carlos title: Replication of Equine arteritis virus is efficiently suppressed by purine and pyrimidine biosynthesis inhibitors date: 2020-04-10 words: 2185 flesch: 34 summary: The IC 50 of IPPA17-A04 was estimated at 0.70 172 µg/ml, i.e. 1.74 µM. GAC50 is not as effective since viability of ED infected cells treated with GAC50 is 173 >80% only at the highest concentrations of 20 or 50 µg/ml ( Figure 3C ) with an IC 50 at 7.2 µg/ml, i.e. 174 30.2 µM. These results show that cell cultures treated with pyrimidine biosynthesis inhibitors did not 175 exhibit cytopathic effects associated to EAV infection, suggesting that EAV replication is also impaired. Same experiment was performed using cell cultures infected 128 with the Bucyrus strain of EAV at a multiplicity of infection (MOI) of 0.5. keywords: cells; eav; equine; ribavirin cache: cord-103181-my4n0vye.txt plain text: cord-103181-my4n0vye.txt item: #116 of 702 id: cord-103187-a255643n author: Mitchell, Evan title: Prophylactic host behaviour discourages pathogen exploitation date: 2019-12-19 words: 3197 flesch: 72 summary: Using feasible parameters and working to zeroth order in χ − χ c , we use the computer 231 algebra software (CAS) Maple (version 2019.1) to investigate the sign of σ as described in 232 equation (14). + γ) is the basic reproductive number [9] We consider the evolution of the level of pathogen exploitation of its host, denoted ξ > 0. keywords: kappa; res cache: cord-103187-a255643n.txt plain text: cord-103187-a255643n.txt item: #117 of 702 id: cord-103204-gt6upfri author: Hölzer, Martin title: PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection date: 2020-05-20 words: 1792 flesch: 32 summary: key: cord-103204-gt6upfri authors: Hölzer, Martin; Marz, Manja title: PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection date: 2020-05-20 journal: bioRxiv DOI: 10.1101/2020.05.18.102731 sha: doc_id: 103204 cord_uid: gt6upfri Summary PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. The different statistical site models that do not allow (neutral models) or allow (selection models) a class of codons to evolve with ω > 1 are compared. keywords: alignment; recombination; selection cache: cord-103204-gt6upfri.txt plain text: cord-103204-gt6upfri.txt item: #118 of 702 id: cord-103208-krann2ir author: Barber-Axthelm, Isaac M title: Coformulation with tattoo ink for immunological assessment of vaccine immunogenicity in the draining lymph node date: 2020-08-29 words: 2934 flesch: 29 summary: In humans, IM vaccination into the deltoids sees antigen drain predominately to the axillary LN, with vaccine responses largely restricted to draining LNs in anatomic proximity to the injection site ( 8 -1 2 ) . These data indicate that the tattoo ink vaccine formulation does not hinder the identification of total or antigen-specific B GC by flow cytometry, and that ink-dyed draining LN are more likely to contain vaccine responses than suggesting that the degree of ink accumulation mirrors antigen load in the LN following vaccination. keywords: drainage; draining; ink; lns; lymph; right; tattoo; vaccine cache: cord-103208-krann2ir.txt plain text: cord-103208-krann2ir.txt item: #119 of 702 id: cord-103213-oinumv1z author: Kalantar, Katrina L. title: IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring date: 2020-04-18 words: 10497 flesch: 41 summary: Github repositories containing open-source code for IDseq pipeline, web application, and benchmarking resources. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences, and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. keywords: abundance; analysis; database; detection; figure; host; idseq; level; mngs; ncbi; pipeline; reads; recall; results; sample; sequences; sequencing; species; taxonomic; tools cache: cord-103213-oinumv1z.txt plain text: cord-103213-oinumv1z.txt item: #120 of 702 id: cord-103249-k35o3gxe author: Johannsen, Leif title: Robotic light touch assists human balance control during maximum forward reaching date: 2019-11-20 words: 3083 flesch: 43 summary: We speculated, therefore, that minimization of the interaction 106 forces and their variability at the contact location during IPT acts as an implicit task constraint and shared goal In the present study, we intended to contrast the effects of human IPT (hIPT) on CR's postural performance 112 against the effects of two different modes of robotic IPT (rIPT) and expected specific costs and benefits on body 113 sway and postural performance due to the robotic response modes. If robotic systems are envisaged as the solution to future shortages in clinical staff and caregivers for the 82 purpose of augmenting of patients' mobility by a provision of balance support, they must show a responsiveness 83 to the social constraints and demands, which govern any routine physical interaction between a patient and a 84 human carer. keywords: contact; control; human; ipt; system cache: cord-103249-k35o3gxe.txt plain text: cord-103249-k35o3gxe.txt item: #121 of 702 id: cord-103271-l9n27ocf author: Carozza, Jacqueline A title: Structure-aided development of small molecule inhibitors of ENPP1, the extracellular phosphodiesterase of the immunotransmitter cGAMP date: 2020-05-31 words: 5717 flesch: 44 summary: Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics. This work suggests that ENPP1 inhibitors could turn cold tumors hot and render them more sensitive to adaptive immune checkpoint inhibitors. keywords: binding; cancer; cgamp; compound; enpp1; fig; inhibitors; interactions; methoxy; potency; structure cache: cord-103271-l9n27ocf.txt plain text: cord-103271-l9n27ocf.txt item: #122 of 702 id: cord-103294-1lrfna4v author: Northrop, Amanda C. title: Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem date: 2020-05-02 words: 596 flesch: 43 summary: At low enrichment rates, ecosystems showed a substantial lag in the recovery of [O2] (clockwise hysteresis). At high enrichment rates, we observed a novel response: changes in [O2] were proportionally larger during the recovery phase than during the enrichment phase (counter-clockwise hysteresis). keywords: enrichment; hysteresis cache: cord-103294-1lrfna4v.txt plain text: cord-103294-1lrfna4v.txt item: #123 of 702 id: cord-103297-4stnx8dw author: Widrich, Michael title: Modern Hopfield Networks and Attention for Immune Repertoire Classification date: 2020-08-17 words: 14116 flesch: 51 summary: A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning Explaining and interpreting LSTMs Solving the protein sequence metric problem Rank-loss support instance machines for miml instance annotation Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires Multiple instance learning: a survey of problem characteristics and applications VDJServer: a cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements Tetramer-visualized gluten-specific CD4+ T cells in blood as a potential diagnostic marker for coeliac disease without oral gluten challenge iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories Support-vector networks Quantifiable predictive features define epitope-specific T cell receptor repertoires On a model of associative memory with huge storage capacity BERT: pre-training of deep bidirectional transformers for language understanding Solving the multiple instance problem with axis-parallel rectangles Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire Predicting antigen-specificity of single T-cells based on TCR CDR3 regions. We apply random and attention-based subsampling of repertoire sequences to reduce over-fitting and decrease computational effort. keywords: attention; classification; data; datasets; deeprc; et al; hopfield; input; learning; lstm; methods; motif; networks; number; repertoire; search; sequences; table cache: cord-103297-4stnx8dw.txt plain text: cord-103297-4stnx8dw.txt item: #124 of 702 id: cord-103301-v4l9sovt author: Bloom, David C. title: Immunization by replication-competent controlled herpesvirus vectors date: 2018-04-11 words: 2337 flesch: 42 summary: Vector replication was activated in some treatment groups by administration of heat and 20 ulipristal as described in Fig. 3 . In a first 2 experiment, virus vectors were administered under anesthesia to the plantar surfaces of 3 both rear feet of adult Swiss Webster outbred female mice (50,000 pfu per animal; 20 4 animals per group). keywords: activation; hsv; replication; virus cache: cord-103301-v4l9sovt.txt plain text: cord-103301-v4l9sovt.txt item: #125 of 702 id: cord-103306-1wc3f1rl author: Sengupta, Sourodip title: Matrix metalloproteinases and tissue inhibitors of metalloproteinases in murine coronavirus-induced neuroinflammation date: 2020-09-18 words: 3586 flesch: 43 summary: Representative immunoblot assay 579 from two independent experiments showed elevated protein levels of TIMP-1 at all examined 580 days following MHV-A59 infection (B). Elevated mRNA and protein levels of tissue inhibitors of metalloproteinases 1 (TIMP-1) in MHV-A59 infection are suggestive of a TIMP-1 mediated host antiviral response. keywords: a59; coronavirus; data; infection; levels; mhv; mrna; p.i; virus cache: cord-103306-1wc3f1rl.txt plain text: cord-103306-1wc3f1rl.txt item: #126 of 702 id: cord-103320-2rpr7aph author: Bhandari, Bikash K. title: Solubility-Weighted Index: fast and accurate prediction of protein solubility date: 2020-03-26 words: 4893 flesch: 38 summary: To improve protein solubility prediction, we optimised the most recently published set of normalised B-factors using the PSI:Biology dataset (Smith et al. 2003 ) Protein solubility, at least in part, depends upon extrinsic factors such as ionic strength, temperature and pH, as well as intrinsic factors-the physicochemical properties of the protein sequence and structure, including molecular weight, amino acid composition, hydrophobicity, aromaticity, isoelectric point, structural propensities and the polarity of surface residues (Wilkinson and Harrison 1991; keywords: acid; amino; et al; fig; flexibility; prediction; protein; residues; sequence; solubility; swi cache: cord-103320-2rpr7aph.txt plain text: cord-103320-2rpr7aph.txt item: #127 of 702 id: cord-103341-q7yqnvm2 author: MacPherson, Ailene title: A General Birth-Death-Sampling Model for Epidemiology and Macroevolution date: 2020-10-11 words: 2675 flesch: 37 summary: First by the set of edges (labeled 1-11) or as a set of critical times (horizontal lines) including: 1) the time of birth events (solid, x i ) 2) terminal sampling times (dashed, y j ), and 3) ancestral sampling times (dotted, z k ). We begin by deriving 115 the likelihood in terms of the edge representation and later demonstrate how to reformulate the likelihood 116 in terms of critical times. keywords: birth; death; sampling; time cache: cord-103341-q7yqnvm2.txt plain text: cord-103341-q7yqnvm2.txt item: #128 of 702 id: cord-103343-k4v5ksvq author: Naim, Nikki title: NHR-49 Acts in Distinct Tissues to Promote Longevity versus Innate Immunity date: 2020-09-11 words: 826 flesch: 41 summary: NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 is influenced differently 369 by, and orchestrates distinct responses to, the acute stress of pathogen attack vs. a We found that NHR-49 expression in neurons alone could rescue the immunity 391 deficits of germline-less, nhr-49;glp-1 mutants, whereas, their lifespan was 392 substantially restored by expression in any somatic tissue. keywords: immunity; longevity; nhr-49 cache: cord-103343-k4v5ksvq.txt plain text: cord-103343-k4v5ksvq.txt item: #129 of 702 id: cord-103345-v555a2ll author: Taylor, Adrian title: The novel roles of choline transporter-like 1 and 2 in ethanolamine transport date: 2020-08-28 words: 3730 flesch: 43 summary: It is well known that various organic cations can inhibit CTL1 mediated Cho transport (20) . Taken together, these data established that CTL1 and CTL2 mediate mitochondrial Etn transport with the same kinetic properties as in the whole cells. keywords: cells; cho; ctl1; ctl2; etn; fig; mitochondria; transport cache: cord-103345-v555a2ll.txt plain text: cord-103345-v555a2ll.txt item: #130 of 702 id: cord-103350-jj9pc4a6 author: Tang, Pingtao title: An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy date: 2020-05-08 words: 4061 flesch: 40 summary: A urinary biomarker profile for children with HIV-associated renal diseases Synergy between basic fibroblast growth factor and HIV-1 Tat protein in induction of Kaposi's sarcoma Progressive glomerulosclerosis and enhanced renal accumulation of basement membrane components in mice transgenic for human immunodeficiency virus type 1 genes Liver bypass significantly increases the transduction efficiency of recombinant adenoviral vectors in the lung, intestine, and kidney Efficient gene transfer to rat renal glomeruli with recombinant adenoviral vectors Mutational analysis of the conserved basic domain of human immunodeficiency virus tat protein Cutting edge: a short polypeptide domain of HIV-1-Tat protein mediates pathogenesis Tat trans-activates the human immunodeficiency virus through a nascent RNA target The interaction between HIV-1 Tat and human cyclin T1 requires zinc and a critical cysteine residue that is not conserved in the murine CycT1 protein Recruitment of a protein complex containing Tat and cyclin T1 to TAR governs the species specificity of HIV-1 Tat The Tat protein of HIV-1 induces tumor necrosis factor-alpha production. Kidney disease in HIV-positive children HIV-associated kidney glomerular diseases: changes with time and HAART Viral load and HIV-associated nephropathy HIV-associated nephropathy in the setting of maximal virologic suppression Renal disease in children with the acquired immunodeficiency syndrome Human immunodeficiency virus (HIV)-associated nephropathy in children from the HIVassociated nephropathy in transgenic mice expressing HIV-1 genes Nephropathy in HIV-transgenic mice A novel HIV-1 transgenic rat model of childhood HIV-1-associated nephropathy Expression of HIV-1 genes in podocytes alone can lead to the full spectrum of HIV-1-associated nephropathy Transgenic and infectious animal models of HIV-associated nephropathy The Tat protein of human immunodeficiency virus type-1 promotes vascular cell growth and locomotion by engaging the alpha5beta1 and alphavbeta3 integrins and by mobilizing sequestered basic fibroblast growth factor Inflammatory cytokines synergize with the HIV-1 Tat protein to promote angiogenesis and Kaposi's sarcoma via induction of basic fibroblast growth factor and the alpha v beta 3 integrin Adenovirus-mediated gene transfer to glomerular cells in newborn mice bFGF and its low affinity receptors in the pathogenesis of HIVassociated nephropathy in transgenic mice HIV-1 upregulates VEGF in podocytes keywords: children; growth; hiv; hivan; kidney; mice; protein; renal; tat cache: cord-103350-jj9pc4a6.txt plain text: cord-103350-jj9pc4a6.txt item: #131 of 702 id: cord-103358-1hbw3yo3 author: Gisbert-Muñoz, Sandra title: MULTIMAP: Multilingual picture naming test for mapping eloquent areas during awake surgeries date: 2020-06-08 words: 4348 flesch: 34 summary: The MULTIMAP test for objects and verbs represents an alternative to the DO 80 monolingual pictorial set currently used in language mapping, providing an open-source, standardized set of up-to-date pictures, where relevant linguistic variables across several languages have been taken into account in picture creation and selection. In studies that have carried out language mapping using verbs, some teams have reported using the same pictures for verb action naming that they use in their object naming tasks (Papagno et al., 2011) , while others have presented pictures depicting actions (Havas et al., 2015) . keywords: brain; language; mapping; naming; objects; spanish; stimulation; verbs cache: cord-103358-1hbw3yo3.txt plain text: cord-103358-1hbw3yo3.txt item: #132 of 702 id: cord-103363-efd80dgn author: Mahan, Margaret title: tbiExtractor: A framework for extracting traumatic brain injury common data elements from radiology reports date: 2019-03-21 words: 2393 flesch: 33 summary: Using the cosine similarity for each pair of radiology reports, one 140 radiology report was randomly selected and all radiology reports with at least 0.70 cosine similarity to 141 that radiology report were collected in a set. Materials and Methods We developed tbiExtractor, which extends pyConTextNLP, a regular expression algorithm using negation detection and contextual features, to create a framework for extracting TBI common data elements from radiology reports. keywords: algorithm; annotators; data; radiology; reports; targets cache: cord-103363-efd80dgn.txt plain text: cord-103363-efd80dgn.txt item: #133 of 702 id: cord-103377-j1mmx7k7 author: Karasik, Agnes title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date: 2020-09-11 words: 11800 flesch: 49 summary: However, given the short time frame of RNase L activation, detection of cryptic peptides in RNase L activated cells has proven to be difficult (data not shown). We did not observe this trend in RNase L KO cells, showing that RNase L activation is required for the process. keywords: activation; analysis; cells; cleavage; codons; data; density; et al; figure; footprints; fragments; frame; mrna; orf; ribosome; rnase; rnase l; start; translation cache: cord-103377-j1mmx7k7.txt plain text: cord-103377-j1mmx7k7.txt item: #134 of 702 id: cord-103396-jiuqk6kg author: Adler, Paul N. title: Short distance non-autonomy and intercellular transfer of chitin synthase in Drosophila date: 2020-05-26 words: 4074 flesch: 57 summary: In wing cuticle I 205 also detected a layered structure that presumably reflects the banding of chitin in the procuticle (Fig 206 5BC ). To determine if the deposition of cuticle followed a similar time course I used a 130 chitin reporter and examined wing cuticle deposition by in vivo imaging (Sobala et al., 2015) . keywords: cells; chitin; cuticle; drosophila; fig; flies; kkv; puncta; pupal cache: cord-103396-jiuqk6kg.txt plain text: cord-103396-jiuqk6kg.txt item: #135 of 702 id: cord-103408-vhrlrd2c author: Mishra, Preet title: Decision Support Systems based on Scientific Evidence: Bibliometric Networks of Invasive Lantana camara date: 2020-08-10 words: 3305 flesch: 39 summary: Combined with this, the knowledge of advanced network analysis tools like Gephi, Pajek etc. can be used then to analyse the metadata from various perspectives. In this paper, we provide ways of developing a holistic research strategy using bibliometric-data driven approaches that integrate network analysis and information management, without the need of full paper access. keywords: analysis; dss; figure; information; metadata; networks; research; tools cache: cord-103408-vhrlrd2c.txt plain text: cord-103408-vhrlrd2c.txt item: #136 of 702 id: cord-103417-2uinislh author: Doi, Hideyuki title: On-site eDNA detection of species using ultra-rapid mobile PCR date: 2020-10-01 words: 1507 flesch: 43 summary: Our ultra-rapid on-site eDNA extraction and measurement method using mobile PCR successfully detected the eDNA of H. molitrix, and analysis took only 30 min. The Ct of mobile PCR was larger than that of qPCR, because the DNA concentration in the field-extracted samples was lower. keywords: detection; edna; method; pcr; site cache: cord-103417-2uinislh.txt plain text: cord-103417-2uinislh.txt item: #137 of 702 id: cord-103421-46owvqw8 author: Saunders, Jaclyn K. title: METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses date: 2020-05-21 words: 5735 flesch: 33 summary: The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. keywords: categories; coronavirus; database; genomes; metatryp; organisms; peptides; portal; protein; taxa; taxonomic cache: cord-103421-46owvqw8.txt plain text: cord-103421-46owvqw8.txt item: #138 of 702 id: cord-103422-ys846i99 author: Xu, Xinhui title: CRISPR-Assisted DNA Detection, a novel dCas9-based DNA detection technique date: 2020-05-13 words: 4281 flesch: 55 summary: We also verified three forms of CADD method by detecting 15 hrHPV plasmids and as many 64 clinical cervical samples. These investigations demonstrate the feasibility and reliability of CADD method. keywords: beads; cadd; crispr; detection; dna; hcr; method; pmd; sgrna cache: cord-103422-ys846i99.txt plain text: cord-103422-ys846i99.txt item: #139 of 702 id: cord-103430-x6zzuu7v author: Contu, Lara title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date: 2020-10-12 words: 8307 flesch: 46 summary: Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus’ hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. b, Flowchart outlining the experimental approach to transiently express N-7 terminally FLAG-tagged (yellow rectangle) SFV proteins in mammalian cells in order to construct a SFV-host protein-protein 8 interactome. keywords: capsid; cells; figure; host; infection; interactors; nsp2; nsp3; proteins; rna; sfv; translation; viral; virus cache: cord-103430-x6zzuu7v.txt plain text: cord-103430-x6zzuu7v.txt item: #140 of 702 id: cord-103432-cdmoazrl author: Richardson, Eve title: A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-Pertussis toxoid antibodies date: 2020-06-02 words: 6562 flesch: 47 summary: en Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. A clonotype is defined as a group of antibody sequences which derive from a common progenitor B cell [10] . keywords: antibodies; antibody; binders; binding; clonotyping; identity; paratype; paratyping; predictions; ptx; sequences cache: cord-103432-cdmoazrl.txt plain text: cord-103432-cdmoazrl.txt item: #141 of 702 id: cord-103435-yufvt44t author: van Aalst, Marvin title: Constructing and analysing dynamic models with modelbase v1.0 - a software update date: 2020-10-02 words: 4087 flesch: 32 summary: Mathematical models based on a system of differential equations that link the dosing regimen with the dynamics of a disease are called pharmacokinetic-pharmacodynamic (PK-PD) models [30] and with the next example we explore how modelbase can be used to develop such models. Mathematical models are accepted as valuable tools in advancing biological and medical research keywords: construction; drug; label; modelbase; modelling; models; process; results; software; systems cache: cord-103435-yufvt44t.txt plain text: cord-103435-yufvt44t.txt item: #142 of 702 id: cord-103448-xa5zgkd3 author: Adachi, Hiroaki title: Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1 date: 2020-10-12 words: 9939 flesch: 43 summary: We performed BLAST (Altschul et al., 1990) using previously identified ZAR1 sequences as queries (Baudin et al. 2017; Schultink et al. 2019; This indicates that the NB-ARC domain of ZAR1-SUB proteins is highly diversified in contrast to the relatively conserved equivalent region of ZAR1 proteins. keywords: arabidopsis; cin; conserved; domain; et al; figure; nlr; nlrs; orthologs; plant; proteins; sequence; species; sub; supplementary; table; zar1 cache: cord-103448-xa5zgkd3.txt plain text: cord-103448-xa5zgkd3.txt item: #143 of 702 id: cord-103460-5thh6syt author: Carlson, Colin J. title: Climate change will drive novel cross-species viral transmission date: 2020-07-14 words: 1439 flesch: 44 summary: Moving forward, the rapid range shifts already observed 532 in many bat species (see main text) could provide an empirical reference point to fit a new allo-533 metric scaling curve (after standardizing those results for the studies' many different method-534 ologies). Counter to expectations, holding warming under 2°C within the century does not reduce new viral sharing, due to greater range expansions—highlighting the need to invest in surveillance even in a low-warming future. keywords: bats; climate; dispersal; sharing; species cache: cord-103460-5thh6syt.txt plain text: cord-103460-5thh6syt.txt item: #144 of 702 id: cord-103462-z3d9lcar author: Wang, Shiyu title: CD4+ T cell subsets present stable relationships in their T cell receptor repertoires date: 2020-11-02 words: 2936 flesch: 54 summary: key: cord-103462-z3d9lcar authors: Wang, Shiyu; Wang, Longlong; Liu, Ya title: CD4+ T cell subsets present stable relationships in their T cell receptor repertoires date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.01.364224 sha: doc_id: 103462 cord_uid: z3d9lcar CD4+ T cells are key components of adaptive immunity. Our findings indicate that the reduce of public clones in differentiation trim the antigen specificity of CD4+ T cells. keywords: clones; repertoire; subsets; tcrb cache: cord-103462-z3d9lcar.txt plain text: cord-103462-z3d9lcar.txt item: #145 of 702 id: cord-103465-6udhvl9n author: Schierding, William title: Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways date: 2020-04-13 words: 6456 flesch: 34 summary: Results 140 genetic variants with regulatory potential are associated with cohesin loci Mitotic cohesin genes (SMC1A, SMC3, STAG1, STAG2, and RAD21), meiotic cohesin genes (SMC1B, STAG3, REC8, and RAD21L1), cohesin support genes (WAPL, NIPBL, PDS5A, PDS5B, and MAU2) and CTCF were investigated to determine if they contain non-coding genetic variants (SNPs) that make contact in 3D with genes and therefore could directly affect gene expression (GWAS-attributed and eQTL-attributed; Table 1, Table S1 ). key: cord-103465-6udhvl9n authors: Schierding, William; Horsfield, Julia; O’Sullivan, Justin title: Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways date: 2020-04-13 journal: bioRxiv DOI: 10.1101/2020.04.11.037358 sha: doc_id: 103465 cord_uid: 6udhvl9n Variants in DNA regulatory elements can alter the regulation of distant genes through spatial-regulatory connections. keywords: analysis; cohesin; connections; disease; eqtl; expression; genes; gwas; human; intolerant; lof; table; variants cache: cord-103465-6udhvl9n.txt plain text: cord-103465-6udhvl9n.txt item: #146 of 702 id: cord-103497-1ls2dvzy author: Ganier, C title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date: 2020-05-29 words: 1431 flesch: 32 summary: key: cord-103497-1ls2dvzy authors: Ganier, C; Du-Harpur, X; Harun, N; Wan, B; Arthurs, C; Luscombe, NM; Watt, FM; Lynch, MD title: CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals date: 2020-05-29 journal: bioRxiv DOI: 10.1101/2020.05.29.123513 sha: doc_id: 103497 cord_uid: 1ls2dvzy Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a wide range of systemic manifestations. We found that CD147 (BSG) but not ACE2 is detectable in vascular endothelial cells within single cell sequencing datasets derived from multiple tissues in healthy individuals. keywords: ace2; cells cache: cord-103497-1ls2dvzy.txt plain text: cord-103497-1ls2dvzy.txt item: #147 of 702 id: cord-103502-asphso2s author: Herrgårdh, Tilda title: An organ-based multi-level model for glucose homeostasis: organ distributions, timing, and impact of blood flow date: 2020-10-21 words: 8166 flesch: 51 summary: Another application of glucose homeostasis models exist for meal response T2D simulator model, developed for pedagogical and motivational purposes (Maas et al. 2015) . Original multi-level model Rejected by Figure 2 Updated glucose distribution among organs Can describe Figure 2 Rejected by Figure 3 Updated glucose dynamic behaviours by improving interstitial fluid insulin Can describe Figure 3 Rejected by Figure 4 Updated glucose dynamic behaviours by redesigning an intracellular model Can describe Figure 4 Rejected by Figure 5 Blood flow has an influence on adipose tissue glucose uptake Rejected by Figure 5 Insulin has an influence on adipose tissue glucose uptake The impact of mathematical modeling on the understanding of diabetes and related complications Model-Based Interspecies Scaling of Glucose Homeostasis The Computational Patient has Diabetes and a COVID Physiologic evaluation of factors controlling glucose tolerance in man. keywords: adipose; blood; data; et al; fig; glucose; glucose uptake; insulin; model; muscle; tissue; uptake cache: cord-103502-asphso2s.txt plain text: cord-103502-asphso2s.txt item: #148 of 702 id: cord-103504-ucqqpra5 author: Zhang, Zhe title: The conserved ER-transmembrane protein TMEM39 coordinates with COPII to promote collagen secretion and prevent ER stress date: 2020-09-20 words: 2882 flesch: 41 summary: key: cord-103504-ucqqpra5 authors: Zhang, Zhe; Luo, Shuo; Barbosa, Guilherme Oliveira; Bai, Meirong; Kornberg, Thomas B.; Ma, Dengke K. title: The conserved ER-transmembrane protein TMEM39 coordinates with COPII to promote collagen secretion and prevent ER stress date: 2020-09-20 journal: bioRxiv DOI: 10.1101/2020.08.17.253450 sha: doc_id: 103504 cord_uid: ucqqpra5 Dysregulation of collagen production and secretion contributes to aging and tissue fibrosis of major organs. RNAi knockdown of the tmem-39 ortholog in Drosophila causes similar defects in collagen secretion from fat body cells. keywords: collagen; copii; fig; rnai; secretion; stress; tmem-39; tmem39a cache: cord-103504-ucqqpra5.txt plain text: cord-103504-ucqqpra5.txt item: #149 of 702 id: cord-103509-hynnba03 author: Wong, Ten-Tsao title: A self-assembled protein nanoparticle serving as a one-shot vaccine carrier date: 2020-09-18 words: 3235 flesch: 44 summary: As shown in figure 1A , when GFP protein with a molecular weight of 27kDa is able to pass through membranes with MWCO of 100kDa, 300kDa and 1000kDa freely, AH3-GFP fusion protein purified from bacterial lysate was prevented from passing through the membrane with an MWCO of 1000kDa. GFP protein has a thermal stable structure that constituted by 11 β-strands and 3 α-helices and some of the loops between strands have been explored as insertion sites for heterologous protein for various purposes (18, 19, 30) . keywords: ah3; complex; fig; fusion; gfp; peptide; protein; vaccine cache: cord-103509-hynnba03.txt plain text: cord-103509-hynnba03.txt item: #150 of 702 id: cord-103511-31njndob author: Broggi, Achille title: Type III interferons disrupt the lung epithelial barrier upon viral recognition date: 2020-05-05 words: 3898 flesch: 50 summary: Although different viruses vary in their virulence and pathogenic potential, 235 the most severe cases of lung RNA viral infections share similar features that suggest an immune 236 pathological etiology. The EpCAMcells were sorted for immune cells as follows: aMac were gated as CD45 + Ly6g -CD11c hi Siglec-F + , monocytes and monocyte-derived cells (Mo) were gated as CD45 + Ly6g -Siglec-F -Ly6C keywords: cells; fig; ifn; infections; lung; mice; poly; production; rna cache: cord-103511-31njndob.txt plain text: cord-103511-31njndob.txt item: #151 of 702 id: cord-103517-1itisiup author: Kwesi-Maliepaard, Eliza Mari title: The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8+ T cells date: 2019-11-18 words: 7915 flesch: 46 summary: Here we show that the histone methyltransferase DOT1L, which marks the nucleosome core on active genes, safeguards normal differentiation of CD8+ T cells. Through our study DOT1L is emerging as a central player in physiology of CD8+ T cells, acting as a barrier to prevent premature differentiation and supporting the licensing of the full effector potential of cytotoxic T cells. keywords: cd44; cd8; cells; differentiation; dot1l; expression; fig; genes; h3k79; histone; memory; mice; t cells; tcr cache: cord-103517-1itisiup.txt plain text: cord-103517-1itisiup.txt item: #152 of 702 id: cord-103523-46hn2249 author: Shaw, Dario R. title: Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria date: 2019-11-26 words: 3320 flesch: 44 summary: However, the mechanism 50 of how anammox bacteria reduce insoluble extracellular electron acceptors has remained 51 unexplored to date. The anammox cells were incubated anoxically for 216 hours in the 87 presence of 15 NH4 + (4 mM) and graphene oxide (GO) as a proxy for insoluble electron acceptor. keywords: anammox; bacteria; eet; electron; fig; nh4; oxidation cache: cord-103523-46hn2249.txt plain text: cord-103523-46hn2249.txt item: #153 of 702 id: cord-103524-1w9tdhdd author: Hao, Siyuan title: Establishment of a Replicon System for Bourbon Virus and Identification of Small Molecules that Efficiently Inhibit Virus Replication date: 2020-04-25 words: 4259 flesch: 52 summary: Surprisingly, at 10 µM, 3 flavonoids (#7, #9, and #135) inhibited BRBV RdRP activity by >50%. Since then, several deaths have been reported to be caused by BRBV infection in the Midwest and Southern United States. keywords: activity; brbv; cells; et al; fig; infection; influenza; virus cache: cord-103524-1w9tdhdd.txt plain text: cord-103524-1w9tdhdd.txt item: #154 of 702 id: cord-103528-3tib5o1m author: Ahmed, Asad title: DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity date: 2020-09-28 words: 3804 flesch: 46 summary: #in56 (number of atoms in 5 or 6 membered rings) • #noncon (ring atoms cannot form conjugated aromatic bonds) • #nonHatm (heavy atoms-nonhydrogen atoms) • RuleOfThree • RuleOfFive (lipinski violations) • QPlogKhsa (binding to human serum albumin) • PercentHuman-OralAbsorption Recent improvements to binding moad: a resource for protein ligand binding affinities and structures Gapped blast and psi-blast: a new generation of protein database search programs Analysis and comparison of 2d fingerprints: insights into database screening performance using eight fingerprint methods The mm/pbsa and mm/gbsa methods to estimate ligandbinding affinities Expert opinion on drug discovery Simboost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines Receptive fields, binocular interaction and functional architecture in the cat's visual cortex Batch normalization: Accelerating deep network training by reducing internal covariate shift Structure of M pro from SARS-CoV-2 and discovery of its inhibitors A series of pdb related databases for everyday needs sc-pdb: a 3d-database of ligandable binding sites-10 years on Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features On the binding affinity of macromolecular interactions: daring to ask why proteins interact Detection of multiscale pockets on protein surfaces using mathematical morphology Adam: A method for stochastic optimization Imagenet classification with deep convolutional neural networks Binding moad (mother of all databases Gradient-based learning applied to document recognition Deepatom: A framework for protein-ligand binding affinity prediction Deep learning in bioinformatics Bindingmoad, a high-quality protein-ligand database Deepdta: deep drug-target binding affinity prediction Pytorch: Tensors and dynamic neural networks in python with strong gpu acceleration. Binding affinity helps in understanding the degree of protein-ligand interactions and has wide protein applications. keywords: affinity; atoms; binding; features; learning; ligand; network; pocket; protein cache: cord-103528-3tib5o1m.txt plain text: cord-103528-3tib5o1m.txt item: #155 of 702 id: cord-103538-vh6ma7k7 author: Smaldino, Paul E. title: Coupled Dynamics of Behavior and Disease Contagion Among Antagonistic Groups date: 2020-10-05 words: 4980 flesch: 45 summary: However, when R 0 is high enough and outgroup aversion induces 258 group differences in behavior adoption, strong homophily among group 2 can lead to larger, albeit delayed, epidemics in the initially-uninfected segment of the population. We model behavior adoption as a susceptible-infectious-susceptible (SIS) process, in which individuals can oscillate between adoption and non-adoption of the behavior indef-120 initely. keywords: adoption; behavior; dynamics; group; homophily; infection; outgroup cache: cord-103538-vh6ma7k7.txt plain text: cord-103538-vh6ma7k7.txt item: #156 of 702 id: cord-103540-x18pz2uz author: Yellman, Christopher M. title: Precise replacement of Saccharomyces cerevisiae proteasome genes with human orthologs by an integrative targeting method date: 2020-03-26 words: 6455 flesch: 42 summary: Discovery to genome engineering Purification and characterization of the in vitro activity of I-Sce I, a novel and highly specific endonuclease encoded by a group I intron The Delitto Perfetto Approach to In Vivo Site-Directed Mutagenesis and Chromosome Rearrangements with Synthetic Oligonucleotides in Yeast A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells Gene Knockouts, in vivo Site-Directed Mutagenesis and Other Modifications Using the Delitto Perfetto System in Saccharomyces cerevisiae In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae Genetic modification stimulated by the induction of a sitespecific break distant from the locus of correction in haploid and diploid yeast Saccharomyces cerevisiae Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas Seamless site-directed mutagenesis of the Saccharomyces cerevisiae genome using CRISPR-Cas9 A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly Homology-integrated CRISPR-cas (HI-CRISPR) system for one-step multigene disruption in saccharomyces cerevisiae Genome-scale engineering of Saccharomyces cerevisiae with singlenucleotide precision Development of CRISPR-Cas systems for genome editing and beyond Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo Internal guide RNA interactions interfere with Cas9-mediated cleavage Genome-scale engineering of Saccharomyces cerevisiae with singlenucleotide precision Supplemental Off-target effects in CRISPR/Cas9-mediated genome engineering Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9 Systematic humanization of yeast genes reveals conserved functions and genetic modularity. New modules for the repeated internal and N-terminal epitope tagging of genes in Saccharomyces cerevisiae System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae A versatile toolbox for PCR-based tagging of yeast genes: New fluorescent proteins, more markers and promoter substitution cassettes Systematic humanization of yeast genes reveals conserved functions and genetic modularity. keywords: cassettes; cells; cerevisiae; dna; dsb; gene; human; proteasome; repair; scei; site; subunits; yeast cache: cord-103540-x18pz2uz.txt plain text: cord-103540-x18pz2uz.txt item: #157 of 702 id: cord-103542-mf721oa9 author: Mazhari, Ramin title: A comparison of non-magnetic and magnetic beads for measuring IgG antibodies against P. vivax antigens in a multiplexed bead-based assay using Luminex® technology (Bio-Plex® 200 or MAGPIX®) date: 2020-08-10 words: 1332 flesch: 35 summary: There are currently two formats that are widely used: non-magnetic beads or magnetic beads. Whilst non-magnetic beads can only be run on flow-based instruments (such as the Luminex® 100/200™ or Bio-Plex® 200), magnetic beads can be run on both these and the newer MAGPIX® instruments. keywords: beads; non; proteins cache: cord-103542-mf721oa9.txt plain text: cord-103542-mf721oa9.txt item: #158 of 702 id: cord-103554-11avjsqu author: Davies, Jennifer L title: Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles date: 2019-10-17 words: 5343 flesch: 50 summary: Within the quadriceps muscle group there was a main effect of muscle on anterior-posterior centre of gravity (p = 0.010), but the magnitude of the difference was very small. Within the quadriceps there was a main effect of muscle on medial-lateral hotspot (p = 0.027) and map volume (p = 0.047), but no post-hoc tests were significant. keywords: coil; emg; et al; limb; mep; motor; muscles; representation; stimulation cache: cord-103554-11avjsqu.txt plain text: cord-103554-11avjsqu.txt item: #159 of 702 id: cord-103563-7a3wdduq author: Nunez-Bajo, Estefania title: Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens date: 2020-03-25 words: 4541 flesch: 35 summary: As shown in Figure 4C , the peak current intensity (measured from the recorded SWVs) increased two to four times in comparison to room temperature when operated at higher temperatures; this is due to enhanced transport of the analyte to the surface of the electrode. We speculate that this could be related to thermal and electrical crosstalk between the heater and the electrochemical sensing structures which introduce additional noise to the electroanalytical measurements at higher temperatures. keywords: amplification; chip; cost; detection; dna; figure; pcr; silicon; temperature; time; trisilix cache: cord-103563-7a3wdduq.txt plain text: cord-103563-7a3wdduq.txt item: #160 of 702 id: cord-103567-nh9i28lu author: Vanachayangkul, Pattaraporn title: Safety, pharmacokinetics, and liver-stage Plasmodium cynomolgi effect of high-dose ivermectin and chloroquine in Rhesus Macaques date: 2020-04-29 words: 3690 flesch: 47 summary: Primer and probe sequences are as follows; P. cynomolgi Fwd: Blood sampling (1ml) for pharmacokinetic time points: just prior to first ivermectin dose, and 444 after first dose 1, 2, 4, 8, 12 hours, then each consecutive day just before dosing, then after the 445 7 th dose at 1, 2, 4, 8, 12 hours, and days 1, 2, 5, 12, 19. 153 154 Primary blood-stage parasitemia greater than 5,000/μl was detected ten days post inoculation 156 for negative and positive control groups and for 2 of 3 macaques in both ivermectin high (1.2 157 mg/kg)-and low (0.3 mg/kg)-dose groups, with remaining macaques from each group reaching 158 greater than 5,000/µl eleven days post inoculation which was 5 and 6 days after the last 159 ivermectin administration. keywords: blood; chloroquine; days; dose; ivermectin; liver; macaques; stage cache: cord-103567-nh9i28lu.txt plain text: cord-103567-nh9i28lu.txt item: #161 of 702 id: cord-103568-zesg4atp author: Iacullo, Carly title: Non-selective inhibition of the motor system following unexpected and expected infrequent events date: 2020-03-26 words: 5562 flesch: 32 summary: Moreover, CSE suppression due to unexpected events occurs at shorter latencies compared to expected infrequent events. Specifically, unexpected events induce CSE suppression even in the absence of motor initiation, which suggests a more drastic type of inhibitory control that is not evoked by expected infrequent events. keywords: cse; et al; events; inhibition; motor; signal; stop; suppression; task cache: cord-103568-zesg4atp.txt plain text: cord-103568-zesg4atp.txt item: #162 of 702 id: cord-103580-6rf1xs0d author: Arokiaraj, Mark Christopher title: A Novel Method of Immunomodulation of Endothelial cells Using Streptococcus Pyogenes and its Lysate date: 2020-05-15 words: 3674 flesch: 36 summary: The bacteria were cultured by seeding, and the colonies were inoculated with endothelial cells. Streptococcus pyogenes and its lysate has immunomodulation actions when tested with endothelial cells, which have pleiotropic functions. keywords: cells; diseases; disorders; factor; growth; heart; immune; lysate; pyogenes; regulation; streptococcus cache: cord-103580-6rf1xs0d.txt plain text: cord-103580-6rf1xs0d.txt item: #163 of 702 id: cord-103592-lkngp2u6 author: Bachmaier, Kurt title: Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury date: 2020-07-02 words: 6330 flesch: 36 summary: We consistently found that CD11b expression levels on PMN in peripheral blood, lung, and liver, were greater on ANP high PMN than on ANP low PMN ( Figure 1E ), and lung ANP high PMN showed the highest CD11b expression ( Figure 1E) , indicating a higher level of inflammatory activation of the ANP high PMN subset. Importantly, we found that CCR1 receptor cell surface expression, consistent with the mRNA data, was significantly greater on lung ANP high PMN than in ANP low PMN before and 3h, 6h, and 12h after LPS stimulation ( Figure 3B ). keywords: anp; beta; expression; figure; high; low; lps; lung; mice; neutrophils; panp; pmn; subset; tissue; treatment cache: cord-103592-lkngp2u6.txt plain text: cord-103592-lkngp2u6.txt item: #164 of 702 id: cord-103597-mt0h06y3 author: Muller, Alana title: Neurophysiological Correlates of the Dunning-Kruger Effect date: 2020-05-20 words: 14191 flesch: 29 summary: Additionally, while the electrophysiological results are compelling in suggesting memory effects contributing to the Dunning-Kruger phenomena, we should be cautious to avoid an over-reliance upon reverse inference Poldrack, 2011) since other cognitive processes also likely contribute to ERP effects of memory, too, such as implicit fluency and conceptual priming (Voss et al., 2014; Voss & Paller, 2010 Leynes & Zish; Leynes & Addante, 2016 ; though see comments in Addante et al., 2012a Under-estimators (those who performed best), on the other hand, exhibited a larger LPC than over-estimators did from 600-900 ms during memory judgments (Figures 7, 8) , indicating that these under-estimators may be making the decisions by reliance upon the clearer details of recollected information, as opposed to the fuzzy sense of familiarity that can come with less accuracy . keywords: confidence; differences; dke; dunning; effect; erp; estimators; et al; familiarity; judgments; kruger; memory; participants; percentile; performance; recollection; self; task; test cache: cord-103597-mt0h06y3.txt plain text: cord-103597-mt0h06y3.txt item: #165 of 702 id: cord-103606-5gbk6t6y author: Fettrow, Tyler title: Walking cadence affects the recruitment of the medial-lateral balance mechanisms date: 2019-06-03 words: 6106 flesch: 44 summary: To test our hypotheses about whether the relative influence of balance mechanisms changes at different cadences, we used R (R Core Team, 2013) and lme4 (Bates et al., 2015) to perform a linear mixed effects analysis. We found distinct changes in the use of balance mechanisms while walking at lower or higher cadences. keywords: ankle; balance; cadence; com; control; foot; foot placement; gait; mechanism; placement; walking cache: cord-103606-5gbk6t6y.txt plain text: cord-103606-5gbk6t6y.txt item: #166 of 702 id: cord-103618-cl7evbr3 author: Wang, Yingxue title: The WD and linker domains of ATG16L1 required for non-canonical autophagy limit lethal respiratory infection by influenza A virus at epithelial surfaces date: 2020-05-07 words: 5705 flesch: 44 summary: This second wave of cytokine expression was resolved by 7 d.p.i in control mice, but δWD mice showed sustained increases in ISG15, IFIT1, IL-1β, TNFα and CCL2 transcripts, co-incident with exacerbated weight loss. This increased susceptibility to IAV was not observed for control mice reconstituted with wild-type marrow, showing that non-canonical autophagy pathways in phagocytes and other leukocytes from control mice were not able to protect δWD mice against lethal IAV infection. keywords: atg16l1; autophagy; cells; cytokine; fig; iav; infection; lc3; lung; mice; virus; δwd cache: cord-103618-cl7evbr3.txt plain text: cord-103618-cl7evbr3.txt item: #167 of 702 id: cord-103625-p55ew8w7 author: Ramana, Chilakamarti V. title: Regulation of early growth response-1 (Egr-1) gene expression by Stat1-independent type I interferon signaling and respiratory viruses date: 2020-08-14 words: 3333 flesch: 34 summary: A shortlist of Egr-1 regulated genes was generated from the TRUUST transcription factor database and published studies in different cell types and under different stimuli (20) (21) (22) 46) . Interrogation of multiple microarray datasets revealed that respiratory viruses including coronaviruses regulated Egr-1 expression in human lung cell lines. keywords: cell; expression; gene; ifn; interferon; lung; response cache: cord-103625-p55ew8w7.txt plain text: cord-103625-p55ew8w7.txt item: #168 of 702 id: cord-103638-n5kpvsvg author: Nguyen, Long T. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 words: 5390 flesch: 48 summary: key: cord-103638-n5kpvsvg authors: Nguyen, Long T.; Smith, Brianna M.; Jain, Piyush K. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.13.036079 sha: doc_id: 103638 cord_uid: n5kpvsvg The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. In order to measure the collateral or trans-cleavage activity of Cas12a, we employed a FRET-based reporter used in DETECTR, 1 composed of a fluorophore (FAM) and a quencher (3IABkFQ) connected by a 5-nucleotide sequence (TTATT), which displays increased fluorescence upon cleavage. keywords: activity; cleavage; crrna; detection; dna; fig; lbcas12a; supplementary; trans cache: cord-103638-n5kpvsvg.txt plain text: cord-103638-n5kpvsvg.txt item: #169 of 702 id: cord-103648-g50g17ti author: Wang, Hao-Yuan title: Total synthesis and biological characterization of SR-A3, a ternatin-related eEF1A inhibitor with enhanced cellular residence time date: 2020-10-08 words: 2184 flesch: 41 summary: Furthermore, the H 1 and C 13 NMR spectra of SR-A3 appeared identical to the corresponding spectra of natural A3 (Figure 4c) . We found that synthetic SR-A3 is indistinguishable from naturally derived A3 and potently inhibits cancer cell proliferation. keywords: figure; synthesis; ternatin-4 cache: cord-103648-g50g17ti.txt plain text: cord-103648-g50g17ti.txt item: #170 of 702 id: cord-103652-yjl7uj2h author: Vickaryous, Nicola title: Remote testing of vitamin D levels across the UK MS population – a case control study date: 2020-10-16 words: 3266 flesch: 47 summary: Conclusions The UK MS population have higher serum 25(OH)D than controls, mainly as a result of vitamin D supplementation. Clinical trials of vitamin D supplementation in MS have failed to provide robust evidence of benefit [8] . keywords: controls; participants; sampling; serum; vitamin cache: cord-103652-yjl7uj2h.txt plain text: cord-103652-yjl7uj2h.txt item: #171 of 702 id: cord-103654-k02z72gb author: Gamboa Arana, Olga Lucia title: Dose-dependent enhancement of motion direction discrimination with transcranial magnetic stimulation of visual cortex date: 2020-06-15 words: 5861 flesch: 26 summary: Lastly, it is worth noting that there is an important movement towards larger and better powered sample sizes in TMS studies. TMS effects on VEPs showed reduced amplitudes in the 80% Pre-Onset condition, an increase for the 120% N2-Onset condition, and monotonic amplitude scaling with stimulation intensity. keywords: component; condition; eeg; effects; et al; intensity; motion; onset; pulse; response; stimulation; tms cache: cord-103654-k02z72gb.txt plain text: cord-103654-k02z72gb.txt item: #172 of 702 id: cord-103674-pmbpx162 author: Kalaycı, Salih title: The Linkage among Sea Transportation, Trade Liberalization and Industrial Development in the context of Carbon Dioxide Emissions: An Empirical Investigation from China date: 2020-07-13 words: 4524 flesch: 41 summary: According to results of FMOLS, DOLS and CCR models there is a long-term stable relationship between sea transportation, trade liberalization, industrial development and carbon dioxide emissions which is proved empirically. In this study, empirical results proved the impact of sea transportation, trade liberalization and industrial development on carbon dioxide emissions for China from 1980 to 2013. keywords: ardl; carbon; development; emissions; energy; growth; liberalization; term; trade cache: cord-103674-pmbpx162.txt plain text: cord-103674-pmbpx162.txt item: #173 of 702 id: cord-103683-xcsal8vk author: Rafie, K. title: The structure of enteric human adenovirus 41 - a leading cause of diarrhea in children date: 2020-10-16 words: 6656 flesch: 41 summary: In both hitherto published HAdV structures, HAdV-C5 (20) and HAdV-D26 (21), there is similarly shaped electron density at the corresponding position of the virus capsid (Fig. 5E ). Figures of protein structures and electron densities were generated using ChimeraX. Prospects of Replication-Deficient Adenovirus Based Vaccine Development against SARS-CoV-2. keywords: adenovirus; capsid; data; density; electron; enteric; f41; fig; hadv; human; model; pix; protein; refinement; resolution; structure cache: cord-103683-xcsal8vk.txt plain text: cord-103683-xcsal8vk.txt item: #174 of 702 id: cord-103688-n7hzpbyf author: Wang, Lina title: VirusDIP: Virus Data Integration Platform date: 2020-06-09 words: 1287 flesch: 34 summary: To promote sharing of virus data, several virus databases and related analyzing tools have been created. Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. keywords: analysis; data; virus cache: cord-103688-n7hzpbyf.txt plain text: cord-103688-n7hzpbyf.txt item: #175 of 702 id: cord-103703-t03r6ny8 author: Nguyen-Tu, Marie-Sophie title: Reduced expression of TCF7L2 in adipocyte impairs glucose tolerance associated with decreased insulin secretion, incretins levels and lipid metabolism dysregulation in male mice date: 2020-05-20 words: 6257 flesch: 43 summary: Thus, our data indicate that loss of Tcf7l2 gene expression in adipocytes leads to impairments on metabolic responses which are dependent on gender, age and nutritional status. In the present study, we used a genetic model of ablation of TCF7L2 gene expression in mature adipocytes to determine whether TCF7L2 plays a role in adipocyte function, independent of its role in adipogenesis. keywords: adipocytes; atcf7l2ko; beta; cell; expression; fatty; glucose; insulin; levels; mice; secretion; tcf7l2; tolerance cache: cord-103703-t03r6ny8.txt plain text: cord-103703-t03r6ny8.txt item: #176 of 702 id: cord-103709-86hv27vh author: Zhang, Dong Yan title: Prefusion spike protein stabilization through computational mutagenesis date: 2020-06-19 words: 3245 flesch: 45 summary: Due to the critical role in viral-host interaction and the exposure of spike protein, it has been a focus of most vaccines’ developments. Thus, since the prefusion spike protein exists in a thermodynamically metastable state 1 , a stabilized mutant conformation is critical for the development of vaccines and drugs. keywords: conservation; pipeline; protein; residues; rmsf; sasa; spike; structure cache: cord-103709-86hv27vh.txt plain text: cord-103709-86hv27vh.txt item: #177 of 702 id: cord-103714-06hhlma3 author: Miller, Mariël title: Examination of a first-in-class bis-dialkylnorspermidine-terphenyl antibiotic in topical formulation against mono and polymicrobial biofilms date: 2020-06-04 words: 2445 flesch: 38 summary: Novel drug approvals for Novel drug approvals for FDA (2019) Novel drug approvals for ecology of bacteria in chronic wounds Outcomes of surgical treatment of diabetic foot 526 osteomyelitis: a series of 185 patients with histopathological confirmation of bone 527 involvement Diagnostic strategies in osteomyelitis Culture of 530 percutaneous bone biopsy specimens for diagnosis of diabetic foot osteomyelitis: 531 concordance with ulcer swab cultures Culture of per-wound 533 bone specimens: a simplified approach for the medical management of diabetic foot 534 osteomyelitis Multiple 536 bacterial species reside in chronic wounds: a longitudinal study Biofilms in chronic 538 wounds Survey of bacterial 540 diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun 541 sequencing The penetration of antibiotics into 543 aggregates of mucoid and non-mucoid Pseudomonas aeruginosa Self-generated diversity produces insurance 546 effects in biofilm communities Biofilm maturity 548 studies indicate sharp debridement opens a time-dependent therapeutic window Topical and systemic antibiotics in the management 551 of periodontal diseases Introduction to biofilm Characterization of biologic properties of wound 555 fluid collected during early stages of wound healing Overview of wound healing in a moist environment In vitro testing of a 559 first-in-class tri-alkylnorspermidine-biaryl antibiotic in an anti-biofilm silicone coating Interaction between polyamines and bacterial outer 562 membranes as investigated with ion-selective electrodes An in vitro 565 biofilm model to examine the effect of antibiotic ointments on biofilms produced by burn 566 wound bacterial isolates Experimental 568 model of biofilm implant-related osteomyelitis to test combination biomaterials using 569 biofilms as initial inocula In vivo efficacy 571 of a silicone -cationic steroid antimicrobial coating to prevent implant-related infection Growth substrate 574 may influence biofilm susceptibility to antibiotics Developing selective media for quantification 576 of multispecies biofilms following antibiotic treatment Selection for 578 Staphylococcus aureus small-colony variants due to growth in the presence of 579 Pseudomonas aeruginosa Microevolution of 581 cytochrome bd oxidase in Staphylococci and its implication in resistance to respiratory 582 toxins released by Pseudomonas Small-colony variant selection as 584 a survival strategy for Staphylococcus aureus in the presence of Pseudomonas 585 aeruginosa Advanced wound 587 care therapies for nonhealing diabetic, venous, and arterial ulcers: a systematic review GlaxoSmithKline (2015) key: cord-103714-06hhlma3 authors: Miller, Mariël; Rogers, Jeffery C.; Badham, Marissa A.; Cadenas, Lousili; Brightwell, Eian; Adams, Jacob; Tyler, Cole; Sebahar, Paul R.; Haussener, Travis J.; Reddy, Hariprassada K.; Looper, Ryan E.; Williams, Dustin L. title: Examination of a first-in-class bis-dialkylnorspermidine-terphenyl antibiotic in topical formulation against mono and polymicrobial biofilms date: 2020-06-04 journal: bioRxiv DOI: 10.1101/2020.06.04.133934 sha: doc_id: 103714 cord_uid: 06hhlma3 Biofilm-impaired tissue is a significant factor in chronic wounds such as diabetic foot ulcers. keywords: aeruginosa; biofilms; cellulose; cfu; drug; growth cache: cord-103714-06hhlma3.txt plain text: cord-103714-06hhlma3.txt item: #178 of 702 id: cord-103715-53v1qoyc author: Bauman, Neda title: Computational image analysis reveals the structural complexity of Toxoplasma gondii tissue cysts date: 2020-05-21 words: 1028 flesch: 40 summary: Vet S2 Data -Fractal dimension and lacunarity of tissue cysts (n=31) S3 Data -Binary images of T. gondii cysts segmented by watershed algorithm (n=31) The objective of this study was to quantify the geometrical complexity of T. gondii cysts by morphological, particle, and fractal analysis, as well as to determine if and how it is impacted by parasite strain, cyst age, and host factors. keywords: analysis; cysts; fractal; gondii cache: cord-103715-53v1qoyc.txt plain text: cord-103715-53v1qoyc.txt item: #179 of 702 id: cord-103733-blam1f4c author: Levade, Inès title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date: 2020-06-24 words: 2669 flesch: 27 summary: key: cord-103733-blam1f4c authors: Levade, Inès; Saber, Morteza M.; Midani, Firas; Chowdhury, Fahima; Khan, Ashraful I.; Begum, Yasmin A.; Ryan, Edward T.; David, Lawrence A.; Calderwood, Stephen B.; Harris, Jason B.; LaRocque, Regina C.; Qadri, Firdausi; Shapiro, B. Jesse; Weil, Ana A. title: Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study date: 2020-06-24 journal: bioRxiv DOI: 10.1101/2020.02.25.960930 sha: doc_id: 103733 cord_uid: blam1f4c Background Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. Updated Global Burden of Cholera in Endemic 420 Countries Cholera epidemic in Yemen, 2016-18: an 422 analysis of surveillance data Defining endemic cholera at three levels of 424 spatiotemporal resolution within Bangladesh Clinical Outcomes in Household Contacts of 426 Patients with Cholera in Bangladesh Cholera transmission: the 428 host, pathogen and bacteriophage dynamic Susceptibility to Vibrio cholerae Infection 430 in a Cohort of Household Contacts of Patients with Cholera in Bangladesh Roles of the intestinal microbiota in pathogen protection Members of the human gut microbiota 435 involved in recovery from Vibrio cholerae infection Bile Salts 437 Modulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae A single gene of a commensal microbe affects host 440 susceptibility to enteric infection Probiotic strains detect and suppress 442 cholera in mice Anti-biofilm Properties of the Fecal Probiotic 444 Lactobacilli Against Vibrio spp Commensal-derived metabolites govern Vibrio cholerae 446 pathogenesis in host intestine Gut Microbial Succession Follows Acute Secretory 448 Diarrhea in Humans Human Gut Microbiota Predicts Susceptibility 450 to Vibrio cholerae Infection MetaPhlAn2 for enhanced metagenomic 452 taxonomic profiling Species-level functional profiling of 454 metagenomes and metatranscriptomes Machine Learning Meta-analysis of 456 Large Metagenomic Datasets: Tools and Biological Insights Fillat MF. keywords: cholerae; cohort; disease; gut; infection; species; table cache: cord-103733-blam1f4c.txt plain text: cord-103733-blam1f4c.txt item: #180 of 702 id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: 5837 flesch: 49 summary: Viral contigs were confirmed by PCR and Sanger sequencing for samples L7, L17, L25 and L37 (Suppl. Of the 11 water filtrate samples tested, two samples from Mongolia (WM3 and WM20) (18.2%) had viral contigs with 100% identity to the Equid herpesvirus 1 and 3 (EHV-1 and EHV-3). keywords: capture; contigs; dna; fig; identity; leeches; pcr; reads; rna; samples; sediment; sequences; suppl; viruses; water; wildlife cache: cord-103735-nil1vv6h.txt plain text: cord-103735-nil1vv6h.txt item: #181 of 702 id: cord-103739-mmkrwj8t author: Snijder, Eric J. title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 words: 3813 flesch: 35 summary: However, it is not clear that DMVs always play the primary role 421 in virus replication that we demonstrate here for CoV. For picornaviruses, for example, virus- were freeze-substituted in a Leica AFS2 system with 0.1% (wt/vol) uranyl acetate as 576 previously described [71] , with the only modification that acetone was replaced by ethanol 577 from the last washing step before Lowycril infiltration onwards. The comprehensive analysis presented here demonstrates that viruses across different CoV 371 genera induce essentially the same type of membrane structures. keywords: autoradiography; coronavirus; cov; dmss; dmvs; membrane; replication; rna; virus cache: cord-103739-mmkrwj8t.txt plain text: cord-103739-mmkrwj8t.txt item: #182 of 702 id: cord-103757-fed21fhu author: McPherson, Malinda J. title: Time-dependent discrimination advantages for harmonic sounds suggest efficient coding for memory date: 2020-10-15 words: 13346 flesch: 42 summary: However, previous studies examining effects of musicianship on pitch discrimination used either pure tone or harmonic complex tone stimuli, and thus do not differentiate between representations of the f0 vs. the spectrum. For harmonic tones, listeners could compare f0 estimates for the two tones or follow the spectrum. keywords: conditions; delay; discrimination; experiment; harmonic; memory; note; participants; pitch; second; sounds; stimuli; tones; trial cache: cord-103757-fed21fhu.txt plain text: cord-103757-fed21fhu.txt item: #183 of 702 id: cord-103770-4svaq0at author: Ogrodzinski, Martin P. title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date: 2019-10-07 words: 671 flesch: 39 summary: key: cord-103770-4svaq0at authors: Ogrodzinski, Martin P.; Lunt, Sophia Y. title: Metabolomic profiling of mouse mammary tumor derived cell lines reveals targeted therapy options for cancer subtypes date: 2019-10-07 journal: bioRxiv DOI: 10.1101/796573 sha: doc_id: 103770 cord_uid: 4svaq0at Breast cancer is a heterogeneous disease with several subtypes that currently do not have targeted therapy options. Metabolites 92 increased in the papillary subtype include fructose bisphosphate (FBP; glycolysis); acetyl-CoA indicating relative metabolite differences between EMT and papillary tumor derived cell lines. keywords: metabolic; subtypes cache: cord-103770-4svaq0at.txt plain text: cord-103770-4svaq0at.txt item: #184 of 702 id: cord-103773-1b961lfz author: Kurokawa, Shunji title: In vivo recellularization of xenogeneic vascular grafts decellularized with high hydrostatic pressure method in a porcine carotid arterial interpose model date: 2020-05-29 words: 2917 flesch: 33 summary: Xenogeneic decellularized vascular grafts from animals potentially substitute for autologous vascular grafts. HHP decellularized vascular grafts may be utilized as new medical products for revascularization surgeries. keywords: arteries; artery; fig; grafts; hhp; implantation; phase; surface; vascular cache: cord-103773-1b961lfz.txt plain text: cord-103773-1b961lfz.txt item: #185 of 702 id: cord-103781-bycskjtr author: Mönke, Gregor title: Optimal time frequency analysis for biological data - pyBOAT date: 2020-06-04 words: 7390 flesch: 49 summary: key: cord-103781-bycskjtr authors: Mönke, Gregor; Sorgenfrei, Frieda A.; Schmal, Christoph; Granada, Adrián E. title: Optimal time frequency analysis for biological data - pyBOAT date: 2020-06-04 journal: bioRxiv DOI: 10.1101/2020.04.29.067744 sha: doc_id: 103781 cord_uid: bycskjtr Methods for the quantification of rhythmic biological signals have been essential for the discovery of function and design of biological oscillators. With this challenge in mind, we have developed pyBOAT, a Python-based fully automatic stand-alone software that integrates multiple steps of non-stationary oscillatory time series analysis into an easy-to-use graphical user interface. keywords: analysis; data; et al; figure; frequency; lter; noise; oscillations; period; power; pyboat; signal; smoothing; spectrum; time; wavelet cache: cord-103781-bycskjtr.txt plain text: cord-103781-bycskjtr.txt item: #186 of 702 id: cord-103788-sxw4l9tt author: Talbot, Steven R. title: One score to rule them all: severity assessment in laboratory mice date: 2020-06-24 words: 6003 flesch: 50 summary: In conclusion, we propose the RELSA score as a validated tool for objective real-time applicability in severity assessment and as a first step towards a unified and accessible risk assessment tool in biomedical research. Therefore, the chosen parameters for severity assessment should be 280 multimodal 30 . keywords: animals; assessment; colitis; data; fig; mice; parameters; relsa; score; set; severity; values; variables cache: cord-103788-sxw4l9tt.txt plain text: cord-103788-sxw4l9tt.txt item: #187 of 702 id: cord-103802-mygo3qx0 author: Li, Yanpeng title: Multiple known and a novel parvovirus associated with an outbreak of feline diarrhea and vomiting date: 2020-03-25 words: 1781 flesch: 33 summary: Of the other 15 affected cats in 280 Shelter 2 a total of 5 individual cats and a sample pool (mixed feces from 3 cats) were Using metagenomics, we found FeBoV1, 2, and 3 and a novel chaphamaparvovirus we named 311 fechavirus in a large fraction of fecal samples and fechavirus in all vomit samples from sick cats 312 in a multi-facility outbreak. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease. keywords: cats; feline; novel; shelter cache: cord-103802-mygo3qx0.txt plain text: cord-103802-mygo3qx0.txt item: #188 of 702 id: cord-103812-ls6zgipi author: Norris, Rachael P. title: Gap junction internalization and processing in vivo: a 3D immuno-electron microscopy study date: 2020-06-30 words: 4810 flesch: 50 summary: A review Differential modulation of rat follicle cell gap junction populations at ovulation Degradation of annular gap junctions of the equine hoof wall Endosome-tocytosol transport of viral nucleocapsids Endocytic processing of connexin43 gap junctions: a morphological study Autophagy: a pathway that contributes to connexin degradation Oral tolerance can be established via gap junction transfer of fed antigens from CXCR1+ macrophages to CD103+ dendritic cells The fine structure of granulosa cell nexuses in rat ovarian follicles Influence of aldehyde fixation on the morphology of endosomes and lysosomes: quantitative analysis and electron tomography Endosomal compartmentalization in three dimensions: implications for membrane fusion Gap junctions Luteinizing hormone causes MAP kinase-dependent phosphorylation and closure of connexin 43 gap junctions in mouse ovarian follicles: one of two paths to meiotic resumption Localization of phosphorylated Connexin 43 using serial section immunogold electron microscopy Colocalization of connexin 43 and connexin 45 but absence of connexin 40 in granulosa cell gap junctions of rat ovary This tissue was used because it has large numbers of Cx43 gap junctions (Okuma et al, 1996 ; Norris et al., 2008 Norris et al., , 2017 Baena et al., 2020) , which are caused to internalize in response to hormone (Larsen et al., 1987) . keywords: cell; connexosomes; cx43; gap; junctions; membrane; sections; vesicles cache: cord-103812-ls6zgipi.txt plain text: cord-103812-ls6zgipi.txt item: #189 of 702 id: cord-103813-w2sb6h94 author: Schumacher, Garrett J. title: Genetic information insecurity as state of the art date: 2020-07-10 words: 6461 flesch: 30 summary: Human genetic information is identifiable and contains sensitive information, but genetic data security is only recently gaining attention. Genetic data is generated in an evolving and distributed cyber-physical ecosystem, with multiple systems that handle data and multiple partners that utilize the data. keywords: data; devices; dna; ecosystem; et al; information; laboratory; material; privacy; samples; security; sequencing; stakeholders; systems cache: cord-103813-w2sb6h94.txt plain text: cord-103813-w2sb6h94.txt item: #190 of 702 id: cord-103830-pu6v53oy author: Pichon, Fabien title: Analysis and annotation of genome-wide DNA methylation patterns in two nonhuman primate species using the Infinium Human Methylation 450K and EPIC BeadChips date: 2020-05-10 words: 5444 flesch: 42 summary: For example, using different selection criteria for probes yielding reliable signals, 61% of human probes were mapped and annotated to the Macaca fascicularis genome and subsequently used to study the impact of birth weight on gene methylation and expression in Macaca fascicularis We thus chose to remove probes presenting a mismatch at 1 or 2 bp from the CpG from the Furthermore, using Pyrosequencing, which as a sequencing-by-synthesis method is not dependent on human probes but uses species-specific amplification and sequencing primers, we validated DNA methylation levels measured by the respective Infinium probes at three CpG positions in each species showing a high correlation between the two orthogonal technologies and validating our approach of selecting reliable probes (Figure 4 ). keywords: 450k; cpg; dna; gene; genome; human; infinium; methylation; mismatches; probes; species cache: cord-103830-pu6v53oy.txt plain text: cord-103830-pu6v53oy.txt item: #191 of 702 id: cord-103853-ar09nzmw author: Wayment-Steele, Hannah K. title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 words: 4331 flesch: 35 summary: key: cord-103853-ar09nzmw authors: Wayment-Steele, Hannah K.; Kladwang, Wipapat; Das, Rhiju title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 journal: bioRxiv DOI: 10.1101/2020.05.29.124511 sha: doc_id: 103853 cord_uid: ar09nzmw The computer-aided study and design of RNA molecules is increasingly prevalent across a range of disciplines, yet little is known about the accuracy of commonly used structure prediction packages in real-world tasks. As more sources of structural data continue to be made available in higher quantity, resolution, and scope, the EternaBench and EternaFold frameworks will allow for the usage of these datasets in continually assessing and improving RNA structure prediction. keywords: chemical; contrafold; data; datasets; figure; mapping; packages; prediction; rna; structure cache: cord-103853-ar09nzmw.txt plain text: cord-103853-ar09nzmw.txt item: #192 of 702 id: cord-103864-4kec8re4 author: Miao, Zhen title: Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets date: 2020-06-04 words: 1821 flesch: 20 summary: Leveraging this newly 564 identified cell type-specific regulatory network will be essential for future studies of cellular 565 reprogramming of precursors into specific kidney cell types and for better understanding 566 homeostatic and maladaptive regeneration. We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. keywords: cell; chromatin; expression; gene; kidney; type cache: cord-103864-4kec8re4.txt plain text: cord-103864-4kec8re4.txt item: #193 of 702 id: cord-103868-iwpiti2h author: Harrison, Angela R. title: The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking date: 2020-08-11 words: 2265 flesch: 35 summary: Nuclear export is not required for STAT1 antagonism, consistent with competitive karyopherin binding being the principal antagonistic mechanism while export mediates return of nuclear VP24 to the cytoplasm for replication functions. Nuclear export is not 27 required for STAT1 antagonism, consistent with competitive karyopherin binding being the 28 principal antagonistic mechanism while export mediates return of nuclear VP24 to the 29 cytoplasm for replication functions. keywords: export; gfp; localisation; vp24 cache: cord-103868-iwpiti2h.txt plain text: cord-103868-iwpiti2h.txt item: #194 of 702 id: cord-103869-ii6qi1bp author: Yang, Liu title: Defining a Global Map of Functional Group Based 3D Ligand-binding Motifs date: 2020-09-28 words: 7445 flesch: 44 summary: Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. As shown in Fig. 1B , our method identified three FA clusters or binding motifs corresponding to triphosphate group, ribose and adenine, respectively. keywords: binding; class; fgs; fig; hydrophobic; interactions; ligand; motifs; pockets; protein cache: cord-103869-ii6qi1bp.txt plain text: cord-103869-ii6qi1bp.txt item: #195 of 702 id: cord-103872-yzqic5vt author: Liu, Zhijin title: Global view on virus infection in non-human primates and implication for public health and wildlife conservation date: 2020-05-13 words: 1312 flesch: 38 summary: Non-human primates (NHPs), as our evolutionary closest relatives, are susceptible to human viruses, and a number of pathogens are known to circulate between humans and NHPs. The most prominent cases of virus transmission from wild NHPs to human are 54 simian foamy virus (SFV), yellow fever virus (YFV), Zika virus (ZIKV), and human 55 immunodeficiency virus (HIV) keywords: centrality; humans; nhps; virus cache: cord-103872-yzqic5vt.txt plain text: cord-103872-yzqic5vt.txt item: #196 of 702 id: cord-103876-2rg2qtdq author: Watkins, Laura C. title: Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics date: 2020-06-20 words: 5532 flesch: 40 summary: World Health Organization The M2 proton channels of influenza A and B viruses Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block Viroporins: structure, function and potential as antiviral targets SARS coronavirus E protein forms cation-selective ion channels Severe acute respiratory syndrome-associated coronavirus 3a protein forms an ion channel and modulates virus release Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity Structure and mechanism of the M2 proton channel of influenza A virus Mechanisms of proton conduction and gating in influenza M2 proton channels from solid-state NMR Effect of cytosolic pH on inward currents reveals structural characteristics of the proton transport cycle in the influenza A protein M2 in cell-free membrane patches of Xenopus oocytes Acid activation mechanism of the influenza A M2 proton channel Put a cork in it: Plugging the M2 viral ion channel to sink influenza In Vitro Pharmacokinetic Optimizations of AM2-S31N Channel Blockers Led to the Discovery of Slow-Binding Inhibitors with Potent Antiviral Activity against Drug-Resistant Influenza A Viruses Exploring the Requirements for the Hydrophobic Scaffold and Polar Amine in inhibitors of M2 from Influenza A Virus Identification of hits as matrix-2 protein inhibitors through the focused screening of a small primary amine library Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations Hydrogen-bonded water molecules in the M2 channel of the influenza A virus guide the binding preferences of ammonium-based inhibitors Computationally Efficient Multiconfigurational Reactive Molecular Dynamics Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase Proton movement and coupling in the POT family of peptide transporters Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux Exchange Pathways in ClC-ec1 Antiporter Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction Computational studies to date have primarily focused on the means of entry into the channel and location of binding, 42-46 but have not deduced specific interactions between the drug, channel, and channel water involved in binding as they relate specifically to similar interactions seen in the PT mechanism. keywords: binding; channel; drug; excess; hydrogen; influenza; protein; proton; water cache: cord-103876-2rg2qtdq.txt plain text: cord-103876-2rg2qtdq.txt item: #197 of 702 id: cord-103888-ggm29vrz author: Nova, Nicole title: Susceptible host availability modulates climate effects on dengue dynamics date: 2020-10-19 words: 1541 flesch: 29 summary: However, the converse 199 scenario would not be true: since dengue does not cause temperature, the shadow 200 attractor constructed using temperature data should not contain information to 201 accurately reconstruct past dengue incidence (Supporting Information). By capturing mechanistic, nonlinear, and context-dependent effects of population susceptibility, temperature, and rainfall on dengue transmission empirically, our model improves forecast skill over recent, state-of-the-art models for dengue incidence. keywords: dengue; incidence; rainfall; temperature cache: cord-103888-ggm29vrz.txt plain text: cord-103888-ggm29vrz.txt item: #198 of 702 id: cord-103892-v6gkubd4 author: Mäkinen, Janne J. title: The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases date: 2020-07-01 words: 8488 flesch: 45 summary: 6-MI allowed the monitoring of RNAP translocation along the DNA following nucleotide incorporation (Supplementary Fig. 1a) . In contrast, the interaction of the conserved Arg with the 3'OH of the 2'dNTP substrates shapes their deoxyribose moiety into the catalytically inert 2'-endo conformation where the 3'OH cannot promote closure of the active site and substrate incorporation is additionally inhibited by the unfavorable geometry of the triphosphate moiety. keywords: 2'dntps; 3'oh; active; data; dna; fig; incorporation; rnaps; site; substrate; supplementary; table; β'arg425 cache: cord-103892-v6gkubd4.txt plain text: cord-103892-v6gkubd4.txt item: #199 of 702 id: cord-103895-dt0ers70 author: Zeng, Xiangrui title: Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis date: 2018-10-16 words: 4509 flesch: 47 summary: Subsequently, we developed a text mining algorithm to automate the annotation of pathway clusters by extracting keywords from pathway descriptions, which also offers more statistically valid summarization compared to leaving user exploring each pathway in a cluster manually and heuristically. Then, to gain more insight into the underlying biological mechanism, pathway analysis (a.k.a. gene set analysis) is usually applied to pursue the functional annotation of the candidate biomarker list. keywords: analysis; cluster; cpi; layer; pathway; schizophrenia; test; text cache: cord-103895-dt0ers70.txt plain text: cord-103895-dt0ers70.txt item: #200 of 702 id: cord-103914-ppgx7mci author: Maughan, Elizabeth F. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 words: 8208 flesch: 38 summary: The differentiated cell types in this slow-turnover tissue are replenished by airway basal cells, which act as multipotent progenitors (Rock et al., 2010; Teixeira et al., 2013) . However, the majority of differentially expressed genes do not have previously described roles in airway basal cells. keywords: adult; age; airway; analysis; basal; cells; children; culture; differences; epithelium; et al; expression; figure; genes; human; lung; medium; paediatric; rna; samples cache: cord-103914-ppgx7mci.txt plain text: cord-103914-ppgx7mci.txt item: #201 of 702 id: cord-103915-rzy7mejb author: Duricki, Denise A. title: Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke date: 2018-07-11 words: 12878 flesch: 48 summary: However, ELISA cannot distinguish exogenous human NT3 from endogenous rat NT3 because the amino acid sequences for mature human and rat NT3 are identical 58,59 . Because ELISA did not allow us to detect any small increases in exogenous human NT3 against the background of endogenous rat NT3 in the CNS, we next used a more sensitive method for measuring trafficking of NT3 across the blood-CNS barrier. keywords: brain; cord; cst; fig; forelimb; group; human; muscle; nerve; neurotrophin-3; nt3; protein; rats; recovery; spinal; stimulation; stroke; time; treatment; triceps; vehicle; weeks; wrist cache: cord-103915-rzy7mejb.txt plain text: cord-103915-rzy7mejb.txt item: #202 of 702 id: cord-103924-mhgnqi80 author: Shin, Donghyuk title: Novel class of OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection date: 2020-04-28 words: 2107 flesch: 44 summary: S1 S1 Prg K63 S1 S1 LotC-host proteins Interactome LotB-host proteins Interactome MRPL12 NDUFS4 RPS12 SF3B5 SLC25A1 SERBP1 NPM1 SPTBN1 PRDX2 UBA52 RPS5 RPS8 RPS27 PPM1B PCNA A crystal structure of LotC catalytic core (LotC14-310) was determined at 2.4 Å and compared with other OTU deubiquitinases, including LotB. Unlike the classical OTU-family, the structures of Legionella OTU-family (LotB and LotC) shows an extended helical lobe between the Cys-loop and the variable loop, which define a novel class of OTU-deubiquitinase. keywords: fig; legionella; lotb; lotc; otu; proteins; ubiquitin cache: cord-103924-mhgnqi80.txt plain text: cord-103924-mhgnqi80.txt item: #203 of 702 id: cord-103925-i73ymrov author: Hill, Chris H. title: Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date: 2020-08-11 words: 11567 flesch: 45 summary: Cardioviruses are genetically diverse and cause common enteric infections in South Asian children Phylogenetic analysis of the species Theilovirus: emerging murine and human pathogens Facets of Theiler's Murine Encephalomyelitis Virus-Induced Diseases: An Update A detailed kinetic analysis of the in vitro synthesis and processing of encephalomyocarditis virus products Proteolytic processing of picornaviral polyprotein Cell-specific proteins regulate viral RNA translation and virus-induced disease However, 2A protein sequences are highly divergent within cardioviruses, and the TMEV protein shares only ~ 27 % pairwise amino acid sequence identity with its EMCV orthologue. keywords: analysis; binding; cells; data; emcv; figure; frameshifting; genome; loop; prf; protein; reads; ribosomal; ribosome; rna; sequence; site; tmev; translation; virus cache: cord-103925-i73ymrov.txt plain text: cord-103925-i73ymrov.txt item: #204 of 702 id: cord-103940-a2cqw8kg author: Shi, Yuejun title: Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins date: 2020-06-09 words: 3221 flesch: 52 summary: Mice sera of HCoV-229E S trimer (orange) and HCoV-229E Since the S1 protein is expressed in a monomeric form, RBD is not restricted by 257 We compared the structures of S trimers and RBDs among alpha-coronaviruses 258 (Figs. 1B and 6A) . keywords: alpha; cov; hcov-229e; rbd; sars; trimer cache: cord-103940-a2cqw8kg.txt plain text: cord-103940-a2cqw8kg.txt item: #205 of 702 id: cord-103946-c5i8btp7 author: Li, Maohua title: Next generation of anti-PD-L1 Atezolizumab with better anti-tumor efficacy in vivo date: 2020-07-01 words: 4397 flesch: 45 summary: In this paper, based on the knowledge of an antibody's 3D conformation changes post antigen binding, we propose a novel way to design antibody drugs without ADCC function by simply inserting a flexible amino acid sequence such as GGGS into the hinge region of the antibody's Fc region. High molecular weight (HMW) aggregations of antibody drugs are the major causes of antidrug antibody (ADA) 3 . keywords: adcc; antibodies; antibody; atezolizumab; binding; cells; human; igg1; maxatezo; region; tumor cache: cord-103946-c5i8btp7.txt plain text: cord-103946-c5i8btp7.txt item: #206 of 702 id: cord-103964-k6jnv87v author: Friedl, Jana title: More than just a ticket canceller: The mitochondrial processing peptidase matures complex precursor proteins at internal cleavage sites date: 2020-07-03 words: 2333 flesch: 43 summary: The regulatory region of the divergent argECBH operon in Escherichia coli K-12 An Early mtUPR: Redistribution of the 523 Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic 524 Aggregates The versatility of the mitochondrial presequence 526 processing machinery: cleavage, quality control and turnover New roles for mitochondrial proteases in health, ageing 528 and disease The NADH Dehydrogenase Nde1 Executes Cell Death after 531 Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface Role of the membrane potential in mitochondrial protein unfolding 534 and import Two distinct membrane potential-dependent steps drive mitochondrial matrix 537 protein translocation The Benefits of Cotranslational Assembly: A Structural Perspective Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome 542 profiling The biosynthesis of insulin and a probable precursor of insulin by a human 544 islet cell adenoma Requirement for the yeast gene LON in 546 intramitochondrial proteolysis and maintenance of respiration N-terminome analysis of the human mitochondrial 549 proteome The N-end rule pathway and regulation by proteolysis Multi-553 omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production 556 Mitochondrial protein turnover: role of the precursor intermediate peptidase Oct1 in protein 557 stabilization Global analysis of the mitochondrial 560 N-proteome identifies a processing peptidase critical for protein stability Mitochondrial targeting sequences may form amphiphilic helices Molecular chaperones cooperate with 563 PIM1 protease in the degradation of misfolded proteins in mitochondria Construction of a set of convenient 565 Saccharomyces cerevisiae strains that are isogenic to S288C Proteomic profiling of the 567 mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein Viral precursor polyproteins: keys of regulation from replication to 570 maturation Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-573 ketoamide inhibitors Δarg5,6) were transformed with plasmids for expression of the indicated Arg5,6 variants and 605 streaked out on plates containing minimal growth medium without arginine Figure 3. Our data suggest that, in addition to its role as “ticket canceller” for the removal of presequences, MPP exhibits a second, widely conserved activity as internal processing peptidase for complex mitochondrial precursor proteins. keywords: arg5; arg5,6; fig; mpp; precursor; proteins cache: cord-103964-k6jnv87v.txt plain text: cord-103964-k6jnv87v.txt item: #207 of 702 id: cord-103990-qvuv289g author: Amster, Guy title: Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations date: 2019-09-09 words: 5520 flesch: 36 summary: A study of 32 mammalian genomes Revising the human mutation rate: implications for understanding human evolution Inferring human population size and separation history from multiple genome sequences Notably, their effects on polymorphism ratios in human populations has garnered considerable interest over the past decade (8) (9) (10) (11) (12) (13) (14) (15) . keywords: estimates; history; mutation; polymorphism; populations; ratios cache: cord-103990-qvuv289g.txt plain text: cord-103990-qvuv289g.txt item: #208 of 702 id: cord-104001-5clslvqb author: Wang, Xiaoqi title: selfRL: Two-Level Self-Supervised Transformer Representation Learning for Link Prediction of Heterogeneous Biomedical Networks date: 2020-10-21 words: 5525 flesch: 43 summary: Based on the above analysis, there are two main problems in link prediction based on network representation learning. Network representation learning plays a significant role in various network analysis tasks, such as community detection, link prediction, and node classification. keywords: hbns; learning; link; meta; network; path; prediction; representation; selfrl cache: cord-104001-5clslvqb.txt plain text: cord-104001-5clslvqb.txt item: #209 of 702 id: cord-104008-luqvw0y8 author: Levinson, Julia title: Investigating the effectiveness of school health services delivered by a health provider: a systematic review of systematic reviews date: 2019-02-07 words: 6731 flesch: 50 summary: In order for policy makers and leaders in school health to make evidence-based recommendations on which services should be available in schools, who should deliver them, and how should they be delivered, more SRs must be done. Through a comprehensive literature search, the 71 overview aimed to identify health areas and specific school health service interventions that 72 have at least some evidence of effectiveness. keywords: children; effectiveness; evidence; health; interventions; overview; review; school; services; srs; studies cache: cord-104008-luqvw0y8.txt plain text: cord-104008-luqvw0y8.txt item: #210 of 702 id: cord-104025-ysxc7rpl author: Cheek, Martin title: Deinbollia onanae (Sapindaceae), a new, Endangered, montane tree species from the Cameroon Highlands date: 2020-10-26 words: 4006 flesch: 50 summary: Index Herbariorum: A global directory of public herbaria and associated staff Notes on Deinbollia species from Cameroon New Sapindaceae from Cameroon and Nigeria Documented extinctions of plant species are increasing, e.g. Oxygyne triandra Schltr. of Cameroon is now known to be globally extinct (Cheek et al., 2018b) . keywords: cameroon; cheek; deinbollia; et al; forest; new; plants; species cache: cord-104025-ysxc7rpl.txt plain text: cord-104025-ysxc7rpl.txt item: #211 of 702 id: cord-104030-eb29t38n author: Morales-Nebreda, Luisa title: Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia date: 2020-06-05 words: 3970 flesch: 26 summary: Gene expression profiling of lung Treg cells during the recovery phase of influenza infection showed that young Treg cells significantly upregulated genes (when compared with aged Treg cells) linked to biologic processes associated with a robust pro-repair signature, including extracellular matrix organization, alveologenesis and vasculogenesis. Interestingly, we found no difference when comparing the suppressive phenotype of young versus aged Treg cells, suggesting that following influenza-induced lung injury, the reparative program of Treg cells is separable and distinct from their suppressive program. keywords: age; cells; figure; infection; influenza; injury; lung; mice; recovery; repair; treg cache: cord-104030-eb29t38n.txt plain text: cord-104030-eb29t38n.txt item: #212 of 702 id: cord-104031-vodwptdo author: Altshuler, Anna title: Capturing limbal epithelial stem cell population dynamics, signature, and their niche date: 2020-07-01 words: 10292 flesch: 45 summary: Indeed, the limbal/corneal epithelium becomes uniformly labeled following 2-weeks of nucleotide pulse 38 10 , i.e., suggesting that the length of cell cycle of both limbal and corneal epithelial cells is shorter than 14 days. Corneal cells: Although a minimal basal expression levels of corneal specific Krt12 mRNA was found in all groups, clusters 6-9 expressed much higher levels of Krt12 (Krt12 hi ) (Fig. 1d) . keywords: analysis; basal; cells; cluster; corneal; cycle; expression; fig; genes; gpha2; ifitm3; krt15; limbus; lineage; markers; mice; niche; outer; qlscs; quiescence; scs; stem cache: cord-104031-vodwptdo.txt plain text: cord-104031-vodwptdo.txt item: #213 of 702 id: cord-104035-ykyr2gvl author: Ivanov, Mark V. title: Boosting the MS1-only proteomics with machine learning allows 2000 protein identifications in 5-minute proteome analysis date: 2020-10-29 words: 1853 flesch: 26 summary: While Significantly Reducing Instrument Time A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes Ultrafast and Comprehensive Peptide Identification in Mass Spectrometry-Based Proteomics Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing SW-Tandem: A Highly Efficient Tool for Large-Scale Peptide Identification with Parallel Spectrum Dot Product on Sunway TaihuLight Fast Quantitative Analysis of TimsTOF PASEF Data with MSFragger and IonQuant Proteomic Analyses Using an Accurate Mass and Time Tag Strategy Accurate Mass Measurements in Proteomics Influence of Mass Resolution on Species Matching in Accurate Mass and Retention Time (AMT) Tag Proteomics Experiments Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach Identification of Phosphorylated Human Peptides by Accurate Mass Measurement Alone Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes Predicting Peptide Retention Times for Proteomics Predictive Chromatography of Peptides and Proteins as a Complementary Tool for Training, Selection, and Robust Calibration of Retention Time Models for Targeted Proteomics Improved Peptide Retention Time Prediction in Liquid Chromatography through Deep Learning Prosit: Proteome-Wide Prediction of Peptide Tandem Mass Spectra by Deep Learning DeepLC can predict retention times for peptides that carry as-yet unseen modifications LightGBM: A Highly Efficient Gradient Boosting Decision Tree A New Method of Separation of Multi-Atomic Ions by Mobility at Atmospheric Pressure Using a High-Frequency Amplitude-Asymmetric Strong Electric Field High-Field Asymmetric Waveform Ion Mobility Spectrometry for Mass Spectrometry-Based Proteomics Enhancement of Mass Spectrometry Performance for Proteomic Analyses Using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Improving Support for Quantification Data Open Source Software for Rapid Proteomics Tools Development Dinosaur: A Refined Open-Source Peptide MS Feature Detector Target-Decoy Search Strategy for Increased Confidence in Large-Scale Protein Identifications by Mass Spectrometry A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach Prediction of Peptide Retention Times in High-Pressure Liquid Chromatography on the Basis of Amino Acid Composition LC-MS Alignment in Theory and Practice: A Comprehensive Algorithmic Review keywords: mass; method; peptide; proteomics; time cache: cord-104035-ykyr2gvl.txt plain text: cord-104035-ykyr2gvl.txt item: #214 of 702 id: cord-104036-790vk1cf author: Liekkinen, Juho title: Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level date: 2020-07-08 words: 6537 flesch: 36 summary: [41] [42] While previous simulations have generated a lot of insight to better understand the behavior of surfactant monolayers, they have been haunted by the insufficiently accurate description of the physical behavior of the lipids at the interface, which is largely due to water models whose quality in describing phenomena at water-monolayer-air interfacial regions is not sufficiently high, 33, 39, 43, 44 and due to incorrect description of the driving forces behind the formation of heterogeneous membranes. 45 To overcome these limitations and provide a detailed and accurate picture of the molecularlevel organization of surfactant monolayers, we used extensive and state-of-the-art all-atom molecular dynamics (MD) simulations of model systems that were validated with experimental Langmuir trough data. keywords: air; area; behavior; domains; fig; interface; lipid; monolayers; phase; pressure; pulmonary; simulations; surface; surfactant; water cache: cord-104036-790vk1cf.txt plain text: cord-104036-790vk1cf.txt item: #215 of 702 id: cord-104037-39kk37fb author: Ma, Jiahao title: Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19 date: 2020-09-21 words: 2729 flesch: 54 summary: Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 Å and 2.6 Å respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. Like the previously reported structure of full-length WT S protein purified in detergent 199 micelles, it is unclear whether the furin cleavage site in our resolved WT S-Trimer 200 structure is cleaved. keywords: fig; protein; structure; trimer cache: cord-104037-39kk37fb.txt plain text: cord-104037-39kk37fb.txt item: #216 of 702 id: cord-104055-47ren7ie author: Lutkenhoff, Evan S. title: EEG power spectra and subcortical pathology in chronic disorders of consciousness date: 2020-09-01 words: 2481 flesch: 34 summary: The mixed-model analysis revealed a significant interaction (F (10, 1309.055) = 16.599, 10 p < 0.001) between diagnostic group (i.e., VS, MCS-, MCS+) and EEG features (i.e., 11 total power, delta, theta, alpha, beta, gamma frequency bands; see Figure 2 and Table 12 1), along with a significant main effect of diagnosis (F (2, 4389.124) = 5.158, p = Predicting DOC level from EEG spectral features 2 As shown in Figure 5a and Table 2 , diagnosis (i.e., VS vs. MCS) was predicted 3 significantly better by the model including EEG components, overall brain atrophy 4 (including both white matter and gray matter), and demographic components (i.e., age, and specificity (sens/spec; 0.79, 0.81, respectively) than both other models (AUC = 1 0.78, sens/spec 0.58/0.78 and AUC = 0.67, sens/spec 0.29/0.89 for the 2 demographics and atrophy and the demographic only models, respectively). In what follows, we address, in a large cohort 18 of patients with chronic DOC, the heretofore untested relationship between observed 19 electrocortical rhythms, patterns of subcortical brain atrophy (including thalamus, 20 brainstem, and basal ganglia), and clinical measures of awareness and arousal. keywords: atrophy; brain; consciousness; data; eeg; patients; power cache: cord-104055-47ren7ie.txt plain text: cord-104055-47ren7ie.txt item: #217 of 702 id: cord-104073-vsa5y7ip author: Warner, Emily F. title: Cross kingdom analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets to ameliorate fungal pathogenicity? date: 2020-09-23 words: 3225 flesch: 45 summary: As expected, there was a positive correlation between GC content 230 and PQS frequency amongst all the fungal species analysed (r=0.5290; p<0.0001; Figure 3A ). The Mucoromycota and Basidiomycota displayed high PQS frequencies relative to GC 220 content (459 and 340 PQS/GC%, respectively; Figure 2C and G). keywords: drug; figure; fungal; genes; kbp; pqs; quadruplex cache: cord-104073-vsa5y7ip.txt plain text: cord-104073-vsa5y7ip.txt item: #218 of 702 id: cord-104081-a3fx8tyd author: Tang, Tiffany title: Proteolytic activation of the SARS-CoV-2 spike S1/S2 site: a re-evaluation of furin cleavage date: 2020-10-05 words: 4017 flesch: 45 summary: ProP predicts furin cleavage sites based on networks derived from experimental data, whereas PiTou uses a combination of a hidden Markov model and biological knowledge-based cumulative probability score functions to characterize a 20 amino acid motif from P14 to P6' that reflects the binding strength and accessibility of the motif in the furin binding pocket. The Coronavirus Spike Protein and Acquisition of Fusion Competence Efficient Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein by the Transmembrane Protease TMPRSS2 Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein Proteolytic processing of middle east respiratory syndrome coronavirus spikes expands virus tropism Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop Proprotein convertase models based on the crystal structures of furin and kexin: Explanation of their specificity The crystal structure of the proprotein processing proteinase furin explains its stringent specificity A Database of 20-residue furin cleavage site motifs, substrates and their associated drugs The pore-forming toxin proaerolysin is activated by furin SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Article SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells Computational prediction of furin cleavage sites by a hybrid method and understanding mechanism underlying diseases Prediction of proprotein convertase cleavage sites SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects The proximal origin of SARS-CoV-2 Receptor usage and cell entry of bat coronavirus HKU4 provide insight into bat-tohuman transmission of MERS coronavirus Production of pseudotyped particles to study highly pathogenic coronaviruses in a biosafety level 2 setting Ca 2+ ions promote fusion of Middle East respiratory syndrome coronavirus with host cells and increase infectivity Coronavirus membrane fusion mechanism offers a potential target for antiviral development Middle East Respiratory Syndrome Coronavirus Spike Protein Is Not Activated Directly by Cellular Furin during Viral Entry into Target Cells α1-Antitrypsin Portland, a bioengineered serpin highly selective for furin: Application as an antipathogenic agent Proteolytic Cleavage of the SARS-CoV-2 Spike Protein and the Role of the Novel S1/S2 Site The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells A Single Immunization with Nucleoside-Modified mRNA Vaccines Elicits keywords: cells; cleavage; cov-2; furin; protein; sars; site cache: cord-104081-a3fx8tyd.txt plain text: cord-104081-a3fx8tyd.txt item: #219 of 702 id: cord-104092-yau3r79c author: Tamming, Renee J. title: Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits date: 2019-04-13 words: 4073 flesch: 40 summary: Atrx loxP mice were mated with C57BL/6 mice expressing Cre recombinase under the control of the αCaMKII gene promoter 19 . The Shank family of scaffold proteins The glycine receptor Cloning and characterization of human CADPS and CADPS2, new members of the Ca2+-dependent activator for secretion protein family Intersectin 1 forms complexes with SGIP1 and Reps1 in clathrin-coated pits Disruption of the direct perforant path input to the CA1 subregion of the dorsal hippocampus interferes with spatial working memory and novelty detection A macromolecular synthesis-dependent late phase of long-term potentiation requiring cAMP in the medial perforant pathway of rat hippocampal slices Abnormal Microglia and Enhanced Inflammation-Related Gene Transcription in Mice with Conditional Deletion of Ctcf in Camk2a-Cre-Expressing Neurons Lipopolysaccharide-induced microglial activation induces learning and memory deficits without neuronal cell death in rats Learning, memory, and glial cell changes following recovery from chronic unpredictable stress Disruption of the perineuronal net in the hippocampus or medial prefrontal cortex impairs fear conditioning Modification of extracellular matrix by enzymatic removal of chondroitin sulfate and by lack of tenascin-R differentially affects several forms of synaptic plasticity in the hippocampus New translational assays for preclinical modelling of cognition in schizophrenia: the touchscreen testing method for mice and rats Synaptic scaffold evolution generated components of vertebrate cognitive complexity X-linked alphathalassemia/mental retardation (ATR-X) syndrome: localization to Xq12-q21.31 by X inactivation and linkage analysis Sexually dimorphic behavior, neuronal activity, and gene expression in Chd8-mutant mice Mecp2 organizes juvenile social behavior in a sex-specific manner MeCP2 Modulates Sex Differences in the Postsynaptic Development of the Valproate Animal Model of Autism Epidemiology of pervasive developmental disorders A higher mutational burden in females supports a female protective model in neurodevelopmental disorders Transcriptomic analysis of autistic brain reveals convergent molecular pathology Human CRMP4 mutation and disrupted Crmp4 expression in mice are associated with ASD characteristics and sexual dimorphism SHANK1 Deletions in Males with Investigation of sex differences in the expression of RORA and its transcriptional targets in the brain as a potential contributor to the sex bias in autism Memory-Related Synaptic Plasticity Is Sexually Dimorphic in Rodent Hippocampus Sex-specific differences in expression of histone demethylases Utx and Uty in mouse brain and neurons miRNA Expression profile after status epilepticus and hippocampal neuroprotection by targeting miR-132 Microarray based analysis of microRNA expression in rat cerebral cortex after traumatic brain injury The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory Supplementary Figure 5: Transcriptional profiling reveals dysregulation of presynaptic genes in Atrx-FoxG1 mice. keywords: atrx; brain; cko; control; expression; figure; gene; learning; male; memory; mice; neurons; synaptic cache: cord-104092-yau3r79c.txt plain text: cord-104092-yau3r79c.txt item: #220 of 702 id: cord-104109-k36jya0b author: Das Jana, Indrani title: Development of a copper-graphene nanocomposite based transparent coating with antiviral activity against influenza virus date: 2020-09-02 words: 1767 flesch: 30 summary: Thermal Properties of the Binary-Filler Hybrid Composites with Graphene and 403 Copper Nanoparticles Plasmonic Properties of Copper Nanoparticles Fabricated by Nanosphere 405 Lithography Copper Nanoparticle/Polymer Composites with Antifungal and Bacteriostatic 407 Properties Cu-Ag Bimetallic Nanoparticles on Reduced Graphene Oxide 409 Nanosheets as Peroxidase Mimic for Glucose and Ascorbic Acid Detection Copper Nanoparticles: Aqueous Phase Synthesis and Conductive Films 412 Fabrication at Low Sintering Temperature Situ Raman Spectroscopy of Copper and Copper Oxide Surfaces during Electrochemical Oxygen Evolution Reaction: Identification of CuIII Oxides as Catalytically Active 415 Species Graphene Synthesis: Relationship to Applications Chemistry with Graphene and Graphene Oxide -419 Challenges for Synthetic Chemists Coronaviruses: An Overview of Their Replication Methods in molecular biology Raman Spectrum of Graphene and Graphene Layers Cu and This data suggested that 30 minutes of preincubation with Cu-Gr 189 composite can lead to more than tenfold reduction in input virus titer that ultimately results in ~50% 190 decrease in reporter activity. keywords: activity; graphene; nano; reporter; virus cache: cord-104109-k36jya0b.txt plain text: cord-104109-k36jya0b.txt item: #221 of 702 id: cord-104122-klvx927g author: Tayfuroglu, Omer title: An Accurate Free Energy Method for Solvation of Organic Compounds and Binding to Proteins date: 2020-05-28 words: 2413 flesch: 34 summary: The method is adopted from ANI-1ccx neural network potentials (Machine Learning) for the The insertion of the ligand to an environment of solvent (solvation free energy) or receptor (binding free energy) can be defined by a coupling parameter, λ. 61 key: cord-104122-klvx927g authors: Tayfuroglu, Omer; Yildiz, Muslum; Pearson, Lee-Wright; Kocak, Abdulkadir title: An Accurate Free Energy Method for Solvation of Organic Compounds and Binding to Proteins date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.26.116459 sha: doc_id: 104122 cord_uid: klvx927g Here, we introduce a new strategy to estimate free energies using single end-state molecular dynamics simulation trajectories. keywords: binding; energies; energy; learning; ligand; methods; simulations cache: cord-104122-klvx927g.txt plain text: cord-104122-klvx927g.txt item: #222 of 702 id: cord-104128-0gyk9cwx author: Morand, Serge title: The accelerated infectious disease risk in the Anthropocene: more outbreaks and wider global spread date: 2020-04-20 words: 7039 flesch: 31 summary: Here, we report on another risk: the accelerated infectious disease risk associated with the number and geographic spread of human infectious disease outbreaks. Using the most complete, reliable, and up-to-date database on human infectious disease outbreaks (GIDEON), we show that the number of disease outbreaks, the number of diseases involved in these outbreaks, and the number of countries affected have increased during the entire Anthropocene. keywords: air; anthropocene; countries; disease; disease outbreaks; et al; global; growth; health; human; mobility; modularity; number; outbreaks; pandemic; spread; travel; world cache: cord-104128-0gyk9cwx.txt plain text: cord-104128-0gyk9cwx.txt item: #223 of 702 id: cord-104133-d01joq23 author: Arthur, Ronan F. title: Adaptive social contact rates induce complex dynamics during epidemics date: 2020-07-14 words: 5242 flesch: 46 summary: A common approach to incorporating behavior into epidemic models is to 64 track co-evolving dynamics of behavior and infection [16, 19, 20] , where behavior 65 represents an i-state of the model [21] . The spread of awareness and its 532 Proceedings of the National Academy of Sciences A review The Dynamics of Physiologically Structured Populations Periodicity in epidemiological models Measles in England and Wales-I: an analysis of factors 544 underlying seasonal patterns Seasonal and interannual cycles of endemic cholera in 547 Bengal 1891-1940 in relation to climate and geography Etiology of Newly Emerging Marine Diseases Epidemic cycles driven by host behaviour Periodic solutions of delay differential equations 552 arising in some models of epidemics A contribution to the mathematical theory of 555 epidemics The Royal Society Modeling infectious diseases in humans and animals Princeton University Press Time series modelling of childhood diseases dynamical systems approach Adaptive human behavior in epidemiological models Choices, beliefs, and infectious disease dynamics Higher disease prevalence can 568 induce greater sociality: a game theoretic coevolutionary model Global stability of an SIR epidemic 571 Global stability for the SEIR model in epidemiology Scipy-based delay differential equation (dde) solver The strategy of building models of complex ecological systems Simple mathematical models with very complicated dynamics Journal of the Fisheries Board of Canada Time-delay versus stability in population models with two and three 587 trophic levels Time delays are not necessarily destabilizing Different epidemic curves for severe acute respiratory 591 Rational epidemics and their public control Group interest versus self-interest in smallpox 596 vaccination policy keywords: behavior; contact; disease; dynamics; epidemic; model; number; time cache: cord-104133-d01joq23.txt plain text: cord-104133-d01joq23.txt item: #224 of 702 id: cord-104138-qagyaegp author: Magee, Michelle title: Effects of face masks on acoustic analysis and speech perception: Implications for peri-pandemic protocols date: 2020-10-08 words: 2188 flesch: 46 summary: Post hoc comparisons showed power (dB/Hz 2 ) was significantly lower between 3-10 kHz for N95 mask and 5-10kHz for surgical and cloth masks when compared to no mask on recordings made using the head-mounted microphone (Figure 2a) . Spectral tilt was lower in recordings produced with the surgical (p=0.016) and N95 masks (p=0.001). keywords: differences; frequency; intelligibility; mask; n95; speech; type cache: cord-104138-qagyaegp.txt plain text: cord-104138-qagyaegp.txt item: #225 of 702 id: cord-104140-o46kvd0b author: McPherson, Malinda J. title: Harmonicity aids hearing in noise date: 2020-09-30 words: 9610 flesch: 44 summary: We observed a 2.38 dB SNR advantage for Inharmonic tones compared to Pure tones, and an additional 1.32 dB SNR advantage for Harmonic tones over Inharmonic tones (averaged across phase conditions). Previous studies have found that it is easier to hear the f0 of harmonic sounds when there is background noise (Hall & Peters, 1981; Houtgast, 1976) , but it was unclear whether such effects would translate to improved discrimination of harmonic tones, compared to inharmonic tones, in noise. keywords: conditions; detection; discrimination; experiment; harmonic; harmonicity; musicians; noise; participants; sounds; speech; tones cache: cord-104140-o46kvd0b.txt plain text: cord-104140-o46kvd0b.txt item: #226 of 702 id: cord-104142-0nfprn2a author: Azmi, Maryam A. title: A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans date: 2020-10-19 words: 5438 flesch: 38 summary: key: cord-104142-0nfprn2a authors: Azmi, Maryam A.; Palmisano, Nicholas J.; Medwig-Kinney, Taylor N.; Moore, Frances E.; Rahman, Rumana; Zhang, Wan; Adikes, Rebecca C.; Matus, David Q. title: A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans date: 2020-10-19 journal: bioRxiv DOI: 10.1101/2020.10.17.344069 sha: doc_id: 104142 cord_uid: 0nfprn2a Authentic research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills as well as foundational research skills in a team-based setting. We designed a laboratory module to provide an authentic research experience to stimulate curiosity, introduce students to experimental techniques, and promote higher-order thinking. keywords: codon; elegans; figure; gfpnco; learning; module; research; rnai; strain; students cache: cord-104142-0nfprn2a.txt plain text: cord-104142-0nfprn2a.txt item: #227 of 702 id: cord-104146-pabh3ajb author: de Lussanet de la Sablonière, Marc H. E. title: Robust, general purpose, digital power line hum filter which is free of deformations and which can be applied to large transients date: 2019-11-04 words: 3465 flesch: 63 summary: key: cord-104146-pabh3ajb authors: de Lussanet de la Sablonière, Marc H. E. title: Robust, general purpose, digital power line hum filter which is free of deformations and which can be applied to large transients date: 2019-11-04 journal: bioRxiv DOI: 10.1101/830463 sha: doc_id: 104146 cord_uid: pabh3ajb Power line interference (“hum noise”) is a common source of noise in recorded biological data. The results also show that the errors of hum filters generally increase with the high-frequency content of the data. keywords: amplitude; data; filter; hum; noise; pms; power cache: cord-104146-pabh3ajb.txt plain text: cord-104146-pabh3ajb.txt item: #228 of 702 id: cord-104157-rivaoo73 author: Noreika, Valdas title: Alertness fluctuations during task performance modulate cortical evoked responses to transcranial magnetic stimulation date: 2019-06-28 words: 10471 flesch: 43 summary: ERP dynamics were additionally studied using data-driven spatiotemporal clustering analyses similar to what we have described previously (Chennu et al., 2013) . In these cases, EEG alpha effects are typically evident only within a relatively short pre-stimulus time period of a few hundred milliseconds (Romei et al., 2008) , and are restricted to sensory or fronto-parietal regions (Capotosto et al., 2009; van Dijk et al., 2008) . keywords: alertness; amplitude; data; drowsy; eeg; et al; hori; level; mep; motor; participants; peak; pulse; sleep; stimulation; tep; time; tms; trials cache: cord-104157-rivaoo73.txt plain text: cord-104157-rivaoo73.txt item: #229 of 702 id: cord-104161-jvbgouv8 author: Pfrieger, Frank W. title: Insight into the workforce advancing fields of science and technology date: 2020-06-02 words: 3054 flesch: 39 summary: key: cord-104161-jvbgouv8 authors: Pfrieger, Frank W. title: Insight into the workforce advancing fields of science and technology date: 2020-06-02 journal: bioRxiv DOI: 10.1101/2020.06.01.128355 sha: doc_id: 104161 cord_uid: jvbgouv8 Advances in biomedicine and other fields of science and technology depend on research teams and their peer-reviewed publications. Progress in biomedicine and other fields of science and technology (S&T) depends on research teams working in specific fields and on the publication of their results by peer-reviewed articles. keywords: field; fig; publication; science; teams; workforce cache: cord-104161-jvbgouv8.txt plain text: cord-104161-jvbgouv8.txt item: #230 of 702 id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 words: 3746 flesch: 42 summary: [22] were primarily concerned with the statistical significance of RNA folding, rather than with distinguishing the relative contributions of base composition and base order. Just as a local arrangement of words conveys specific meaning to a text, so base order better reflects local evolutionary pressures. keywords: base; composition; folding; genome; order; regions; rna; sars; structure cache: cord-104162-fe51v2pt.txt plain text: cord-104162-fe51v2pt.txt item: #231 of 702 id: cord-104169-2sbc1guz author: Satish, Swarup title: The impact of preprint servers in the formation of novel ideas date: 2020-10-08 words: 4804 flesch: 54 summary: Because the enumeration of all possible partitions is impossible, Pelt (Killick et al., 2012) relies on a pruning rule. A number of studies propose different ideas to quantify originality in science and technology (Cozzens et al., 2010; Alexander et al., 2013; Rzhetsky et al., 2015; Rotolo et al., 2015; Wang and Chai, 2018; Shibayama and Wang, 2020) or their impact on the other works (Shi et al., 2010; Shahaf et al., 2012; Sinatra et al., 2016; Hutchins et al., 2016; Wesley-Smith et al., 2016; Herrmannova et al., 2018b,a; Zhao et al., 2019; Bornmann et al., 2019; Small et al., 2019) . keywords: biorxiv; et al; novel; novelty; phrases; publication; pubmed; research; time cache: cord-104169-2sbc1guz.txt plain text: cord-104169-2sbc1guz.txt item: #232 of 702 id: cord-193356-hqbstgg7 author: None title: cord-193356-hqbstgg7 date: None words: 14115 flesch: 51 summary: A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning Explaining and interpreting LSTMs Solving the protein sequence metric problem Rank-loss support instance machines for miml instance annotation Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires Multiple instance learning: a survey of problem characteristics and applications VDJServer: a cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements Tetramer-visualized gluten-specific CD4+ T cells in blood as a potential diagnostic marker for coeliac disease without oral gluten challenge iReceptor: a platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories Support-vector networks Quantifiable predictive features define epitope-specific T cell receptor repertoires On a model of associative memory with huge storage capacity BERT: pre-training of deep bidirectional transformers for language understanding Solving the multiple instance problem with axis-parallel rectangles Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire Predicting antigen-specificity of single T-cells based on TCR CDR3 regions. We apply random and attention-based subsampling of repertoire sequences to reduce over-fitting and decrease computational effort. keywords: attention; classification; data; datasets; deeprc; et al; hopfield; input; learning; lstm; methods; motif; networks; number; repertoire; search; sequences; table cache: cord-193356-hqbstgg7.txt plain text: cord-193356-hqbstgg7.txt item: #233 of 702 id: cord-252097-4kslllaq author: Kaur, S. title: Local computational methods to improve the interpretability and analysis of cryo-EM maps date: 2020-06-19 words: 5989 flesch: 46 summary: More importantly, these approaches do not require input parameters as fitted atomic models or local resolution maps, which reduces the possibility of overfitting. B-factor maps provide complementary information to local resolution maps, though usually these results are correlated. keywords: cryo; et al; factor; figure; map; maps; resolution cache: cord-252097-4kslllaq.txt plain text: cord-252097-4kslllaq.txt item: #234 of 702 id: cord-252597-ea78sjcs author: Ramazzotti, Daniele title: VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples date: 2020-10-19 words: 10711 flesch: 36 summary: Homoplasy detection (clonal variants). As specified above, VERSO STEP #2 is executed on groups of samples with identical clonal genotype: the rationale is that the transmission of minor variants implicates the concurrent transfer of clonal variants, excluding the rare cases in which the VF of a clonal variant significantly decreases in a given host, for instance due to mutation losses (e.g., via recombination-associated deletions or via multiple mutations hitting an already mutated genome location [34] ) or to complex horizontal evolution phenomena (e.g., super-infections keywords: analysis; clonal; cov-2; data; evolution; genomic; host; intra; mutations; samples; sars; sequencing; step; transmission; variants; verso cache: cord-252597-ea78sjcs.txt plain text: cord-252597-ea78sjcs.txt item: #235 of 702 id: cord-252910-7qvnj6c8 author: Li, Xin title: The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date: 2020-09-21 words: 4198 flesch: 46 summary: Recombination, Reservoirs, and the Modular Spike: Mechanisms of Coronavirus Cross-Species Transmission Bioinformatics Analysis of the 2019 Novel Coronavirus Genome A Furin Cleavage Site Was Discovered in the S Protein of the 2019 Novel Coronavirus Novel Coronavirus Leads to Insights into Its Virulence The Architecture of SARS-CoV-2 Transcriptome A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein SARS coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination Attenuation of replication by a 29 nucleotide deletion in SARScoronavirus acquired during the early stages of human-to-human transmission Genomewide Association Study of Severe Covid-19 with Respiratory Failure Potential impact of SARS-CoV-2 infection on the thymus Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2. key: cord-252910-7qvnj6c8 authors: Li, Xin; Jin, Xiufeng; Chen, Shunmei; Wang, Liangge; Yau, Tung On; Yang, Jianyi; Hong, Zhangyong; Ruan, Jishou; Duan, Guangyou; Gao, Shan title: The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-19 pandemics date: 2020-09-21 journal: bioRxiv DOI: 10.1101/2020.07.22.213926 sha: doc_id: 252910 cord_uid: 7qvnj6c8 keywords: betacoronavirus; cov; cov-2; junction; orf8; recombination; rmyn02; sars cache: cord-252910-7qvnj6c8.txt plain text: cord-252910-7qvnj6c8.txt item: #236 of 702 id: cord-253447-4w6caxwu author: Zeng, Xin title: Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy date: 2020-04-20 words: 2892 flesch: 50 summary: The wells were washed and blocked with 1% PVA, and then the mixture of antibody library (10 10 pfu per well) and free RBD-His protein (100ng per well) was added. A specific binder of target protein was added during the binding step for the selection of blocking antibodies. keywords: ace2; antibodies; antibody; binding; biopanning; cov-2; rbd; sars cache: cord-253447-4w6caxwu.txt plain text: cord-253447-4w6caxwu.txt item: #237 of 702 id: cord-253987-83h861lp author: Tada, Takuya title: A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture date: 2020-09-17 words: 6860 flesch: 40 summary: Soluble ACE2 proteins (10 µg) were mixed with 20 µl nickel beads for 1 hour at 4°C. The antiviral activity of ACE2 proteins against live virus was similar to pseudotyped virus, except that in the live virus assay, the wild-type and H345A microbodies were of similar potency. keywords: ace2; ace2 microbody; activity; cells; cov-2; et al; figure; infection; microbody; protein; sars; soluble; spike; virus cache: cord-253987-83h861lp.txt plain text: cord-253987-83h861lp.txt item: #238 of 702 id: cord-254636-3lr008th author: Shishir, Tushar Ahmed title: In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh date: 2020-08-16 words: 2976 flesch: 44 summary: Rapid detection of selective pressure on individual sites of codon alignments DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks AputativediacidicmotifintheSARS-CoVORF6proteininfluencesitssubcellularlocalizationandsuppressionofexpressionofco -transfectedexpressionconstructs SARS-CoV accessory protein 7a directly interacts with human LFA-1 Severe Acute Respiratory Syndrome Coronavirus Gene 7 Products Contribute to Virus-Induced Apoptosis Severe Acute Respiratory Syndrome Coronavirus ORF7a Inhibits Bone Marrow Stromal Antigen 2 Virion Tethering through a Novel Mechanism of Glycosylation Interference The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I. bioRxiv The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19 COVID-2019: All mutations were synonymous and found this gene conserved In summary, mutation analysis revealed point mutations as well as deletion of base pairs. keywords: bangladesh; cov-2; isolates; mutations; protein; sars; sequences cache: cord-254636-3lr008th.txt plain text: cord-254636-3lr008th.txt item: #239 of 702 id: cord-254772-1xzkfl8g author: Pandolfi, Laura title: Neutrophil extracellular traps induce the epithelial-mesenchymal transition: implications in post-COVID-19 fibrosis date: 2020-11-09 words: 4252 flesch: 45 summary: The aim of this study is to assess the capacity of NETs to drive epithelial-mesenchymal transition (EMT) of lung epithelial cells and to analyze the involvement of NETs in COVID-19. Given these premises, the aim of this study is to assess whether NETosis may drive the EMT also in lung epithelial cells. keywords: a549; cells; covid-19; emt; fig; lung; nets; neu; patients; pma cache: cord-254772-1xzkfl8g.txt plain text: cord-254772-1xzkfl8g.txt item: #240 of 702 id: cord-254855-gmy9zyad author: He, Sijia title: PSGL-1 inhibits the virion incorporation of SARS-CoV and SARS-CoV-2 spike glycoproteins and impairs virus attachment and infectivity date: 2020-07-06 words: 1714 flesch: 38 summary: Nevertheless, it remains to be determined whether PSGL-1 is expressed in SARS coronavirus target cells in the lungs, and, if 6 so, whether its expression can impair viral infection. Together, these results demonstrate that PSGL-1 expression in the virus-producer cells severely diminishes the infectivity of virions bearing SARS coronavirus S proteins. keywords: cells; cov; cov-2; psgl-1; sars cache: cord-254855-gmy9zyad.txt plain text: cord-254855-gmy9zyad.txt item: #241 of 702 id: cord-255069-9xueqdri author: Leary, Shay title: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date: 2020-04-11 words: 1824 flesch: 33 summary: Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA HIV evolution: CTL escape mutation and reversion after transmission Molecular footprints reveal the impact of the protective HLA-A*03 allele in hepatitis C virus infection Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level Cross-species transmission of the newly identified coronavirus 2019-nCoV Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission HIV protease resistance and viral fitness Selection of viral adaptations to polymorphic host responses mediated by T cells, NKcells, antibodies and antiviral drugs are well described for other RNA viruses such as HIV and HCV 4, 11 . keywords: cov-2; nucleocapsid; polymorphisms; sars; strains cache: cord-255069-9xueqdri.txt plain text: cord-255069-9xueqdri.txt item: #242 of 702 id: cord-255325-tl5fm2yu author: Goletic, Teufik title: Phylogenetic pattern of SARS-CoV-2 from COVID-19 patients from Bosnia and Herzegovina: lessons learned to optimize future molecular and epidemiological approaches date: 2020-06-19 words: 1727 flesch: 41 summary: [12] , was shown to be G in BH isolates, assigning all four BiH isolates to G clade together with European sequences (Italy, Austria, France, Sweden, Cyprus, England). [6] , and the cycle threshold (Ct) values were 17,1; 21,3; 24,6 and 20,4 for Livno, Banja Luka, Tuzla and Sarajevo samples, respectively. Livno and Banja Luka samples WGS was performed according to the ARTIC amplicon sequencing protocol for MinION for nCoV-2019, which uses two primer pools to generate the sequence, as described elsewhere [7] . keywords: bih; gisaid; samples; sarajevo; sars; sequences cache: cord-255325-tl5fm2yu.txt plain text: cord-255325-tl5fm2yu.txt item: #243 of 702 id: cord-255371-o9oxchq6 author: Nguyen, Thanh Thi title: Genomic Mutations and Changes in Protein Secondary Structure and Solvent Accessibility of SARS-CoV-2 (COVID-19 Virus) date: 2020-07-10 words: 5655 flesch: 52 summary: For the mutation detection purpose, we apply a dynamic programming algorithm to protein AA sequences to get global pairwise alignments between a reference sequence and a query sequence. There have been various protein secondary structure prediction programs in the literature and many of those were developed based on artificial intelligence models using protein AA sequences such as JPred4 [29] , Spider2 keywords: accessibility; cov-2; gene; mutations; number; protein; sars; sequences; solvent; structure; virus cache: cord-255371-o9oxchq6.txt plain text: cord-255371-o9oxchq6.txt item: #244 of 702 id: cord-255440-ls1l2mlg author: Tindle, Courtney title: Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19 date: 2020-10-18 words: 9984 flesch: 41 summary: Organoids and monolayers used for lung cell type studies were lysed using RNA lysis buffer followed by RNA CoV2 studies were lysed in TRI-Reagent and RNA was extracted using Zymo Research Direct-zol RNA Miniprep. Organoid and monolayer cell-type gene expression was measured by qRT-PCR using 2x SYBR Green qPCR Master Mix. As for personalization, our model is derived from adult lung stem cells from deep lung biopsies; each organoid line was established from one patient. keywords: airway; ali; alveolar; at2; cells; cov-2; covid-19; epithelial; et al; expression; fig; gene; host; human; lung; media; model; monolayers; organoids; pneumocytes; response; rna; sars; signatures; type cache: cord-255440-ls1l2mlg.txt plain text: cord-255440-ls1l2mlg.txt item: #245 of 702 id: cord-255515-7se14455 author: Graudenzi, Alex title: Mutational Signatures and Heterogeneous Host Response Revealed Via Large-Scale Characterization of SARS-COV-2 Genomic Diversity date: 2020-07-06 words: 8285 flesch: 41 summary: We employed VERSO, a framework introduced in [12] for the reconstruction of high-resolution models of viral evolution from raw sequencing data of viral samples. In this respect, raw sequencing data of viral samples can be effectively employed to deliver a high-resolution picture of intra-host heterogeneity, which might underlie different clinical outcomes and affect the efficacy of anti-viral therapies. keywords: analysis; cov-2; host; number; processes; samples; sars; signature; substitution; variants cache: cord-255515-7se14455.txt plain text: cord-255515-7se14455.txt item: #246 of 702 id: cord-255552-k1retwa4 author: Gassen, Nils C. title: Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics date: 2020-04-15 words: 1215 flesch: 11 summary: N Engl 216 Antiviral potential of ERK/MAPK and PI3K/AKT/mTOR signaling 218 modulation for Middle East respiratory syndrome coronavirus infection as identified 219 by temporal kinome analysis The SARS-coronavirus-host interactome: identification of cyclophilins 221 as target for pan-coronavirus inhibitors As AKT1 inhibition results in BECN1 up-regulation and autophagy induction (10, 31), SARS-CoV-2 174 growth inhibition was expected. keywords: autophagy; coronavirus; niclosamide; protein; sars cache: cord-255552-k1retwa4.txt plain text: cord-255552-k1retwa4.txt item: #247 of 702 id: cord-255755-5jccb3nh author: Saha, Sovan title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date: 2020-04-23 words: 3670 flesch: 54 summary: key: cord-255755-5jccb3nh authors: Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Nasipuri, Mita title: Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network date: 2020-04-23 journal: bioRxiv DOI: 10.1101/2020.04.12.038216 sha: doc_id: 255755 cord_uid: 5jccb3nh It has been reported that SARS-CoV has ∼89% genetic similarities with n-CoV. With this hypothesis, the current work focuses on the identification of spreader nodes in SARS-CoV protein interaction network. keywords: cov; edges; level; network; nodes; sars; spreader cache: cord-255755-5jccb3nh.txt plain text: cord-255755-5jccb3nh.txt item: #248 of 702 id: cord-255791-ghrlj6b2 author: Pruijssers, Andrea J. title: Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice date: 2020-04-27 words: 3469 flesch: 41 summary: 159 To determine whether RDV exerts antiviral 160 effect on SARS-CoV-2 in vivo, we constructed a chimeric mouse-adapted SARS-CoV-1 variant encoding 161 the target of RDV antiviral activity, the RdRp, of SARS-CoV-2 (SARS1/SARS2-RdRp) (Fig. 5A) . The lowest levels of RDV-TP were observed following RDV treatment of Vero E6 cells and were 146 approximately 4-and 20-fold lower than those observed in Calu3 2B4 and HAE cultures, respectively. keywords: antiviral; cells; coronavirus; cultures; ec50; fig; human; rdv; sars cache: cord-255791-ghrlj6b2.txt plain text: cord-255791-ghrlj6b2.txt item: #249 of 702 id: cord-255888-znfgh78m author: Fisher, Dale title: Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food date: 2020-08-18 words: 1819 flesch: 52 summary: Efforts to avert the risk of COVID-19 outbreaks seeded by contaminated food must begin at the source; that is food processing premises. While it can be confidently argued that transmission via contaminated food is not a major infection route, the potential for movement of contaminated items to a region with no COVID-19 and initiate an outbreak is an important hypothesis. keywords: cov-2; food; sars cache: cord-255888-znfgh78m.txt plain text: cord-255888-znfgh78m.txt item: #250 of 702 id: cord-255895-6at9gelt author: Han, Namshik title: Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies date: 2020-08-25 words: 4746 flesch: 43 summary: Our data-driven unsupervised approach and biological