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              <name>Title</name>
              <description>A name given to the resource</description>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Asymptomatic Middle East Respiratory Syndrome coronavirus infection using a serologic survey in Korea</text>
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                <text>Yeong Jun Song, Jeong-Sun Yang, Hee Jung Yoon, Hae-Sung Nam, Soon Young Lee, Hae Kwan Cheong, Woo Jung Park, Sung-Han Park, Bo Youl Choi, Sung Soon Kim, Moran Ki</text>
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                <text>OBJECTIVES The rates of asymptomatic infection with Middle East Respiratory Syndrome (MERS) coronavirus vary. A serologic study was conducted to determine the asymptomatic MERS infection rate in healthcare workers and non-healthcare workers by exposure status. METHODS Study participants were selected from contacts of MERS patients based on a priority system in 4 regions strongly affected by the 2015 MERS outbreak. A sero-epidemiological survey was performed in 1,610 contacts (average duration from exposure to test, 4.8 months), and the collected sera were tested using an enzyme-linked immunespecific assay (ELISA), immunofluorescence assay (IFA), and plaque reduction neutralization antibody test (PRNT). Among the 1,610 contacts, there were 7 ELISA-positive cases, of which 1 exhibited positive IFA and PRNT results. RESULTS The asymptomatic infection rate was 0.060% (95% confidence interval, 0.002 to 0.346). The asymptomatic MERS case was a patient who had been hospitalized with patient zero on the same floor of the hospital at the same time. The case was quarantined at home for 2 weeks after discharge, and had underlying diseases, including hypertension, angina, and degenerative arthritis. CONCLUSIONS The asymptomatic infection was acquired via healthcare-associated transmission. Thus, it is necessary to extend serologic studies to include inpatient contacts who have no symptoms.</text>
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                <text>2018</text>
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            <name>Subject</name>
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                <text>Asymptomatic infection, Epidemiology, Middle East respiratory syndrome coronavirus, nosocomial infections, Outbreak, Enzyme-linked immunespecific assay</text>
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                <text>DOI: 10.4178/epih.e2018014</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>EN</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Possible zoonotic viral threats associated with bats in southern Ukraine</text>
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                <text>Oksana Yurchenko, Dmytro Dubina, Dmytro Sokolovskyi, Oleksandr Gaidash</text>
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                <text>The paper is devoted to evaluation of some bat species inhabiting Ukraine as potential reservoir hosts of highly dangerous viruses including lyssaviruses, MERS-CoV-related coronaviruses, and arboviruses. Repeated catches of bats by a domestic cat were described. Laboratory examination of the caught bats did not detect infection with coronaviruses or arboviruses such as West Nile, tick-borne encephalitis, Crimean-Congo hemorrhagic fever, Tribec and Uukuniyemi viruses. The analysis of the literature showed the possibility of persistence of dangerous viruses among examined bat species. The fact that domestic cats may prey on bats that are potential reservoir hosts of dangerous viruses should be considered as a risk factor for infection of humans and cats with lyssaviruses causing rabies, and infection of humans with coronaviruses that may be associated with severe respiratory diseases.</text>
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                <text>2017</text>
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                <text>Chiroptera, Arboviruses, coronaviruses, lyssaviruses, pets, biological risk for humans</text>
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                <text>DOI: 10.15407/ptt2017.15.150</text>
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                <text>Праці Теріологічної школи</text>
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                <text>National Academy of Sciences of Ukraine. National Museum of Natural History</text>
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                <text>Zoology</text>
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            <description>A language of the resource</description>
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                  <text>Coronavirus</text>
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              <description>An account of the resource</description>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis.</text>
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                <text>Steven B Smith, William Dampier, Aydin Tozeren, James R. Brown, Michal Magid-Slav</text>
