Datasets:

---

param-bharat

/

ragbench-context-relevance-filtered

like 1

[ "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: Five of the novel viruses identified in this study were assigned to established genera. Two of these, KOOLV and YATV, clustered within the existing Ephemerovirus clade, and possessed the characteristic genome organization of ephemeroviruses, including a non-structural glycoprotein gene followed by a viroporin Newly proposed genera are indicated by a † symbol. Cytorhabdovirus, novirhabdovirus and nucleorhabdovirus outgroup sequences were excluded from the tree as they were too divergent to establish a reliable rooting. The tree is therefore rooted arbitrarily on one of two basal clades that comprise viruses isolated from mosquitoes.", "Title: Serious Invasive Saffold Virus Infections in Children, 2009\nPassage: During the past few years, intensive searches for new viruses, using conventional virologic methods and metagenomics, have resulted in the discovery of several new viruses. During the past decade, the family Picornaviridae has grown as the number of recognized genera has increased from 6 to 12 ; the numbers of species, types, and subtypes have increased even more. However, only viruses from 3 genera have been fi rmly established as being capable of causing clinically signifi cant disease in humans. Viruses from other genera have so far been detected only in noninvasively collected human sample material such as fecal and", "Title: Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections\nPassage: , , . In 2007, a first member of the Marseilleviridae family also related to NCLDVs, Acanthamoeba polyphaga marseillevirus , was isolated from water collected from a cooling tower in Paris, France, using a method based on Acanthamoeba polyphaga culture . This virus was named in honor of its amoebal host and of the name of the French city, Marseille, where it was discovered . The Marseillevirus was characterized by a 368-kb genome, 457 genes, and a minimum of 49 proteins . Furthermore, the first member of the second branch of Mimiviridae family, Cafeteria roenbergensis virus , was described in", "Title: Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts\nPassage: We also detected a sequence related to the large segment of members of the family Bunyaviridae in adult culicine mosquitoes. The contig contained a single long ORF that showed greatest similarity to members of the genus Phlebovirus, and the currently unclassified GOUV which was originally detected in specimens of the mosquito genera Anopheles , Culex and Uranotaenia in West Africa. Here, we provide evidence for a related novel virus from mosquitoes collected in France. Further field studies are necessary to allow the potential full isolation of this strain, which considering its divergence from GOUV, may constitute a novel genus within" ]

[ [ "1a", "Title: Serious Invasive Saffold Virus Infections in Children, 2009" ], [ "1b", "Passage: During the past few years, intensive searches for new viruses, using conventional virologic methods and metagenomics, have resulted in the discovery of several new viruses." ], [ "1c", "During the past decade, the family Picornaviridae has grown as the number of recognized genera has increased from 6 to 12 ; the numbers of species, types, and subtypes have increased even more." ], [ "1d", "However, only viruses from 3 genera have been fi rmly established as being capable of causing clinically signifi cant disease in humans." ], [ "1e", "Viruses from other genera have so far been detected only in noninvasively collected human sample material such as fecal and" ] ]

[ "0b", "0c", "0d", "1b", "1c", "1d", "2d", "2e", "3c", "3d", "3e" ]

[ "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: Five of the novel viruses identified in this study were assigned to established genera. Two of these, KOOLV and YATV, clustered within the existing Ephemerovirus clade, and possessed the characteristic genome organization of ephemeroviruses, including a non-structural glycoprotein gene followed by a viroporin Newly proposed genera are indicated by a † symbol. Cytorhabdovirus, novirhabdovirus and nucleorhabdovirus outgroup sequences were excluded from the tree as they were too divergent to establish a reliable rooting. The tree is therefore rooted arbitrarily on one of two basal clades that comprise viruses isolated from mosquitoes.", "Title: Serious Invasive Saffold Virus Infections in Children, 2009\nPassage: During the past few years, intensive searches for new viruses, using conventional virologic methods and metagenomics, have resulted in the discovery of several new viruses. During the past decade, the family Picornaviridae has grown as the number of recognized genera has increased from 6 to 12 ; the numbers of species, types, and subtypes have increased even more. However, only viruses from 3 genera have been fi rmly established as being capable of causing clinically signifi cant disease in humans. Viruses from other genera have so far been detected only in noninvasively collected human sample material such as fecal and", "Title: Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections\nPassage: , , . In 2007, a first member of the Marseilleviridae family also related to NCLDVs, Acanthamoeba polyphaga marseillevirus , was isolated from water collected from a cooling tower in Paris, France, using a method based on Acanthamoeba polyphaga culture . This virus was named in honor of its amoebal host and of the name of the French city, Marseille, where it was discovered . The Marseillevirus was characterized by a 368-kb genome, 457 genes, and a minimum of 49 proteins . Furthermore, the first member of the second branch of Mimiviridae family, Cafeteria roenbergensis virus , was described in", "Title: Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts\nPassage: We also detected a sequence related to the large segment of members of the family Bunyaviridae in adult culicine mosquitoes. The contig contained a single long ORF that showed greatest similarity to members of the genus Phlebovirus, and the currently unclassified GOUV which was originally detected in specimens of the mosquito genera Anopheles , Culex and Uranotaenia in West Africa. Here, we provide evidence for a related novel virus from mosquitoes collected in France. Further field studies are necessary to allow the potential full isolation of this strain, which considering its divergence from GOUV, may constitute a novel genus within" ]

