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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples</text>
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                <text>Maley Carlo C, Venkatesh Santosh S, Liu Zhandong</text>
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                <text>Abstract Background Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. Results We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes. Virtually all possible (&gt; 98%) 12 bp oligomers appear in vertebrate genomes while &lt; 2% of 19 bp oligomers are present. Other species showed different ranges of &gt; 98% to &lt; 2% of possible oligomers in D. melanogaster (12–17 bp), C. elegans (11–17 bp), A. thaliana (11–17 bp), S. cerevisiae (10–16 bp) and E. coli (9–15 bp). Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy. Conclusion Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect novel microbes in human tissues.</text>
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                <text>2008</text>
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                <text>DOI: 10.1186/1471-2164-9-509</text>
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                <text>BMC Genomics</text>
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                <text>BMC</text>
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                <text>Genetics, Biotechnology</text>
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                <text>Sequence-dependent fluorescence of cyanine dyes on microarrays.</text>
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                <text>Christy Agbavwe, Mark M. Somoza</text>
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                <text>Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5'-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5' guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5'-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.</text>
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                <text>2011</text>
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                <text>DOI: 10.1371/journal.pone.0022177</text>
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                <text>PLoS ONE</text>
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                <text>Public Library of Science (PLoS)</text>
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                  <text>Agricultura sostenible</text>
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                  <text>Dominio científico: Agricultura sostenible</text>
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                <text>SEQUÊNCIAS DIDÁTICAS INVESTIGATIVAS E ARGUMENTAÇÃO NO ENSINO DE ECOLOGIA</text>
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              <elementText elementTextId="174418">
                <text>Marcelo Tadeu Motokane</text>
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                <text>Este artículo presenta los principios que basan la producción  de las Secuencias Didácticas Investigativas (SDI) del grupo de  investigación LINCE (Lenguaje y Enseñanza de las Ciencias). Tales  secuencias tienen enfoque en la enseñanza de la ecología y utilizan el  proceso de alfabetización científica y de la enseñanza por investigación  para promover la producción de argumentos en aula y justificar su  importancia para el aprendizaje de la ciencia. Las secuencias presentan  problemas científicos que llevan a la construcción de argumentos. Las  aplicaciones y los análisis de las secuencias didácticas han señalado que  hay espacio para el desarrollo de argumentos hablados y escritos. Todavía,  ha sido un desafío construir orientaciones para que el profesor pueda  mediar las actividades con finalidad de producir argumentos válidos,  basados en conocimientos científicos en sus justificativas.</text>
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                <text>2015</text>
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              <elementText elementTextId="174421">
                <text>Ensaio Pesquisa em Educação em Ciências</text>
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                <text>Universidade Federal de Minas Gerais</text>
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                <text>Education (General)</text>
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                <text>&lt;a href="http://www.redalyc.org/articulo.oa?id=129543057007" target="_blank" rel="noreferrer noopener"&gt;http://www.redalyc.org/articulo.oa?id=129543057007&lt;/a&gt;</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Sequencing for Surveillance of Emerging Infectious Diseases: from Laboratory to Field</text>
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                <text>Lihua Wang, Jishu Shi</text>
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                <text>Emerging infectious diseases (EIDs) have affected both human and animal populations throughout history, and can be grouped into four categories: 1) newly identified pathogens, 2) zoonotic pathogens, 3) pathogens or vectors adapted to new environments, and 4) pathogens with enhanced virulence. In recent decades, several EIDs have threatened the global community and drawn both public and scientific attention. These include human immunodeficiency virus/acquired immune deficiency syndrome, severe acute respiratory syndrome, Middle East respiratory syndrome, influenza strains H7N9 (bird flu) and H1N1 (swine flu), Ebola virus disease, expanded multidrug-resistant Mycobacterium tuberculosis and other antimicrobial-resistant microorganisms, and most recently, Zika virus disease. These events underscore the need for comprehensive surveillance and quick response systems to combat today’s EIDs and prevent those of tomorrow.</text>
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                <text>2016</text>