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                <text>Pandemic and seasonal respiratory viruses are a major global health concern. Given the genetic diversity of respiratory viruses and the emergence of drug resistant strains, the targeted disruption of human host-virus interactions is a potential therapeutic strategy for treating multi-viral infections. The availability of large-scale genomic datasets focused on host-pathogen interactions can be used to discover novel drug targets as well as potential opportunities for drug repositioning.In this study, we performed a large-scale analysis of microarray datasets involving host response to infections by influenza A virus, respiratory syncytial virus, rhinovirus, SARS-coronavirus, metapneumonia virus, coxsackievirus and cytomegalovirus. Common genes and pathways were found through a rigorous, iterative analysis pipeline where relevant host mRNA expression datasets were identified, analyzed for quality and gene differential expression, then mapped to pathways for enrichment analysis. Possible repurposed drugs targets were found through database and literature searches. A total of 67 common biological pathways were identified among the seven different respiratory viruses analyzed, representing fifteen laboratories, nine different cell types, and seven different array platforms. A large overlap in the general immune response was observed among the top twenty of these 67 pathways, adding validation to our analysis strategy. Of the top five pathways, we found 53 differentially expressed genes affected by at least five of the seven viruses. We suggest five new therapeutic indications for existing small molecules or biological agents targeting proteins encoded by the genes F3, IL1B, TNF, CASP1 and MMP9. Pathway enrichment analysis also identified a potential novel host response, the Parkin-Ubiquitin Proteasomal System (Parkin-UPS) pathway, which is known to be involved in the progression of neurodegenerative Parkinson's disease.Our study suggests that multiple and diverse respiratory viruses invoke several common host response pathways. Further analysis of these pathways suggests potential opportunities for therapeutic intervention.</text>
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                <text>DOI: 10.1371/journal.pone.0033174</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure.</text>
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                <text>Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown</text>
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                <text>K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this data structure is considerably more memory efficient than any exact data structure. In exchange, the use of a Count-Min Sketch introduces a systematic overcount for k-mers; moreover, only the counts, and not the k-mers, are stored. Here we analyze the speed, the memory usage, and the miscount rate of khmer for generating k-mer frequency distributions and retrieving k-mer counts for individual k-mers. We also compare the performance of khmer to several other k-mer counting packages, including Tallymer, Jellyfish, BFCounter, DSK, KMC, Turtle and KAnalyze. Finally, we examine the effectiveness of profiling sequencing error, k-mer abundance trimming, and digital normalization of reads in the context of high khmer false positive rates. khmer is implemented in C++ wrapped in a Python interface, offers a tested and robust API, and is freely available under the BSD license at github.com/ged-lab/khmer.</text>
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                <text>2014</text>
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                <text>DOI: 10.1371/journal.pone.0101271</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV).</text>
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                <text>The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.</text>
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                <text>DOI: 10.1371/journal.pone.0123126</text>
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                <text>Correction: Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants.</text>
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                <text>Monica K. Borucki, Victoria Lao, Mona Hwang, Shea Gardner, Danielle Adney, Vincent Munster, Richard Bowen, Jonathan E Allen</text>
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                <text>[This corrects the article DOI: 10.1371/journal.pone.0146251.].</text>
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                <text>DOI: 10.1371/journal.pone.0154424</text>
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                <text>PLoS ONE</text>
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                  <text>Coronavirus</text>
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              <description>An account 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>Impact of the Regulators SigB, Rot, SarA and sarS on the Toxic Shock Tst Promoter and TSST-1 Expression in Staphylococcus aureus.</text>
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              <elementText elementTextId="2566">
                <text>Diego O. Andrey, Ambre Jousselin, Maite Villanueva, Adriana Renzoni, Antoinette Monod, Christine Barras, Natalia Rodríguez, William L Kelley</text>
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                <text>Staphylococcus aureus is an important pathogen manifesting virulence through diverse disease forms, ranging from acute skin infections to life-threatening bacteremia or systemic toxic shock syndromes. In the latter case, the prototypical superantigen is TSST-1 (Toxic Shock Syndrome Toxin 1), encoded by tst(H), and carried on a mobile genetic element that is not present in all S. aureus strains. Transcriptional regulation of tst is only partially understood. In this study, we dissected the role of sarA, sarS (sarH1), RNAIII, rot, and the alternative stress sigma factor sigB (σB). By examining tst promoter regulation predominantly in the context of its native sequence within the SaPI1 pathogenicity island of strain RN4282, we discovered that σB emerged as a particularly important tst regulator. We did not detect a consensus σB site within the tst promoter, and thus the effect of σB is likely indirect. We found that σB strongly repressed the expression of the toxin via at least two distinct regulatory pathways dependent upon sarA and agr. Furthermore rot, a member of SarA family, was shown to repress tst expression when overexpressed, although its deletion had no consistent measurable effect. We could not find any detectable effect of sarS, either by deletion or overexpression, suggesting that this regulator plays a minimal role in TSST-1 expression except when combined with disruption of sarA. Collectively, our results extend our understanding of complex multifactorial regulation of tst, revealing several layers of negative regulation. In addition to environmental stimuli thought to impact TSST-1 production, these findings support a model whereby sporadic mutation in a few key negative regulators can profoundly affect and enhance TSST-1 expression.</text>
