# bib

id: cord-018103-czjjnlkf
author: Moon, Sanghoon
title: Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome
date: 2006
extension: .txt
mime: text/plain
words: 2352
sentence: 147
flesch: 64
cache: cache/cord-018103-czjjnlkf.txt
txt: txt/cord-018103-czjjnlkf.txt
summary:
  There are few computer programs available for public use to identify frameshift sites from genomic sequences. We have developed a web-based application program called FSFinder2 for predicting frameshift sites of general type.


id: cord-018865-melttpiq
author: Yu, Tian-fei
date: 2012
extension: .txt
mime: text/plain
words: 2194
sentence: 88
flesch: 46
cache: cache/cord-018865-melttpiq.txt
txt: txt/cord-018865-melttpiq.txt
title:
  Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems

summary:
  Although site B is conformation dependent, MAbs specific for this site can bind TGEV spike protein by immunoblotting providing that the samples were not treated with 2-mercaptoethanol. It is recognized by MAbs in Western blot analysis after treatment of the virus with 2.5% SDS and 5% 2-mercaptoethanol; It is represented by synthetic nonapeptides derived from TGEV spike protein [9] ; It is present in recombinant products expressed in bacteria, which do not reconstitute the native spike protein [10] ; and it is formed in the absence of glycosylation [8] .


id: cord-346532-4xpnd93d
author: Strömich, Léonie
title: Allosteric Hotspots in the Main Protease of SARS-CoV-2
date: 2020-11-06
extension: .txt
mime: text/plain
words: 2371
sentence: 84
flesch: 48
cache: cache/cord-346532-4xpnd93d.txt
txt: txt/cord-346532-4xpnd93d.txt
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.


id: cord-260657-yf8fvx7k
author: Bekaert, Michaël
date: 2005-01-07
extension: .txt
mime: text/plain
words: 2966
sentence: 118
flesch: 50
cache: cache/cord-260657-yf8fvx7k.txt
txt: txt/cord-260657-yf8fvx7k.txt
title:
  An Extended Signal Involved in Eukaryotic −1 Frameshifting Operates through Modification of the E Site tRNA

summary:
  E site tRNA nus members do not carry Ϫ1 frameshift sites but, is thus sufficiently connected to the P site to suggest rather, use ϩ1 frameshifting to express their polymerase that it very likely plays a role in promoting the stability domain. By using a sensitive search program based on hidden Markov models (HMM), we identified 74 viruses carrying frameshift sites among 1500 fully sequenced virus genomes.


id: cord-300117-rlpzejjt
author: Coutard, B.
date: 2020-02-10
extension: .txt
mime: text/plain
words: 3047
sentence: 83
flesch: 35
cache: cache/cord-300117-rlpzejjt.txt
txt: txt/cord-300117-rlpzejjt.txt
title:
  The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

summary:
  Insertion of furin like cleavage site is surrounded by a black frame. However, in the other less pathogenic circulating human CoV, the S2′ cleavage site only exhibits a monobasic R↓S sequence (Fig. 2) with no basic residues at either P2 and/or P4 needed to allow furin cleavage, suggesting a less efficient cleavage or higher restriction at the entry step depending on the cognate proteases expressed by target cells.


id: cord-013443-x74uxdi4
author: Daniel, Dennis A.
date: 2020-06-25
extension: .txt
mime: text/plain
words: 3161
sentence: 110
flesch: 39
cache: cache/cord-013443-x74uxdi4.txt
txt: txt/cord-013443-x74uxdi4.txt
title:
  Pediatric Resident Engagement With an Online Critical Care Curriculum During the Intensive Care Rotation*

summary:
  ICU resident rotation directors created individualized curricula for each site that covered core concepts in pediatric critical care medicine. We did not include test attempts occurring prior to the ICU rotation in the time-of-use analysis due to the significant heterogeneity in resident clinical rotations immediately prior to the ICU rotation.


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
extension: .txt
mime: text/plain
words: 3300
sentence: 152
flesch: 53
cache: cache/cord-274409-4ugdxbmy.txt
txt: txt/cord-274409-4ugdxbmy.txt
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.


id: cord-259195-bmz8995u
author: Huang, Chih-Cheng
title: AlGaN/GaN high electron mobility transistors for protein–peptide binding affinity study
date: 2013-03-15
extension: .txt
mime: text/plain
words: 3468
sentence: 154
flesch: 55
cache: cache/cord-259195-bmz8995u.txt
txt: txt/cord-259195-bmz8995u.txt
summary:
  It is very important to identify the number of binding sites on the receptor and the dissociation constants between the receptor and ligands at different binding sites. Instead, through the analysis of surface coverage ratio versus the ligand concentration in the binding-site model, the number of binding sites of a receptor and the dissociation constants can be determined.


id: cord-315951-5gsbtfag
author: Kiemer, Lars
title: Coronavirus 3CL(pro )proteinase cleavage sites: Possible relevance to SARS virus pathology
date: 2004-06-06
extension: .txt
mime: text/plain
words: 3773
sentence: 140
flesch: 43
cache: cache/cord-315951-5gsbtfag.txt
txt: txt/cord-315951-5gsbtfag.txt
summary:
  Implications for cap-dependent and cap-independent translational initiation A transcriptionally active form of TFIIIC is modified in poliovirus-infected HeLa cells Poliovirus proteinase 3C converts an active form of transcription factor IIIC to an inactive form: a mechanism for inhibition of host cell polymerase III transcription by poliovirus DNA binding domain and subunit interactions of transcription factor IIIC revealed by dissection with poliovirus 3C protease Inhibition of host cell transcription by poliovirus: cleavage of transcription factor CREB by poliovirus-encoded protease 3Cpro Cleavage of transcriptional activator Oct-1 by poliovirus encoded protease 3Cpro An RNA polymerase II transcription factor inactivated in poliovirus-infected cells copurifies with transcription factor TFIID Poliovirus 3C protease-mediated degradation of transcriptional activator p53 requires a cellular activity Stimulation of p53-mediated transcriptional activation by the p53-binding proteins, 53BP1 and 53BP2 Poliovirus infection results in structural alteration of a microtubule-associated protein Poliovirus protease 3C mediates cleavage of microtubule-associated protein 4 Alveolar epithelial type I cells contain transport proteins and transport sodium, supporting an active role for type I cells in regulation of lung liquid homeostasis Gene expression associated with interferon alfa antiviral activity in an HCV replicon cell line Treatment of SARS with human interferons Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS GenBank: update A mathematical theory of communication. We propose that a deeper understanding of coronavirus proteinase function and substrate specificity may benefit further research by: i) increasing the understanding of substrate specificity determinants which may direct studies focusing on the development of specific proteinase inhibitors and ii) providing a method for screening cellular target proteins for potential coronavirus proteinase cleavage sites.