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                <text>emerging infectious diseases, Surveillance, Sequencing</text>
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                <text>DOI: 10.11979/idtm.201601001</text>
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                <text>Infectious Diseases and Translational Medicine</text>
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                <text>International Biological and Medical Journals Publishing House Co., Limited</text>
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                <text>Infectious and parasitic diseases</text>
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                <text>Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding</text>
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                <text>Julien Fouret, Julien Fouret, Frédéric G. Brunet, Martin Binet, Martin Binet, Noémie Aurine, Francois Enchéry, Séverine Croze, Marie Guinier, Abdelghafar Goumaidi, Doris Preininger, Jean-Nicolas Volff, Marc Bailly-Bechet, Joël Lachuer, Joël Lachuer, Branka Horvat, Catherine Legras-Lachuer, Catherine Legras-Lachuer</text>
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                <text>Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.</text>
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                <text>bats, Nipah virus, Pteropus medius, Pteropus giganteus, hybrid genome assembly, secondary scaffolding</text>
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                <text>10.3389/fmicb.2020.01807</text>
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                <text>Epidemiology and Health</text>
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                <text>Korean Society of Epidemiology</text>
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                <text>Microbiology</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Sequential Emergence and Wide Spread of Neutralization Escape Middle East Respiratory Syndrome Coronavirus Mutants, South Korea, 2015</text>
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              <elementText elementTextId="21695">
                <text>Yeon Sook Kim, Abdimadiyeva Aigerim, Uni Park, Yu-Ri Kim, Ji-Young Rhee, Jae-Phil Choi, Wan Beom Park, Sangwon Park, Yeonjae Kim, Dong-Gyun Lim, Kyung-Soo Inn, Eung Soo Hwang, Myung Sik Choi, Nam-Hyuk Cho</text>
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                <text>The unexpectedly large outbreak of Middle East respiratory syndrome in South Korea in 2015 was initiated by an infected traveler and amplified by several “superspreading” events. Previously, we reported the emergence and spread of mutant Middle East respiratory syndrome coronavirus bearing spike mutations (I529T or D510G) with reduced affinity to human receptor CD26 during the outbreak. To assess the potential association of spike mutations with superspreading events, we collected virus genetic information reported during the outbreak and systemically analyzed the relationship of spike sequences and epidemiology. We found sequential emergence of the spike mutations in 2 superspreaders. In vivo virulence of the mutant viruses seems to decline in human patients, as assessed by fever duration in affected persons. In addition, neutralizing activity against these 2 mutant viruses in serum samples from mice immunized with wild-type spike antigen were gradually reduced, suggesting emergence and wide spread of neutralization escapers during the outbreak.</text>
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                <text>2019</text>
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                <text>Middle East respiratory syndrome coronavirus, MERS-CoV, Superspreading, Spike, antibody neutralization, Viruses</text>
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                <text>DOI: 10.3201/eid2506.181722</text>
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                <text>Emerging Infectious Diseases</text>
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                <text>Centers for Disease Control and Prevention</text>
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            <description>The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant</description>
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                <text>Infectious and parasitic diseases, Medicine</text>
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            <description>A language of the resource</description>
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                  <text>Dominio científico: Coronavirus</text>
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      <name>Text</name>
      <description>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.</description>
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                <text>Sequential introduction of single room isolation and hand hygiene campaign in the control of methicillin-resistant &lt;it&gt;Staphylococcus aureus &lt;/it&gt;in intensive care unit</text>
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              <elementText elementTextId="21492">
                <text>Cheng Vincent CC, Tai Josepha WM, Chan W. M., Lau Eric HY, Chan Jasper FW, To Kelvin KW, Li Iris WS, Ho PL, Yuen KY</text>
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            <description>An account of the resource</description>
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              <elementText elementTextId="21493">
