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                <text>Theory versus data: how to calculate R0?</text>
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                <text>To predict the potential severity of outbreaks of infectious diseases such as SARS, HIV, TB and smallpox, a summary parameter, the basic reproduction number R(0), is generally calculated from a population-level model. R(0) specifies the average number of secondary infections caused by one infected individual during his/her entire infectious period at the start of an outbreak. R(0) is used to assess the severity of the outbreak, as well as the strength of the medical and/or behavioral interventions necessary for control. Conventionally, it is assumed that if R(0)&gt;1 the outbreak generates an epidemic, and if R(0)</text>
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                <text>DOI: 10.1371/journal.pone.0000282</text>
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                <text>Albrecht von Brunn, Carola Teepe, Jeremy C. Simpson, Rainer Pepperkok, Caroline C Friedel, Ralf Zimmer, Rhonda Roberts, Ralph Baric, Jürgen Haas</text>
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                <text>The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies.</text>
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                <text>DOI: 10.1371/journal.pone.0000459</text>
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                <text>Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.</text>
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                <text>Olga V Matveeva, Aleksey Y Ogurtsov, Nafisa N Nazipova, Svetlana A Shabalina</text>
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                <text>Off-target oligoprobe's interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array. The database included two types of probes with signals derived from (i) a combination of specific signal and cross-hybridization and (ii) genomic cross-hybridization only. All probes from the database were grouped into bins according to their sequence characteristics, where both hybridization signals were averaged separately. For selection of specific probes, we analyzed the following sequence characteristics: vulnerability to self-folding, nucleotide composition bias, numbers of G nucleotides and GGG-blocks, and occurrence of probe's k-mers in the human genome. Increases in bin ranges for these characteristics are simultaneously accompanied by a decrease in hybridization specificity-the ratio between specific and cross-hybridization signals. However, both averaged hybridization signals exhibit growing trends along with an increase of probes' binding energy, where the hybridization specific signal increases significantly faster in comparison to the cross-hybridization. The same trend is evident for the S function, which serves as a combined evaluation of probe binding energy and occurrence of probe's k-mers in the genome. Application of S allows extracting a larger number of specific probes, as compared to using only binding energy. Thus, we showed that high values of specific and cross-hybridization signals are not mutually exclusive for probes with high values of binding energy and S. In this study, the application of a new set of sequence characteristics allows detection of probes that are highly specific to their targets for array design and other bio-techniques that require selection of specific probes.</text>
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                <text>DOI: 10.1371/journal.pone.0199162</text>
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                <text>The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome.</text>
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                <text>Meznah Almutairy, Eric Torng</text>
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                <text>One of the most common ways to search a sequence database for sequences that are similar to a query sequence is to use a k-mer index such as BLAST. A big problem with k-mer indexes is the space required to store the lists of all occurrences of all k-mers in the database. One method for reducing the space needed, and also query time, is sampling where only some k-mer occurrences are stored. Most previous work uses hard sampling, in which enough k-mer occurrences are retained so that all similar sequences are guaranteed to be found. In contrast, we study soft sampling, which further reduces the number of stored k-mer occurrences at a cost of decreasing query accuracy. We focus on finding highly similar local alignments (HSLA) over nucleotide sequences, an operation that is fundamental to biological applications such as cDNA sequence mapping. For our comparison, we use the NCBI BLAST tool with the human genome and human ESTs. When identifying HSLAs, we find that soft sampling significantly reduces both index size and query time with relatively small losses in query accuracy. For the human genome and HSLAs of length at least 100 bp, soft sampling reduces index size 4-10 times more than hard sampling and processes queries 2.3-6.8 times faster, while still achieving retention rates of at least 96.6%. When we apply soft sampling to the problem of mapping ESTs against the genome, we map more than 98% of ESTs perfectly while reducing the index size by a factor of 4 and query time by 23.3%. These results demonstrate that soft sampling is a simple but effective strategy for performing efficient searches for HSLAs. We also provide a new model for sampling with BLAST that predicts empirical retention rates with reasonable accuracy by modeling two key problem factors.</text>
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                <text>DOI: 10.1371/journal.pone.0179046</text>