id: cord-048327-xgwbl8em
author: Henderson, Clark M.
title: Antisense-induced ribosomal frameshifting
date: 2006-08-18
extension: .txt
mime: text/plain
words: 4342
sentence: 140
flesch: 37
cache: cache/cord-048327-xgwbl8em.txt
txt: txt/cord-048327-xgwbl8em.txt
summary:
  Similarly, for +1 frameshift sites, the identity of the codons in the P-and A-sites of the ribosome is critical for efficient frameshifting. However, visual examination of upstream codons does not reveal an obvious À1 or +1 frameshift site.


id: cord-356264-q0yqnlyl
author: Armijos-Jaramillo, Vinicio
date: 2020-03-23
extension: .txt
mime: text/plain
words: 4990
sentence: 178
flesch: 45
cache: cache/cord-356264-q0yqnlyl.txt
txt: txt/cord-356264-q0yqnlyl.txt
title:
  SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability

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.


id: cord-009730-lc8712xm
author: HODKINSON, I. D.
date: 2008-03-14
extension: .txt
mime: text/plain
words: 5267
sentence: 261
flesch: 60
cache: cache/cord-009730-lc8712xm.txt
txt: txt/cord-009730-lc8712xm.txt
title:
  The distribution, abundance and host plant relationships of Salix‐ feeding psyllids (Homoptera: Psylloidea) in arctic Alaska

summary:
  comm.) showed that levels of soluble nitrogen, the food source of psyllids, are greater in female catkins than in any other plant component growing on the Alaskan tundra. The life cycle was generally closely synchronized with the period of catkin development.


id: cord-332948-h297ukuu
author: Olotu, Fisayo A.
date: 2020-10-16
extension: .txt
mime: text/plain
words: 5186
sentence: 203
flesch: 42
cache: cache/cord-332948-h297ukuu.txt
txt: txt/cord-332948-h297ukuu.txt
title:
  Leaving no stone unturned: Allosteric targeting of SARS-CoV-2 Spike protein at putative druggable sites disrupts human angiotensin-converting enzyme interactions at the receptor binding domain.

summary:
  Assessment of Binding Site Prediction Methods and a Protocol for Validation of Predicted Binding Sites Identifying and characterizing binding sites and assessing druggability Fpocket: An open source platform for ligand pocket detection PrankWeb: a web server for ligand binding site prediction and visualization New method for fast and accurate binding-site identification and analysis Therapeutic target-site variability in α 1-antitrypsin characterized at high J o u r n a l P r e The N protein makes up the nucleocapsid and other viral genome-related processes 21 while the M protein is the most abundant of the four, playing major roles in maintaining viral structural integrity as well as coordinating other structural proteins.


id: cord-024166-t3qxscbp
author: Losvik, Mary H.
date: 2008-06-28
extension: .txt
mime: text/plain
words: 5581
sentence: 226
flesch: 55
cache: cache/cord-024166-t3qxscbp.txt
txt: txt/cord-024166-t3qxscbp.txt
title:
  Plant species diversity in an old, traditionally managed hay meadow compared to abandoned hay meadows in southwest Norway

summary:
  The grasslands may have high species numbers, up to well above 60 per m2 (Willems 1978 (Willems , 1982 Kull & Zobel 1991) . In time sites B-D will turn into deciduous woodland with a closed canopy and the indicators of traditional management and common grassland species will even- 1.7) 19(4.5)


id: cord-010628-71rkpco4
author: WISE, E. J.
date: 2006-05-29
extension: .txt
mime: text/plain
words: 5531
sentence: 263
flesch: 57
cache: cache/cord-010628-71rkpco4.txt
txt: txt/cord-010628-71rkpco4.txt
title:
  Studies on the Ephemeroptera of a Northumbrian river system: I. Serial distribution and relative abundance

summary:
  However, there was no marked successionai replacement of abundant species along the main river course and discontinuous distributions were confined to the scarce species. The adverse effects of the deposition of suspended inorganic sediments on stream faunas, caused by sand and gravel washings etc., have already been noted (e.g. Stuart, 1959; Cordone & Kelly, 1961; Hamilton, 1961; Chutter, 1969) .


id: cord-328681-jf2mj16z
author: Yang, Ziheng
title: Statistical methods for detecting molecular adaptation
date: 2000-12-01
extension: .txt
mime: text/plain
words: 5618
sentence: 228
flesch: 42
cache: cache/cord-328681-jf2mj16z.txt
txt: txt/cord-328681-jf2mj16z.txt
summary:
  Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila Reduced nucleotide variability at an androgen-binding protein locus (Abpa) in house mice: evidence for positive natural selection Positive selection and sequence arrangements generate extensive polymorphism in the gamete recognition protein bindin A rapidly evolving homeobox at the site of a hybrid sterility gene Rapid evolution of a homeodomain: evidence for positive selection Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive darwinian selection? Identification of regions in which positive selection may operate in S-RNase of Rosaceae: implications for Sallele-specific recognition sites in S-RNase Evolution of Sry genes Nucleotide sequence evolution at the k-casein locus: evidence for positive selection within the family Bovidae Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus Accelerated evolution in the protein-coding regions is universal in crotalinae snake venom gland phospholipase A 2 isozyme genes Molecular evolution of the COX7A gene family in primates Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates Evolution of hemopoietic ligands and their receptors: influence of positive selection on correlated replacements throughout ligand and receptor proteins The molecular evolution of vertebrate growth hormones: a pattern of near-stasis interrupted by sustained bursts of rapid changes Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperatures Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila The test of positive selection then involves two major steps: first, to test whether sites exist where Ͼ 1, which is achieved by a likelihood-ratio test comparing a model that does not allow for such sites with a more general model that does; and second, to use the Bayes theorem to identify positively selected sites when they exist.