[ [ "2a", "Title: Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections" ], [ "2b", "Passage: , , ." ], [ "2c", "In 2007, a first member of the Marseilleviridae family also related to NCLDVs, Acanthamoeba polyphaga marseillevirus , was isolated from water collected from a cooling tower in Paris, France, using a method based on Acanthamoeba polyphaga culture ." ], [ "2d", "This virus was named in honor of its amoebal host and of the name of the French city, Marseille, where it was discovered ." ], [ "2e", "The Marseillevirus was characterized by a 368-kb genome, 457 genes, and a minimum of 49 proteins ." ], [ "2f", "Furthermore, the first member of the second branch of Mimiviridae family, Cafeteria roenbergensis virus , was described in" ] ]

[ "0b", "0c", "0d", "1b", "1c", "1d", "2d", "2e", "3c", "3d", "3e" ]

[ "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: Five of the novel viruses identified in this study were assigned to established genera. Two of these, KOOLV and YATV, clustered within the existing Ephemerovirus clade, and possessed the characteristic genome organization of ephemeroviruses, including a non-structural glycoprotein gene followed by a viroporin Newly proposed genera are indicated by a † symbol. Cytorhabdovirus, novirhabdovirus and nucleorhabdovirus outgroup sequences were excluded from the tree as they were too divergent to establish a reliable rooting. The tree is therefore rooted arbitrarily on one of two basal clades that comprise viruses isolated from mosquitoes.", "Title: Serious Invasive Saffold Virus Infections in Children, 2009\nPassage: During the past few years, intensive searches for new viruses, using conventional virologic methods and metagenomics, have resulted in the discovery of several new viruses. During the past decade, the family Picornaviridae has grown as the number of recognized genera has increased from 6 to 12 ; the numbers of species, types, and subtypes have increased even more. However, only viruses from 3 genera have been fi rmly established as being capable of causing clinically signifi cant disease in humans. Viruses from other genera have so far been detected only in noninvasively collected human sample material such as fecal and", "Title: Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections\nPassage: , , . In 2007, a first member of the Marseilleviridae family also related to NCLDVs, Acanthamoeba polyphaga marseillevirus , was isolated from water collected from a cooling tower in Paris, France, using a method based on Acanthamoeba polyphaga culture . This virus was named in honor of its amoebal host and of the name of the French city, Marseille, where it was discovered . The Marseillevirus was characterized by a 368-kb genome, 457 genes, and a minimum of 49 proteins . Furthermore, the first member of the second branch of Mimiviridae family, Cafeteria roenbergensis virus , was described in", "Title: Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts\nPassage: We also detected a sequence related to the large segment of members of the family Bunyaviridae in adult culicine mosquitoes. The contig contained a single long ORF that showed greatest similarity to members of the genus Phlebovirus, and the currently unclassified GOUV which was originally detected in specimens of the mosquito genera Anopheles , Culex and Uranotaenia in West Africa. Here, we provide evidence for a related novel virus from mosquitoes collected in France. Further field studies are necessary to allow the potential full isolation of this strain, which considering its divergence from GOUV, may constitute a novel genus within" ]

[ [ "3a", "Title: Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts" ], [ "3b", "Passage: We also detected a sequence related to the large segment of members of the family Bunyaviridae in adult culicine mosquitoes." ], [ "3c", "The contig contained a single long ORF that showed greatest similarity to members of the genus Phlebovirus, and the currently unclassified GOUV which was originally detected in specimens of the mosquito genera Anopheles , Culex and Uranotaenia in West Africa." ], [ "3d", "Here, we provide evidence for a related novel virus from mosquitoes collected in France." ], [ "3e", "Further field studies are necessary to allow the potential full isolation of this strain, which considering its divergence from GOUV, may constitute a novel genus within" ] ]

