# bib

id: cord-007073-soov8q3q
author: Wang, Claire Y T
date: 2019-08-13
extension: .txt
mime: text/plain
words: 3973
sentence: 176
flesch: 47
cache: cache/cord-007073-soov8q3q.txt
txt: txt/cord-007073-soov8q3q.txt
title:
  Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study

summary:
  Beyond seroprevalence, few studies describe the epidemiology and clinical characteristics of PeV infections in the community A similar pattern of PeV infection, but with lower incidence rates, was observed in 200 Finnish children enrolled between 1996 and 2007 where by age 12 months 22% had PeV detected in their stools on at least 1 occasion, which increased to 48% approaching their second birthday [15] .


id: cord-103081-k7ev5qkn
author: Janosevic, Danielle
date: 2020-05-30
extension: .txt
mime: text/plain
words: 4512
sentence: 201
flesch: 49
cache: cache/cord-103081-k7ev5qkn.txt
txt: txt/cord-103081-k7ev5qkn.txt
title:
  The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline

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.


id: cord-342012-1w3x0g42
author: Wu, Joseph T.
title: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China
date: 2020-03-19
extension: .txt
mime: text/plain
words: 5333
sentence: 209
flesch: 48
cache: cache/cord-342012-1w3x0g42.txt
txt: txt/cord-342012-1w3x0g42.txt
summary:
  Public health control measures widely imposed in China since the Wuhan alert have also kept case numbers down elsewhere, so that their health systems are not nearly as overwhelmed beyond surge capacity, thus again perhaps leading to better outcomes 6, 8 . Let G be the cumulative number of death cases in Wuhan as of 25 February 2020 (time T).


id: cord-103638-n5kpvsvg
author: Nguyen, Long T.
date: 2020-04-14
extension: .txt
mime: text/plain
words: 5390
sentence: 206
flesch: 48
cache: cache/cord-103638-n5kpvsvg.txt
txt: txt/cord-103638-n5kpvsvg.txt
title:
  Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

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.


id: cord-325155-lqzgz6p3
author: Gallo, Juan E.
title: Hypertension and the roles of the 9p21.3 risk locus: classic findings and new association data
date: 2020-09-15
extension: .txt
mime: text/plain
words: 5291
sentence: 155
flesch: 34
cache: cache/cord-325155-lqzgz6p3.txt
txt: txt/cord-325155-lqzgz6p3.txt
summary:
  Risk alleles were defined as those for which mean difference or beta was positive (continuous variables), for which effect size was greater than one (dichotomous variables), or that were explicitly labeled as 'risk allele'. Basic statistical analysis in genetic case-control studies The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals Genomewide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits Genomes Project Consortium.


id: cord-265418-yqe9vdj1
author: Kumar, Nilesh
title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis
date: 2020-04-11
extension: .txt
mime: text/plain
words: 5303
sentence: 247
flesch: 47
cache: cache/cord-265418-yqe9vdj1.txt
txt: txt/cord-265418-yqe9vdj1.txt
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 .


id: cord-006034-xfyavk3m
author: Gil-Cruz, Cristina
date: 2016-10-31
extension: .txt
mime: text/plain
words: 5519
sentence: 194
flesch: 39
cache: cache/cord-006034-xfyavk3m.txt
txt: txt/cord-006034-xfyavk3m.txt
title:
  Fibroblastic reticular cells regulate intestinal inflammation via IL-15-mediated control of group 1 ILCs

summary:
  chaperones IL-15 to stable dendritic cell membrane complexes that activate NK cells via trans presentation An innately dangerous balancing act: intestinal homeostasis, inflammation, and colitis-associated cancer Initial and innate responses to viral infections--pattern setting in immunity or disease Dendritic cells prime natural killer cells by trans-presenting interleukin 15 Differential responses of immune cells to type I interferon contribute to host resistance to viral infection Intraepithelial type 1 innate lymphoid cells are a unique subset of IL-12-and IL-15-responsive IFN-γ-producing cells Mesenchymal cells of the intestinal lamina propria ANOVA with Tukey's post-test or two-way ANOVA with Benferroni's post-test. The particular confines of these immune reactions are generated by fibroblastic reticular cells (FRCs) that not only provide structural support and guidance to immune cells but also actively participate in shaping immune responsiveness 11, 12 .


id: cord-013658-vygiate7
author: Yang, Jian
date: 2020-06-01
extension: .txt
mime: text/plain
words: 6490
sentence: 253
flesch: 37
cache: cache/cord-013658-vygiate7.txt
txt: txt/cord-013658-vygiate7.txt
title:
  Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes

summary:
  However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l).


id: cord-322129-uyswj4ow
author: Melin, Amanda D.
title: Comparative ACE2 variation and primate COVID-19 risk
date: 2020-10-27
extension: .txt
mime: text/plain
words: 6328
sentence: 227
flesch: 40
cache: cache/cord-322129-uyswj4ow.txt
txt: txt/cord-322129-uyswj4ow.txt
summary:
  Some of our results, such as the uniform conservation of ACE2 binding sites among catarrhines, backed up by the demonstrated high susceptibility of humans and other catarrhines to SARS-CoV-2, should give a good degree of confidence of high levels of risk. Great apes, COVID-19 and the SARS CoV-2 joint statement of the IUCN SSC Wildlife Health Specialist Group and the Primate Specialist Group Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus.


