32 10 20655 https://www.socictopen.socict.org/files/original/ad0763f407e85c42cf30ff4b24086684.pdf 42bfe17ad4f87c1baec6db9af37c0a3b Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. Creator An entity primarily responsible for making the resource Malcolm S. Hill, April L Hill, José López, Kevin J Peterson, Shirley Pomponi, María C. Díaz, Robert W. Thacker, Maja Adamska, Nicole Boury-Esnault, Paco Cárdenas, Andia Chaves-Fonnegra, Elizabeth Danka, Bre-Onna De Laine, Dawn Formica, Eduardo Hajdu, Gisele Lôbo-Hajdu, Sarah Klontz, Christine C Morrow, Jignasa Patel, Bernard Picton, Davide Pisani, Deborah Pohlmann, Niamh E Redmond, John Reed, Stacy Richey, Ana Riesgo, Ewelina Rubin, Zach Russell, Klaus Rützler, Erik A Sperling, Michael di Stefano, James E Tarver, Allen G. Collins Description An account of the resource Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa(p), Myxospongiae(p), Spongillida(p), Haploscleromorpha(p) (the marine haplosclerids) and Democlavia(p). We found conflicting results concerning the relationships of Keratosa(p) and Myxospongiae(p) to the remaining demosponges, but our results strongly supported a clade of Haploscleromorpha(p)+Spongillida(p)+Democlavia(p). In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillida(p)) are sister to Haploscleromorpha(p) rather than part of Democlavia(p). Within Keratosa(p), we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiae(p), Chondrosida and Verongida were monophyletic. A well-supported clade within Democlavia(p), Tetractinellida(p), composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlavia(p). Within Tetractinellida(p), we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida.These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets. Date A point or period of time associated with an event in the lifecycle of the resource 2013 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0050437 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/c66bd2ac48d82368168ea6db6796b0d4.pdf b8db253af67ae0e364a7a745c055379d Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross. Creator An entity primarily responsible for making the resource Lisa E Gralinski, Martin T. Ferris, David L Aylor, Alan C. Whitmore, Richard Green, Matthew B. Frieman, Damon Deming, Vineet D. Menachery, Darla R. Miller, Ryan J Buus, Timothy A. Bell, Gary A. Churchill, David W. Threadgill, Michael G. Katze, Leonard McMillan, William Valdar, Mark T. Heise, Fernando Pardo-Manuel de Villena, Ralph S. Baric Description An account of the resource New systems genetics approaches are needed to rapidly identify host genes and genetic networks that regulate complex disease outcomes. Using genetically diverse animals from incipient lines of the Collaborative Cross mouse panel, we demonstrate a greatly expanded range of phenotypes relative to classical mouse models of SARS-CoV infection including lung pathology, weight loss and viral titer. Genetic mapping revealed several loci contributing to differential disease responses, including an 8.5Mb locus associated with vascular cuffing on chromosome 3 that contained 23 genes and 13 noncoding RNAs. Integrating phenotypic and genetic data narrowed this region to a single gene, Trim55, an E3 ubiquitin ligase with a role in muscle fiber maintenance. Lung pathology and transcriptomic data from mice genetically deficient in Trim55 were used to validate its role in SARS-CoV-induced vascular cuffing and inflammation. These data establish the Collaborative Cross platform as a powerful genetic resource for uncovering genetic contributions of complex traits in microbial disease severity, inflammation and virus replication in models of outbred populations. Date A point or period of time associated with an event in the lifecycle of the resource 2015 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pgen.1005504 Source A related resource from which the described resource is derived PLoS Genetics Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Genetics Language A language of the resource EN https://www.socictopen.socict.org/files/original/7930c56dd3129b985308956aa328215e.pdf 441600cdb2947525d31bf52d6b21a3a1 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource From the Beginning Until Today: Current Status of SARS Creator An entity primarily responsible for making the resource Can Polat EYIGUN Date A point or period of time associated with an event in the lifecycle of the resource 2005 Subject The topic of the resource severe acute respiratory syndrome virus, coronavirus, Respiratory syndrome, Severe, Acute Identifier An unambiguous reference to the resource within a given context DOI: Source A related resource from which the described resource is derived Flora Infeksiyon Hastalıkları ve Klinik Mikrobiyoloji Dergisi Publisher An entity responsible for making the resource available Bilimsel Tip Yayinevi Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Infectious and parasitic diseases, Microbiology Language A language of the resource EN, TR