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                <text>2015</text>
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                <text>DOI: 10.1371/journal.pone.0135579</text>
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                <text>PLoS ONE</text>
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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>Asymptomatic COVID-19 Infection Management: The Key to Stop COVID-19</text>
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            <description>An entity primarily responsible for making the resource</description>
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                <text>Rachid Ait Addi, Abdelhafid Benksim, Mohamed Amine, Mohamed Cherkaoui</text>
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                <text>The COVID-19 disease, emerged in December 2019, has spread rapidly, with new cases confirmed in multiple countries. Many efforts to contain the virus are ongoing, such as containment, individual measures of protection, the authorization of use of some drugs as chloquorine in some countries. Also, it has been known that symptomatic and asymptomatic people whom are infected by COVID-19 have the same contagiousness which expose a far greater portion of the population to virus and increase the late diagnosis and thereafter enhance COVID-19 mortality. Thereafter, it is fundamental to review our COVID-19 screening approach and enlarge COVID-19 testing to the general population by using rapid testing appliances such as rapid SARS-CoV-2 IgG-IgM combined antibody since another appliance more efficient will be performed.</text>
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                <text>COVID-19, Pandemic, screening, diagnosis</text>
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                <text>DOI: 10.5799/jcei/7866</text>
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                <text>Journal of Clinical and Experimental Investigations</text>
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                <text>Association of Health Investigations</text>
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                <text>Medicine</text>
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                <text>EN, TR</text>
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              <name>Title</name>
              <description>A name given to the resource</description>
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                  <text>Coronavirus</text>
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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>COVID-19 Tragic Pandemic: Concerns over Unintentional “Directed Accelerated Evolution” of Novel Coronavirus (SARS-CoV-2) and Introducing a Modified Treatment Method for ARDS</text>
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              <elementText elementTextId="2546">
                <text>A Ghadimi Moghadam, M. Haghani, JJ Bevelacqua, A. Jafarzadeh, A Kaveh-Ahangar, S.M.J. Mortazavi, S A R Mortazavi</text>
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                <text>Global health authorities are trying to work out the current status of the novel coronavirus (COVID-19) outbreak and explore methods to reduce the rate of its transmission to healthy individuals. In this viewpoint we provide insights concerning how health care professionals can unintentionally shift the novel coronavirus type to more drug-resistant forms. It is worth noting that viruses usually have different sensitivities to physical and chemical damaging agents such antiviral drugs, UV and heat ranging from extremely sensitive (ES) to extremely resistant (ER) based on a bell-shaped curve. Given this consideration, the widespread infection of people with such ER viruses would be a real disaster. Here, we introduce a modified treatment method for COVID-19-associated pneumonia. In this proposed method, COVID-19 patients will receive a single dose of 100, 180 or 250 mSv X-ray radiation that is less than the maximum annual radiation dose of the residents of high background radiation areas of Ramsar that is up to 260 mSv. In contrast with antiviral drugs, a single dose of either 100, 180 or 250 mSv of low LET X-rays cannot exert a significant selective pressure on the novel coronavirus (SARS-CoV-2) and hence does not lead to directed accelerated evolution of these viruses. Moreover, Low Dose Radiation (LDR) has the capacity of modulating excessive inflammatory responses, regulating lymphocyte counts, and controling bacterial co-infections in patients with COVID-19.</text>
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                <text>2020</text>
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                <text>coronavirus, X-rays, respiratory distress syndrome, Radiation Dosage, selective pressure, directed evolution</text>
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            <description>An unambiguous reference to the resource within a given context</description>
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