id: cord-007199-ol2du7ph
author: Kliger, Yossef
title: Predicting proteolytic sites in extracellular proteins: only halfway there
date: 2008-04-15
extension: .txt
mime: text/plain
words: 5796
sentence: 245
flesch: 44
cache: cache/cord-007199-ol2du7ph.txt
txt: txt/cord-007199-ol2du7ph.txt
summary:
  Currently, most computational approaches are protease-oriented and rely on proteolytic site data of specific enzymes (Blom et al., 1996; Cai et al., 1998; Kiemer et al., 2004; Yang and Berry, 2004) . key: cord-007199-ol2du7ph authors: Kliger, Yossef; Gofer, Eyal; Wool, Assaf; Toporik, Amir; Apatoff, Avihay; Olshansky, Moshe title: Predicting proteolytic sites in extracellular proteins: only halfway there date: 2008-04-15 journal: Bioinformatics DOI: 10.1093/bioinformatics/btn084 sha: doc_id: 7199 cord_uid: ol2du7ph Motivation: Many secretory proteins are synthesized as inactive precursors that must undergo post-translational proteolysis in order to mature and become active.


id: cord-009716-oxahu8nz
author: Lawes, Roger A.
date: 2006-10-27
extension: .txt
mime: text/plain
words: 6003
sentence: 274
flesch: 49
cache: cache/cord-009716-oxahu8nz.txt
txt: txt/cord-009716-oxahu8nz.txt
title:
  Comparing agglomerative clustering and three weed classification frameworks to assess the invasiveness of alien species across spatial scales

summary:
  This approach differs from those proposed by the authors of previous frameworks as species are classified using all available data acquired from an extensive, multiscale landscape survey of species frequency and cover. This data set contained information on species frequency and cover at a range of spatial scales.


id: cord-317061-0bx704ao
author: Wu, Andong
date: 2015-10-02
extension: .txt
mime: text/plain
words: 6019
sentence: 197
flesch: 45
cache: cache/cord-317061-0bx704ao.txt
txt: txt/cord-317061-0bx704ao.txt
title:
  Prediction and biochemical analysis of putative cleavage sites of the 3C-like protease of Middle East respiratory syndrome coronavirus

summary:
  The substrate specificity of coronaviruses 3CLpro is determined by the residues from P4 to P2 positions of cleavage sites, especially depending on the P1, P2 and P1 positions, which would benefit the prediction of cleavage site and design the broadspectrum inhibitors of coronaviruses 3CLpro (Chuck et al., 2011; Hegyi and Ziebuhr, 2002) . Our study points out a new direction regarding the prediction and identification of cleavage sites of proteases and contributes to understanding the mechanism of coronaviral polyprotein processing.


id: cord-010307-sxh5mq1q
author: MILNE, D. J.
date: 2005-11-23
extension: .txt
mime: text/plain
words: 6439
sentence: 289
flesch: 49
cache: cache/cord-010307-sxh5mq1q.txt
txt: txt/cord-010307-sxh5mq1q.txt
title:
  Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas

summary:
  At each site we used a range of sampling techniques to maximize the likelihood of obtaining a full inventory of bat species (Kuenzi & Morrison 1998; Murray et al . 1999; The occurrence of bat species within the derived groups and habitat types is summarized in Table 2 and the geographical distribution of sites (classified according to group) is shown in Fig.


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-276405-yfvu83r9
author: Brat, Gabriel A.
date: 2020-08-19
extension: .txt
mime: text/plain
words: 5733
sentence: 241
flesch: 43
cache: cache/cord-276405-yfvu83r9.txt
txt: txt/cord-276405-yfvu83r9.txt
title:
  International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium

summary:
  RESTful API The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system Scalable collaborative infrastructure for a learning healthcare system (SCILHS): architecture SHRINE: enabling nationally scalable multi-site disease studies Overview of data collection and analysis The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories Accrual to Clinical Trials (ACT): a clinical and translational science award consortium network A translational engine at the national scale: informatics for integrating biology and the bedside Case-fatality rate and characteristics of patients dying in relation to COVID-19 in Italy An interactive web-based dashboard to track COVID-19 in real time Prediction models for diagnosis and prognosis of covid-19 infection: systematic review and critical appraisal Laboratory abnormalities in patients with COVID-2019 infection Impact of selective mapping strategies on automated laboratory result notification to public health authorities Learning from the crowd in terminology mapping: the LOINC experience Standardizing laboratory data by mapping to LOINC Evaluating congruence between laboratory LOINC value sets for quality measures, public health reporting, and mapping common tests Early vision for the CTSA Program Trial Innovation Network: a perspective from the National Center for Advancing Translational Sciences Launching PCORnet, a national patient-centered clinical research network German medical informatics initiative The COVID-19 Global Rheumatology Alliance: collecting data in a pandemic Recent developments in clinical terminologies-SNOMED CT, LOINC, and RxNorm i2b2: Informatics for Integrating Biology & the Bedside CTSA ACT Network i2b2 and SHRINE Ontology with 1-1 SHRINE Adapter Mapping File (Github The Unified Medical Language System (UMLS): integrating biomedical terminology All authors approved the manuscript. Aggregate laboratory data have limited ability to identify general trends in the admitted population.


