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                  <text>Dominio científico: Coronavirus</text>
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                <text>Microorganisms Causing Community-Acquired Acute Bronchitis: The Role of Bacterial Infection.</text>
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                <text>Jiyoung Park, Sunghoon Park, Sun Hwa Lee, Myung Goo Lee, Yong  Bum Park, Kil Chan Oh, Jae-Myung Lee, Do Il Kim, Ki-Hyun Seo, Kyeong-Cheol Shin, Kwang Ha Yoo, Yongchun Ko, Seung Hun Jang, Ki Suck Jung, Yong Il Hwang</text>
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                <text>Although acute bronchitis is quite common, there is relatively limited information regarding the microorganisms that are involved in this illness.We performed a prospective study of acute bronchitis at 31 hospitals and clinics in Korea from July 2011 to June 2012. Sputum specimens were collected for polymerase chain reaction (PCR) and culture of microorganisms.Of the 811 enrolled patients, 291 had acceptable sputum specimens that were included for analysis of the etiologic distribution. With multiplex PCR testing, viruses were identified in 36.1% (105/291), most commonly rhinovirus (25.8%) and coronavirus (3.8%). Typical bacteria were isolated in 126/291 (43.3%) patients. Among these patients Haemophilus influenzae (n = 39) and Streptococcus pneumoniae (n = 30) were isolated most commonly; atypical bacteria were identified in 44 (15.1%) patients. Bacteria-only, virus-only, and mixed infections (bacteria plus virus) accounted for 36.7% (98/291), 17.2% (50/291), and 18.9% (55/291) of infections, respectively. In particular, 52.4% of patients with viral infection had a concurrent bacterial infection, and rhinovirus was the most common virus in mixed infections (40/55). Additionally, infections with typical bacteria were more common in patients with chronic lung disease (p = 0.029), and typical bacterial infections showed a trend towards a higher prevalence with older age (p = 0.001).Bacteria were associated with almost half of community-acquired acute bronchitis cases. Additional studies are required to further illuminate the role of bacteria and to identify patient groups most likely to benefit from antibiotic treatment.</text>
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                <text>DOI: 10.1371/journal.pone.0165553</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>COMPARISON OF STRESS PROTEINS PARTICIPATION IN ADAPTATION MECHANISMS OF BAIKALIAN AND PALEARCTIC AMPHIPOD (AMPHIPODA; CRUSTACEA) SPECIES</text>
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                <text>Timofeyev M.A., Shatilina Zh.M., Bedulina D.S., Protopopova M.V., Grabelnych, O. I., Pobezhimova, T. P., Kolesnichenko A.V.</text>
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                <text>The aim of the present study was a study of the influence different stressful factor on syntheses and activity of the stress proteins (HSP70, sHSP and peroxidase) of freshwater organism. Six freshwater amphipod species were investigated: Eulimnogammarus cyaneus (Dyb.), E verrucosus (Gerstf.), E vittatus (Dyb.) - endemic species from Lake Baikal which were compared with Palearctic species - Gammarus lacustris Sars., G tigrinus (Sexton), Chaetogammarus ischnus (Stebbins). It was shown expression of sHSP by heat and toxic stresses for all amphipods species. Oxidative stress induced HSP70 for Palearctic species G tigrinus and C ischnus but not for baikalian species. Heat stress did not caused the increase of HSP70 level for Baikalian species of amphipods. The activity of the peroxidase was decrease by heat and toxic stresses. Oxidative stress caused the increase of peroxidase activity for Palearctic species, and the decrease for Baikalian once.</text>
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                <text>2006</text>
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                <text>Baikal, Heat-shock proteins, peroxidase, amphipods, stress adaptation</text>
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                <text>Journal of Stress Physiology &amp; Biochemistry</text>
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                <text>Vikol publishing" ST Kolesnichenko V.V."</text>
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                <text>Biochemistry</text>
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                <text>Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans.</text>
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                <text>Christina Osborne, Paul M. Cryan, Thomas J O'Shea, Lauren M. Oko, Christina Ndaluka, Charles H Calisher, Andrew D Berglund, Mead L Klavetter, Richard A. Bowen, Kathryn V. Holmes, Samuel R. Dominguez</text>
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                <text>Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.</text>
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                <text>DOI: 10.1371/journal.pone.0019156</text>
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                <text>PLoS ONE</text>
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                <text>A post-synaptic scaffold at the origin of the animal kingdom.</text>
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                <text>Onur Sakarya, Kathryn A Armstrong, Maja Adamska, Marcin Adamski, I-Fan Wang, Bruce Tidor, Bernard M. Degnan, Todd H Oakley, Kenneth S. Kosik</text>