https://www.socictopen.socict.org/files/original/97688a83c7820ec079fc0a0bb53c6921.pdf b81116f9ad3803fd7740bb250e9dfbc5 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Multi-Organ Damage in Human Dipeptidyl Peptidase 4 Transgenic Mice Infected with Middle East Respiratory Syndrome-Coronavirus. Creator An entity primarily responsible for making the resource Guangyu Zhao, Yuting Jiang, Hongjie Qiu, Tongtong Gao, Yang Zeng, Yan Guo, Hong Yu, Junfeng Li, Zhihua Kou, Lanying Du, Wen-Jie Tan, Shibo Jiang, Shihui Sun, Yusen Zhou Description An account of the resource The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes severe acute respiratory failure and considerable extrapumonary organ dysfuction with substantial high mortality. For the limited number of autopsy reports, small animal models are urgently needed to study the mechanisms of MERS-CoV infection and pathogenesis of the disease and to evaluate the efficacy of therapeutics against MERS-CoV infection. In this study, we developed a transgenic mouse model globally expressing codon-optimized human dipeptidyl peptidase 4 (hDPP4), the receptor for MERS-CoV. After intranasal inoculation with MERS-CoV, the mice rapidly developed severe pneumonia and multi-organ damage, with viral replication being detected in the lungs on day 5 and in the lungs, kidneys and brains on day 9 post-infection. In addition, the mice exhibited systemic inflammation with mild to severe pneumonia accompanied by the injury of liver, kidney and spleen with neutrophil and macrophage infiltration. Importantly, the mice exhibited symptoms of paralysis with high viral burden and viral positive neurons on day 9. Taken together, this study characterizes the tropism of MERS-CoV upon infection. Importantly, this hDPP4-expressing transgenic mouse model will be applicable for studying the pathogenesis of MERS-CoV infection and investigating the efficacy of vaccines and antiviral agents designed to combat MERS-CoV infection. Date A point or period of time associated with an event in the lifecycle of the resource 2015 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0145561 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/7444b6c7020b00ff799837d599792904.pdf 0535468fe8a638044206677243ef96cf Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Development of a protocol for the auto-generation of explicit aqueous-phase oxidation schemes of organic compounds Creator An entity primarily responsible for making the resource P. Bräuer, C. Mouchel-Vallon, A. Tilgner, A. Mutzel, O. Böge, M. Rodigast, L. Poulain, D. van Pinxteren, R. Wolke, B. Aumont, H. Herrmann Description An account of the resource This paper presents a new CAPRAM–GECKO-A protocol for mechanism auto-generation of aqueous-phase organic processes. For the development, kinetic data in the literature were reviewed and a database with 464 aqueous-phase reactions of the hydroxyl radical with organic compounds and 130 nitrate radical reactions with organic compounds has been compiled and evaluated. Five different methods to predict aqueous-phase rate constants have been evaluated with the help of the kinetics database: gas–aqueous phase correlations, homologous series of various compound classes, radical reactivity comparisons, Evans–Polanyi-type correlations, and structure–activity relationships (SARs). The quality of these prediction methods was tested as well as their suitability for automated mechanism construction. Based on this evaluation, SARs form the basis of the new CAPRAM–GECKO-A protocol. Evans–Polanyi-type correlations have been advanced to consider all available H atoms in a molecule besides the H atoms with only the weakest bond dissociation enthalpies (BDEs). The improved Evans–Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 and organic compounds reactions. Extensive tests have been performed on essential parameters and on highly uncertain parameters with limited experimental data. These sensitivity studies led to further improvements in the new CAPRAM–GECKO-A protocol but also showed current limitations. Biggest uncertainties were observed in uptake processes and the estimation of Henry's law coefficients as well as radical chemistry, in particular the degradation of alkoxy radicals. Previous estimation methods showed several deficits, which impacted particle growth. For further evaluation, a 1,3,5-trimethylbenzene oxidation experiment has been performed in the aerosol chamber “Leipziger Aerosolkammer” (LEAK) at high relative humidity conditions and compared to a multiphase mechanism using the Master Chemical Mechanism (MCMv3.2) in the gas phase and using a methylglyoxal oxidation scheme of about 600 reactions generated with the new CAPRAM–GECKO-A protocol in the aqueous phase. While it was difficult to evaluate single particle constituents due to concentrations close to the detection limits of the instruments applied, the model studies showed the importance of aqueous-phase chemistry in respect to secondary organic