id: cord-314166-79323mzd
author: Vanderford, Thomas H.
date: 2006-12-11
extension: .txt
mime: text/plain
words: 6458
sentence: 196
flesch: 36
cache: cache/cord-314166-79323mzd.txt
txt: txt/cord-314166-79323mzd.txt
title:
  Adaptation of a Diverse Simian Immunodeficiency Virus Population to a New Host Is Revealed through a Systematic Approach to Identify Amino Acid Sites under Selection

summary:
  To identify specific amino acid sites that may be responsible for the disparate evolutionary patterns of viruses replicating in the 2 monkey species, we applied 3 site-bysite analyses to detect particular codons under selection. In these studies, analysis of the ratio of nonsynonymous to synonymous substitutions have revealed particular genes or amino acid sites that are under positive diversifying selection pressure due to immune responses against these sites.


id: cord-262318-qpztmdnw
author: Guo, Jingxu
title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors
date: 2020-07-16
extension: .txt
mime: text/plain
words: 6366
sentence: 208
flesch: 47
cache: cache/cord-262318-qpztmdnw.txt
txt: txt/cord-262318-qpztmdnw.txt
summary:
  Studies have indicated that norovirus 3CL proteases have a preferential order of processing the polyprotein, for example, the Southampton virus 3CL pro has a preference for cleavage at LQ-GP and LQ-GK, but it can also cleave at ME-GK, FE-AP and LE-GG (Hussey et al., 2011) . A further 10 compounds were found to bind in the central cavity of this putative tetrameric form of the enzyme. Expression and purification of SV3CP was conducted using the method described by Hussey et al., (2011) .


id: cord-263033-4790dhc5
author: Laptev, I. G.
title: Posttranscriptional modification of messenger RNAs in eukaryotes
date: 2015-12-11
extension: .txt
mime: text/plain
words: 6798
sentence: 330
flesch: 53
cache: cache/cord-263033-4790dhc5.txt
txt: txt/cord-263033-4790dhc5.txt
summary:
  Regions distant from the mRNA ends may contain N6 methyladenosine (m 6 A), 5 methylcytidine (m 5 C), pseudouridine (Ψ), and inosine (I), which were believed to play only a minor role because their pro portion in cell RNA is extremely low as compared with the standard nucleotides. In addition to RNA methylation, demethylation occurs as an opposite process.


id: cord-332855-u0amf1oh
author: Parsons, Lisa M.
date: 2019-03-22
extension: .txt
mime: text/plain
words: 7009
sentence: 318
flesch: 54
cache: cache/cord-332855-u0amf1oh.txt
txt: txt/cord-332855-u0amf1oh.txt
title:
  Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding

summary:
  Glycosylation sites in the spike protein are highly conserved across viral genotypes, suggesting an important role for this modification in the virus life cycle. glycomics analysis revealed that glycosylation sites have specific proportions of N-glycan subtypes.


id: cord-028681-e2zh6092
author: Koide, Takashi
title: It Never Rains but It Pours: Analyzing and Detecting Fake Removal Information Advertisement Sites
date: 2020-06-11
extension: .txt
mime: text/plain
words: 8082
sentence: 383
flesch: 60
cache: cache/cord-028681-e2zh6092.txt
txt: txt/cord-028681-e2zh6092.txt
summary:
  Since our system is specialized for collecting and detecting FRAD sites, which are the important platforms used by attackers to distribute fake AV software, detecting software distribution sites is out of scope for this paper. They click on download buttons on the FRAD sites and are navigated to software distribution sites ( 2 ) .


id: cord-271514-sls3bsm0
author: Dean, Natalie E.
title: Ensemble Forecast Modeling for the Design of COVID-19 Vaccine Efficacy Trials
date: 2020-09-15
extension: .txt
mime: text/plain
words: 2501
sentence: 105
flesch: 36
cache: cache/cord-271514-sls3bsm0.txt
txt: txt/cord-271514-sls3bsm0.txt
summary:
  key: cord-271514-sls3bsm0 authors: Dean, Natalie E.; Pastore y Piontti, Ana; Madewell, Zachary J.; Cummings, Derek A.T; Hitchings, Matthew D.T.; Joshi, Keya; Kahn, Rebecca; Vespignani, Alessandro; Elizabeth Halloran, M.; Longini, Ira M. title: Ensemble Forecast Modeling for the Design of COVID-19 Vaccine Efficacy Trials date: 2020-09-15 journal: Vaccine DOI: 10.1016/j.vaccine.2020.09.031 sha: doc_id: 271514 cord_uid: sls3bsm0 To rapidly evaluate the safety and efficacy of COVID-19 vaccine candidates, prioritizing vaccine trial sites in areas with high expected disease incidence can speed endpoint accrual and shorten trial duration. Selecting vaccine trial sites where disease incidence is highest during the study period can accelerate the accrual of endpoints.


id: cord-024619-0wihqs9i
author: Parvin, Farhana
date: 2020-05-11
extension: .txt
mime: text/plain
words: 8447
sentence: 343
flesch: 42
cache: cache/cord-024619-0wihqs9i.txt
txt: txt/cord-024619-0wihqs9i.txt
title:
  Accessibility and site suitability for healthcare services using GIS-based hybrid decision-making approach: a study in Murshidabad, India

summary:
  Spat DOI: 10.1007/s41324-020-00330-0 sha: doc_id: 24619 cord_uid: 0wihqs9i Healthcare accessibility and site suitability analysis is an elongated and complex task that requires evaluation of different decision factors. The present study aimed to utilize spatial tools to integrate different spatial and aspatial information for spatial analysis of healthcare accessibility and inaccessibility which support to propose new health infrastructures in inaccessible areas in Murshidabad district of West Bengal, India.