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                <text>Infectious Bronchitis Virus as a Vector for the Expression of Heterologous Genes.</text>
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                <text>Kirsten Bentley, María Armesto, Paul Britton</text>
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            <description>An account of the resource</description>
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                <text>The avian coronavirus infectious bronchitis virus (IBV) is the causative agent of the respiratory disease infectious bronchitis of domestic fowl, and is controlled by routine vaccination. To explore the potential use of IBV as a vaccine vector a reverse genetics system was utilised to generate infectious recombinant IBVs (rIBVs) expressing the reporter genes enhanced green fluorescent protein (eGFP) or humanised Renilla luciferase (hRluc). Infectious rIBVs were obtained following the replacement of Gene 5 or the intergenic region (IR) with eGFP or hRluc, or the replacement of ORFs 3a and 3b with hRluc. The replacement of Gene 5 with an IBV codon-optimised version of the hRluc gene also resulted in successful rescue of infectious rIBV. Reporter gene expression was confirmed by fluorescence microscopy, or luciferase activity assays, for all successfully rescued rIBVs following infection of primary chick kidney (CK) cells. The genetic stability of rIBVs was analysed by serial passage on CK cells. Recombinant IBV stability varied depending on the genome region being replaced, with the reporter genes maintained up to at least passage 8 (P8) following replacement of Gene 5, P7 for replacement of the IR and P5 for replacement of ORFs 3a and 3b. Codon-optimisation of the hRluc gene, when replacing Gene 5, resulted in an increase in genome stability, with hRluc expression stable up to P10 compared to P8 for standard hRluc. Repeated passaging of rIBVs expressing hRluc at an MOI of 0.01 demonstrated an increase in stability, with hRluc expression stable up to at least P12 following the replacement of Gene 5. This study has demonstrated that heterologous genes can be incorporated into, and expressed from a range of IBV genome locations and that replacement of accessory Gene 5 offers a promising target for realising the potential of IBV as a vaccine vector for other avian pathogens.</text>
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                <text>DOI: 10.1371/journal.pone.0067875</text>
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                <text>PLoS ONE</text>
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                <text>Public Library of Science (PLoS)</text>
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              <name>Title</name>
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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>Human coronaviruses associated with upper respiratory tract infections in three rural areas of Ghana.</text>
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            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="2668">
                <text>Michael Owusu, Augustina Annan, Victor Max Corman, Richard Larbi, Priscilla Anti, Jan Felix Drexler, Olivia Agbenyega, Yaw Adu-Sarkodie, Christian Drosten</text>
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            <description>An account of the resource</description>
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                <text>Acute respiratory tract infections (ARI) are the leading cause of morbidity and mortality in developing countries, especially in Africa. This study sought to determine whether human coronaviruses (HCoVs) are associated with upper respiratory tract infections among older children and adults in Ghana.We conducted a case control study among older children and adults in three rural areas of Ghana using asymptomatic subjects as controls. Nasal/Nasopharyngeal swabs were tested for Middle East respiratory syndrome coronavirus (MERS-CoV), HCoV-22E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 using Reverse Transcriptase Real-Time Polymerase Chain Reaction.Out of 1,213 subjects recruited, 150 (12.4%) were positive for one or more viruses. Of these, single virus detections occurred in 146 subjects (12.0%) and multiple detections occurred in 4 (0.3%). Compared with control subjects, infections with HCoV-229E (OR = 5.15, 95%CI = 2.24-11.78), HCoV-OC43 (OR = 6.16, 95%CI = 1.77-21.65) and combine HCoVs (OR = 2.36, 95%CI = 1.5 = 3.72) were associated with upper respiratory tract infections. HCoVs were found to be seasonally dependent with significant detections in the harmattan season (mainly HCoV-229E) and wet season (mainly HCoV-NL63). A comparison of the obtained sequences resulted in no differences to sequences already published in GenBank.HCoVs could play significant role in causing upper respiratory tract infections among adults and older children in rural areas of Ghana.</text>
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                <text>2014</text>
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                <text>DOI: 10.1371/journal.pone.0099782</text>
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            <description>A related resource from which the described resource is derived</description>
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              <elementText elementTextId="2672">
                <text>PLoS ONE</text>
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            <description>An entity responsible for making the resource available</description>
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                <text>Public Library of Science (PLoS)</text>
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            <description>A language of the resource</description>