id: cord-336209-grpi7gnc
author: Allen, Cameron
date: 2020-08-12
extension: .txt
mime: text/plain
words: 6687
sentence: 209
flesch: 31
cache: cache/cord-336209-grpi7gnc.txt
txt: txt/cord-336209-grpi7gnc.txt
title:
  Delivering an enabling environment and multiple benefits for land degradation neutrality: Stakeholder perceptions and progress

summary:
  The analysis is based on a global survey of LDN stakeholders and a review of national LDN Target Setting Programme (TSP) reports from a wide selection of countries. LDN implementation also requires that associated policy procedures in day-to-day operations are in place to enforce, monitor, and verify the impacts of national policies (Chasek et al., 2015) .


id: cord-004126-u6ts87ur
author: Furuyama, Wakako
date: 2020-01-10
extension: .txt
mime: text/plain
words: 6045
sentence: 235
flesch: 44
cache: cache/cord-004126-u6ts87ur.txt
txt: txt/cord-004126-u6ts87ur.txt
title:
  A single dose of a vesicular stomatitis virus-based influenza vaccine confers rapid protection against H5 viruses from different clades

summary:
  Cumulative number of confirmed human cases for avian influenza A(H5N1) reported to WHO Novel Eurasian highly pathogenic avian influenza A H5 viruses in wild birds Novel reassortant influenza A(H5N8) viruses among inoculated domestic and wild ducks Intercontinental spread of Asian-origin H5N8 to North America through Beringia by migratory birds Reassortant highly pathogenic influenza A H5N2 virus containing gene segments related to Eurasian H5N8 in British Columbia Novel reassortant highly pathogenic H5N6 avian influenza viruses in poultry in China Characterization of three H5N5 and one H5N8 highly pathogenic avian influenza viruses in China Avian flu: isolation of drug-resistant H5N1 virus Lethal H5N1 influenza viruses escape host anti-viral cytokine responses Scientific barriers to developing vaccines against avian influenza viruses Universal vaccines and vaccine platforms to protect against influenza viruses in humans and agriculture Emerging vaccines for influenza Resistance to influenza virus and vesicular stomatitis virus conferred by expression of human MxA protein Vesicular stomatitis virus-based vaccines against Lassa and Ebola viruses An effective AIDS vaccine based on live attenuated vesicular stomatitis virus recombinants A VSV-based Zika virus vaccine protects mice from lethal challenge Single-dose liveattenuated Nipah virus vaccines confer complete protection by eliciting antibodies directed against surface glycoproteins VSV-EBOV rapidly protects macaques against infection with the 2014/15 Ebola virus outbreak strain The vesicular stomatitis virus-based Ebola virus vaccine: from concept to clinical trials Ebola: lessons on vaccine development Keeping your cool -doing Ebola research during an emergency Single-dose live-attenuated vesicular stomatitis virus-based vaccine protects African green monkeys from Nipah virus disease Protective efficacy of a bivalent recombinant vesicular stomatitis virus vaccine in the Syrian hamster model of lethal Ebola virus infection Characterization of a bivalent vaccine capable of inducing protection against both Ebola and cross-clade H5N1 influenza in mice Vesicular stomatitis virus-based vaccine protects hamsters against lethal challenge with Andes virus A single immunization with soluble recombinant trimeric hemagglutinin protects chickens against highly pathogenic avian influenza virus H5N1 Recombinant trimeric HA protein immunogenicity of H5N1 avian influenza viruses and their combined use with inactivated or adenovirus vaccines Vesicular stomatitis virus vectors expressing avian influenza H5 HA induce cross-neutralizing antibodies and long-term protection Poultry and the influenza H5N1 outbreak in Hong Kong, 1997: abridged chronology and virus isolation H5N1 highly pathogenic avian influenza: timeline of major events Brief literature review for the WHO global influenza research agenda-highly pathogenic avian influenza H5N1 risk in humans Potent vesicular stomatitis virus-based avian influenza vaccines provide long-term sterilizing immunity against heterologous challenge Single low-dose VSV-EBOV vaccination protects cynomolgus macaques from lethal Ebola challenge Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1) Antigenic and genetic characteristics of zoonotic influenza viruses and development of candidate vaccine viruses for pandemic preparedness Haemagglutination-inhibiting antibody to influenza virus Cross-clade immunity in cats vaccinated with a canarypoxvectored avian influenza vaccine Towards a universal influenza vaccine: different approaches for one goal Enhanced immunogenicity of stabilized trimeric soluble influenza hemagglutinin Antibodies are necessary for rVSV/ZEBOV-GP-mediated protection against lethal Ebola virus challenge in nonhuman primates Ebola haemorrhagic fever VSVDeltaG/EBOV GP-induced innate protection enhances natural killer cell activity to increase survival in a lethal mouse adapted Ebola virus infection Cell culture-based influenza vaccines: a necessary and indispensable investment for the future Ebola vaccines in clinical trial: the promising candidates Properties of replication-competent vesicular stomatitis virus vectors expressing glycoproteins of filoviruses and arenaviruses We thank the animal care staff of the Rocky Mountain Veterinary Branch (NIAID, NIH) for their support of the animal experiments. Next, we performed a series of studies measuring the rate and extent of vaccine virus growth over time.