id: cord-000294-2g471tb4
author: Rhodin, Michael H. J.
title: A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding
date: 2010-08-12
extension: .txt
mime: text/plain
words: 8182
sentence: 280
flesch: 49
cache: cache/cord-000294-2g471tb4.txt
txt: txt/cord-000294-2g471tb4.txt
summary:
  Thus, the structural changes observed are indicative of changes in the full 'dynamic potential' of the ribosome as opposed to conformations locked in by e.g. occupation of binding sites by tRNAs or ribosome-associated factors. Ribosomal protein L11 of Saccharomyces cerevisiae is an essential, highly conserved component of the 60S subunit (in bacteria and archaea, the homologous protein is named L5; the yeast nomenclature is used throughout this text to minimize confusion).


id: cord-267326-355q6k6k
author: Gu, Xiaoqiong
title: Geospatial distribution of viromes in tropical freshwater ecosystems
date: 2018-06-15
extension: .txt
mime: text/plain
words: 8436
sentence: 298
flesch: 35
cache: cache/cord-267326-355q6k6k.txt
txt: txt/cord-267326-355q6k6k.txt
summary:
  Viral communities in different reservoirs in terms of land use impact were compared and the majority of viral communities were largely conserved and stable at the family level with Myoviridae, Siphoviridae and Podoviridae as the main family level, and small differences observed in Dicistroviridae and other families (Fig. 2B) . Bacteriophage observations and evolution The marine viromes of four oceanic regions The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes Globally mobile populations and the spread of emerging pathogens Prevalence and genetic diversity of waterborne pathogenic viruses in surface waters of tropical urban catchments Prevalence and genotypes of human noroviruses in tropical urban surface waters and clinical samples in Singapore Identification of viral pathogen diversity in sewage sludge by metagenome analysis Genomic analysis of uncultured marine viral communities The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments Oxygen minimum zones harbour novel viral communities with low diversity Spatial and temporal variability across life's hierarchies in the terrestrial Antarctic Human and bovine viruses in the Milwaukee River watershed: hydrologically relevant representation and relations with environmental variables Metagenomic analysis of coastal RNA virus communities Human norovirus transmission and evolution in a changing world Bacteria-phage interactions in natural environments Functional metagenomic profiling of nine biomes Metagenomic analysis of RNA viruses in a fresh water lake Zoonotic hepatitis E virus: classification, animal reservoirs and transmission routes Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara Global consequences of land use A latitudinal diversity gradient in planktonic marine bacteria Cyclovirus CyCV-VN species distribution is not limited to Vietnam and extends to Viral metagenomics analysis of planktonic viruses in East Lake Diarrhea and enteric emerging viruses in HIV-infected patients Bacteriophages: update on application as models for viruses in water Unbiased detection of respiratory viruses by use of RNA sequencing-based metagenomics: a systematic comparison to a commercial PCR panel Enteric viruses and diarrhea in HIV-infected patients Ecology drives the worldwide distribution of human diseases Novoalign.


id: cord-321150-ev6acl7b
author: Lam, Ha Minh
title: Improved Algorithmic Complexity for the 3SEQ Recombination Detection Algorithm
date: 2017-10-03
extension: .txt
mime: text/plain
words: 3189
sentence: 121
flesch: 44
cache: cache/cord-321150-ev6acl7b.txt
txt: txt/cord-321150-ev6acl7b.txt
summary:
  To illustrate improved runtimes and memory usage of the new 3SEQ algorithm, we searched for recombinants among large sequence data sets of dengue virus serotype 2, Ebola virus, the coronavirus responsible for Middle-East Respiratory Syndrome (MERS) and Zika virus; see table 1. Ebola virus sequences were restricted to human viruses sampled in Africa after December 1, 2013.


id: cord-285910-rw2byz31
author: Stahl, Guillaume
date: 2002-04-01
extension: .txt
mime: text/plain
words: 4726
sentence: 179
flesch: 49
cache: cache/cord-285910-rw2byz31.txt
txt: txt/cord-285910-rw2byz31.txt
title:
  Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding

summary:
  The mechanism of frame disruption varies between sites. Despite the number and phylogenetic ubiquity of such sites, we do not yet understand how these signals stimulate frameshift errors.


id: cord-316968-rowoylge
author: Zhang, Wenjuan
title: Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes
date: 2006
extension: .txt
mime: text/plain
words: 3536
sentence: 154
flesch: 44
cache: cache/cord-316968-rowoylge.txt
txt: txt/cord-316968-rowoylge.txt
summary:
  Maximum likelihood (ML) method with codon-substitution models is a powerful statistic tool for detecting amino acid sites under positive selection and adaptive evolution. It is employed not only to select the best phylogenic tree that fit the real data [1] , but also to detect select pressure on sites under different codon substitution models, especially for amino acid sites undergoing positive selection [8] .


id: cord-327069-vjlisnui
author: Driscoll, Amanda J.
title: Standardization of Laboratory Methods for the PERCH Study
date: 2017-06-15
extension: .txt
mime: text/plain
words: 4734
sentence: 191
flesch: 38
cache: cache/cord-327069-vjlisnui.txt
txt: txt/cord-327069-vjlisnui.txt
summary:
  Site laboratories received uniform training, equipment, and reagents for core testing methods. The standardization of laboratory methods in the PERCH study was equally important to ensure comparability across study sites and for accurate and meaningful interpretation of pneumonia etiology results.


id: cord-336034-13u8njtt
author: Scott, Shannon D
date: 2009-10-13
extension: .txt
mime: text/plain
words: 6036
sentence: 232
flesch: 44
cache: cache/cord-336034-13u8njtt.txt
txt: txt/cord-336034-13u8njtt.txt
title:
  Barriers and supports to implementation of MDI/spacer use in nine Canadian pediatric emergency departments: a qualitative study

summary:
  [15] elements thought to influence research use: the evidence-based innovation (MDI spacers), the potential adopter, and the practice environment. Rather, the decision to adopt MDI spacers requires support and decisions at levels ranging from the individual practitioner, parents, department, institution, and regional levels.