[ "0b", "0c", "0d", "1b", "1c", "1d", "2d", "2e", "3c", "3d", "3e" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: NDV has also been explored as a vaccine vector for humans. Two NHP studies assessed the immunogenicity and efficacy of an rNDV expressing the HA or NA of A/Vietnam/1203/2004 . Intranasal and intratracheal delivery of the rNDV-HA or rNDV-NA vaccines induced both serum and mucosal antibody responses and protected from HPAIV challenge . NDV has limited clinical data; however, phase I and phase I/II clinical trials have shown that the NDV vector is well-tolerated, even at high doses delivered intravenously . While these results are promising, additional studies are needed to advance NDV as a human vaccine vector for influenza.", "Title: Viral vector-based influenza vaccines\nPassage: one single study, cross-reactive cellular immune responses against A viruses were observed after vaccination with a NDV-H5 construct. 168 The immunogenicity of recombinant NDV expressing the HA and NA genes of influenza virus A/Vietnam/1203/04 was tested in non-human primates. Both constructs induced VN and local IgA antibody responses and afforded protection from A challenge infection. 169, 170 Small numbers of clinical trials have been performed with NDV, which showed that the vector is well tolerated.", "Title: Viral vector-based influenza vaccines\nPassage: Newcastle disease virus is a single-stranded negative sense RNA paramyxovirus that causes disease in poultry. NDV has several favorable properties as a vaccine vector; no preexisting immunity in humans exists, NDV can easily be attenuated and reverse genetics systems to rescue recombinant NDV are in place. Thus far, NDV has been extensively characterized as an influenza vaccine vector in poultry, where it serves as a bivalent vaccine capable of inducing immunity against both NDV and influenza virus. As an added advantage, NDV is easily administered to poultry through nasal spray, drinking water or ocular drops. An overview of NDV-based influenza", "Title: Viral vector-based influenza vaccines\nPassage: The first study using NDV as a vaccine vector for influenza was NDV-H1, that expressed the HA gene of influenza virus A/ WSN/1933. Complete protection of mice against homologous challenge infection was achieved, demonstrating that NDV can be used as an influenza vaccine vector. 148 Consequently, a recombinant NDV expressing HA genes of A viruses has been licensed as a poultry vaccine in some countries and was shown to have a protective effect against challenge infection with A viruses in chickens and ducks in various studies. The NDV based A vaccine offered only partial cross-clade protection, but was immunogenic in" ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: NDV has also been explored as a vaccine vector for humans." ], [ "0c", "Two NHP studies assessed the immunogenicity and efficacy of an rNDV expressing the HA or NA of A/Vietnam/1203/2004 ." ], [ "0d", "Intranasal and intratracheal delivery of the rNDV-HA or rNDV-NA vaccines induced both serum and mucosal antibody responses and protected from HPAIV challenge ." ], [ "0e", "NDV has limited clinical data; however, phase I and phase I/II clinical trials have shown that the NDV vector is well-tolerated, even at high doses delivered intravenously ." ], [ "0f", "While these results are promising, additional studies are needed to advance NDV as a human vaccine vector for influenza." ] ]

[ "0b", "0e", "1e", "2c", "2e" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: NDV has also been explored as a vaccine vector for humans. Two NHP studies assessed the immunogenicity and efficacy of an rNDV expressing the HA or NA of A/Vietnam/1203/2004 . Intranasal and intratracheal delivery of the rNDV-HA or rNDV-NA vaccines induced both serum and mucosal antibody responses and protected from HPAIV challenge . NDV has limited clinical data; however, phase I and phase I/II clinical trials have shown that the NDV vector is well-tolerated, even at high doses delivered intravenously . While these results are promising, additional studies are needed to advance NDV as a human vaccine vector for influenza.", "Title: Viral vector-based influenza vaccines\nPassage: one single study, cross-reactive cellular immune responses against A viruses were observed after vaccination with a NDV-H5 construct. 168 The immunogenicity of recombinant NDV expressing the HA and NA genes of influenza virus A/Vietnam/1203/04 was tested in non-human primates. Both constructs induced VN and local IgA antibody responses and afforded protection from A challenge infection. 169, 170 Small numbers of clinical trials have been performed with NDV, which showed that the vector is well tolerated.", "Title: Viral vector-based influenza vaccines\nPassage: Newcastle disease virus is a single-stranded negative sense RNA paramyxovirus that causes disease in poultry. NDV has several favorable properties as a vaccine vector; no preexisting immunity in humans exists, NDV can easily be attenuated and reverse genetics systems to rescue recombinant NDV are in place. Thus far, NDV has been extensively characterized as an influenza vaccine vector in poultry, where it serves as a bivalent vaccine capable of inducing immunity against both NDV and influenza virus. As an added advantage, NDV is easily administered to poultry through nasal spray, drinking water or ocular drops. An overview of NDV-based influenza", "Title: Viral vector-based influenza vaccines\nPassage: The first study using NDV as a vaccine vector for influenza was NDV-H1, that expressed the HA gene of influenza virus A/ WSN/1933. Complete protection of mice against homologous challenge infection was achieved, demonstrating that NDV can be used as an influenza vaccine vector. 148 Consequently, a recombinant NDV expressing HA genes of A viruses has been licensed as a poultry vaccine in some countries and was shown to have a protective effect against challenge infection with A viruses in chickens and ducks in various studies. The NDV based A vaccine offered only partial cross-clade protection, but was immunogenic in" ]