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
extension: .txt
mime: text/plain
words: 6656
sentence: 220
flesch: 41
cache: cache/cord-103683-xcsal8vk.txt
txt: txt/cord-103683-xcsal8vk.txt
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.


id: cord-001270-l8aa9cl3
author: Wongsrikeao, Pimprapar
title: Antiviral restriction factor transgenesis in the domestic cat
date: 2011-09-11
extension: .txt
mime: text/plain
words: 6277
sentence: 246
flesch: 41
cache: cache/cord-001270-l8aa9cl3.txt
txt: txt/cord-001270-l8aa9cl3.txt
summary:
  To investigate whether more than one transgene could be expressed in cat embryos in a single step by PVSMI, we microinjected 418 oocytes with single-or dual-transgene lentiviral vectors. A practical capability for cat transgenesis is needed to realize the distinctive potential of research on this neurobehaviorally complex, accessible species for advancing human and feline health.


id: cord-295482-qffg6r91
author: Wong, Alan H. M.
title: Receptor-binding loops in alphacoronavirus adaptation and evolution
date: 2017-11-23
extension: .txt
mime: text/plain
words: 6621
sentence: 244
flesch: 42
cache: cache/cord-295482-qffg6r91.txt
txt: txt/cord-295482-qffg6r91.txt
summary:
  The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding Pre-fusion structure of a human coronavirus spike protein Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains Contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution Effects of human anti-spike protein receptor binding domain antibodies on severe acute respiratory syndrome coronavirus neutralization escape and fitness The Evolution and Emergence of RNA Viruses Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes Clinical isolates of human coronavirus 229E bypass the endosome for cell entry The role of mutational robustness in RNA virus evolution HIV pathogenesis: dynamics and genetics of viral populations and infected cells Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains The behaviour of recent isolates of human respiratory coronavirus in vitro and in volunteers: evidence of heterogeneity among 229E-related strains Differences in neutralizing antigenicity between laboratory and clinical isolates of HCoV-229E isolated in Japan in 2004-2008 depend on the S1 region sequence of the spike protein The X-ray crystal structure of human aminopeptidase N reveals a novel dimer and the basis for peptide processing Structural bases of coronavirus attachment to host aminopeptidase N and its inhibition by neutralizing antibodies Mutational analysis of aminopeptidase N, a receptor for several group 1 coronaviruses, identifies key determinants of viral host range Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection Human coronavirus 229E: receptor binding domain and neutralization by soluble receptor at 37 degrees C Broadly neutralizing antiviral antibodies As such, adaptation in a new species, changes in tissue tropism, and differences in receptor expression levels can all lead to changes in receptor binding affinity 29, 31, 48 .


id: cord-256652-ent4vu3z
author: Tan, Joshua
date: 2018-03-19
extension: .txt
mime: text/plain
words: 6596
sentence: 227
flesch: 37
cache: cache/cord-256652-ent4vu3z.txt
txt: txt/cord-256652-ent4vu3z.txt
title:
  A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein

summary:
  The ability of monoclonal antibodies and serum to prevent PfSPZ invasion and traversal in vitro was tested as previously described 44, 48 . To test specific antibody binding, ELISA plates were either directly coated with 1 μg ml −1 of recombinant PfCSP (Sanaria ® , sequence previously shown 21 ), 2 μg ml −1 of peptide 22-110 or 1 μg ml −1 of peptide 282-383, or first with 10 μg ml −1 of avidin (Sigma-Aldrich), followed by 10 μg ml −1 of NANP18 (NANPNANPNANPNANPNA), NPDP19 (KQPADGNPDPNANPNVDPN), NPDP15 (KQPADGNPDPNANPN) or various NPDP19 peptide mutants.


id: cord-320325-sjab8zsk
author: Mendez, Aaron S
date: 2018-12-14
extension: .txt
mime: text/plain
words: 6521
sentence: 236
flesch: 45
cache: cache/cord-320325-sjab8zsk.txt
txt: txt/cord-320325-sjab8zsk.txt
title:
  Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX

summary:
  Our data suggest that this is likely because the K2-31 RNA lacks the additional residues necessary for SOX binding site found in both LIMD1 and GFP. This mutant has been previously identified to block SOX cleavage in vivo (20) .


id: cord-288824-sygnmiun
author: Lam, SD
date: 2020-08-19
extension: .txt
mime: text/plain
words: 7363
sentence: 315
flesch: 48
cache: cache/cord-288824-sygnmiun.txt
txt: txt/cord-288824-sygnmiun.txt
title:
  SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

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.


id: cord-340907-j9i1wlak
author: Zarai, Yoram
title: Evolutionary selection against short nucleotide sequences in viruses and their related hosts
date: 2020-04-27
extension: .txt
mime: text/plain
words: 8168
sentence: 336
flesch: 41
cache: cache/cord-340907-j9i1wlak.txt
txt: txt/cord-340907-j9i1wlak.txt
summary:
  The virus and host coding sequences and association information was retrieved from a published database. We provide various novel discoveries that may shed light on the evolution of viral DNA sequences and on the virus co-evolution with its respective hosts.


id: cord-263868-ewnf96cz
author: Srivastava, Mayank
title: Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor
date: 2020-08-04
extension: .txt
mime: text/plain
words: 7640
sentence: 312
flesch: 45
cache: cache/cord-263868-ewnf96cz.txt
txt: txt/cord-263868-ewnf96cz.txt
summary:
  We devised and synthesized a multifunctional chemical probe ( Fig. 1a; Supplementary Figs. 1-3) bearing a labeling group that conjugates the probe to the ZIKV surface, a photo-reactive group that allows for covalent crosslinking of ZIKV proteins to interacting host cell proteins upon UV exposure, and an isolation tag of biotin for purifying the interacting proteins for quantitative MS analysis, thus facilitating the investigation of host-pathogen interactomes in a time-resolved manner (Fig. 1b) . 4F2 cell-surface antigen heavy chain (SLC3A2) was reported interacting with ZIKV NS4B protein and was indicated as a candidate host factor for ZIKV infection 12 .