id: cord-332165-31tbc31x
author: Rustmeier, Nils H.
title: The Symmetry of Viral Sialic Acid Binding Sites—Implications for Antiviral Strategies
date: 2019-10-14
extension: .txt
mime: text/plain
words: 5842
sentence: 250
flesch: 38
cache: cache/cord-332165-31tbc31x.txt
txt: txt/cord-332165-31tbc31x.txt
summary:
  Due to the surface-exposed binding mode and the weak individual interactions between sialic acids and their cognate virus proteins, modifying sialic acid to achieve high-affinity binding is challenging. Å resolution X-ray crystal structure of the rotavirus inner capsid particle at 3.8 a resolution Sigma 1 protein of mammalian reoviruses extends from the surfaces of viral particles The GM2 Glycan Serves as a Functional Coreceptor for Serotype 1 Reovirus Crystal structure of reovirus attachment protein sigma1 in complex with sialylated oligosaccharides Three-dimensional visualization of the rotavirus hemagglutinin structure Comparison of human, simian, and bovine rotaviruses for requirement of sialic acid in hemagglutination and cell adsorption Role of sialic acids in rotavirus infection Sialic acid dependence in rotavirus host cell invasion


id: cord-304421-xpj6c0vx
author: Piñón, Josefina D.
date: 1999-10-25
extension: .txt
mime: text/plain
words: 7410
sentence: 265
flesch: 51
cache: cache/cord-304421-xpj6c0vx.txt
txt: txt/cord-304421-xpj6c0vx.txt
title:
  Further Requirements for Cleavage by the Murine Coronavirus 3C-like Proteinase: Identification of a Cleavage Site within ORF1b

summary:
  cleavage site situated between the putative polymerase (POL) and zinc finger (Zn) domains (the POL2Zn site) (Fig. 2) . Recombinant MBP-3CLpro enzyme (1.27 mg/ml in elution buffer supplemented with 20% glycerol and 2 mM DTT, 17.5 M enzyme) was incubated with synthetic peptide ORF1a (0.02 to 0.6 mM in 10% DMSO), with the sequence H 2 N-Thr-Thr-Ser-Phe-Leu-Gln2Ser-Gly-Ile-Val-Lys-Met-Val-Ser-COOH, corresponding to ORF1a amino acids 3328 to 3341 (arrow indicates cleavage site) or ORF1b peptide (0.02 to 0.25 mM in 10% DMSO), with the sequence H 2 N-Arg-Ser-Ala-Val-Leu-Gln2Ser-Val-Gly-Ala-Cys-Val-Val-Cys-Ser-COOH, corresponding to ORF1b amino acids 934 to 948 (arrow indicates cleavage site) in a final reaction volume of 100 l.


id: cord-346965-0oq2n0af
author: Liu, Zhi-Ping
title: Bridging protein local structures and protein functions
date: 2008-04-18
extension: .txt
mime: text/plain
words: 14492
sentence: 605
flesch: 38
cache: cache/cord-346965-0oq2n0af.txt
txt: txt/cord-346965-0oq2n0af.txt
summary:
  Supplement 4: corrections and additions Kernel-based machine learning protocol for predicting DNA-binding proteins Inferring functional relationships of proteins from local sequence and spatial surface patterns CASTp: computed atlas of surface topography of proteins pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins Protein surface analysis for function annotation in high-throughput structural genomics pipeline Statistical analysis and prediction of protein-protein interfaces Flu virus proton channel analyzed: structures of key surface protein suggest different drug mechanisms Insights into protein-protein interfaces using a Bayesian network prediction method A tour of structural genomics Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces Identify catalytic triads of serine hydrolases by support vector machines The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with gene ontology Ligand binding: functional site location, similarity and docking Predicting functionally important residues from sequence conservation Analysis and prediction of functionally important sites in proteins Prediction of interface residues in proteinprotein complexes by a consensus neural network method: test against NMR data Prediction of linear B-cell epitopes using amino acid pair antigenicity scale Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design Prediction of protein cellular attributes using pseudo amino acid composition (Erratum: ibid Structural bioinformatics and its impact to biomedical science A novel approach to predict active sites of enzyme molecules Predicting protein-protein interactions from sequences in a hybridization space MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM Recent progresses in protein subcellular location prediction Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms Prediction of protein structural classes Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS (Erratum: ibid High-throughput identification of interacting protein-protein binding sites Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families Predicting calciumbinding sites in proteins-a graph theory and geometry approach Practical limits of function prediction Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus Robust recognition of zinc binding sites in proteins Protein function in the post-genomic era Prediction of functionally important residues based solely on the computed energetics of protein structure Predicting DNA-binding proteins: approached from Chou's pseudo amino acid composition and other specific sequence features Prediction of protein-protein interaction sites in heterocomplexes with neural networks SURFACE: a database of protein surface regions for functional annotation Functional annotation by identification of local surface similarities: a novel tool for structural genomics HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter Effective function annotation through catalytic residue conservation Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins Surprising similarities in structure comparison A method for localizing ligand binding pockets in protein structures SiteBase: a database for structurebased protein-ligand binding site comparison Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships Structural genomics: computational methods for structure analysis Exploiting 3D structural templates for detection of metal-binding sites in protein structures Uncovering network systems within protein structures Using a neural network and spatial clustering to predict the location of active sites in enzymes Distance-based identification of spatial motifs in proteins using constrained frequent subgraph mining LIGSITE csc : predicting ligand binding sites using the Connolly surface and degree of conservation LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins Protein structure comparison by alignment of distance matrices Mapping the protein universe An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements Global mapping of the protein structure space and application in structure-based inference of protein function Prediction of functional sites in proteins using conserved functional group analysis PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins PDBSite: a database of the 3D structure of protein functional sites A new bioinformatic approach to detect common 3D sites in protein structures Principles of protein-protein interactions Searching for functional sites in protein structures Protein-RNA interactions: a structural analysis Using electrostatic potentials to predict DNA-binding sites on DNAbinding proteins Quantitative assessment of relationship between sequence similarity and function similarity Shape variation in protein binding pockets and their ligands KEGG: An approach for clustering protein pockets into similar groups Analysis of protein surface patterns by pocket similarity network Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity An overview of the structures of protein-DNA complexes Amino acidbase interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Protein-protein interaction: structurally conserved residues distinguish between binding sites and exposed protein surfaces A combined algorithm for genome-wide prediction of protein function Statistical models for discerning protein structures containing the DNA-binding helix-turn helix motif Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons SCOP: a structural classification of proteins database for the investigation of sequences and structures On the nature of cavities on protein surfaces: application to the identification of drug-binding sites ProMate: a structure based prediction program to identify the location of protein-protein binding sites Predicted protein-protein interaction sites from local sequence information CATH-a hierarchic classification of protein domain structures SSAP: sequential structure alignment program for protein structure comparison From protein structure to function Inference of protein function from protein structure Prediction of functional sites by analysis of sequence and structure conservation Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks Automatic prediction of protein function and detection of functional sites from structure The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Molecular shape comparisons in searches for active sites and functional similarity Twilight zone of protein sequence alignments The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution A structural perspective on protein-protein interactions Computational methods of analysis of protein-protein interactions Integrating structure, bioinformatics, and enzymology to discover function-BioH, a new carboxylesterase from Escherichia coli A new method to detect related function among proteins independent of sequence and fold homology Structure and mechanism of the M2 proton channel of influenza A virus Predicting enzyme function from sequence: a systematic appraisal Network-based prediction of protein function EzyPred: a top-down approach for predicting enzyme functional classes and subclasses Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition Using pseudo amino acid composition to predict protein subcellular location: approached with amino acid composition distribution Protein structure alignment by incremental combinatorial extension (CE) of the optimal path SiteEngines: recognition and comparison of binding sites and protein-protein interfaces Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity Hierarchical protein structure alignment using both secondary structure and atomic representations Identifying structural motifs in proteins Predicting metal-binding site residues in low-resolution structural models Annotation in three dimensions.