[ [ "1a", "Title: Viral vector-based influenza vaccines" ], [ "1b", "Passage: one single study, cross-reactive cellular immune responses against A viruses were observed after vaccination with a NDV-H5 construct." ], [ "1c", "168 The immunogenicity of recombinant NDV expressing the HA and NA genes of influenza virus A/Vietnam/1203/04 was tested in non-human primates." ], [ "1d", "Both constructs induced VN and local IgA antibody responses and afforded protection from A challenge infection." ], [ "1e", "169, 170 Small numbers of clinical trials have been performed with NDV, which showed that the vector is well tolerated." ] ]

[ "0b", "0e", "1e", "2c", "2e" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: NDV has also been explored as a vaccine vector for humans. Two NHP studies assessed the immunogenicity and efficacy of an rNDV expressing the HA or NA of A/Vietnam/1203/2004 . Intranasal and intratracheal delivery of the rNDV-HA or rNDV-NA vaccines induced both serum and mucosal antibody responses and protected from HPAIV challenge . NDV has limited clinical data; however, phase I and phase I/II clinical trials have shown that the NDV vector is well-tolerated, even at high doses delivered intravenously . While these results are promising, additional studies are needed to advance NDV as a human vaccine vector for influenza.", "Title: Viral vector-based influenza vaccines\nPassage: one single study, cross-reactive cellular immune responses against A viruses were observed after vaccination with a NDV-H5 construct. 168 The immunogenicity of recombinant NDV expressing the HA and NA genes of influenza virus A/Vietnam/1203/04 was tested in non-human primates. Both constructs induced VN and local IgA antibody responses and afforded protection from A challenge infection. 169, 170 Small numbers of clinical trials have been performed with NDV, which showed that the vector is well tolerated.", "Title: Viral vector-based influenza vaccines\nPassage: Newcastle disease virus is a single-stranded negative sense RNA paramyxovirus that causes disease in poultry. NDV has several favorable properties as a vaccine vector; no preexisting immunity in humans exists, NDV can easily be attenuated and reverse genetics systems to rescue recombinant NDV are in place. Thus far, NDV has been extensively characterized as an influenza vaccine vector in poultry, where it serves as a bivalent vaccine capable of inducing immunity against both NDV and influenza virus. As an added advantage, NDV is easily administered to poultry through nasal spray, drinking water or ocular drops. An overview of NDV-based influenza", "Title: Viral vector-based influenza vaccines\nPassage: The first study using NDV as a vaccine vector for influenza was NDV-H1, that expressed the HA gene of influenza virus A/ WSN/1933. Complete protection of mice against homologous challenge infection was achieved, demonstrating that NDV can be used as an influenza vaccine vector. 148 Consequently, a recombinant NDV expressing HA genes of A viruses has been licensed as a poultry vaccine in some countries and was shown to have a protective effect against challenge infection with A viruses in chickens and ducks in various studies. The NDV based A vaccine offered only partial cross-clade protection, but was immunogenic in" ]

[ [ "2a", "Title: Viral vector-based influenza vaccines" ], [ "2b", "Passage: Newcastle disease virus is a single-stranded negative sense RNA paramyxovirus that causes disease in poultry." ], [ "2c", "NDV has several favorable properties as a vaccine vector; no preexisting immunity in humans exists, NDV can easily be attenuated and reverse genetics systems to rescue recombinant NDV are in place." ], [ "2d", "Thus far, NDV has been extensively characterized as an influenza vaccine vector in poultry, where it serves as a bivalent vaccine capable of inducing immunity against both NDV and influenza virus." ], [ "2e", "As an added advantage, NDV is easily administered to poultry through nasal spray, drinking water or ocular drops." ], [ "2f", "An overview of NDV-based influenza" ] ]

[ "0b", "0e", "1e", "2c", "2e" ]