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              <name>Title</name>
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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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      <elementSet elementSetId="1">
        <name>Dublin Core</name>
        <description>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/.</description>
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          <element elementId="50">
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            <description>A name given to the resource</description>
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                <text>Distinct immune response in two MERS-CoV-infected patients: can we go from bench to bedside?</text>
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            <description>An entity primarily responsible for making the resource</description>
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              <elementText elementTextId="2659">
                <text>Emmanuel Faure, Julien Poissy, Anne Goffard, Clement Fournier, Eric Kipnis, Marie Titecat, Perinne Bortolotti, Laura Martinez, Sylvain Dubucquoi, Rodrigue Dessein, Philippe Gosset, Daniel MATHIEU, Benoit Guery</text>
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            <description>An account of the resource</description>
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                <text>One year after the occurrence of the first case of infection by the Middle East Respiratory Syndrome coronavirus (MERS-CoV) there is no clear consensus on the best treatment to propose. The World Health Organization, as well as several other national agencies, are still working on different clinical approaches to implement the most relevant treatment in MERS-CoV infection. We compared innate and adaptive immune responses of two patients infected with MERS-CoV to understand the underlying mechanisms involved in the response and propose potential therapeutic approaches. Broncho-alveolar lavage (BAL) of the first week and sera of the first month from the two patients were used in this study. Quantitative polymerase chain reaction (qRTPCR) was performed after extraction of RNA from BAL cells of MERS-CoV infected patients and control patients. BAL supernatants and sera were used to assess cytokines and chemokines secretion by enzyme-linked immunosorbent assay. The first patient died rapidly after 3 weeks in the intensive care unit, the second patient still recovers from infection. The patient with a poor outcome (patient 1), compared to patient 2, did not promote type-1 Interferon (IFN), and particularly IFNα, in response to double stranded RNA (dsRNA) from MERS-CoV. The absence of IFNα, known to promote antigen presentation in response to viruses, impairs the development of a robust antiviral adaptive Th-1 immune response. This response is mediated by IL-12 and IFNγ that decreases viral clearance; levels of both of these mediators were decreased in patient 1. Finally, we confirm previous in vitro findings that MERS-CoV can drive IL-17 production in humans. Host recognition of viral dsRNA determines outcome in the early stage of MERS-CoV infection. We highlight the critical role of IFNα in this initial stage to orchestrate a robust immune response and bring substantial arguments for the indication of early IFNα treatment during MERS-CoV infection.</text>
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                <text>2014</text>
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            <description>An unambiguous reference to the resource within a given context</description>
            <elementTextContainer>
              <elementText elementTextId="2662">
                <text>DOI: 10.1371/journal.pone.0088716</text>
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            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="2663">
                <text>PLoS ONE</text>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
            <elementTextContainer>
              <elementText elementTextId="2664">
                <text>Public Library of Science (PLoS)</text>
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            <name>Coverage</name>
            <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>Science, Medicine</text>
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            <description>A language of the resource</description>
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  <item itemId="286" public="1" featured="0">
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              <name>Title</name>
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                  <text>Coronavirus</text>
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              <name>Description</name>
              <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>Virus survey in populations of two subspecies of bent-winged bats (Miniopterus orianae bassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses.</text>
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              <elementText elementTextId="2650">
                <text>Peter H Holz, Linda F Lumsden, Julian Druce, Alistair R Legione, Paola Vaz, Joanne M Devlin, Jasmin Hufschmid</text>