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
extension: .txt
mime: text/plain
words: 8488
sentence: 316
flesch: 45
cache: cache/cord-103892-v6gkubd4.txt
txt: txt/cord-103892-v6gkubd4.txt
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.


id: cord-003318-abs9rvjk
author: Liu, Ming
title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity
date: 2018-05-01
extension: .txt
mime: text/plain
words: 7893
sentence: 360
flesch: 46
cache: cache/cord-003318-abs9rvjk.txt
txt: txt/cord-003318-abs9rvjk.txt
summary:
  Likewise, E-17β-G (9a) was acetylated by EcSGA1 to form monoacetylated products 9b-9e in a ratio of 80:10:6:4. shown in Supplementary Information Fig. 1B and Supplementary Information Fig. S4 ) was first assessed as sugar Table S3 ).


id: cord-015527-ph576eji
author: Mostajo, Nelly F
date: 2019-09-30
extension: .txt
mime: text/plain
words: 8399
sentence: 305
flesch: 48
cache: cache/cord-015527-ph576eji.txt
txt: txt/cord-015527-ph576eji.txt
title:
  A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

summary:
  Other ncRNAs are currently unknown from bat genomes or not well documented. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 RNA-Seq gene expression estimation with read mapping uncertainty Rfam: an RNA family database Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families Non-coding RNA analysis using the Rfam database Infernal 1.0: inference of RNA alignments Infernal 1.1: 100-fold faster RNA homology searches RALEE--RNA Alignment editor in Emacs RNAmmer: consistent and rapid annotation of ribosomal RNA genes tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Matching of Soulmates: coevolution of snoRNAs and their targets Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing LNCipedia 5: towards a reference set of human long non-coding RNAs MITOS: Improved de novo metazoan mitochondrial genome annotation A comprehensive study of de novo genome assemblers: current challenges and future prospective Genome-wide signatures of convergent evolution in echolocating mammals A high-resolution map of human evolutionary constraint using 29 mammals Comparative analysis of bat genomes provides insight into the evolution of flight and immunity The genomes of two bat species with long constant frequency echolocation calls Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing The Egyptian rousette genome reveals unexpected features of bat antiviral immunity Reference sequence (RefSeq) database at [NCBI: current status, taxonomic expansion, and functional annotation sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis)


id: cord-343107-oj1re34k
author: Zhou, Haixia
date: 2019-07-11
extension: .txt
mime: text/plain
words: 8683
sentence: 317
flesch: 45
cache: cache/cord-343107-oj1re34k.txt
txt: txt/cord-343107-oj1re34k.txt
title:
  Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein

summary:
  It indicated that the combination of 7D10 with MERS-27 exhibited neither synergy nor antagonism. Mechanism of 7D10 neutralization. Here, we showed that 7D10 neutralization is not solely dependent on DPP4-binding competition, and its inhibition of the S trimer conformational transition after cell attachment also plays a significant role in the neutralization.


id: cord-342047-pm3i54mb
author: Du Preez, Andrea
date: 2020-09-21
extension: .txt
mime: text/plain
words: 8842
sentence: 279
flesch: 27
cache: cache/cord-342047-pm3i54mb.txt
txt: txt/cord-342047-pm3i54mb.txt
title:
  The type of stress matters: repeated injection and permanent social isolation stress in male mice have a differential effect on anxiety- and depressive-like behaviours, and associated biological alterations

summary:
  Mice were exposed to one of four experimental conditions after an initial 1week habituation period: (i) stress-free control group (socially-housed in pairs and injection naive-Group 1); (ii) repeated injection stress (sociallyhoused in pairs and repeatedly injected-Group 2); (iii) social isolation stress (permanent social isolation and injection naive-Group 3); and (iv) combined stress (permanent isolation and repeatedly injected-Group 4). We first assessed the behavioural effects associated with chronic stress exposure and found that all stress-exposed mice, irrespective of the type of stress, exhibited significantly increased anxiety-like behaviour in the OFT (Fig. 2a) relative to control animals, as shown by significantly less time in the centre of the OFT arena (−59% in repeatedly injected animals, −92% in the socially isolated mice and −74% in animals exposed to combined stress spent (Fig. 2a) ).


id: cord-198395-v15queyh
author: Storch, David-Maximilian
title: Incentive-driven discontinuous transition to high ride-sharing adoption
date: 2020-08-25
extension: .txt
mime: text/plain
words: 8961
sentence: 430
flesch: 48
cache: cache/cord-198395-v15queyh.txt
txt: txt/cord-198395-v15queyh.txt
summary:
  When ζ > the system is in a low-sharing regime where users request shared rides at low numbers of users S but the number of shared ride requests saturates and becomes constant at high S (S share < S, light green triangles, red line in panel b). Fraction of shared ride requests from different origins (red) served by the four major for-hire vehicle transportation service providers in New York City by destination zone (January -December 2019)


id: cord-013614-j6h338qa
author: Liu, Xiaojing
title: ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells
date: 2020-04-30
extension: .txt
mime: text/plain
words: 8241
sentence: 405
flesch: 50
cache: cache/cord-013614-j6h338qa.txt
txt: txt/cord-013614-j6h338qa.txt
summary:
  Gene knockout cells were cultured with DNA damage chemicals at IC 20 for 12 days (from Day 0 to Day 12) before harvested for genomic DNA purification. Interestingly, ERCC6L2 deficient cells were depleted upon Zeocin treatment which induces DSBs (Fig. 1d ), but not in the presence of Cisplatin or Veliparib treatment which creates ICLs and SSBs, respectively (Fig. 1e ).