[ "Title: Recent developments in antiviral agents against enterovirus 71 infection\nPassage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease . Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes . Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses . X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial. Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms . However, in studies of natural infection, it did not significantly affect viral loads or symptom severity .", "Title: Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir\nPassage: is considerably lower than the values reported for favipiravir or galidesivir . The triphosphate form of remdesivir was shown to inhibit the RSV RdRp surrogate for EBOV RdRp . No significant inhibition was seen with human RNA Pol II and human mitochondrial RNA polymerase . The biochemical data obtained with purified recombinant RSV RdRp and a recent study with NiV RdRp point to delayed chain termination as a possible mechanism of action . Delayed chain termination refers to inhibition of RNA synthesis a few residues downstream of the incorporated inhibitor. However, the inhibition results have yet to be translated in", "Title: Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity\nPassage: suggests that inhibition of RdRp activity is the main mechanism of action for 5FU. As we did not identify mutations that mediate ribavirin or 5-azacytidine resistance, we cannot say whether mutagenic or nonmutagenic mechanisms are dominant for these drugs." ]

[ [ "0a", "Title: Recent developments in antiviral agents against enterovirus 71 infection" ], [ "0b", "Passage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease ." ], [ "0c", "Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes ." ], [ "0d", "Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses ." ], [ "0e", "X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam" ] ]

[ "0b", "0c", "0e", "1b" ]

[ "Title: Recent developments in antiviral agents against enterovirus 71 infection\nPassage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease . Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes . Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses . X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial. Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms . However, in studies of natural infection, it did not significantly affect viral loads or symptom severity .", "Title: Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir\nPassage: is considerably lower than the values reported for favipiravir or galidesivir . The triphosphate form of remdesivir was shown to inhibit the RSV RdRp surrogate for EBOV RdRp . No significant inhibition was seen with human RNA Pol II and human mitochondrial RNA polymerase . The biochemical data obtained with purified recombinant RSV RdRp and a recent study with NiV RdRp point to delayed chain termination as a possible mechanism of action . Delayed chain termination refers to inhibition of RNA synthesis a few residues downstream of the incorporated inhibitor. However, the inhibition results have yet to be translated in", "Title: Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity\nPassage: suggests that inhibition of RdRp activity is the main mechanism of action for 5FU. As we did not identify mutations that mediate ribavirin or 5-azacytidine resistance, we cannot say whether mutagenic or nonmutagenic mechanisms are dominant for these drugs." ]

[ [ "1a", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics" ], [ "1b", "Passage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial." ], [ "1c", "Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms ." ], [ "1d", "However, in studies of natural infection, it did not significantly affect viral loads or symptom severity ." ] ]

[ "0b", "0c", "0e", "1b" ]

[ "Title: Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection\nPassage: Acute respiratory viral infections are among the most common reasons for patient visits in primary and acute care settings . Many viruses cause such acute respiratory illness including human rhinovirus , respiratory syncytial virus and influenza. These viruses can be associated with a range of clinical severity from asymptomatic to mild, self-limited illness to respiratory failure and death. Influenza alone causes 25 to 50 million infections annually in the USA, resulting in several hundred thousand hospitalizations and 20-40,000 deaths .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of", "Title: Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016\nPassage: Acute respiratory infections are a group of diseases that are caused by different microorganisms where viral etiologies are responsible for 80% of cases. 1 Influenza and noninfluenza viruses are responsible for significant annual morbidity and mortality across all age groups. 2 On average, influenza viruses infect 5% to 15% of the global population, resulting in 3 to 5 million cases of severe illness and between 260 000 and 650 000 deaths every year worldwide. The heaviest burden is among high-risk groups that include pregnant women, children under 59 months, the elderly, individuals with chronic medical conditions. 3 In 2015, it" ]

[ [ "0a", "Title: Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection" ], [ "0b", "Passage: Acute respiratory viral infections are among the most common reasons for patient visits in primary and acute care settings ." ], [ "0c", "Many viruses cause such acute respiratory illness including human rhinovirus , respiratory syncytial virus and influenza." ], [ "0d", "These viruses can be associated with a range of clinical severity from asymptomatic to mild, self-limited illness to respiratory failure and death." ], [ "0e", "Influenza alone causes 25 to 50 million infections annually in the USA, resulting in several hundred thousand hospitalizations and 20-40,000 deaths ." ] ]