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                <text>The evolution of complex sub-cellular structures such as the synapse requires the assembly of multiple proteins, each conferring added functionality to the integrated structure. Tracking the early evolution of synapses has not been possible without genomic information from the earliest branching animals. As the closest extant relatives to the Eumetazoa, Porifera (sponges) represent a pivotal group for understanding the evolution of nervous systems, because sponges lack neurons with clearly recognizable synapses, in contrast to eumetazoan animals.We show that the genome of the demosponge Amphimedon queenslandica possesses a nearly complete set of post-synaptic protein homologs whose conserved interaction motifs suggest assembly into a complex structure. In the critical synaptic scaffold gene, dlg, residues that make hydrogen bonds and van der Waals interactions with the PDZ ligand are 100% conserved between sponge and human, as is the motif organization of the scaffolds. Expression in Amphimedon of multiple post-synaptic gene homologs in larval flask cells further supports the existence of an assembled structure. Among the few post-synaptic genes absent from Amphimedon, but present in Eumetazoa, are receptor genes including the entire ionotropic glutamate receptor family.Highly conserved protein interaction motifs and co-expression in sponges of multiple proteins whose homologs interact in eumetazoan synapses indicate that a complex protein scaffold was present at the origin of animals, perhaps predating nervous systems. A relatively small number of crucial innovations to this pre-existing structure may represent the founding changes that led to a post-synaptic element.</text>
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                <text>DOI: 10.1371/journal.pone.0000506</text>
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                <text>PLoS ONE</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>ERROR CORRECTION METHOD FOR SEQUENCING DATA WITH INSERTIONS AND DELETIONS</text>
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            <name>Creator</name>
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              <elementText elementTextId="789">
                <text>A. V. Alexandrov, A. A. Shalyto</text>
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                <text>Subject of Research.A method for error correction for sequencing reads of a haploid organism with insertions and deletions was developed. It was tested on two libraries: a synthesized dataset for Escherichia coli bacterium and a real dataset of reads for Pseudomonas stutzeri. Method. The method is based on using k-mers but only for finding reads that are close to each other. For the close reads a consensus string is created which is then used for correcting errors in the initial reads. Main Results. The algorithm is implemented as a separated program. The program has been tested on both real and synthesized data. The method performance is higher than that of the other known methods (N50 metric was used as well as total contig length and maximal contig length as metrics for comparison). Practical Relevance. The method can be used together with known genome assembly methods not suitable for application with the reads containing insertion and deletion errors.</text>
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                <text>2016</text>
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                <text>genome assembly, error correction, insertions and deletions errors</text>
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                <text>DOI: 10.17586/2226-1494-2016-16-1-108-114</text>
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              <elementText elementTextId="794">
                <text>Naučno-tehničeskij Vestnik Informacionnyh Tehnologij, Mehaniki i Optiki</text>
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              <elementText elementTextId="795">
                <text>Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University)</text>
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                <text>Optics. Light, Electronic computers. Computer science</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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                <text>First report of bovine rotavirus and bovine coronavirus seroprevalance in goats in Turkey</text>
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              <elementText elementTextId="799">
                <text>Gumusova Okur S., Yazici Z., Albayrak H., Çakiroglu D.</text>
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                <text>In this study, bovine coronavirus (BCV) and bovine rotavirus (BRV) seroprevalances were detected by ELISA in 107 goat blood serum samples obtained from five different provinces of Northern Turkey. The results of the study reflected 41.12% and 82.24% seropositivity against BCV and BRV, respectively, in the goat sera. BCV seroprevalance in mature goats is determined for the first time with this study. Furthermore, this is the first statement of BRV and BCV seroprevalances in the mature goat population in Turkey.</text>
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            <name>Date</name>
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                <text>2007</text>
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            <name>Subject</name>
            <description>The topic of the resource</description>
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                <text>BRV, BCV, ELISA, goat, Seroprevalance</text>
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                <text>DOI: 10.2298/VETGL0702075G</text>
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              <elementText elementTextId="804">
                <text>Veterinarski Glasnik</text>
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                <text>Faculty of Veterinary Medicine, Belgrade</text>
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                <text>Veterinary medicine</text>
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            <description>A language of the resource</description>
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                <text>SR</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>THE MOLECULAR EVOLUTION OF THE MOST DANGEROUS EMERGING VIRUS INFECTIONS</text>
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            <name>Creator</name>
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              <elementText elementTextId="809">
                <text>Popov N.N., Kolotova TYu</text>