id: cord-348972-r94fhpe0
author: Gussow, Ayal B.
title: Machine-learning approach expands the repertoire of anti-CRISPR protein families
date: 2020-07-29
extension: .txt
mime: text/plain
words: 9657
sentence: 401
flesch: 49
cache: cache/cord-348972-r94fhpe0.txt
txt: txt/cord-348972-r94fhpe0.txt
summary:
  We show that this method is significantly predictive of Acrs, compile a collection of 2500 previously undetected predicted Acrs families and examine the top candidates in detail, including experimental validation. Consequently, we removed protein families with an average directon size of more than five genes.


id: cord-024810-z323cl40
author: Wicaksono, Irmandy
date: 2020-04-23
extension: .txt
mime: text/plain
words: 9626
sentence: 373
flesch: 47
cache: cache/cord-024810-z323cl40.txt
txt: txt/cord-024810-z323cl40.txt
title:
  A tailored, electronic textile conformable suit for large-scale spatiotemporal physiological sensing in vivo

summary:
  Bluetooth low energy-based washable wearable activity motion and electrocardiogram textronic monitoring and communicating system BioWatch: estimation of heart and breathing rates from wrist motions Theory and developments in an unobtrusive cardiovascular system representation: ballistocardiography Epidermal mechano-acoustic sensing electronics for cardiovascular diagnostics and human-machine interfaces Annual International Conference of the IEEE Engineering in Medicine and Biology-Proceedings SensorKnit: architecting textile sensors with machine knitting. Sensor data in these figures are separated in terms of their respective location: on the posterior side, anterior side, both arms, and the neck.


id: cord-315483-l6dm82pp
author: Santhakumar, Diwakar
date: 2018-05-01
extension: .txt
mime: text/plain
words: 10827
sentence: 401
flesch: 39
cache: cache/cord-315483-l6dm82pp.txt
txt: txt/cord-315483-l6dm82pp.txt
title:
  Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses

summary:
  The second exon codes the rest of the ORF (1435 bps) and 3′ untranslated regions (UTR) for chicken IFIT5 gene. Chicken cells were transfected with 500 ng of mammalian expression vectors encoding V5-tagged chIFIT5 for 24 hours and were left untreated (NDV-) or were treated with 1 MOI of NDV-GFP (NDV+) for another 24 hours before fixation, staining for nucleus (blue), chIFIT5 (red) and GFP marker (NDV).


id: cord-288916-i8ukefp8
author: Gómez-Herranz, Maria
title: The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis
date: 2019-04-02
extension: .txt
mime: text/plain
words: 11737
sentence: 510
flesch: 45
cache: cache/cord-288916-i8ukefp8.txt
txt: txt/cord-288916-i8ukefp8.txt
summary:
  However, as the oesophagus squamous epithelium also exhibits IFITM1 protein expression in the basal cells of normal squamous epithelium (Protein Atlas, Supplementary Fig. 4) , and the normal oesophagus is not noted for HPV infection, we would suggest that the expression of IFITM1 protein in basal cells is not related to HPV status. Attenuation of IFITM1 protein expression can inhibit growth, invasion, and/or migration of cancer cells [34] .


id: cord-318079-jvx1rh7g
author: Hinch, R.
date: 2020-09-22
extension: .txt
mime: text/plain
words: 5365
sentence: 249
flesch: 43
cache: cache/cord-318079-jvx1rh7g.txt
txt: txt/cord-318079-jvx1rh7g.txt
title:
  OpenABM-Covid19 - an agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

summary:
  We therefore took the decision to model interactions using three social networks (household/occupational/random) with non-pharmaceutical interventions affecting each network differently. Modelling contact tracing requires the model to keep a record of previous interventions for a set number of days.


id: cord-333145-a20dlaxn
author: Johnson, Todd A.
title: Association of an IGHV3-66 gene variant with Kawasaki disease
date: 2020-10-26
extension: .txt
mime: text/plain
words: 6446
sentence: 218
flesch: 41
cache: cache/cord-333145-a20dlaxn.txt
txt: txt/cord-333145-a20dlaxn.txt
summary:
  In previous literature, polyclonal activation and increase of B cells [34, 35] and detection of auto-antibodies against components of vascular endothelial cells or neutrophils in peripheral blood of acute KD patients have been documented [36, 37] . However, a recent transcriptomic study revealed downregulation of genes related to BCR signaling in acute KD patients [39] .


id: cord-350286-n7ylgqfu
author: Giri, Rajanish
date: 2020-04-03
extension: .txt
mime: text/plain
words: 15857
sentence: 672
flesch: 51
cache: cache/cord-350286-n7ylgqfu.txt
txt: txt/cord-350286-n7ylgqfu.txt
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

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.


id: cord-286217-3uklf2u2
author: Jiang, He-wei
title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses
date: 2020-07-14
extension: .txt
mime: text/plain
words: 6841
sentence: 316
flesch: 49
cache: cache/cord-286217-3uklf2u2.txt
txt: txt/cord-286217-3uklf2u2.txt
summary:
  One part of a sub-microarray showed the IgG responses of two controls, i.e., LC169 and NC96 against N proteins, N-Cter and N-Nter indicates the C-terminal and N-terminal of N protein, respectively. Indeed, a variety of protein microarrays have already been constructed and successfully applied to serum antibody profiling, such as the Mycobacterium tuberculosis proteome microarray 21 , the SARS-CoV protein microarray 12 , the Dengue virus protein microarray 22 and the influenza virus protein microarray 23 .