                <text>Abstract Background After renovation of the adult intensive care unit (ICU) with installation of ten single rooms, an enhanced infection control program was conducted to control the spread of methicillin-resistant Staphylococcus aureus (MRSA) in our hospital. Methods Since the ICU renovation, all patients colonized or infected with MRSA were nursed in single rooms with contact precautions. The incidence of MRSA infection in the ICU was monitored during 3 different phases: the baseline period (phase 1); after ICU renovation (phase 2) and after implementation of a hand hygiene campaign with alcohol-based hand rub (phase 3). Patients infected with extended spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella species were chosen as controls because they were managed in open cubicles with standard precautions. Results Without a major change in bed occupancy rate, nursing workforce, or the protocol of environmental cleansing throughout the study period, a stepwise reduction in ICU onset nonbacteraemic MRSA infection was observed: from 3.54 (phase 1) to 2.26 (phase 2, p = 0.042) and 1.02 (phase 3, p = 0.006) per 1000-patient-days. ICU onset bacteraemic MRSA infection was significantly reduced from 1.94 (phase 1) to 0.9 (phase 2, p = 0.005) and 0.28 (phase 3, p = 0.021) per 1000-patient-days. Infection due to ESBL-producing organisms did not show a corresponding reduction. The usage density of broad-spectrum antibiotics and fluoroquinolones increased from phase 1 to 3. However a significant trend improvement of ICU onset MRSA infection by segmented regression analysis can only be demonstrated when comparison was made before and after the severe acute respiratory syndrome (SARS) epidemic. This suggests that the deaths of fellow healthcare workers from an occupational acquired infection had an overwhelming effect on their compliance with infection control measures. Conclusion Provision of single room isolation facilities and promotion of hand hygiene practice are important. However compliance with infection control measures relies largely on a personal commitment, which may increase when personal safety is threatened.</text>
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                <text>2010</text>
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                <text>DOI: 10.1186/1471-2334-10-263</text>
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                <text>BMC Infectious Diseases</text>
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                <text>BMC</text>
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                <text>Infectious and parasitic diseases</text>
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                <text>Sequential introduction of single room isolation and hand hygiene campaign in the control of methicillin-resistant &lt;it&gt;Staphylococcus aureus &lt;/it&gt;in intensive care unit</text>
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                <text>Cheng Vincent CC, Tai Josepha WM, Chan WM, Lau Eric HY, Chan Jasper FW, To Kelvin KW, Li Iris WS, Ho PL, Yuen KY</text>
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            <description>An account of the resource</description>
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                <text>Abstract Background After renovation of the adult intensive care unit (ICU) with installation of ten single rooms, an enhanced infection control program was conducted to control the spread of methicillin-resistant Staphylococcus aureus (MRSA) in our hospital. Methods Since the ICU renovation, all patients colonized or infected with MRSA were nursed in single rooms with contact precautions. The incidence of MRSA infection in the ICU was monitored during 3 different phases: the baseline period (phase 1); after ICU renovation (phase 2) and after implementation of a hand hygiene campaign with alcohol-based hand rub (phase 3). Patients infected with extended spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella species were chosen as controls because they were managed in open cubicles with standard precautions. Results Without a major change in bed occupancy rate, nursing workforce, or the protocol of environmental cleansing throughout the study period, a stepwise reduction in ICU onset nonbacteraemic MRSA infection was observed: from 3.54 (phase 1) to 2.26 (phase 2, p = 0.042) and 1.02 (phase 3, p = 0.006) per 1000-patient-days. ICU onset bacteraemic MRSA infection was significantly reduced from 1.94 (phase 1) to 0.9 (phase 2, p = 0.005) and 0.28 (phase 3, p = 0.021) per 1000-patient-days. Infection due to ESBL-producing organisms did not show a corresponding reduction. The usage density of broad-spectrum antibiotics and fluoroquinolones increased from phase 1 to 3. However a significant trend improvement of ICU onset MRSA infection by segmented regression analysis can only be demonstrated when comparison was made before and after the severe acute respiratory syndrome (SARS) epidemic. This suggests that the deaths of fellow healthcare workers from an occupational acquired infection had an overwhelming effect on their compliance with infection control measures. Conclusion Provision of single room isolation facilities and promotion of hand hygiene practice are important. However compliance with infection control measures relies largely on a personal commitment, which may increase when personal safety is threatened.</text>
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                <text>10.1186/1471-2334-10-263</text>
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                <text>Infectious and parasitic diseases</text>
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                <text>Antonio Gil Olcina</text>
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                <text>Las sequías de 1841–42 y, sobre todo, 1846–50 en el sureste ibérico, tan próximas y particularmente graves, entre las peores de que hay noticia histórica, movieron a la convocatoria de un certamen nacional para seleccionar la mejor memoria sobre las causas de este tipo de fenómenos en las provincias de Murcia y Almería; con la finalidad de eliminar su causas y, si no era posible, atenuar sus efectos. El Gobierno de España se hacía así eco de la posibilidad de un cambio climático por deforestación.</text>
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