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                <text>In this paper we reviewed what is known about the emerging viruses, the hosts that they originate in, and the molecular events that drive their emergence. When a pathogen crosses over from animals to humans, or an existing human disease suddenly increases in incidence, the infectious disease is said to be ‘emerging’. Most of the emerging pathogens originate from nonhuman animal species which has been termed natural reservoirs. The number of emerging infectious diseases has increased over the last few decades, driven by both anthropogenic and environmental factors such as population growth, urbanization, global travel and trade, intensification of livestock production. Now it has been believed that the emergence process may include four steps. On the first step the exposure of the humans to a novel virus occures. On the second step the subset of the viruses overcome the cross-species barrier. Host shifts have resulted in multiple human pandemics, such as HIV from chimps the H1N1, ‘‘spanish flu’’ from birds, SARS-CoV and virus Ebola from bats. Then some viruses enables to transmit from one human to another. And on the last step the viruses that are sufficiently transmissible between humans cause outbreaks and become endemic in human populations without the requirement of a natural reservoir. This review aims to discuss the molecular mechanisms that govern virus cross-species transmission and following stage, using the emergence of HIV, SARS-CoV, virus Ebola and influenza virus A as the models.Populations of many viruses harbour abundant genetic variability due to a combination of high mutation, recombination or reassortation rates and large population sizes. Mutations and recombinations has been associated with the increases in virulence, the evasion of host immunity and the evolution of resistance to antivirals. Genetic alterations in one species may results in the acquisition of variations that allow them to overcome cross species barriers and infect new hosts. Really, many recently emerged human diseases are caused by viruses that display active recombination or reassortment. The continual shuffling of genes of influenza A represents a example of the key role of reassortment for the new virus emergence. Available data demonstrate the possible origin of SARS-CoV from recombination of different bat SL-CoVs viruses strains. However in other cases the emergence of a specific virus cannot be directly attributed to its ability to recombine. For example, although SIV recombines at a high rate in natural reservoirs, there is no evidence that recombination assisted the cross-species transfer of the virus from the chimpanzee into humans. But mutagenesis and recombination actively shape the further molecular history of HIV in humans. Also it is not proved that recombination precede the cross-species jump of the Ebola virus. In summary, the available data suggest that although recombination, reassortment and mutagenesis is sometimes directly involved to the process of cross-species transmission, it is not a necessary precursor to successful viral emergence. Further investigations are required to reveal the role of genetic change in the history of virus emergence. We believe that comprehensive description of molecular evolution of new viruses has led to a better understanding of the causes and predictability of infection emergence.</text>
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                <text>2016</text>
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            <name>Subject</name>
            <description>The topic of the resource</description>
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              <elementText elementTextId="812">
                <text>Emerging viruses, four stage of the emergence, Natural reservoir, recombination, reassotment, Mutagenesis, HIV-1, HIV-2, SIV, SARS-CoV, virus Ebola, influenza virus A</text>
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                <text>DOI: </text>
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              <elementText elementTextId="814">
                <text>Anali Mečnikìvsʹkogo Institutu</text>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
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              <elementText elementTextId="815">
                <text>Mechnikov Institute of Microbiology and immunology</text>
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                <text>Medicine (General)</text>
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                  <text>Dominio científico: Coronavirus</text>
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                <text>Human Mycobacterium tuberculosis CD8 T Cell Antigens/Epitopes Identified by a Proteomic Peptide Library.</text>
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                <text>David M Lewinsohn, Gwendolyn M Swarbrick, Meghan E Cansler, Megan D Null, Veena Rajaraman, Marisa M Frieder, David R Sherman, Shannon McWeeney, Deborah A. Lewinsohn</text>
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                <text>Identification of CD8(+) T cell antigens/epitopes expressed by human pathogens with large genomes is especially challenging, yet necessary for vaccine development. Immunity to tuberculosis, a leading cause of mortality worldwide, requires CD8(+) T cell immunity, yet the repertoire of CD8 antigens/epitopes remains undefined. We used integrated computational and proteomic approaches to screen 10% of the Mycobacterium tuberculosis (Mtb) proteome for CD8 Mtb antigens. We designed a weighting schema based upon a Multiple Attribute Decision Making:framework to select 10% of the Mtb proteome with a high probability of containing CD8(+) T cell epitopes. We created a synthetic peptide library consisting of 15-mers overlapping by 11 aa. Using the interferon-γ ELISPOT assay and Mtb-infected dendritic cells as antigen presenting cells, we screened Mtb-specific CD8(+) T cell clones restricted by classical MHC class I molecules (MHC class Ia molecules), that were isolated from Mtb-infected humans, against this library. Three novel CD8 antigens were unambiguously identified: the EsxJ family (Rv1038c, Rv1197, Rv3620c, Rv2347c, Rv1792), PE9 (Rv1088), and PE_PGRS42 (Rv2487c). The epitopes are B5701-restricted EsxJ24-34, B3905-restricted PE953-67, and B3514-restricted PE_PGRS4248-56, respectively. The utility of peptide libraries in identifying unknown epitopes recognized by classically restricted CD8(+) T cells was confirmed, which can be applied to other intracellular pathogens with large size genomes. In addition, we identified three novel Mtb epitopes/antigens that may be evaluated for inclusion in vaccines and/or diagnostics for tuberculosis.</text>