id: cord-341968-uc8i9h0m
author: Izaguirre, Gonzalo
title: The Proteolytic Regulation of Virus Cell Entry by Furin and Other Proprotein Convertases
date: 2019-09-09
extension: .txt
mime: text/plain
words: 7895
sentence: 306
flesch: 39
cache: cache/cord-341968-uc8i9h0m.txt
txt: txt/cord-341968-uc8i9h0m.txt
summary:
  The experimental inactivation of the PC cleavage site of several herpes viruses did not severely affect viral cell entry into cells growing in vitro; however, the lack of PC cleavage reduced virus spread and replication in vivo [36, 37] . PC cleavage site motifs in the coat proteins L1 and L2 of HPV types.


id: cord-338980-pygykil7
author: Rahaman, Jordon
date: 2016-11-09
extension: .txt
mime: text/plain
words: 5807
sentence: 222
flesch: 45
cache: cache/cord-338980-pygykil7.txt
txt: txt/cord-338980-pygykil7.txt
title:
  Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses

summary:
  (C) NSP14, based on PDB id 5C8T A computationally optimized broadly reactive antigen (COBRA) based H5N1 VLP vaccine elicits broadly reactive antibodies in mice and ferrets Computationally optimized antigens to overcome influenza viral diversity Rapid evolution of virus sequences in intrinsically disordered protein regions Molecular pathology of emerging coronavirus infections MRBAYES: Bayesian inference of phylogenetic trees ETE 3: Reconstruction, analysis, and visualization of phylogenomic data Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses The rapid generation of mutation data matrices from protein sequences MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivity Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses Bayesian model of protein primary sequence for secondary structure prediction Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data The PSIPRED protein structure prediction server Metagenomics and future perspectives in virus discovery Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses Marked variability in the extent of protein disorder within and between viral families Cross host transmission in the emergence of MERS coronavirus MrBayes 3: Bayesian phylogenetic inference under mixed models Exploring the viral world through metagenomics The evolution of protein structures and structural Ensembles under functional constraint The challenge of protein structure determination-lessons from structural genomics Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human Epidemiology, genetic recombination, and pathogenesis of coronaviruses Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans The DISOPRED server for the prediction of protein disorder Genetic relatedness of the novel human group C betacoronavirus to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5 World Health Organization. Protein sequences were identified by individual BLAST searches with MERS-CoV (Taxonomy ID: 1335626) proteins ORF1ab (YP_009047202.1; polyprotein), S protein (YP_009047204.1), M protein (YP_009047210.1), E protein (YP_009047209.1), and N protein (YP_009047211.1) against coronaviruses.


id: cord-351115-dy81dtnk
author: Wang, Chen
title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome
date: 2020-10-20
extension: .txt
mime: text/plain
words: 6145
sentence: 199
flesch: 39
cache: cache/cord-351115-dy81dtnk.txt
txt: txt/cord-351115-dy81dtnk.txt
summary:
  Overall, these results show that predicted ET drug sites can recover experimentally tested drug binding pockets and suggest new sites that can be targeted in computational docking approaches. In addition, because these sites are conserved across multiple coronavirus genera, these predicted ET drug sites are anticipated to be relevant for identifying inhibitors of SARS-CoV-2 as well as more distantly related coronaviruses.