[ "0b", "0c", "0d", "1a", "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection\nPassage: Acute respiratory viral infections are among the most common reasons for patient visits in primary and acute care settings . Many viruses cause such acute respiratory illness including human rhinovirus , respiratory syncytial virus and influenza. These viruses can be associated with a range of clinical severity from asymptomatic to mild, self-limited illness to respiratory failure and death. Influenza alone causes 25 to 50 million infections annually in the USA, resulting in several hundred thousand hospitalizations and 20-40,000 deaths .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of", "Title: Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016\nPassage: Acute respiratory infections are a group of diseases that are caused by different microorganisms where viral etiologies are responsible for 80% of cases. 1 Influenza and noninfluenza viruses are responsible for significant annual morbidity and mortality across all age groups. 2 On average, influenza viruses infect 5% to 15% of the global population, resulting in 3 to 5 million cases of severe illness and between 260 000 and 650 000 deaths every year worldwide. The heaviest burden is among high-risk groups that include pregnant women, children under 59 months, the elderly, individuals with chronic medical conditions. 3 In 2015, it" ]

[ [ "1a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "1b", "Passage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration." ], [ "1c", "Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration." ], [ "1d", "This also increases the chances of allergens coming into contact with airway immune cells." ], [ "1e", "For example, IFV infection was found to induce oncostatin M which causes tight junction opening ." ], [ "1f", "Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening" ] ]

[ "0b", "0c", "0d", "1a", "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection\nPassage: Acute respiratory viral infections are among the most common reasons for patient visits in primary and acute care settings . Many viruses cause such acute respiratory illness including human rhinovirus , respiratory syncytial virus and influenza. These viruses can be associated with a range of clinical severity from asymptomatic to mild, self-limited illness to respiratory failure and death. Influenza alone causes 25 to 50 million infections annually in the USA, resulting in several hundred thousand hospitalizations and 20-40,000 deaths .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of", "Title: Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016\nPassage: Acute respiratory infections are a group of diseases that are caused by different microorganisms where viral etiologies are responsible for 80% of cases. 1 Influenza and noninfluenza viruses are responsible for significant annual morbidity and mortality across all age groups. 2 On average, influenza viruses infect 5% to 15% of the global population, resulting in 3 to 5 million cases of severe illness and between 260 000 and 650 000 deaths every year worldwide. The heaviest burden is among high-risk groups that include pregnant women, children under 59 months, the elderly, individuals with chronic medical conditions. 3 In 2015, it" ]

[ [ "2a", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management" ], [ "2b", "Passage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD." ], [ "2c", "Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common." ], [ "2d", "79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda." ], [ "2e", "In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of" ] ]

[ "0b", "0c", "0d", "1a", "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection\nPassage: Acute respiratory viral infections are among the most common reasons for patient visits in primary and acute care settings . Many viruses cause such acute respiratory illness including human rhinovirus , respiratory syncytial virus and influenza. These viruses can be associated with a range of clinical severity from asymptomatic to mild, self-limited illness to respiratory failure and death. Influenza alone causes 25 to 50 million infections annually in the USA, resulting in several hundred thousand hospitalizations and 20-40,000 deaths .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of", "Title: Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016\nPassage: Acute respiratory infections are a group of diseases that are caused by different microorganisms where viral etiologies are responsible for 80% of cases. 1 Influenza and noninfluenza viruses are responsible for significant annual morbidity and mortality across all age groups. 2 On average, influenza viruses infect 5% to 15% of the global population, resulting in 3 to 5 million cases of severe illness and between 260 000 and 650 000 deaths every year worldwide. The heaviest burden is among high-risk groups that include pregnant women, children under 59 months, the elderly, individuals with chronic medical conditions. 3 In 2015, it" ]

[ [ "3a", "Title: Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016" ], [ "3b", "Passage: Acute respiratory infections are a group of diseases that are caused by different microorganisms where viral etiologies are responsible for 80% of cases." ], [ "3c", "1 Influenza and noninfluenza viruses are responsible for significant annual morbidity and mortality across all age groups." ], [ "3d", "2 On average, influenza viruses infect 5% to 15% of the global population, resulting in 3 to 5 million cases of severe illness and between 260 000 and 650 000 deaths every year worldwide." ], [ "3e", "The heaviest burden is among high-risk groups that include pregnant women, children under 59 months, the elderly, individuals with chronic medical conditions." ], [ "3f", "3 In 2015, it" ] ]

[ "0b", "0c", "0d", "1a", "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: provided input to the outline, multiple versions of the manuscript and gave approval to the final draft.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: 2 days to be hospitalised.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

[ [ "3a", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020" ], [ "3b", "Passage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong." ], [ "3c", "Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020." ], [ "3d", "Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ] ]

[ "3a", "3b", "3c" ]