aerosol (SOA) formation and particle growth. The new protocol forms the basis for further CAPRAM mechanism development towards a new version 4.0. Moreover, it can be used as a supplementary tool for aerosol chambers to design and analyse experiments of chemical complexity and help to understand them on a molecular level. Date A point or period of time associated with an event in the lifecycle of the resource 2019 Identifier An unambiguous reference to the resource within a given context DOI: 10.5194/acp-19-9209-2019 Source A related resource from which the described resource is derived Atmospheric Chemistry and Physics Publisher An entity responsible for making the resource available Copernicus Publications Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Physics, Chemistry Language A language of the resource EN https://www.socictopen.socict.org/files/original/ff313a6116972844d73ee4334771211d.pdf 219258d913b64a74cf10e95fad65a0f0 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. Creator An entity primarily responsible for making the resource Abdulkadir Elmas, Xiao-Dong Wang, Jacqueline M. Dresch Description An account of the resource Understanding the molecular machinery involved in transcriptional regulation is central to improving our knowledge of an organism's development, disease, and evolution. The building blocks of this complex molecular machinery are an organism's genomic DNA sequence and transcription factor proteins. Despite the vast amount of sequence data now available for many model organisms, predicting where transcription factors bind, often referred to as 'motif detection' is still incredibly challenging. In this study, we develop a novel bioinformatic approach to binding site prediction. We do this by extending pre-existing SVM approaches in an unbiased way to include all possible gapped k-mers, representing different combinations of complex nucleotide dependencies within binding sites. We show the advantages of this new approach when compared to existing SVM approaches, through a rigorous set of cross-validation experiments. We also demonstrate the effectiveness of our new approach by reporting on its improved performance on a set of 127 genomic regions known to regulate gene expression along the anterio-posterior axis in early Drosophila embryos. Date A point or period of time associated with an event in the lifecycle of the resource 2017 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0185570 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/c338e258661123599f82c258979a8f1d.pdf c42f0fa61b891f3d86edc71397981440 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods. Creator An entity primarily responsible for making the resource Mohd Jaseem Khan, Amanda Cristina Trabuco, Helda Liz Alfonso, Mario Luis Figueiredo, Weber Cheli Batista, Soraya Jabur Badra, Luiz Tadeu Figueiredo, Marco Aurélio Lavrador, Victor Hugo Aquino Description An account of the resource Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n = 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. Date A point or period of time associated with an event in the lifecycle of the resource 2016 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pntd.0005017 Source A related resource from which the described resource is derived PLoS Neglected Tropical Diseases Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Arctic medicine. Tropical medicine, Public aspects of medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/b8f3655d7571a4fa230a38ac2f8921d9.pdf c39cfb38dae6363becbb5c07a6e6a89b Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. Creator An entity primarily responsible for making the resource Anh Ha Lien Do, H. Rogier van Doorn, My Ngoc Nghiem, Juliet E. Bryant, Thanh Hang thi Hoang, Quang Ha Do, Tan Le Van, Tan Thanh Tran, Bridget Wills, Vinh Chau van Nguyen, Minh Hien Vo, Cong Khanh Vo, Minh-Dung Nguyen, Jeremy Farrar, Tinh Hien Tran, Menno D de Jong Description An account of the resource The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized children in resource-limited tropical countries where morbidity and mortality caused by ARIs are highest. Improved etiological insight is needed to improve clinical management and prevention.We conducted a three-year prospective descriptive study of severe respiratory illness among children from 2 months to 13 years of age within the largest referral hospital for infectious diseases in southern Vietnam.Molecular detection for 15 viral species and subtypes was performed on three types of respiratory specimens (nose, throat swabs and nasopharyngeal aspirates) using a multiplex RT-PCR kit (Seeplex™ RV detection, Seegene) and additional monoplex real-time RT-PCRs.A total of 309 children were enrolled from November 2004 to January 2008. Viruses were identified in 72% (222/309) of cases, including respiratory syncytial virus (24%), influenza virus A and B (17%), human bocavirus (16%), enterovirus (9%), human coronavirus (8%), human metapneumovirus (7%), parainfluenza virus 