id: cord-271693-7tg21up3
author: Zheng, Fan
title: Identifying persistent structures in multiscale ‘omics data
date: 2020-10-03
extension: .txt
mime: text/plain
words: 4895
sentence: 230
flesch: 43
cache: cache/cord-271693-7tg21up3.txt
txt: txt/cord-271693-7tg21up3.txt
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.


id: cord-268645-5op2m7pu
author: Wu, Zhiqiang
date: 2015-08-11
extension: .txt
mime: text/plain
words: 5953
sentence: 194
flesch: 40
cache: cache/cord-268645-5op2m7pu.txt
txt: txt/cord-268645-5op2m7pu.txt
title:
  Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases

summary:
  key: cord-268645-5op2m7pu authors: Wu, Zhiqiang; Yang, Li; Ren, Xianwen; He, Guimei; Zhang, Junpeng; Yang, Jian; Qian, Zhaohui; Dong, Jie; Sun, Lilian; Zhu, Yafang; Du, Jiang; Yang, Fan; Zhang, Shuyi; Jin, Qi title: Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date: 2015-08-11 journal: The ISME Journal DOI: 10.1038/ismej.2015.138 sha: doc_id: 268645 cord_uid: 5op2m7pu Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. In conclusion, the understanding of the viral community characteristics, genetics and ecological distribution of bat viruses could enable the rapid identification of novel viruses with variant genomes and could thus facilitate the tracing of EIDs in bats.


id: cord-322286-2de6r1h6
author: Vandewege, Michael W
date: 2020-07-22
extension: .txt
mime: text/plain
words: 6217
sentence: 239
flesch: 38
cache: cache/cord-322286-2de6r1h6.txt
txt: txt/cord-322286-2de6r1h6.txt
title:
  Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

summary:
  Selection analyses among bat genes have generally been limited to few species for specific purposes (Shen et al. 2010; From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation.


id: cord-346054-k84rcpav
author: Niespodziana, Katarzyna
title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze
date: 2018-06-18
extension: .txt
mime: text/plain
words: 7427
sentence: 248
flesch: 39
cache: cache/cord-346054-k84rcpav.txt
txt: txt/cord-346054-k84rcpav.txt
summary:
  3a (right column) results from the PCR testing performed using VP4-VP2specific primers in 108 of the 120 children 35 , which showed that the nucleic acid-based detection of virus strains was negative for approximately 25% of children with increases of RV peptide-specific IgG levels which may indicate a higher sensitivity of serology vs. PCR in these children. There were also 14 children without increases of RV peptide-specific antibody responses who had positive PCR results (Fig. 3a, bottom) .


id: cord-351837-vasuu70k
author: Shannon, Ashleigh
date: 2020-09-17
extension: .txt
mime: text/plain
words: 6551
sentence: 244
flesch: 43
cache: cache/cord-351837-vasuu70k.txt
txt: txt/cord-351837-vasuu70k.txt
title:
  Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis

summary:
  Accepted: 10 August 2020; Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage RNA 3′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex Discovery of an RNA virus 3′→5′ exoribonuclease that is critically involved in coronavirus RNA synthesis High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants Understanding the mechanism of the broad-spectrum antiviral activity of favipiravir (T-705): key role of the F1 motif of the viral polymerase Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus Remdesivir is a direct-acting antiviral that inhibits RNAdependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency Nucleoside analogues for the treatment of coronavirus infections Favipiravir as a potential countermeasure against neglected and emerging RNA viruses Determining the mutation bias of favipiravir in influenza virus using next-generation sequencing Antiviral efficacy of favipiravir against Ebola virus: a translational study in cynomolgus macaques The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent Expression, purification, and characterization of SARS coronavirus RNA polymerase One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors Structure of the RNA-dependent RNA polymerase from COVID-19 virus Structure of replicating SARS-CoV-2 polymerase Continuous and discontinuous RNA synthesis in coronaviruses Synthesis of T-705-ribonucleoside and T-705-ribonucleotide and studies of chemical stability Cell line-dependent activation and antiviral activity of T-1105, the non-fluorinated analogue of T-705 (favipiravir) Prodrugs of the phosphoribosylated forms of hydroxypyrazinecarboxamide pseudobase T-705 and its de-fluoro analogue T-1105 as potent influenza virus inhibitors T-705 (Favipiravir) induces lethal mutagenesis in influenza A H1N1 viruses in vitro Extinction of west nile virus by favipiravir through lethal mutagenesis Lethal mutagenesis of hepatitis C virus induced by favipiravir Favipiravir elicits antiviral mutagenesis during virus replication in vivo Mechanism of action of T-705 ribosyl triphosphate against influenza virus RNA polymerase The ambiguous basepairing and high substrate efficiency of T-705 (Favipiravir) Ribofuranosyl 59-triphosphate towards influenza A virus polymerase Signatures of nucleotide analog incorporation by an RNAdependent RNA polymerase revealed using high-throughput magnetic tweezers Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics Polymerase (3Dpol): assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub) Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability A quantitative stopped-flow fluorescence assay for measuring polymerase elongation rates Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex Characterization of the elongation complex of dengue virus RNA polymerase: assembly, kinetics of nucleotide incorporation, and fidelity Structure-function relationships underlying the replication fidelity of viral RNA-dependent RNA polymerases Viral mutation rates A comprehensive superposition of viral polymerase structures Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity The SARScoronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension A second, non-canonical RNA-dependent RNA polymerase in SARS Coronavirus Identification and characterization of a human coronavirus 229E nonstructural protein 8-associated RNA 3′-terminal adenylyltransferase activity Global Kinetic Explorer: a new computer program for dynamic simulation and fitting of kinetic data In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication Phylogenetically based establishment of a dengue virus panel, representing all available genotypes, as a tool in dengue drug discovery Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral We thank Magali Gilles and Karine Alvarez for excellent technical support, as well as Prs. C. Drosten and F. Drexler for providing the SARS-CoV-2 through EVA-GLOBAL (European Union's Horizon 2020 programme, GA 871029). As with all positive strand RNA viruses, an RdRp lies at the core of the viral replication machinery and for CoVs this is the nsp12 protein.