[ "Title: Influenza A H1N1 2009 (Swine Flu) and Pregnancy\nPassage: The reluctance to be vaccinated is mainly due to worries about the side effects. Experience from the 2009/2010 pandemic confirmed the safety profile of the vaccine. Over 350 million doses of the vaccine were administered worldwide during the pandemic with no adverse long term effects noted in both the pregnant and non pregnant populations .", "Title: Travellers and influenza: risks and prevention\nPassage: with vaccination. During the H1N1 pandemic, influenza vaccines proved to be safe and effective for pregnant women and their unborn babies; findings very similar to studies of seasonal influenza vaccination in this high risk group. 67, 68 In line with these recommendations, the advice might be broadened to pregnant women travelling to influenza endemic areas and possibly to persons in close contact with pregnant women or other high-risk individuals, like partners and close family members ] or travel partners.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Maternal vaccination to prevent disease in the youngest infants has been shown to be effective for tetanus, influenza and pertussis . Influenza vaccination during pregnancy is safe, provides reasonable maternal protection against influenza, and also protects infants for a limited period from confirmed influenza infection and 50.4% in South Africa ). However as antibody levels drop sharply after birth, infant protection does not persist much beyond 8 weeks . Recently respiratory syncytial virus vaccination in pregnancy has been shown to be safe and immunogenic, and a phase-3 clinical trial of efficacy at preventing respiratory syncytial virus disease in infants is", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: The need to protect neonates and infants in the first 6 months of life from influenza is so important that many health authorities have recommended influenza vaccinations of pregnant women . Studies have shown that vaccination during pregnancy is effective in reducing influenza cases for at least one influenza season ." ]

[ [ "0a", "Title: Influenza A H1N1 2009 (Swine Flu) and Pregnancy" ], [ "0b", "Passage: The reluctance to be vaccinated is mainly due to worries about the side effects." ], [ "0c", "Experience from the 2009/2010 pandemic confirmed the safety profile of the vaccine." ], [ "0d", "Over 350 million doses of the vaccine were administered worldwide during the pandemic with no adverse long term effects noted in both the pregnant and non pregnant populations ." ] ]

[ "0c", "0d", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Influenza A H1N1 2009 (Swine Flu) and Pregnancy\nPassage: The reluctance to be vaccinated is mainly due to worries about the side effects. Experience from the 2009/2010 pandemic confirmed the safety profile of the vaccine. Over 350 million doses of the vaccine were administered worldwide during the pandemic with no adverse long term effects noted in both the pregnant and non pregnant populations .", "Title: Travellers and influenza: risks and prevention\nPassage: with vaccination. During the H1N1 pandemic, influenza vaccines proved to be safe and effective for pregnant women and their unborn babies; findings very similar to studies of seasonal influenza vaccination in this high risk group. 67, 68 In line with these recommendations, the advice might be broadened to pregnant women travelling to influenza endemic areas and possibly to persons in close contact with pregnant women or other high-risk individuals, like partners and close family members ] or travel partners.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Maternal vaccination to prevent disease in the youngest infants has been shown to be effective for tetanus, influenza and pertussis . Influenza vaccination during pregnancy is safe, provides reasonable maternal protection against influenza, and also protects infants for a limited period from confirmed influenza infection and 50.4% in South Africa ). However as antibody levels drop sharply after birth, infant protection does not persist much beyond 8 weeks . Recently respiratory syncytial virus vaccination in pregnancy has been shown to be safe and immunogenic, and a phase-3 clinical trial of efficacy at preventing respiratory syncytial virus disease in infants is", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: The need to protect neonates and infants in the first 6 months of life from influenza is so important that many health authorities have recommended influenza vaccinations of pregnant women . Studies have shown that vaccination during pregnancy is effective in reducing influenza cases for at least one influenza season ." ]

[ [ "1a", "Title: Travellers and influenza: risks and prevention" ], [ "1b", "Passage: with vaccination." ], [ "1c", "During the H1N1 pandemic, influenza vaccines proved to be safe and effective for pregnant women and their unborn babies; findings very similar to studies of seasonal influenza vaccination in this high risk group." ], [ "1d", "67, 68 In line with these recommendations, the advice might be broadened to pregnant women travelling to influenza endemic areas and possibly to persons in close contact with pregnant women or other high-risk individuals, like partners and close family members ] or travel partners." ] ]