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                <text>While bats are often viewed as carriers of infectious disease agents, little research has been conducted on the effects these potential pathogens may have on the bat populations themselves. The southern bent-winged bat (Miniopterus orianae bassanii) is a critically endangered subspecies endemic to south-eastern Australia. Population numbers of this bat have been declining for the past 50 years, but the reasons for this are unclear. As part of a larger study to determine if disease could be a contributing factor to this decline, 351 southern bent-winged bats from four locations were captured, and oral swabs were collected and tested for the presence of potentially pathogenic viruses. Results were compared with those obtained from 116 eastern bent-winged bats (Miniopterus orianae oceanensis) from three different locations. The eastern bent-winged bat is a related but more common and widespread subspecies whose geographical range overlaps partly with southern bent-winged bats. Herpesviruses were detected in bent-winged bats from all seven locations. At least six novel herpesviruses (five betaherpesviruses and one gammaherpesvirus) were identified. The prevalence of herpesvirus infection was higher in eastern bent-winged bats (44%, 51/116), compared to southern bent-winged bats (27%, 95/351), although this varied across the locations and sampling periods. Adenoviruses and a range of different RNA viruses (lyssaviruses, filoviruses, coronaviruses and henipaviruses) were also tested for but not detected. The detected herpesviruses did not appear to be associated with obvious ill health, and may thus not be playing a role in the population decline of the southern bent-winged bat. The detection of multiple novel herpesviruses at a high prevalence of infection is consistent with our understanding of bats as hosts to a rich diversity of viruses.</text>
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                <text>2018</text>
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              <elementText elementTextId="2653">
                <text>DOI: 10.1371/journal.pone.0197625</text>
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              <elementText elementTextId="2654">
                <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>Dominio científico: Coronavirus</text>
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                <text>Using motor imagery to study the neural substrates of dynamic balance.</text>
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                <text>Murielle Ursulla Ferraye, Bettina Debû, Lieke Heil, Mark Carpenter, Bastiaan Roelof Bloem, Ivan Toni</text>
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            <description>An account of the resource</description>
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                <text>This study examines the cerebral structures involved in dynamic balance using a motor imagery (MI) protocol. We recorded cerebral activity with functional magnetic resonance imaging while subjects imagined swaying on a balance board along the sagittal plane to point a laser at target pairs of different sizes (small, large). We used a matched visual imagery (VI) control task and recorded imagery durations during scanning. MI and VI durations were differentially influenced by the sway accuracy requirement, indicating that MI of balance is sensitive to the increased motor control necessary to point at a smaller target. Compared to VI, MI of dynamic balance recruited additional cortical and subcortical portions of the motor system, including frontal cortex, basal ganglia, cerebellum and mesencephalic locomotor region, the latter showing increased effective connectivity with the supplementary motor area. The regions involved in MI of dynamic balance were spatially distinct but contiguous to those involved in MI of gait (Bakker et al., 2008; Snijders et al., 2011; Crémers et al., 2012), in a pattern consistent with existing somatotopic maps of the trunk (for balance) and legs (for gait). These findings validate a novel, quantitative approach for studying the neural control of balance in humans. This approach extends previous reports on MI of static stance (Jahn et al., 2004, 2008), and opens the way for studying gait and balance impairments in patients with neurodegenerative disorders.</text>
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            <name>Date</name>
            <description>A point or period of time associated with an event in the lifecycle of the resource</description>
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              <elementText elementTextId="2643">
                <text>2014</text>
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          <element elementId="43">
            <name>Identifier</name>
            <description>An unambiguous reference to the resource within a given context</description>
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              <elementText elementTextId="2644">
                <text>DOI: 10.1371/journal.pone.0091183</text>
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          <element elementId="48">
            <name>Source</name>
            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="2645">
                <text>PLoS ONE</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="45">
            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
            <elementTextContainer>
              <elementText elementTextId="2646">
                <text>Public Library of Science (PLoS)</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="38">
            <name>Coverage</name>
            <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>Science, Medicine</text>
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            <name>Language</name>
            <description>A language of the resource</description>
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              <elementText elementTextId="2648">
                <text>EN</text>
              </elementText>
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        <src>https://www.socictopen.socict.org/files/original/efee94f90ebab107ab179d1eef3b3d71.pdf</src>