id: cord-323307-nu9ib62h
author: Dong, Dong
title: The genomes of two bat species with long constant frequency echolocation calls
date: 2016-10-26
extension: .txt
mime: text/plain
words: 7643
sentence: 300
flesch: 44
cache: cache/cord-323307-nu9ib62h.txt
txt: txt/cord-323307-nu9ib62h.txt
summary:
  Our result showed more visual perception genes have become pseudogenes in rhinolophoid bats, and it is reasonable to speculate that some visual perception gene may have undergone relaxed natural selection in echolocating bats. The result based on nucleotide data was in line with previous analysis that bats are a sister group to odd-toed ungulates, whereas the result based on amino acid data supported that bat bats are sister group to the Fereuungulata (Carnivores + Perissodactyla + Cetartiodactyla).


id: cord-282566-rgo5sj5i
author: Bernard, Sandra C
title: Pathogenic Neisseria meningitidis utilizes CD147 for vascular colonization
date: 2014-06-01
extension: .txt
mime: text/plain
words: 7525
sentence: 276
flesch: 33
cache: cache/cord-282566-rgo5sj5i.txt
txt: txt/cord-282566-rgo5sj5i.txt
summary:
  Here, we report that the immunoglobulin superfamily member CD147 (also called extracellular matrix metalloproteinase inducer (EMMPRIN) or Basigin) is a critical host receptor for the meningococcal pilus components PilE and PilV. Interfering with this interaction potently inhibited the primary attachment of meningococci to human endothelial cells in vitro and prevented colonization of vessels in human brain tissue explants ex vivo and in humanized mice in vivo. The capacity of pathogenic capsulated meningococci to interact tightly with human endothelial cells relies on the expression of type IV pili 3, 5 .


id: cord-354003-ko45l1qv
author: Scarpin, M Regina
title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation
date: 2020-10-15
extension: .txt
mime: text/plain
words: 16889
sentence: 551
flesch: 36
cache: cache/cord-354003-ko45l1qv.txt
txt: txt/cord-354003-ko45l1qv.txt
summary:
  Total RNA was extracted from one set of samples in polysome buffer with cycloheximide; an aliquot of this RNA was used to build RNA-Seq libraries after protease treatment and depletion of rRNA, and the rest of the RNA was used for ribosome footprint profiling (Hsu et al., 2016; Ingolia et al., 2009) . [Hsu et al., 2011; Yu et al., 2011] ) and to orthogonal experimental approaches in Arabidopsis (e.g. cell suspension culture proteomics ), we defined a core set of bona fide TOR-sensitive phosphoproteins in Arabidopsis, including LARP1.


id: cord-299605-j1ewxk4q
author: Lin, Jing-wen
date: 2017-02-03
extension: .txt
mime: text/plain
words: 6678
sentence: 247
flesch: 43
cache: cache/cord-299605-j1ewxk4q.txt
txt: txt/cord-299605-j1ewxk4q.txt
title:
  Signatures of malaria-associated pathology revealed by high-resolution whole-blood transcriptomics in a rodent model of malaria

summary:
  AS and CB infected mice showed comparable iRBC loads (parasitemia multiplied by total RBC numbers), despite the fact that higher peak The total numbers of infected red blood cells (iRBC) per ml of blood (b) and the parasitemia (percentage of infected iRBC) (c) in the mice infected with AS or CB parasites. Moreover, the RBC loss in CB infected mice is longer lasting, even after the peak of infection at 12 dpi (Fig. 1d,e) .