id: cord-289443-46w52de3
author: Sironi, Manuela
title: Evolutionary insights into host–pathogen interactions from mammalian sequence data
date: 2015-03-18
extension: .txt
mime: text/plain
words: 9373
sentence: 305
flesch: 31
cache: cache/cord-289443-46w52de3.txt
txt: txt/cord-289443-46w52de3.txt
summary:
  PLoS Pathog MHC class I antigen presentation: learning from viral evasion strategies An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles The intertransmembrane region of Kaposi's sarcoma-associated herpesvirus modulator of immune recognition 2 contributes to B7-2 downregulation The Nef protein of HIV-1 induces loss of cell surface costimulatory molecules CD80 and CD86 in APCs Members of adenovirus species B utilize CD80 and CD86 as cellular attachment receptors Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a single binding site Hiding lipid presentation: viral interference with CD1d-restricted invariant natural killer T (iNKT) cell activation A threonine-based targeting signal in the human CD1d cytoplasmic tail controls its functional expression Evolutionary history of copynumber-variable locus for the low-affinity Fcγ receptor: mutation rate, autoimmune disease, and the legacy of helminth infection One of the few studies of helminth-driven selective pressure in mammals that also integrates evolutionary analysis with epidemiological information Thrombosis as an intravascular effector of innate immunity Dual host-virus arms races shape an essential housekeeping protein An extremely interesting study extending the arms race scenario to a housekeeping protein, the transferrin receptor Evolutionary reconstructions of the transferrin receptor of caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs Escape from bacterial iron piracy through rapid evolution of transferrin Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes Niemann-Pick C1 (NPC1)/ NPC1-like1 chimeras define sequences critical for NPC1's function as a flovirus entry receptor Cell entry by a novel European filovirus requires host endosomal cysteine proteases and Niemann-Pick C1 Multiple cationic amphiphiles induce a Niemann-Pick C phenotype and inhibit Ebola virus entry and infection Inhibition of ebola virus infection: identification of Niemann-Pick C1 as the target by optimization of a chemical probe Small molecule inhibitors reveal Niemann-Pick C1 is essential for Ebola virus infection Evolutionary analysis of the contact system indicates that kininogen evolved adaptively in mammals and in human populations Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations Induction of vascular leakage through release of bradykinin and a novel kinin by cysteine proteinases from Staphylococcus aureus Viral immune modulators perturb the human molecular network by common and unique strategies Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers PAML 4: phylogenetic analysis by maximum likelihood Accuracy and power of Bayes prediction of amino acid sites under positive selection Bayes empirical Bayes inference of amino acid sites under positive selection Detecting individual sites subject to episodic diversifying selection High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes Class of multiple sequence alignment algorithm affects genomic analysis Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment The effects of alignment error and alignment filtering on the sitewise detection of positive selection Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites A random effects branchsite model for detecting episodic diversifying selection Modeling the site-specific variation of selection patterns along lineages Performance of standard and stochastic branch-site models for detecting positive selection among coding sequences Statistical properties of the branch-site test of positive selection Towards a systems understanding of MHC class I and MHC class II antigen presentation CD1 antigen presentation: how it works The authors declare no competing interests. In this case the branch of the phylogeny leading to these species may show significant evidence of positive selection .


id: cord-034684-ehaiqye5
author: Peterson, Ryan R.
title: Over the Caribbean Top: Community Well-Being and Over-Tourism in Small Island Tourism Economies
date: 2020-11-05
extension: .txt
mime: text/plain
words: 15697
sentence: 490
flesch: 25
cache: cache/cord-034684-ehaiqye5.txt
txt: txt/cord-034684-ehaiqye5.txt
summary:
  Exemplary of this continued tourism rhetoric is the recent Caribbean push towards inclusive tourism development by focusing on the market acceptance of new tourism services and how community tourism can support product differentiation with the ultimate benefit being the creation of a distinctive tourism brand that stimulate economic growth, productivity, and competitiveness (CTO 2019). Peterson et al. 2017) , and conceptualizes over-tourism from a contextualized perspective in which both norms and networks of purpose, power, people, and place take center stage in social construction of tourism development and institutional behaviors (Cloutier et al. 2019;


id: cord-103085-vf4qyvft
author: Seitz, Christian
title: Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase
date: 2020-11-02
extension: .txt
mime: text/plain
words: 9741
sentence: 368
flesch: 42
cache: cache/cord-103085-vf4qyvft.txt
txt: txt/cord-103085-vf4qyvft.txt
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.


id: cord-275307-d7htyfcl
author: Gaglia, Marta Maria
date: 2015-12-08
extension: .txt
mime: text/plain
words: 10873
sentence: 450
flesch: 53
cache: cache/cord-275307-d7htyfcl.txt
txt: txt/cord-275307-d7htyfcl.txt
title:
  Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

summary:
  In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. To dissect the specificity of SOX cleavage across the mRNA transcriptome, we designed an approach to map SOX cleavage sites in endogenous mRNAs using PARE


id: cord-022955-vy0qgtll
title: Proteases
date: 2005-06-20
extension: .txt
mime: text/plain
words: 36483
sentence: 1524
flesch: 40
cache: cache/cord-022955-vy0qgtll.txt
txt: txt/cord-022955-vy0qgtll.txt
summary:
  Specific molecular associations or shared scaffolds between the involved proteases and/or protein inhibitors and defined three-dimensional structures have also been reported. It was used affinity chromatography, electrophoresis, western-blotting, ELISA, determination of proteins activity.


id: cord-001835-0s7ok4uw
title: Abstracts of the 29th Annual Symposium of The Protein Society
date: 2015-10-01
extension: .txt
mime: text/plain
words: 138771
sentence: 5463
flesch: 38
cache: cache/cord-001835-0s7ok4uw.txt
txt: txt/cord-001835-0s7ok4uw.txt
summary:
  In conclusion, the analysis of hydropathic environments strongly suggests that the orientation of a residue in a three-dimensional structure is a direct consequence of its hydropathic environment, which leads us to propose a new paradigm, interaction homology, as a key factor in protein structure. In computer simulation modeling of protein structure in a solvent medium, explicit, implicit, effectivemedium, approaches are often adopted to incorporate the effects of solvation.