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          <name>Dublin Core</name>
          <description>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/.</description>
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            <element elementId="50">
              <name>Title</name>
              <description>A name given to the resource</description>
              <elementTextContainer>
                <elementText elementTextId="1">
                  <text>Coronavirus</text>
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            <element elementId="41">
              <name>Description</name>
              <description>An account of the resource</description>
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                  <text>Dominio científico: Coronavirus</text>
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          </elementContainer>
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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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        <name>Dublin Core</name>
        <description>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/.</description>
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          <element elementId="50">
            <name>Title</name>
            <description>A name given to the resource</description>
            <elementTextContainer>
              <elementText elementTextId="2630">
                <text>The Review of Our Chronic Osteomyelitis Cases</text>
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          <element elementId="39">
            <name>Creator</name>
            <description>An entity primarily responsible for making the resource</description>
            <elementTextContainer>
              <elementText elementTextId="2631">
                <text>Özlem KANDEMİR, Volkan ÖZTUNA, Mehmet Colak, Elif Şahin, Ali  KAYA</text>
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          <element elementId="41">
            <name>Description</name>
            <description>An account of the resource</description>
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                <text>In this study, we have presented the laboratory and clinical findings, and treatment and follow-up results of 32 patients with osteomyelitis treated in both Infectious Disease Clinics and Orthopaedics &amp; Traumatology departments of our university hospital between January 1999 and December 2001. Eleven female patients with a mean age of 45.9 ± 20.0 (15-80), and twenty-one male patients with a mean age of 53.4 ± 15.5 (28-82) were included in this study. The patients have had several risk factors rendering them predisposed to osteomyelitis. Staphylococcus aureus was the most frequently isolated microorganism (%46). The mean pretreatment and posttreatment C-reactive protein levels and sedimentation rates were different and the difference was statistically significant; but we could not find any difference between the white blood cell counts (p= 0.000, p= 0.022, p= 0.258 respectively). Despite of the medical and surgical treatment modalities, recurrence of the disease was detected in 6 patients. The mean time of treatment was 10.2 ± 9.3 (5-24) weeks and the mean follow up was 15.5 ± 7.5 (6-27) months. In conclusion, chronic osteomyelitis needs long term follow-up because of high rate of recurrence and resistance to treatment.</text>
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          <element elementId="40">
            <name>Date</name>
            <description>A point or period of time associated with an event in the lifecycle of the resource</description>
            <elementTextContainer>
              <elementText elementTextId="2633">
                <text>2002</text>
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          <element elementId="49">
            <name>Subject</name>
            <description>The topic of the resource</description>
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              <elementText elementTextId="2634">
                <text>Chronic osteomyelitis, Risk factors, clinical findings, laboratory findings</text>
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          <element elementId="43">
            <name>Identifier</name>
            <description>An unambiguous reference to the resource within a given context</description>
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              <elementText elementTextId="2635">
                <text>DOI: </text>
              </elementText>
            </elementTextContainer>
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          <element elementId="48">
            <name>Source</name>
            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="2636">
                <text>Flora Infeksiyon Hastalıkları ve Klinik Mikrobiyoloji Dergisi</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="45">
            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
            <elementTextContainer>
              <elementText elementTextId="2637">
                <text>Bilimsel Tip Yayinevi</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="38">
            <name>Coverage</name>
            <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>
            <elementTextContainer>
              <elementText elementTextId="2638">
                <text>Infectious and parasitic diseases, Microbiology</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="44">
            <name>Language</name>
            <description>A language of the resource</description>
            <elementTextContainer>
              <elementText elementTextId="2639">
                <text>EN, TR</text>
              </elementText>
            </elementTextContainer>
          </element>
        </elementContainer>
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