id: cord-284015-vvtv492b
author: Nikaido, Masato
title: Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera
date: 2020-09-23
extension: .txt
mime: text/plain
words: 8601
sentence: 346
flesch: 43
cache: cache/cord-284015-vvtv492b.txt
txt: txt/cord-284015-vvtv492b.txt
summary:
  RepbaseSubmitter and censor Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences Repbase update, a database of repetitive elements in eukaryotic genomes PAML 4: a program package for phylogenetic analysis by maximum likelihood The PyMOL molecular graphics system A genomic approach to examine the complex evolution of laurasiatherian mammals A molecular phylogeny for bats illuminates biogeography and the fossil record Characterization of the mitochondrial genome of Rousettus leschenaulti Dynamics of genome size evolution in birds and mammals Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring, and morphological innovation Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome 5S rRNA-derived and tRNA-derived SINEs in fruit bats Origin of avian genome size and structure in non-avian dinosaurs Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates Loss of LINE-1 activity in the megabats Reviving the dead: history and reactivation of an extinct L1 Viral encounters with 2 0 ,5 0 -oligoadenylate synthetase and RNase L during the interferon antiviral response RNase L restricts the mobility of engineered retrotransposons in cultured human cells Restricting retrotransposons: a review LINE-mediated retrotransposition of marked Alu sequences The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals A cluster of olfactory receptor genes linked to frugivory in bats Genomic and genetic evidence for the loss of umami taste in bats Extreme variability among mammalian V1R gene families Prenatal development supports a single origin of laryngeal echolocation in bats Evolution of the sweet taste receptor gene Tas1r2 in bats Frequent expansions of the bitter taste receptor gene repertoire during evolution of mammals in the Euarchontoglires clade Formyl peptide receptor-like proteins are a novel family of vomeronasal chemosensors Adaptive evolution of formyl peptide receptors in mammals Molecular organization of vomeronasal chemoreception From genes to social communication: molecular sensing by the vomeronasal organ Evolution of V1R pheromone receptor genes in vertebrates: diversity and commonality Widespread losses of vomeronasal signal transduction in bats Trpc2 pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss A single pheromone receptor gene conserved across 400 million years of vertebrate evolution Inactivation of ancV1R as a predictive signature for the loss of vomeronasal system in mammals Vomeronasal organ in bats and primates: extremes of structural variability and its phylogenetic implications Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling A novel family of putative pheromone receptors in mammals with a topographically organized and sexually dimorphic distribution A multigene family encoding a diverse array of putative pheromone receptors in mammals The male mouse pheromone ESP1 enhances female sexual receptive behaviour through a specific vomeronasal receptor Sexual rejection via a vomeronasal receptor-triggered limbic circuit First evidence for functional vomeronasal 2 receptor genes in primates Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land A renaissance in trace amines inspired by a novel gpcr family A second class of chemosensory receptors in the olfactory epithelium Trace amine-associated receptors: ligands, neural circuits, and behaviors Molecular evolution and functional divergence of trace amine-associated receptors MHC-dependent mate choice is linked to a trace-amine-associated receptor gene in a mammal WebGestalt, a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit Pangolin genomes and the evolution of mammalian scales and immunity Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins Adaptive evolution in the glucose transporter 4 gene Slc2a4 in Old World fruit bats (family: pteropodidae) It is possible that megabats re-allocated the diversity in chemosensory receptor genes as a sensory trade-off, given that megabats have experienced the secondary loss of echolocation ability, which is one of the most specialized senses in bats.


id: cord-102481-obig3mu1
author: Alić, Ivan
date: 2020-01-31
extension: .txt
mime: text/plain
words: 10739
sentence: 373
flesch: 45
cache: cache/cord-102481-obig3mu1.txt
txt: txt/cord-102481-obig3mu1.txt
title:
  “Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain”

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.


id: cord-252597-ea78sjcs
author: Ramazzotti, Daniele
date: 2020-10-19
extension: .txt
mime: text/plain
words: 10711
sentence: 357
flesch: 36
cache: cache/cord-252597-ea78sjcs.txt
txt: txt/cord-252597-ea78sjcs.txt
title:
  VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

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


id: cord-103915-rzy7mejb
author: Duricki, Denise A.
date: 2018-07-11
extension: .txt
mime: text/plain
words: 12878
sentence: 506
flesch: 48
cache: cache/cord-103915-rzy7mejb.txt
txt: txt/cord-103915-rzy7mejb.txt
title:
  Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke

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.


id: cord-354743-mjaqt6wk
author: Enard, David
title: Viruses are a dominant driver of protein adaptation in mammals
date: 2016-05-17
extension: .txt
mime: text/plain
words: 13699
sentence: 511
flesch: 46
cache: cache/cord-354743-mjaqt6wk.txt
txt: txt/cord-354743-mjaqt6wk.txt
summary:
  This includes well-known antiviral VIPs ( Figure 6A) , antiviral VIPs where adaptation was previously unknown across mammals ( Figure 6B) , and non-antiviral VIPs with diverse, well-studied functions in the mammalian hosts ( Figure 6C ). The reduction in pN/pS in non-immune VIPs is very similar to the reduction observed in the entire set of VIPs ( Figure 3C ).


id: cord-292862-ezrkg0dc
author: Myerson, Jacob W.
date: 2020-04-18
extension: .txt
mime: text/plain
words: 14319
sentence: 610
flesch: 42
cache: cache/cord-292862-ezrkg0dc.txt
txt: txt/cord-292862-ezrkg0dc.txt
title:
  Supramolecular Organization Predicts Protein Nanoparticle Delivery to Neutrophils for Acute Lung Inflammation Diagnosis and Treatment

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.


id: cord-262470-nkql7h9x
author: Muus, Christoph
date: 2020-04-20
extension: .txt
mime: text/plain
words: 17614
sentence: 592
flesch: 41
cache: cache/cord-262470-nkql7h9x.txt
txt: txt/cord-262470-nkql7h9x.txt
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

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.


id: cord-013784-zhgjmt2j
author: Tang, Min
date: 2020-06-04
extension: .txt
mime: text/plain
words: 13724
sentence: 601
flesch: 40
cache: cache/cord-013784-zhgjmt2j.txt
txt: txt/cord-013784-zhgjmt2j.txt
title:
  Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions

summary:
  e Gene set enrichment analysis (GSEA) of the glioblastoma tissue vs cell culture signature as defined in d when applied to RNA-seq data comparing the 3D tetra-culture system with sphere cell culture. Data was derived from Miller et al. 36 g GSEA of the glioblastoma tissue vs cell culture signature as defined in f when applied to RNA-seq data comparing the 3D tetraculture system with sphere cell culture.


# url

id: cord-013784-zhgjmt2j
domain: media.addgene.org
url:
  https://media.addgene.org/cms/filer_public/61/16/611619f4-0926-4a07-b5c7-e286a8ecf7f5/broadgpp-sequencing-protocol