validation has uncovered 160 approved drugs not currently in clinical trials, which can be investigated immediately for repurposing and two drugs that show promise as anti-viral drugs. We constructed a SARS-CoV-2-induced protein (SIP) network, based on disease signatures defined by COVID-19 multi-omic datasets(Bojkova et al., 2020; Gordon et al., 2020), and cross-examined these pathways against approved drugs. keywords: analysis; covid-19; drugs; figure; infection; network; pathways; proteins; replication; sars; sip; sulfasalazine cache: cord-255895-6at9gelt.txt plain text: cord-255895-6at9gelt.txt item: #251 of 702 id: cord-255997-oer5lxxr author: Onodi, Fanny title: SARS-CoV-2 induces activation and diversification of human plasmacytoid pre-dendritic cells date: 2020-07-10 words: 4250 flesch: 44 summary: First, we asked whether SARS-CoV-2 was able to induce pDC activation, and diversification into IFNproducing and/or T cell stimulating effectors, as we previously described for influenza virus A (Flu) (Alculumbre et al., 2018) . PDC activation and diversification was observed with two independent primary SARS-CoV-2 strains (Fig 1C) , which both induced similar proportions of P1-P3 subsets. keywords: activation; cells; cov-2; fig; ifn; infection; pdc; production; sars; type cache: cord-255997-oer5lxxr.txt plain text: cord-255997-oer5lxxr.txt item: #252 of 702 id: cord-256572-sqz8yc7b author: Huo, Jiandong title: Neutralization of SARS-CoV-2 by destruction of the prefusion Spike date: 2020-05-06 words: 5392 flesch: 48 summary: Whilst this work was being prepared for publication a paper reporting that CR3022 does not neutralise SARS-CoV-2 and describing the structure of the complex with the RBD at 3.1 Å resolution was published (Yuan et al., 2020) . (Yuan et al., 2020) . keywords: ace2; antibody; binding; cov-2; cr3022; epitope; et al; figure; rbd; receptor; sars; spike; structure cache: cord-256572-sqz8yc7b.txt plain text: cord-256572-sqz8yc7b.txt item: #253 of 702 id: cord-256607-wpywh8c9 author: Itokawa, Kentaro title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by the ARTIC Network’s multiplex PCR date: 2020-06-01 words: 1418 flesch: 50 summary: These amplicons 134 seemed equally weak in all three primer sets rather than specific in N1 primer set. Finally, we further compared the V1, V3 and N1 primer 142 sets for three other clinical samples using a standard temperature program ( = 65 °C). keywords: amplicons; primer; set cache: cord-256607-wpywh8c9.txt plain text: cord-256607-wpywh8c9.txt item: #254 of 702 id: cord-258360-fqrn02lr author: Lee, Jimmy title: No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia date: 2020-06-19 words: 2838 flesch: 35 summary: They were confiscated at holding facilities, ports or borders prior to shipment, and had not yet been exposed to multiple potential sources of infection, unlike the confiscated animals in China reported by Xiao et al., (2020) and Lam et al., (2020) . Recently, four different groups have identified coronaviruses in imported Sunda or Malayan pangolins (Manis javanica) seized in raids on wildlife traders in China ( Liu et al., 2019; Lam et al., 2020; Xiao et al., 2020; Zhang et al., 2020) . keywords: coronavirus; et al; pangolins; sars; sunda; trade; wildlife cache: cord-258360-fqrn02lr.txt plain text: cord-258360-fqrn02lr.txt item: #255 of 702 id: cord-258630-mvz2l3yj author: Liu, Tiantian title: A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples date: 2020-11-10 words: 11054 flesch: 48 summary: Furthermore, when the samples contained high viral input, both P1 and P7 could achieve high viral genome coverage (min10X) at lower read depths as compared to all other protocols (Fig. 3b) . To evaluate the variability of viral load on the SARS-CoV-2 WGS performance, we compared the SARS-CoV-2, human, and bacterial reference mapping rates between low (1K copies) and high viral inputs (250K and 1M copies) across seven protocols (Fig. 2d-f ). keywords: cov-2; coverage; data; fig; genome; input; primer; protocols; reads; rna; samples; sars; sequencing; snv; suppl cache: cord-258630-mvz2l3yj.txt plain text: cord-258630-mvz2l3yj.txt item: #256 of 702 id: cord-258650-aeyf0yu1 author: Joshi, Bhrugesh title: deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early-Stage Comprehension in Pandemic Situations specifically for COVID-19 date: 2020-04-02 words: 1999 flesch: 50 summary: As we know the fact that the similar virus has already been known, it becomes crucial to collect and organize this information from the ocean of research articles. [10] , that means that it will take a substantial amount of time to comprehend and find useful information from thousands of research articles published. keywords: articles; coronavirus; mining; research; system cache: cord-258650-aeyf0yu1.txt plain text: cord-258650-aeyf0yu1.txt item: #257 of 702 id: cord-258914-g6pv8zz9 author: Proud, Pamela C. title: Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model date: 2020-09-25 words: 1195 flesch: 31 summary: Scheduled culls were performed for 6/24 ferrets on day 3 p.c. and 18/24 ferrets on Origin and evolution of pathogenic coronaviruses Evolutionary history, potential intermediate animal host, and cross-462 species analyses of SARS-CoV-2 Epidemiology and cause of severe acute respiratory 465 syndrome (SARS) in Guangdong, People's Republic of China Isolation of a Novel Coronavirus from a Man with Pneumonia 470 in Saudi Arabia Genomic characterisation and epidemiology of 2019 novel 473 coronavirus: implications for virus origins and receptor binding The trinity of 476 COVID-19: immunity, inflammation and intervention Clinical characteristics of 24 asymptomatic infections with COVID-479 19 screened among close contacts in Nanjing, China. bioRxiv Ferret models of viral pathogenesis Mapping influenza transmission in the ferret model 532 to transmission in humans Receptor Recognition by 534 the Novel Coronavirus from Wuhan: an Analysis Based on Decade Structural Studies of SARS Coronavirus Pathology of Experimental SARS Coronavirus 538 Infection in Cats and Ferrets Susceptibility of ferrets, cats, dogs, and other domesticated animals 541 to SARS-coronavirus 2 Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human 545 Airways The Role of TLR2 in 547 TLR-Dependent Human Mucosal Epithelial Cell 550 Responses to Microbial Pathogens keywords: coronavirus; ferret; sars; urt; virus cache: cord-258914-g6pv8zz9.txt plain text: cord-258914-g6pv8zz9.txt item: #258 of 702 id: cord-259084-lwh3rww4 author: Anderson, Cole title: Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2 date: 2020-05-22 words: 1007 flesch: 41 summary: In this study, we examined the feasibility of pooling nasopharyngeal swab specimens submitted 44 for COVID-19 testing using the CDC 2019-nCoV RT-PCR diagnostic panel without compromising 45 clinical sensitivity. Available at Update: FDA Issues first Emergency Use Authorization for Point 172 of Care Diagnostic | FDA Pooling nasopharyngeal/throat swab specimens to increase testing 176 capacity for influenza viruses by PCR Pooling of sera for human 178 immunodeficiency virus (HIV) testing: An economical method for use in developing 179 countries Pooling of clinical 181 specimens prior to testing for Chlamydia trachomatis by PCR is accurate and cost saving High throughput screening of 16 million serologically negative blood 184 donors for hepatitis B virus, hepatitis C virus and human immunodeficiency virus type-1 185 by nucleic acid amplification testing with specific and sensitive multiplex reagent in 186 Utility of pooled urine specimens for detection of Chlamydia trachomatis 188 and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics 189 in Mumbai, India, by PCR Evaluation of COVID-19 RT-qPCR test in multi-sample pools Pooling of samples for testing for SARS-CoV-2 in asymptomatic people Increasing testing throughput and case detection with a 195 pooled-sample Bayesian approach in the context of COVID-19 BioFire COVID-19 Test Emergency Use Authorization keywords: covid-19; pooling; specimens; testing cache: cord-259084-lwh3rww4.txt plain text: cord-259084-lwh3rww4.txt item: #259 of 702 id: cord-259246-azt5sr9w author: Peng, Qi title: Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date: 2020-10-19 words: 3229 flesch: 46 summary: Besides, the cyanogroup in the ribose ring may cause steric clash with polymerase residues during elongation, resulting in aberrant termination of RNA synthesis 29,31 . Due to the key roles of polymerase complex for viral replication, it has long been thought of as a promising antiviral drug target 25 . keywords: complex; favipiravir; fig; polymerase; residues; rna; sars; structure; template cache: cord-259246-azt5sr9w.txt plain text: cord-259246-azt5sr9w.txt item: #260 of 702 id: cord-259261-fmuozy3w author: Bickler, Stephen W. title: AGE IS ASSOCIATED WITH INCREASED EXPRESSION OF PATTERN RECOGNITION RECEPTOR GENES AND ACE2, THE RECEPTOR FOR SARS-COV-2: IMPLICATIONS FOR THE EPIDEMIOLOGY OF COVID-19 DISEASE date: 2020-06-16 words: 2041 flesch: 43 summary: The highest case fatality rates are in the 80 years and older age group (7.8%), with the lowest in the 0-9 years age group (0.00161%) (3) . Older age was associated with increased expression of PRR genes, ACE2 and four genes that encode proteins that have been shown to interact with SAR2-CoV-2 proteins. keywords: age; cov-2; expression; genes; prr; sars cache: cord-259261-fmuozy3w.txt plain text: cord-259261-fmuozy3w.txt item: #261 of 702 id: cord-259340-1ir19s25 author: Das, Rohit Pritam title: Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach date: 2020-07-01 words: 1644 flesch: 44 summary: In this connection, epitope based peptide design have remarkable privilege than conventional vaccine development. Prediction of B-cell epitope is a crucial step in epitope base vaccine design [28] . keywords: cell; cov-2; peptide; protein; sars; vaccine cache: cord-259340-1ir19s25.txt plain text: cord-259340-1ir19s25.txt item: #262 of 702 id: cord-259620-qigfstxt author: Yang, Chen title: Kidney injury molecule-1 is a potential receptor for SARS-CoV-2 date: 2020-10-10 words: 3424 flesch: 44 summary: Clinical Characteristics of Coronavirus Disease 2019 in China Q: Product of natural evolution (SARS, MERS, and SARS-CoV-2); deadly diseases, from SARS to SARS-CoV-2 Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways C: In-vitro renal epithelial cell infection reveals a viral kidney tropism as a potential mechanism for acute renal failure during Middle East Respiratory Syndrome (MERS) Consistent with our findings, latest clinical reports combined with mutational scanning suggest that V367F may lead to enhanced viral infectivity of SARS-CoV-2 28, 29 . keywords: ace2; binding; cov-2; figure; kidney; kim1; patients; rbd; sars cache: cord-259620-qigfstxt.txt plain text: cord-259620-qigfstxt.txt item: #263 of 702 id: cord-260054-iihgc5nr author: Cavallo, Luigi title: D936Y and Other Mutations in the Fusion Core of the SARS-Cov-2 Spike Protein Heptad Repeat 1 Undermine the Post-Fusion Assembly date: 2020-06-08 words: 4079 flesch: 50 summary: Other, less frequent, mutations were S939F and then S929I, L938F and S940F. Overall, such mutations appeared to be late ones, emerging starting from the end of February or even mid March 2020, and were mainly localized in Europe and USA. From these sequences, we extracted the nucleotide sequences of the spike protein and translated them to protein sequences with in-house scripts. keywords: conformation; cov-2; fusion; mutations; protein; sars; sequences; spike cache: cord-260054-iihgc5nr.txt plain text: cord-260054-iihgc5nr.txt item: #264 of 702 id: cord-260315-uau554jj author: Ramirez, Santseharay title: Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds date: 2020-10-04 words: 2280 flesch: 35 summary: We demonstrated that the Huh7.5-adapted virus exhibited a >3-Log10 increase in infectivity titers (TCID50) in Huh7.5 cells, with titers of ~8 Log10TCID50/mL, and >2-Log10 increase in the human lung cancer cell line Calu-1, with titers of ~6 Log10TCID50/mL. Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. The enhanced ability of the virus to replicate and propagate in human cells permitted screening of a panel of nine nucs, including broad-spectrum compounds. Limited SARS-CoV-2 replication and propagation occurs in human cells, which are the most relevant testing platforms. keywords: cells; cov-2; huh7.5; sars; virus cache: cord-260315-uau554jj.txt plain text: cord-260315-uau554jj.txt item: #265 of 702 id: cord-260352-rhd0qqyn author: Bhattacharyya, Sumit title: Increased Expression of Chondroitin Sulfotransferases following AngII may Contribute to Pathophysiology Underlying Covid-19 Respiratory Failure: Impact may be Exacerbated by Decline in Arylsulfatase B Activity date: 2020-06-25 words: 2761 flesch: 43 summary: 4- ARSB activation requires oxygen for post-translational modification and activation, and ARSB activity is lower in hypoxic conditions [12, 13] ; b) decline in ARSB is associated with increased IL-6 expression in human bronchial epithelial cells and in patients with cystic fibrosis and asthma [14] ; c) decline in ARSB replicates effects of hypoxia and generation of sulfate by ARSB may be important in mitochondrial metabolism [12, 15] ; d) accumulation of sulfated glycosaminoglycans when ARSB is reduced can contribute to inflammation and pulmonary pathophysiology, as in cystic fibrosis [16] ; e) in patients with moderate COPD, refractoriness to oxygen therapy was associated with gene mutations regulating ARSB expression In this brief report, we present data indicating that stimulation of vascular smooth muscle cells by AngII leads to increased expression of two chondroitin sulfotransferases (CHST11 and CHST15), which are required for the synthesis of the sulfated glycosaminoglycans chondroitin 4-sulfate (C4S) and chondroitin 4,6-disulfate (CSE). keywords: activity; arsb; cells; chondroitin; decline; expression; il-6; patients cache: cord-260352-rhd0qqyn.txt plain text: cord-260352-rhd0qqyn.txt item: #266 of 702 id: cord-260481-twk5kvd3 author: Täufer, Matthias title: Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing date: 2020-08-18 words: 3855 flesch: 55 summary: However, pool testing is typically performed via an adaptive testing strategy which requires a feedback loop in the lab and at least two PCR runs to confirm positive results. A small modification of our strategy might furthermore allow for an improvement of the false negative rate -even compared to usual adaptive pool testing strategies: even though commonly used, pooling samples can potentially dilute samples close to the identification threshold of the PCR and increase the probaility of false negatives. keywords: pool; positive; size; testing cache: cord-260481-twk5kvd3.txt plain text: cord-260481-twk5kvd3.txt item: #267 of 702 id: cord-260508-z11exbyu author: Wang, Hongru title: Synonymous mutations and the molecular evolution of SARS-Cov-2 origins date: 2020-10-12 words: 4705 flesch: 45 summary: The 7 ML tree using sequence from the ACE2 contact residue region supports the clustering of SARS-8 CoV-2 and GD410721, but with unusual long external branches for all strains except SARS-9 CoV-2, possibly reflecting smaller recombination regions within the ACE2 contact residue region. However, 15 these analyses alone do not distinguish between recombination into RaTG13 from an unknown 16 source as previously hypothesized (Boni, et al. 2020 ) and recombination between SARS-CoV-2 17 and GD410721 as proposed as one possible explanation by Lam et al. . keywords: cov-2; divergence; ratg13; recombination; sars cache: cord-260508-z11exbyu.txt plain text: cord-260508-z11exbyu.txt item: #268 of 702 id: cord-260793-bb4h255w author: Brann, David H. title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia date: 2020-05-18 words: 12011 flesch: 46 summary: medRxiv A primer on viral-associated olfactory loss in the era of COVID-19 Sudden and Complete Olfactory Loss Function as a Possible Symptom of COVID-19 European Patients with mild-to-moderate Coronavirus Disease SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ACE2 Efficient replication of severe acute respiratory syndrome coronavirus in mouse cells is limited by murine angiotensin-converting enzyme 2 A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts Middle East respiratory syndrome coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto host cells The Laboratory Mouse Comparative anatomy, physiology, and function of the upper respiratory tract Phagocytic cells in the rat olfactory epithelium after bulbectomy Supporting cells as phagocytes in the olfactory epithelium after bulbectomy Ionic conductances in sustentacular cells of the mouse olfactory epithelium Novel role of cystic fibrosis transmembrane conductance regulator in maintaining adult mouse olfactory neuronal homeostasis Olfactory epithelium: Cells, clinical disorders, and insights from an adult stem cell niche Stem and progenitor cells of the mammalian olfactory epithelium: Taking poietic license Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes A single-cell atlas of the human healthy airways A cellular census of human lungs identifies novel cell states in health and in asthma A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans Single-cell analysis of olfactory neurogenesis and differentiation in adult humans SARS-CoV-2 Entry Genes Are Most Highly Expressed in Nasal Goblet and Ciliated Cells within Human Airways Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome Dnmt3a Regulates Global Gene Expression in Olfactory Sensory Neurons and Enables Odorant-Induced Transcription Molecular Architecture of the Mouse Nervous System Pericytes and Neurovascular Function in the Healthy and Diseased Brain Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. If humans also exhibit a similar relationship between mRNA and protein (a reasonable possibility given the precise match in olfactory cell types that express CoV-2 cell entry genes between the two species), then ACE2 protein is likely to be broadly expressed in human dorsal sustentacular cells. keywords: ace2; bulb; cell types; cells; cov-2; data; dataset; entry; epithelium; expression; figure; genes; human; infection; mice; mouse; neurons; olfactory; osns; respiratory; seq; sustentacular; tmprss2; types; wom cache: cord-260793-bb4h255w.txt plain text: cord-260793-bb4h255w.txt item: #269 of 702 id: cord-261435-wcn4bjnw author: Ren, Xianwen title: Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients date: 2020-10-29 words: 8612 flesch: 49 summary: We first analyzed the compositional changes of the broad categories of immune cells for 206 PBMCs in different COVID-19 patient groups. 499 500 Such interaction distinctions not only existed among epithelial cells, but also impacted their 501 interactions with immune cells. keywords: age; cells; cov-2; covid-19; covid-19 patients; cytokine; differences; disease; figure; patients; plasma; sars; subtypes; types cache: cord-261435-wcn4bjnw.txt plain text: cord-261435-wcn4bjnw.txt item: #270 of 702 id: cord-261662-d0tg9i90 author: Andres, Cristina title: Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients date: 2020-06-08 words: 4688 flesch: 43 summary: Our results indicate that the mutant S would have a large impact on the S protein, and suggest that the virus could produce free S1, which may have implications regarding the candidacy of S protein as a target for vaccination and antiviral treatment strategies. Abbreviations: ACE2, angiotensin converting enzyme 2; mRNA, messenger RNA; NAb; neutralizing antibodies; pp1a, polyprotein 1a; RdRp, RNA-dependent RNA polymerase; S, spike; S1, subunit S1 at the N-terminal domain of the S protein, which includes receptor binding domain (RBD); S2, subunit S2 located at the C-terminal domain of S protein, which includes fusion peptide (FP), heptad repeat (HR) domain 1 and 2, and the transmembrane domain (TM); ss, single stranded; ss+RNA, single-stranded positive sense RNA; TMPRS22, human serine protease TMPRSS2 Replication error, quasispecies populations and extreme evolution rates of RNA viruses Basic concepts in RNA virus evolution Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission Covid-19 -Navigating the Uncharted A Review of SARS-CoV-2 and the Ongoing Clinical Trials Mechanisms of coronavirus cell entry mediated by the viral spike protein SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor CD209L keywords: cell; cov-2; deletions; human; infection; patients; protein; receptor; rna; sars; virus cache: cord-261662-d0tg9i90.txt plain text: cord-261662-d0tg9i90.txt item: #271 of 702 id: cord-261688-njlxrxv6 author: Yang, Ziwei title: Suppression of MDA5-mediated antiviral immune responses by NSP8 of SARS-CoV-2 date: 2020-08-12 words: 2541 flesch: 38 summary: Here, we revealed that NSP8 protein of SARS-CoV-2 directly blocks the activation of the cytosolic viral dsRNA sensor MDA5 and significantly downregulates antiviral immune responses. The polyubiquitination of MDA5 was 165 analyzed in the presence or absence of NSP8 expression. keywords: k63; mda5; nsp8; polyubiquitination; responses; rna; sars cache: cord-261688-njlxrxv6.txt plain text: cord-261688-njlxrxv6.txt item: #272 of 702 id: cord-261718-zqoggwnk author: Pietschmann, Jan title: Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies date: 2020-06-03 words: 1189 flesch: 33 summary: Specific antibodies were retained within the IFC and labelled with an isotype specific biotinylated antibody. Here, a new point-of-care approach for SARS-CoV-2 specific antibody detection in human serum based on magnetic immuno-detection is described and compared to standard ELISA. keywords: cov-2; detection; protein; sars cache: cord-261718-zqoggwnk.txt plain text: cord-261718-zqoggwnk.txt item: #273 of 702 id: cord-261855-qpbgq5d8 author: Walker, Susanne N. title: SARS-CoV-2 assays to detect functional antibody responses that block ACE2 recognition in vaccinated animals and infected patients date: 2020-06-18 words: 2556 flesch: 44 summary: One such approach to help augment the methods listed 95 above is an enzyme-linked immunosorbent assay (ELISA) employed in a competitive manner to determine levels of ACE2 receptor blocking antibodies in a sample. In addition, recent advances 97 of portable and field-deployable surface plasmon resonance (SPR) devices(22) and widespread 98 availability of SPR instruments in research laboratories make SPR an additional platform for 99 measuring ACE2 receptor blocking. keywords: ace2; assay; binding; fig; receptor; sera; spike cache: cord-261855-qpbgq5d8.txt plain text: cord-261855-qpbgq5d8.txt item: #274 of 702 id: cord-261877-4y37676n author: Xu, Cong title: Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM date: 2020-06-30 words: 8815 flesch: 45 summary: Unlike the observations made with SARS-CoV and MERS-CoV S trimers, we did not detect S trimer with two RBD domains up with bound ACE2 (Kirchdoerfer et al., 2018; Pallesen et al., 2017) . Our data suggested there is one RBD in the up conformation and is trapped with ACE2 in the S-ACE2 complex; ACE2 can greatly shift the conformational landscape of S trimer, and trigger continuous swing motions of ACE2-RBD in the context of the S trimer resulting in conformational dynamics in S1 subunits. keywords: ace2; binding; conformational; cov-2; et al; fig; particles; rbd; receptor; s trimer; sars; spike; state; structure; trimer cache: cord-261877-4y37676n.txt plain text: cord-261877-4y37676n.txt item: #275 of 702 id: cord-261961-u4d0vvmq author: St-Germain, Jonathan R. title: A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research date: 2020-08-28 words: 2741 flesch: 25 summary: A number of virus protein interactions were also detected with components of the UFMylation system (DDRGK1, CDK5RAP3, UFL1 and UFSP2), which was recently shown to play a key role in ER-phagy 10 , highlighting interesting links between specific autophagy pathways and SARS-CoV-2. As a whole, the virus-host interactome is significantly enriched in proteins associated with the endoplasmic reticulum (ER)/nuclear, Golgi and plasma membranes, and ER-Golgi trafficking vesicles ( Even amongst those viral proteins that appear to localize exclusively to the ER-Golgi-PM endomembrane membrane system, specificity in virus-host interactomes was observed, likely reflecting preferences for interactions with different subsets of membrane proteins and/or localization to unique membrane lipid nanodomains. keywords: approaches; data; host; mass; membrane; proteins; proteomics; replication; sars; virus cache: cord-261961-u4d0vvmq.txt plain text: cord-261961-u4d0vvmq.txt item: #276 of 702 id: cord-262119-s6hc7fxs author: Ostaszewski, Marek title: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms date: 2020-10-27 words: 12366 flesch: 31 summary: COVID-19 pathways featured in the previous section cover mechanisms reported so far. By aligning our efforts, we strive to provide COVID-19 specific pathway models, synchronize content with similar resources and encourage discussion and feedback at every stage of the curation process. keywords: activation; acute; analysis; apoptosis; cell; community; coronavirus; cov-2; covid-19; covid-19 disease; data; diagrams; disease; disease map; expression; host; human; infection; interactions; interferon; map; mechanisms; modelling; models; pathway; patients; protein; response; sars; syndrome; systems; type cache: cord-262119-s6hc7fxs.txt plain text: cord-262119-s6hc7fxs.txt item: #277 of 702 id: cord-262145-i29e3fge author: Huang, Kuan-Ying A. title: Breadth and function of antibody response to acute SARS-CoV-2 infection in humans date: 2020-10-19 words: 2974 flesch: 40 summary: Data are presented as mean ± 823 standard error of the mean ACE2-blocking activity of anti-RBD antibody compared to ACE2-Fc (see methods): +, partial; ++ Abbreviations: IFA, immunofluorescence; RBD, receptor-binding domain; PRNT, plaque reduction 835 neutralisation assay The presence of pre-existing immune memory to betacoronavirus that cross-react with 322 SARS-CoV-2 is supported by the accumulation of somatic mutations in the genes 323 encoding cross-reactive antibodies isolated from COVID-19 patients (Figures 2c and 324 2d, Supplemental Tables 2 and 3 ). keywords: ace2; anti; antibodies; antibody; binding; mabs; rbd; sars cache: cord-262145-i29e3fge.txt plain text: cord-262145-i29e3fge.txt item: #278 of 702 id: cord-262470-nkql7h9x author: Muus, Christoph title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells date: 2020-04-20 words: 17614 flesch: 41 summary: In order to avoid spurious associations in cell types with very few ACE2 + cells and due to very low expression of ACE2, we subsampled ACE2cells to the number of ACE2 + cells within each cell type and discarded cell types containing fewer than 5 cells expressing either ACE2 or fewer than 5 cells expressing the other gene being tested after the subsampling procedure. Focusing on pathogenesis, in addition to key subsets in the lung, airways and gut, we identified ACE2 + cells that co-express either TMPRSS2 or CTSL in diverse organs, many of which have been associated with severe disease. keywords: ace2; ace2 expression; age; airway; analysis; associations; at2 cells; cell types; cells; coronavirus; cov-2; covid-19; ctsl; data; data fig; datasets; expression; fig; genes; human; infection; lung; model; patients; programs; samples; sars; secretory; seq; sex; smoking; tissue; tmprss2; type cache: cord-262470-nkql7h9x.txt plain text: cord-262470-nkql7h9x.txt item: #279 of 702 id: cord-262485-sx2q5ol4 author: Davda, Jayeshkumar Narsibhai title: An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance date: 2020-06-08 words: 3259 flesch: 48 summary: 6 In order to compare the performance of RT-nPCR with that of standard RT-qPCR we tested RNA samples that had tested positive by RT-qPCR. Based on E gene result RdRp and Orf1b were tested with 5 µl of RNA sample by following Confirmatory assay given by ICMR-NIV https://main.icmr.nic.in/sites/default/files/upload_documents/2_SOP_for_Confirmatory_As say_for_2019_nCoV.pdf. keywords: npcr; pcr; rna; samples; sars; test; testing cache: cord-262485-sx2q5ol4.txt plain text: cord-262485-sx2q5ol4.txt item: #280 of 702 id: cord-262573-wdgbno9p author: Begum, Feroza title: Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India date: 2020-05-03 words: 1616 flesch: 56 summary: We downloaded all the sequences from West Bengal (Figure 1 ) and performed a nucleotide translation to obtain respective spike protein sequences. key: cord-262573-wdgbno9p authors: Begum, Feroza; Mukherjee, Debica; Thagriki, Dluya; Das, Sandeepan; Tripathi, Prem Prakash; Banerjee, Arup Kumar; Ray, Upasana title: Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India date: 2020-05-03 journal: bioRxiv DOI: 10.1101/2020.04.28.066985 sha: doc_id: 262573 cord_uid: wdgbno9p India has recently started sequencing SARS-CoV2 genome from clinical isolates. keywords: bengal; protein; sequences; spike cache: cord-262573-wdgbno9p.txt plain text: cord-262573-wdgbno9p.txt item: #281 of 702 id: cord-262602-on0w55x0 author: Muruato, Antonio E. title: A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation date: 2020-05-22 words: 884 flesch: 44 summary: Here we report on a fluorescence-based SARS-CoV-2 neutralization assay that detects SARS-CoV-2 neutralizing antibodies in COVID-19 patient specimens and yields comparable results to plaque reduction neutralizing assay, the gold standard of serological testing. Next, we evaluated the specificity of reporter neutralization assay using potentially cross-7 1 reactive sera and interfering substances (Table 1) . keywords: assay; covid-19; reporter cache: cord-262602-on0w55x0.txt plain text: cord-262602-on0w55x0.txt item: #282 of 702 id: cord-262726-lfuxhlki author: Diallo, Aïssatou Bailo title: Daytime variation in SARS-CoV-2 infection and cytokine production date: 2020-09-11 words: 1157 flesch: 43 summary: key: cord-262726-lfuxhlki authors: Diallo, Aïssatou Bailo; Gay, Laetitia; Coiffard, Benjamin; Leone, Marc; Mezouar, Soraya; Mege, Jean-Louis title: Daytime variation in SARS-CoV-2 infection and cytokine production date: 2020-09-11 journal: bioRxiv DOI: 10.1101/2020.09.09.290718 sha: doc_id: 262726 cord_uid: lfuxhlki S. Ray and A. Reddy recently anticipated the implication of circadian rhythm in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of the coronavirus disease (Covid-19). Using Cosinor analysis, we showed that Bmal1 and Clock transcripts exhibited circadian rhythm in monocytes with an acrophase and a bathyphase at Zeitgeber Time (ZT)6 and ZT17. keywords: cov-2; infection; sars cache: cord-262726-lfuxhlki.txt plain text: cord-262726-lfuxhlki.txt item: #283 of 702 id: cord-262958-tmp6yxlv author: Pinto, Dora title: Structural and functional analysis of a potent sarbecovirus neutralizing antibody date: 2020-04-09 words: 2248 flesch: 42 summary: Subsequently, two rounds 443 of 3D classification with 50 iterations each (angular sampling 7.5˚ for 25 iterations and 444 1.8˚ with local search for 25 iterations), using our previously reported closed SARS-445 CoV-2 S structure 6 as initial model, were carried out using Relion 51 without imposing 446 symmetry to separate distinct SARS-CoV-2 S conformations. bioRxiv Genomic characterisation and epidemiology of 2019 novel 605 coronavirus: implications for virus origins and receptor binding Structure of SARS coronavirus spike 608 receptor-binding domain complexed with receptor Occupancy and mechanism in antibody-611 mediated neutralization of animal viruses IgG Fc engineering to modulate antibody 614 effector functions Alveolar macrophages are critical for broadly-reactive antibody-617 mediated protection against influenza A virus in mice Differential Fc-Receptor Engagement Drives an 620 A neutralizing antibody selected from plasma cells that binds to 623 group 1 and group 2 influenza keywords: antibody; cells; cov-2; fig; s309; sars cache: cord-262958-tmp6yxlv.txt plain text: cord-262958-tmp6yxlv.txt item: #284 of 702 id: cord-263008-w6twrjzr author: Yin, Rui title: Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide date: 2020-07-15 words: 3689 flesch: 40 summary: Inferring 78 the lethality of novel coronavirus is possible by identifying the patterns from a large 79 number of coronavirus sequences. The predictive performance is evaluated by accuracy, precision, sensitivity, and F1 score 221 of all models in the prediction tasks of coronavirus lethality. keywords: analysis; coronavirus; human; learning; lethality; machine; novel; prediction; sars; sequences cache: cord-263008-w6twrjzr.txt plain text: cord-263008-w6twrjzr.txt item: #285 of 702 id: cord-263090-29n9tsk9 author: Roy, Susmita title: Dynamical asymmetry exposes 2019-nCoV prefusion spike date: 2020-04-21 words: 4634 flesch: 47 summary: An investigation for small globular proteins SWISS-MODEL: homology modelling of protein structures and complexes The human coronavirus HCoV-229E S-protein structure and receptor binding SMOG 2: A Versatile Software Package for Generating Structure-Based Models The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. An investigation for small globular proteins SWISS-MODEL: homology modelling of protein structures and complexes The human coronavirus HCoV-229E S-protein structure and receptor binding SMOG 2: A Versatile Software Package for Generating Structure-Based Models The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. keywords: chain; head; inter; protein; rbd; sars; spike; state cache: cord-263090-29n9tsk9.txt plain text: cord-263090-29n9tsk9.txt item: #286 of 702 id: cord-263594-jd9ako6c author: Kang, Sisi title: A COVID-19 antibody curbs SARS-CoV-2 nucleocapsid protein-induced complement hyper-activation date: 2020-09-11 words: 2520 flesch: 41 summary: The complex structure of N protein RNA binding domain with the highest binding affinity mAb nCoV396 reveals the epitopes and antigen’s allosteric changes. One Sentence Summary B cell profiling, structural determination, and protease activity assays identify a functional antibody to N protein. mechanics despite the severity of hypoxemia (7). keywords: antibodies; antibody; complement; cov-2; fig; protein; sars cache: cord-263594-jd9ako6c.txt plain text: cord-263594-jd9ako6c.txt item: #287 of 702 id: cord-263780-8jejswuk author: Wang, Nan title: Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of 2019-nCoV Spike pseudotyped virus date: 2020-08-14 words: 1606 flesch: 52 summary: The expression of ACE2 protein in ACE2 h cells was significantly higher than that 208 in other cells, indicating that ACE2 h cells were successfully constructed. 212 As shown in Figure 1B , CQ and HCQ had no significant effect on the activity of ACE2 h cells when 213 the concentration was less than 50 μM, and the survival rate of ACE2 h cells could be reduced in a dose-dependent manner when the concentration was above 50 μM. The inhibition of HCQ on the 215 activity of ACE2 h cells was more significant than that of CQ. keywords: ace2; cells; hcq; lc3 cache: cord-263780-8jejswuk.txt plain text: cord-263780-8jejswuk.txt item: #288 of 702 id: cord-263825-g8p2lsr0 author: Maldonado, Lucas L. title: Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects date: 2020-06-25 words: 3433 flesch: 44 summary: CPB correlation is included in the left for each cluster relating the 670 CPB of human genes (horizontal axis) and CPB of the viral genes to 6) using a hierarchical method 672 of viral genes forSARS (NC_038294) of the human host and human genes based on the 673 molecular features. Furthermore, as demonstrated in our clustering analysis, codon 497 pair usage seems to be dependent on the dinucleotide bias and the human CPB was 498 higher for human genes than for viruses genes as previously reported (Kames et al., 499 2020; Kunec and Osterrieder, 2016) . keywords: bias; codon; cov-2; genes; host; human; sars; usage; virus cache: cord-263825-g8p2lsr0.txt plain text: cord-263825-g8p2lsr0.txt item: #289 of 702 id: cord-263970-9w6ciglv author: Marquez-Miranda, Valeria title: Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date: 2020-10-22 words: 2886 flesch: 51 summary: key: cord-263970-9w6ciglv authors: Marquez-Miranda, Valeria; Rojas, Maximiliano; Duarte, Yorley; Diaz-Franulic, Ignacio; Holmgren, Miguel; Cachau, Raul E.; Gonzalez-Nilo, Fernando D. title: Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites date: 2020-10-22 journal: bioRxiv DOI: 10.1101/2020.10.22.349522 sha: doc_id: 263970 cord_uid: 9w6ciglv SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. ORF3a is believed to form ion channels keywords: cavity; domain; ions; orf3a; potential; structure cache: cord-263970-9w6ciglv.txt plain text: cord-263970-9w6ciglv.txt item: #290 of 702 id: cord-264012-q2quyijg author: Lim, Su Bin title: ACE2-expressing endothelial cells in aging mouse brain date: 2020-07-11 words: 2141 flesch: 38 summary: Overall, this work reveals an outline of ACE2 distribution in the mouse brain and identify putative brain host cells that may underlie the selective susceptibility of the aging brain to viral infection. In light of such controversy regarding neuropathological features, a more comprehensive assessment on the distribution of ACE2 in a cell type-specific manner is required to identify putative brain host cells. keywords: ace2; brain; cells; covid-19; human; seq cache: cord-264012-q2quyijg.txt plain text: cord-264012-q2quyijg.txt item: #291 of 702 id: cord-264031-0y7xbgun author: Wierbowski, Shayne D. title: A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions date: 2020-10-13 words: 5081 flesch: 22 summary: Our finding that disease mutations and viral proteins 197 affect human proteins at distinct sites is consistent with a two-hit hypothesis of comorbidities whereby 198 proteins whose function is already affected by genetic background may be further compromised by viral 199 infection. Disruption of native protein-protein interactions is one mechanism of disease 189 pathology, and disease mutations are known to be enriched along protein interfaces 70, 71 . keywords: cov-2; disease; human; interaction; interactome; interface; mutations; population; protein; sars; structural; variants; viral cache: cord-264031-0y7xbgun.txt plain text: cord-264031-0y7xbgun.txt item: #292 of 702 id: cord-264051-ps0x2es1 author: Li, Wei title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date: 2020-11-05 words: 8954 flesch: 43 summary: Such discrepancies may be owing to the binding of hyaluronan and its ligand CD44, which can induce the death of activated T cells (McKallip et al., 2002) . Noteworthily, as the antiviral immunity guardian, T cells are reduced significantly in COVID-19 patients (Diao et al., 2020) , which is negatively correlated with survival rates. keywords: cov-2; covid-19; et al; expression; g t; gene; hek293 t; host; human; hyaluronan; level; patients; rna; sars; t c; t cells; t t; virus cache: cord-264051-ps0x2es1.txt plain text: cord-264051-ps0x2es1.txt item: #293 of 702 id: cord-264204-4ablrwuo author: Guintivano, Jerry title: Psychiatric Genomics Research During the COVID-19 Pandemic: A Survey of Psychiatric Genomics Consortium Researchers date: 2020-10-08 words: 4002 flesch: 37 summary: (16.2%), offer greater support to early career researchers (e.g. advocate for junior researchers, create support groups for early career researchers) (14.9%), provide support for researchers directly impacted by COVID-19 (e.g. leniency for those who see patients and other caregivers, support career advancement for those directly affected by COVID-19) (10.8%) , provide funding to support researchers (e.g. bridge funding to sustain PGC research especially among junior researchers and those not part of core PGC funding) (10.8%), and provide online training (e.g. statistical genetics and other key topic courses) (8.1%). We modeled our questionnaire after Weissman et al (Weissman et al., 2020) and assessed: (a) the impact of COVID-19 on PGC research now and in the foreseeable future; (b) the level of concern about COVID-19-related disruptions of research and the potential impact of these disruptions on individuals' careers; (c) strategies that respondents thought to be effective in coping with COVID-19-related research disruptions; and (d) respondents' suggestions for how the PGC or the field should respond to help researchers move through and beyond the current crisis. keywords: career; covid-19; pgc; research; researchers; respondents; responses cache: cord-264204-4ablrwuo.txt plain text: cord-264204-4ablrwuo.txt item: #294 of 702 id: cord-264296-0x90yubt author: Sawmya, Shashata title: Analyzing hCov genome sequences: Applying Machine Intelligence and beyond date: 2020-06-03 words: 5017 flesch: 56 summary: Thus, every resulting time-step represents a date (Tk for Cluster k) and contains the clusters of genome sequences of the countries/states. Notably, we do not consider any alignmentbased method since it is not computationally feasible for us to align thousands of viral sequences for analysis and clustering purposes [4] . keywords: analysis; coronavirus; countries; features; genome; learning; pipeline; sars; sequences; strain; tree cache: cord-264296-0x90yubt.txt plain text: cord-264296-0x90yubt.txt item: #295 of 702 id: cord-264919-0jlg2gkc author: Hopp, Marie-Thérèse title: Unravelling the debate on heme effects in COVID-19 infections date: 2020-06-12 words: 7102 flesch: 40 summary: Clinical observations revealed their upregulation in COVID-19 patients as well as during hemolytic events (Dutra and Bozza, 2014; Humayun et al., 2020; Ye et al., 2020) , which highlights even more the TLR4 signaling pathway in both situations. COVID-19 is caused by infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is accompanied by pneumonia, acute respiratory distress syndrome (ARDS) associated with a cytokine storm, and death in the most severe cases (Ye et al., 2020; Zhou et al., 2020a) . keywords: ace2; binding; cell; cov-2; covid-19; et al; figure; heme; interaction; motifs; patients; protein; sars; system; tmprss2 cache: cord-264919-0jlg2gkc.txt plain text: cord-264919-0jlg2gkc.txt item: #296 of 702 id: cord-265277-ymvrserl author: Crooke, Stephen N. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 words: 4637 flesch: 38 summary: Prior immunization with severe acute respiratory syndrome (SARS)-434 associated coronavirus (SARS-CoV) nucleocapsid protein causes severe pneumonia in mice 435 infected with SARS-CoV Characterization of the receptor-binding domain (RBD) of 2019 novel 537 coronavirus: implication for development of RBD protein as a viral attachment inhibitor and 538 vaccine Quantitative comparison of the efficiency of antibodies against S1 and S2 540 subunit of SARS coronavirus spike protein in virus neutralization and blocking of receptor 541 binding: implications for the functional roles of S2 subunit Neutralizing epitopes of the SARS-CoV S-protein cluster independent of 543 repertoire, antigen structure or mAb technology Identification and characterization of novel neutralizing epitopes in the 545 receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic 546 determinants in inactivated SARS-CoV vaccine Discovery of 548 naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass 549 spectrometry for vaccine development Development of Autologous C5 Vaccine Nanoparticles to Reduce 551 Intravascular Hemolysis in Vivo Plug-and-Display: decoration of Virus-Like Particles via isopeptide 553 bonds for modular immunization A novel candidate HPV vaccine: MS2 phage VLP displaying a tandem HPV 555 L2 peptide offers similar protection in mice to Gardasil-9 Targeted 557 immunomodulation using antigen-conjugated nanoparticles Scoring function for automated assessment of protein structure 560 template quality GalaxyPepDock: a protein-peptide docking tool based 562 on interaction similarity and energy optimization World Health Organization (2020) Draft landscape of COVID-19 candidate vaccines Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine 428 development Immunization with SARS coronavirus vaccines leads to pulmonary 430 immunopathology on challenge with the SARS virus Vaccine efficacy in senescent mice challenged with recombinant SARS-432 CoV bearing epidemic and zoonotic spike variants keywords: cell; class; cov-2; epitopes; hla; peptides; protein; sars; vaccine cache: cord-265277-ymvrserl.txt plain text: cord-265277-ymvrserl.txt item: #297 of 702 id: cord-265418-yqe9vdj1 author: Kumar, Nilesh title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis date: 2020-04-11 words: 5303 flesch: 47 summary: It is also important to note that PHB is also targeted by viral proteins of SARS-CoV 34 . Human-viral interactome landscapes of several viruses have previously shown that viral proteins interact with nodes corresponding to high degree (hubs) and high betweenness (bottlenecks), and such structural features have been previously used to predict viral targets 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . keywords: cov-2; csps; fig; human; network; proteins; sars; viral cache: cord-265418-yqe9vdj1.txt plain text: cord-265418-yqe9vdj1.txt item: #298 of 702 id: cord-265453-z6aux01t author: Bierig, Tobias title: Design, expression, purification and characterization of a YFP-tagged 2019-nCoV spike receptor-binding domain construct date: 2020-09-29 words: 3459 flesch: 52 summary: Cell culture experiments, protein purification and biochemical analysis were performed by R.M.B., T.B. and G.C.. The solution was incubated at 4 o C with occasional agitation until the next batch of secreted protein became available. keywords: cells; domain; expression; medium; nta; protein; spike; yfp cache: cord-265453-z6aux01t.txt plain text: cord-265453-z6aux01t.txt item: #299 of 702 id: cord-266444-rw94yls8 author: Dominguez Andres, Ana title: SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells date: 2020-08-19 words: 5655 flesch: 34 summary: Thus, to maximize the discovery of ORF9c dysregulated proteins, results from both technologies were combined. Together with the observations on cellular immune pathways, this association with 16 the UBP suggested that ORF9c induces changes in UBP components that alter the stability of cellular proteins implicated in cytokine signaling, antigen presentation, innate immunity, and the cell cycle. keywords: analysis; cells; changes; cov-2; data; fig; immune; mg132; orf9c; pathways; proteasome; proteins; sars; signaling; table cache: cord-266444-rw94yls8.txt plain text: cord-266444-rw94yls8.txt item: #300 of 702 id: cord-266869-fs8dn7ir author: Kim, So Young title: Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry date: 2020-04-15 words: 3834 flesch: 45 summary: In: World Health Organization Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites Middle East Respiratory Syndrome Coronavirus Spike Protein Is Not Activated Directly by Cellular Furin during Viral Entry into Target Cells SARS coronavirus, but not human coronavirus NL63, utilizes cathepsin L to infect ACE2-expressing cells Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2 Inhibition of SARS pseudovirus cell entry by lactoferrin binding to heparan sulfate proteoglycans Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC Glycosaminoglycans in infectious disease Mechanisms of coronavirus cell entry mediated by the viral spike protein Interaction of Zika Virus Envelope Protein with Glycosaminoglycans Proteoglycans and Sulfated Glycosaminoglycans Copper regulates the interactions of antimicrobial piscidin peptides from fish mast cells with formyl peptide receptors and heparin Molecular modeling of protein-glycosaminoglycan interactions Glycosaminoglycan-protein interactions: definition of consensus sites in glycosaminoglycan binding proteins The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade Software News and Updates AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking Matrix proteoglycans as effector molecules for epithelial cell function Comparison of Low-Molecular-Weight Heparins Prepared From Bovine Lung Heparin and Porcine Intestine Heparin Thermodynamic Analysis of the Heparin Interaction with a Basic Cyclic Peptide Using Isothermal Titration Calorimetry Kinetic Model for FGF, FGFR, and Proteoglycan Signal Transduction Complex Assembly Further evidence that periodate cleavage of heparin occurs primarily through the antithrombin binding site Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry Cleavage of Group 1 Coronavirus Spike Proteins: How Furin Cleavage Is Traded Off against Heparan Sulfate Binding upon Cell Culture Adaptation Heparin enhances the furin cleavage of HIV-1 gp160 peptides Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. During this step, heavily sulfated HS chains span inter-domain channel containing GAG-binding site 2 on each monomer in the trimeric SGP and binds site 1 within the RBD in an open conformation (Fig 5) . keywords: binding; cell; cov-2; fig; gag; host; sars; sgp; site; surface cache: cord-266869-fs8dn7ir.txt plain text: cord-266869-fs8dn7ir.txt item: #301 of 702 id: cord-267115-6jqdi417 author: Giobbe, Giovanni Giuseppe title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 words: 8091 flesch: 38 summary: Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. While R-spondin 1,Wnt-3A and Noggin withdrawal led to more differentiated morphology, CHIR99021 (GSK-3 inhibitor) proved to be essential in the formation of fetal gastric organoids starting from single cells (Fig. 2a) . keywords: analysis; cells; cov-2; data; degs; expression; fig; gastric; human; infection; organoids; pcw; pediatric; rna; samples; sars; stages; virus cache: cord-267115-6jqdi417.txt plain text: cord-267115-6jqdi417.txt item: #302 of 702 id: cord-267223-pf799wbw author: de Lamballerie, Claire Nicolas title: Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model date: 2020-05-19 words: 1184 flesch: 7 summary: In the present study, to better understand the biological impact of superinfection we sought to determine and compare the host transcriptional response to SARS-CoV-2 versus Aspergillus superinfection, using a model of reconstituted humain airway epithelium. In the present study, to better 24 understand the biological impact of superinfection we sought to determine and compare the 25 host transcriptional response to SARS-CoV-2 versus Aspergillus superinfection, using a model 26 of reconstituted humain airway epithelium. keywords: cell; regulation; response; superinfection cache: cord-267223-pf799wbw.txt plain text: cord-267223-pf799wbw.txt item: #303 of 702 id: cord-267482-afqfymbq author: Ryu, Seungjin title: Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model date: 2020-09-12 words: 8214 flesch: 40 summary: For example, epithelial cell specific induction of hACE2 (K18-hACE2) as a model of SARS-CoV-2 infection demonstrated that post intranasal inoculation, animals develop lung inflammation and pneumonia driven by infiltration of monocytes, neutrophils and T cells . Interestingly, some of the most striking changes occurred in T cells, where ketogenesis led to a substantial increase in ϒδ but not αβ T cells ( Figure 6C and Figure S6B ). keywords: a59; aging; cells; cov-2; covid-19; et al; expression; figure; infection; inflammasome; inflammation; mcov; mice; model; mouse; nlrp3; sars; ϒδ t cache: cord-267482-afqfymbq.txt plain text: cord-267482-afqfymbq.txt item: #304 of 702 id: cord-267536-rvhwl4ea author: Miyashita, L title: Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells date: 2020-05-27 words: 1095 flesch: 46 summary: Objective To assess the effect of traffic-derived PM10 on human airway epithelial cell ACE2 expression in vitro. Since the effect of traffic-related PM on the expression of ACE2 in human airway cell populations is not known we sought, in this study, to assess ACE2 expression in human airway epithelial cells exposed to traffic-derived PM 10 in vitro. Traffic-derived PM 10 was collected as dry particles using a high-volume cyclone placed within 2 metres of Marylebone Road, London, UK (8). keywords: ace2; cells; expression cache: cord-267536-rvhwl4ea.txt plain text: cord-267536-rvhwl4ea.txt item: #305 of 702 id: cord-267613-hsc2x36j author: Dittmar, Mark title: Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2 date: 2020-06-19 words: 7574 flesch: 43 summary: Remdesivir and hydroxylchloroquine were antiviral against SARS-CoV-2 in Huh7.5 cells with IC50s that were greater than 10-fold lower than those observed in Vero cells (Fig 2b) . However, the majority of the antivirals that were validated in Huh7.5 cells were not active in Vero cells. keywords: activity; antiviral; calu-3; cells; coronavirus; cov-2; cyclophilin; cyclosporine; drugs; entry; fig; huh7.5; infection; sars; vero; virus cache: cord-267613-hsc2x36j.txt plain text: cord-267613-hsc2x36j.txt item: #306 of 702 id: cord-267831-uu883ofc author: Kang, Yuan-Lin title: Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2 date: 2020-06-15 words: 1272 flesch: 5 summary: Lassa virus entry requires a trigger-induced 658 receptor switch Old world 660 arenaviruses enter the host cell via the multivesicular body and depend on the 661 endosomal sorting complex required for transport Coincidence detection in phosphoinositide signaling PIKfyve, a mammalian ortholog of 665 yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Analogues as Inhibitors by Virtual Drug Screening and Chemical Synthesis Vacuolin-1 potently and reversibly inhibits autophagosome-703 lysosome fusion by activating RAB5A Randomized, double-blind, placebo-controlled trial of the 705 oral interleukin-12/23 inhibitor apilimod mesylate for treatment of active Crohn's 706 disease Apilimod inhibits the production of IL-12 and IL-23 and 708 reduces dendritic cell infiltration in psoriasis The phosphatidylinositol-3-phosphate 5-kinase inhibitor 710 apilimod blocks filoviral entry and infection Ebola virus requires phosphatidylinositol (3,5) bisphosphate 712 production for efficient viral entry Visualization of Ebola Virus Fusion Triggering in the Endocytic Pathway A phase 1/2A trial of STA 5326 inhibitor, in patients with active moderate to severe Crohn's disease Brief report: a phase IIa, randomized, double-blind, 720 placebo-controlled trial of apilimod mesylate patients with rheumatoid arthritis Arbidol and Other Low-Molecular-Weight Drugs That 723 Inhibit Lassa and Ebola Viruses Identification of Combinations of Approved Drugs With Synergistic Activity Against Ebola Virus in Cell Cultures Characterization of VPS34-IN1, a selective inhibitor of 728 Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein 729 kinase is a downstream target of class III phosphoinositide 3-kinase Evidence that TMPRSS2 activates the severe acute 732 respiratory syndrome coronavirus spike protein for membrane fusion and reduces 733 viral control by the humoral immune response A transmembrane serine protease is linked to the severe 735 acute respiratory syndrome coronavirus receptor and activates virus entry Efficient activation of the severe acute respiratory 738 syndrome coronavirus spike protein by the transmembrane protease TMPRSS2 SARS-CoV-2 Cell Entry Depends on ACE2 and 741 TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Characterization of severe acute respiratory syndrome-744 associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Identification of apilimod as a first-in-class PIKfyve kinase 747 inhibitor for treatment of B-cell non-Hodgkin lymphoma The VP1 750 subunit of JC polyomavirus recapitulates early events in viral trafficking and is a 751 novel tool to study polyomavirus entry The Phosphoinositide Kinase PIKfyve Promotes 753 Small molecule inhibitors reveal Niemann-Pick C1 is 756 essential for Ebola virus infection Endosome-to-cytosol transport of viral nucleocapsids Protease inhibitors targeting coronavirus and filovirus entry Tracking the Fate of Genetically Distinct Vesicular 762 Stomatitis Virus Matrix Proteins Highlights the Role for Late Domains in 763 Assembly Uptake of rabies virus into 765 epithelial cells by clathrin-mediated endocytosis depends upon actin A 768 forward genetic strategy reveals destabilizing mutations in the Ebolavirus 769 glycoprotein that alter its protease dependence during cell entry Efficient recovery of infectious 772 vesicular stomatitis virus entirely from cDNA clones Genome engineering using the CRISPR-Cas9 system Identification and characterization of a novel broad 777 spectrum virus entry inhibitor A highly conserved cryptic epitope in the receptor-binding 779 domains of SARS-CoV-2 and SARS-CoV The first five seconds in the 781 life of a clathrin-coated pit 614 We thank Walter J. Atwood for providing the parental SVG-A cells, Eric Marino, Justin 615 H. Houser and Tegy John Vadakkan for maintaining the spinning disc confocal *** ** ** *** *** *** *** A Table I Table II keywords: cell; entry; kinase; pikfyve; sars; virus cache: cord-267831-uu883ofc.txt plain text: cord-267831-uu883ofc.txt item: #307 of 702 id: cord-267845-18hb5ndr author: Resende, Paola Cristina title: SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms date: 2020-05-01 words: 1621 flesch: 38 summary: Demultiplexed Fastq files generated from the Illumina sequencing data were used as an input for the analysis. The protocols described herein can be applied to different sequencing platforms, such as Sanger, Illumina and Oxford Nanopore, and therefore are useful, accessible and adaptable to laboratories with different resources and sequencing facilities. keywords: genomes; pcr; protocol; samples; sars; sequencing cache: cord-267845-18hb5ndr.txt plain text: cord-267845-18hb5ndr.txt item: #308 of 702 id: cord-268034-7id7sfsu author: Auerswald, Heidi title: Assessment of Inactivation Procedures for SARS-CoV-2 date: 2020-05-28 words: 1620 flesch: 35 summary: Untreated virus isolates had a concentration of viable virus up to 6.67 x 10 5 187 (isolate 2310) before treatment (Table 1) Previous studies have been conducted on the effectiveness of chemical inactivation 220 techniques on SARS-CoV-2 [11, 12] , the majority of these based on infectious agents of concern 221 such as Ebola Therefore, formaldehyde treatment does not appear to be a 247 solution for increased molecular SARS-CoV-2 testing; however, it does remain a viable alternative 248 for sample inactivation or disinfection. keywords: cov-2; inactivation; sars; treatment; virus cache: cord-268034-7id7sfsu.txt plain text: cord-268034-7id7sfsu.txt item: #309 of 702 id: cord-268224-5tbb8df1 author: Di Gioacchino, Andrea title: The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2 date: 2020-08-27 words: 7109 flesch: 54 summary: The absence of a straightforward correlation between global CpG force and the pathology of a coronavirus in humans calls for a finer, local analysis of CpG forces we report below. CpG forces could be related to the evolutionary constraint to lower or increase CpG number, under the pressure of host PRRs that recognize a pathogen. keywords: codon; cov-2; cpg; evolution; fig; force; genome; human; mutations; sars; sequence cache: cord-268224-5tbb8df1.txt plain text: cord-268224-5tbb8df1.txt item: #310 of 702 id: cord-268339-jxm69ndw author: Karamitros, Timokratis title: SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies date: 2020-03-28 words: 3766 flesch: 46 summary: In detail, intra-host SNVs colocalized with the probe of RdRP_SARSr reaction (15, The de novo assembly of the viral genomes revealed intra-host genomic rearrangements. Here, we explore intra-host genomic variants and low-frequency polymorphic quasispecies in Next Generation Sequencing (NGS) data derived from patients infected by SARS-CoV-2. keywords: c c; g c; genome; genomic; host; intra; sars; u c; u g; u u cache: cord-268339-jxm69ndw.txt plain text: cord-268339-jxm69ndw.txt item: #311 of 702 id: cord-268795-tjmx6msm author: Sardar, Rahila title: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis date: 2020-03-21 words: 2258 flesch: 40 summary: As a host defense mechanism, a repertoire of host miRNAs also target invading viruses. To predict host miRNAs targeting the virus, we collected a list of experimentally verified antiviral miRNAs with their targets from VIRmiRNA database (11) . keywords: analysis; coronavirus; cov2; genomes; host; mirnas; sars cache: cord-268795-tjmx6msm.txt plain text: cord-268795-tjmx6msm.txt item: #312 of 702 id: cord-268894-amfv3z2y author: Nguyen-Contant, Phuong title: S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit date: 2020-07-21 words: 4676 flesch: 45 summary: Our key findings are as follows: (i) the presence of IgG 223 reactive to the S2 subunit of SARS-CoV-2 in most unexposed subjects, likely reflecting cross-224 reactivity to HCoVs, (ii) markedly increased levels of IgG against the SARS-CoV-2 S and N 225 proteins, including reactivity to the RBD and S2 subunit of S, in convalescent subjects, (iii) 226 increased IgG binding to the S protein of the OC43 HCoV, but not 229E HCoV, in convalescent 227 subjects, reflecting greater cross-reactivity between S2 subunits of betacoronaviruses, (iv) strong 228 formation of IgG MBCs reactive with the RBD and S2 subunit of the SARS-CoV-2 S protein in 229 convalescent subjects, and (v) formation of IgG MBCs reactive with the S protein of OC43, but 230 not 229E, in convalescent subjects, consistent with S2 subunit cross-reactivity between 231 Approximately one-third of our cohort of non-SARS-CoV-2-exposed subjects had low 233 levels of IgG against the SARS-CoV-2 S and N proteins. (D) Comparison of serum 533 IgG concentrations (upper panels) and IgG MBC numbers CoV-2 S (left-hand side) and N (right-hand side) proteins. keywords: cov-2; igg; infection; mbcs; rbd; sars; subjects cache: cord-268894-amfv3z2y.txt plain text: cord-268894-amfv3z2y.txt item: #313 of 702 id: cord-269285-2r40mico author: Resnick, Samuel J. title: A simplified cell-based assay to identify coronavirus 3CL protease inhibitors date: 2020-08-29 words: 1943 flesch: 53 summary: Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. Given the potential for protease inhibitors in the treatment of viral illnesses, small molecule inhibitors 183 of coronavirus 3CL proteases represent a promising avenue for treating infections caused by this 184 large family of viruses. keywords: assay; author; funder; preprint cache: cord-269285-2r40mico.txt plain text: cord-269285-2r40mico.txt item: #314 of 702 id: cord-270049-54t3w94z author: Campione, Elena title: Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date: 2020-08-17 words: 2029 flesch: 35 summary: Coronavirus are spherical, enveloped viruses Then, the efficacy of different concentrations of bLf in inhibiting SARS-CoV-2 infection was tested 161 on Vero E6 and Caco-2 cells according to different experimental procedures: i) control: untreated 162 SARS-CoV-2 and cells; ii) bLf pre-incubated with virus inoculum for 1 h at 37°C before cell 163 infection; iii) cells pre-incubated with bLf for 1 h at 37°C before virus infection; iv) bLf added 164 together with virus inoculum at the moment of infection step; v) virus and cells separately pre-165 incubated with bLf for 1 h at 37°C before infection. key: cord-270049-54t3w94z authors: Campione, Elena; Lanna, Caterina; Cosio, Terenzio; Rosa, Luigi; Conte, Maria Pia; Iacovelli, Federico; Romeo, Alice; Falconi, Mattia; Del Vecchio, Claudia; Franchin, Elisa; Lia, Maria Stella; Minieri, Marilena; Chiaramonte, Carlo; Ciotti, Marco; Nuccetelli, Marzia; Terrinoni, Alessandro; Iannuzzi, Ilaria; Coppeda, Luca; Magrini, Andrea; Moricca, Nicola; Sabatini, Stefano; Rosapepe, Felice; Bartoletti, Pier Luigi; Bernardini, Sergio; Andreoni, Massimo; Valenti, Piera; Bianchi, Luca title: Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: randomized clinical trial, in vitro and in silico preliminary evidences date: 2020-08-17 journal: bioRxiv DOI: 10.1101/2020.08.11.244996 sha: doc_id: 270049 cord_uid: 54t3w94z The current treatments against SARS-CoV-2 have proved so far inadequate. keywords: blf; cov-2; figure; lactoferrin; sars cache: cord-270049-54t3w94z.txt plain text: cord-270049-54t3w94z.txt item: #315 of 702 id: cord-270257-5f95gve3 author: Jeon, Sangeun title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date: 2020-03-28 words: 1148 flesch: 44 summary: Drug repositioning represents the only feasible option to address this global challenge and a panel of 48 FDA-approved drugs that have been pre-selected by an assay of SARS-CoV was screened to identify potential antiviral drug candidates against SARS-CoV-2 infection. key: cord-270257-5f95gve3 authors: Jeon, Sangeun; Ko, Meehyun; Lee, Jihye; Choi, Inhee; Byun, Soo Young; Park, Soonju; Shum, David; Kim, Seungtaek title: Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs date: 2020-03-28 journal: bioRxiv DOI: 10.1101/2020.03.20.999730 sha: doc_id: 270257 cord_uid: 5f95gve3 COVID-19 is an emerging infectious disease and was recently declared as a pandemic by WHO. keywords: coronavirus; drug; sars cache: cord-270257-5f95gve3.txt plain text: cord-270257-5f95gve3.txt item: #316 of 702 id: cord-270329-t60t639i author: Schloer, Sebastian title: Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro date: 2020-10-16 words: 1057 flesch: 26 summary: While remdesivir and the host-directed drugs itraconazole or fluoxetine target independent 297 pathways, we found that drug combinations together with remdesivir (ItraRem and 298 FluoRem) showed stronger antiviral activities against SARS-CoV-2 than the remdesivir 299 monotherapy. Drug treatments were well-tolerated and potent impaired viral replication was observed with all drug treatments. keywords: drug; itraconazole; remdesivir; sars cache: cord-270329-t60t639i.txt plain text: cord-270329-t60t639i.txt item: #317 of 702 id: cord-270550-if748w2n author: Bailey, Adam L. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 words: 5824 flesch: 40 summary: Figure 1 : ACE2 is expressed in the human heart and in stem cell derived cardiomyocytes. After infection with SARS-CoV-2, engineered tissues display typical features of myocarditis, including cardiomyocyte cell death, impaired cardiac contractility, and innate immune cell activation. keywords: ace2; cardiomyocytes; cell; cms; cov-2; expression; fig; hpsc; human; infected; infection; mock; sars; tissues cache: cord-270550-if748w2n.txt plain text: cord-270550-if748w2n.txt item: #318 of 702 id: cord-270698-9w3ap3gz author: Guo, Hua title: Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes date: 2020-05-13 words: 2501 flesch: 40 summary: In 537 this study, bat ACE2 sequences were either amplified or downloaded from NCBI and 538 SARSr-CoV spike sequences were downloaded from NCBI; the database accession 539 numbers are listed in Table S2 . Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiency in cells transiently expressing bat ACE2 variants. keywords: ace2; bat; coronavirus; cov; human; sars; spike cache: cord-270698-9w3ap3gz.txt plain text: cord-270698-9w3ap3gz.txt item: #319 of 702 id: cord-270919-0hldozml author: Cortey, Martí title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date: 2020-05-17 words: 1066 flesch: 36 summary: The species of origin of SARS-CoV-2 has not been fully 32 identified, but the virus seems to be related to SARS-CoV and other coronaviruses found 33 in bats and other mammal species, although different from them (Chan et The SARS-CoV-2 genome size is around 30 kb with the typical gene structure known in 36 other betacoronaviruses: starting from the 5′, more than two-thirds of the genome 37 comprises orf1ab encoding polyproteins (nsp1 to nsp15), while the last third consists of 38 genes encoding major structural proteins; including spike (S or ORF2), envelope (E or 39 ORF4), membrane (M or ORF5), and nucleocapsid (N or ORF9) proteins. key: cord-270919-0hldozml authors: Cortey, Martí; Li, Yanli; Díaz, Ivan; Clilverd, Hepzibar; Darwich, Laila; Mateu, Enric title: SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins date: 2020-05-17 journal: bioRxiv DOI: 10.1101/2020.05.16.099499 sha: doc_id: 270919 cord_uid: 0hldozml The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naïve human population. keywords: coronavirus; cov-2; protein; sars cache: cord-270919-0hldozml.txt plain text: cord-270919-0hldozml.txt item: #320 of 702 id: cord-271693-7tg21up3 author: Zheng, Fan title: Identifying persistent structures in multiscale ‘omics data date: 2020-10-03 words: 4895 flesch: 43 summary: The goal of the first phase is to detect network communities, i.e. groups of densely connected biological entities. Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. keywords: analysis; cell; communities; community; data; fig; hidef; human; networks; protein; supplementary cache: cord-271693-7tg21up3.txt plain text: cord-271693-7tg21up3.txt item: #321 of 702 id: cord-271849-wxmr8eki author: Meysman, Pieter title: Tracking SARS-CoV-2 T cells with epitope-T-cell receptor recognition models date: 2020-09-09 words: 2930 flesch: 50 summary: In addition, using such models on longitudinal data reveals a potential difference in temporal dynamics between T cells predicted to react against epitopes that are unique to SARS-CoV-2 and those that are shared among other coronaviruses. T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV Understanding the T cell immune response in SARS coronavirus infection Long-lived effector/central memory T-cell responses to severe acute respiratory syndrome coronavirus (SARS-CoV) S antigen in recovered SARS patients SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls T cell responses in patients with COVID-19 Kinetics of SARS-CoV-2 specific IgM and IgG responses in COVID-19 patients Convergent Antibody Responses to SARS-CoV-2 Neutralizing Antibody Responses to SARS-CoV-2 in a COVID-19 Recovered Patient Cohort and Their Implications medRxiv Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans In silico identification of vaccine targets for 2019-nCoV Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2 Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV Potential T-cell and B-cell Epitopes of 2019-nCoV SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors. keywords: cell; cov-2; data; epitopes; sars; tcr cache: cord-271849-wxmr8eki.txt plain text: cord-271849-wxmr8eki.txt item: #322 of 702 id: cord-271970-i35pic5o author: Boris, Bonaventure title: A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor date: 2020-10-28 words: 6369 flesch: 39 summary: With the aim of identifying new cellular inhibitors of HIV-1, we have developed a strategy in which we took advantage of the ability of type 1 interferon (IFN) to potently inhibit HIV-1 infection, in order to create a cellular environment hostile to viral replication. Similarly, the overexpression of a dominant-negative mutant of DDX42 positively impacted HIV-1 infection, whereas wild-type DDX42 overexpression potently inhibited HIV-1 infection. keywords: cas9; cd4; cells; ddx42; et al; figure; genome; human; ifn; infection; populations; renilla; replication; rna; type; virus cache: cord-271970-i35pic5o.txt plain text: cord-271970-i35pic5o.txt item: #323 of 702 id: cord-271971-rstmd0va author: Matsumura, Yasufumi title: Comparison of 12 molecular detection assays for SARS-CoV-2 date: 2020-06-25 words: 1208 flesch: 48 summary: The CDC N2 and NIID N2 assays exhibited 104 100% sensitivity; thus, their results were equal to the defined reference standard. The CDC protocol requires both N1 and N2 assays, and a sample will be 109 considered positive if both produced positive results. keywords: assays; cdc cache: cord-271971-rstmd0va.txt plain text: cord-271971-rstmd0va.txt item: #324 of 702 id: cord-271978-j5enftje author: Zoltán, Köntös title: In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) date: 2020-11-10 words: 2912 flesch: 40 summary: The virucidal activity of Essential Iodine Drops against SARS-CoV-2 was tested in three dilutions; 1:1; 2:1 and 3:1. Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1 Air, Surface Environmental, and Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From a Symptomatic Patient Modality of human expired aerosol size distributions Small droplet aerosols in poorly ventilated spaces and SARS-CoV-2 transmission Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis Mask use during COVID-19: A risk adjusted strategy The Use of Povidone Iodine Nasal Spray and Mouthwash During the Current COVID-19 Pandemic May Protect Healthcare Workers and Reduce Cross Infection A Comparison of the Effectiveness of Tincture of Iodine and Potassium Iodide on Chronic Sinusitis Patients with Biofilm Povidone-Iodine Use in Sinonasal and Oral Cavities: A Review of Safety in the COVID-19 Era In Vitro Efficacy of Povidone-Iodine Nasal And Oral Antiseptic Preparations Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) Rapid In-Vitro Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Using Povidone-Iodine Oral Antiseptic Rinse ACE2 receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia An unusual complication of late onset allergic contact dermatitis to povidone iodine in oral & maxillofacial surgery -a report of 2 cases Anaphylactic reaction to povidone secondary to drug ingestion in a young child I am particularly grateful for the service given by Jonna B. Westover with The Institute for Antiviral Research at Utah State University. keywords: covid-19; eid; iodine; pvp; sars; seconds; virus cache: cord-271978-j5enftje.txt plain text: cord-271978-j5enftje.txt item: #325 of 702 id: cord-272513-umuiovrd author: Bindayna, Khalid Mubarak title: Variant analysis of SARS-CoV-2 genomes in the Middle East date: 2020-10-09 words: 3034 flesch: 54 summary: key: cord-272513-umuiovrd authors: Bindayna, Khalid Mubarak; Crinion, Shane title: Variant analysis of SARS-CoV-2 genomes in the Middle East date: 2020-10-09 journal: bioRxiv DOI: 10.1101/2020.10.09.332692 sha: doc_id: 272513 cord_uid: umuiovrd Background Coronavirus (COVID-19) was introduced into society in late 2019 and has now reached over 26 million cases and 850,000 deaths. If we explore the structure and common variants of SARS-CoV-2 strains in these populations, we expect to learn more about how the virus spread. keywords: alignment; analysis; data; file; middle; samples; variants cache: cord-272513-umuiovrd.txt plain text: cord-272513-umuiovrd.txt item: #326 of 702 id: cord-272626-bw9lbzvt author: Pizzorno, Andrés title: Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia date: 2020-04-02 words: 2057 flesch: 24 summary: On top of that, we observed an additional 1.3 log10 reduction in nasal HAE viral titers for the remdesivir-diltiazem combination when compared with remdesivir monotherapy. As previously observed in structural studies of other coronaviruses, notably SARS-CoV and MERS-CoV (15-18), we distinguished characteristic clusters in the perinuclear region of infected HAE cells. keywords: cov-2; covid-19; fig; hae; nasal; remdesivir; sars cache: cord-272626-bw9lbzvt.txt plain text: cord-272626-bw9lbzvt.txt item: #327 of 702 id: cord-272869-381qupdn author: Mirvakili, Seyed M title: Reverse Pneumatic Artificial Muscles for Application in Low-Cost Artificial Respirators date: 2020-05-21 words: 6041 flesch: 54 summary: Constant pressure ventilators can be noninvasive or invasive. Positive pressure ventilators were first introduced in the early 1950s to treat polio patients with respiratory paralysis (3) . keywords: air; device; end; figure; motor; pressure; rate; syringe; ventilation; ventilators; volume cache: cord-272869-381qupdn.txt plain text: cord-272869-381qupdn.txt item: #328 of 702 id: cord-272986-ebgusf3o author: Cao, Yipeng title: Computational Study of Ions and Water Permeation and Transportation Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel date: 2020-05-17 words: 4342 flesch: 48 summary: A new coronavirus associated with human respiratory disease in China Structure validation by Cα geometry: ϕ, ψ and Cβ deviation Molecular dynamics simulations of membrane channels and transporters A single polar residue and distinct membrane topologies impact the function of the infectious bronchitis coronavirus E protein SARS coronavirus E protein forms cation-selective ion channels MERS coronavirus envelope protein has a single transmembrane domain that forms pentameric ion channels Ion channels of excitable membranes Theoretical and computational models of biological ion channels Functional annotation of ion channel structures by molecular simulation Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants Effect of field direction on electrowetting in a nanopore Voltage gating of a biomimetic nanopore: Electrowetting of a hydrophobic barrier Viroporins: structure and biological functions Ion channel voltage sensors: structure, function, and pathophysiology Designing a hydrophobic barrier within biomimetic nanopores STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate 376-Relaxation studies on cell membranes and lipid bilayers in the high electric field range CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures COVID-19 infection: origin, transmission, and characteristics of human coronaviruses The disintegration of the ion equilibrium of the intracellular area affect the charges coming from the cell through ion channels in the cell membrane, changing the pH and making it easier for the virus to fuse with the cell membrane. keywords: channel; coronavirus; e protein; ion; ions; pore; protein; sars; water cache: cord-272986-ebgusf3o.txt plain text: cord-272986-ebgusf3o.txt item: #329 of 702 id: cord-273083-xrydkiu4 author: Pahmeier, Felix title: A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date: 2020-09-01 words: 1003 flesch: 38 summary: key: cord-273083-xrydkiu4 authors: Pahmeier, Felix; Neufeldt, Christoper J; Cerikan, Berati; Prasad, Vibhu; Pape, Costantin; Laketa, Vibor; Ruggieri, Alessia; Bartenschlager, Ralf; Cortese, Mirko title: A versatile reporter system to monitor virus infected cells and its application to dengue virus and SARS-CoV-2 date: 2020-09-01 journal: bioRxiv DOI: 10.1101/2020.08.31.276683 sha: doc_id: 273083 cord_uid: xrydkiu4 Positive-strand RNA viruses have been the etiological agents in several major disease outbreaks over the last few decades. In order to generate a reporter system that can specifically indicate virus infection, we 219 designed a construct expressing a GFP fusion protein that could selectively be cleaved 220 by viral proteases. keywords: reporter; system; virus cache: cord-273083-xrydkiu4.txt plain text: cord-273083-xrydkiu4.txt item: #330 of 702 id: cord-273416-332stbjl author: Liu, Tianyuan title: Transcriptional differences for COVID-19 Disease Map genes between males and females indicate a different basal immunophenotype relevant to the disease date: 2020-10-01 words: 2741 flesch: 35 summary: Using DeCovid, we analyzed the extent of gene expression differences among demographic groups across different COVID-19 affected tissues (Table 1) . We used data from the GTEx database, which contains RNA-seq profiles for hundreds of demographically diverse healthy individuals in multiple tissues and allows us to interrogate COVID-19 genes globally or individually. keywords: covid-19; differences; disease; expression; genes cache: cord-273416-332stbjl.txt plain text: cord-273416-332stbjl.txt item: #331 of 702 id: cord-273613-cpiveo7j author: Cao, Xia title: Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach date: 2020-09-29 words: 3518 flesch: 34 summary: The parental nAb STI-1499 and the affinity-matured derivative STI-2020 were characterized for their biochemical and function properties in vitro and in vivo against prevalent clinical isolates of SARS CoV-2. Antibody treatments were administered intravenously (i.v.) with monoclonal antibodies (mAbs) against SARS-CoV-2 Spike, or isotype control mAb in up to 350 µl of sterile PBS at 1 hour-post inoculation. keywords: animals; antibodies; antibody; binding; nabs; sars; spike; sti-1499; sti-2020; treatment; virus cache: cord-273613-cpiveo7j.txt plain text: cord-273613-cpiveo7j.txt item: #332 of 702 id: cord-273645-czh3zfb3 author: Lu, Shuaiyao title: Comparison of SARS-CoV-2 infections among 3 species of non-human primates date: 2020-07-17 words: 2204 flesch: 60 summary: Most of swab samples saw the second peaks of viral RNA on 6-8 dpi. In some swab samples from old world monkeys, viral RNA was still detectable on 14 dpi ( Figure 3A ). keywords: cov-2; monkeys; sars cache: cord-273645-czh3zfb3.txt plain text: cord-273645-czh3zfb3.txt item: #333 of 702 id: cord-273882-tqdcb3oo author: Pratibha, title: Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses date: 2020-08-21 words: 1959 flesch: 55 summary: Next, we analyzed protein sequences of 26 viruses (Figures 2, 3 , and Supplementary Figures 1 -4) to search for a ubiquitous forbidden order in each one of them. COVID-19 case study A novel numerical representation for proteins: Three-dimensional Chaos Game Representation and its Extended Natural Vector Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses Could an unrelated live attenuated vaccine serve as a preventive measure to dampen septic inflammation associated with COVID-19 infection? keywords: cov-2; order; protein; sars; sequence cache: cord-273882-tqdcb3oo.txt plain text: cord-273882-tqdcb3oo.txt item: #334 of 702 id: cord-273891-7w334xgt author: Kirchdoerfer, Robert N. title: Receptor binding and proteolysis do not induce large conformational changes in the SARS-CoV spike date: 2018-03-31 words: 3321 flesch: 42 summary: We were 136 further able to identify S1 RBD conformations at the non-ACE2 occupied RBD positions to 137 represent each population of S1 RBD conformations among ACE2-bound S. 138 As hypothesized by previous structural work 15-17,22 , the S1 RBD recognizes ACE2 with 139 an 'up' S1 RBD conformation. Fine sorting of S1 RBD positions of the trypsin-224 cleaved S reveals a very similar distribution of 'up' S1 RBD conformations available for receptor 225 binding as in the uncleaved samples, although we additionally observe a small proportion of S1 226 RBD in the all-'down' conformation (Fig. 5c) . keywords: ace2; coronavirus; cov; host; rbd; sars cache: cord-273891-7w334xgt.txt plain text: cord-273891-7w334xgt.txt item: #335 of 702 id: cord-274114-fglyfz8p author: Minervina, Anastasia A. title: Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection date: 2020-10-01 words: 5579 flesch: 49 summary: Theravajan et al. showed that activated CD8+HLA-DR+CD38+ T cells in a mild case of COVID-19 significantly expand following symptom onset, reaching their peak frequency of 12% of CD8+ T cells on day 9 after symptom onset, and contract thereafter From each blood sample we isolated PBMCs (peripheral blood mononuclear cells, in two biological replicates), CD4+, and CD8+ T cells. keywords: cd4; cd8; cells; clones; day; fig; infection; memory; sars; tcrbeta cache: cord-274114-fglyfz8p.txt plain text: cord-274114-fglyfz8p.txt item: #336 of 702 id: cord-274409-4ugdxbmy author: Laskar, Rezwanuzzaman title: Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India date: 2020-10-19 words: 3300 flesch: 53 summary: The maximum variants affecting protein sequence were present in NSP3 (63) followed by Spike (S) protein with 49 variants. Composition and distribution of variable sites (Table 1 ) and its negative value indicated the significance of these variable sites. keywords: disease; genome; mutations; protein; samples; sars; sites; variants cache: cord-274409-4ugdxbmy.txt plain text: cord-274409-4ugdxbmy.txt item: #337 of 702 id: cord-274528-mr81o9cu author: Li, Fei title: Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide date: 2020-09-12 words: 6496 flesch: 43 summary: Moreover, we observed distinct AR binding patterns between prostate cells and lung cells and a lack of direct binding of AR to TMPRSS2 in human lung cells. Camostat mesylate but not enzalutamide inhibited infection of LuOs with SARS-CoV-2-S, 41 confirming that enzalutamide could not protect lung cells against SARS-CoV-2 infection (Fig. keywords: cells; cov-2; entry; enzalutamide; expression; fig; infection; lung; mice; prostate; sars; tmprss2 cache: cord-274528-mr81o9cu.txt plain text: cord-274528-mr81o9cu.txt item: #338 of 702 id: cord-275173-ely3aen3 author: Pickering, Brad S. title: Susceptibility of domestic swine to experimental infection with SARS-CoV-2 date: 2020-09-10 words: 1919 flesch: 39 summary: Nat Microbiol Transmission of SARS-CoV-2 383 in Domestic Cats A pneumonia outbreak associated with 385 a new coronavirus of probable bat origin Hematology and biochemistry 389 reference intervals for Ontario commercial nursing pigs close to the time of weaning The biomedical piglet: 392 establishing reference intervals for haematology and clinical chemistry parameters of two age groups 393 with and without iron supplementation Recombinant 395 nipah virus vaccines protect pigs against challenge Experimental inoculation study indicates swine as a 397 potential host for Hendra virus Detection of 2019 novel 399 coronavirus (2019-nCoV) by real-time RT-PCR A Genomic Perspective on the Origin and Emergence of SARS-CoV-2 SARS-CoV-2 in fruit bats, 403 ferrets, pigs, and chickens: an experimental transmission study. Vector-Borne and Zoonotic Diseases Nipah virus: a recently 370 emergent deadly paramyxovirus Fatal encephalitis due to 372 Nipah virus among pig-farmers in Malaysia Japanese encephalitis 374 virus infection, diagnosis and control in domestic animals Veterinary Vaccines and Their Importance to Animal Health and Public Health. keywords: animals; blood; cov-2; dpi; sars; study cache: cord-275173-ely3aen3.txt plain text: cord-275173-ely3aen3.txt item: #339 of 702 id: cord-275252-4e3cn50u author: Rad SM, Ali Hosseini title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 words: 4369 flesch: 45 summary: While perfect matches of miRNA to target viral sequences results in miRNA-induced silencing complex (miRISC)-mediate destruction of viral RNA, imperfect matches interfere with translation [15] . C=18.4%) and enrichment of codons in in pyrimidines is likely due to APOBEC editing of viral RNA and the fact that Nsp14 (proof-reading) does not remove U (the product of cytosine deamination) keywords: cov-2; figure; genome; host; mirna; mutations; rna; sars; sites; structure; target; virus cache: cord-275252-4e3cn50u.txt plain text: cord-275252-4e3cn50u.txt item: #340 of 702 id: cord-275690-83nrzfon author: Stanifer, Megan L. title: Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells date: 2020-04-24 words: 4699 flesch: 40 summary: SARS-CoV-2 infection of the gastrointestinal tract is supported by the fact that ACE2, the virus receptor (Hoffmann et al., 2020) , is expressed in intestinal epithelial cells (Zhao et al., 2020) (Lukassen et al., 2020) (Wu et al., 2020a) (Venkatakrishnan et al., 2020) and single cell sequencing analysis suggest that its expression is even higher on intestinal cells compared to lung cells (Xu et al., 2020a) Here, we engaged in studying SARS-CoV-2 infection of human intestinal cells. keywords: cells; cov-2; fig; ifn; infection; sars; type cache: cord-275690-83nrzfon.txt plain text: cord-275690-83nrzfon.txt item: #341 of 702 id: cord-276017-2375ipkk author: Chen, Dongsheng title: Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife date: 2020-06-14 words: 4133 flesch: 50 summary: Furthermore, we screened the expression patterns of receptors for 144 viruses, resulting in a comprehensive atlas of virus target cells. Taken together, our work provides a novel and fundamental strategy to screen virus target cells and susceptible species, based on single-cell transcriptomes we generated for domesticated animals and wildlife, which could function as a valuable resource for controlling current pandemics and serve as an early warning system for coping with future infectious disease threats. keywords: ace2; cat; cells; cov-2; lung; sars; target; tmprss2; ¢ â; � ¢ cache: cord-276017-2375ipkk.txt plain text: cord-276017-2375ipkk.txt item: #342 of 702 id: cord-277253-vy0mvzeb author: Liu, Hongbo title: Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro date: 2020-04-11 words: 2280 flesch: 42 summary: A Review of Historical Classics, Research Evidence and Current Prevention Programs A comprehensive review on phytochemistry, pharmacology, and flavonoid biosynthesis of Scutellaria baicalensis Baicalein and baicalin as Zika virus inhibitors Anti-H1N1 virus, cytotoxic and Nrf2 activation activities of chemical constituents from Scutellaria baicalensis Inhibition of HIV replication by baicalin and S. baicalensis extracts in H9 cell culture Extract of Scutellaria baicalensis inhibits dengue virus replication Efficacy of Scutellaria baicalensis for the Treatment of Hand, Foot, and Mouth Disease Associated with Encephalitis in Patients Infected with EV71: A Multicenter, Retrospective Analysis A targeted strategy to analyze untargeted mass spectral data: Rapid chemical profiling of Scutellaria baicalensis using ultra-high performance liquid chromatography coupled with hybrid quadrupole orbitrap mass spectrometry and key ion filtering Inhibition of SARS-CoV 3CL protease by flavonoids Characteristics of flavonoids as potent MERS-CoV 3C-like protease inhibitors 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism Therapeutic Effects of Breviscapine in Cardiovascular Diseases: A Review Identification of myricetin and scutellarein as novel chemical inhibitors of the SARS coronavirus helicase, nsP13 Metabolism of constituents in Huangqin-Tang, a prescription in traditional Chinese medicine, by human intestinal flora Hepatic metabolism and disposition of baicalein via the coupling of conjugation enzymes and transporters-in vitro and in vivo evidences Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase Maturation mechanism of severe acute respiratory syndrome (SARS) coronavirus 3C-like proteinase In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Within the 20 years of the 21st century, there are already three outbreaks of CoV-causing global epidemics, including SARS, MERS, and COVID-19. keywords: 3cl; activity; baicalensis; cov-2; pro; sars cache: cord-277253-vy0mvzeb.txt plain text: cord-277253-vy0mvzeb.txt item: #343 of 702 id: cord-277487-jgbjxgh1 author: Graham, Simon P. title: Evaluation of the immunogenicity of prime-boost vaccination with the replication-deficient viral vectored COVID-19 vaccine candidate ChAdOx1 nCoV-19 date: 2020-06-20 words: 5084 flesch: 44 summary: For analysis of T cell responses in pigs, overlapping 16mer peptides offset by 4 residues based on the predicted amino acid sequence of the entire S protein from SARS-CoV-2 Wuhan-Hu-1 isolate (NCBI Reference Sequence: NC_045512.2) were designed and synthesised (Mimotopes, Melbourne, Australia) and reconstituted in sterile 40% acetonitrile (Sigma-Aldrich) at a concentration of 3 mg/mL. Three pools of synthetic peptides representing residues 1-331 (Pool 1), 332-748 (Pool 2) and 749-1273 (Pool 3) were prepared for use to stimulate T cells in IFN-γ ELISpot and intracellular cytokine staining (ICS) assays. We show here that T cell responses are higher in pigs that received a prime-boost vaccination when compared to prime only at day 42, whilst comparing responses 14 days after last immunisation demonstrates the prime-boost regimen trended toward a higher response. keywords: antibody; boost; cells; chadox1; cov-2; mice; ncov-19; pigs; prime; responses; sars; titres cache: cord-277487-jgbjxgh1.txt plain text: cord-277487-jgbjxgh1.txt item: #344 of 702 id: cord-277648-9kxwkcbl author: Overholt, Kalon J. title: Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution date: 2020-06-19 words: 10011 flesch: 34 summary: Notably, the concerted TNF-α/NF-κB pathway enrichment across BALF cell types is indicative of a strong upregulation of TNFAIP3 and NFKBIA. Exploring the expression of these 16 ligands across the diversity of BALF cell types indicates that MPs and neutrophils may act as sender cells signaling to the epithelium, as suggested in recent reports [21, 28, 53] . keywords: analysis; ards; balf; cell; control; covid-19; disease; donors; expression; figure; gene; ligands; lung; patients; severity; type cache: cord-277648-9kxwkcbl.txt plain text: cord-277648-9kxwkcbl.txt item: #345 of 702 id: cord-278869-7zr1118b author: Ravichandran, Supriya title: Antibody repertoire induced by SARS-CoV-2 spike protein immunogens date: 2020-05-13 words: 2386 flesch: 39 summary: Immunity Antigenic fingerprinting of H5N1 avian influenza 405 using convalescent sera and monoclonal antibodies reveals potential vaccine and diagnostic 406 targets Vaccines with MF59 Adjuvant Expand the 409 Antibody Repertoire to Target Protective Sites of Pandemic Avian H5N1 Influenza Virus Human antibody 412 repertoire after VSV-Ebola vaccination identifies novel targets and virus-neutralizing IgM 413 antibodies Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked 416 Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins AS03-adjuvanted H5N1 vaccine promotes antibody diversity 420 and affinity maturation, NAI titers, cross-clade H5N1 neutralization, but not H1N1 cross-subtype 421 neutralization MF59 adjuvant enhances diversity and affinity of antibody-mediated 424 immune response to pandemic influenza vaccines High-Affinity 427 H7 Head and Stalk Domain-Specific Antibody Responses to an Inactivated Influenza H7N7 Vaccine After Priming With Live Attenuated Influenza Vaccine Longitudinal Human Antibody Repertoire against Complete Viral Proteome from Ebola Virus Survivor Reveals Protective Sites for Vaccine Design intravenous immunoglobulin for adults with influenza A or B infection (FLU-IVIG): a double-blind, 437 randomised, placebo-controlled trial Antigenic Fingerprinting of Respiratory Syncytial Virus (RSV)-A-Infected 440 Hematopoietic Cell Transplant Recipients Reveals Importance of Mucosal Anti-RSV G Antibodies 441 in Control of RSV Infection in Humans The 443 COVID-19 vaccine development landscape Characterization of the receptor-445 binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as 446 a viral attachment inhibitor and vaccine A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2 H5 N-terminal beta sheet promotes oligomerization of H7-HA1 that induces better 452 antibody affinity maturation and enhanced protection against H7N7 and H7N9 viruses compared 453 to inactivated influenza vaccine 456 Differential human antibody repertoires following Zika infection and the implications for 457 serodiagnostics and disease outcome 2020) with a single receptor-binding domain (RBD) in the up conformation, wherever available using UCSF Chimera software. Although S2 contains the fusion peptide, it does not appear to be as immunogenic, 186 compared with S1 or RBD, in generating binding antibodies to the intact spike (S1+S2) 187 ectodomain, as observed in both IgG ELISA and SPR. keywords: antibody; domain; rbd; s1+s2; spike cache: cord-278869-7zr1118b.txt plain text: cord-278869-7zr1118b.txt item: #346 of 702 id: cord-279474-c5y2lygj author: Bozzo, Caterina Prelli title: IFITM proteins promote SARS-CoV-2 infection of human lung cells date: 2020-08-18 words: 1116 flesch: 35 summary: (D) Alignment of the Spike amino acid sequences from SARS-CoV-2 Alanine substitutions are color coded. IFITM-Family Proteins: The Cell's First Line of Antiviral Defense Severe respiratory illness caused by a novel 649 coronavirus Imbalanced host response to SARS-CoV-2 drives 653 development of COVID-19 A sensitive and specific enzyme-based assay 655 detecting HIV-1 virion fusion in primary T lymphocytes High-efficiency transformation of mammalian cells by plasmid 657 DNA Regulation of the trafficking and 659 antiviral activity of IFITM3 by post-translational modifications The broad-spectrum antiviral functions of IFIT and IFITM 661 proteins PSGL-1 restricts HIV-1 infectivity by blocking virus particle attachment to target cells More than meets the I: The diverse antiviral and 737 cellular functions of interferon-induced transmembrane proteins Opposing activities of IFITM proteins in SARS-CoV-740 2 infection IFITM proteins -Cellular inhibitors of 742 viral entry Intracellular detection of viral nucleic acids Vpu modulates DNA repair to suppress 747 innate sensing and hyper-integration of HIV-1 IFITM proteins inhibit entry driven by the 749 Spike protein: Evidence for Cholesterol-Independent Mechanisms Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3 Cholesterol 25-hydroxylase suppresses SARS-CoV-2 replication by blocking 756 membrane fusion Antiviral Protection by IFITM3 keywords: cells; cov-2; infection; proteins; sars cache: cord-279474-c5y2lygj.txt plain text: cord-279474-c5y2lygj.txt item: #347 of 702 id: cord-279576-wt4crton author: Fajardo, Álvaro title: Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples date: 2020-05-13 words: 4858 flesch: 42 summary: Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques can be difficult to perform given the limited supply of reagents in low and middle income countries. Since all these protocols are based on the use of fluorogenic probes and one-step reagents (cDNA synthesis followed by PCR amplification in the same tube), these techniques are limited to the use of more specific reagents and can be quite expensive. keywords: amplification; cov-2; detection; green; qpcr; samples; sars; sybr; time cache: cord-279576-wt4crton.txt plain text: cord-279576-wt4crton.txt item: #348 of 702 id: cord-279629-t1xjy12y author: Nazneen Akhand, Mst Rubaiat title: Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine date: 2020-04-15 words: 6731 flesch: 37 summary: ( Figure 10E ) indicated low chance of deformation of vaccine protein V3. Protein sequence of the spike, envelope, membrane and nucleocapsid were also retrieved from the corresponding genome sequences found in NCBI (Supplementary File 1). keywords: analysis; cell; coronavirus; covid-19; different; epitopes; et al; figure; novel; prediction; protein; sars; server; spike; study; table; vaccine cache: cord-279629-t1xjy12y.txt plain text: cord-279629-t1xjy12y.txt item: #349 of 702 id: cord-280025-4hmecfi0 author: Korber, B title: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 date: 2020-05-05 words: 11191 flesch: 46 summary: Because Spike mutations are rare, we set a low threshold for a site to be deemed of interest for further tracking. The same tree expanded to show interesting patterns of Spike mutations that we are tracking against the backdrop of the phylogenetic tree based on the full genome. keywords: analysis; antibody; coronavirus; cov-2; d614; data; et al; fig; form; g614; gisaid; mutation; recombination; sars; sequences; sites; spike; time cache: cord-280025-4hmecfi0.txt plain text: cord-280025-4hmecfi0.txt item: #350 of 702 id: cord-280198-bhjw6xc5 author: Olaleye, Omonike A. title: Discovery of Clioquinol and Analogues as Novel Inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 Infection, ACE2 and ACE2 - Spike Protein Interaction In Vitro date: 2020-08-14 words: 1831 flesch: 23 summary: The crystal structure of full length human ACE2 revealed that the RBD on SARS-CoV-2 419 S1 binds directly to the metallopeptidase domain (MPD) of ACE2 receptor 40,41 , that consists of 420 amino acid residues that coordinates zinc, providing further support for the utility of zinc chelators The strengths of our study includes, the use of a rapid multi-prong approach via three World Health Organization (WHO) Director-General's opening remarks at the media briefing on 520 COVID-19 Coronavirus disease 2019 (COVID-19) Situation Report A novel coronavirus from patients with pneumonia in China Clinical features of patients infected with 2019 novel coronavirus in Wuhan Potential Effects of Coronaviruses 527 on the Cardiovascular System: A Review Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, 530 China: A Retrospective Case Series Study Clinical characteristics of coronavirus disease 2019 in China Potential Antiviral Drugs Under Evaluation for the Treatment of COVID-19 COVID-19 Treatment Guidelines Current updates on the European and WHO registered clinical trials of 544 coronavirus disease 2019 (COVID-19) Clioquinol, an alternative antimicrobial agent against 550 common pathogenic microbe Effect of clioquinol, an 8-hydroxyquinoline derivative, on 552 rotavirus infection in mice RNA dependent DNA polymerase 554 (reverse transcriptase) from avian myeloblastosis virus: a zinc metalloenzyme Characterization of Clioquinol and Analogs as Novel Inhibitors of Methionine 557 Aminopeptidases from Mycobacterium tuberculosis Killing of non-replicating Mycobacterium tuberculosis by 8-33 Structure and function of the methionine aminopeptidases Control of protein life-span by N-terminal methionine 599 excision Zinc supplementation for the treatment or prevention of 601 disease: Current status and future perspectives Pyrithione and 8-hydroxyquinolines transport lead 603 across erythrocyte membranes Clioquinol and pyrithione activate TRPA1 605 by increasing intracellular Zn2+ Zinc-binding compounds induce cancer cell death via 608 distinct modes of action Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 Quantitative mRNA expression profiling of 621 ACE 2, a novel homologue of angiotensin converting enzyme Angiotensin converting 624 enzyme-2 Structure of SARS coronavirus 631 spike receptor-binding domain complexed with receptor Receptor Recognition Mechanisms of Coronaviruses: a Decade of Structural Studies Cryo-EM structure of the SARS coronavirus spike 635 glycoprotein in complex with its host cell receptor ACE2 Cleavage of the SARS coronavirus spike glycoprotein by airway proteases 638 enhances virus entry into human bronchial epithelial cells in vitro Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a 647 prerequisite conformational state for receptor binding Host cell proteases: Critical determinants of coronavirus tropism 649 and pathogenesis Characterization of a Highly 651 Conserved Domain within the Severe Acute Respiratory Syndrome Coronavirus Spike Protein 652 S2 Domain with Characteristics of a Viral Fusion Peptide Adapting Cell-Based Assays to the High-654 Throughput Screening Platform: keywords: ace2; analogues; clq; coronavirus; covid-19; sars cache: cord-280198-bhjw6xc5.txt plain text: cord-280198-bhjw6xc5.txt item: #351 of 702 id: cord-280392-ij5gtesw author: Gultom, Mitra title: Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2 date: 2020-11-10 words: 2258 flesch: 29 summary: Longitudinal Fecal Screening In Malayan Tigers Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict 354 potential intermediate hosts of SARS-CoV-2 SARS-CoV-2 spike protein predicted to form complexes with host receptor protein 356 orthologues from a broad range of mammals Livestock susceptibility to infection 358 with Middle East respiratory syndrome coronavirus Limited susceptibility of chickens, turkeys, and mice to pandemic (H1N1) 2009 virus Susceptibility of pigs and chickens to SARS coronavirus The contribution of animal models to the understanding of the host 364 range and virulence of influenza A viruses Influenza virus reservoirs and intermediate hosts: dogs, 366 horses, and new possibilities for influenza virus exposure of humans Emerging influenza D virus threat: What we know so far! For both rhesus macaques and cats, SARS-141 CoV-2 antigen-positive cells predominantly overlapped with the non-ciliated cell populations, 142 irrespective of the incubation temperature. keywords: ace2; aec; cat; cells; cov-2; sars; species cache: cord-280392-ij5gtesw.txt plain text: cord-280392-ij5gtesw.txt item: #352 of 702 id: cord-280454-etf32afd author: Moustaqil, Mehdi title: SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts date: 2020-06-05 words: 10177 flesch: 51 summary: (*) the protein sequences for Cotton rats (Sigmodon hispidus) and Minks (Neovison vison) were found using tblastn against shotgun genomes, with the Query AAH7172.1 for IRF3 protein [(Isoform 1) Homo sapiens] and NP_653288.1 for NACHT, LRR and PYD domains-containing protein 12 (C) Schematic representation of TAB1 protein structure with the location of the identified cleavage sites on the primary sequence. keywords: 3clpro; cell; cleavage; coronavirus; cov-2; covid-19; expression; fig; fragments; gfp; human; irf3; nlrp12; plpro; protease; proteins; sars; sites; species; tab1; terminal cache: cord-280454-etf32afd.txt plain text: cord-280454-etf32afd.txt item: #353 of 702 id: cord-280922-w6a5ec06 author: Sen, Sanjana title: Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score date: 2020-10-29 words: 4144 flesch: 46 summary: Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. Here, ELISA and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide-range of disease states. keywords: abs; cov-2; covid-19; disease; epitopes; patients; sars; severity; αep9 cache: cord-280922-w6a5ec06.txt plain text: cord-280922-w6a5ec06.txt item: #354 of 702 id: cord-280979-0vaarrji author: Gauttier, V. title: Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date: 2020-08-14 words: 4320 flesch: 18 summary: Our in-vivo results showed that a single injection of selected CD8 T cell epitopes induces memory viral-specific T-cell responses with a phenotype of tissue-resident memory T cells (Trm). Th1-biasing immunization using CD8 T cells optimized peptide vaccination may offer an important alternative and complementary approach with a history of safe administration, may be developed and updated rapidly, and should avoid safety pitfalls in the pursuit of a COVID-19 vaccine 8, 13, 14 . keywords: cd8; cell; covid-19; epitopes; hla; memory; peptide; responses; sars; vaccine; virus cache: cord-280979-0vaarrji.txt plain text: cord-280979-0vaarrji.txt item: #355 of 702 id: cord-280994-w8dtfjel author: Peng, Qi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 words: 2124 flesch: 41 summary: Python-based system for macromolecular structure solution Mechanism of nucleic acid unwinding by SARS-CoV helicase Biochemical characterization of a 555 recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying 556 viral RNA templates Shaping the flavivirus replication complex: It is 558 curvaceous! Fast and accurate defocus estimation from 621 electron micrographs Transmission of 2019-nCoV infection from an 624 asymptomatic contact in Germany Insights into RNA 626 synthesis, capping, and proofreading mechanisms of SARS-coronavirus Viral RNA polymerase: a promising antiviral target 628 for influenza A virus One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Coronaviridae and SARS-associated coronavirus strain HSR1 Clinical characteristics of 138 hospitalized patients with 2019 novel 638 coronavirus-infected pneumonia in Wuhan, China Structural basis for the inhibition of the RNA-dependent RNA polymerase 641 from SARS-CoV-2 by Remdesivir. keywords: cov; nsp12; nsp7; nsp8; polymerase; rna; sars cache: cord-280994-w8dtfjel.txt plain text: cord-280994-w8dtfjel.txt item: #356 of 702 id: cord-281141-ouno4jpl author: Mahajan, Swapnil title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 words: 6239 flesch: 46 summary: Stained cells were analyzed in BD Accuri C6 Plus to detect the expression of activation markers IFN- and CD137 (4-1BB) on CD4 and CD8 T cells. medRxiv Revealing factors determining immunodominant responses against dominant epitopes Identifying specificity groups in the T cell receptor repertoire Clonally diverse CTL response to a dominant viral epitope recognizes potential epitope variants Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity Limited T cell receptor repertoire diversity in tuberculosis patients correlates with clinical severity A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells Direct link between mhc polymorphism, T cell avidity, and diversity in immune defense SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection Convergent antibody responses to SARS-CoV-2 in convalescent individuals Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19 High neutralizing antibody titer in intensive care unit patients with COVID-19 The Immune Epitope Database (IEDB): 2018 update NetMHCpan, a method for MHC class I binding prediction beyond humans Reliable prediction of T-cell epitopes using neural networks with novel sequence representations A simple method for displaying the hydropathic character of a protein NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data keywords: cd8; cd8 t; cell; cov-2; donors; epitopes; figure; hla; peptide; response; sars; spike cache: cord-281141-ouno4jpl.txt plain text: cord-281141-ouno4jpl.txt item: #357 of 702 id: cord-281565-v8s2ski3 author: Belmonte-Reche, Efres title: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date: 2020-08-20 words: 4584 flesch: 42 summary: To compare between virus species, we calculated the density of potential quadruplex sequences per 100000 nucleotides (Density = 100000 × ℎ ). So, we investigated the differences between them through genome alignments and found that most of the sequence versions amongst species (6 out of 8) were still able to form potential quadruplex structures even with modifications. keywords: 2019; dna; genome; ncov; potential; quadruplex; sequences; structures; viruses cache: cord-281565-v8s2ski3.txt plain text: cord-281565-v8s2ski3.txt item: #358 of 702 id: cord-281679-xmbnpawj author: Meekins, David A. title: Susceptibility of swine cells and domestic pigs to SARS-CoV-2 date: 2020-08-16 words: 3412 flesch: 40 summary: In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. SARS-CoV-2 is a member of the Betacoronavirus genus that includes the pathogenic human viruses SARS-CoV-1 and MERS-CoV keywords: animal; cell; coronavirus; cov-2; infection; pigs; porcine; sars; study cache: cord-281679-xmbnpawj.txt plain text: cord-281679-xmbnpawj.txt item: #359 of 702 id: cord-281684-m3m4mhye author: Fagre, Anna C. title: A potent SARS-CoV-2 neutralizing human monoclonal antibody that reduces viral burden and disease severity in Syrian hamsters date: 2020-09-28 words: 3726 flesch: 32 summary: respiratory syndrome coronavirus spike glycoprotein to avoid neutralization escape Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein The establishment of reference sequence for SARS-CoV-2 and variation analysis Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Structural basis of receptor recognition by SARS-CoV-2 Evaluation of human monoclonal antibody 80R for immunoprophylaxis of severe acute respiratory syndrome by an animal study, epitope mapping, and analysis of spike variants Human monoclonal antibody as prophylaxis for SARS coronavirus infection in ferrets Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirusspecific human monoclonal antibody Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Pathogenesis and transmission of SARS-CoV-2 in golden hamsters Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Human neutralizing antibodies elicited by SARS-CoV-2 infection A human monoclonal antibody blocking SARS-CoV-2 infection A human neutralizing antibody targets the receptor binding site of SARS-CoV-2 Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model A SARS-CoV-2 infection model in mice demonstrates protection by neutralizing antibodies Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters Identification of oxidative stress and Toll-like receptor 4 signaling as a key pathway of acute lung injury SARS-CoV-2 and myocardial injury: a role for Nox2? Prospects for the use of regulators of oxidative stress in the comprehensive treatment of the novel Coronavirus Disease 2019 (COVID-19) and its complications Is macrophages heterogeneity important in determining COVID-19 lethality? We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. keywords: ace2; antibody; avgn; binding; coronavirus; cov-2; human; infection; protein; receptor; sars; spike cache: cord-281684-m3m4mhye.txt plain text: cord-281684-m3m4mhye.txt item: #360 of 702 id: cord-281699-pxof67pl author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-08-13 words: 3093 flesch: 43 summary: We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates, and nsp14 mutations as potential predictors for high mutability strains. Our results show that nsp14 mutations show the most consistent association with mutations between MoE and the whole genome. keywords: cov-2; genome; isolates; moe; mutations; sars cache: cord-281699-pxof67pl.txt plain text: cord-281699-pxof67pl.txt item: #361 of 702 id: cord-281717-kzd9vvci author: Digard, Paul title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 words: 4475 flesch: 34 summary: Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. No differences in CpG composition between coronavirus genera were 104 apparent, although the gamma genus exhibited a tighter range (Fig 2B) . keywords: composition; coronavirus; cov-2; cpg; host; human; sars; sequences; viruses cache: cord-281717-kzd9vvci.txt plain text: cord-281717-kzd9vvci.txt item: #362 of 702 id: cord-282372-nmii30mc author: Youk, Jeonghwan title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 words: 5127 flesch: 42 summary: Bulk RNA and single cell RNA sequencing datasets will be uploaded on the European Genome-Phenome Archive (EGA). We have established feeder-free, 3D hAT2 organoids (hereafter referred to as hAOs; definition of organoid is available at ref. 24 ) with defined factors which support molecular and functional identity of hAT2 cells over multiple passages, showing substantial improvements from the previous application of co-culture models [25] [26] [27] . keywords: alveolar; cells; cov-2; data; dpi; fig; genes; haos; hat2; human; infected; infection; rna; sars cache: cord-282372-nmii30mc.txt plain text: cord-282372-nmii30mc.txt item: #363 of 702 id: cord-282604-xp71rkxc author: Nikolaev, EN title: Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein date: 2020-05-25 words: 2185 flesch: 47 summary: [6] , which has a structure similar to SARS-CoV-2 structure, it can be concluded that the number of copies of E, M, and N proteins is much larger than that of S, but the E and M are relatively short and tightly membrane-bound proteins, what makes them difficult to extract, detect, and identify. The detection of viral proteins in body fluids by mass-spectrometry based methods could serve as a complementary diagnostic tool. keywords: detection; mass; proteins; samples; sars; virus cache: cord-282604-xp71rkxc.txt plain text: cord-282604-xp71rkxc.txt item: #364 of 702 id: cord-282795-kje7rn57 author: Zheng, Yue title: Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions date: 2020-09-21 words: 491 flesch: 37 summary: Enveloped viruses are known to efficiently package their core elements with heterologous 30 envelope glycoproteins, giving rise to the so called 'pseudotypes' or 'pseudoviruses ' Neutralization titers NT50 and NT80 were calculated using Prism 8 (GraphPad, US). None of these sera had Characterization of 162 spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with 163 SARS-CoV Veesler D: Structure, Function, and 165 Antigenicity of the SARS-CoV-2 Spike Glycoprotein The 167 D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases 168 infectivity High-efficiency gene 170 transfer into CD34 keywords: cov-2; sars; virus cache: cord-282795-kje7rn57.txt plain text: cord-282795-kje7rn57.txt item: #365 of 702 id: cord-282878-8qgsq2km author: Fignani, Daniela title: SARS-CoV-2 receptor Angiotensin I-Converting Enzyme type 2 (ACE2) is expressed in human pancreatic β-cells and in the human pancreas microvasculature date: 2020-10-23 words: 7592 flesch: 31 summary: We also identified ACE2 positive cells in the pancreatic ducts, even though only some scattered cells with a clear ACE2 signal were detected (Figure 1, panel-c and -d) . The elaboration process consisted in the comparison between the peak list obtained in silico considering the expected aminoacidic sequence of human ACE2 protein (Uniprot ID: Q9BYF1), trypsin as digestion enzyme and eventual modifications (carbamidomethylation, oxidation, etc.). keywords: ace2; analysis; cells; cov-2; diabetes; endoc; expression; figure; human; infection; insulin; islets; pancreas; protein; sars; βh1 cache: cord-282878-8qgsq2km.txt plain text: cord-282878-8qgsq2km.txt item: #366 of 702 id: cord-283109-ka3n9pft author: Arumugam, Arunkumar title: The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step date: 2020-04-08 words: 1728 flesch: 47 summary: Our data using both high (Ct < 35) and low (Ct >35) target concentrations suggest that since RT-qPCR is highly sensitive, using raw samples or minimal sample preparation steps might not reduce the test sensitivity as most patients tend to have a higher viral load. Long assay time, partly caused by slow sample preparation steps, has created a large backlog when testing patient samples suspected of COVID-19. keywords: cov-2; samples; sars cache: cord-283109-ka3n9pft.txt plain text: cord-283109-ka3n9pft.txt item: #367 of 702 id: cord-284045-scd3f8vk author: Pape, Constantin title: Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera date: 2020-10-07 words: 5631 flesch: 46 summary: 506 507 Quantitation and Scoring 508 To distinguish infected cells from control cells we use the dsRNA virus marker channel: infected 510 cells show a signal in this channel while the non-infected control cells should ideally be invisible 511 (see Fig. 3 ). Preferential 129 antibody binding to infected compared to non-infected cells indicates the presence of specific 130 SARS-CoV-2 antibodies in the examined serum. keywords: analysis; antibodies; cells; control; cov-2; detection; fig; images; sars; sera; serum cache: cord-284045-scd3f8vk.txt plain text: cord-284045-scd3f8vk.txt item: #368 of 702 id: cord-284068-sbon3aes author: Mok, Chee Keng title: Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis date: 2020-06-22 words: 1803 flesch: 33 summary: Using this method, we identified 31 compounds from the pre-infection treatment screen and 90 compounds from the post-infection treatment screen with activity against SARS-CoV-2 (Table S4) . To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. keywords: compounds; cov-2; infection; library; sars; vitamin cache: cord-284068-sbon3aes.txt plain text: cord-284068-sbon3aes.txt item: #369 of 702 id: cord-284102-rovyvv45 author: Wagner, Teresa R. title: NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response date: 2020-09-28 words: 2921 flesch: 36 summary: From this, we can assume that 227 our RBD Nbs covering large parts of the RBD:ACE2 interface might be suitable to monitor the 228 emergence and presence of neutralizing antibodies in patients. In contrast, NM1228 169 (Nb-Set1) as well as NM1230 (Nb-Set2) contacted the RBD at amino acid residues overlapping 170 with the RBD:ACE2 binding interface, whereas NM1230 additionally covers parts of the spike-171 like loop region on one edge of the ACE2 interface at the top front/ lower left side (Front View, 172 which did not contact any amino acid residues involved in the RBD:ACE2 interface but rather 179 binds to the opposite site (Front View, Figure 5 ). keywords: ace2; binding; cov-2; nbs; rbd; sars cache: cord-284102-rovyvv45.txt plain text: cord-284102-rovyvv45.txt item: #370 of 702 id: cord-284191-05djnz4p author: Bert, Nina Le title: Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals date: 2020-05-27 words: 1959 flesch: 42 summary: Half of them (9/18) possess T cells targeting the ORF-1 coded proteins NSP7 and 13, which were rarely detected in COVID-19- and SARS-recovered patients. All of them trigger antibody and T cell responses in infected patients: however, antibody levels appear to wane relatively quicker than T cells. keywords: cells; cov-2; covid-19; sars cache: cord-284191-05djnz4p.txt plain text: cord-284191-05djnz4p.txt item: #371 of 702 id: cord-284354-aoti88v7 author: Lupala, Cecylia S. title: Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2 date: 2020-05-04 words: 977 flesch: 28 summary: A Novel Coronavirus from Patients with Pneumonia in China Genomic characterisation and epidemiology of 2019 novel coronavirus: 287 implications for virus origins and receptor binding Evolution of the novel coronavirus from the ongoing Wuhan outbreak 289 and modeling of its spike protein for risk of human transmission Angiotensin-converting enzyme 2 is a functional receptor for the SARS 292 coronavirus A 193-Amino Acid Fragment 294 of the Structural and functional basis of SARS-CoV-2 entry by using human 297 ACE2 Trilogy of ACE2: A peptidase 299 in the renin-angiotensin system, a SARS receptor, and a partner for amino acid 300 transporters Angiotensin-converting 302 enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential 303 therapeutic target SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is 305 Blocked by a Clinically Proven Protease Inhibitor Mice transgenic for human angiotensin-converting enzyme 2 provide a 308 model for SARS coronavirus infection Angiotensin-converting enzyme 2 protects from severe acute lung failure A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS 312 coronavirus-induced lung injury Structure, Function, and Antigenicity of the SARS-CoV-2 Spike 314 Cryo-EM structure of the 2019-nCoV spike in the prefusion 316 conformation Computational simulations reveal the binding dynamics between human 318 ACE2 and the receptor binding domain of SARS-CoV-2 spike protein The first-in-class 321 peptide binder to the SARS-CoV-2 spike protein Inhibition of SARS-CoV-2 infections in 324 engineered human tissues using clinical-grade soluble human ACE2 Computational Design of Peptides to Block Binding of 327 the SARS-CoV-2 Spike Protein to Human ACE2 Identification of critical determinants on 330 ACE2 for SARS-CoV entry and development of a potent entry inhibitor A web-based graphical user 333 interface for CHARMM Optimization of the additive CHARMM all-atom protein force field 335 targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 Dihedral 336 Constraint Solver for molecular simulations GROMACS: Figure 7 illustrates the binding energy 239 dependency on helical contents, especially the helicity of free peptides (solid black circles in 240 Figure 7) . keywords: binding; coronavirus; cov-2; sars cache: cord-284354-aoti88v7.txt plain text: cord-284354-aoti88v7.txt item: #372 of 702 id: cord-284627-qvz63m93 author: Banerjee, Shuvam title: Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence date: 2020-04-09 words: 3697 flesch: 54 summary: A C>T G>T T>C C>T C>T AGC>AGT TTT>TAT TAC>TAT GGA>GTA TTT>TTC GAC>GAT TCA>TTA S2839S F3071Y Y346Y G196V F87F D128D S197L S NS S On the origin and continuing evolution of SARS-CoV-2 Genetic diversity and evolution of SARS-CoV-2 Mechanisms of viral mutation The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known. keywords: cov-2; genome; mutations; protein; sars cache: cord-284627-qvz63m93.txt plain text: cord-284627-qvz63m93.txt item: #373 of 702 id: cord-285088-krim73zt author: Wang, Deguo title: One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay date: 2020-04-21 words: 1807 flesch: 38 summary: NO external funding The COVID-19 epidemic Chest Imaging Appearance of COVID-19 Infection Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Loop-mediated isothermal amplification of DNA Accelerated reaction by loop-mediated isothermal amplification using loop primers Development and evaluation of a loop-mediated isothermal amplification (LAMP) method for detecting Listeria monocytogenes in raw milk Rapid Detection of Listeria monocytogenes in raw milk with loop-mediated isothermal amplification and chemosensor Evaluation and improvement of LAMP assays for detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Methods Six specific LAMP primers targeting the N gene of COVID-19 were designed, the RT-LAMP reaction system was optimized with plasmid pUC57 containing N gene sequence, the detection limit was determined with a serial dilution of the plasmid pUC57 containing N gene sequence, and the one-pot real-time RT-LAMP assay and one-pot visual RT-LAMP assay for the detection of COVID-19 were established. keywords: amplification; assay; lamp; pot; time cache: cord-285088-krim73zt.txt plain text: cord-285088-krim73zt.txt item: #374 of 702 id: cord-285159-gytebbua author: Eydoux, Cecilia title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 words: 3620 flesch: 51 summary: Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. keywords: assay; concentration; cov; nsp12; nsp7l8; rna; sars cache: cord-285159-gytebbua.txt plain text: cord-285159-gytebbua.txt item: #375 of 702 id: cord-285592-0in22wzv author: Lemoine, Frédéric title: COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM date: 2020-05-25 words: 3757 flesch: 57 summary: # New DNA mutations (does not apply to GISAID sequences).  Mut_New_List: List of new mutations (does not apply to GISAID sequences). keywords: genomes; gisaid; msa; number; reference; sequences cache: cord-285592-0in22wzv.txt plain text: cord-285592-0in22wzv.txt item: #376 of 702 id: cord-286001-pu1fetq7 author: Zang, Ruochen title: TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes date: 2020-04-23 words: 2056 flesch: 33 summary: bioRxiv Structure, Function, and Evolution of Coronavirus Spike Proteins The 676 cutting edge: membrane-anchored serine protease activities in the pericellular 677 microenvironment TMPRSS2 activates the human coronavirus 229E for 679 cathepsin-independent host cell entry and is expressed in viral target cells in the 680 respiratory epithelium Simultaneous treatment of human bronchial epithelial cells with serine and 683 cysteine protease inhibitors prevents severe acute respiratory syndrome 684 coronavirus entry Fields Virology Enteric involvement of severe acute respiratory syndrome-689 associated coronavirus infection Viral Shedding and Antibody Response in 37 Patients With 691 Clinical infectious 692 diseases : an official publication of the Infectious Diseases Society of America 693 62 Site-specific N-glycosylation Characterization of Recombinant SARS CoV-2 Spike Proteins using High-Resolution Mass Spectrometry. A new coronavirus associated with human respiratory disease in A pneumonia outbreak associated with a new coronavirus of 584 probable bat origin SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 Functional assessment of cell entry and receptor 588 usage for SARS-CoV-2 and other lineage B betacoronaviruses Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Peyrin-Biroulet, Diarrhea during 600 COVID-19 infection: pathogenesis, epidemiology, prevention and management Clinical characteristics 604 of COVID-19 patients with digestive symptoms in Hubei, China: a 605 descriptive, cross-sectional, multicenter study Gastrointestinal Manifestations of SARS-CoV-2 Infection Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review 608 and Meta-analysis First Case of 2019 Novel Coronavirus in the United States Molecular and serological investigation of 2019-nCoV infected 612 patients: implication of multiple shedding routes Prolonged presence of SARS-CoV-2 viral RNA in faecal samples Evidence for Gastrointestinal Infection of SARS-CoV-2 Virological assessment of hospitalized patients with COVID-619 2019 Tissue-specific amino acid transporter partners ACE2 and 621 collectrin differentially interact with hartnup mutations ACE2 links amino acid malnutrition to microbial ecology and 624 intestinal inflammation Rotavirus VP3 targets MAVS for degradation to inhibit type III 626 interferon expression in intestinal epithelial cells Innate immune response to homologous rotavirus infection in the 628 small intestinal villous epithelium at single-cell resolution Controlling Epithelial Polarity: A Human Enteroid Model for Host-632 Human VP8* keywords: cell; cov-2; fig; infection; sars; tmprss4; virus cache: cord-286001-pu1fetq7.txt plain text: cord-286001-pu1fetq7.txt item: #377 of 702 id: cord-286466-scokdxp2 author: Tani, Hideki title: Evaluation of SARS-CoV-2 neutralizing antibodies using a vesicular stomatitis virus possessing SARS-CoV-2 spike protein date: 2020-08-23 words: 2559 flesch: 43 summary: Clinical features of patients infected with 2019 279 novel coronavirus in Wuhan Remdesivir for the treatment of COVID-19: A systematic review 282 of the literature Current epidemiological and clinical features of 284 COVID-19; a global perspective from Virology, epidemiology, 286 pathogenesis, and control of COVID-19 Current status on the development of 288 pseudoviruses for enveloped viruses Pseudotyped lentiviral vectors: One vector Generation of VSV pseudotypes using recombinant DeltaG-VSV for 292 studies on virus entry, identification of entry inhibitors, and immune responses to vaccines Recombinant nucleoprotein-based enzyme-linked immunosorbent assay for detection of 296 immunoglobulin G antibodies to Crimean-Congo hemorrhagic fever virus Vesicular stomatitis virus pseudotyped with severe acute respiratory 300 syndrome coronavirus spike protein Protease-mediated entry via the 302 endosome of human coronavirus 229E Involvement of ceramide in the propagation of Japanese encephalitis virus Development of genetic diagnostic 308 methods for detection for novel coronavirus 2019(nCoV-2019) in Japan Analysis of VSV pseudotype virus infection mediated by 311 rubella virus envelope proteins Analysis of Lujo virus cell entry using 314 pseudotype vesicular stomatitis virus Characterization of glycoprotein-mediated entry of severe fever with 317 thrombocytopenia syndrome Virus Protocol and 320 reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for 321 neutralization assays indicated dilutions of sera from two different convalescent . As a result, the inhibition of pseudotyped virus infection was specifically observed in both serum and whole blood and was also correlated with the results of the IFA. keywords: blood; cov-2; covid-19; crnt; sars; sera cache: cord-286466-scokdxp2.txt plain text: cord-286466-scokdxp2.txt item: #378 of 702 id: cord-286810-kq2gu5cc author: Klein, Joshua A. title: Assignment of coronavirus spike protein site-specific glycosylation using GlycReSoft date: 2020-05-31 words: 2583 flesch: 50 summary: Some methods use oxonium ions to constrain the range of glycopeptide glycans in a manner that complements use of peptide + Y ions for assigning glycan composition. Approaches for estimating glycan search spaces have been described using biosynthetic simulation keywords: data; figure; glycan; glycopeptide; glycosylation; protein; search cache: cord-286810-kq2gu5cc.txt plain text: cord-286810-kq2gu5cc.txt item: #379 of 702 id: cord-287172-h8zoplkm author: Ghobrial, Moheb title: The human brain vasculature shows a distinct expression pattern of SARS-CoV-2 entry factors date: 2020-10-21 words: 7030 flesch: 42 summary: Most interestingly, the viral entry-associated protease CTSB but not TMPRSS2 is highly expressed in brain vascular endothelial cells whereas CTSL but not TMPRSS2 is highly expressed in vascular endothelial cells of peripheral organs. Moreover, CTSB was co-expressed in adult and fetal brain endothelial cells with genes and pathways involved in innate immunity and inflammation, angiogenesis, blood-brain-barrier permeability, vascular metabolism, and coagulation, providing a potential explanation for the role of brain endothelial cells in clinically observed (neuro)vascular symptoms in COVID-19 patients. keywords: c c; c t; e c; f c; k c; l c; s c; s e; s f; s l; s s; t s cache: cord-287172-h8zoplkm.txt plain text: cord-287172-h8zoplkm.txt item: #380 of 702 id: cord-287205-k64svq6n author: Pollet, Jeroen title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice date: 2020-11-05 words: 4302 flesch: 42 summary: This demonstrates that bound RBD proteins are structurally and possibly functionally 308 active and that after adsorption the protein does not undergo any significant conformational changes 309 that could result in the loss of possible key epitopes around the receptor-binding motif (RBM). Currently, there are several types of COVID-19 vaccine candidates in 444 advanced clinical trials 6,40-45 . keywords: alhydrogel; antigen; binding; covid-19; n1c1; protein; rbd219; sars; titers; vaccine cache: cord-287205-k64svq6n.txt plain text: cord-287205-k64svq6n.txt item: #381 of 702 id: cord-287372-ya5uvoki author: Böszörményi, Kinga P. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 words: 3984 flesch: 48 summary: However, in the second week of infection, cynomolgus macaques 188 showed more, but still mild, clinical symptoms than rhesus macaques. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model Epub 2020/04/19 Hydroxychloroquine use against SARS-CoV-2 infection in non-human primates CoV-2 infection protects against rechallenge in rhesus macaques Ocular conjunctival inoculation of 620 SARS-CoV-2 can cause mild COVID-19 in rhesus macaques 623 Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2 Development of an inactivated 630 vaccine candidate for SARS-CoV-2 Alphavirus-derived replicon RNA vaccine induces SARS-CoV-2 neutralizing antibody and T cell 635 responses in mice and nonhuman primates Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques DNA 642 vaccine protection against SARS-CoV-2 in rhesus macaques Intradermal-646 delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 647 challenge model 649 Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates A vaccine targeting the RBD of the S 653 protein of SARS-CoV-2 induces protective immunity A 656 macaque model of HIV-1 infection SIV infection of rhesus macaques of 660 Chinese origin: a suitable model for HIV infection in humans Nonhuman Primate Model of Tuberculosis Experimental animal modelling for TB vaccine development Pandemic Swine-Origin H1N1 Influenza Virus Replicates to Higher Levels and Induces More 671 Fever and Acute Inflammatory Cytokines in Cynomolgus versus Rhesus Monkeys and Can 672 Replicate in Common Marmosets C-reactive protein levels in the early stage of COVID-19 Kidney involvement in COVID-19 and rationale for extracorporeal 679 therapies Management of acute kidney injury in patients with 682 COVID-19 Kidney disease is associated 685 with in-hospital death of patients with COVID-19 Severe Hypercoagulability in Patients Admitted to Intensive Care Unit for Acute Respiratory 690 COVID-19 and its implications for thrombosis and 693 anticoagulation Respiratory disease in rhesus macaques inoculated with SARS-CoV-2 The cytokine storm in COVID-701 19: An overview of the involvement of the chemokine/chemokine-receptor system Clinical features of patients infected 705 with 2019 novel coronavirus in Wuhan A role for CT in COVID-19? keywords: animals; cov-2; covid-19; cynomolgus; infection; macaques; rhesus; sars; species; study cache: cord-287372-ya5uvoki.txt plain text: cord-287372-ya5uvoki.txt item: #382 of 702 id: cord-287658-c2lljdi7 author: Lopez-Rincon, Alejandro title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 words: 4786 flesch: 46 summary: These methods rely on the assumption that cDNA sequences share common features, and their order prevails among different sequences 19, 20 . We then validate the discovered sequences on datasets not used during the training of the CNN, and show how to exploit them to create a novel, highly informative set of sequence features (e.g. viral sequences). keywords: bps; coronavirus; cov-2; data; learning; primer; samples; sars; sequences; set; virus cache: cord-287658-c2lljdi7.txt plain text: cord-287658-c2lljdi7.txt item: #383 of 702 id: cord-288644-ywaefpe8 author: Rodon, Jordi title: Pre-clinical search of SARS-CoV-2 inhibitors and their combinations in approved drugs to tackle COVID-19 pandemic date: 2020-10-20 words: 7597 flesch: 44 summary: To detect any drugassociated cytotoxic effect, Vero E6 cells were equally cultured in the presence of increasing drug concentrations, but in the absence of virus. A constant concentration of a clinical isolate of SARS-CoV-2 (ID EPI_ISL_510689) was mixed with increasing concentrations of hydroxychloroquine and added to Vero E6 cells. keywords: activity; cells; cov-2; drugs; effect; inhibitors; sars; supp; table; vero cache: cord-288644-ywaefpe8.txt plain text: cord-288644-ywaefpe8.txt item: #384 of 702 id: cord-288705-f3zqhpx1 author: Slaine, Patrick title: Thiopurines activate an antiviral unfolded protein response that blocks viral glycoprotein accumulation in cell culture infection model date: 2020-10-01 words: 6063 flesch: 32 summary: To test this directly, we performed HCoV-285 with the strong effect on infectious virion production, we also observed significant, dose-294 dependent reductions in viral protein accumulation due to 6-TG and 6-TGo treatment in HCoV-295 OC43-infected HCT-8 cells (Fig. 6C , the main band recognized by the anti-OC43 antibody is 296 consistent with the size of the nucleocapsid N protein). 396 Our data also highlight the sensitivity of membrane anchored viral proteins to 6-TG treatment. keywords: accumulation; cells; fig; iav; infected; protein; replication; tgo; treatment; upr cache: cord-288705-f3zqhpx1.txt plain text: cord-288705-f3zqhpx1.txt item: #385 of 702 id: cord-288824-sygnmiun author: Lam, SD title: SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals date: 2020-08-19 words: 7363 flesch: 48 summary: Previous work contrasted the binding energy of the S-protein of SARS-CoV and SARS-CoV-2 with human ACE2 protein [24, 25, 32] . We show the residues that P(2)-PPI2 reports as stabilising or destabilising for the SARS-CoV-2 S-protein:ACE2 animal complex for DC ( Supplementary Fig. 8 ) and DCEX (Supplementary Fig. 9 ) residues. keywords: ace2; animals; binding; complex; cov-2; human; infection; protein; residues; sars; species; supplementary; δδg cache: cord-288824-sygnmiun.txt plain text: cord-288824-sygnmiun.txt item: #386 of 702 id: cord-289367-zna8qkkv author: Wirden, Marc title: Multicenter comparison of the Cobas 6800 system with the RealStar RT-PCR kit for the detection of SARS-CoV-2 date: 2020-06-30 words: 1195 flesch: 46 summary: Conclusions In this comparison, both RealStar® and Cobas® assays provided comparable qualitative results and a high correlation when both tests were positive. Bland-Altman analysis showed that the mean difference (Cobas® minus RealStar®) was + 3.3 Ct, with a SD of + 2.3 Ct. keywords: cobas; sars cache: cord-289367-zna8qkkv.txt plain text: cord-289367-zna8qkkv.txt item: #387 of 702 id: cord-290290-wyx9ib7s author: Sinegubova, Maria V. title: High-level expression of the monomeric SARS-CoV-2 S protein RBD 320-537 in stably transfected CHO cells by the EEF1A1-based plasmid vector date: 2020-11-05 words: 6012 flesch: 43 summary: We developed a simple purification scheme that consistently yielded up to 30 mg of RBD protein per liter of the simple shake flask cell culture. This All cell populations, secreting RBD proteins, were analyzed by the quantitative PCR and it was found, that increased productivity of populations, adapted to higher concentrations of MTX corresponds to higher copy numbers of target gene (Fig 3C) . keywords: antigen; cell; cho; cov-2; culture; days; domain; expression; fig; protein; rbd; rbdv2; sars; spike; target; tests cache: cord-290290-wyx9ib7s.txt plain text: cord-290290-wyx9ib7s.txt item: #388 of 702 id: cord-290445-vb53bih9 author: Ahmed, Shiek SSJ title: Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery date: 2020-04-23 words: 3796 flesch: 37 summary: This result confirms the hijack of host hub proteins and their molecular pathways for SARS-CoV2 machinery. For instance, eight differentially expressed hub proteins were noticed in the receptor-mediated network (S1 Table) . keywords: cov-2; cov2; host; hubs; network; proteins; receptor; replication; sars cache: cord-290445-vb53bih9.txt plain text: cord-290445-vb53bih9.txt item: #389 of 702 id: cord-290694-jmav8xi4 author: Bridgland, Victoria M. E. title: Why the COVID-19 pandemic is a traumatic stressor date: 2020-09-22 words: 1104 flesch: 46 summary: key: cord-290694-jmav8xi4 authors: Bridgland, Victoria M. E.; Moeck, Ella K.; Green, Deanne M.; Swain, Taylor L.; Nayda, Diane; Matson, Lucy A.; Hutchison, Nadine P.; Takarangi, Melanie K.T. title: Why the COVID-19 pandemic is a traumatic stressor date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.22.307637 sha: doc_id: 290694 cord_uid: jmav8xi4 The COVID-19 pandemic does not fit into prevailing Post-traumatic Stress Disorder (PTSD) models, or diagnostic criteria, yet emerging research shows traumatic stress symptoms as a result of this ongoing global stressor. The PTSD 531 Checklist for DSM-5 (PCL-5) Post-traumatic stress disorder and 533 psychological distress in Chinese youths following the COVID-19 emergency At what sample size do correlations stabilize? keywords: covid-19; participants; stress cache: cord-290694-jmav8xi4.txt plain text: cord-290694-jmav8xi4.txt item: #390 of 702 id: cord-291012-y0ufzx93 author: Ye, Qing title: SARS-CoV-2 infection causes transient olfactory dysfunction in mice date: 2020-11-10 words: 1864 flesch: 31 summary: Interestingly, some respiratory viruses, such as influenza virus, respiratory syncytial CoV-2 infection on olfactory system, groups of 6-8 weeks old hACE2 mice were 81 intranasally infected with 5.4 × 10 5 plaque-forming units (PFU) of SARS-CoV-2. Robust viral nucleocapsid (N) protein was detected in the 89 lung from SARS-CoV-2 infected hACE2 mice, but not from the control animals 90 ( Figure S1B ). keywords: cells; cov-2; dpi; olfactory; positive; sars cache: cord-291012-y0ufzx93.txt plain text: cord-291012-y0ufzx93.txt item: #391 of 702 id: cord-291156-zxg3dsm3 author: Bernasconi, Anna title: Empowering Virus Sequences Research through Conceptual Modeling date: 2020-05-01 words: 4605 flesch: 34 summary: The manuscript is organized as follows: Section 2 overviews current technologies available for virus sequence data management. Many other resources link to viral sequence data, including: drug databases, particularly interesting as they provide information about clinical studies (see ClinicalTrials 10 ), protein sequences databases (e.g., UniProtKB/Swiss-Prot [32] ), and cell lines databases (e.g., Cellosaurus [3] ). keywords: cov2; covid-19; data; database; entity; genomic; information; model; sars; sequence; vcm; virus cache: cord-291156-zxg3dsm3.txt plain text: cord-291156-zxg3dsm3.txt item: #392 of 702 id: cord-291420-40xsypzt author: Nelson-Sathi, Shijulal title: Mutational landscape and in silico structure models of SARS-CoV-2 Spike Receptor Binding Domain reveal key molecular determinants for virus-host interaction date: 2020-10-01 words: 2283 flesch: 44 summary: In addition, RBD mutations identified in this study can serve as a molecular directory for experimental biologists to perform functional validation experiments. For the Maximum-likelihood phylogeny reconstruction, we have used the SARS-CoV-2 genomes containing RBD mutations, and 10 genomes were sampled as representatives for each known subtype with Wuhan RefSeq strain as root. keywords: ace2; binding; cov-2; interface; mutations; rbd; sars cache: cord-291420-40xsypzt.txt plain text: cord-291420-40xsypzt.txt item: #393 of 702 id: cord-291523-4dtk1kyh author: Nguyen, Thanh Thi title: Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence date: 2020-07-01 words: 5362 flesch: 54 summary: Specifically, SARS-CoV-2, bat CoV RaTG13 and Guangdong pangolin CoV are grouped together in cluster 2 while bat SARS CoVs are divided into 2 clusters, i.e. bat SARS CoV ZXC21 and bat SARS CoV ZC45 are in cluster 2 whereas other bat SARS CoVs are in cluster 3. 7C , while 3 members of the Merbecovirus sub-genus (i.e. Pipistrellus bat CoV HKU5, Tylonycteris bat CoV HKU4 and MERS CoV) are divided into 3 clusters (12, 2 and 4) or members of the Sarbecovirus cluster are separated themselves into 2 clusters '1 and 11, sequences of SARS-CoV-2 still join the cluster 11' with other members of Sarbecovirus such as 3 bat viruses (bat SARS CoV ZC45, bat SARS CoV ZXC21, bat CoV RaTG13) and 7 pangolin CoVs. keywords: bat; cluster; clustering; cov-2; fig; pangolin; sars; sequences cache: cord-291523-4dtk1kyh.txt plain text: cord-291523-4dtk1kyh.txt item: #394 of 702 id: cord-291590-24psoaer author: Ogando, Natacha S. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 words: 4335 flesch: 33 summary: Part A: 882 Emergence of the hypercycle Viral quasispecies evolution Mutational fitness effects in RNA and single-stranded DNA viruses: common 886 patterns revealed by site-directed mutagenesis studies Viral mutation rates Lack of evidence for proofreading mechanisms 891 associated with an RNA virus polymerase Mutation rates among RNA viruses Error catastrophe and antiviral strategy Selforganization of matter and the evolution of biological macromolecules Discovery of the first 899 insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus 900 genomes The 902 footprint of genome architecture in the largest genome expansion in RNA viruses A planarian 905 nidovirus expands the limits of RNA genome size Description and 907 initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new 908 family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus 909 Alphaletovirus Unique and conserved features of genome and proteome of SARS-912 coronavirus, an early split-off from the coronavirus group 2 lineage Exoribonuclease superfamilies: structural analysis and 914 phylogenetic distribution Purification and characterization of Escherichia coli RNase 916 T Structural basis for the 3'-5' exonuclease activity of Escherichia coli 918 DNA polymerase I: a two metal ion mechanism A general two-metal-ion mechanism for catalytic RNA 922 Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA 923 synthesis Structural basis 925 and functional analysis of the SARS coronavirus nsp14-nsp10 complex Structural and molecular basis of mismatch correction 929 and ribavirin excision from coronavirus RNA High fidelity of murine hepatitis virus 931 replication is decreased in nsp14 exoribonuclease mutants Infidelity of SARS-CoV Nsp14-exonuclease mutant 934 virus replication is revealed by complete genome sequencing A live, impaired-936 fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal 937 disease keywords: activity; coronavirus; cov; exon; fig; mers; nsp14; replication; rna; sars cache: cord-291590-24psoaer.txt plain text: cord-291590-24psoaer.txt item: #395 of 702 id: cord-291677-zcbyhsf1 author: Wilamowski, M. title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 words: 5370 flesch: 45 summary: We determined crystal structures of Nsp10/16 that revealed the states before and after the methylation reaction, for the first time illustrating coronavirus Nsp10/16 complexes with the m7GpppAm2′-O Cap-1, where 2′OH of ribose is methylated. Extended Data Table 1 contains details of number of chips and detector distances used for data collection for Nsp10/16 SSX structures. keywords: 2′-o; cap-1; complex; cov-2; crystallography; data; fig; mrna; nsp10/16; nsp16; rna; sam; sars; ssx; structure cache: cord-291677-zcbyhsf1.txt plain text: cord-291677-zcbyhsf1.txt item: #396 of 702 id: cord-291710-ixun0c8g author: Su, Haixia title: Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date: 2020-04-14 words: 2577 flesch: 40 summary: Accordingly, baicalin and baicalein are identified as novel non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro with single-digit micromolar potency. key: cord-291710-ixun0c8g authors: Su, Haixia; Yao, Sheng; Zhao, Wenfeng; Li, Minjun; Liu, Jia; Shang, WeiJuan; Xie, Hang; Ke, Changqiang; Gao, Meina; Yu, Kunqian; Liu, Hong; Shen, Jingshan; Tang, Wei; Zhang, Leike; Zuo, Jianping; Jiang, Hualiang; Bai, Fang; Wu, Yan; Ye, Yang; Xu, Yechun title: Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.13.038687 sha: doc_id: 291710 cord_uid: ixun0c8g Human infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause coronavirus disease 19 (COVID-19) and there is currently no cure. keywords: 3clpro; baicalein; binding; cov-2; inhibitors; protease; protein; sars cache: cord-291710-ixun0c8g.txt plain text: cord-291710-ixun0c8g.txt item: #397 of 702 id: cord-292670-12prczym author: Urra, José Miguel title: The antibody response to the glycan α-Gal correlates with COVID-19 disease symptoms date: 2020-07-14 words: 2103 flesch: 26 summary: The results showed that while the inflammatory response and the anti-SARS-CoV-38 2 (Spike) IgG antibody titers increased, reduction in anti-α-Gal IgE, IgM and IgG antibody 39 titers and alteration of anti-α-Gal antibody isotype composition correlated with COVID-19 40 severity. Based on the fact that natural antibodies against α-Gal are produced in response to bacteria 317 with this modification in the microbiota [10], our hypothesis is that the dysbacteriosis observed 318 in COVID-19 patients [28] translates into a reduction in total anti-α-Gal antibody titers and 319 alteration of anti-α-Gal antibody isotype composition due to the reduction in the microbiota of 320 α-Gal-containing commensal bacteria and other still uncharacterized mechanisms ( Figure 5) that may be implicated in the human protection to COVID-19. keywords: antibody; covid-19; gal; patients; response cache: cord-292670-12prczym.txt plain text: cord-292670-12prczym.txt item: #398 of 702 id: cord-292862-ezrkg0dc author: Myerson, Jacob W. title: Supramolecular Organization Predicts Protein Nanoparticle Delivery to Neutrophils for Acute Lung Inflammation Diagnosis and Treatment date: 2020-04-18 words: 14319 flesch: 42 summary: Our data thus indicate that NAP tropism for neutrophils in inflamed mouse lungs may be recapitulated in human lungs. 6, 10, 14, 18 Single cell suspensions prepared from mouse lungs were probed by flow cytometry to further characterize pulmonary neutrophils in naïve mice and in mice following LPS-induced inflammation. keywords: albumin; anti; cells; data; dbco; figure; human; igg; inflammation; injury; liposomes; lps; lungs; lysozyme; mice; minutes; nanoparticles; naps; naïve; neutrophils; nps; protein; pulmonary; uptake cache: cord-292862-ezrkg0dc.txt plain text: cord-292862-ezrkg0dc.txt item: #399 of 702 id: cord-292985-w62xaa4f author: Römer, Rudolf A. title: Flexibility and mobility of SARS-CoV-2-related protein structures date: 2020-07-12 words: 5209 flesch: 54 summary: Molecular dynamics simulations and multiple X-ray structure analyses Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy Structure of M pro from COVID-19 virus and discovery of its inhibitors Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs Protein conformational flexibility modulates kinetics and thermodynamics of drug binding Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses Protein flexibility and dynamics using constraint theory Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic Conformational change of proteins arising from normal mode calculations On the potential of normal mode analysis for solving difficult molecular replacement problems ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Normal mode analysis and applications in biological physics Constrained geometric simulation of diffusive motion in proteins Docking of Photosystem I Subunit C Using a Constrained Geometric Simulation Protein flexibility is key to cisplatin crosslinking in calmodulin Inhibition of HIV-1 protease: the rigidity perspective Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions The flexibility and dynamics of protein disulfide isomerase Something in the way she moves': We have downloaded protein structure files as deposited on the Protein Data Bank, 35 including all PDB codes that came up when using SARS-CoV-2 and Covid-19 as search terms, as well as minor variations in spelling. keywords: cluster; cov-2; cut; domain; flexibility; motion; protein; rigidity; sars; structure cache: cord-292985-w62xaa4f.txt plain text: cord-292985-w62xaa4f.txt item: #400 of 702 id: cord-293274-ysr1l557 author: Perisé-Barrios, Ana Judith title: Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain date: 2020-09-22 words: 4140 flesch: 48 summary: In dogs, canine enteric coronavirus (CCoV), an α-CoV, causes an enteritis of variable severity (rarely fatal) and develop immunity; however some of the recovered dogs become carriers with the ability to infect other dogs. Our findings show that sick dogs presented severe alveolar or interstitial pattern, with pulmonary opacity, parenchymal abnormalities, and bilateral lesions. keywords: animals; canine; cov-2; covid-19; dogs; igg; infection; sars cache: cord-293274-ysr1l557.txt plain text: cord-293274-ysr1l557.txt item: #401 of 702 id: cord-293428-8hj06hzt author: Yang, Jianling title: Cytotoxicity evaluation of chloroquine and hydroxychloroquine in multiple cell lines and tissues by dynamic imaging system and PBPK model date: 2020-04-24 words: 1859 flesch: 41 summary: We compared the 237 R TTCC data collected from heart, liver, kidney, lung, and revealed HCQ has shown 238 significantly safe profiles than that of upon CQ treatment (9). As a result, our data 246 shows that kidney, lung and heart are prone to the toxicity of CQ, otherwise lung and 247 kidney are relative vulnerable upon HCQ treatment ( Figure 5 ). keywords: covid-19; hcq; heart; kidney; toxicity cache: cord-293428-8hj06hzt.txt plain text: cord-293428-8hj06hzt.txt item: #402 of 702 id: cord-293640-pgrrurrc author: Tripathi, Satyendra C title: Renal carcinoma is associated with increased risk of coronavirus infections date: 2020-07-06 words: 3730 flesch: 39 summary: The Tumor Immune Estimation Resource (TIMER) (https://cistrome.shinyapps.io/timer/) platform comprised of the immune infiltrate data from the TCGA patients (Li et al., 2016 (Li et al., , 2017 ) was used to investigate the association between CoV receptors expression and the infiltration level of B cell, CD4+ T cell, CD8+ T cell, neutrophil, macrophage and dendritic cell. The correlation among CoV receptors expression and with immune infiltration level was determined by the TIMER interface using Spearman's correlation analysis and statistical significance, and the strength of the correlation was determined using the following guide for the absolute value: 0.00-0.19 weak, 0.20-0.59 moderate, 0.60-1.0 strong. keywords: ace2; cancer; cell; cov; expression; immune; receptors; tissues cache: cord-293640-pgrrurrc.txt plain text: cord-293640-pgrrurrc.txt item: #403 of 702 id: cord-293826-2p7dqacd author: Lee, Cheryl Yi-Pin title: Neutralizing antibodies from early cases of SARS-CoV-2 infection offer cross-protection against the SARS-CoV-2 D614G variant date: 2020-10-09 words: 1314 flesch: 35 summary: Given that a majority of the developing antibody-mediated therapies and serological assays are based on the S antigen of the original Wuhan reference sequence, it is crucial to determine if humoral immunity acquired from the original SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against the novel prevailing D614G variant. Given that a majority of the developing antibody-mediated therapies 68 and serological assays are based on the S antigen of the original Wuhan reference 69 sequence, it is crucial to determine if humoral immunity acquired from the original 70 SARS-CoV-2 isolate is able to induce cross-detection and cross-protection against 71 the novel prevailing D614G variant. keywords: cov-2; d614; sars cache: cord-293826-2p7dqacd.txt plain text: cord-293826-2p7dqacd.txt item: #404 of 702 id: cord-294120-8fxrqorg author: Guebre-Xabier, Mimi title: NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge date: 2020-08-19 words: 872 flesch: 49 summary: Funding for certain studies was provided by the Coalition for Epidemic Preparedness 198 Author contributions conceptualization of 201 experiments, generation of data and analysis, and interpretation of the results drafting and making critical revisions with 204 the help of others SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 214 elicits immunogenicity in baboons and protection in mice First-in-Human Trial of a SARS CoV 2 Recombinant Spike Protein 218 Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Virological assessment of hospitalized patients with COVID-2019 Infection with novel 227 coronavirus (SARS-CoV-2) causes pneumonia in Rhesus macaques SARS-CoV-2 infection protects against rechallenge in rhesus macaques Development of an inactivated 233 vaccine candidate for SARS-CoV-2 Neeltje van Doremalen ChAdOx1 nCoV-19 237 vaccination prevents SARS-CoV-2 pneumonia in rhesus macaques DNA 240 vaccine protection against SARS-CoV-2 in rhesus macaques Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate 248 model Authors MGX, NP, JHT, BZ, SM, KL, ADP, MJM, GG, GS and LE are current or past 207 employees of Novavax, Inc., a for-profit organization, and these authors own stock or 208 hold stock options. In contrast, SARS-CoV-2 anti-S antibody in convalescent human sera was 157 6.9-to 14.2-fold less with at GMT EC 50 of 23,614 ( Figure 1B) . keywords: macaques; nvx; sars; vaccine cache: cord-294120-8fxrqorg.txt plain text: cord-294120-8fxrqorg.txt item: #405 of 702 id: cord-294275-pp0vlaye author: Li, Jingjing title: Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow date: 2020-06-03 words: 2368 flesch: 48 summary: The study design ( Figure 2 ) for SARS-CoV-2 detection is based on LAMP rapid amplification of specific genes and sequenced by nanopore Flongle workflow. Amplification reaction can be done less than 30 minutes in a friendly environment. keywords: amplification; cov-2; lamp; nanopore; reads cache: cord-294275-pp0vlaye.txt plain text: cord-294275-pp0vlaye.txt item: #406 of 702 id: cord-295257-iguhy1z8 author: Calcagnile, Matteo title: ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study date: 2020-04-24 words: 4793 flesch: 35 summary: Pandemics: waves of disease, waves of hate from the Plague of Athens to A.I.D.S Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? Genomic modulators of the immune response Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan Mechanisms of coronavirus cell entry mediated by the viral spike protein Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry Protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection Cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Cleavage of the SARS coronavirus spike glycoprotein by airway proteases enhances virus entry into human bronchial epithelial cells in vitro A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation COVID-19 and the cardiovascular system Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. FireDock 34 was used to estimate the effects of removal of glycosidic residues or chains on ACE2 interaction with SARS-CoV-2 Spike RBD by calculating ΔG values. keywords: ace2; binding; cov-2; fig; interaction; models; protein; receptor; residues; sars; snps; spike cache: cord-295257-iguhy1z8.txt plain text: cord-295257-iguhy1z8.txt item: #407 of 702 id: cord-295545-ruxz77i8 author: Hennighausen, Lothar title: Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers date: 2020-05-11 words: 1666 flesch: 41 summary: To explore the possibility that Ace2 gene expression in SARS-CoV-2 target cells is regulated not only by interferons but also by a range of cytokines through the family of STAT transcription factors, we mined available scRNA-seq data (Ziegler, 2020) (Table 1) . We have tested this premise and explored whether Ace2 is activated in mouse mammary tissue through STAT transcription factors. keywords: ace2; expression; sars; stat cache: cord-295545-ruxz77i8.txt plain text: cord-295545-ruxz77i8.txt item: #408 of 702 id: cord-295560-0rpguepv author: Yan, Kexin title: Simple rapid in vitro screening method for SARS-CoV-2 anti-virals that identifies potential cytomorbidity-associated false positives date: 2020-10-14 words: 1883 flesch: 46 summary: Another limitation of using 107 virus-induced CPE as a read-out for anti-viral drugs is sensitivity. key: cord-295560-0rpguepv authors: Yan, Kexin; Rawle, Daniel J.; Le, Thuy T.T.; Suhrbier, Andreas title: Simple rapid in vitro screening method for SARS-CoV-2 anti-virals that identifies potential cytomorbidity-associated false positives date: 2020-10-14 journal: bioRxiv DOI: 10.1101/2020.10.13.338541 sha: doc_id: 295560 cord_uid: 0rpguepv The international SARS-CoV-2 pandemic has resulted in an urgent need to identify new anti-viral drugs for treatment of COVID-19 patients. keywords: activity; anti; drug cache: cord-295560-0rpguepv.txt plain text: cord-295560-0rpguepv.txt item: #409 of 702 id: cord-295765-c7o2ukm6 author: Silvas, Jesus A. title: Inhibitors of VPS34 and lipid metabolism suppress SARS-CoV-2 replication date: 2020-07-20 words: 2249 flesch: 40 summary: The use of compounds known to target specific host 51 factors may also elucidate key pathways needed for virus replication. 176 The capacity of the system to differentiate different levels of virus replication was first 177 assessed. keywords: cells; cov-2; orlistat; replication; sars; virus; vps34 cache: cord-295765-c7o2ukm6.txt plain text: cord-295765-c7o2ukm6.txt item: #410 of 702 id: cord-296007-1gsgd22t author: Mohseni, Amir Hossein title: Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date: 2020-09-12 words: 2332 flesch: 43 summary: Designing of multi-hit peptides vaccine sequence 1 3 7 A set of high immunogenic hit peptides derived from N and S proteins of SARS-CoV-2 with high binding 1 3 8 events to HLA-A0201, HLA-B0801, HLA-B3501, HLA-B3508, HLA-B4405, and HLA-E were selected 1 3 9 on the basis of their solvent exposed residues and hydrophobicity scales. The binding events among hit peptides derived from N proteins related to HLA-A0201 2 1 9 Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV keywords: cov; figure; hla; peptide; sars cache: cord-296007-1gsgd22t.txt plain text: cord-296007-1gsgd22t.txt item: #411 of 702 id: cord-296187-nnv2e7gr author: Mulgaonkar, Nirmitee title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 words: 4966 flesch: 50 summary: key: cord-296187-nnv2e7gr authors: Mulgaonkar, Nirmitee; Wang, Haoqi; Mallawarachchi, Samavath; Fernando, Sandun; Martina, Byron; Ruzek, Daniel title: Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19 date: 2020-08-18 journal: bioRxiv DOI: 10.1101/2020.06.18.158196 sha: doc_id: 296187 cord_uid: nnv2e7gr The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. VSV-G particles cells do not carry spike proteins and thus, no significant entry inhibition occurred, suggesting that entry inhibition is likely mediated through the spike protein. keywords: ace2; binding; cells; cov-2; fusion; imatinib; kinase; protein; rbd; receptor; sars; spike; vsv cache: cord-296187-nnv2e7gr.txt plain text: cord-296187-nnv2e7gr.txt item: #412 of 702 id: cord-296237-i9cti2ok author: Díez, José-María title: Cross-neutralization activity against SARS-CoV-2 is present in currently available intravenous immunoglobulins date: 2020-06-19 words: 3746 flesch: 41 summary: The life cycle of SARS coronavirus in Vero E6 cells Crossneutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals Lack of crossneutralization by SARS patient sera towards SARS-CoV-2 Protective antiviral antibodies that lack neutralizing activity: precedents and evolution of concepts COVID-19: consider cytokine storm syndromes and immunosuppression High-dose intravenous immunoglobulin as a therapeutic option for deteriorating patients with Coronavirus Disease Effect of regular intravenous immunoglobulin therapy on prognosis of severe pneumonia in patients with COVID-19 The Efficacy of Intravenous Immunoglobulin Therapy for Severe 2019-nCoV Infected Pneumonia Jordi Bozzo PhD, CMPP and Michael K. James PhD (Grifols) are acknowledged for medical writing and editorial support in the preparation of this manuscript. An Outbreak of Human Coronavirus OC43 Infection and Serological Cross-reactivity with SARS Coronavirus Cross-reactive antibodies in convalescent SARS patients' sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests Antigenic crossreactivity between severe acute respiratory syndromeassociated coronavirus and human coronaviruses 229E and OC43 Currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus 2 antigens Construction of a severe acute respiratory syndrome coronavirus infectious cDNA clone and a replicon to study coronavirus RNA synthesis Search for SARS-CoV-2 inhibitors in currently approved drugs to tackle COVID-19 pandemia Engineering a replication-competent, propagation-defective Middle East respiratory syndrome coronavirus as a vaccine candidate Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans Comparative host gene transcription by microarray analysis early after infection of the Huh7 cell line by SARS coronavirus and human coronavirus 229E keywords: antibodies; coronavirus; cov; cov-2; cross; human; ivig; mers; neutralization; sars cache: cord-296237-i9cti2ok.txt plain text: cord-296237-i9cti2ok.txt item: #413 of 702 id: cord-296268-kb7fgfaq author: Mendonça, Luiza title: SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging date: 2020-11-05 words: 2650 flesch: 38 summary: CryoFIB/SEM images clearly reveal virus exiting tunnels in 3D at the cell 269 periphery connecting to cell membrane ( Figure 5A -B, Movie 2). This likely resulted from the 270 fusion of very large multi-virus containing vesicles with cell membrane, i.e. egress through exocytosis. keywords: assembly; cell; cov-2; cryo; replication; sars; series; tilt cache: cord-296268-kb7fgfaq.txt plain text: cord-296268-kb7fgfaq.txt item: #414 of 702 id: cord-296649-h6oyjz56 author: Scherf-Clavel, Oliver title: Tissue Level Profiling of SARS-CoV-2 antivirals in mice to predict their effects: comparing Remdesivir’s active metabolite GS-441 524 vs. the clinically failed Hydroxychloroquine date: 2020-11-06 words: 5084 flesch: 48 summary: A prophylactic effect of HCQ could be studied infecting the current mouse model after long term (1-3 weeks) treatment with HCQ (5mg/kg per day) in order to reach high HCQ tissue concentration at the time of infection. GS-441 524 and HCQ concentrations were quantified in mouse plasma and several mouse tissue homogenates by two liquid chromatography/tandem mass spectrometry (LC-MS/MS) methods using an SCIEX API 6500 TM triple quadrupole (GS-441 524) and an API 5500 triple quadrupole (HCQ) mass spectrometer (SCIEX, Concord, Ontario, Canada). keywords: blood; distribution; gs-441; hcq; mice; min; pharmacokinetics; plasma; rem; remdesivir; tissue cache: cord-296649-h6oyjz56.txt plain text: cord-296649-h6oyjz56.txt item: #415 of 702 id: cord-296657-mymndjvd author: Higuchi, Yusuke title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 words: 3531 flesch: 42 summary: key: cord-296657-mymndjvd authors: Higuchi, Yusuke; Suzuki, Tatsuya; Arimori, Takao; Ikemura, Nariko; Kirita, Yuhei; Ohgitani, Eriko; Mazda, Osam; Motooka, Daisuke; Nakamura, Shota; Matsuura, Yoshiharu; Matoba, Satoaki; Okamoto, Toru; Takagi, Junichi; Hoshino, Atsushi title: High affinity modified ACE2 receptors prevent SARS-CoV-2 infection date: 2020-09-16 journal: bioRxiv DOI: 10.1101/2020.09.16.299891 sha: doc_id: 296657 cord_uid: mymndjvd The SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor via receptor binding domain (RBD) to enter into the cell. High affinity modified ACE2 fused with Fc is the promising strategy to neutralize SARS-CoV-2. keywords: ace2; affinity; binding; cells; cov-2; fig; mutant; rbd; sars cache: cord-296657-mymndjvd.txt plain text: cord-296657-mymndjvd.txt item: #416 of 702 id: cord-296981-tded20ih author: Gilmore, Kerry title: In vitro efficacy of Artemisinin-based treatments against SARS-CoV-2 date: 2020-10-05 words: 3165 flesch: 38 summary: Therefore, we set out to determine whether A. annua extracts, as well as pure artemisinin, artesunate, and artemether are active against SARS-CoV-2 in vitro. While A. annua extracts have been considered natural combination therapies as they contain several bioactive compounds, 21 the WHO discourages the use of non-pharmaceutical forms of artemisinin as a therapeutic option for malaria due to lack of standardization with its sourcing and preparation, implying risks of suboptimal efficacy and resistance development. keywords: annua; artemisinin; cov-2; extracts; sars cache: cord-296981-tded20ih.txt plain text: cord-296981-tded20ih.txt item: #417 of 702 id: cord-296997-ba7f2mf3 author: Sikora, Mateusz title: Map of SARS-CoV-2 spike epitopes not shielded by glycans date: 2020-07-03 words: 5826 flesch: 50 summary: The model fits high-resolution cryoET electron density data of S proteins on the surface of virions extracted from a culture of infected cells remarkably well They are located on distinct S domains that could fold independently and present these epitopes in a native-like manner. keywords: accessibility; binding; cov-2; epitope; fig; glycans; membrane; model; protein; residues; sars; spike; surface cache: cord-296997-ba7f2mf3.txt plain text: cord-296997-ba7f2mf3.txt item: #418 of 702 id: cord-297021-fzfl08qa author: Manomaipiboon, Anan title: The new silicone N99 half-piece respirator, VJR-NMU N99: A novel and effective tool to prevent COVID-19 date: 2020-07-23 words: 3112 flesch: 53 summary: The remaining 41 people (21 males and 20 females) chose the proper size of silicone respirators to perform the qualitative fit testing. To meet the need for FFRs during a pandemic, Navamindradhiraj University has invented a new model of silicone N99 facepiece respirator by using the silicone mask and the HEPA filter normally used in the operating room (CareStar or SafeStar, Draeger, Germany) (Fig 1) . keywords: filter; fit; mask; n99; protection; respirators; silicone; test cache: cord-297021-fzfl08qa.txt plain text: cord-297021-fzfl08qa.txt item: #419 of 702 id: cord-297044-tpp40j0g author: Jin, Zhenming title: Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug Carmofur date: 2020-04-28 words: 1151 flesch: 51 summary: To verify this result, we fixed infected cells and 97 stained them using anti-sera against viral nucleocapsid protein (NP) and observed a decrease in NP levels after Carmofur treatment (Fig. 2b) . Here we determined the inhibitory 94 effect of Carmofur against SARS-CoV-2 infection on Vero E6 cells, as previously 95 described 20 (Fig. 2) . keywords: carmofur; fig; pro; sars cache: cord-297044-tpp40j0g.txt plain text: cord-297044-tpp40j0g.txt item: #420 of 702 id: cord-297684-9q3oopaz author: Dobaño, Carlota title: Highly sensitive and specific multiplex antibody assays to quantify immunoglobulins M, A and G against SARS-CoV-2 antigens date: 2020-06-12 words: 5205 flesch: 30 summary: The multiplex nature of the assay will allow to test this hypothesis in the future with the addition of antigens to related coronaviruses 229E, HKU1, NL63 and OC43 in the same assay panel, by comparing the patterns of antibody reactivity, in order to address the significance of this in immunity to Here, antibody responses to M were very marginal and did not contribute to higher assay sensitivity and this could partly be because the purity of the protein was not high. bioRxiv Antigenic crossreactivity between severe acute respiratory syndrome-associated coronavirus and human coronaviruses 229E and OC43 SARS-CoV-2 specific antibody responses in COVID-19 patients Beyond the Spike: identification of viral targets of the antibody response to SARS-CoV-2 in COVID-19 patients. keywords: antibodies; antibody; antigens; assays; cov-2; covid-19; days; igg; samples; sars; sensitivity; symptoms cache: cord-297684-9q3oopaz.txt plain text: cord-297684-9q3oopaz.txt item: #421 of 702 id: cord-297747-kifqgskc author: Lupala, Cecylia S. title: Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein date: 2020-03-27 words: 4596 flesch: 48 summary: For ACE2 residues near the binding interface (within 4.0 Å of the RBD), the RMSD is smaller than 0.43 Å compared to the SARS-RBD/ACE2 complex. The residues near the CoV2-RBD/ACE2 interface (defined as the combined set of ACE2 residues within 4.0 Å of RBD and the RBD residues within 4.0 Å of the ACE2) exhibited a difference of 0.43 Å RMSD, which is comparable to the difference between the two independently reported crystal models (an RMSD of 0.25 Å for the same comparison). keywords: ace2; ace2 complex; binding; cov2; crystal; rbd; residues; sars; simulations; spike; structure cache: cord-297747-kifqgskc.txt plain text: cord-297747-kifqgskc.txt item: #422 of 702 id: cord-297754-d4xnj551 author: Aktas, Emre title: Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site date: 2020-09-03 words: 2894 flesch: 65 summary: An example is QKG89654(A845D) and QKV35819 (A845V)have the same position but different mutation .The other example is QKG91034(Q836P) and QKG81751(Q836L). According to 347 whole sequences of spike protein ,the most common mutations are D614G (39 mutations), H49Y(3 mutations), Y453F (8 mutations), G261D(6 mutations), A845S (4 mutations), T676I(2 mutations), S254F(2 mutations), I197V(2 mutations) respectively and others have only one mutation are shown on the table 2 .It is clear that same mutation can occur different position. keywords: asia; binding; d614; damage; figure; mutations; residue; rsa; spike; structure cache: cord-297754-d4xnj551.txt plain text: cord-297754-d4xnj551.txt item: #423 of 702 id: cord-297775-ug4ovsws author: Hosie, Margaret J title: Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date: 2020-09-23 words: 1999 flesch: 42 summary: Currently, there is no evidence that domestic cats have played any role in the epidemiology of the COVID-19 pandemic, but a better understanding of how efficiently virus is transmitted from humans to cats will require cats in COVID-19 households to be monitored. key: cord-297775-ug4ovsws authors: Hosie, Margaret J; Epifano, Ilaria; Herder, Vanessa; Orton, Richard J; Stevenson, Andrew; Johnson, Natasha; MacDonald, Emma; Dunbar, Dawn; McDonald, Michael; Howie, Fiona; Tennant, Bryn; Herrity, Darcy; Da Silva Filipe, Ana; Streicker, Daniel G; Willett, Brian J; Murcia, Pablo R; Jarrett, Ruth F; Robertson, David L; Weir, William title: Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK date: 2020-09-23 journal: bioRxiv DOI: 10.1101/2020.09.23.309948 sha: doc_id: 297775 cord_uid: ug4ovsws Two cats from different COVID-19-infected households in the UK were found to be infected with SARS-CoV-2 from humans, demonstrated by immunofluorescence, in situ hybridisation, reverse transcriptase quantitative PCR and viral genome sequencing. keywords: cat; cov-2; human; sars; transmission cache: cord-297775-ug4ovsws.txt plain text: cord-297775-ug4ovsws.txt item: #424 of 702 id: cord-297786-jz1d1m2e author: Hasan, Md. Mahbub title: Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes date: 2020-08-26 words: 3273 flesch: 48 summary: According to a recent study on 48,635 of SARS CoV-2 genome sequences, 353,341 mutation events have been observed globally in comparison to the reference genome of Wuhan. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (95.6%) in Bangladeshi isolates. keywords: analysis; bangladesh; cov-2; d614; genomes; mutations; sars; sequences; virus cache: cord-297786-jz1d1m2e.txt plain text: cord-297786-jz1d1m2e.txt item: #425 of 702 id: cord-297787-t9neub6d author: Fu, Ziyang title: Structural basis for the inhibition of the papain-like protease of SARS-CoV-2 by small molecules date: 2020-07-18 words: 2159 flesch: 45 summary: that the original pocket in MERS PLpro might be too shallow to allow GRL0617 to bind with 130 extensive contacts, and the naphthalene moiety of GRL0617 would also be in steric clash with the 131 pocket of MERS PLpro ( Fig. S4C) . We showed that PLpro preferably cleaves the K48-ubiquitin linkage while also being capable of cleaving ISG15 modification. keywords: cov-2; fig; grl0617; isg15; plpro; sars cache: cord-297787-t9neub6d.txt plain text: cord-297787-t9neub6d.txt item: #426 of 702 id: cord-297826-2nruf2g7 author: Tian, Jing-Hui title: SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 elicits immunogenicity in baboons and protection in mice date: 2020-06-30 words: 2676 flesch: 45 summary: 310 PBMCs were collected 7 days after the second immunization (day 28) and T cell CoV2373 alone or 1 µg NVXCoV2373/Matrix-M (Fig. 8E) . Anti-S protein IgG titers were detected within 21-days of a single priming immunization 288 in animals immunized with NVX-CoV2373/Matrix-M across all the dose levels (GMT = 289 1,249-19,000). keywords: cov2373; fig; matrix; mice; nvx; sars cache: cord-297826-2nruf2g7.txt plain text: cord-297826-2nruf2g7.txt item: #427 of 702 id: cord-298172-iyxyennq author: Guo, Youjia title: Potent mouse monoclonal antibodies that block SARS-CoV-2 infection date: 2020-10-02 words: 4577 flesch: 36 summary: With the development of humanized mouse antibodies and subsequent generation of fully human antibodies by various techniques, monoclonal antibodies have become widely used in therapy and prophylaxis for cancer, autoimmune diseases, and viral pathogens (Walker & Burton, 2018) . Instead, monoclonal antibodies produced by hybridomas are secreted into the culture supernatant, thus their production is straightforward and of low cost, and their quality is stable. keywords: ace2; antibodies; antibody; cov-2; et al; monoclonal; s1d7; s3d8; sars; spike cache: cord-298172-iyxyennq.txt plain text: cord-298172-iyxyennq.txt item: #428 of 702 id: cord-298242-iuskpoug author: Yu, Alvin title: A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion date: 2020-10-02 words: 3609 flesch: 34 summary: AA protein models (see discussion below) were subsequently simulated and coarsegrained to generate the CG models ( Figure 2 and see sections below). Several computational approaches have been developed to build or refine CG models using data from AA or fine-grained simulations. keywords: data; model; molecular; protein; sars; simulations; spike; structure; virion cache: cord-298242-iuskpoug.txt plain text: cord-298242-iuskpoug.txt item: #429 of 702 id: cord-298321-8871aifz author: Laamarti, Meriem title: Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum date: 2020-07-01 words: 2152 flesch: 44 summary: We observed two domains rich in non-synonymous mutations, the first, nsp3-Multi domain due to its large size compared to other non-structural proteins and previously described as playing a different role in SARS-CoV-2 infection (29) . Focusing on non-synonymous mutations, 29 (47.54%) were distributed in five genes (ORF1ab, spike, membrane, nucleocapsid and ORF3a) with variable frequencies. keywords: countries; cov-2; genomes; mutations; sars; tunisia cache: cord-298321-8871aifz.txt plain text: cord-298321-8871aifz.txt item: #430 of 702 id: cord-298326-f5q7j3iu author: Nick, Benjamin C. title: Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV) date: 2020-06-19 words: 2759 flesch: 42 summary: 239 Mutant P184A, which had shown a temperature-sensitive EOP of 1.39 x 10 -2 , failed to exhibit 240 replication kinetics that were significantly different for wild-type or the other MHV IDL strains. These data demonstrate that MHV nsp5 IDL mutation 232 R186A is associated with reduced nsp5 activity at 40°C, whereas no appreciable difference in 233 processing at 40°C was detected for mutant P184A. 234 To assess the impact of elevated temperature on replication of the recovered MHV IDL mutant 236 viruses, we repeated the MOI 0.01 replication assay in DBT-9 cells at 40°C (Fig. 2B) . keywords: idl; mhv; nsp5; protease; residues cache: cord-298326-f5q7j3iu.txt plain text: cord-298326-f5q7j3iu.txt item: #431 of 702 id: cord-298716-pubhq564 author: Bryche, Bertrand title: Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters date: 2020-06-16 words: 3563 flesch: 47 summary: Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria. Interestingly, SARS-CoV-1 (Netland et al., 2008 ) was described as a virus able to use this olfactory pathway. keywords: cells; cov-2; fig; infection; olfactory; sars cache: cord-298716-pubhq564.txt plain text: cord-298716-pubhq564.txt item: #432 of 702 id: cord-299737-r34d0rx7 author: Grant, Paul R title: Extraction-free COVID-19 (SARS-CoV-2) diagnosis by RT-PCR to increase capacity for national testing programmes during a pandemic date: 2020-04-08 words: 1385 flesch: 54 summary: Capacity can be significantly increased without the extraction step but is dependent on the number of safety cabinets for swab processing and number of real time PCR thermal cyclers. We recommend this method is explored further by other medical laboratories using alternative PCR reagents to improve the resilience and capacity of virology laboratories during the pandemic. keywords: extraction; pcr; rna cache: cord-299737-r34d0rx7.txt plain text: cord-299737-r34d0rx7.txt item: #433 of 702 id: cord-300078-svu06v9c author: Haghani, Milad title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature date: 2020-06-01 words: 6373 flesch: 43 summary: Covid-19 studies seem to have been distributed across a broader variety of journals and subject areas. Covid-19 studies also display the involvement of authors from a broader variety of countries compared to SARS and MRS. keywords: cluster; covid-19; items; literature; mers; number; research; sars; studies; terms cache: cord-300078-svu06v9c.txt plain text: cord-300078-svu06v9c.txt item: #434 of 702 id: cord-300194-nsp53lv6 author: Rath, Soumya Lipsa title: Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations date: 2020-06-19 words: 4305 flesch: 48 summary: Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. keywords: binding; domain; protein; receptor; sars; spike; temperature; virus cache: cord-300194-nsp53lv6.txt plain text: cord-300194-nsp53lv6.txt item: #435 of 702 id: cord-300272-95o8yd7h author: Thépaut, Michel title: DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist date: 2020-08-10 words: 6871 flesch: 40 summary: Even more noteworthy nowadays, DC-SIGN and L-SIGN (herein after collectively referred to as DC/L-SIGN) have also been reported to be involved in the enhancement of SARS-CoV-1 infection (Jeffers et al., 2004; Marzi et al., 2004; Yang et al., 2004) . Thus, their role in SARS-CoV-2 infection deserves attention and we focused on DC-SIGN and L-SIGN because of their involvement in SARS-CoV-1 infections (Jeffers et al., 2004; Marzi et al., 2004; Yang et al., 2004) . keywords: cells; clrs; cov-2; et al; figure; glycan; infection; lectin; protein; sars; sign; spike; surface; type; virus cache: cord-300272-95o8yd7h.txt plain text: cord-300272-95o8yd7h.txt item: #436 of 702 id: cord-300423-q2i328sz author: Bai, Lei title: Co-infection of influenza A virus enhances SARS-CoV-2 infectivity date: 2020-10-14 words: 1475 flesch: 57 summary: To study the interaction between IAV and SARS-CoV-2, A549 (a hypotriploid alveolar A549 was converted to be highly sensitive (up to 10,000-fold) against the pSARS-CoV-2 72 virus after different doses of IAV infections (from low MOI of 0.01 to high MOI of 1, also 73 shown by pSARS-CoV-2 with mCherry reporter in Fig. Mice were infected with 3x10 5 PFU of SARS-CoV-2 with or without 90 2000 PFU of IAV pre-infection and were then sacrificed two days later after SARS-CoV-2 91 infection (the experimental scheme is shown in Fig. 2A) . keywords: cov-2; iav; infection; sars cache: cord-300423-q2i328sz.txt plain text: cord-300423-q2i328sz.txt item: #437 of 702 id: cord-300707-k9uk14b3 author: Bouwman, Kim M. title: Multimerization- and glycosylation-dependent receptor binding of SARS-CoV-2 spike proteins date: 2020-09-04 words: 2332 flesch: 39 summary: 120 To illustrate the expression yields of SARS spike proteins or domains thereof 121 we measured the fluorescence in the cell culture supernatant (Fig 1C) . afford additional means for fluorescent-based experiments [13] , and thus are 101 attractive to be fused to RBD proteins. keywords: binding; cov-2; fig; proteins; rbd; sars; trimeric cache: cord-300707-k9uk14b3.txt plain text: cord-300707-k9uk14b3.txt item: #438 of 702 id: cord-300783-pvn2qq0f author: Sadykov, Mukhtar title: Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction date: 2020-08-07 words: 937 flesch: 42 summary: UpA dinucleotide frequencies on RNA virus replication and characterization of 287 the innate cellular pathways underlying virus attenuation and enhanced 288 replication Imbalanced Host Response to SARS CoV-2 Drives Development of COVID-19 RStudio: Integrated 294 Development for R Diverse mechanisms used by cellular restriction factors 297 to inhibit virus infections The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2 Evidence for 312 host-dependent RNA editing in the transcriptome of SARS-CoV-2 Patterns of evolution and host 315 gene mimicry in influenza and other RNA viruses Dinucleotide evolutionary dynamics in 318 influenza A virus Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to 330 Adaptation and Evolution in Natural Infection SnapShot: Antiviral Restriction Factors ViennaRNA Package 2.0 Molecular Mechanism of 338 RNA Recognition by Zinc-Finger Antiviral Protein Mansky 341 LM. We find that the majority of dinucleotide 124 losses were due to C>U changes, in agreement with a recent study by Rice and et al. 2020 ). keywords: cov-2; cpg; sars cache: cord-300783-pvn2qq0f.txt plain text: cord-300783-pvn2qq0f.txt item: #439 of 702 id: cord-300847-ycuiso0g author: Li, Wei title: Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models date: 2020-06-02 words: 2815 flesch: 44 summary: After washing, bound hACE2-Fc was detected by using HRP conjugated streptavidin After washing, bound CR3022 was detected by using HRP conjugated anti human Fc antibody. Thus, to generate high affinity and safe mAbs we used eight very large (size ~ 10 11 clones each) naive human antibody libraries in Fab, scFv or VH format using PBMCs from 490 individuals total obtained before the SARS-CoV-2 outbreak. keywords: ab1; cov-2; fig; human; igg1; rbd; sars cache: cord-300847-ycuiso0g.txt plain text: cord-300847-ycuiso0g.txt item: #440 of 702 id: cord-301233-nenw0f81 author: Naydenova, Katerina title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 words: 4082 flesch: 42 summary: However, in the influenza RNA polymerase this site is occupied by the trisphosphate of the incoming rNTP (PDB 6SZV [30] ). The RNA template, 5'-rUrUrUrUrUrCrArUrArArCrUrUrArArUrCrUrCrAr CrArUrArGrCrArCrUrG-3', and RNA primer 5'-rCrArGrUrGrCrUrArUrGrUr GrArGrArUrUrArArGrUrUrArU-3' were prepared by solid phase synthesis on anÄKTA oligopilot plus 10 (GE Healthcare). keywords: complex; cov-2; favipiravir; fig; polymerase; primer; rdrp; rna; rtp; sars; structure cache: cord-301233-nenw0f81.txt plain text: cord-301233-nenw0f81.txt item: #441 of 702 id: cord-301535-eui41zyg author: Chandler-Brown, Devon title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 words: 4149 flesch: 45 summary: Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Since a major limitation for increasing testing capacity has been supply chain and lab workflow bottlenecks related to RNA extraction, we next attempted to detect SARS-CoV-2 directly from the specimen matrix (viral transport medium). keywords: cov-2; covid-19; gce; qpcr; qsanger; rna; sars; sequence; spike cache: cord-301535-eui41zyg.txt plain text: cord-301535-eui41zyg.txt item: #442 of 702 id: cord-302146-51hof7it author: Cross, Thomas J. title: Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease date: 2020-05-15 words: 3668 flesch: 37 summary: The solid arcs around the outside of the diagram indicate M pro mutations; color coding corresponds to the geographical source. Whether and how M pro mutations have affected viral fitness is not yet known, but at least three mutants have remained in the population long enough to accumulate another mutation: L220F to A191V/L220F, G15S to G15S/D48E and G15S/V35L, and K90R to V77A/K90R. It is worth noting that although a single variant A191V exists, the A191V/L220F double variant likely stemmed from an L220F ancestor due to its shared lineage with L220F single variants. keywords: analysis; mutations; pro; protease; protein; residues; sars; structure; variants cache: cord-302146-51hof7it.txt plain text: cord-302146-51hof7it.txt item: #443 of 702 id: cord-302160-4yfvspaq author: Ruetalo, Natalia title: Rapid and efficient inactivation of surface dried SARS-CoV-2 by UV-C irradiation date: 2020-10-07 words: 1866 flesch: 41 summary: Rapid inactivation of 223 SARS-CoV-2 with deep-UV LED irradiation 225 Effectiveness of 222-nm ultraviolet light on disinfecting SARS-CoV-2 surface contamination 228 Susceptibility of SARS-CoV-2 to UV irradiation An 230 Infectious cDNA Clone of SARS-CoV-2 No touch' technologies for environmental 232 decontamination: focus on ultraviolet devices and hydrogen peroxide systems Williamson 237 BN, et al. 168 Effect of ultraviolet germicidal irradiation on viral aerosols Role of ultraviolet (UV) disinfection in infection control and 208 environmental cleaning Role of Ultraviolet Disinfection in 210 the Prevention of Surgical Site Infections Stability of SARS 212 coronavirus in human specimens and environment and its sensitivity to heating and UV 213 irradiation Large-scale preparation of UV-inactivated SARS coronavirus 215 virions for vaccine antigen Inactivation of the coronavirus 217 that induces severe acute respiratory syndrome, SARS-CoV UV Dose) Achieve Incremental Log Inactivation of Bacteria, Protozoa, Viruses and Algae keywords: cov-2; sars cache: cord-302160-4yfvspaq.txt plain text: cord-302160-4yfvspaq.txt item: #444 of 702 id: cord-302608-fw4pmaoc author: Huang, Jiao-Mei title: Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) date: 2020-03-19 words: 1894 flesch: 45 summary: Ninth report of the International Committee on Taxonomy of Viruses Fast gapped-read alignment with Bowtie 2 MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Bats are natural reservoirs of SARS-like coronaviruses Naturally occurring mutations in PB1 affect influenza A virus replication fidelity, virulence, and adaptability Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination Middle East respiratory syndrome coronavirus (MERS-CoV): challenges in identifying its source and controlling its spread The molecular biology of coronaviruses IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies Severe acute respiratory syndrome From SARS coronavirus to novel animal and human coronaviruses Jalview Version 2-a multiple sequence alignment editor and analysis workbench Mechanisms of host receptor adaptation by severe acute respiratory syndrome coronavirus Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission Management and prevention of SARS in China A novel coronavirus from patients with pneumonia in China Figure 2b and Table S1 describe that all key amino acid residues of RBD (except two positions) are completely homologues between SARS-CoV-2 (Wuhan-Hu-1_MN908947) and pangolin CoVs (pangolin/Guandong/1/2019 and pangolin/Guangdong/lung08), supporting our postulation of recombination event in S-protein gene. keywords: cov-2; covs; pangolin; sars cache: cord-302608-fw4pmaoc.txt plain text: cord-302608-fw4pmaoc.txt item: #445 of 702 id: cord-302733-rfuyd041 author: Dellicour, Simon title: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages date: 2020-10-21 words: 3728 flesch: 34 summary: Indeed, locally reduced transmission rates will not automatically be associated with a notable decrease in the average velocity or distance travelled by lineage dispersal events, which could in turn limit the effectiveness of localised lockdown measures in containing local upsurge of the virus circulation. Firstly, we investigated if the lockdown was associated with a change in lineage dispersal velocity. keywords: belgium; cov-2; dispersal; phylogeographic; sars; sequences; time; tree cache: cord-302733-rfuyd041.txt plain text: cord-302733-rfuyd041.txt item: #446 of 702 id: cord-302920-jkr438p9 author: Gasser, Romain title: Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2 date: 2020-10-09 words: 424 flesch: 23 summary: In this regard, we and others recently reported that the neutralization activity of plasma from COVID-19 patients decreases rapidly during the first weeks after recovery. Potent neutralizing 413 antibodies from COVID-19 patients define multiple targets of vulnerability Rituximab for granulomatosis with 416 polyangiitis in the pandemic of covid-19: lessons from a case with severe pneumonia Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor COVID-19 in persons with multiple sclerosis 423 treated with ocrelizumab -A pharmacovigilance case series Post-rituximab immunoglobulin M (IgM) 426 hypogammaglobulinemia intracytoplasmic tyrosine residue of HIV-1 envelope glycoprotein is critical for basolateral 429 targeting of viral budding in MDCK cells keywords: covid-19; igm cache: cord-302920-jkr438p9.txt plain text: cord-302920-jkr438p9.txt item: #447 of 702 id: cord-303069-ss6g3jkg author: Jakhar, Renu title: An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date: 2020-05-26 words: 3387 flesch: 44 summary: The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. The Allergenicity of predicted epitopes was analyzed by AllerTOP Tool keywords: binding; cell; envelope; epitopes; mhc; prediction; protein; vaccine cache: cord-303069-ss6g3jkg.txt plain text: cord-303069-ss6g3jkg.txt item: #448 of 702 id: cord-303399-s1hbpvn7 author: Straus, Marco R. title: SPINT2 inhibits proteases involved in activation of both influenza viruses and metapneumoviruses date: 2019-08-31 words: 6433 flesch: 58 summary: At 18 hours post transfection we infected MDCK cells with A/CA/04/09 (H1N1) 2 at a MOI of 0.1 and subsequently added SPINT2 protein at different concentrations. SPINT2 protein was eluted by a 1-hour incubation 8 with ULP1-6xHis. keywords: author; cells; cleavage; funder; hmpv; matriptase; peer; preprint; spint2 cache: cord-303399-s1hbpvn7.txt plain text: cord-303399-s1hbpvn7.txt item: #449 of 702 id: cord-303832-1kcqhgjw author: Dai, Manman title: Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets date: 2020-09-06 words: 834 flesch: 50 summary: SARS-CoV-2 41 attached on salmon or suspended in culture medium stored at 4°C remained viable for at least 8 42 days, while these stored at 25°C resulted in attenuating infectivity very quickly. In this study, we detected the titer (50% tissue culture infectious dose/mL, TCID 50 /mL) of 35 viable SARS-CoV-2 attached on salmon or untreated SARS-CoV-2 in culture medium stored at 36 4°C, the temperature in refrigerators or cold rooms for the temporary storage of fish, or 25°C, the 37 regular room temperature, respectively, using end-point titration assay on Vero E6 cells as 38 described previously (8). keywords: sars cache: cord-303832-1kcqhgjw.txt plain text: cord-303832-1kcqhgjw.txt item: #450 of 702 id: cord-303868-aes92l6s author: Steffen, Tara L. title: The receptor binding domain of SARS-CoV-2 spike is the key target of neutralizing antibody in human polyclonal sera date: 2020-08-22 words: 6106 flesch: 36 summary: To measure the functional effect of S1, S2, and RBD antibody depletion on virus specific neutralization we evaluated post-depletion neutralization activity by FRNT (Supplemental figure 3 ). This data has been further represented as % binding neutralizing antibodies based on the pre depletion FRNT50 values (Supplemental Figure 3D) . keywords: antibodies; antibody; binding; cov-2; infection; rbd; response; sars; spike cache: cord-303868-aes92l6s.txt plain text: cord-303868-aes92l6s.txt item: #451 of 702 id: cord-304356-jyp9gjh9 author: Grant, Rogan A. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 words: 7464 flesch: 38 summary: We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. Single cell RNA-Seq of flow-sorted BAL cells: keywords: alveolar; analysis; bal; cells; controls; cov-2; covid-19; data; figure; flow; infection; macrophages; patients; pneumonia; rna; samples; sars; seq; type cache: cord-304356-jyp9gjh9.txt plain text: cord-304356-jyp9gjh9.txt item: #452 of 702 id: cord-304544-tqtdjh2m author: Enes, Ak title: Transcriptional response of signalling pathways to SARS-CoV-2 infection in normal human bronchial epithelial cells date: 2020-06-20 words: 3748 flesch: 41 summary: Although virus entry protein ACE2 has low expression in NHBE cells, pathogen response pathways are strongly activated within 24 hours of infection. We find that response generated in H1N1 infection is much stronger in the Influenza A pathway as expected, but other immune response pathways such as IL-17, NFκB and TNF pathways yielded a stronger response in SARS-CoV-2 infection, which may explain the severity and higher mortality rates of inflammation in patients when compared to swine flu. keywords: cells; cov-2; infection; pathway; response; sars cache: cord-304544-tqtdjh2m.txt plain text: cord-304544-tqtdjh2m.txt item: #453 of 702 id: cord-304792-8sdxqmkb author: Khan, Md. Abdullah-Al-Kamran title: SARS-CoV-2 proteins exploit host’s genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology date: 2020-05-08 words: 2988 flesch: 25 summary: We have identified miRNA hsa-miR-429 whose transcription factor was also upregulated and targets were downregulated and this miRNA can have pivotal role in suppression of host immune responses. Integrating the experimentally validated host interactome proteins and differentially expressed host genes due to SARS-CoV-2 infection, we have taken a blend of computational and knowledgebase approach to delineate the interplay between host and SARS-CoV-2 in various signaling pathways. keywords: cov-2; figure; genes; host; human; infection; pathways; response; sars; signaling cache: cord-304792-8sdxqmkb.txt plain text: cord-304792-8sdxqmkb.txt item: #454 of 702 id: cord-305054-4d84b2g6 author: Liu, Yuan title: The selection of reference genome and the search for the origin of SARS-CoV-2 date: 2020-08-11 words: 2176 flesch: 56 summary: key: cord-305054-4d84b2g6 authors: Liu, Yuan; Yan, Changhui title: The selection of reference genome and the search for the origin of SARS-CoV-2 date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.08.10.245290 sha: doc_id: 305054 cord_uid: 4d84b2g6 We investigated how the selection of reference genome affect the resulting CoV genome assembly. keywords: genome; hu-1; ratg13; reference cache: cord-305054-4d84b2g6.txt plain text: cord-305054-4d84b2g6.txt item: #455 of 702 id: cord-305496-t8ykkekl author: Stone, E. Taylor title: Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay date: 2020-08-21 words: 7239 flesch: 49 summary: This goal was guided by previous studies that 118 have suggested that the use of Vero cells from varying origins can impact viral titer These results suggest that these 275 gastric adenocarcinoma cell lines can support infection, replication and egress of SARS-CoV-2 as 276 well as, or in some cases better than, Vero cell lines. keywords: assay; cell; cov-2; figure; human; infection; lines; sars; vero; virus cache: cord-305496-t8ykkekl.txt plain text: cord-305496-t8ykkekl.txt item: #456 of 702 id: cord-305589-ofpna4k1 author: Schubert, Katharina title: SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation date: 2020-07-07 words: 4099 flesch: 45 summary: The 5.9 Å and 4.3 Å maps of the Nsp1-43S PIC shown in Extended Data Fig. 1 and 3 The high-resolution cryo-EM maps of the complete 40S-Nsp1 complex, the 40S body and the Viral and Cellular mRNA Translation in Coronavirus-Infected Cells Severe acute respiratory syndrome coronavirus nsp1 protein suppresses host gene expression by promoting host mRNA degradation The Architecture of SARS-CoV-2 Transcriptome The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Human Coronaviruses: A Review of Virus-Host Interactions Identification and Characterization of Severe Acute Respiratory Syndrome Coronavirus Replicase Proteins Mechanisms and enzymes involved in SARS coronavirus genome expression A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein SARS coronavirus nsp1 protein induces template-dependent endonucleolytic cleavage of mRNAs: Viral mRNAs are resistant to nsp1-induced RNA cleavage Severe Acute Respiratory Syndrome Coronavirus Protein nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation Novel β-Barrel Fold in the Nuclear Magnetic Resonance Structure of the Replicase Nonstructural Protein 1 from the Severe Acute Respiratory Syndrome Coronavirus Severe Acute Respiratory Syndrome Coronavirus nsp1 Suppresses Host Gene Expression, Including That of Type I Interferon, in Infected Cells Severe Acute Respiratory Syndrome Coronavirus Evades Antiviral Signaling: Role of nsp1 and Rational Design of an Attenuated Strain Coronavirus non-structural protein 1 is a major pathogenicity factor: Implications for the rational design of coronavirus vaccines Human NMD ensues independently of stable ribosome stalling Genomic variance of the 2019-nCoV coronavirus Middle East Respiratory Syndrome Coronavirus nsp1 Inhibits Host Gene Expression by Selectively Targeting mRNAs Transcribed in the Nucleus while Sparing mRNAs of Cytoplasmic Origin Structural and Functional Insights into Human Re-initiation Complexes MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy Gctf: Real-time CTF determination and correction New tools for automated high-resolution cryo-EM structure determination in RELION-3 Prevention of overfitting in cryo-EM structure determination Algorithms for rapid unsupervised cryo-EM structure determination Integrated Tools for Structural and Sequence Alignment and Analysis Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION Features and development of Coot Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix MolProbity: All-atom structure validation for macromolecular crystallography Structural Insights into the Mammalian Late-Stage Initiation Complexes The Phyre2 web portal for protein modeling, prediction and analysis Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex Structure and interactions of the translation initiation factor eIF1 Deciphering key features in protein structures with the new ENDscript server Our structural data suggest that SARS-CoV-2 Nsp1 inhibits translation by sterically occluding the entrance region of the mRNA channel and interfering with binding of cellular mRNAs (Fig. 4a,b) . keywords: 40s; data; fig; mrna; nsp1; protein; ribosomal; sars; terminal; translation cache: cord-305589-ofpna4k1.txt plain text: cord-305589-ofpna4k1.txt item: #457 of 702 id: cord-305858-gp1u4kh7 author: Song, Xiang title: High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients date: 2020-07-19 words: 4909 flesch: 42 summary: The data suggests that SARS-CoV-2 virus may not directly attack blood immune cells lacking the ACE2 expression. To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. keywords: ace2; blood; cells; cov-2; covid-19; expression; figure; human; macrophages; sars; tissue; usa cache: cord-305858-gp1u4kh7.txt plain text: cord-305858-gp1u4kh7.txt item: #458 of 702 id: cord-306901-uuwgpuhw author: Roy, Sylvie title: Efficient production of Moloney murine leukemia virus-like particles pseudotyped with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein date: 2020-09-16 words: 4245 flesch: 40 summary: Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-445 2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques Immunogenicity of a DNA 457 vaccine candidate for COVID-19 CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing 461 responses in nonhuman primates Development of an Inactivated 465 Vaccine Candidate, BBIBP-CorV, with Potent Protection against SARS-CoV-2 Development of an inactivated vaccine 470 candidate for SARS-CoV-2 Phase 1/2 study of COVID-19 RNA vaccine BNT162b1 in adults Immunogenicity and safety of 479 a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years 480 or older: a randomised, double-blind, placebo-controlled, phase 2 trial Intradermal-486 delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 487 challenge model Retroviral vectors pseudotyped with severe acute respiratory syndrome coronavirus S 490 protein The contribution of the cytoplasmic 492 retrieval signal of severe acute respiratory syndrome coronavirus to intracellular 493 accumulation of S proteins and incorporation of S protein into virus-like particles Intracellular targeting signals contribute to 496 localization of coronavirus spike proteins near the virus assembly site Cytoplasmic tail of coronavirus spike protein has 498 intracellular targeting signals Genetic analysis of the SARS-coronavirus spike glycoprotein functional domains 501 involved in cell-surface expression and cell-to-cell fusion Aromatic amino acids in the juxtamembrane domain of severe acute respiratory syndrome 504 coronavirus spike glycoprotein are important for receptor-dependent virus entry and cell-505 cell fusion Vesicular stomatitis virus pseudotyped with severe acute respiratory 508 syndrome coronavirus spike protein 510 Efficient human hematopoietic cell transduction using RD114-and GALV-pseudotyped 511 retroviral vectors produced in suspension and serum-free media Discrimination between 513 exosomes and HIV-1: purification of both vesicles from cell-free supernatants Highly purified human immunodeficiency virus type 1 reveals a 516 virtual absence of Vif in virions The Improbability of the Rapid Development of a Vaccine for SARS-CoV-2 DNA vaccine protection against SARS-CoV-2 in rhesus macaques Single-shot Ad26 vaccine protects against SARS-CoV-2 in rhesus 534 macaques Human 536 immunodeficiency viral vector pseudotyped with the spike envelope of severe acute 537 respiratory syndrome coronavirus transduces human airway epithelial cells and dendritic 538 cells Retroviruses pseudotyped with the severe acute 541 respiratory syndrome coronavirus spike protein efficiently infect cells expressing 542 angiotensin-converting enzyme 2 Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric 547 viruses Protocol and Reagents 550 for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization 551 We could conclude that 131 the production of recombinant viral particles was robust from stable producers expressing DS and 132 inefficient with the full-length version of SARS CoV-2 S. 133 The deletion of the 19 amino acid cytoplasmic tail of S does not enhance its fusogenicity. keywords: cells; coronavirus; cov-2; fig; protein; sars; vaccine cache: cord-306901-uuwgpuhw.txt plain text: cord-306901-uuwgpuhw.txt item: #459 of 702 id: cord-306924-dw35dlx3 author: Wohlers, Inken title: COVID-19 risk haplogroups differ between populations, deviate from Neanderthal haplotypes and compromise risk assessment in non-Europeans date: 2020-11-03 words: 802 flesch: 44 summary: key: cord-306924-dw35dlx3 authors: Wohlers, Inken; Calonga-Solís, Verónica; Jobst, Jan-Niklas; Busch, Hauke title: COVID-19 risk haplogroups differ between populations, deviate from Neanderthal haplotypes and compromise risk assessment in non-Europeans date: 2020-11-03 journal: bioRxiv DOI: 10.1101/2020.11.02.365551 sha: doc_id: 306924 cord_uid: dw35dlx3 Recent genome wide association studies (GWAS) have identified genetic risk factors for developing severe COVID-19 symptoms. Haplogroup H3 has highest risk probability and 81 is the most common risk haplogroup in Europeans and Americans (Fig. 1b) . keywords: covid-19; risk cache: cord-306924-dw35dlx3.txt plain text: cord-306924-dw35dlx3.txt item: #460 of 702 id: cord-307242-e20gtx0z author: Jegouic, Sophie M. title: Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping date: 2020-05-22 words: 3462 flesch: 44 summary: Nevertheless, we found that S protein fragments prepared for gel electrophoresis using non-reducing loading buffer could be used successfully for epitope mapping of 2 S reactive monoclonal antibodies, 3G9, an unpublished mouse mAb generated to SARS S, and CR3022, a human mAb also isolated originally to SARS [19] but shown to cross-react with SARS-CoV-2. Recombinant baculovirus stocks were used to infect small scale cultures (1 x 10 6 cells) for confirmation of S protein expression. keywords: antibody; cells; cov-2; expression; figure; fragments; protein; sars cache: cord-307242-e20gtx0z.txt plain text: cord-307242-e20gtx0z.txt item: #461 of 702 id: cord-307504-cogk5kig author: Zhu, Yuanmei title: Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity date: 2020-03-28 words: 1956 flesch: 32 summary: Can Interact with 494 the N-Terminal Structural and functional 497 characterization of HIV-1 cell fusion inhibitor T20 A Novel Coronavirus from 339 Patients with Pneumonia in China Coronaviruses post-SARS: update on replication and pathogenesis Structure, Function, and Evolution of Coronavirus Spike Proteins Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structure, Function, and 346 Antigenicity of the SARS-CoV-2 Spike Glycoprotein Receptor Recognition by the Novel Coronavirus from 348 Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus Tectonic conformational 350 changes of a coronavirus spike glycoprotein promote membrane fusion Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: 354 implications for virus fusogenic mechanism and identification of fusion inhibitors keywords: cell; coronavirus; cov-2; fusion; protein; sars cache: cord-307504-cogk5kig.txt plain text: cord-307504-cogk5kig.txt item: #462 of 702 id: cord-307536-qeo5dfxg author: Feng, Ye title: Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2) date: 2020-06-30 words: 1000 flesch: 50 summary: In this study, we performed an in silico approach to identify the antigenic B-cell epitopes and human-leukocyte-antigen (HLA) restricted T-cell epitopes, and designed a panel of multi-epitope peptide vaccines. This study screened antigenic B-cell and T-cell epitopes in all encoded proteins of SARS-CoV-2, and further designed multi-epitope based peptide vaccine against viral structural proteins. keywords: cell; epitopes; peptides cache: cord-307536-qeo5dfxg.txt plain text: cord-307536-qeo5dfxg.txt item: #463 of 702 id: cord-307701-fujejfwb author: Gaurav, Shubham title: Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype date: 2020-06-07 words: 2076 flesch: 49 summary: Studies on SARS-CoV-2 are being carried out at an unprecedented rate to tackle this threat. Our results corroborate with the earlier reported 29-nucleotide deletion in SARS, which was frequent during the early stage of human-to-human transmission. keywords: cov-2; genome; mutation; protein; sars; structure cache: cord-307701-fujejfwb.txt plain text: cord-307701-fujejfwb.txt item: #464 of 702 id: cord-307811-6e3j0pn7 author: Hao, Wei title: Binding of the SARS-CoV-2 Spike Protein to Glycans date: 2020-07-02 words: 5709 flesch: 47 summary: Binding of the subunits and S proteins of SARS-CoV-2, SARS-CoV, and MERS-CoV to a HS microarray. Additionally, we found that the binding preferences of the RBDs, S1 subunits and full-length S proteins of SARS-CoV and MERS-CoV are similar to those of the subunits and S protein of SARS-CoV-2, although small differences are observed (Fig. keywords: acid; binding; cell; cov-2; microarray; protein; sars; sulfate; surface; virus cache: cord-307811-6e3j0pn7.txt plain text: cord-307811-6e3j0pn7.txt item: #465 of 702 id: cord-308310-wtmjt3hf author: Zha, Lisha title: Development of a COVID-19 vaccine based on the receptor binding domain displayed on virus-like particles date: 2020-05-14 words: 2022 flesch: 48 summary: Unreacted SMPH and RBD proteins were removed using Amicon-Ultra 0.5, 100K (Merck-Millipore, Burlington, Mass). The coupling reactions were performed with 0.3x molar excess of RBD, 0.3x RBD, or equal molar amount of RBD regarding the CuMVTT (shaking at 23°C for 3 hours at 1200 rpm on DSG Titertek; Flow Laboratories, Irvine, United Kingdom). keywords: ace2; protein; rbd; sars; vaccine; virus cache: cord-308310-wtmjt3hf.txt plain text: cord-308310-wtmjt3hf.txt item: #466 of 702 id: cord-308428-zw26usmh author: Walter, Justin D. title: Highly potent bispecific sybodies neutralize SARS-CoV-2 date: 2020-11-10 words: 10557 flesch: 48 summary: Although the global resolution of the spike protein in complex with both sybodies is around 3 Å, the local resolution of the RBDs with bound sybodies was only in the range of 6-7 Å, presumably due to conformational flexibility (Fig. S6) . Loop 0.180 Phylogene c tree of RBD sybodies. keywords: ace2; binding; conformation; cov-2; cryo; data; fig; fusion; neutralization; protein; rbd; s-2p; sars; sb#15; sb#68; spike; sybodies; sybody cache: cord-308428-zw26usmh.txt plain text: cord-308428-zw26usmh.txt item: #467 of 702 id: cord-309289-vm0k7hfx author: Rothan, Hussin A. title: The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells date: 2020-04-14 words: 1467 flesch: 36 summary: Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Auranofin treatment dramatically reduced the expression of SARS-COV-2-induced cytokines in human cells. keywords: auranofin; cells; cov-2; infection; sars cache: cord-309289-vm0k7hfx.txt plain text: cord-309289-vm0k7hfx.txt item: #468 of 702 id: cord-309411-2dfiwo65 author: Paris, Kristina A. title: Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology date: 2020-06-23 words: 4736 flesch: 51 summary: To answer this question, we need to consider that viral particles in the respiratory system are under small external strains from, e.g., shear flow in the respiratory airways, when engaging cell surface receptors. On the other hand, if only a small number of cell surface receptors are available, then receptor diffusion will be the limiting step to accrue the critical number of receptors needed for endocytosis, and longer RBD/ACE2 dwelling times will be required. keywords: ace2; binding; cell; cov1; cov2; receptor; sars; state cache: cord-309411-2dfiwo65.txt plain text: cord-309411-2dfiwo65.txt item: #469 of 702 id: cord-309512-d8n9711b author: Bacus, Michael G. title: Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses date: 2020-05-05 words: 1026 flesch: 35 summary: For example, bat hosts that belong to genetically 212 unrelated taxa were mixed in some BetaCoV groups. In the succeeding discussions, we will present two deviant phenomena that 286 exemplify this: cross-taxon transmission of CoVs and bat hosts with multi-CoV lineages. keywords: bat; bats; betacovs; host cache: cord-309512-d8n9711b.txt plain text: cord-309512-d8n9711b.txt item: #470 of 702 id: cord-309556-xv3413k1 author: Chow, Ryan D. title: The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2 date: 2020-04-15 words: 5772 flesch: 41 summary: Lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts, pericytes and CD4+ Tcm cells increase in abundance with age. We showed that lung epithelial cells, macrophages, and Th1 cells decrease in abundance with age, whereas fibroblasts and pericytes increase in abundance with age. keywords: age; aging; cell; cluster; cov-2; covid-19; data; expression; factors; figure; genes; human; infection; lung; sars cache: cord-309556-xv3413k1.txt plain text: cord-309556-xv3413k1.txt item: #471 of 702 id: cord-310017-c8rd714a author: Popa, Alexandra title: Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria date: 2020-07-17 words: 5576 flesch: 39 summary: Together, these results from two superspreading events (Tyrol-1, 5 Vienna-1) demonstrate the power of deep viral genome sequencing in combination with detailed epidemiological data for observing viral mutation on their way from emergence at low frequency to fixation. The patientspecific dynamics of viral mutation frequencies may indicate influences of both host-intrinsic 30 factors such as immune responses and overall state of their health as well as extrinsic factors such as different treatment protocols. keywords: analysis; cases; cluster; cov-2; data; epidemiological; fig; genome; mutations; samples; sars; sequences; transmission cache: cord-310017-c8rd714a.txt plain text: cord-310017-c8rd714a.txt item: #472 of 702 id: cord-310230-9wfb43gt author: Ghorbani, Mahdi title: Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations date: 2020-06-27 words: 3482 flesch: 45 summary: Fine Mapping and Functional Characterization Development and Characterization of a Severe Acute Respiratory Syndrome-Associated Coronavirus-Neutralizing Human Monoclonal Antibody That Provides Effective Immunoprophylaxis in Mice Neutralizing Human Monoclonal Antibodies to Severe Acute Respiratory Syndrome Coronavirus: Target, Mechanism of Action, and Therapeutic Potential Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants Vaccine Efficacy in Senescent Mice Challenged with Recombinant SARS-CoV Bearing Epidemic and Zoonotic Spike Variants Structural Basis for Potent Cross-Neutralizing Human Monoclonal Antibody Protection against Lethal Human and Zoonotic Severe Acute Respiratory Syndrome Coronavirus Challenge Escape from Human Monoclonal Antibody Neutralization Affects In Vitro and In Vivo Fitness of Severe Acute Respiratory Syndrome Coronavirus Disease and Diplomacy: GISAID's Innovative Contribution to Global Health Structural Basis for Receptor Recognition by the Novel Coronavirus from Wuhan MCSM-PPI2: predicting the effects of mutations on protein The SARS Coronavirus S Glycoprotein Receptor Binding Domain: Residues K479 and S487 in SARS-Civet are in close proximity with these hotspots and mutations at these residues caused SARS to bind ACE2 with significantly higher affinity than SARS-Civet and played a major role in civet-to-human and human-to-human transmission of SARS coronavirus in 2002. keywords: ace2; binding; coronavirus; human; mutations; ncov-2019; rbd; receptor; sars cache: cord-310230-9wfb43gt.txt plain text: cord-310230-9wfb43gt.txt item: #473 of 702 id: cord-310464-lkdkdque author: Rayko, Mikhail title: Quality control of low-frequency variants in SARS-CoV-2 genomes date: 2020-05-07 words: 1704 flesch: 51 summary: Prompt access to original raw sequencing data is needed to perform accurate and reproducible analysis. We used the following keywords for GISAID database to get information about sequencing methods: Illumina, Nanopore, Ion Torrent, Sanger, dbnseq. keywords: data; genomes; singletons; variants cache: cord-310464-lkdkdque.txt plain text: cord-310464-lkdkdque.txt item: #474 of 702 id: cord-310477-vniokol0 author: Pontes, Camila title: Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs date: 2020-08-21 words: 4383 flesch: 32 summary: The SDP analysis is based on a vectorial representation of protein sequences and amino acid positions in a multidimensional space to simultaneously identify the family segregation and the residue positions that better explain the sources of variation of the family (15) . More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). keywords: ace2; analysis; binding; cov; cov-2; protein; receptor; sars; sdps; spike cache: cord-310477-vniokol0.txt plain text: cord-310477-vniokol0.txt item: #475 of 702 id: cord-310752-zl2g9wqo author: Sato, Taku title: Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats date: 2020-05-15 words: 2141 flesch: 38 summary: Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. keywords: ace2; epithelium; expression; sars; tmprss2 cache: cord-310752-zl2g9wqo.txt plain text: cord-310752-zl2g9wqo.txt item: #476 of 702 id: cord-311066-62edsbfc author: Cox, Brian J. title: Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2 date: 2020-06-24 words: 2928 flesch: 56 summary: TRS independent transcripts were detected as likely non-polyadenylated. To explore if TRS independent transcripts are common in other human CoV pathogens, I assessed SARS-CoV(Josset et al., 2014; Xiong et al., 2014) and MERS (Data: PRJNA233943; publication not known) using previously published polyA independent RNA sequencing data sets that also used ribosome depletion of total RNA. keywords: cov; cov-2; independent; rna; sars; sequence; trs cache: cord-311066-62edsbfc.txt plain text: cord-311066-62edsbfc.txt item: #477 of 702 id: cord-311114-ggcpsjk8 author: Radhakrishnan, Chandni title: Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions date: 2020-09-09 words: 4386 flesch: 46 summary: Genetic variants compiled from a total of 1,855 high-quality genomes from India and 32,286 global genomes were considered for analysis. We have also added 89 new variants (2.61%) to the Indian repertoire of genetic variants. keywords: analysis; epidemiology; genomes; india; kerala; sars; sequencing; study; table; variants; virus cache: cord-311114-ggcpsjk8.txt plain text: cord-311114-ggcpsjk8.txt item: #478 of 702 id: cord-311214-eqwxkwqa author: Kumar, Roshan title: Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution date: 2020-04-16 words: 2731 flesch: 54 summary: 132 To determine the evolutionary pressure on viral proteins, dN/dS values were calculated for 9 134 ORFs of all strains. [36] and IntAct [37] for predicting their interaction against host proteins. keywords: cov-2; figure; isolates; proteins; sars; strains; usa cache: cord-311214-eqwxkwqa.txt plain text: cord-311214-eqwxkwqa.txt item: #479 of 702 id: cord-311240-o0zyt2vb author: Motayo, Babatunde Olarenwaju title: Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences date: 2020-07-27 words: 3104 flesch: 42 summary: There has been paucity of data on the genetic evolution of SARSCoV-2 sequences from Africa, despite the increasing number of genome sequence submissions into the GISAID database from Africa; there were 97 whole genome sequences available in the GISAID database as at 24 th April 2020. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. keywords: africa; analysis; et al; genome; sarscov-2; sequences; virus cache: cord-311240-o0zyt2vb.txt plain text: cord-311240-o0zyt2vb.txt item: #480 of 702 id: cord-311333-shvtfxog author: Fukumoto, Tatsuya title: Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification date: 2020-05-28 words: 415 flesch: 51 summary: Nasopharyngeal swab, sputum and saliva samples were collected from 9 patients who 69 were admitted to our hospital after a diagnosis of COVID-19. Sputum and saliva samples were self-collected in a sterilized PP Screw cup 50 74 (Asiakizai Co., Ltd., Tokyo, Japan). keywords: detection; samples cache: cord-311333-shvtfxog.txt plain text: cord-311333-shvtfxog.txt item: #481 of 702 id: cord-311445-b6bc6vwd author: Bansal, Kanika title: Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin date: 2020-10-12 words: 2751 flesch: 50 summary: Since horseshoe bat SARS strains RaTG13 and RmYN02 are known to be the closest strains to SARS-CoV-2, we have compared CUP of these two strains with SARS-CoV-2 (figure 2). The closest match to SARS-CoV-2 is RaTG13 (96% identity) isolated from the Rhinolophus affinis bat (Zhou et al., 2020) , followed by pangolin SARS viruses with 91% identity (Zhou et al., 2020) . keywords: bat; cov-2; cup; genes; sars cache: cord-311445-b6bc6vwd.txt plain text: cord-311445-b6bc6vwd.txt item: #482 of 702 id: cord-311843-un6urdb1 author: Baray, Juwel Chandra title: BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response date: 2020-09-30 words: 3180 flesch: 54 summary: In Mice Self-Amplifying RNA SARS-CoV-2 Lipid Nanoparticle Vaccine 706 Candidate Induces High Neutralizing Antibody Titers in Mice Alnylam Launches Era of RNAi Drugs Capping, and Proofreading Mechanisms of SARS-Coronavirus Exoribonuclease Activity Are Susceptible to Lethal Mutagenesis: Evidence for 715 Proofreading and Potential Therapeutics Molecular Architecture of Early Dissemination and 722 Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area Tracking Changes in 731 SARS-CoV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 D614G Spike Variant Does Not Alter IgG, IgM, 735 or IgA Spike Seroassay Performance SARS-CoV-2 Viral Spike G614 Mutation Exhibits 785 Higher Case Fatality Rate The Spike D614G Mutation Increases SARS-CoV-2 Infection of Multiple 789 The D614G Mutation in the SARS-CoV-2 Spike Protein Reduces S1 Shedding 793 and Increases Infectivity Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: 796 Enhanced Infectivity and Therapeutic Opportunity Spike Mutation D614G Alters SARS-CoV-2 Fitness and Neutralization 802 The Effect 804 of Size and Charge of Lipid Nanoparticles Prepared by Microfluidic Mixing on Their 805 Lymph Node Transitivity and Distribution Lipid-Based Nanoparticles in the Systemic 808 Delivery of SiRNA Virus-like Particles Induces a Strong Antiviral-like Immune Response in Mice Type 1/Type 2 Immunity in Infectious Diseases IgG Subclass Co-Expression Brings Harmony to the Quartet Model of 818 Flow cytometric analysis of total T cell (CD4 + ) populations producing IL-6 on mouse splenocyte upon SARS-CoV-2 S protein stimulation. keywords: cells; column; cov-2; mice; sars; step; vaccine cache: cord-311843-un6urdb1.txt plain text: cord-311843-un6urdb1.txt item: #483 of 702 id: cord-312038-g76cpjp7 author: Brunaugh, Ashlee D. title: Broad-Spectrum, Patient-Adaptable Inhaled Niclosamide-Lysozyme Particles are Efficacious Against Coronaviruses in Lethal Murine Infection Models date: 2020-10-07 words: 11069 flesch: 39 summary: Though hLYS is surface active, it appeared to only slightly enhance the dissolution of NIC compared to NIC particles blended with lactose (F). We have previously demonstrated that hen egg white lysozyme is robust to processinduced aggregation using typical particle engineering techniques (51) , which provided part of the rationale for its selection as a therapeutically active carrier for the aerosol delivery of NIC particles. keywords: activity; cells; cov-2; covid-19; delivery; dose; drug; fig; formulation; hlys; infection; lung; mers; mice; nic; niclosamide; particles; powder; sars; spray; study; treatment cache: cord-312038-g76cpjp7.txt plain text: cord-312038-g76cpjp7.txt item: #484 of 702 id: cord-312228-wbyqmvhs author: Xiao, Minfeng title: Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples date: 2020-03-19 words: 3253 flesch: 40 summary: To further com-157 pare the sensitivity of different methods, we plotted the number of HCoV-19 reads per million 158 (HCoV-19-RPM) of total sequencing reads against the viral concentration for each sample. For metatranscriptomic sequencing of clinical samples, raw sequencing data of a single se-427 quence lane (approximately 60-75 Gb per sample) was used to simultaneously assess the 428 RNA expression patterns of human, bacteria and viruses in clinical samples from COVID-429 19 patients. keywords: amplicon; capture; fig; genome; hcov-19; reads; samples; sequencing cache: cord-312228-wbyqmvhs.txt plain text: cord-312228-wbyqmvhs.txt item: #485 of 702 id: cord-312305-ll29frwc author: Sun, Shihui title: Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 date: 2020-11-11 words: 4757 flesch: 44 summary: Additionally, immunostaining of lung sections showed a significant infiltration of CD68 + macrophages and Ly-6G + neutrophils in MASCp36 infected mice ( fig. Aged mice challenged with high dose of MASCp36 developed typical respiratory symptoms and exhibited features like ruffled fur, hunched back, and reduced activity. keywords: binding; complex; cov-2; covid-19; disease; fig; lung; mace2; mascp36; mice; model; mouse; rbdmascp36; sars cache: cord-312305-ll29frwc.txt plain text: cord-312305-ll29frwc.txt item: #486 of 702 id: cord-312414-g5px0b65 author: Takagi, Akira title: An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2 date: 2020-09-19 words: 4093 flesch: 51 summary: Front 603 immunol 11:1729 Longitudinal analyses 610 reveal immunological misfiring in severe COVID-19 Origin and evolution of pathogenic coronaviruses Efficient induction of 615 cytotoxic T lymphocytes specific for severe acute respiratory syndrome 616 (SARS)-associated coronavirus by immunization with surface-linked liposomal 617 peptides derived from a non-structural polyprotein 1a SYFPEITHI: database for MHC ligands and peptide motifs A hybrid approach for predicting promiscuous 622 MHC class I restricted T cell epitopes ProPred1: Prediction of promiscuous MHC class-I 624 binding sites The immune epitope database (IEDB) Cytotoxic T 630 lymphocytes recognize a fragment of influenza virus matrix protein in association 631 with HLA-A2 An optimal viral peptide recognized by 633 CD8 + T cells binds very tightly to the restricting class I major histocompatibility 634 complex protein on intact cells but not to the purified class I protein 1-restricted education and cytolytic activity of CD8 + T lymphocytes from 638 beta2 microglobulin (beta2m) HLA-A2.1 monochain transgenic H-2D b beta2m 639 double knockout mice A 641 sequence homology and bioinformatics approach can predict candidate targets for 642 immune responses to SARS-CoV-2 COVID-19 coronavirus vaccine design using 644 reverse vaccinology and machine learning SARS-CoV-2-specific T cell 649 immunity in cases of COVID-19 and SARS, and uninfected controls Selective 655 and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans Sette A. 660 2020. One week later, spleen cells 170 of immunized mice were prepared, stimulated in vitro with a relevant peptide for 5 hours, 171 and stained for their expression of cell-surface CD8 and intracellular interferon-gamma 172 (IFN-. As shown in Fig. 2 , the intracellular cytokine staining (ICS) assay showed that 173 significant numbers of IFN--producing CD8+ T cells were elicited in mice immunized 174 with 18 liposomal peptides including pp1a-38, -52, -84, -103, -445, -597, -641, -1675, 175 -2785, -2884, -3083, -3403, -3467, -3583, -3662, -3710, -3732, and -3886, revealing that 176 these 18 peptides are HLA-A*02:01-restricted CTL epitopes derived from SARS-CoV-2 177 pp1a. keywords: cd8; cells; ctl; epitopes; mice; peptides; sars cache: cord-312414-g5px0b65.txt plain text: cord-312414-g5px0b65.txt item: #487 of 702 id: cord-312473-7i7efdp2 author: Sidhom, John-William title: Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date: 2020-06-20 words: 1182 flesch: 31 summary: Select overlapping epitopes were highlighted showing a shared SNVT motif and corresponding specific TCRs were represented with a seqlogo (bottom). key: cord-312473-7i7efdp2 authors: Sidhom, John-William; Baras, Alexander S. title: Analysis of SARS-CoV-2 specific T-cell receptors in ImmuneCode reveals cross-reactivity to immunodominant Influenza M1 epitope date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.20.160499 sha: doc_id: 312473 cord_uid: 7i7efdp2 Adaptive Biotechnologies and Microsoft have recently partnered to release ImmuneCode, a database containing SARS-CoV-2 specific T-cell receptors derived through MIRA, a T-cell receptor (TCR) sequencing based sequencing approach to identify antigen-specific TCRs. keywords: sars; specific; tcrs cache: cord-312473-7i7efdp2.txt plain text: cord-312473-7i7efdp2.txt item: #488 of 702 id: cord-312524-ee5xw1r8 author: Moustafa, Ahmed M. title: Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread date: 2020-06-08 words: 2060 flesch: 51 summary: Going forward whole genome sequences will be useful for identifying emerging 50 clones or hotspots of reemergence. Our tool (GNUVID) allows for 185 fast sequence typing and clustering of whole genome sequences in a rapidly changing 186 pandemic. keywords: ccs; figure; genome; sars; sequence cache: cord-312524-ee5xw1r8.txt plain text: cord-312524-ee5xw1r8.txt item: #489 of 702 id: cord-312702-fruzsn26 author: Finch, Courtney L. title: Characteristic and quantifiable COVID-19-like abnormalities in CT- and PET/CT-imaged lungs of SARS-CoV-2-infected crab-eating macaques (Macaca fascicularis) date: 2020-05-14 words: 2796 flesch: 24 summary: Based on the rather limited X-97 ray findings in the lungs of reported NHP models of SARS-CoV-2 infection with either 98 mild or no clinical signs (11, 25, 27-29), we turned to high-resolution chest CT and 99 PET/CT to characterize lung abnormalities in infected NHPs toward longitudinal 100 quantitative comparison. 161 CT images can be used for quantification of lung abnormalities using measures of 162 volume or radiodensity, i.e., total lung volume (LV); average radiodensity in the total 163 lung volume (LD); hyperdense volume (HV), a volume of lung in which radiodensity 164 (Hounsfield units, HU) is above a pre-defined threshold; and average radiodensity in the 165 hyperdense volume (hyperdensity, HD). keywords: abnormalities; coronavirus; covid-19; disease; lung; macaques; sars cache: cord-312702-fruzsn26.txt plain text: cord-312702-fruzsn26.txt item: #490 of 702 id: cord-312999-3erodkv9 author: Hassan, Sk. Sarif title: Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2 date: 2020-09-06 words: 3924 flesch: 42 summary: Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. keywords: amino; cov-2; disorder; mutations; orf10; pangolin; protein; sars; sequence cache: cord-312999-3erodkv9.txt plain text: cord-312999-3erodkv9.txt item: #491 of 702 id: cord-313215-diqfmitr author: Luo, Lei title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date: 2020-07-09 words: 1594 flesch: 43 summary: We highly recommend that persons no matter COVID-19 cases or Note: Environmental specimens were tested by RT-PCR testing; 5 positive environmental specimens of asymptomatic COVID-19 cases were excluded in bars of symptoms onset to sampling. key: cord-313215-diqfmitr authors: Luo, Lei; Liu, Dan; Zhang, Hao; Li, Zhihao; Zhen, Ruonan; Zhang, Xiru; Xie, Huaping; Song, Weiqi; Liu, Jie; Huang, Qingmei; Liu, Jingwen; Yang, Xingfen; Chen, Zongqiu; Mao, Chen title: Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases date: 2020-07-09 journal: bioRxiv DOI: 10.1101/2020.07.09.195008 sha: doc_id: 313215 cord_uid: diqfmitr Background Little is known about the SARS-CoV-2 contamination of environmental surfaces and air in non-health care settings among COVID-19 cases. keywords: cases; covid-19; specimens; surfaces cache: cord-313215-diqfmitr.txt plain text: cord-313215-diqfmitr.txt item: #492 of 702 id: cord-313247-55loucvc author: Pipes, Lenore title: Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny date: 2020-10-07 words: 2549 flesch: 58 summary: An alternative to outgroup rooting is molecular clock rooting, which is based on the assumption that mutations occur at an approximately constant rate, or at a rate that can be modeled and predicted using statistical models (e.g., using a relaxed molecular clock such as Drummond et al. Methods for inferring phylogenetic trees that assume an ultrametric tree (i.e. a tree that perfectly follows a molecular clock), such as unweighted pair group method with arithmetic mean (UPGMA; Sokal and Michener, 1958) , directly infers a rooted tree. keywords: cov-2; rooting; sars; tree cache: cord-313247-55loucvc.txt plain text: cord-313247-55loucvc.txt item: #493 of 702 id: cord-313505-2lr4xara author: Resende, Paola Cristina title: Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil date: 2020-06-18 words: 1147 flesch: 38 summary: We also detected two other well-supported (SH-aLRT 228 > 80%) monophyletic clades of small size (n = 2-11) mostly composed by Brazilian sequences 229 ( Supplementary Fig. 1) . The prevalence of the sub-clade 211 B.1.1 in our sample (92%) was much higher than that observed in other Brazilian sequences 212 available in GISAID (36%) (Fig. 1C) phylogenetic tree, consistent with the hypothesis of multiple independent introductions (Fig. 2) (Fig. 2) . keywords: biorxiv; cov-2; fig; sars; sequences cache: cord-313505-2lr4xara.txt plain text: cord-313505-2lr4xara.txt item: #494 of 702 id: cord-313571-umcbulcw author: Martínez-Murcia, Antonio title: In silico design and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012 date: 2020-05-05 words: 1192 flesch: 40 summary: Results from reference laboratories 100% correlated with these obtained by suing reference methods and received an evaluation with 100% of diagnostic sensitivity and specificity. Standard calibration curves of the qPCR were performed from ten-fold 202 dilution series (Figure 3a Only three months ago, an outbreak of severe pneumonia caused by the novel coronavirus SARS-225 CoV-2 started in Wuhan (China) and rapidly expanded to almost all areas worldwide. keywords: cov-2; covid-19; sars cache: cord-313571-umcbulcw.txt plain text: cord-313571-umcbulcw.txt item: #495 of 702 id: cord-313795-jr3n3uo9 author: McAuley, Julie L. title: Liquid chalk is an antiseptic against SARS-CoV-2 and influenza A respiratory viruses date: 2020-11-02 words: 1416 flesch: 34 summary: Chalk was applied before or after virus inoculum and recovery of infectious virus was determined to mimic the use in the gym. Norovirus was not 192 rendered non-infectious when treated with gym chalk, regardless of whether the virus was 193 added to dry chalk, or chalk was added to virus inoculum As different alcohols are the major constituents of liquid chalk, we additionally 198 evaluated the impact of alcohol alone on the recovery of infectious virus. keywords: chalk; cov-2; norovirus; sars; virus cache: cord-313795-jr3n3uo9.txt plain text: cord-313795-jr3n3uo9.txt item: #496 of 702 id: cord-313805-6mnclfeg author: Suzuki, Yuichiro J. title: SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells date: 2020-10-12 words: 2299 flesch: 48 summary: The treatment of human pulmonary artery smooth muscle cells or human pulmonary artery endothelial cells with recombinant SARS-CoV-2 spike protein S1 subunit (Val16 – Gln690) at 10 ng/ml (0.13 nM) caused an activation of MEK phosphorylation. Human pulmonary artery smooth muscle cells and human pulmonary artery endothelial cells were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA), and rat pulmonary artery smooth muscle cells were purchased from Cell Applications (San Diego, CA, USA). keywords: cells; cov-2; mek; protein; sars; spike cache: cord-313805-6mnclfeg.txt plain text: cord-313805-6mnclfeg.txt item: #497 of 702 id: cord-313910-bwe2f7xf author: Bojadzic, Damir title: Small-Molecule In Vitro Inhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2 date: 2020-10-22 words: 7111 flesch: 40 summary: bioRxiv Experimental design and analysis and their reporting II: updated and simplified guidance for authors and peer reviewers Scaffolds for blocking protein-protein interactions Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods Rationalizing the chemical space of protein-protein interaction inhibitors Metabolism of azo dyes: implication for detoxication and activation Toxicological significance of azo dye metabolism by human intestinal microbiota Novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms Identification of novel small-molecule inhibitors of severe acute respiratory syndrome-associated coronavirus by chemical genetics Development and validation of a high-throughput screen for inhibitors of SARS CoV and its application in screening of a 100,000-compound library Targeting membrane-bound viral RNA synthesis reveals potent inhibition of diverse coronaviruses including the middle East respiratory syndrome virus Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay. medRxiv Inhibitors of viral entry Cell entry mechanisms of SARS-CoV-2 Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine Cytokine storm in a phase 1 trial of the anti-CD28 monoclonal antibody TGN1412 London's disastrous drug trial has serious side effects for research Small molecules drive big improvements in immunooncology therapies Postmarket safety events among novel therapeutics approved by the US Food and Drug Administration between 2001 and 2010 COVID-19: Drug targets and potential treatments The spike protein of SARS-CoV -a target for vaccine and therapeutic development Investigation of ACE2 Nterminal fragments binding to SARS-CoV-2 Spike RBD. keywords: ace2; activity; binding; compounds; cov-2; dri; entry; ppi; protein; sars; smis cache: cord-313910-bwe2f7xf.txt plain text: cord-313910-bwe2f7xf.txt item: #498 of 702 id: cord-314072-av3r7it7 author: Liu, Zhuoming title: Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization date: 2020-11-08 words: 1113 flesch: 41 summary: Comparison of escape mutants with S sequence variants isolated in humans. Remarkably, we identified mutants that escaped neutralization by convalescent human sera, suggesting that some humans induce a narrow repertoire of neutralizing antibodies. keywords: cov-2; escape; fig; sars cache: cord-314072-av3r7it7.txt plain text: cord-314072-av3r7it7.txt item: #499 of 702 id: cord-314321-klb8oe9q author: Chen, Serena H. title: Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date: 2020-04-18 words: 3176 flesch: 46 summary: Here, to obtain deeper insights into S protein structure for biological understanding and therapeutic targeting, we employ a combined molecular dynamics (MD) simulation and artificial intelligence (AI) methodology on a series of coronavirus S proteins. To better understand S protein structure keywords: coronavirus; cov-2; domain; fig; protein; protomer; sars; structures cache: cord-314321-klb8oe9q.txt plain text: cord-314321-klb8oe9q.txt item: #500 of 702 id: cord-314329-rzda8x62 author: Wells, Stephen A. title: Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure date: 2020-03-12 words: 4115 flesch: 46 summary: Protein structure is shown as spheres and coloured by amino acid type. Protein structure is shown as spheres and coloured by amino acid type. keywords: crystal; interactions; mode; motion; protease; protein; residues; site; structure cache: cord-314329-rzda8x62.txt plain text: cord-314329-rzda8x62.txt item: #501 of 702 id: cord-314445-4cb4a9r5 author: McNamara, Ryan P. title: High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States date: 2020-06-19 words: 1966 flesch: 27 summary: Influenza Other Respir Viruses Structural basis of receptor recognition by SARS-CoV-2 GISAID: Global initiative on sharing all influenza data -from vision to 609 reality Prospects for inferring very large phylogenies by using the 612 neighbor-joining method Coronavirus Disease 2019 in Children -United States Rapid reconstruction of SARS-CoV-2 using a synthetic 619 genomics platform Aerosol and Surface Stability of SARS-CoV-622 2 as Compared with SARS-CoV-1 Emergence of genomic diversity and recurrent mutations in SARS-626 An outbreak of severe Kawasaki-like disease at the Italian epicentre of the SARS-629 CoV-2 epidemic: an observational cohort study Antigenicity of the SARS-CoV-2 Spike Glycoprotein Receptor Recognition by the Novel 635 Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus Receptor Recognition by the Novel 638 Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is 496 Mediated by the Viral Polymerase and the Proofreading Exoribonuclease The proximal origin of 499 SARS-CoV-2 Presymptomatic SARS-CoV-2 Infections and Transmission in 502 a Skilled Nursing Facility SARS-CoV-2 viral spike G614 mutation exhibits higher case 504 fatality rate Covid-19 in Critically Ill Patients in the Seattle 507 Region -Case Series Genomic variance of the 2019-nCoV coronavirus Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in 512 China: a descriptive study Molecular evolution of the SARS coronavirus during the course of the 515 SARS epidemic in China Detection of 2019 novel coronavirus (2019-nCoV) by real-519 time RT-PCR The species 522 Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-523 Could the D614 G substitution in the 525 SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Coast-to-Coast Spread of SARS-CoV-2 during the Early 529 Epidemic in the United States Phylogenetic network analysis of SARS-531 CoV-2 genomes Genomic epidemiology of hCoV-19 Characterization of the RNA 535 components of a putative molecular switch in the 3' untranslated region of the murine coronavirus 536 genome A live, 538 impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of 539 lethal disease Evaluation of a 541 recombination-resistant coronavirus as a broadly applicable Clinical Characteristics of Coronavirus Disease 2019 in China Nextstrain: real-time tracking of pathogen evolution Temporal dynamics in viral shedding and transmissibility of COVID-19 SARS-CoV-2 Transmission from 554 Presymptomatic Meeting Attendee Faster quantitative real-time PCR protocols may 557 lose sensitivity and show increased variability SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 561 and Is Blocked by a Clinically Proven Protease Inhibitor MAFFT multiple sequence alignment software version 7: 564 improvements in performance and usability Infection and Rapid Transmission of SARS-CoV-2 in Ferrets Functional assessment of cell entry and receptor usage 573 for SARS-CoV-2 and other lineage B betacoronaviruses Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia Efficiency clustering for low-density 579 microarrays and its application to QPCR Antibody responses to SARS-CoV-2 in patients with COVID-19 Genomic Epidemiology of SARS-CoV-2 in Guangdong Province Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins 589 and receptor binding Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins 592 and receptor binding US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe 596 Acute Respiratory Syndrome Coronavirus 2 The neighbor-joining method: a new method for reconstructing 599 phylogenetic trees Burden of respiratory viral infection in persons with 603 human immunodeficiency virus. keywords: coronavirus; cov-2; covid-19; figure; novel; sars; u.s cache: cord-314445-4cb4a9r5.txt plain text: cord-314445-4cb4a9r5.txt item: #502 of 702 id: cord-315702-pn8247j2 author: Sahakijpijarn, Sawittree title: Development of Remdesivir as a Dry Powder for Inhalation by Thin Film Freezing date: 2020-09-22 words: 2305 flesch: 29 summary: Figure 5B 417 demonstrates an expansion of 1H-NMR spectra for selected TFF remdesivir powder formulations and 418 remdesivir unprocessed powder. In conclusion, TFF technology produces high potency remdesivir dry powder formulations for inhalation suitable to treat patients with COVID-19 on an outpatient basis and earlier in the disease course where effective antiviral therapy can reduce related morbidity and mortality. keywords: drug; formulations; freezing; inhalation; powder; remdesivir; tff; water cache: cord-315702-pn8247j2.txt plain text: cord-315702-pn8247j2.txt item: #503 of 702 id: cord-315760-9g8901v6 author: Teng, Xufei title: Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades date: 2020-08-30 words: 3539 flesch: 42 summary: Another notion is that higher MAF within-271 clade mutations (such as MAF>0.2) are mostly non-synonymous mutations, indicating 272 selection at work ( Figure S4 ). Coronaviruses lacking 600 exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and 601 potential therapeutics Rampant C-->U Hypermutation in the Genomes of SARS-CoV-2 and Other 603 Coronaviruses: Causes and Consequences for Their Short-and Long-Term Evolutionary Evidence for host-606 dependent RNA editing in the transcriptome of SARS-CoV-2 A scenario on the stepwise evolution of the genetic code A content-centric organization of the genetic code On the organizational dynamics of the genetic code The pendulum model for genome compositional dynamics: from the four 614 nucleotides to the twenty amino acids An accessory to 616 the 'Trinity': SR-As are essential pathogen sensors of extracellular dsRNA, mediating entry and 617 leading to subsequent type I IFN responses SARS coronavirus pathogenesis: host innate immune responses and 619 viral antagonism of interferon Codon--anticodon pairing: the wobble hypothesis The transcript-centric mutations in human genomes Distinct contributions of replication 624 and transcription to mutation rate variation of human genomes Compositional gradients 627 in Gramineae genes Asymmetric substitution patterns in the two DNA strands of bacteria Comparative analysis of rodent and small 631 mammal viromes to better understand the wildlife origin of emerging infectious diseases Viral load of SARS-CoV-2 in clinical 634 samples Detection of SARS-CoV-2 in Different 636 Types of Clinical Specimens A dynamic 638 nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology On the origin and continuing evolution 641 of SARS-CoV-2 disease and diplomacy: GISAID's innovative 643 contribution to global health A Novel Bat keywords: clade; cov-2; figure; genome; mutations; permutations; sars cache: cord-315760-9g8901v6.txt plain text: cord-315760-9g8901v6.txt item: #504 of 702 id: cord-315982-iuez41zj author: Achdout, Hagit title: COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning date: 2020-10-30 words: 4127 flesch: 48 summary: 10mM compound stocks dissolved in DMSO were provided by Enamine (Ukraine). Non-covalent compounds are also analysed by NMR. keywords: assay; cells; compounds; data; dmso; medium; mpro; pbs; plates; protease; sars; virus cache: cord-315982-iuez41zj.txt plain text: cord-315982-iuez41zj.txt item: #505 of 702 id: cord-317123-0tdfvlqd author: Tan, Xiaotian title: Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples date: 2020-04-21 words: 4164 flesch: 46 summary: First, S1 protein is immobilized on the capillary inner surface through a poly-histidine mediation approach (see Figures S1 and S2(A) for details). To evaluate the differences in antibody's affinity towards SARS-CoV-2 S1 and SARS-CoV S1, we performed a side-by-side study with these two types of S1 proteins for all three clones of antibodies. keywords: antibodies; antibody; cov-2; detection; igg; protein; sars cache: cord-317123-0tdfvlqd.txt plain text: cord-317123-0tdfvlqd.txt item: #506 of 702 id: cord-317523-idji1l0a author: Xu, Huanzhou title: SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway date: 2020-10-27 words: 1196 flesch: 30 summary: With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention. To assess if ORF3a also 135 mediates activation of other prominent inflammasomes including NLRP1 and NLRC4, we 136 depleted each of these molecules but were unable to block cleavage of pro-caspase 1 (Fig.2G) , 137 indicating that ORF3a predominantly activates the NLRP3 inflammasome. keywords: activation; inflammasome; nlrp3; orf3a cache: cord-317523-idji1l0a.txt plain text: cord-317523-idji1l0a.txt item: #507 of 702 id: cord-317628-1inxq7t5 author: Cuccarese, Michael F. title: Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery date: 2020-08-14 words: 9597 flesch: 35 summary: However, the immune system is vastly complex and dependent on cell type and context; reliably intervening in such a highly interdependent process is a formidable drug discovery challenge. Taken together these findings suggest that SARS-CoV-2 entry protease inhibitor activity varies across cell type and species; however, remdesivir and GS-441524 show strong rescue of the viral phenoprint in all cell types tested. keywords: cells; compounds; covid-19; cytokine; data; disease; dose; fig; image; immune; infection; inhibitors; perturbation; phenoprint; response; sars; screening; stimuli; storm; tgf; tnf; type cache: cord-317628-1inxq7t5.txt plain text: cord-317628-1inxq7t5.txt item: #508 of 702 id: cord-318253-vp22xd8p author: Parisi, Ortensia Ilaria title: “Monoclonal-type” plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers date: 2020-05-28 words: 1865 flesch: 21 summary: The biological challenges to recognition Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan Surface functionalization of polypropylene devices with hemocompatible DMAAm and NIPAAm grafts for norfloxacin sustained release Coronaviruses: an overview of their replication and pathogenesis Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig Structure of SARS coronavirus spike receptor-binding domain complexed with receptor Bat-to-human: spike features determining 'host jump'of coronaviruses SARS-CoV, MERS-CoV, and beyond Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding Molecularly imprinted polymers as receptor mimics for selective cell recognition Modified Polyacrylamide Microspheres as Immunosorbent: The genome analysis of the novel coronavirus revealed that it belongs to the subgenus Sarbecovirus of the genus Betacoronavirus and it is closely related (88% identity) to two bat-SARS-like coronavirus (bat-SL-CoVZC45 and bat-SL-CoVZXC21) with which it forms a distinct lineage (Lu et al., 2020; Pradhan et al., 2020) . keywords: coronavirus; protein; sars; spike cache: cord-318253-vp22xd8p.txt plain text: cord-318253-vp22xd8p.txt item: #509 of 702 id: cord-318444-sgm24q1i author: Walter, Justin D. title: Sybodies targeting the SARS-CoV-2 receptor-binding domain date: 2020-05-16 words: 5915 flesch: 38 summary: Concave ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCX-VXVGXXYXGQGTQVTVS Phylogene c tree of RBD sybodies. Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. keywords: binders; binding; cov-2; elisa; fig; fusion; protein; rbd; sars; selection; spike; sybodies; sybody; tbs; vyfp cache: cord-318444-sgm24q1i.txt plain text: cord-318444-sgm24q1i.txt item: #510 of 702 id: cord-318478-fn0gcxbb author: Ziv, Omer title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 words: 5768 flesch: 44 summary: RNA viruses comprise the dominant component of the eukaryotic virome (Dolja and Koonin, 2018) . Genome cyclization plays an essential role in the replication of a number of RNA viruses, including flaviviruses (Hahn et al., 1987; Ziv et al., 2018) . keywords: chimeric; coronavirus; cov-2; et al; figure; genome; interactions; rna; sars; sequence; sgmrna; structure cache: cord-318478-fn0gcxbb.txt plain text: cord-318478-fn0gcxbb.txt item: #511 of 702 id: cord-318499-uihof6k6 author: Beddingfield, Brandon title: The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date: 2020-06-16 words: 1560 flesch: 38 summary: key: cord-318499-uihof6k6 authors: Beddingfield, Brandon; Iwanaga, Naoki; Zheng, Wenshu; Roy, Chad J.; Hu, Tony Y.; Kolls, Jay; Bix, Gregory title: The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.15.153387 sha: doc_id: 318499 cord_uid: uihof6k6 Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting ACE2 binding with the SARS-CoV-2 spike protein. We performed similar assays to investigate ACE2 binding to α5β1, using a mixture of ATN-161 and human ACE2 protein (hACE2). keywords: atn-161; binding; cells; cov-2; sars; spike cache: cord-318499-uihof6k6.txt plain text: cord-318499-uihof6k6.txt item: #512 of 702 id: cord-319100-3gdawhfn author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 words: 4628 flesch: 41 summary: Finally, to establish whether these effects were limited to testing of RNA viruses, a sample of bovine herpesvirus-1 was tested in the same model and range of dilutions. It is also important to recognise that these observations reflect the outcome of contact between viral nucleic acid and VTM for less than 1 hour in each instance. keywords: acid; nucleic; results; rna; samples; sars; transport; virus; vtm cache: cord-319100-3gdawhfn.txt plain text: cord-319100-3gdawhfn.txt item: #513 of 702 id: cord-319447-xanewi59 author: Sun, Jiya title: Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection date: 2020-05-01 words: 3254 flesch: 40 summary: Using time-series profiling of the virus genome and host transcriptome at the same time during SARS-CoV-2 infection coupled with comparative transcriptome analysis, we found that, compared to SARS-CoV and MERS-CoV, SARS-CoV-2 induces strong host cell responses at the very early stage of infection that not only favor its high infectivity to host cells but also restrict its pathogenesis. While recent efforts have been focused on transcriptome analysis of host responses to SARS-CoV-2 infection at a certain time point in certain cell lines [5, 6] , the transcriptional dynamics of host responses to the virus infection has remained largely unexplored. keywords: cells; cov-2; figure; host; infection; mers; sars; virus cache: cord-319447-xanewi59.txt plain text: cord-319447-xanewi59.txt item: #514 of 702 id: cord-320054-wqpr8v3p author: Yuan, Xianlin title: The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date: 2020-08-24 words: 2591 flesch: 51 summary: key: cord-320054-wqpr8v3p authors: Yuan, Xianlin; li, liangping title: The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes date: 2020-08-24 journal: bioRxiv DOI: 10.1101/2020.08.24.264895 sha: doc_id: 320054 cord_uid: wqpr8v3p SARS-CoV-2 has rapidly transmitted worldwide and results in the COVID-19 pandemic. In order to investigate the influences of the above common 9 mutations of 299 S protein on B cell epitopes, we compared the predicted epitopes of reference and 300 mutant S protein, analyzed the association of epitope changes among mutations and 301 determined the influence of mutation on B cell epitopes. keywords: cell; cov-2; epitopes; protein; sars cache: cord-320054-wqpr8v3p.txt plain text: cord-320054-wqpr8v3p.txt item: #515 of 702 id: cord-320165-1b6sycgv author: Guo, Qirui title: Small molecules inhibit SARS-COV-2 induced aberrant inflammation and viral replication in mice by targeting S100A8/A9-TLR4 axis date: 2020-09-09 words: 6781 flesch: 48 summary: For mice infection assay, WT mice were inoculated intranasally with VSV (10 7 PFU), EMCV (10 7 PFU), HSV-1 (10 6 PFU) after anesthesia. For mice infection assay, Ifnar -/mice were inoculated intranasally with MHV-A59 (10 5 PFU) after anesthesia or Ifnar -/mice were inoculated intraperitoneally with MHV-A59 (10 6 PFU). keywords: cov-2; dpi; expression; figure; genes; immune; infection; mhv; mice; neutrophils; s100a8; sars cache: cord-320165-1b6sycgv.txt plain text: cord-320165-1b6sycgv.txt item: #516 of 702 id: cord-320417-01l27d99 author: Wang, Hai-Long title: The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date: 2020-10-14 words: 5014 flesch: 46 summary: The differences in viral clade populations from separate regions are clearly displayed in Figures 4 and 5 . key: cord-320417-01l27d99 authors: Wang, Hai-Long title: The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping date: 2020-10-14 journal: bioRxiv DOI: 10.1101/2020.10.13.338038 sha: doc_id: 320417 cord_uid: 01l27d99 I performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide. keywords: clade; covid-19; genome; inter; mutation; recombination; rna; sars; sequences; sequencing; snp; virus cache: cord-320417-01l27d99.txt plain text: cord-320417-01l27d99.txt item: #517 of 702 id: cord-320490-3jmo35jc author: Ismail, Saba title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 words: 6758 flesch: 46 summary: The count for other salt bridges from TLR3 to MEPVC is in following order: Asp124-Arg706 (mean, 3, max,7 and min,3), Glu98-Lys679 (mean, 5, max,10 and min,4), Asp402-Arg641 (mean, 12, max, 18 and min, 4), Glu146-Arg706 (mean,7 max,11 and min,3), Glu146-Lys679 (mean,5 max,13 and min,2), Glu272-Lys655 Gln722-Side 0.02% The vital hydrogen bond interactions involved between TLR3 receptor and MEPVC shortlisted by VMD were subjected to a novel AFD analysis to elucidate 3D movements of MEPVC atoms with respect to a reference TLR3 residues atom in simulation time. Residue wise decomposition of net binding energy into TLR3 receptor and MEPVC interacting residues. keywords: binding; complex; coronavirus; energy; epitopes; immune; interactions; kcal; mepvc; mol; protein; receptor; residues; sars; spike; structure; system; tlr3; vaccine cache: cord-320490-3jmo35jc.txt plain text: cord-320490-3jmo35jc.txt item: #518 of 702 id: cord-321027-64y43o0y author: Andreano, Emanuele title: Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients date: 2020-05-09 words: 2294 flesch: 41 summary: Supernatants from each cell were tested by ELISA for spike protein binding, and positive antibodies were further tested for neutralization of spike binding to receptor(s) on Vero E6 cells and for virus neutralization in vitro. Single-cell RNA-seq analyses to evaluate the expression levels of ACE2 in different human 73 organs have shown that SARS-CoV-2, through the S-protein, can invade human cells in different 74 major physiological systems including the respiratory, cardiovascular, digestive and urinary 75 systems, thus enhancing the possibility of spreading and infection (7). keywords: antibodies; cov-2; mabs; protein; sars cache: cord-321027-64y43o0y.txt plain text: cord-321027-64y43o0y.txt item: #519 of 702 id: cord-321049-9ozn6il7 author: de Almeida, Paula Rodrigues title: SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR date: 2020-05-01 words: 1312 flesch: 42 summary: In this experiment three primer-probe assays were applied to titrate viral genomic copies per microliter. Additional information about viral titration methods in different samples are necessary to estimate viral pathogenicity, to assess treatment success, estimate viral degree of transmissibility and viral survival in different surfaces and situations. keywords: dpcr; precision; sars cache: cord-321049-9ozn6il7.txt plain text: cord-321049-9ozn6il7.txt item: #520 of 702 id: cord-321050-yabt72jf author: Tuttle, Kathryn D. title: JAK1 inhibition blocks lethal sterile immune responses: implications for COVID-19 therapy date: 2020-04-09 words: 4128 flesch: 37 summary: Remarkably, Dp16 mice were profoundly sensitive to the treatment, which was largely tolerated by WT mice (Figure 2A ). Remarkably, Dp16 mice display lethal immune responses upon challenge with viral mimetic molecules, such as the TLR3 agonist poly-I:C keywords: cytokine; dp16; figure; ifn; immune; liver; mice; p(i; treatment cache: cord-321050-yabt72jf.txt plain text: cord-321050-yabt72jf.txt item: #521 of 702 id: cord-321155-dty18esg author: Zhang, Rongxin title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 words: 4936 flesch: 47 summary: G-Quadruplex Telomere DNA-and TERRA-Binding Protein TLS/FUS G-quadruplex preferentially forms at the very 3′ end of vertebrate telomeric DNA An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance A Gquadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells RNA Gquadruplexes at upstream open reading frames cause DHX36-and DHX9-dependent translation of human mRNAs More Than Just a Kink in Microbial Genomes G-quadruplexes in viruses: function and potential therapeutic applications G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy The SARS-unique domain (SUD) of SARS coronavirus contains two macrodomains that bind G-quadruplexes LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands Anti-HIV-1 activity of the G-quadruplex ligand BRACO-19 Zika Virus Genomic RNA Possesses Conserved G-Quadruplexes Characteristic of the Flaviviridae Family The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA Chemical Targeting of a G-Quadruplex RNA in the Ebola Virus L Gene New scoring system to identify RNA G-quadruplex folding An U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 words: 3506 flesch: 37 summary: Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations. Sequence substitutions were characterised by a preponderance of cytidine to uridine (C->U) transitions. keywords: c->u; changes; coronaviruses; cov-2; fig; rna; sars; sequence; substitutions cache: cord-326257-rcv8sh22.txt plain text: cord-326257-rcv8sh22.txt item: #548 of 702 id: cord-326282-uxn64olw author: Lu, Maolin title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 words: 3272 flesch: 43 summary: 5 The strength of the presented smFRET approach is revealed by the capacity to examine the dynamic properties of the S protein in real time, including: 1) the distinct conformational states that it spontaneously transits under physiological conditions; 2) the impact of sequence alterations on S protein dynamics; and 3) the responses of the S protein to cognate hACE2 receptor and antibody recognition. key: cord-326282-uxn64olw authors: Lu, Maolin; Uchil, Pradeep D.; Li, Wenwei; Zheng, Desheng; Terry, Daniel S.; Gorman, Jason; Shi, Wei; Zhang, Baoshan; Zhou, Tongqing; Ding, Shilei; Gasser, Romain; Prévost, Jérémie; Beaudoin-Bussières, Guillaume; Anand, Sai Priya; Laumaea, Annemarie; Grover, Jonathan R.; Liu, Lihong; Ho, David D.; Mascola, John R.; Finzi, Andrés; Kwong, Peter D.; Blanchard, Scott C.; Mothes, Walther title: Real-time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles date: 2020-09-13 journal: bioRxiv DOI: 10.1101/2020.09.10.286948 sha: doc_id: 326282 cord_uid: uxn64olw SARS-CoV-2 spike (S) mediates entry into cells and is critical for vaccine development against COVID-19. keywords: conformation; cov-2; fig; fret; hace2; protein; rbd; sars cache: cord-326282-uxn64olw.txt plain text: cord-326282-uxn64olw.txt item: #549 of 702 id: cord-326337-s0fp5z1q author: Chan, Kui K. title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants date: 2020-10-19 words: 4597 flesch: 40 summary: Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. 