1-3 (6%), adenovirus (5%), and human rhinovirus A (4%). Co-infections with multiple viruses were detected in 20% (62/309) of patients. When combined, diagnostic yields in nose and throat swabs were similar to nasopharyngeal aspirates.Similar to other parts in the world, RSV and influenza were the predominant viral pathogens detected in Vietnamese hospitalized children. Combined nasal and throat swabs are the specimens of choice for sensitive molecular detection of a broad panel of viral agents. Further research is required to better understand the clinical significance of single versus multiple viral coinfections and to address the role of bacterial (co-)infections involved in severe respiratory illness. Date A point or period of time associated with an event in the lifecycle of the resource 2011 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0018176 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/a73176cf6613ae226f10820665f4e85d.pdf bbc6cd57e0b3d8e2ad94fb2147ce58a4 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches. Creator An entity primarily responsible for making the resource Meznah Almutairy, Eric Torng Description An account of the resource Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. Date A point or period of time associated with an event in the lifecycle of the resource 2018 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0189960 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN https://www.socictopen.socict.org/files/original/30287a6558bc107af568d798ea0e3928.pdf 30f83adff648ccf13bb4fc50eee777d4 Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Coronavirus Description An account of the resource Dominio científico: Coronavirus Text A resource consisting primarily of words for reading. Examples include books, letters, dissertations, poems, newspapers, articles, archives of mailing lists. Note that facsimiles or images of texts are still of the genre Text. Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Epidemiology characteristics of human coronaviruses in patients with respiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou. Creator An entity primarily responsible for making the resource Su-Fen Zhang, Jiu-Ling Tuo, Xu-Bin Huang, Xun Zhu, Dingmei Zhang, Kai Zhou, Lei Yuan, Hong-Jiao Luo, Bo-Jian Zheng, Kwok-yung Yuen, Mengfeng Li, Kai-Yuan Cao, Lin Xu Description An account of the resource Human coronavirus (HCoV) is one of the most common causes of respiratory tract infection throughout the world. To investigate the epidemiological and genetic variation of HCoV in Guangzhou, south China, we collected totally 13048 throat and nasal swab specimens from adults and children with fever and acute upper respiratory infection symptoms in Gunazhou, south China between July 2010 and June 2015, and the epidemiological features of HCoV and its species were studied. Specimens were screened for HCoV by real-time RT-PCR, and 7 other common respiratory viruses were tested simultaneously by PCR or real-time PCR. HCoV was detected in 294 cases (2.25%) of the 13048 samples, with most of them inpatients (251 cases, 85.4% of HCoV positive cases) and young children not in nursery (53.06%, 156 out of 294 HCoV positive cases). Four HCoVs, as OC43, 229E, NL63 and HKU1 were detected prevalent during 2010-2015 in Guangzhou, and among the HCoV positive cases, 60.20% were OC43, 16.67% were 229E, 14.97% were NL63 and 7.82% were HKU1. The month distribution showed that totally HCoV was prevalent in winter, but differences existed in different species. The 5 year distribution of HCoV showed a peak-valley distribution trend, with the detection rate higher in 2011 and 2013 whereas lower in 2010, 2012 and 2014. The age distribution revealed that children (especially those 50 years) were both high risk groups to be infected by HCoV. Of the 294 HCoV positive patients, 34.69% (101 cases) were co-infected by other common respiratory viruses, and influenza virus was the most common co-infecting virus (30/101, 29.70%). Fifteen HCoV-OC43 positive samples of 2013-2014 were selected for S gene sequencing and phylogenetic analysis, and the results showed that the 15 strains could be divided into 2 clusters in the phylogenetic tree, 12 strains of which formed a separate cluster that was closer to genotype G found in Malaysia. It was revealed for the first time that genotype B and genotype G of HCoV-OC43 co-circulated and the newly defined genotype G was epidemic as a dominant genotype during 2013-2014 in Guanzhou, south China. Date A point or period of time associated with an event in the lifecycle of the resource 2018 Identifier An unambiguous reference to the resource within a given context DOI: 10.1371/journal.pone.0191789 Source A related resource from which the described resource is derived PLoS ONE Publisher An entity responsible for making the resource available Public Library of Science (PLoS) Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Science, Medicine Language A language of the resource EN