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                <text>2013</text>
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                <text>DOI: 10.1371/journal.pone.0067016</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>Science, Medicine</text>
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                <text>Comparative pathology of rhesus macaque and common marmoset animal models with Middle East respiratory syndrome coronavirus.</text>
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                <text>Pin Yu, Yanfeng Xu, Wei Deng, Lin-Lin Bao, Lan HUANG, Yuhuan Xu, Yanfeng Yao, Chuan Qin</text>
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                <text>Middle East respiratory syndrome (MERS), which is caused by a newly discovered coronavirus (CoV), has recently emerged. It causes severe viral pneumonia and is associated with a high fatality rate. However, the pathogenesis, comparative pathology and inflammatory cell response of rhesus macaques and common marmosets experimentally infected with MERS-CoV are unknown. We describe the histopathological, immunohistochemical, and ultrastructural findings from rhesus macaque and common marmoset animal models of MERS-CoV infection. The main histopathological findings in the lungs of rhesus macaques and common marmosets were varying degrees of pulmonary lesions, including pneumonia, pulmonary oedema, haemorrhage, degeneration and necrosis of the pneumocytes and bronchial epithelial cells, and inflammatory cell infiltration. The characteristic inflammatory cells in the lungs of rhesus macaques and common marmosets were eosinophils and neutrophils, respectively. Based on these observations, the lungs of rhesus macaques and common marmosets appeared to develop chronic and acute pneumonia, respectively. MERS-CoV antigens and viral RNA were identified in type I and II pneumocytes, alveolar macrophages and bronchial epithelial cells, and ultrastructural observations showed that viral protein was found in type II pneumocytes and inflammatory cells in both species. Correspondingly, the entry receptor DDP4 was found in type I and II pneumocytes, bronchial epithelial cells, and alveolar macrophages. The rhesus macaque and common marmoset animal models of MERS-CoV can be used as a tool to mimic the oncome of MERS-CoV infections in humans. These models can help to provide a better understanding of the pathogenic process of this virus and to develop effective medications and prophylactic treatments.</text>
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                <text>2017</text>
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                <text>DOI: 10.1371/journal.pone.0172093</text>
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              <elementText elementTextId="832">
                <text>PLoS ONE</text>
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                <text>Public Library of Science (PLoS)</text>
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                <text>Science, Medicine</text>
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                <text>EN</text>
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        <src>https://www.socictopen.socict.org/files/original/1f8e2746eb99d98ecbc51a459fabf5ed.pdf</src>
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              <name>Title</name>
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                  <text>Coronavirus</text>
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                  <text>Dominio científico: Coronavirus</text>
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          <element elementId="50">
            <name>Title</name>
            <description>A name given to the resource</description>
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                <text>Structure activity relationship and modeling studies of inhibitors of lysine specific demethylase 1.</text>
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            <name>Creator</name>
            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="837">
                <text>Chao Zhou, Fangrui Wu, Lianghao Lu, Liping Wei, Eric Pai, Yuan Yao, Yongcheng Song</text>
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                <text>Post-translational modifications of histone play important roles in gene transcription. Aberrant methylation of histone lysine sidechains have been often found in cancer. Lysine specific demethylase 1 (LSD1), which can demethylate histone H3 lysine 4 (H3K4) and other proteins, has recently been found to be a drug target for acute myeloid leukemia. To understand structure activity/selectivity relationships of LSD1 inhibitors, several series of cyclopropylamine and related compounds were synthesized and tested for their activities against LSD1 and related monoamine oxidase (MAO) A and B. Several cyclopropylamine containing compounds were found to be highly potent and selective inhibitors of LSD1. A novel series cyclopropylimine compounds also exhibited strong inhibitory activity against LSD1. Structure activity relationships (SAR) of these compounds are discussed. Docking studies were performed to provide possible binding models of a representative compound in LSD1 and MAO-A. Moreover, these modeling studies can rationalize the observed SARs and selectivity.</text>
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                <text>2017</text>
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                <text>DOI: 10.1371/journal.pone.0170301</text>
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              <elementText elementTextId="841">
                <text>PLoS ONE</text>
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                <text>Public Library of Science (PLoS)</text>
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                <text>Science, Medicine</text>
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                <text>EN</text>
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