216 Soluble ACE2 2 .v2.4 has three mutations from wild type ACE2: T27Y buried within the RBD 233 interface, and L79T and N330Y at the interface periphery ( Figure 5A) . keywords: ace2; binding; cov-2; decoy; figure; human; mutations; rbd; receptor; sars; type cache: cord-326337-s0fp5z1q.txt plain text: cord-326337-s0fp5z1q.txt item: #550 of 702 id: cord-326380-9ecsp66y author: Griesemer, Sara B title: Assessment of sample pooling for clinical SARS-CoV-2 testing date: 2020-05-27 words: 2239 flesch: 43 summary: To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Methods for pooling vary widely and testing large numbers of pooled samples is not possible without an inherent loss of sensitivity. keywords: detection; pooling; pools; samples; specimens; testing cache: cord-326380-9ecsp66y.txt plain text: cord-326380-9ecsp66y.txt item: #551 of 702 id: cord-326441-w8iyh59u author: Bhattacharjee, Sayan title: Transmission of allosteric response within the homotrimer of SARS-CoV-2 spike upon recognition of ACE2 receptor by the receptor-binding domain date: 2020-09-06 words: 2438 flesch: 36 summary: key: cord-326441-w8iyh59u authors: Bhattacharjee, Sayan; Bhattacharyya, Rajanya; Sengupta, Jayati title: Transmission of allosteric response within the homotrimer of SARS-CoV-2 spike upon recognition of ACE2 receptor by the receptor-binding domain date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.09.06.284901 sha: doc_id: 326441 cord_uid: w8iyh59u The pathogenesis of novel SARS-CoV-2 virus initiates through recognition of ACE2 receptor (Angiotensin-converting enzyme 2) of the host cells by the receptor-binding domain (RBD) located at spikes of the virus. The receptor-binding domain (RBD) that interacts with ACE2 receptor of the host belongs to the S1 subunit, while the S2 subunit anchors on the viral membrane. keywords: ace2; allosteric; binding; protein; rbd; receptor; spike cache: cord-326441-w8iyh59u.txt plain text: cord-326441-w8iyh59u.txt item: #552 of 702 id: cord-326666-melz5fq4 author: Sun, Weitao title: The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe date: 2020-09-03 words: 1726 flesch: 47 summary: Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from 496 Greater Horseshoe Bats through Recombination Expression, post-translational 499 modification and biochemical characterization of proteins encoded by subgenomic mRNA8 of the 500 severe acute respiratory syndrome coronavirus Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal 506 Pneumonia in SARS-CoV-Infected Mice The establishment of reference sequence 508 for SARS-CoV-2 and variation analysis Emerging SARS-CoV-510 2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant The single-cell RNA-seq data analysis on the 537 receptor ACE2 expression reveals the potential risk of different human organs vulnerable to Wuhan 538 2019-nCoV infection Frontiers of Specific ACE2 Expression in Cholangiocytes 540 May Cause Liver Damage After 2019-nCoV Infection Priapism in a 543 patient with coronavirus disease 2019 (COVID-19): A case report Clinical characteristics of 2019 546 novel coronavirus infection in China SARS coronavirus spike protein-induced innate immune 549 response occurs via activation of the NF-κB pathway in human monocyte macrophages in vitro Human Coronavirus: Host-Pathogen Interaction. Compared with SARS-speculated that some genes of the two viruses may also exist in the human genome or that the viruses may 111 may accelerate adaptation in humans through increasing HGS of the ORF6 and ORF8 genes and 112 selecting the M37F mutation. keywords: cov-2; genome; hgs; mutation; sars cache: cord-326666-melz5fq4.txt plain text: cord-326666-melz5fq4.txt item: #553 of 702 id: cord-326736-jd6fvaop author: Bosco-Lauth, Angela M. title: Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats date: 2020-05-29 words: 924 flesch: 21 summary: Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. The remaining two 127 cats were euthanized at 30 DPI and necropsied; these cats will be referred to as contact cats Step qRT-PCR system (Invitrogen), with the following modification; the initial reverse Tissues from cats were fixed in 10% buffered formalin for 12 days and transferred to 70% with their pets, there is minimal risk of a potentially exposed cat infecting another human. keywords: cats; infection; sars; transmission cache: cord-326736-jd6fvaop.txt plain text: cord-326736-jd6fvaop.txt item: #554 of 702 id: cord-326866-nbd4arhx author: Fox, Charles W. title: The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic date: 2020-05-29 words: 1948 flesch: 42 summary: key: cord-326866-nbd4arhx authors: Fox, Charles W. title: The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic date: 2020-05-29 journal: bioRxiv DOI: 10.1101/2020.05.29.123455 sha: doc_id: 326866 cord_uid: nbd4arhx Observations made from papers submitted to preprint servers, and the speculation of editors on social media platforms, suggest that women are submitting fewer papers to scholarly journals than are men during the COVID-19 pandemic. Women were similarly represented among submitting authors (the person who submitted the manuscript to ScholarOne Manuscripts); 39.1% of submitting authors were women (averaged across journals), though this varied among journals from a high of 51.2% to a low of 30.4% ( Figure 1B ). keywords: covid; journals; submissions; women cache: cord-326866-nbd4arhx.txt plain text: cord-326866-nbd4arhx.txt item: #555 of 702 id: cord-326882-bbn1tfq5 author: Li, Quan title: Genetic Variability of Human Angiotensin-Converting Enzyme 2 (hACE2) Among Various Ethnic Populations date: 2020-04-14 words: 1677 flesch: 45 summary: To explore the variability in genetic polymorphisms and expression in human ACE2 (hACE2), we set out to determine if there were any differences between the Asian and Caucasian populations for ACE2 polymorphisms and compare the variability of hACE2 expression in peripheral blood among eight different populations. Further attention has been drawn to the ACE2 receptor as antimalarials, which can interfere with ACE2 expression, have resulted in increased clearing of the SARS-CoV-2 clearance among Covid-19 patients 12. keywords: covid-19; expression; hace2; populations; sars cache: cord-326882-bbn1tfq5.txt plain text: cord-326882-bbn1tfq5.txt item: #556 of 702 id: cord-327431-dnppshnv author: Hognon, Cécilia title: Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses date: 2020-05-27 words: 2465 flesch: 33 summary: However, the removal of the mRNA necessary to produce these signaling factors by viral SUD may impair the apoptosis/survival response pathways allowing massive cell infection. In particular, we can easily distinguish between a first mode of binding in which the G4 mainly interacts with only one SUD monomer, called monomeric binding mode, and a second one in which the nucleic acid is firmly placed at the interface between the two protein monomeric subunits, referred as dimeric binding mode. keywords: binding; domain; mode; rna; sars; sud cache: cord-327431-dnppshnv.txt plain text: cord-327431-dnppshnv.txt item: #557 of 702 id: cord-327520-qj7coqfr author: Wei, Yulong title: Coronavirus genomes carry the signatures of their habitats date: 2020-06-13 words: 1397 flesch: 29 summary: key: cord-327520-qj7coqfr authors: Wei, Yulong; Silke, Jordan R.; Aris, Parisa; Xia, Xuhua title: Coronavirus genomes carry the signatures of their habitats date: 2020-06-13 journal: bioRxiv DOI: 10.1101/2020.06.13.149591 sha: doc_id: 327520 cord_uid: qj7coqfr Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. 209 Next, among 2666 high sequence quality and complete SARS-CoV-2 genomes from CNCB, we records of tissue infection are located in Supplemental File S1). keywords: apobec3; cpg; fig; sars; tissues cache: cord-327520-qj7coqfr.txt plain text: cord-327520-qj7coqfr.txt item: #558 of 702 id: cord-327711-welf0eb1 author: Zhou, Daming title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient date: 2020-06-13 words: 4867 flesch: 45 summary: Surface plasmon resonance (SPR) measurements for EY6A Fab showed high affinity binding to immobilised SARS-CoV-2 RBD (KD = 2 nM, although the value for immobilised EY6A IgG was somewhat higher) as derived from the kinetic data (Methods, Extended Data Fig. 1 , Extended Data Table 1 ). EY6A Fab binds tightly (KD of 2 nM) the receptor binding domain (RBD) of the viral Spike glycoprotein and a 2.6Å crystal structure of an RBD/EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. keywords: ace2; antibody; binding; complex; cov-2; data; epitope; ey6a; fab; fig; rbd; sars; spike; structure cache: cord-327711-welf0eb1.txt plain text: cord-327711-welf0eb1.txt item: #559 of 702 id: cord-327808-k3jec87p author: Zhu, Yunkai title: The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission date: 2020-08-25 words: 2767 flesch: 51 summary: The gene-edited cells were infected with 177 pseudovirus bearing the Sdel virus S protein or, as a control, the glycoprotein of suggest that these genes mediate Sdel virus entry. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. keywords: figure; sars; sdel; virus cache: cord-327808-k3jec87p.txt plain text: cord-327808-k3jec87p.txt item: #560 of 702 id: cord-327912-wfjdxgxh author: Swann, Heather title: Minimal system for assembly of SARS-CoV-2 virus like particles date: 2020-08-24 words: 1698 flesch: 52 summary: S protein appears more highly enriched in cells vs VLPs suggesting that not all expressed S protein is released on VLPs. Notably, nanogold labels not only decorate the VLPs but also proximal areas, suggestive of S protein dissociating from VLPs during surface deposition. keywords: figure; protein; sars; virus; vlps cache: cord-327912-wfjdxgxh.txt plain text: cord-327912-wfjdxgxh.txt item: #561 of 702 id: cord-328073-bqeffvzl author: Limonta, Daniel title: Nodosome inhibition as a novel broad-spectrum antiviral strategy against arboviruses and SARS-CoV-2 date: 2020-11-06 words: 1889 flesch: 46 summary: (D) Cells were counted in 10 different fields for quantitation of infected cells after GSK583 or DMSO treatment. The studies were prompted by the observation that infection of human fetal brain cells with Zika virus (ZIKV) induces expression of nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a host factor that was found to promote ZIKV replication and spread. keywords: cells; cov-2; human; nod2; rna; sars; spectrum cache: cord-328073-bqeffvzl.txt plain text: cord-328073-bqeffvzl.txt item: #562 of 702 id: cord-328187-9zd79gai author: Zhang, Yali title: Virus-free and live-cell visualizing SARS-CoV-2 cell entry for studies of neutralizing antibodies and compound inhibitors date: 2020-07-22 words: 3106 flesch: 48 summary: Cell images 24 involved in Figure 6D and Figure CRBT. At a 21 concentration below than 10 nM, the cMFI of SARS-CoV2-STG was approximately 10-22 fold higher than that of SARS-CoV2-RBG. keywords: cell; cov-2; cov2; crbt; csbt; figure; sars; stg cache: cord-328187-9zd79gai.txt plain text: cord-328187-9zd79gai.txt item: #563 of 702 id: cord-328189-jpkxjn6e author: Brielle, Esther S. title: The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor date: 2020-03-12 words: 2988 flesch: 44 summary: Similar to the SARS-2002 virus, the COVID-19 virus enters the host cell by RBD binding to the host cell ACE2 receptor (7, 11, 12) . MERS RBD structure was taken from the complex with the neutralizing antibody CDC2-C2 (PDB 6C6Z, resolution 2.1Å) and structurally aligned onto SARS-2002 RBD in complex with ACE2 receptor. keywords: ace2; binding; covid-19; fig; interface; rbd; receptor; sars-2002 cache: cord-328189-jpkxjn6e.txt plain text: cord-328189-jpkxjn6e.txt item: #564 of 702 id: cord-328257-kl4wh2zg author: Xu, H title: Hydroxychloroquine increased psychiatric-like behaviors and disrupted the expression of related genes in the mouse brain date: 2020-09-28 words: 4856 flesch: 46 summary: Our results did not reveal a significant effect of HCQ treatment on working memory, but total exploration time was decreased after HCQ administration, which also suggests that the drugs increased anxiety. To the best of our knowledge, this study is the first to test the psychiatric effect of HCQ in an animal model, and our results suggest that, in healthy mice, HCQ administration can induce persistent behavioral changes and disrupt gene expression in the brain. keywords: days; dose; drug; effect; expression; group; hcq; mice; time cache: cord-328257-kl4wh2zg.txt plain text: cord-328257-kl4wh2zg.txt item: #565 of 702 id: cord-328585-1rkrrx8a author: Lu, Shuai title: The immunodominant and neutralization linear epitopes for SARS-CoV-2 date: 2020-08-27 words: 2961 flesch: 39 summary: Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. To assess 8 neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with 178 D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT 179 cells which stably expressed ACE2. keywords: antibodies; cov-2; epitopes; sars; virus cache: cord-328585-1rkrrx8a.txt plain text: cord-328585-1rkrrx8a.txt item: #566 of 702 id: cord-328636-1q71gjwt author: Arora, Kajal title: Multi-Antigenic Virus-like Particle of SARS CoV-2 produced in Saccharomyces cerevisiae as a vaccine candidate date: 2020-05-19 words: 2250 flesch: 46 summary: However, a band at ~80kDa was observed for S protein (Figure 1 ) which is due to detection of the S2 domain of S protein. kDa protein, suggesting cleavage of S protein by the cellular protease into its two fragments, S1 and the S2, which were found to be coexisting together on the microsomal membrane, and would would get incorporated into the a VLP as it assembles at the ER-Golgi interface. keywords: analysis; expression; protein; vaccine; vlp; vlps cache: cord-328636-1q71gjwt.txt plain text: cord-328636-1q71gjwt.txt item: #567 of 702 id: cord-328644-odtue60a author: Comandatore, Francesco title: Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes date: 2020-05-28 words: 6537 flesch: 37 summary: If a functional role for this mutation will be demonstrated, this pattern seems to indicate that different variants might have different fitness when interacting with different host's haplotypes, i.e. in case Asian and European have different haplotypes concerning some of the proteins interacting with the Spike, like for instance Furin. When focusing on single Clades across all macro-regions previously defined, we find a heterogeneous situation with different variants increasing in time in different countries. keywords: coronavirus; et al; frequency; position; present; protein; sars; sequences; spike; time; variants; virus cache: cord-328644-odtue60a.txt plain text: cord-328644-odtue60a.txt item: #568 of 702 id: cord-328659-miujzgtd author: Mishra, Akhilesh title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 words: 6074 flesch: 47 summary: Individual mutations as well as co-occurring mutations can act as lineage defining mutations. A single lineage defining mutation G26144T first reported from North America on the 22 nd January 2020 represents our C1 lineage. keywords: cov-2; defining; editing; figure; genomes; lineage; mutations; nucleotide; rna; sars; sequences; substitutions; virus cache: cord-328659-miujzgtd.txt plain text: cord-328659-miujzgtd.txt item: #569 of 702 id: cord-328695-nptfd6c2 author: Tengs, Torstein title: A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species date: 2020-06-29 words: 1971 flesch: 42 summary: Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function. We have previously reported the presence of a 41-43 nucleotide long hairpin-forming element, referred to as stemloop II-like motif (s2m) keywords: sars; viruses cache: cord-328695-nptfd6c2.txt plain text: cord-328695-nptfd6c2.txt item: #570 of 702 id: cord-328960-46zui1sl author: Hillen, Hauke S. title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 words: 4556 flesch: 54 summary: From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses A new coronavirus associated with human respiratory disease in China A pneumonia outbreak associated with a new coronavirus of probable bat origin The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets Nucleosides for the treatment of respiratory RNA virus infections Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus Race to find COVID-19 treatments accelerates Arguments in favour of remdesivir for treating SARS-CoV-2 infections Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity Viral replication. When added to a minimal RNA substrate (Fig. 1b) , the purified proteins gave rise to RNA-dependent RNA extension activity, which depended on the presence of nsp8 and nsp7 (Fig. 1c) . keywords: buffer; ml-1; nsp12; nsp7; nsp8; rdrp; rna; sars; structure cache: cord-328960-46zui1sl.txt plain text: cord-328960-46zui1sl.txt item: #571 of 702 id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 words: 9327 flesch: 53 summary: Interactive drawing and editing of the RNA secondary structure Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond Simplified Estimation from Censored Normal Samples CONTRAfold: RNA secondary structure prediction without physics-based models Implications of RNA structure on the annealing of a potent antisense RNA directed against the human immunodeficiency virus type 1 MUSCLE: Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. keywords: base; cov-2; dms; et al; figure; fse; genome; rna; sars; sequence; stem; structure; î¼l cache: cord-329102-2y49kcwu.txt plain text: cord-329102-2y49kcwu.txt item: #572 of 702 id: cord-329118-0gq5yusk author: Xiang, Boyu title: ScRNA-seq discover cell cluster change under OAB: ACE2 expression reveal possible alternation of 2019-nCoV infectious pathway date: 2020-06-06 words: 1565 flesch: 45 summary: key: cord-329118-0gq5yusk authors: Xiang, Boyu; Hu, Xiangyu; Li, Haoxuan; Ma, Li; Zhou, Hao; Wei, Ling; Fan, Jue; Zheng, Ji title: ScRNA-seq discover cell cluster change under OAB: ACE2 expression reveal possible alternation of 2019-nCoV infectious pathway date: 2020-06-06 journal: bioRxiv DOI: 10.1101/2020.06.05.137380 sha: doc_id: 329118 cord_uid: 0gq5yusk Objective Previous study indicated that bladder cells which express ACE2 were a potential infection route of 2019-nCov. Result In pubic database (healthy human and mice bladder), ACE2 expression in humans and mice is concentrated in bladder epithelial cells. keywords: ace2; bladder; cells; expression cache: cord-329118-0gq5yusk.txt plain text: cord-329118-0gq5yusk.txt item: #573 of 702 id: cord-329129-t84pu00z author: Zuo, J title: Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection date: 2020-11-02 words: 3502 flesch: 39 summary: A comparative overview Persistence of Antibodies against Middle East Respiratory Syndrome Coronavirus Duration of antibody responses after severe acute respiratory syndrome SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls Recovery from the Middle East respiratory syndrome is associated with antibody and T-cell responses Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals Healthcare workers with mild / asymptomatic SARS-CoV-2 infection show T cell responses and neutralising antibodies after the first wave Circulating CXCR5(+)CXCR3(+)PD-1(lo) It was noteworthy that CD4 T cells responses against SARS-CoV-2 outnumbered CD8 effector cells by ratio of 2 to 1. keywords: cell; cov-2; infection; responses; sars; spike cache: cord-329129-t84pu00z.txt plain text: cord-329129-t84pu00z.txt item: #574 of 702 id: cord-329240-atisrhas author: Fedorenko, Aliza title: Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces date: 2020-06-16 words: 4499 flesch: 43 summary: Thus, RH and hydration conditions are not sufficient to explain virus survival, indicating that the suspended medium, and association with saliva components in particular, likely affect physicochemical properties that determine virus survival. The factors that affect virus survival in droplets that settle on surfaces are complex and not well understood. keywords: microdroplets; saliva; sars; surfaces; survival; virus; viruses; water cache: cord-329240-atisrhas.txt plain text: cord-329240-atisrhas.txt item: #575 of 702 id: cord-329395-4k8js9v2 author: Ratcliff, Jeremy title: Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA date: 2020-07-01 words: 1667 flesch: 35 summary: As determined by 50% endpoint detection, the sensitivities of three RT-qPCRs and nested PCR methods varied substantially depending on the transcript target with no method approaching single copy detection. 19 An alternative, more cost-effective diagnostic method for SARS-CoV-2 RNA is nested PCR. 20 Nested PCR is based on the use of two sequential PCR amplifications wherein the secondary set 21 of primers target sequences nested within the amplicon produced by the first round amplification. keywords: cov-2; detection; pcr; rna; sars cache: cord-329395-4k8js9v2.txt plain text: cord-329395-4k8js9v2.txt item: #576 of 702 id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 words: 4827 flesch: 47 summary: Visualizing an unseen enemy; mobilizing structural biology to counter COVID-19 RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education Announcing the worldwide Protein Data Bank Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation AUSPEX: a graphical tool for X-ray diffraction data analysis The PDB_REDO Server for Macromolecular Structure Model Optimization Errors in protein structures This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. keywords: cov-2; data; errors; map; model; pdb; polymerase; protein; rna; sars; structures cache: cord-329504-91te3nu8.txt plain text: cord-329504-91te3nu8.txt item: #577 of 702 id: cord-329840-f3dsu36p author: Hati, Sanchita title: Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin Converting Enzyme 2 Receptor date: 2020-05-11 words: 2502 flesch: 41 summary: In particular, the interaction of viral spike proteins with ACE2 is a critical step in the viral replication cycle. [3] [4] The role of oxidative stress on the binding of viral proteins on the host cell surface receptors is a relatively underexplored area of biomedical research. keywords: ace2; binding; cov; cov-2; disulfide; protein; sars cache: cord-329840-f3dsu36p.txt plain text: cord-329840-f3dsu36p.txt item: #578 of 702 id: cord-329855-pr7g6ivu author: Kalfaoglu, Bahire title: T-cell hyperactivation and paralysis in severe COVID-19 infection revealed by single-cell analysis date: 2020-05-30 words: 5370 flesch: 41 summary: medRxiv Structure and function of the interleukin 2 receptor: affinity conversion model Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19 Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis Role of Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand in Immune Response to Influenza Virus Infection in Mice TNF Superfamily Networks: bidirectional and interference pathways of the herpesvirus entry mediator (TNFSF14) The Measles Virus Receptor SLAMF1 Can Mediate Particle Endocytosis CD161intCD8+ T cells: a novel population of highly functional, memory CD8+ T cells enriched within the gut A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo Controversies concerning thymus-derived regulatory T cells: fundamental issues and a new perspective Self-antigen-driven activation induces instability of regulatory T cells during an inflammatory autoimmune response Plasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells Signal transducer and activator of transcription 4 limits the development of adaptive regulatory T cells TGF-beta-induced Foxp3 inhibits T(H)17 cell differentiation by antagonizing RORgammat function Functional delineation and differentiation dynamics of human CD4+ T cells expressing the FoxP3 transcription factor The PD-1/PD-L1 Axis and Virus Infections: A Delicate Balance Interleukin-10 production by effector T cells: Th1 cells show self control The Biology of T Regulatory Type 1 Cells and Their Therapeutic Application in Immune-Mediated Diseases IL-10 Receptor Signaling Is Essential for TR1 Cell Function In Vivo IL-10: The Master Regulator of Immunity to Infection Control of regulatory T-cell differentiation and function by T-cell receptor signalling and Foxp3 transcription factor complexes Immunological Genome Project, C. The Immunological Genome Project: networks of gene expression in immune cells Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells Foxp3 controls regulatory T-cell function by interacting with AML1/Runx1 A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme Plasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells Self-antigen-driven activation induces instability of regulatory T cells during an inflammatory autoimmune response Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease Letter to the Editor: Obesity as a risk factor for greater severity of COVID-19 in patients with metabolic associated fatty liver disease Statins induce the accumulation of regulatory T cells in atherosclerotic plaque Regulatory T cells and IL-10 levels are reduced in patients with vulnerable coronary plaques Drug Insight: the role of leptin in human physiology and pathophysiology-emerging clinical applications A Key Role of Leptin in the Control of Regulatory T Cell Proliferation Are Regulatory T Cells Defective in Type 1 Diabetes and Can We Fix Them? Metabolic Pathways in Immune Cell Activation and Quiescence Sugars and fat -A healthy way to generate functional regulatory T cells Control of T(H)17/T(reg) balance by hypoxia-inducible factor 1 Restriction of PD-1 function by cis-PD-L1/CD80 interactions is required for optimal T cell responses Local Blockade of Epithelial PDL-1 in the Airways Enhances T Cell Function and Viral Clearance during Influenza Virus Infection Expression of Programmed Death-1 Ligand (PD-L) 1, PD-L2, B7-H3, and Inducible Costimulator Ligand on Human Respiratory Tract Epithelial Cells and Regulation by Respiratory Syncytial Virus and Type 1 and 2 Cytokines SnapShot: effector and memory T cell differentiation Tissue-Derived Hedgehog Proteins Modulate Th Differentiation and Disease Foxp3-Deficient Regulatory T Cells Do Not Revert into Conventional Effector CD4+ T Cells but Constitute a Unique Cell Subset Comprehensive Integration of Single-Cell Data clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters MO is supported by MRC project grant (MR/S000208/1) and is currently a Visiting Associate Next, we asked if human naïve and memory CD4 + T cells can express FURIN upon receiving TCR signals. keywords: cd25; cd4; cells; covid-19; expression; fig; foxp3; furin; patients cache: cord-329855-pr7g6ivu.txt plain text: cord-329855-pr7g6ivu.txt item: #579 of 702 id: cord-330031-c1n994j6 author: Kratzel, Annika title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date: 2020-03-17 words: 755 flesch: 37 summary: key: cord-330031-c1n994j6 authors: Kratzel, Annika; Todt, Daniel; V’kovski, Philip; Steiner, Silvio; Gultom, Mitra L.; Thao, Tran Thi Nhu; Ebert, Nadine; Holwerda, Melle; Steinmann, Jörg; Niemeyer, Daniela; Dijkman, Ronald; Kampf, Günter; Drosten, Christian; Steinmann, Eike; Thiel, Volker; Pfaender, Stephanie title: Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols date: 2020-03-17 journal: bioRxiv DOI: 10.1101/2020.03.10.986711 sha: doc_id: 330031 cord_uid: c1n994j6 The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 is a major burden for health care systems worldwide. Subsequent 23 regression analysis revealed similar inactivation profiles compared to SARS-CoV, 24 1 pathogenic human CoVs (Fig. 1A) . keywords: hand; sars cache: cord-330031-c1n994j6.txt plain text: cord-330031-c1n994j6.txt item: #580 of 702 id: cord-330213-reb9vo7x author: Miladi, Milad title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 words: 3215 flesch: 47 summary: RNA modifications are essential modulators of RNA stability and function. The recent invention of direct RNA sequencing protocols using nanopores enable unbiased detection of RNA modification. keywords: data; genome; modification; reads; rna; sars; sgrnas; sites; trs cache: cord-330213-reb9vo7x.txt plain text: cord-330213-reb9vo7x.txt item: #581 of 702 id: cord-330337-d41imvo7 author: Basu, Souradip title: Impact of clade specific mutations on structural fidelity of SARS-CoV-2 proteins date: 2020-10-20 words: 6430 flesch: 42 summary: Our final scoring revealed that ORF8 protein mutation L84S was the most disruptive of the mutations under study. In our analyses we have been able to clearly show that mutations caused significant changes in protein structures where highest RMSD value was observed for S protein (5.67), while maximum number of mismatches were observed in case of N protein (24 out of 419). keywords: analysis; binding; cell; cov-2; epitopes; et al; mutant; mutations; protein; sars; score; structures; type cache: cord-330337-d41imvo7.txt plain text: cord-330337-d41imvo7.txt item: #582 of 702 id: cord-330384-yujbcwg5 author: Al-Mulla, Fahd title: A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine date: 2020-05-16 words: 4695 flesch: 43 summary: Finally, our data illustrate a significant correlation between ACE2 variants identified in people from Middle Eastern origins that can be further explored to explain the variation in COVID-19 infection and mortality rates globally. Notably, in our data, Kuwaiti individuals carrying ACE2 missense variants were all males. keywords: ace2; cov-2; furin; gene; populations; protein; receptor; sars; table; tmprss2; variants cache: cord-330384-yujbcwg5.txt plain text: cord-330384-yujbcwg5.txt item: #583 of 702 id: cord-330473-f03ka7bd author: Yuan, Meng title: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV date: 2020-03-14 words: 1573 flesch: 52 summary: A recent study has shown that CR3022, which is a human 49 neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4), can bind to the RBD of SARS-CoV-2 (5). In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. keywords: binding; cr3022; rbd; sars cache: cord-330473-f03ka7bd.txt plain text: cord-330473-f03ka7bd.txt item: #584 of 702 id: cord-330743-o11d0aa1 author: Yu, Xi title: Broad-spectrum virucidal activity of bacterial secreted lipases against flaviviruses, SARS-CoV-2 and other enveloped viruses date: 2020-05-25 words: 4488 flesch: 47 summary: Incubation of the culture supernatant but not the bacterial lysates resulted in significant suppression of DENV ( Figure 1B ) and ZIKV ( Figure 1C ) infectivity in Vero cells, indicating that an extracellular effector(s) secreted by Csp_BJ was responsible for viral inhibition. Either the upper retentate (proteins and large peptides) or the lower liquid filtrate (small molecule compounds and short peptides) was mixed with the viruses for incubation in Vero cells ( Figure 1D ). keywords: activity; cbae-1; cbaes; cells; denv; figure; infection; viral; virus; zikv cache: cord-330743-o11d0aa1.txt plain text: cord-330743-o11d0aa1.txt item: #585 of 702 id: cord-331611-pwj226j0 author: Shrimp, Jonathan H. title: An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 date: 2020-06-23 words: 3907 flesch: 37 summary: Meyer et al. examined several peptide AMC substrates for TMPRSS2 and used a biochemical assay to assess modified peptide substrates as TMPRSS2 inhibitors, some with observed inhibition constants of approximately 20 nM 13 . A validated inhibitor of TMPRSS2 protease activity would be a valuable tool for studying the impact TMPRSS2 has in viral entry and potentially be an effective antiviral therapeutic. keywords: activity; amc; assay; cov-2; inhibitor; nafamostat; preprint; sars; tmprss2 cache: cord-331611-pwj226j0.txt plain text: cord-331611-pwj226j0.txt item: #586 of 702 id: cord-331680-qlzhtxs0 author: Goryachev, A.N. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 words: 4113 flesch: 43 summary: antisense oligonucleotides consists in administering to the body of the patient a drug containing single-strand DNA chains which is complementary to any site of single-strand DNA or RNA, for example, virus RNA. Table 2 Genetic target sequences of the coronavirus genome for TRS1 and TRS2 drugs Name Nucleotide sequence of virus RNA (5 '-3') site trs1 GATCTGTTCTCTAAACGAAC site trs2 CTGTTCTCTAAACGAACTTTA * keywords: antisense; cells; drug; oligonucleotide; rna; sars; sequence; study; virus cache: cord-331680-qlzhtxs0.txt plain text: cord-331680-qlzhtxs0.txt item: #587 of 702 id: cord-331701-izkz1hz4 author: Eden, John-Sebastian title: An emergent clade of SARS-CoV-2 linked to returned travellers from Iran date: 2020-03-17 words: 1273 flesch: 40 summary: Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases. keywords: cov-2; data; iran; sars; sequencing cache: cord-331701-izkz1hz4.txt plain text: cord-331701-izkz1hz4.txt item: #588 of 702 id: cord-331786-wgt7kg6f author: Diego-Martin, Borja title: Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities date: 2020-10-13 words: 7052 flesch: 38 summary: We carried out a final agroinfiltration for recombinant antibody production using a total of 112 plants, equivalent to approximately 2.5 kilograms of fresh plant material. For antibody production we used wild-type and RNAi ΔXT/FT glycoengineered N. benthamiana plant lines, the latter lacking plantspecific Xylose and Fucose glycosylation (Strasser et al., 2008) . keywords: agroinfiltration; antibodies; antibody; benthamiana; buffer; cov-2; expression; fig; plant; production; protein; rbd; sars; scale cache: cord-331786-wgt7kg6f.txt plain text: cord-331786-wgt7kg6f.txt item: #589 of 702 id: cord-331888-lbtuvdv3 author: de Souza, Dalton Garcia Borges title: Forecasting COVID-19 cases at the Amazon region: a comparison of classical and machine learning models date: 2020-10-09 words: 2435 flesch: 55 summary: All those numbers caught the attention of many researchers, that presented models 11 to attend the concerns from the Brazilian government and population, such as when the 12 outbreak will peak, how long it will last, and how many will be infected or die [4, 5] . In each pair of models we can observe how the Holt-Winters perform in comparison 214 to an other model and considering the periods we classify as (1) exponential increasing, 215 (2) after sudden daily decreasing and (3) stability of daily new cases. keywords: arima; cases; covid-19; data; forecasting; models; regression cache: cord-331888-lbtuvdv3.txt plain text: cord-331888-lbtuvdv3.txt item: #590 of 702 id: cord-332134-88wfcc3y author: Li, Tingting title: A potent synthetic nanobody targets RBD and protects mice from SARS-CoV-2 infection date: 2020-09-24 words: 2070 flesch: 43 summary: Taken together, SR4 169 and MR17, and probably MR3, neutralize SARS-CoV-2 by competitively blocking the For biparatopic fusion, we first identified two sybodies, namely LR1 and LR5 (Fig. 208 3A, 3B), that could bind RBD in addition to MR3 using the BLI assay. The results showed that MR3 could block ACE2 (Fig. 2G) , and SR4 167 and MR17 (Fig. 2H, 2I) , suggesting it also binds to at least part of the RBM, although 168 the possibility of allosteric inhibition remains to be investigated. keywords: binding; cov-2; fig; mr17; mr3; rbd; sars cache: cord-332134-88wfcc3y.txt plain text: cord-332134-88wfcc3y.txt item: #591 of 702 id: cord-332178-0xyrmk5a author: Chadchan, Sangappa B. title: The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization date: 2020-06-24 words: 2459 flesch: 37 summary: SUMMARY ANSWER ACE2 protein is highly expressed in human endometrial stromal cells during the secretory phase and is essential for human endometrial stromal cell decidualization. The effect of ACE2 knockdown on morphological and molecular changes of human endometrial stromal cell decidualization were assessed. keywords: ace2; angiotensin; cells; decidualization; expression; human; sars; stromal cache: cord-332178-0xyrmk5a.txt plain text: cord-332178-0xyrmk5a.txt item: #592 of 702 id: cord-332185-a96r1k7a author: Zhang, Shuyuan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 words: 1234 flesch: 44 summary: The overall structures of homotrimeric RaTG13 and PCoV_GX spikes resemble the 107 previously reported pre-fusion structures of coronavirus spikes (Fig. 1A ). key: cord-332185-a96r1k7a authors: Zhang, Shuyuan; Qiao, Shuyuan; Yu, Jinfang; Zeng, Jianwei; Shan, Sisi; Lan, Jun; Tian, Long; Zhang, Linqi; Wang, Xinquan title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.21.307439 sha: doc_id: 332185 cord_uid: a96r1k7a In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. keywords: cov-2; rbd; receptor; sars; spike cache: cord-332185-a96r1k7a.txt plain text: cord-332185-a96r1k7a.txt item: #593 of 702 id: cord-332271-slouuryl author: Baker, Jeremy D. title: A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease date: 2020-08-27 words: 2694 flesch: 41 summary: Infection usually resolves without active medical intervention, but for a subset of 46 cases infection can progress to viral pneumonia and a variety of complications including acute lung 47 targetable activities for COVID-19, the coronavirus Mpro seems a likely choice for rapid drug 66 To accelerate drug development we employed a drug repurposing strategy, an approach of utilizing 68 previously approved drugs for new indications 12,13 . Based upon previous successful antiviral drug development for HIV-1 and hepatitis C, the SARS-CoV-2 main protease (Mpro) appears an attractive target for drug development. keywords: compounds; drug; mpro; protease; repurposing; sars; screen cache: cord-332271-slouuryl.txt plain text: cord-332271-slouuryl.txt item: #594 of 702 id: cord-332374-cbiw6yvb author: Israeli, Ofir title: Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction date: 2020-06-10 words: 1052 flesch: 47 summary: COVID-19 genetic diagnostics process include RNA extraction from Oronasopharyngeal swabs followed by reverse transcriptase quantitative PCR (RT-qPCR) targeting viral genes [2] . Potentially, eliminating RNA extraction would greatly simplify the diagnostic procedure, reducing both cost and time to answer, while allowing testing to continue in case of reagent shortages. keywords: extraction; rna; samples cache: cord-332374-cbiw6yvb.txt plain text: cord-332374-cbiw6yvb.txt item: #595 of 702 id: cord-332539-v1bfm57x author: Gohl, Daryl M. title: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2 date: 2020-05-11 words: 5055 flesch: 46 summary: The tailed amplicon approach, developed here, enriches first strand cDNA using ARTIC v3 primers containing adapter tails. We thank Sean Wang and Matt Plumb from the Minnesota Department of Heath for helpful discussions and for sharing ARTIC v3 primers. keywords: amplicon; artic; cov-2; coverage; figure; read; samples; sars; sequencing cache: cord-332539-v1bfm57x.txt plain text: cord-332539-v1bfm57x.txt item: #596 of 702 id: cord-333089-ufyzqgqk author: Aguilar-Pineda, Jorge Alberto title: Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry date: 2020-07-29 words: 6978 flesch: 45 summary: Our findings that estrogens interfere with S protein and ACE2 interactions in silico that is associated with reduced S protein uptake in an in vitro model of SARS-CoV-2 infectivity in cultured human endothelial cells are consistent with prior studies demonstrating that estrogens have antiviral properties against HIV, Ebola and hepatitis viruses 33 . We then examined the ability of estrogen molecules to interfere with S protein uptake into pulmonary epithelial cells using an in vivo model of SARS-CoV2 infectivity. keywords: 17β; ace2; cells; cov-2; diol; entry; equol; estrogen; figure; glycan; interactions; molecules; protein; rbd; receptor; residues; sars cache: cord-333089-ufyzqgqk.txt plain text: cord-333089-ufyzqgqk.txt item: #597 of 702 id: cord-333420-qqyg9um9 author: Zhu, Xun title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date: 2020-10-09 words: 462 flesch: 44 summary: key: cord-333420-qqyg9um9 authors: Zhu, Xun; Chang, Ti-Cheng; Webby, Richard; Wu, Gang title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates date: 2020-10-09 journal: bioRxiv DOI: 10.1101/2020.10.08.330456 sha: doc_id: 333420 cord_uid: qqyg9um9 idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Nextflow enables reproducible computational workflows An interactive web-based dashboard to track COVID-19 in real time GISAID -Clade and lineage nomenclature aids in genomic epidemiology of active hCoV-19 139 viruses Haplotype-based variant detection from short-read sequencing Introductions and early spread of SARS-CoV-2 in the New York City area Year-letter Genetic Clade Naming for SARS-CoV-2 on Nextstain.org Datahike is a durable Datalog database powered by an 147 efficient Datalog query engine Clinical and virological data of the first cases of COVID-19 in Europe: a case series The Lancet Infectious Fast and accurate short read alignment with Burrows-Wheeler transform The sequence alignment/map format and SAMtools Tracking the COVID-19 pandemic in Australia using genomics A new coronavirus associated with human respiratory disease in China keywords: covid-19; sars cache: cord-333420-qqyg9um9.txt plain text: cord-333420-qqyg9um9.txt item: #598 of 702 id: cord-333703-1ku3jc9s author: Kraus, Aurora title: A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2 date: 2020-11-08 words: 8459 flesch: 39 summary: 521 Interestingly, we did not observe any changes in ace2 expression after 3h immersion with SARS-522 CoV-2 S RBD protein. 300 There are copious amounts of immune cells in the teleost olfactory organ ( Intranasal delivery of SARS-CoV-2 S RBD induces inflammatory responses and 318 widespread loss of olfactory receptor expression in adult zebrafish olfactory organ 319 320 The cellular landscape of the zebrafish olfactory epithelium was affected by SARS-CoV-2 S 321 RBD treatment and time ( Figure 4A -D). keywords: ace2; cell; cov-2; covid-19; et al; expression; figure; gene; infection; larvae; olfactory; protein; rbd; responses; s rbd; sars; treatment; type; zebrafish cache: cord-333703-1ku3jc9s.txt plain text: cord-333703-1ku3jc9s.txt item: #599 of 702 id: cord-334220-sqvfr31q author: Messina, Francesco title: Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome date: 2020-11-03 words: 4228 flesch: 28 summary: We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. The ubiquitin proteasome system deletes viral proteins to control the infection, but the virus can use them for its propagation (34) . keywords: cov-2; covid-19; host; human; infection; interactions; interactome; pathways; patients; proteins; sars cache: cord-334220-sqvfr31q.txt plain text: cord-334220-sqvfr31q.txt item: #600 of 702 id: cord-334300-hnrmaytm author: Ventura Fernandes, Bianca H title: Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date: 2020-10-20 words: 1803 flesch: 24 summary: key: cord-334300-hnrmaytm authors: Ventura Fernandes, Bianca H; Feitosa, Natália Martins; Barbosa, Ana Paula; Bomfim, Camila Gasque; Garnique, Anali M. B.; Gomes, Francisco I. F.; Nakajima, Rafael T.; Belo, Marco A. A.; Eto, Silas Fernandes; Fernandes, Dayanne Carla; Malafaia, Guilherme; Manrique, Wilson G.; Conde, Gabriel; Rosales, Roberta R. C.; Todeschini, Iris; Rivero, Ilo; Llontop, Edgar; Sgro, German G.; Oka, Gabriel Umaji; Bueno, Natalia F; Ferraris, Fausto K.; de Magalhaes, Mariana T. Q.; Medeiros, Renata J.; Gomes, Juliana M. M; de Souza Junqueira, Mara; Conceição, Katia; Pontes, Letícia G.; Condino-Neto, Antonio; Perez, Andrea C.; Barcellos, Leonardo J. G.; Correa junior, Jose Dias; Dorlass, Erick G.; Camara, Niels O. S; Durigon, Edison Luiz; Cunha, Fernando Q.; Nóbrega, Rafael H.; Machado-Santelli, Glaucia M.; Farah, Chuck; Veras, Flávio P; Galindo-Villegas, Jorge; Costa-Lotufo, Leticia; Cunha, Thiago M.; Chammas, Roger; Guzzo, Cristiane R.; Carvalho, Luciani R; Charlie-Silva, Ives title: Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction date: 2020-10-20 journal: bioRxiv DOI: 10.1101/2020.10.20.346262 sha: doc_id: 334300 cord_uid: hnrmaytm Establishing new experimental animal models to assess the safety and immune response to the antigen used in the development of COVID-19 vaccine is an imperative issue. The zebrafish reference genome sequence 906 and its relationship to the human genome Zebrafish as an 909 alternative animal model in human and animal vaccination research Potential of mucoadhesive 912 nanocapsules in drug release and toxicology in zebrafish Zebrafish as tools for drug discovery Developing Covid-19 Vaccines at 917 Pandemic Speed A Comprehensive Review of Animal Models 920 for Coronaviruses: SARS-CoV-2, SARS-CoV, and MERS-CoV Comparison of SARS-CoV-2 923 infections among 3 species of non-human Affiliations Non-invasive bioluminescence imaging of HCoV-925 OC43 infection and therapy in the central nervous system of live mice An alpaca nanobody neutralizes 928 SARS-CoV-2 by blocking receptor interaction Equine hyperimmune globulin raised 931 against the SARS-CoV-2 spike glycoprotein has extremely high neutralizing 932 titers Development of a 934 hyperimmune equine serum therapy for COVID-19 in Argentina Serological survey of SARS-CoV-2 for experimental, 937 domestic, companion and wild animals excludes intermediate hosts of 35 938 different species of animals The Zebrafish Disease and Drug Screening Model: A Strong 941 Ally Against Covid-19 Tracking Mechanisms of Viral Dissemination In Vivo A Contemporary View of Coronavirus 946 Antibody responses to SARS-CoV-2 in 948 patients with COVID-19 Maternal transfer and protective role of 951 antibodies in zebrafish Danio rerio Role of maternally derived immunity in fish Breast Milk-fed Infant of COVID-956 19  SARS-CoV-2 S1 and S2 subunits-and nucleocapsid protein-reactive SIgM/IgM IgA antibodies in human milk Acute transverse myelitis after 963 COVID-19 pneumonia Pathological findings of COVID-19 associated with 966 acute respiratory distress syndrome Patients -An MRI-based 3-month Follow-up Study Cerebral Venous Thrombosis Associated 972 with COVID-19 Effects of COVID-19 on the Nervous System Respiratory Syndrome Coronavirus Infection Causes Neuronal Death in the 981 Absence of Encephalitis in Mice Transgenic for Human ACE2 Pathological study of the 2019 novel coronavirus 984 disease (COVID-19) through postmortem core biopsies COVID-19 Infection 987 and Neurological Complications: Present Findings and Future Predictions COVID-19-associated acute necrotizing 990 myelitis Pathogenesis and Diagnosis of Viral 993 Infections of the Nervous System Neurologic and Radiographic Findings 996 Associated With COVID-19 Infection in Children keywords: animal; cov-2; covid-19; human; sars; study; zebrafish cache: cord-334300-hnrmaytm.txt plain text: cord-334300-hnrmaytm.txt item: #601 of 702 id: cord-334313-v2syspu6 author: Long, S. Wesley title: Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas date: 2020-05-03 words: 4531 flesch: 42 summary: GISAID sequences containing greater than 1% N characters, and Houston sequences with greater than 5% N characters were removed from consideration. Machine learning models were trained to predict patient metadata categories including mortality, length of stay, inpatient versus outpatient status, ICU admission, overall outcome, gender, age, and ethnicity from viral sequence data. keywords: acid; amino; cov-2; covid-19; disease; houston; patients; sars; strains; viral; virus cache: cord-334313-v2syspu6.txt plain text: cord-334313-v2syspu6.txt item: #602 of 702 id: cord-334394-qgyzk7th author: Edgar, Robert C. title: Petabase-scale sequence alignment catalyses viral discovery date: 2020-08-10 words: 8139 flesch: 49 summary: Innovative fields such as high-throughput functional viromics [39] leverage these broad and rapidly growing collections of viral sequences, and can inform evidence-based policies responding to emerging pandemics [40, 41] . Accurate annotation of CoV genomes is challenging due to ribosomal frameshifts and polyproteins which are cleaved into maturation proteins [56] , and thus previously-annotated viral genomes offer a guide to accurate gene-calls and protein functional predictions. keywords: alignment; annotation; assembly; contigs; cov; coverage; data; family; figure; genome; identity; rdrp; reads; reference; rna; sequence; sequencing; serratus; sra; study; tree; virus cache: cord-334394-qgyzk7th.txt plain text: cord-334394-qgyzk7th.txt item: #603 of 702 id: cord-334584-xh41koro author: Dilucca, Maddalena title: Temporal evolution and adaptation of SARS-COV 2 codon usage date: 2020-05-29 words: 3958 flesch: 49 summary: It is tempting to speculate that N gene accumulates mutations that are do not affect its structure and function, but rather enable it to evade the host's immune responses and enhance SARS-CoV-2's pathogenicity. RSCU measures codon usage bias within a family of synonymous codons. keywords: codon; codon usage; cov-2; genes; proteins; sars; usage; values cache: cord-334584-xh41koro.txt plain text: cord-334584-xh41koro.txt item: #604 of 702 id: cord-334624-chnibsa1 author: Hayn, Manuel title: Imperfect innate immune antagonism renders SARS-CoV-2 vulnerable towards IFN-γ and -λ date: 2020-10-30 words: 5379 flesch: 46 summary: Our data showed that ORF3a and ORF7a are the most potent autophagy antagonists of SARS-CoV-2 206 ( Fig. SARS-CoV-1 ORF6 is about 4-fold less potent in antagonizing type I IFN signaling (Fig. 243 4b) but induces higher levels of autophagy (Fig. 4c) . keywords: autophagy; cov-2; fig; ifn; nsp15; orf3a; proteins; sars; signaling; treatment; type cache: cord-334624-chnibsa1.txt plain text: cord-334624-chnibsa1.txt item: #605 of 702 id: cord-334891-4jgtxg07 author: Choudhury, Abhigyan title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 words: 2937 flesch: 43 summary: The Brazilian Journal of Infectious Diseases Recognition of GU-rich polyadenylation regulatory 13 elements by human CstF-64 protein Coronavirus infections and immune responses The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 18 (SARS CoV-2 or n-COV19), the Cause of COVID-19 Identifying discriminative classification-based motifs 21 in biological sequences Learning Framework for 1 Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary 2 Information Predicting RNA-Protein Interactions Using Only 5 Sequence Information HDOCK: a web server for protein-protein 8 and protein-DNA/RNA docking based on a hybrid strategy PLIP: fully automated 11 protein-ligand interaction profiler iMODS: internal coordinates 14 normal mode analysis server Designing of a novel multi-epitope peptide based 17 vaccine against Brugia malayi: 15 Our study focuses principally on the interactions of the intracellular TLRs with the mRNA 16 fragments, and molecular docking studies play a pivotal role in this study by precisely Table S1 . keywords: binding; complex; cov-2; figure; mrna; protein; sars; studies; tlrs cache: cord-334891-4jgtxg07.txt plain text: cord-334891-4jgtxg07.txt item: #606 of 702 id: cord-335075-6wo2o5pp author: Bangaru, Sandhya title: Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate date: 2020-08-06 words: 4725 flesch: 40 summary: SARS: the first pandemic of the 21st century A Novel Coronavirus from Patients with Pneumonia in China Mechanisms of coronavirus cell entry mediated by the viral spike protein SARS-CoV-2 SPIKE PROTEIN: an optimal immunological target for vaccines SARS-CoV-2 Vaccines: Status Report Developing Covid-19 Vaccines at Pandemic Speed Structure, Function, and Evolution of Coronavirus Spike Proteins Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex The proximal origin of SARS-CoV-2 A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients Human coronaviruses OC43 and HKU1 bind to 9-O-acetylated sialic acids via a conserved receptor-binding site in spike protein domain A Identification of sialic acid-binding function for the Middle East respiratory syndrome coronavirus spike glycoprotein Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors Structural basis of receptor recognition by SARS-CoV-2 Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis. Initial 2D classifications revealed the presence of 2 distinct classes: free spike trimers and dimers of trimers ( Figure 2A ). keywords: binding; conformation; cov-2; figure; glycans; protein; residues; sars; spike; structure; trimers cache: cord-335075-6wo2o5pp.txt plain text: cord-335075-6wo2o5pp.txt item: #607 of 702 id: cord-335118-oa9jfots author: Taka, E. title: Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor date: 2020-09-21 words: 5314 flesch: 50 summary: In SMD simulations of SARS-CoV-2, Cα atoms of ACE2 residues S19-S43, T78-P84, Q325-N330, G352-I358, and P389-R393 were kept fixed, whereas Cα atoms of RBD residues K417-I418, G446-F456, Y473-A475, and N487-Y505 were steered (Fig. 3A) . CR1 releasing last when SARS-CoV-2 RBD was pulled away from ACE2 PD. keywords: ace2; binding; cov-2; cr1; fig; interactions; protein; rbd; sars; simulations cache: cord-335118-oa9jfots.txt plain text: cord-335118-oa9jfots.txt item: #608 of 702 id: cord-335443-iv2gs3kg author: Kim, Youngchang title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 words: 5475 flesch: 48 summary: Protein science : a publication of the Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease Trifluridine/Tipiracil (Lonsurf) for the Treatment of Metastatic Colorectal Cancer Turkey coronavirus non-structure protein NSP15--an endoribonuclease The severe acute respiratory syndrome coronavirus Nsp15 protein is an endoribonuclease that prefers manganese as a cofactor Mutational analysis of the SARS virus Nsp15 endoribonuclease: identification of residues affecting hexamer formation Functional plasticity of antibacterial EndoU toxins Structural and functional analyses of the severe acute respiratory syndrome coronavirus endoribonuclease Nsp15 Major genetic marker of nidoviruses encodes a replicative endoribonuclease Bovine pancreatic ribonuclease: fifty years of the first enzymatic reaction mechanism Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism Bovine pancreatic ribonuclease A as a model of an enzyme with multiple substrate binding sites Crystal structure of ribonuclease A.d(ApTpApApG) complex. Tipiracil, an uracil derivative, binds to Nsp15 uracil site in a manner consistent with competitive inhibition. keywords: base; binding; cov-2; endoribonuclease; fig; nsp15; rna; rnase; sars; site; structures; tipiracil; uracil cache: cord-335443-iv2gs3kg.txt plain text: cord-335443-iv2gs3kg.txt item: #609 of 702 id: cord-335652-v98gv5uf author: Salazar, Cecilia title: Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay date: 2020-05-10 words: 2077 flesch: 41 summary: Sequencing of SARS-CoV-2 positive samples was performed according to the primalseq [5] approach on the MinION sequencing platform (Oxford Nanopore Technologies, United Kingdom) using the V2 primer pools. The application of rapid genomic epidemiology during local outbreaks allows to identify main routes of virus introduction and estimate spatio-temporal dynamics which can be used to improve contingency measures. keywords: cov-2; covid-19; sars; sequencing; uruguay cache: cord-335652-v98gv5uf.txt plain text: cord-335652-v98gv5uf.txt item: #610 of 702 id: cord-336012-8klkojpo author: Harilal, Divinlal title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 words: 3042 flesch: 36 summary: Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. Even with higher throughput sequencing (NovaSeq SP flowcell), shotgun sequencing requires an allocation of 1TB of data for ~250 sequenced samples. keywords: cost; cov-2; data; genome; sars; sequencing; table; usa; virus cache: cord-336012-8klkojpo.txt plain text: cord-336012-8klkojpo.txt item: #611 of 702 id: cord-336343-qbcb9qi3 author: Agarwal, Ajay title: in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA date: 2020-06-16 words: 2333 flesch: 53 summary: AllerTOP v2 (https://www.ddg-pharmfac.net/AllerTOP/) was used for determining the allergenicity of selected epitopes. For MHC Class-I T-cell epitope prediction for ORF1ab leader proteins, NetMHCpan EL 4.0 method was used. keywords: analysis; cell; class; epitopes; mhc; proteins cache: cord-336343-qbcb9qi3.txt plain text: cord-336343-qbcb9qi3.txt item: #612 of 702 id: cord-336522-y9nzsv95 author: Rosenke, Kyle title: Inhibition of SARS-CoV-2 in Vero cell cultures by peptide-conjugated morpholino-oligomers date: 2020-09-30 words: 1726 flesch: 41 summary: Using an MOI of 0.01, virus growth rose steadily and reached peak growth at 72 hrs post-136 infection ( Fig. 1B and H) AUG PPMO was not nearly as effective as the other 4 antiviral PPMO used in this study ( Figure 146 1C and I). 35 Results: PPMO designed to base-pair with sequence in the 5'-terminal region or the leader 36 transcription regulatory sequence-region of SARS-CoV-2 genomic RNA were highly 37 efficacious, reducing viral titers by up to 4-6 log10 in cell cultures at 48-72 hours post-infection, 38 in a non-toxic and dose-responsive manner. keywords: cell; cov-2; ppmo; sars; sequence cache: cord-336522-y9nzsv95.txt plain text: cord-336522-y9nzsv95.txt item: #613 of 702 id: cord-336560-m5u6ryy9 author: Boudewijns, Robbert title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 words: 5039 flesch: 37 summary: Of note, these receptor knockouts did not affect ACE2 expression in hamster lungs (Fig. S9A ), while interferon-stimulated genes (ISG) 27 such as MX-2 (strongly induced by IFNα/STAT2 signaling) and IP-10 (induced by both type I and type II IFNs) showed a differential expression pattern when comparing the different genotypes, triggered by SARS-CoV-2 infection (Fig. S9B) . The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . keywords: covid-19; disease; fig; hamsters; infection; interferon; levels; lung; mice; rna; sars; stat2; type; virus cache: cord-336560-m5u6ryy9.txt plain text: cord-336560-m5u6ryy9.txt item: #614 of 702 id: cord-336628-0evl3wnd author: Neufeldt, Christopher J. title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 words: 5906 flesch: 41 summary: One hour after infection cells were treated with the indicated drugs at the given concentrations. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. keywords: activation; cells; cgas; cov-2; infection; levels; response; rna; sars; sting; virus cache: cord-336628-0evl3wnd.txt plain text: cord-336628-0evl3wnd.txt item: #615 of 702 id: cord-336793-9bbyu1qx author: Matsuyama, Shutoku title: The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells date: 2020-08-24 words: 713 flesch: 52 summary: These observations indicate that the suppressive effect of ciclesonide on viral replication is specific to coronaviruses, highlighting it as a candidate drug for the treatment of COVID-19 patients. A novel coronavirus from patients with 301 pneumonia in China Drug treatment options for the 2019-new coronavirus (2019-nCoV) Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-306 nCoV) in vitro The inhaled corticosteroid ciclesonide blocks coronavirus RNA replication by targeting viral Therapeutic 351 potential of ciclesonide inahalation for COVID-19 pneumonia: keywords: ciclesonide; replication cache: cord-336793-9bbyu1qx.txt plain text: cord-336793-9bbyu1qx.txt item: #616 of 702 id: cord-336938-03366q9t author: Thacker, Vivek V title: Rapid endothelialitis and vascular inflammation characterise SARS-CoV-2 infection in a human lung-on-chip model date: 2020-08-10 words: 2822 flesch: 34 summary: NRP1 expression was between one and four orders of magnitude higher than ACE2 expression both in monoculture and on-chip (Fig. S1A, 1D) , with a10-fold higher expression in endothelial cells compared to epithelial cells that was retained on-chip ( Fig S1B) . Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses The protein expression profile of ACE2 in human tissues Upregulation of angiotensin converting enzyme 2 by shear stress reduced inflammation and proliferation in vascular endothelial cells Neuropilin-1/ keywords: cells; dpi; endothelial; epithelial; fig; human; infection; sars cache: cord-336938-03366q9t.txt plain text: cord-336938-03366q9t.txt item: #617 of 702 id: cord-337701-56tmg38b author: Xiao, Yan title: Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2 date: 2020-07-06 words: 2124 flesch: 41 summary: For the ORF 1b gene assay, the CVs of mean Ct 145 values were 0.26%-4.45%, 0.29%-1.76%, 0.71%-6.52% in intra-assay, and 146 2.17%-5.12%, 0.30-1.57%, 2.63%-4.34% in inter-assay of IPBCAMS assays, WHO 147 assays, and CCDC assays, respectively. A LOD of 10 genomic copies per 127 reaction was observed for both the N gene assay and the ORF 1b gene assay of all the 128 three qRT-PCR assays, although the Ct values for N gene assay of WHO assays and 129 ORF 1b gene assay of CCDC assays were higher than 35 cycles (Table 2) . keywords: assays; gene; pcr cache: cord-337701-56tmg38b.txt plain text: cord-337701-56tmg38b.txt item: #618 of 702 id: cord-337973-djqzgc1k author: Hao, Siyuan title: Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium date: 2020-08-28 words: 2632 flesch: 36 summary: Methods for establishing 575 primary cultures Well-differentiated 577 human airway epithelial cell cultures Culturing the unculturable: human coronavirus HKU1 580 infects, replicates, and produces progeny virions in human ciliated airway epithelial cell cultures Systematic 599 assembly of a full-length infectious clone of human coronavirus NL63 Avian Influenza virus glycoproteins restrict virus replication and 603 spread through human airway epithelium at temperatures of the proximal airways Human coronavirus 229E infects polarized airway epithelia from 607 the apical surface Infection and Propagation of Human Rhinovirus C in 610 Human Airway Epithelial Cells ACE2 receptor expression and severe acute respiratory 613 syndrome coronavirus infection depend on differentiation of human airway epithelia SARS-CoV replication and pathogenesis in 616 an in vitro model of the human conducting airway epithelium Characterization and Treatment of 620 SARS-CoV-2 in Nasal and Bronchial Human Airway Epithelia An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 626 in human airway epithelial cell cultures and multiple coronaviruses in mice Morphogenesis 630 and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Our observation that SARS-CoV-2 was unable to infect epithelial cells from the 299 basolateral side supports that the viral entry receptor ACE2 is polarly expressed at the apical 300 side 30, 31 . keywords: airway; cells; cov-2; hae; infection; sars cache: cord-337973-djqzgc1k.txt plain text: cord-337973-djqzgc1k.txt item: #619 of 702 id: cord-338055-2d6n4cve author: Hassan, Sk. Sarif title: A unique view of SARS-CoV-2 through the lens of ORF8 protein date: 2020-08-26 words: 5951 flesch: 45 summary: Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. The web-server 60 'QUARK' was used for prediction of the secondary structure of ORF8 proteins [32, 33] . keywords: amino; bat; cov; cov-2; mutations; orf8; pangolin; protein; sars; sequence cache: cord-338055-2d6n4cve.txt plain text: cord-338055-2d6n4cve.txt item: #620 of 702 id: cord-338296-2hk7h132 author: Malla, Tek Narsingh title: Ebselen Reacts with SARS Coronavirus-2 Main Protease Crystals date: 2020-08-23 words: 490 flesch: 62 summary: Fig. 2 shows a comparison of 87 diffraction patterns collected from untreated crystals (Fig. 2a) , and crystals treated with the Ebselen 88 (Fig. 2b) . SARS CoV-2 3CLpro in its functional, dimeric form 1 . keywords: crystals; ebselen cache: cord-338296-2hk7h132.txt plain text: cord-338296-2hk7h132.txt item: #621 of 702 id: cord-338543-q6cl5kjp author: Salguero, Francisco J. title: Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19 date: 2020-09-17 words: 1095 flesch: 42 summary: However, comparison of the summed MP 1-3-specific response indicated that 304 significantly higher SFU frequencies were present in the animals euthanised at the In general, there was a trend for spike protein peptide-specific IFN-γ SFU 311 frequencies measured in PBMC samples collected from cynomolgus macaques to 312 be greater than those detected in rhesus macaques, although these differences did 313 not reach statistical significance. In rhesus macaques, low levels of viral RNA were detected 157 from one dpc to nine dpc. keywords: cynomolgus; dpc; macaques; rhesus cache: cord-338543-q6cl5kjp.txt plain text: cord-338543-q6cl5kjp.txt item: #622 of 702 id: cord-338734-laeocs3j author: Lima, Amorce title: Validation and Comparison of a Modified CDC Assay with two Commercially Available Assays for the Detection of SARS-CoV-2 in Respiratory Specimen date: 2020-06-30 words: 2537 flesch: 51 summary: 281 A closer look at the Ct value differences between the modified CDC SARS-CoV-2 assay 282 and the commercial assays suggests that there is not a significant difference between the 283 modified CDC SARS-CoV-2 assay and NeuMoDx SARS-CoV-2; however, there seems to be a 284 greater difference in Ct values between DiaSorin Simplexa CoV-2 Direct assay and the modified 285 CDC SARS-CoV-2 assay, with DiaSorin having lower Ct values. DiaSorin Simplexa CoV-2 Direct assay involves a simple operation procedure that 300 does not include an extraction step; it has, however, much lower throughput than NeuMoDx. keywords: assay; cdc; cov-2; samples; sars cache: cord-338734-laeocs3j.txt plain text: cord-338734-laeocs3j.txt item: #623 of 702 id: cord-339012-4juhmjaj author: Hou, Wei title: Rapid host response to an infection with Coronavirus. Study of transcriptional responses with Porcine Epidemic Diarrhea Virus date: 2020-07-28 words: 6784 flesch: 39 summary: Differential expressed genes (DEGs) in PEDV infected cells were compared to DEGs responding in Vero cells infected with Mammalian Orthoreovirus (MRV). A decrease in CT-values for PEDV was not observed before 6 h post inoculation (6 h.p.i), indicating that replication in PEDV infected cells started later than was observed for MRV (at 4 h.p.i). keywords: cells; coronavirus; cov-2; degs; expression; file; genes; infection; mrv; pedv; processes; response; sars; vero; virus cache: cord-339012-4juhmjaj.txt plain text: cord-339012-4juhmjaj.txt item: #624 of 702 id: cord-339431-kyr5lv15 author: Saçar Demirci, Müşerref Duygu title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 words: 2325 flesch: 35 summary: Since viruses would need to use at least some members of host miRNA biogenesis pathway elements, viral miRNAs should be similar to host miRNAs to a certain degree. For instance, through targeting specific human genes by viral miRNAs, it is possible to form an environment suitable for survival and replication of the virus. keywords: coronavirus; cov-2; genes; human; mirnas; sars; virus cache: cord-339431-kyr5lv15.txt plain text: cord-339431-kyr5lv15.txt item: #625 of 702 id: cord-339665-nwwutduy author: Patel, Ami title: Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model date: 2020-07-29 words: 5279 flesch: 44 summary: This vaccine candidate induced neutralizing and ACE2-blocking antibodies, as well as T cell responses in mice and guinea pigs. This anamnestic response was characterized by expansion of neutralizing antibody responses, including those against the now dominantly circulating G614 variant, as well as the rapid expansion of T cell responses. keywords: animals; cells; challenge; cov-2; covid-19; et al; ino-4800; protein; responses; sars; spike; vaccine cache: cord-339665-nwwutduy.txt plain text: cord-339665-nwwutduy.txt item: #626 of 702 id: cord-339720-d1stzy8w author: Zhao, Yuan title: Susceptibility of tree shrew to SARS-CoV-2 infection date: 2020-04-30 words: 2579 flesch: 53 summary: key: cord-339720-d1stzy8w authors: Zhao, Yuan; Wang, Junbin; Kuang, Dexuan; Xu, Jingwen; Yang, Mengli; Ma, Chunxia; Zhao, Siwen; Li, Jingmei; Long, Haiting; Ding, Kaiyun; Gao, Jiahong; Liu, Jiansheng; Wang, Haixuan; Li, Haiyan; Yang, Yun; Yu, Wenhai; Yang, Jing; Zheng, Yinqiu; Wu, Daoju; Lu, Shuaiyao; Liu, Hongqi; Peng, Xiaozhong title: Susceptibility of tree shrew to SARS-CoV-2 infection date: 2020-04-30 journal: bioRxiv DOI: 10.1101/2020.04.30.029736 sha: doc_id: 339720 cord_uid: d1stzy8w Since SARS-CoV-2 became a pandemic event in the world, it has not only caused huge economic losses, but also a serious threat to global public health. No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39° C) particular in female animals during infection. keywords: cov-2; infection; sars; shrews; tree; virus cache: cord-339720-d1stzy8w.txt plain text: cord-339720-d1stzy8w.txt item: #627 of 702 id: cord-339772-q814d6l7 author: Pach, Szymon title: ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study date: 2020-05-14 words: 3767 flesch: 52 summary: Similarly, the mutation H353K in rat and mouse ACE2 Bp A should result in a hydrogen bond network comparable to hamster protein and therefore enhancing the RBD binding. We compared ACE2 residues with direct contact to the RBD (distance of max. keywords: ace2; binding; cov-2; rat; rbd; residue; sars; species cache: cord-339772-q814d6l7.txt plain text: cord-339772-q814d6l7.txt item: #628 of 702 id: cord-340240-dk48pdqa author: Kuo, Tsun-Yung title: Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 date: 2020-08-11 words: 1248 flesch: 41 summary: Vaccine Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the 380 SARS virus. An eosinophil-specific colony-stimulating factor with activity for human cells Immunization with SARS coronavirus vaccines leads to 407 pulmonary immunopathology on challenge with the SARS virus Systems and their Potential Applications in Hepatitis B Vaccines keywords: cov-2; covid-19; cpg; s-2p; sars cache: cord-340240-dk48pdqa.txt plain text: cord-340240-dk48pdqa.txt item: #629 of 702 id: cord-340291-bah2ege0 author: Kohmer, Niko title: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity date: 2020-05-10 words: 1003 flesch: 41 summary: Currently there are many S 57 protein based commercially or in-house developed assays available, but there is limited data on how 58 these tests perform with clinical samples and if the detected IgG antibodies provide protective 59 immunity. Lateral flow assays can be 167 used by less experienced personnel in a point-of-care setting, generating results in short time. keywords: assays; igg cache: cord-340291-bah2ege0.txt plain text: cord-340291-bah2ege0.txt item: #630 of 702 id: cord-340432-vm6m0kb4 author: Srivastava, Sukrit title: Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide date: 2020-09-06 words: 2667 flesch: 28 summary: bioRxiv GalaxyWEB server for protein structure prediction and 1522 refinement Defensins as anti-1525 inflammatory compounds and mucosal adjuvants New ways to boost molecular dynamics simulations Reliable B cell epitope 1529 predictions: impacts of method development and improved benchmarking In silico identification of vaccine targets for 2019-1532 nCoV Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations 1535 Predicted to Target Human Haplotype Distributions Structure validation by Calpha geometry: 1538 phi, psi and Cbeta deviation Efficient identification of mutated cancer 1542 antigens recognized by T cells associated with durable tumor regressions 1545 ff14SB: improving the accuracy of protein side chain and backbone parameters from 1546 ff99SB Escort service for cross-priming Multi-epitope based peptide 1549 vaccine design against SARS-CoV-2 using its spike protein Synonymous codon usage pattern in glycoprotein gene of 1551 rabies virus VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-1554 based vaccine adjuvants 045512&tracks=[key:sequence_track,name:Sequence,display_name:Sequence,id:STD6 1559 49220238,annots:Sequence,ShowLabel:false,ColorGaps:false Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 1564 antigens Prediction of MHC class II binding affinity using 1566 SMM-align, a novel stabilization matrix alignment method Identifying MHC class I 1569 epitopes by predicting the TAP transport efficiency of epitope precursors ElliPro: a new 1572 structure-based tool for the prediction of antibody epitopes Sequence-based prediction of vaccine targets for inducing T cell responses to SARS-1576 CoV-2 utilizing the bioinformatics predictor RECON. RAMPAGE analysis for all the MPVs (A) CTL-MPV-1381 1 Work flow concept chart from Ag-Patch (antigenic 1401 patch) identification to in vivo trial for the proposed MPVs against SARS-CoV-2 Design of multi epitope-based peptide vaccine against E 1409 protein of human 2019-nCoV: An immunoinformatics approach Preliminary identification of potential 1412 vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV 1413 immunological studies Genome based Evolutionary study of SARS-CoV-2 towards the 1416 Prediction of Epitope Based Chimeric Vaccine Quantitative and 1418 qualitative analyses of the immune responses induced by a multivalent minigene DNA 1419 vaccine Assembly and export of MHC class I peptide 1421 ligands Energetics based epitope screening in SARS CoV-2 1423 (COVID 19) spike glycoprotein by Immuno-informatic analysis aiming to a suitable 1424 vaccine development Immunoinformatics-aided identification of T cell and B cell 1426 epitopes in the surface glycoprotein of 2019-nCoV keywords: cov-2; epitope; multi; patches; protein; sars; vaccine cache: cord-340432-vm6m0kb4.txt plain text: cord-340432-vm6m0kb4.txt item: #631 of 702 id: cord-340516-9dfaqsv7 author: Moore, Anne C. title: Pre-clinical studies of a recombinant adenoviral mucosal vaccine to prevent SARS-CoV-2 infection date: 2020-09-06 words: 6704 flesch: 40 summary: We are developing oral vaccines for multiple indications, including influenza and noroviruses, delivered in a tablet form for people. We and others 17 have observed that transgene expression by vaccine vectors orally administered to mice can be suppressed in their intestinal environment, so immunogenicity was assessed following intranasal (i.n.) keywords: antibodies; antibody; antigen; cells; cov-2; iga; immunogenicity; infection; protein; rad; responses; sars; vaccine; virus cache: cord-340516-9dfaqsv7.txt plain text: cord-340516-9dfaqsv7.txt item: #632 of 702 id: cord-341502-jlzufa28 author: Lee, Sungyul title: The SARS-CoV-2 RNA interactome date: 2020-11-02 words: 5853 flesch: 37 summary: As for viral proteins, the N protein was the most strongly enriched one, as expected ( Figure 1D ). PARP12, a cytoplasmic mono-ADP-ribosylation (MARylation) enzyme, is also known to have broad antiviral activity against RNA viruses such as Venezuelan equine encephalitis virus (Togaviridae), vesicular stomatitis virus (Rhabdoviridae), Rift Valley fever virus (Phenuiviridae), encephalomyocarditis virus (Picornaviridae), and Zika virus (Flaviviridae) by multiple mechanisms including blocking cellular RNA translation (Atasheva et al., 2014; Welsby et al., 2014) or triggering proteasome-mediated destabilization of viral proteins (Li et al., 2018) . keywords: cells; cov-2; figure; host; interactome; mrna; probe; proteins; rna; rnas; rnp; sars; translation; viral; virus cache: cord-341502-jlzufa28.txt plain text: cord-341502-jlzufa28.txt item: #633 of 702 id: cord-341768-k86gsfng author: Suresh, Voddu title: Tissue distribution of ACE2 protein in Syrian golden hamster (Mesocricetus auratus) and its possible implications in SARS-CoV-2 related studies date: 2020-06-29 words: 2545 flesch: 34 summary: key: cord-341768-k86gsfng authors: Suresh, Voddu; Parida, Deepti; Minz, Aliva P.; Senapati, Shantibhusan title: Tissue distribution of ACE2 protein in Syrian golden hamster (Mesocricetus auratus) and its possible implications in SARS-CoV-2 related studies date: 2020-06-29 journal: bioRxiv DOI: 10.1101/2020.06.29.177154 sha: doc_id: 341768 cord_uid: k86gsfng Recently, the Syrian golden hamster (Mesocricetus auratus) has been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. The alignment of ACE2 protein of different species has suggested that the S protein may interact more efficiently with Cricetidae ACE2 than murine ACE2 10 . keywords: ace2; cells; expression; hamster; human; protein; sars; tissue cache: cord-341768-k86gsfng.txt plain text: cord-341768-k86gsfng.txt item: #634 of 702 id: cord-342010-5mkf67os author: Levasseur, Anthony title: Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients date: 2020-09-04 words: 5392 flesch: 87 summary: C T T P 4 0 2 L 1 4 1 0 5 n s p 3 A T > X 1 5 1 5 n s p 1 G T T > keywords: g t; n s; s p; t c; t t cache: cord-342010-5mkf67os.txt plain text: cord-342010-5mkf67os.txt item: #635 of 702 id: cord-342015-bz2vab6e author: Ouadfeul, Sid-Ali title: Multifractal Analysis of SARS-CoV-2 Coronavirus genomes using the wavelet transform date: 2020-08-16 words: 1387 flesch: 42 summary: Fractal character of nucleic acids distribution in DNA sequences has been widely studied by the scientific community; many papers have been published in literature. Arneodo et al (1996) published a paper deals with the study of the Long-Range Correlation (LRC) character of DNA sequences using the 1D continuous wavelet transform method. keywords: dna; sequences; wavelet cache: cord-342015-bz2vab6e.txt plain text: cord-342015-bz2vab6e.txt item: #636 of 702 id: cord-342456-5gp3cry0 author: Hoagland, Daisy A. title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 words: 4520 flesch: 37 summary: We then searched for FDA-approved compounds that induce or suppress the expression of these genes using drug signatures extracted from other independent transcriptome studies . Consensus analysis was performed by counting gene overlap in the top 50 up or down differentially expressed genes based on the consensus L1000FWD and RNA-seq signatures generated from the A549-ACE2 cells. keywords: cells; cov-2; drugs; rna; sars; seq; signatures; virus cache: cord-342456-5gp3cry0.txt plain text: cord-342456-5gp3cry0.txt item: #637 of 702 id: cord-342599-558yn6pu author: Rinchai, Darawan title: A modular framework for the development of targeted Covid-19 blood transcript profiling panels date: 2020-05-22 words: 5236 flesch: 36 summary: These data could, for instance, be used to refine the delineation of Covid-19 module sets. Immunological relevance: Lists of immunologically relevant genes were retrieved from Immport (44) , and were used along with membership to IPA pathways (Ingenuity Pathway Analysis, QIAGEN, Germantown MD) to annotate transcripts comprising Covid-19 module sets. keywords: abundance; blood; coronavirus; covid-19; data; immune; module; panel; patients; profiling; repertoire; sars; sets; transcripts cache: cord-342599-558yn6pu.txt plain text: cord-342599-558yn6pu.txt item: #638 of 702 id: cord-342657-od48cntc author: Klemm, Theresa title: Mechanism and inhibition of SARS-CoV-2 PLpro date: 2020-06-19 words: 1717 flesch: 51 summary: The S2 site in SARS2 PLpro 1037 a, A previous structure of SARS PLpro bound to a non-hydrolysable, Lys48-linked 1038 diubiquitin probe (pdb 5e6j, 20 ) explained the noted preference of PLpro for longer 1039 While the proximal ubiquitin unit occupies the S1 site in a highly 1040 similar fashion in SARS~ b, Superposition of ubiquitin tail in SARS2 PLpro, and 1086 compound 3j in SARS PLpro (pdb 4ovz, 29 ) shows an identical binding for 1087 compounds in SARS2 PLpro and highlights the change in Tyr268 Compounds rac3j and rac3k, racemic 1089 versions of 3j and 3k from 29 , and their in vitro biochemical IC50 values determined by 1090 the HTS assay technical triplicate and in three independent experiments (as for 1091 rac5c in Figure 4c). keywords: data; fig; isg15; plpro; sars2 cache: cord-342657-od48cntc.txt plain text: cord-342657-od48cntc.txt item: #639 of 702 id: cord-342942-1s32o9m8 author: Stamatakis, George title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 words: 4077 flesch: 38 summary: Only a subset of generated peptides was predicted to bind with sufficient affinity onto at least one HLA: 23% for ERAP1, 22% for ERAP2, 6% for ERAP1/ERAP2 mixture and 21% for IRAP (peptide sequences are listed in Table 1a ). key: cord-342942-1s32o9m8 authors: Stamatakis, George; Samiotaki, Martina; Mpakali, Anastasia; Panayotou, George; Stratikos, Efstratios title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 journal: bioRxiv DOI: 10.1101/2020.06.22.164681 sha: doc_id: 342942 cord_uid: 1s32o9m8 Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. keywords: cov-2; erap1; hla; irap; mixture; peptides; sars; trimming cache: cord-342942-1s32o9m8.txt plain text: cord-342942-1s32o9m8.txt item: #640 of 702 id: cord-343027-ks3fn9pq author: Fraser, Nicholas title: Preprinting the COVID-19 pandemic date: 2020-09-18 words: 5713 flesch: 48 summary: Only marginally 135 faster screening was detected for COVID-19 preprints than for non-COVID-19 preprints (Fig. 2B) when 136 adjusting for differences between servers (two-way ANOVA, interaction term; F1,14808 = 69.13, p < 137 0.001). COVID-19 preprints 185 did not discernibly differ in number of versions compared with non-COVID-19 preprints ( Mann-Whitney, p < 0.001) keywords: biorxiv; covid-19; data; fig; medrxiv; non; pandemic; preprints; research; time cache: cord-343027-ks3fn9pq.txt plain text: cord-343027-ks3fn9pq.txt item: #641 of 702 id: cord-343317-97n1j0jj author: Duan, Xiaohua title: Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids date: 2020-05-02 words: 3780 flesch: 49 summary: However, such transgenic animals fail to fully recapitulate the cellular phenotype and host response of human cells 11, 12 . Using disease-relevant normal colonic human cells, we screened 1280 FDA-approved compounds and identified MPA and QNHC, two drugs that can block the entry of SARS-CoV-2 into human cells. keywords: cells; cos; cov-2; entry; fig; hpsc; infection; organoids; pseudo; sars; virus cache: cord-343317-97n1j0jj.txt plain text: cord-343317-97n1j0jj.txt item: #642 of 702 id: cord-343476-0chuwvg6 author: MacLean, Oscar A. title: Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans date: 2020-05-29 words: 1386 flesch: 45 summary: dN/dS was approximately 0.6 in singletons, suggesting that 40% of nonsynonymous mutations are strongly deleterious and therefore never observed in the population. It is important to consider that the observed frequencies are likely to differ from true global frequencies due to biased sampling of infections in the pandemic 4 , and so we caution against overinterpretation of specific mutation frequencies. keywords: mutations; sars; selection cache: cord-343476-0chuwvg6.txt plain text: cord-343476-0chuwvg6.txt item: #643 of 702 id: cord-343517-vf32wxkx author: Lokman, Syed Mohammad title: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach date: 2020-04-11 words: 2752 flesch: 43 summary: Based on the phylogenetic studies, the SARS-CoV-2 is categorized as a member of the genus Betacoronavirus, the same lineage that includes SARS coronavirus (SARS-CoV) The neighbor-joining method: a new method for reconstructing phylogenetic trees Bootstrap confidence levels for phylogenetic trees Evolutionary divergence and convergence in proteins SWISS-MODEL: homology modelling of protein structures and complexes Structure validation by Calpha geometry: Phi, psi and Cbeta deviation Pymol: An open-source molecular graphics tool Receptor recognition mechanisms of coronaviruses: a decade of structural studies A Parvovirus B19 synthetic genome: Sequence features and functional competence Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Long-term protection from SARS coronavirus infection conferred by a single immunization with an attenuated VSV-based vaccine Human monoclonal antibodies against highly conserved HR1 and HR2 domains of the SARS-CoV spike protein are more broadly neutralizing A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: Implication for developing therapeutics and vaccines Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: keywords: coronavirus; cov-2; domain; glycoprotein; protein; receptor; sars; spike; variations cache: cord-343517-vf32wxkx.txt plain text: cord-343517-vf32wxkx.txt item: #644 of 702 id: cord-343586-28ezisog author: Rocca, María Florencia title: A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs date: 2020-05-07 words: 1500 flesch: 40 summary: Binary peak matching tables were exported to summarize the presence of peak classes. All raw spectra were imported into the Bionumerics database with x-axis trimming to a minimum of 1960 m/z. Baseline subtraction (with a rolling disc with a size of 50 points), noise computing (continuous wavelet transformation, CWT), smooth (Kaiser Window with a window size of 20 points and beta of 10 points), and peak detection (CWT with a minimum signal to noise ratio of 1) were performed. keywords: cov-2; peak; samples; sars; spectra cache: cord-343586-28ezisog.txt plain text: cord-343586-28ezisog.txt item: #645 of 702 id: cord-344236-qp3ianzf author: Ali, Fedaa title: ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity date: 2020-05-08 words: 2478 flesch: 45 summary: In addition, the frequency of I468V which enhance ACE2 interaction with SARS-CoV-2 was observed in more than 1% of the East Asian population. The sequencing projects will not only help us test the association between ACE2 variants and risk/severity of infection in certain populations, it will also allow more accurate analysis of variants for other host genes involved in the viral entry and pathogenicity 21 . keywords: ace2; binding; populations; protein; sars; variants cache: cord-344236-qp3ianzf.txt plain text: cord-344236-qp3ianzf.txt item: #646 of 702 id: cord-344560-662pfa61 author: Yamamoto, Norio title: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro date: 2020-04-08 words: 1422 flesch: 57 summary: Saquinavir (C max /EC 50 = 0.73, C trough /EC 50 = 0.07), atazanavir (C max /EC 50 = 0.93, C trough /EC 50 = 0.19), amprenavir (C max /EC 50 = 0.46, C trough /EC 50 = 0.09), darunavir (C max /EC 50 = 0.27, C trough /EC 50 = 0.05), and indinavir (C max /EC 50 = 0.21, C trough /EC 50 = 0.004) could not reach one in the C max -EC 50 ratio. Nelfinavir (C max /EC 50 = 6.23, C trough /EC 50 = 3.43), lopinavir (C max /EC 50 = 2.72, C trough /EC 50 = 1.97), and tipranavir (C max /EC 50 = 6.46, C trough keywords: trough cache: cord-344560-662pfa61.txt plain text: cord-344560-662pfa61.txt item: #647 of 702 id: cord-344909-0o55l4iy author: Cross, Robert W. title: Use of convalescent serum reduces severity of COVID-19 in nonhuman primates date: 2020-10-14 words: 5723 flesch: 40 summary: Differences in clinical parameters of the LD-treated group with untreated control animals from this study or historical control animals were minimal; however, the lack of infectious SARS-CoV-2 in the BAL samples from all of the LD-treated animals and reduced lung pathology suggest that an antiviral effect was present despite the lower concentration of neutralizing antibodies in the dose of convalescent sera administered. Prothrombin time (PT) was largely unaffected, yet a significantly prolonged coagulation time was noted at 4 dpi for activated partial thromboplastin time (aPTT) in HD versus control group (p=0.0459; two-way ANOVA with Tukey's multiple comparison); decreases in levels of thrombocytes were more notable in control animals; and increases in circulating fibrinogen were generally more pronounced in the control group compared to either of the experimental groups ( Figure S1 ). keywords: animals; control; convalescent; cov-2; covid-19; dpi; et al; sars; sera; treatment cache: cord-344909-0o55l4iy.txt plain text: cord-344909-0o55l4iy.txt item: #648 of 702 id: cord-344949-9zyz4hll author: Luban, Jeremy title: The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines date: 2020-08-05 words: 5571 flesch: 36 summary: Normalized percent numbers of nucleocapsid positive cells were plotted against Log10 transforms of PTC299 concentrations and the IC50 was estimated using non-linear regression (goodness-of-fit R-squared = 0.9653). The percentages in red denote the respective extents to which the relative levels of specific nucleotides are reduced during PTC299 treatment (100 nM) of cultured HT1080 fibrosarcoma cells for 8 hours (Cao et al., 2019) keywords: cells; cov-2; covid-19; culture; et al; production; ptc299; replication; sars; system cache: cord-344949-9zyz4hll.txt plain text: cord-344949-9zyz4hll.txt item: #649 of 702 id: cord-345299-4k7qymqd author: Xiong, Hua-Long title: Several FDA-approved drugs effectively inhibit SARS-CoV-2 infection in vitro date: 2020-06-05 words: 1479 flesch: 38 summary: Re-purposing of approved drugs may be a faster way to find treatment for COVID-19. In this study, the anti-SARS-Cov-2 potentiality of 1403 FDA approved drugs were quantitatively evaluated by the pseudovirus-based assay. keywords: cov-2; drugs; infection; sars cache: cord-345299-4k7qymqd.txt plain text: cord-345299-4k7qymqd.txt item: #650 of 702 id: cord-345405-ngpsgn63 author: Tremiliosi, Guilherme C. title: Ag nanoparticles-based antimicrobial polycotton fabrics to prevent the transmission and spread of SARS-CoV-2 date: 2020-06-26 words: 6262 flesch: 36 summary: A Fourier transform Raman study Application of Raman Spectroscopy for Differentiation Among Cotton and Viscose Fibers Dyed with Several Dye Classes Raman spectroscopic investigation of acetylation of raw cotton Spectrochim Physicochemical modifications accompanying UV laser induced surface structures on poly(ethylene terephthalate) and their effect on adhesion of mesenchymal cells Chemical depth profiling of photovoltaic backsheets after accelerated laboratory weathering Reliab Graphene/cotton composite fabrics as flexible electrode materials for electrochemical capacitors RSC Adv Eco-friendly cationic modification of cotton fabrics for improving utilization of reactive dyes RSC Adv Characterization of cotton fabric scouring by FT-IR ATR spectroscopy Pine Cone and Boron Compounds Effect as Reinforcement on Mechanical and Flammability Properties of Polyester Composites Open Chem Influence of Stacking Sequence on the Mechanical and Dynamic Mechanical Properties of Cotton/Glass Fiber Reinforced Polyester Multi-Finishing of Polyester and Polyester Cotton Blend Fabrics Activated by Enzymatic Treatment and Loaded with Antibacterial cotton fabric with enhanced durability prepared using silver nanoparticles and carboxymethyl chitosan Synthesis and optical properties of composite films from P3HT and sandwich-like Ag-C-Ag nanoparticles RSC Adv Laundering durable antibacterial cotton fabrics grafted with pomegranate-shaped polymer wrapped in silver nanoparticle aggregations Sci Silver-cotton nanocomposites: Nano-design of microfibrillar structure causes morphological changes and increased tenacity Sci Enhancing the surface affinity with silver nano-particles for antibacterial cotton fabric by coating carboxymethyl chitosan and l-cysteine Application of silver nanoparticles to cotton fabric as an antibacterial textile finish Fibers Polym Preparation of cotton fibers with antibacterial silver nanoparticles Antimicrobial activity and cytotoxicity of cotton fabric coated with conducting polymers, polyaniline or polypyrrole, and with deposited silver nanoparticles Antibacterial properties of cotton fabric treated with silver nanoparticles Durable antibacterial and cross-linking cotton with colloidal silver nanoparticles and butane tetracarboxylic acid without yellowing Colloids Surfaces B Biointerfaces A New Method of Finishing of Cotton Fabric by in Situ Synthesis of Silver Nanoparticles Ind Controlled synthesis of Ag nanoparticles with different morphologies and their antibacterial properties Ag Nanoparticles/α-Ag 2 WO 4 Composite Formed by Electron Beam and Femtosecond Irradiation as Peiris M. and Poon L. L. M. 2020 Stability of SARS-CoV-2 in different environmental conditions The Lancet Microbe Protease inhibitors: Silver bullets for chronic hepatitis C infection? Ag nanoparticles (AgNPs) acquire special attention due to its specificity and environment friendly approach with a wide application in industry and medicine due to its antibacterial, antifungal, larvicidal and anti-parasitic characters. keywords: activity; antibacterial; application; control; fabric; nanoparticles; nps; polycotton; properties; samples; silver; surface; test; virus cache: cord-345405-ngpsgn63.txt plain text: cord-345405-ngpsgn63.txt item: #651 of 702 id: cord-345499-hq5um68k author: Xiong, Rui title: Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 date: 2020-03-12 words: 5301 flesch: 46 summary: Several independent studies searching for HTAs collectively end up to compounds targeting the host's pyrimidine synthesis pathway to inhibit virus infections, which indicates that the replication of viruses is widely dependent on the host pyrimidine synthesis [11] [12] Acute viral infections, such as influenza virus, SARS-CoV, MERS-CoV, Ebola virus, Zika virus, and the very recent SARS-CoV-2 are an increasing and probably lasting global threat 1 . keywords: antiviral; cells; dhodh; drug; fig; influenza; replication; s312; s416; sars; spectrum; virus cache: cord-345499-hq5um68k.txt plain text: cord-345499-hq5um68k.txt item: #652 of 702 id: cord-346299-2s9j01q7 author: Salim Khan, S Muhammad title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date: 2020-09-04 words: 1411 flesch: 45 summary: Immunity and Ageing List of hospitals across District Srinagar Age and gender distribution of the population in District Srinagar and the 406 estimated population Estimated number of infections in District Srinagar Age-and gender-standardized seroprevalence key: cord-346299-2s9j01q7 authors: Salim Khan, S Muhammad; Qurieshi, Mariya Amin; Haq, Inaamul; Majid, Sabhiya; Bhat, Arif Akbar; Nabi, Sahila; Ganai, Nisar Ahmad; Zahoor, Nazia; Nisar, Auqfeen; Chowdri, Iqra Nisar; Qazi, Tanzeela Bashir; Kousar, Rafiya; Lone, Abdul Aziz; Sabah, Iram; Nabi, Shahroz; Sumji, Ishtiyaq Ahmad; Kawoosa, Misbah Ferooz; Ayoub, Shifana title: Seroprevalence of SARS-CoV-2 specific IgG antibodies in District Srinagar, northern India – a cross-sectional study date: 2020-09-04 journal: bioRxiv DOI: 10.1101/2020.09.04.282640 sha: doc_id: 346299 cord_uid: 2s9j01q7 Background Prevalence of IgG antibodies against SARS-CoV-2 infection provides essential information for deciding disease prevention and mitigation measures. keywords: antibodies; cov-2; sars; seroprevalence; study cache: cord-346299-2s9j01q7.txt plain text: cord-346299-2s9j01q7.txt item: #653 of 702 id: cord-346335-el45v0a5 author: Tan, H.S. title: Fourier spectral density of the coronavirus genome date: 2020-08-11 words: 4647 flesch: 47 summary: Beyond the specific linear form of the correlation function postulated in (6), it is also representative of a large class of correlation functions of the form where τ ≡ l − j,κ is a small constant andτ =κ |τ | M . Thus, (6) could approximate correlation functions of the general form F κ |τ | M whereκ is a small dimensionless parameter, and For example, if the correlation function turns out to be an exponentially decaying function of the form e − B|τ | M with B 1, then to a good approximation we can identify κ ∼ B. The power-law decay in (A) parametrizes the decay of the envelope whereas the model in (6) could account for non-vanishing local minima in the low-frequency domain. keywords: density; domain; frequency; function; genome; protein; sequence cache: cord-346335-el45v0a5.txt plain text: cord-346335-el45v0a5.txt item: #654 of 702 id: cord-346532-4xpnd93d author: Strömich, Léonie title: Allosteric Hotspots in the Main Protease of SARS-CoV-2 date: 2020-11-06 words: 2371 flesch: 48 summary: Site 1 and 2 have a 151 high score of 0.97 and 0.96, respectively and score much higher than a randomly sampled site would score with 0.53 152 (95% CI: 0.53-0.54) for a a site of the size of site 1 or 0.52 (95% CI: 0.51-0.53) for a site of the size of site 2. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. keywords: allosteric; bond; protease; residues; score; site cache: cord-346532-4xpnd93d.txt plain text: cord-346532-4xpnd93d.txt item: #655 of 702 id: cord-346546-yffwd0dc author: Douangamath, Alice title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date: 2020-05-27 words: 4101 flesch: 44 summary: Non-covalent fragments were soaked (Collins et al., 2017) , 123 whereas electrophile fragments were both soaked and co-crystallized as previously described 124 (Resnick et al., 2019) , to ensure that as many of the mass spectrometry hits as possible were 125 structurally observed. 615 MichelaNglo: sculpting protein views on web pages without coding An improved model for fragment-619 based lead generation at AstraZeneca Structure-based design,synthesis, and 622 biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors Conservation of substrate specificities among coronavirus main 625 proteases From SARS to MERS: crystallographic studies on coronaviral proteases 627 enable antiviral drug design Critical 629 assessment of important regions in the subunit association and catalytic action of the 630 severe acute respiratory syndrome coronavirus main protease Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like 634 protease cause different conformational changes in crystal structure Structure of M(pro) from SARS-CoV-2 and discovery of its 640 inhibitors Integration, scaling, space-group assignment and post-refinement. keywords: compounds; coronavirus; covalent; data; design; fragments; hits; inhibitors; protease; protein; sars; structure cache: cord-346546-yffwd0dc.txt plain text: cord-346546-yffwd0dc.txt item: #656 of 702 id: cord-346670-34wfy52f author: Gobeil, Sophie M-C. title: D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction date: 2020-10-12 words: 7110 flesch: 45 summary: The D614G mutation alters S protein conformational dynamics. We observed an increased proportion of the 3-RBD-down S compared to the uncleaved D614G S ectodomain, thus reporting a change in the RBD conformational dynamics upon furin cleavage. keywords: cleavage; cov-2; d614; d614 g; ectodomain; et al; figure; furin; gsas; rbd; sars; spike cache: cord-346670-34wfy52f.txt plain text: cord-346670-34wfy52f.txt item: #657 of 702 id: cord-346978-ubkqny8j author: Ranoa, Diana Rose E. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 words: 6480 flesch: 41 summary: We next sought to evaluate saliva collection buffers as a means to enhance viral RNA stability, but also to increase uniformity between saliva samples and to decrease sample viscosity. 35 Using intact, γ-irradiated SARS-CoV-2 spiked into fresh human saliva, which was then heat treated at 95°C for 30 min, we observed outstanding virus detection when saliva samples were combined with either Tris-Borate-EDTA (TBE) or TE buffer ( Figure 3A) . keywords: control; cov-2; detection; ms2; qpcr; saliva; samples; sars cache: cord-346978-ubkqny8j.txt plain text: cord-346978-ubkqny8j.txt item: #658 of 702 id: cord-347441-8ow952d8 author: Parvez, Md Sorwer Alam title: Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism date: 2020-06-07 words: 1027 flesch: 52 summary: Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. For three spike protein models, this study found that a domain of spike protein instead of whole protein, 130 amino acid ranging from 345 to 527, was involved in the interactions. keywords: analysis; isolates; sars cache: cord-347441-8ow952d8.txt plain text: cord-347441-8ow952d8.txt item: #659 of 702 id: cord-347472-n6811ens author: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 words: 6274 flesch: 49 summary: DNA samples were diluted in nuclease free water supplemented with 0.01% Tween-20, RNA samples were diluted in nuclease-free water. All samples contained genomic DNA and generated extraction control positive signals well above the CDC assay threshold (40 cycles, horizontal dashed line). keywords: assay; cdc; control; dna; extraction; probe; qpcr; reverse; rna; samples; signal cache: cord-347472-n6811ens.txt plain text: cord-347472-n6811ens.txt item: #660 of 702 id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 words: 3709 flesch: 30 summary: Obtaining these antigenic epitopes using the immune-informatics approach will help inform which epitopes to use in the construct of protein vaccines against SARS-CoV-2 using proteins other than the spike protein. Homology modelling of protein structures and complexes LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins IntFOLD: An integrated server for modelling protein structures and functions from amino acid sequences The I-TASSER Suite: protein structure and function prediction FALCON: keywords: analysis; coronavirus; cov-2; epitopes; hla; proteins; residues; sars; server; structural; vaccine cache: cord-347714-vxxhglx7.txt plain text: cord-347714-vxxhglx7.txt item: #661 of 702 id: cord-347804-kxhasabe author: Luo, Ruibang title: Tracking cytosine depletion in SARS-CoV-2 date: 2020-10-26 words: 1086 flesch: 55 summary: key: cord-347804-kxhasabe authors: Luo, Ruibang; Wong, Yat-Sing; Lam, Tak-Wah title: Tracking cytosine depletion in SARS-CoV-2 date: 2020-10-26 journal: bioRxiv DOI: 10.1101/2020.10.26.354787 sha: doc_id: 347804 cord_uid: kxhasabe Motivation Danchin et al. have pointed out that cytosine drives the evolution of SARS-CoV-2. However, the percentage of cytosine is higher in SARS (mortality level 4) and MERS (mortality level 5). keywords: cov-2; cytosine; sars cache: cord-347804-kxhasabe.txt plain text: cord-347804-kxhasabe.txt item: #662 of 702 id: cord-347982-omxcdiwt author: Basso, Fernanda Gisele title: Cooperative efforts on developing vaccines and therapies for COVID-19 Cooperative efforts for COVID-19 date: 2020-09-06 words: 3436 flesch: 30 summary: Social Network Analysis technique was used to build cooperation networks and apply metrics that characterize these connections. Organizations which are in cooperation networks that are more heterogeneous tend to be associated with better economic performance [8] . keywords: cooperation; covid-19; development; innovation; networks; organizations; partnerships cache: cord-347982-omxcdiwt.txt plain text: cord-347982-omxcdiwt.txt item: #663 of 702 id: cord-348159-v5hrcl5k author: Sang, Eric R. title: Epigenetic Evolution of ACE2 and IL-6 Genes as Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates date: 2020-09-10 words: 2081 flesch: 32 summary: First, annotation of ENCODE 140 epigenetic datasets discovered similarity of H3K4me3 and H3K27ac markers between IL-6 141 and ACE2 gene promoters in both humans and mice; however, significantly higher Z-142 scores and enrichment of H3K4me3 and H3K27ac in human IL-6 and ACE2 genes were 143 detected than in their mouse orthologs, respectively [55] . To confirm that, we conducted cross-species 139 comparative analysis between IL-6 and ACE2 genes. keywords: ace2; covid-19; genes; il-6; isgs; non cache: cord-348159-v5hrcl5k.txt plain text: cord-348159-v5hrcl5k.txt item: #664 of 702 id: cord-348635-1pb2ag9j author: Anand, Praveen title: SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery date: 2020-04-30 words: 1665 flesch: 41 summary: The overlap of the cell-types expressing ACE2 and ENaC-ɑ, and similar spatial distributions at the apical surfaces, suggest that SARS-CoV-2 may be leveraging the protease network responsible for ENaC cleavage. (b) The cartoon representation of human ENaC protein is depicted (PDB ID: 6BQN; chain in green), highlighting the ENaC-ɑ chain in green. keywords: cov-2; enac; peptide; sars cache: cord-348635-1pb2ag9j.txt plain text: cord-348635-1pb2ag9j.txt item: #665 of 702 id: cord-348727-o38uplxe author: Beaudoin-Bussières, Guillaume title: Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date: 2020-07-09 words: 921 flesch: 41 summary: 60 While it remains to be formally demonstrated, neutralizing activity is considered an important 61 determinant of convalescent plasma efficacy (11) and regulatory agencies have been 62 recommending specific thresholds for qualifying convalescent plasma prior to its release. key: cord-348727-o38uplxe authors: Beaudoin-Bussières, Guillaume; Laumaea, Annemarie; Anand, Sai Priya; Prévost, Jérémie; Gasser, Romain; Goyette, Guillaume; Medjahed, Halima; Perreault, Josée; Tremblay, Tony; Lewin, Antoine; Gokool, Laurie; Morrisseau, Chantal; Bégin, Philippe; Tremblay, Cécile; Martel-Laferrière, Valérie; Kaufmann, Daniel E.; Richard, Jonathan; Bazin, Renée; Finzi, Andrés title: Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals date: 2020-07-09 journal: bioRxiv DOI: 10.1101/2020.07.09.194639 sha: doc_id: 348727 cord_uid: o38uplxe In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to COVID-19 patients. keywords: convalescent; plasma; sars cache: cord-348727-o38uplxe.txt plain text: cord-348727-o38uplxe.txt item: #666 of 702 id: cord-348729-kejlm425 author: Liu, Xiaoyu title: Neutralizing Antibodies Isolated by a site-directed Screening have Potent Protection on SARS-CoV-2 Infection date: 2020-05-04 words: 3541 flesch: 46 summary: It shares 79% nucleotide sequence identity with SARS-CoV-1 4 . Notably, a recent study performed a systematic bioinformatics analysis to predict the potential B cell epitope and T cell epitope of SARS-CoV-2 18 . keywords: ace2; antibodies; antibody; cov-2; figure; rbd; sars cache: cord-348729-kejlm425.txt plain text: cord-348729-kejlm425.txt item: #667 of 702 id: cord-349015-5oisrm5s author: Liu, Zhe title: Identification of a common deletion in the spike protein of SARS-CoV-2 date: 2020-04-02 words: 1182 flesch: 41 summary: In this study, we identified two variants from the first Guangdong SARS-CoV-2 cell strain, with deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. By sequencing the whole genome of SARS-CoV-2, we identified two variants having deletion mutations on polybasic cleavage site (PRRAR) and its flank sites. keywords: cov-2; deletion; sars cache: cord-349015-5oisrm5s.txt plain text: cord-349015-5oisrm5s.txt item: #668 of 702 id: cord-349364-vert186n author: Márquez-López, Cristina title: SARS-CoV-2 protein Nsp1 alters actomyosin cytoskeleton and phenocopies arrhythmogenic cardiomyopathy-related PKP2 mutant date: 2020-09-14 words: 5256 flesch: 36 summary: The graphs show that the median value of the Young's modulus measured in HL-1 PKP2 cells was higher than that measured in HL-1 R735X cells ( Figure 1B ). Images from the top central area of cells revealed a scarcity of F-actin filaments in the area above the nucleus of cells expressing the R735X mutant (46.05%±0.73% in PKP2 cells vs. 26.05%±1.48% in R735X cells; p<0.0001, ****; n=11) ( Figure 1C ). keywords: actin; actomyosin; cardiomyopathy; cells; cytoskeleton; et al; figure; mutant; myh10; myh9; nsp1; pkp2; protein; r735x cache: cord-349364-vert186n.txt plain text: cord-349364-vert186n.txt item: #669 of 702 id: cord-349684-2tioh80m author: Pezzotti, Giuseppe title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 words: 5401 flesch: 43 summary: Dermatol Res Pract An Overview of Copper Toxicity Relevance to Public Health Silicon Nitride and Related Materials Orthopedic Applications of Silicon Nitride Ceramics Bioactive Silicon Nitride: A New Therapeutic Material for Situ Spectroscopic Screening of Osteosarcoma Living Cells on Stoichiometry-Modulated Silicon Nitride Bioceramic Surfaces Silicon Nitride: A Synthetic Mineral for Vertebrate Biology Human Osteoblasts Grow Transitional Si/N Apatite in Quickly Osteointegrated Si3N4 Cervical Insert Decreased Bacteria Activity on Si3N4 Surfaces Compared with PEEK or Titanium Anti-Infective and Osteointegration Properties of Silicon Nitride, Poly (Ether Ether Ketone), and Titanium Implants A Spontaneous Solid-State NO Donor to Fight Antibiotic Resistant Bacteria. These investigators also showed rapid HuCoV-229E inactivation (within a few minutes) for simulated fingertip contamination on Cu surfaces. keywords: aln; cells; cov-2; fig; inactivation; min; nitride; rna; sars; si3n4; silicon; surface; tmprss2; virus cache: cord-349684-2tioh80m.txt plain text: cord-349684-2tioh80m.txt item: #670 of 702 id: cord-349794-mhviub6e author: Le, Brian L. title: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 date: 2020-10-23 words: 3814 flesch: 35 summary: Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). Here, we applied our existing computational drug repositioning pipeline to identify drug profiles with significantly reversed differential gene expression compared to predicted inhibitors (including one tested in Calu-3) were incubated with SARS-CoV-2 infected human embryonic kidney 293T cells overexpressing ACE2 (293T-ACE2) with viral replication determined using an immunofluorescence-based assay. keywords: cells; cov-2; covid-19; data; drug; expression; gene; hits; human; sars; signature cache: cord-349794-mhviub6e.txt plain text: cord-349794-mhviub6e.txt item: #671 of 702 id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 words: 15857 flesch: 51 summary: Evaluation of intrinsic disorder in non-structural proteins of Bat CoV. Table 7 : Predicted MoRF residues in Human SARS proteins. Supplementary Table 10 : Predicted nucleotide-binding residues in Human SARS proteins. keywords: analysis; bat cov; binding; coronavirus; cov; cov-2; disorder; domain; figure; human; mean; protein; regions; residues; rna; sars; sars cov; sequence; structure; syndrome; table; terminal; viral; viruses cache: cord-350286-n7ylgqfu.txt plain text: cord-350286-n7ylgqfu.txt item: #672 of 702 id: cord-350558-qfdp4ov9 author: Shaban, Mohammed Samer title: Inhibiting coronavirus replication in cultured cells by chemical ER stress date: 2020-08-26 words: 5088 flesch: 45 summary: Pearson correlation matrix confirmed a 91 progressive loss of correlation between mRNA levels and protein levels for this pathway over a time 92 course from 3 h to 24 h p.i. The ER is critically involved in surveying the quality and fidelity of membrane and secreted protein 40 synthesis, as well as the folding, assembly, transport and degradation of these proteins (Wang & 41 Kaufman, 2016). keywords: anti; cells; cov; data; fig; infection; p.i; pathways; protein; replication; stress; thapsigargin; virus cache: cord-350558-qfdp4ov9.txt plain text: cord-350558-qfdp4ov9.txt item: #673 of 702 id: cord-350627-4pgish5x author: Zhao, Yu title: Single-cell RNA expression profiling of ACE2,thereceptor of SARS-CoV-2 date: 2020-01-26 words: 1879 flesch: 52 summary: We used FindClusters in Seurat to identify cell clusters for each author/funder. Identification of cell clusters was performed on the final aligned object guided by marker genes. keywords: ace2; cells; expression; preprint; receptor cache: cord-350627-4pgish5x.txt plain text: cord-350627-4pgish5x.txt item: #674 of 702 id: cord-350817-tmszrtju author: Hoepel, Willianne title: Anti-SARS-CoV-2 IgG from severely ill COVID-19 patients promotes macrophage hyper-inflammatory responses date: 2020-07-13 words: 5645 flesch: 39 summary: Moreover, the hyper-inflammatory response induced by anti-Spike IgG can be specifically counteracted in vitro by use of the active component of fostamatinib, an FDA- and EMA-approved therapeutic small molecule inhibitor of Syk. Combined, these data hint towards the involvement of anti-Spike IgG in severe cases of COVID-19. keywords: anti; antibodies; cells; covid-19; cytokine; figure; human; igg; macrophages; patients; polyic; production; sars; serum; spike cache: cord-350817-tmszrtju.txt plain text: cord-350817-tmszrtju.txt item: #675 of 702 id: cord-350821-0qfoc553 author: Jahromi, Reza title: Synergistic effects of anionic surfactants on coronavirus (SARS-CoV-2) virucidal efficiency of sanitizing fluids to fight COVID-19 date: 2020-06-01 words: 1944 flesch: 41 summary: Evaporation time increased by 17-63% when surfactant agents were added to the liquid. The surrounding environment was isolated to eliminate possible air convection, and the room temperature was maintained at ~27 ºC. The exact amount of evaporation time was recorded for each sprayed liquid. keywords: coronavirus; evaporation; liquid; solution; time; virucidal cache: cord-350821-0qfoc553.txt plain text: cord-350821-0qfoc553.txt item: #676 of 702 id: cord-350935-p6euuop3 author: Doğan, Tunca title: CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations date: 2020-09-15 words: 7070 flesch: 40 summary: In CROssBAR knowledge graphs (CROssBAR-KG), biological components/terms (i.e., drugs/compounds, genes/proteins, bio-processes/pathways, phenotypes/diseases) are represented as nodes, and their known or predicted pairwise relationships are annotated as edges (a protein and its coding gene is treated as one merged term/entry/node). Currently, CROssBAR knowledge graphs do not include PubChem data due to both elevated computational demand (the sizes of PubChem collections are large) and high redundancy (a large portion of bioactivity data points in PubChem and ChEMBL databases are shared). keywords: biomedical; compound; covid-19; crossbar; data; database; disease; genes; graph; knowledge; nodes; proteins; terms cache: cord-350935-p6euuop3.txt plain text: cord-350935-p6euuop3.txt item: #677 of 702 id: cord-351011-v4zmksio author: Golden, Joseph W. title: Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease date: 2020-07-09 words: 4705 flesch: 45 summary: Transcriptomic profiling in mouse lungs indicated that female mice that succumbed to disease had modestly lower levels of IL-6, CXCl-2 and IL-1RA 315 suggesting a less intense inflammatory response. Other recently reported SARS-CoV-2 murine models involved transduction of mouse lungs with 260 a replication-incompetent Adenovirus virus or an adeno associated virus (AAV) encoding the hACE2 gene (35, 36) . keywords: cells; cov-2; disease; fig; hace2; infection; k18; lung; mice; sars cache: cord-351011-v4zmksio.txt plain text: cord-351011-v4zmksio.txt item: #678 of 702 id: cord-351321-6d2mn5ok author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window date: 2020-06-19 words: 6251 flesch: 46 summary: By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. This was repeated several times to obtain a one third dilution cascade of viral peptides. keywords: cov-2; detection; mass; min; nasopharyngeal; peptides; proteins; samples; sars; swabs; virus cache: cord-351321-6d2mn5ok.txt plain text: cord-351321-6d2mn5ok.txt item: #679 of 702 id: cord-351472-ch004jxy author: Vashi, Yoya title: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens date: 2020-04-10 words: 1336 flesch: 59 summary: The S protein structure further validated the presence of predicted peptides on the surface. T1105, B:Q1106, B:R1107, B:N1108, B:F1109, B:Y1110, B:E1111, B:P1112, B:Q1113, B:I1114, B:I1115, B:T1116, B:T1117, B:D1118, B:N1119, B:T1120, B:F1121, B:V1122, B:S1123, B:G1124, B:N1125, B:C1126, B:D1127, B:V1128, B:V1129, B:I1130, B:G1131, B:I1132, B:V1133, B:N1134, B:N1135, B:T1136, B:V1137, B:Y1138 C:A1087, C:H1088, C:F1089, C:P1090, C:R1091, C:E1092, C:G1093, C:V1094, C:F1095, C:V1096, C:S1097, C:N1098, C:G1099, C:T1100, C:H1101, C:W1102, C:F1103, C:V1104, C:T1105, C:Q1106, C:R1107, C:N1108, C:F1109, C: keywords: epitopes cache: cord-351472-ch004jxy.txt plain text: cord-351472-ch004jxy.txt item: #680 of 702 id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 words: 2444 flesch: 26 summary: There 122 are direct RNA-RNA interactions for 4 genes, and RNA-protein interactions for the rest 123 ( Figure 2 ). 777 MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by 778 translocation along 3' UTRs 780 Identification of novel argonaute-associated proteins APOBEC3G inhibits 783 microRNA-mediated repression of translation by interfering with the interaction between 784 MicroRNA silencing through RISC recruitment of eIF6 Virus Escape and Manipulation of Cellular 788 Nonsense-Mediated mRNA Decay Provides Antiviral Activity against RNA Viruses by Enhancing RIG-I-MAVS-Independent 791 IFN Induction Not applicable. keywords: cell; cov-2; genes; infection; lncrnas; protein; rna; sars cache: cord-351559-az4pgi9k.txt plain text: cord-351559-az4pgi9k.txt item: #681 of 702 id: cord-352073-rdhjj72g author: Taniwaki, S.A title: Resource optimization in COVID-19 diagnosis date: 2020-06-26 words: 1920 flesch: 42 summary: Although rayon swabs showed better performance, cotton swabs could be used as alternative type for clinical sample collection. This manuscript reports on the optimization of the Charité and the CDC RT-qPCR protocols for SARS-CoV-2 detection regarding concentration and volumes of reagents for both probe and intercalant agent-based platforms, as well as on the substitution of rayon swabs for cotton swabs for sample collection. keywords: cov-2; qpcr; reaction; sars; swabs cache: cord-352073-rdhjj72g.txt plain text: cord-352073-rdhjj72g.txt item: #682 of 702 id: cord-352943-ztonp62x author: Nagpal, Sunil title: What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date: 2020-08-20 words: 2780 flesch: 35 summary: Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes date: 2020-08-20 journal: bioRxiv DOI: 10.1101/2020.08.20.258772 sha: doc_id: Such an assumption can potentially enable classification of the entire genome corpus by identifying mutation signatures (equivalent to topics in document) through topic modeling. keywords: document; genomes; mutation; sars; signatures; topic; words cache: cord-352943-ztonp62x.txt plain text: cord-352943-ztonp62x.txt item: #683 of 702 id: cord-353099-38bz0acw author: Tang, Mei San title: Association between SARS-CoV-2 neutralizing antibodies and commercial serological assays date: 2020-07-02 words: 1035 flesch: 40 summary: However, there was an 210 increase in the ratio observed in high neutralizing titer patients (6.3, 95% CI; 5.7-6.9) 211 compared to low titer patients (5.1, 95% CI; 4.1-6.1) on the Abbott assay and the EI 212 assay (8.2, 7.1-9.2 vs. 6.1, 4.6-7.6) (Supplemental Table 1 all three commercial assays correlated with higher neutralizing titers, this was not 246 universally true. While a negative result on SARS-CoV-2 serological assays is likely to be associated 255 with the absence of neutralizing antibody titers, a positive result is not reliable for 256 predicting the presence of neutralizing antibodies. keywords: assays; sars cache: cord-353099-38bz0acw.txt plain text: cord-353099-38bz0acw.txt item: #684 of 702 id: cord-353129-ivbf4kuq author: Faryami, Ahmad title: Open source 3D printed Ventilation Device date: 2020-05-22 words: 2334 flesch: 42 summary: While the steady increase in pressure observed by a gradual pressurization is best represented by a sinusoidal wave, the handheld digital manometer was not capable of providing a sufficient passage for the flow of large volume air displaced to measure pressure changes through a cycle. Furthermore, the flexible air chamber is best used when providing positive pressure necessary during the inhalation. keywords: air; device; height; pressure; setup cache: cord-353129-ivbf4kuq.txt plain text: cord-353129-ivbf4kuq.txt item: #685 of 702 id: cord-353161-mtq6yh25 author: Rodrigues, João PGLM title: Insights on cross-species transmission of SARS-CoV-2 from structural modeling date: 2020-06-05 words: 6174 flesch: 51 summary: SARS-CoV-2 neg species lack important polar and charged ACE2 residues On further inspection, we find that SARS-CoV-2 neg models rank worse due to a substantial decrease in electrostatic energy (Figure 3 ), indicating loss of polar interface contacts, namely hydrogen bonds and saltbridges ( Figure 4) . HADDOCK score of individual ACE2 interface residues. keywords: ace2; binding; cov-2; haddock; interface; models; neg; rbd; residues; sars; sequence; species cache: cord-353161-mtq6yh25.txt plain text: cord-353161-mtq6yh25.txt item: #686 of 702 id: cord-353209-qkhfp66l author: Steiner, Daniel J. title: Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients date: 2020-06-16 words: 2527 flesch: 36 summary: 15 We have previously reported the utility of influenza antigen arrays fabricated on the AIR platform for assessment of anti-influenza antibodies in human, animal, and avian serum, 16, 17 both as a tool for viral surveillance and for assessment of the efficacy of a candidate vaccine. Other coronavirus antigens including nucleocapsid (N) are also likely candidates for addition to the array, as they are known to produce an immune response (as seen in the ELISA results, for example). keywords: air; antibodies; antibody; antigen; array; cov-2; influenza; sars cache: cord-353209-qkhfp66l.txt plain text: cord-353209-qkhfp66l.txt item: #687 of 702 id: cord-353554-98uzivsk author: Zhang, Zheng title: Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors date: 2018-03-08 words: 2191 flesch: 55 summary: Thus, during the 408 process of searching for protein receptors, the protein with high level of glycosylation 409 could provide a basal attachment ability for the virus, and should be the preferred 410 receptor for the virus. Further correlation analysis between viral receptors and the tissue and host specificity of the virus shows that the virus receptor similarity was a significant predictor for mammalian virus cross-species. keywords: host; proteins; receptor; species; virus cache: cord-353554-98uzivsk.txt plain text: cord-353554-98uzivsk.txt item: #688 of 702 id: cord-353731-7xn7m662 author: Heaton, Brook E. title: SRSF protein kinases 1 and 2 are essential host factors for human coronaviruses including SARS-CoV-2 date: 2020-08-18 words: 2241 flesch: 32 summary: Much attention has been focused on targeting viral proteins 65 and their associated enzymatic activities. In addition to targeting viral proteins directly, other antiviral development strategies 72 attempt to target host factors that the virus requires to complete its lifecycle. keywords: cov-2; phosphorylation; protein; sars; srpk1; viral cache: cord-353731-7xn7m662.txt plain text: cord-353731-7xn7m662.txt item: #689 of 702 id: cord-353742-k4gxww2c author: Arévalo, AP title: Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date: 2020-11-02 words: 722 flesch: 11 summary: Overall results demonstrated that viral infection induces the typical MHV disease in infected animals, with livers showing severe hepatocellular necrosis surrounded by a severe lymphoplasmacytic inflammatory infiltration associated with a high hepatic viral load (52,158 AU), while ivermectin administration showed a better health status with lower viral load (23,192 AU; p<0.05) and few livers with histopathological damage (p<0.05), not showing statistical differences with control mice (P=NS). key: cord-353742-k4gxww2c authors: Arévalo, AP; Pagotto, R; Pórfido, J; Daghero, H; Segovia, M; Yamasaki, K; Varela, B; Hill, M; Verdes, JM; Duhalde Vega, M; Bollati-Fogolín, M; Crispo, M title: Ivermectin reduces coronavirus infection in vivo: a mouse experimental model date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.363242 sha: doc_id: 353742 cord_uid: k4gxww2c SARS-CoV2 is a single strand RNA virus member of the type 2 coronavirus family, responsible for causing COVID-19 disease in humans. keywords: coronavirus; infection; ivermectin; mice cache: cord-353742-k4gxww2c.txt plain text: cord-353742-k4gxww2c.txt item: #690 of 702 id: cord-353777-t8q99tlq author: Jia, Yong title: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity date: 2020-04-11 words: 3222 flesch: 46 summary: By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Highlights Based on the currently available genome sequence data, we proved that SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak. keywords: cov-2; human; mutation; protein; receptor; sars cache: cord-353777-t8q99tlq.txt plain text: cord-353777-t8q99tlq.txt item: #691 of 702 id: cord-353877-wzndpcq3 author: Albagi, Sahar Obi Abd title: A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date: 2020-05-20 words: 3749 flesch: 49 summary: Spike peptide (EVFNATRFASVYAWN) interacts with HLA-DPA1*01:03/DPB1*02:01 allele by forming hydrogen bonds with the amino acids Val2, Ser10, Tyr12, Tyr40A, Glu59A, hydrophobic bonds with the amino acids Val2, Phe8, Tyr40A, Ala41A, Ala42A, Asn93A, Leu101A, Leu104A, Trp14, Tyr174A, and pi-pi bonds with the aromatic amino acid Phe8, Ser10, Tyr12, Trp14, Tyr174A. This finding indicates the higher binding affinity of Spike peptide MIAQYTSAL to the MHC I HLA-C1203 allele and supports the MDockPeP keywords: allele; amino; binding; bonds; hla; mhc; nucleocapsid; peptides; spike cache: cord-353877-wzndpcq3.txt plain text: cord-353877-wzndpcq3.txt item: #692 of 702 id: cord-353911-hp6s6ebh author: Petráš, Marek title: Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein date: 2020-11-03 words: 2122 flesch: 42 summary: Vaccine Preparation, characterization and 505 preliminary in vivo studies of inactivated SARS-CoV vaccine Immunization with SARS coronavirus vaccines leads to 510 pulmonary immunopathology on challenge with the SARS virus RNA-Based COVID-19 Vaccine 518 BNT162b2 Selected for a Pivotal Efficacy Study. Design of a Multiepitope-Based Peptide Vaccine 370 against the E Protein of Human COVID-19: An Immunoinformatics Approach Guidelines for the use of flow cytometry and cell sorting in 375 immunological studies (second edition) Inactivated virus vaccines from 378 chemistry to prophylaxis: merits, risks and challenges Safety and immunogenicity of the ChAdOx1 nCoV-386 19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, 387 randomised controlled trial Development of an inactivated vaccine candidate for SARS-CoV-2 An in-silico 397 approach to develop of a multi-epitope vaccine candidate against SARS-CoV-2 398 envelope (E) protein. keywords: antibodies; mice; protein; sars; vaccine; virus cache: cord-353911-hp6s6ebh.txt plain text: cord-353911-hp6s6ebh.txt item: #693 of 702 id: cord-354315-yfn9vaan author: Meirson, Tomer title: Structural basis of SARS-CoV-2 spike protein induced by ACE2 date: 2020-05-24 words: 5201 flesch: 37 summary: Due to inconsistencies in the reported composition of disulfide bonds in the RBD in different structures (Lavillette, et al., 2006; Song, et al., 2018; Walls, et al., 2020; Wrapp, et al., 2020; Yuan, et al., 2017) and to account for possible errors in modeling disulfide bonds (Carpentier, et al., 2010; Kleywegt and Jones, 1995; Villa and Lasker, 2014; Wlodawer, et al., 2008) , we used Disulfide by Design 2.0 (DbD2) to calculate χ3 torsion angles and bond energies (Craig and Dombkowski, 2013) . The DbD2 algorithm could accurately predict the chiralities and positions of disulfide bonds based on energy function, reflecting the geometric characteristics of disulfide bonds among high-quality crystal structures (Craig and Dombkowski, 2013; Wiedemann, et al., 2020) . keywords: ace2; coronavirus; cov-2; disulfide; et al; figure; helix; protein; rbd; receptor; sars; structures cache: cord-354315-yfn9vaan.txt plain text: cord-354315-yfn9vaan.txt item: #694 of 702 id: cord-354725-lqio7l8k author: Arumugam, Arunkumar title: A Rapid COVID-19 RT-PCR Detection Assay for Low Resource Settings date: 2020-04-30 words: 3492 flesch: 60 summary: (Table 3) Rapid PCR Rapid PCR was conducted using two water baths maintained at 95°C and 55°C ( Table 4) . PCR tubes used in this study was Cepheid SmartCycler reaction tubes and thin-walled polypropylene PCR tubes (Cat. keywords: covid-19; minutes; pcr; samples; tubes; water cache: cord-354725-lqio7l8k.txt plain text: cord-354725-lqio7l8k.txt item: #695 of 702 id: cord-354868-pqn59ojj author: Yao, Hebang title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2 date: 2020-09-25 words: 3260 flesch: 49 summary: To screen RBD binders by size exclusion chromatography (SEC) using unpurified sybodies, RBD was fluorescently labelled as follows. Crystallographic studies reveal that SR31 binds to RBD at a conserved and ‘greasy’ site distal to RBM. keywords: antibodies; binding; cov-2; fig; nanobodies; rbd; sars; sr31 cache: cord-354868-pqn59ojj.txt plain text: cord-354868-pqn59ojj.txt item: #696 of 702 id: cord-355397-y69bk5jc author: Caruso, Ícaro P. title: Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date: 2020-09-06 words: 5131 flesch: 44 summary: We probed dsRNAs’ Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event. keywords: complex; dsns; dsrna; dstrs; figure; melting; model; ntd; protein cache: cord-355397-y69bk5jc.txt plain text: cord-355397-y69bk5jc.txt item: #697 of 702 id: cord-355728-wivk0bm0 author: Schoof, Michael title: An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation date: 2020-08-17 words: 3664 flesch: 60 summary: Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. A prototypical example of this class is nanobody Nb6, which 129 binds to Spike* and to RBD alone with a KD of 210 nM and 41 nM, respectively ( Fig. keywords: binding; fig; mnb6; nb6; rbd; spike; tri cache: cord-355728-wivk0bm0.txt plain text: cord-355728-wivk0bm0.txt item: #698 of 702 id: cord-355758-tk7eturq author: Berrio, Alejandro title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 words: 2181 flesch: 28 summary: The first is Nsp4, which encodes a similarities to, but also notable differences from, that of SARS-Cov-2 (Fig 1) . In the case of Nsp4 protein, two nearly adjacent nonsynonymous substitutions at residues 380 430 and 382 occurred on the branch leading to SARS-CoV-2 ( Fig 3B) . keywords: coronavirus; cov-2; protein; rna; sars; selection; structure cache: cord-355758-tk7eturq.txt plain text: cord-355758-tk7eturq.txt item: #699 of 702 id: cord-355811-aq7p1uxo author: Węglarz-Tomczak, Ewelina title: Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds date: 2020-05-21 words: 2014 flesch: 49 summary: Interestingly, all derivatives except 1a blocked completely PL pro CoV2 at a high concentration of the inhibitor (20μM), but only some of them ( 1c , 1d , 1e and 2d , 2e ) inhibited PL pro SARS while rest of them failed. The inhibitor was screened against recombinant PL pro SARS and PL pro CoV2 at 37°C in the assay buffer as described above. keywords: cov-2; cov2; ebselen; pro; sars cache: cord-355811-aq7p1uxo.txt plain text: cord-355811-aq7p1uxo.txt item: #700 of 702 id: cord-356005-zhwtlik6 author: Yazhini, Arangasamy title: D614G substitution enhances the stability of trimeric SARS-CoV-2 spike protein date: 2020-11-02 words: 2628 flesch: 37 summary: Several studies to characterize the new virus expressing G614 variant show that it exhibits increased infectivity compared to the ancestral virus having D614 spike protein. Here, using in-silico mutagenesis and energy calculations, we analyzed inter-residue interaction energies and thermodynamic stability of the dominant (G614) and the ancestral (D614) variants of spike protein trimer in ‘closed’ and ‘partially open’ conformations. keywords: d614; frustration; protein; spike cache: cord-356005-zhwtlik6.txt plain text: cord-356005-zhwtlik6.txt item: #701 of 702 id: cord-356090-oj3d9ail author: Gorgun, D. title: Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane date: 2020-10-27 words: 6071 flesch: 42 summary: A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster A review of coronavirus disease-2019 (COVID-19) Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus Coronavirus membrane fusion mechanism offers a potential target for antiviral development Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin Mechanisms of viral membrane fusion and its inhibition Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme Virus membrane-fusion proteins: more than one way to make a hairpin Coronavirus binding and entry. To analyze the ensemble of FP membrane binding configurations captured in the 18 HMMM simulations where stable membrane binding was observed, clustering was performed using the z-distances between the the side chain COM and the membrane lipid phosphate plane. keywords: binding; cov2; fig; fusion; lipid; loop; membrane; mode; protein; residues; sars cache: cord-356090-oj3d9ail.txt plain text: cord-356090-oj3d9ail.txt item: #702 of 702 id: cord-356264-q0yqnlyl author: Armijos-Jaramillo, Vinicio title: SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability date: 2020-03-23 words: 4990 flesch: 45 summary: To resolve these ambiguities in positive selection sites we calculate putative selection sites with CODEML (using Bayes Empirical Bayes from M2 and M8 models) and FUBAR with different datasets reflecting the addition of novel sequences to online repositories (broad, closer, closer without MN996532 and MT084071 and closer without MT084071) and we obtain different results. This result does not disregard the presence of positive selection sites in SARS-CoV-2, nonetheless, it shows the limitation of the methods to identify with precision specific sites under positive selection in a precise taxon of a phylogenetic tree. keywords: coronavirus; cov-2; hace2; human; protein; receptor; sars; selection; sites cache: cord-356264-q0yqnlyl.txt plain text: cord-356264-q0yqnlyl.txt