[ "0c", "0d", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Influenza A H1N1 2009 (Swine Flu) and Pregnancy\nPassage: The reluctance to be vaccinated is mainly due to worries about the side effects. Experience from the 2009/2010 pandemic confirmed the safety profile of the vaccine. Over 350 million doses of the vaccine were administered worldwide during the pandemic with no adverse long term effects noted in both the pregnant and non pregnant populations .", "Title: Travellers and influenza: risks and prevention\nPassage: with vaccination. During the H1N1 pandemic, influenza vaccines proved to be safe and effective for pregnant women and their unborn babies; findings very similar to studies of seasonal influenza vaccination in this high risk group. 67, 68 In line with these recommendations, the advice might be broadened to pregnant women travelling to influenza endemic areas and possibly to persons in close contact with pregnant women or other high-risk individuals, like partners and close family members ] or travel partners.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Maternal vaccination to prevent disease in the youngest infants has been shown to be effective for tetanus, influenza and pertussis . Influenza vaccination during pregnancy is safe, provides reasonable maternal protection against influenza, and also protects infants for a limited period from confirmed influenza infection and 50.4% in South Africa ). However as antibody levels drop sharply after birth, infant protection does not persist much beyond 8 weeks . Recently respiratory syncytial virus vaccination in pregnancy has been shown to be safe and immunogenic, and a phase-3 clinical trial of efficacy at preventing respiratory syncytial virus disease in infants is", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: The need to protect neonates and infants in the first 6 months of life from influenza is so important that many health authorities have recommended influenza vaccinations of pregnant women . Studies have shown that vaccination during pregnancy is effective in reducing influenza cases for at least one influenza season ." ]

[ [ "2a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "2b", "Passage: Maternal vaccination to prevent disease in the youngest infants has been shown to be effective for tetanus, influenza and pertussis ." ], [ "2c", "Influenza vaccination during pregnancy is safe, provides reasonable maternal protection against influenza, and also protects infants for a limited period from confirmed influenza infection and 50.4% in South Africa )." ], [ "2d", "However as antibody levels drop sharply after birth, infant protection does not persist much beyond 8 weeks ." ], [ "2e", "Recently respiratory syncytial virus vaccination in pregnancy has been shown to be safe and immunogenic, and a phase-3 clinical trial of efficacy at preventing respiratory syncytial virus disease in infants is" ] ]

[ "0c", "0d", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Influenza A H1N1 2009 (Swine Flu) and Pregnancy\nPassage: The reluctance to be vaccinated is mainly due to worries about the side effects. Experience from the 2009/2010 pandemic confirmed the safety profile of the vaccine. Over 350 million doses of the vaccine were administered worldwide during the pandemic with no adverse long term effects noted in both the pregnant and non pregnant populations .", "Title: Travellers and influenza: risks and prevention\nPassage: with vaccination. During the H1N1 pandemic, influenza vaccines proved to be safe and effective for pregnant women and their unborn babies; findings very similar to studies of seasonal influenza vaccination in this high risk group. 67, 68 In line with these recommendations, the advice might be broadened to pregnant women travelling to influenza endemic areas and possibly to persons in close contact with pregnant women or other high-risk individuals, like partners and close family members ] or travel partners.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Maternal vaccination to prevent disease in the youngest infants has been shown to be effective for tetanus, influenza and pertussis . Influenza vaccination during pregnancy is safe, provides reasonable maternal protection against influenza, and also protects infants for a limited period from confirmed influenza infection and 50.4% in South Africa ). However as antibody levels drop sharply after birth, infant protection does not persist much beyond 8 weeks . Recently respiratory syncytial virus vaccination in pregnancy has been shown to be safe and immunogenic, and a phase-3 clinical trial of efficacy at preventing respiratory syncytial virus disease in infants is", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: The need to protect neonates and infants in the first 6 months of life from influenza is so important that many health authorities have recommended influenza vaccinations of pregnant women . Studies have shown that vaccination during pregnancy is effective in reducing influenza cases for at least one influenza season ." ]

[ [ "3a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "3b", "Passage: The need to protect neonates and infants in the first 6 months of life from influenza is so important that many health authorities have recommended influenza vaccinations of pregnant women ." ], [ "3c", "Studies have shown that vaccination during pregnancy is effective in reducing influenza cases for at least one influenza season ." ] ]

[ "0c", "0d", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: In this study, the commonly identified viruses in patients with COPD exacerbations requiring ED visits were PIV3, Inf A virus, and human rhinovirus. This result was similar to the finding of Cameron et al from a study in Australia in which the most frequently detected viral etiologies were Inf A, PIV3, and rhinovirus. 21 In a recent review of eight studies, picornavirus was the most common virus in western countries and influenza virus was most common in Asia. 7 H. influenzae was the most common bacterial pathogen in COPD exacerbations in a previous study. 4 Pseudomonas aeruginosa and Klebsiella pneumoniae", "Title: Antiviral immunity is impaired in COPD patients with frequent exacerbations\nPassage: bacterial detection at exacerbation versus stable state, suggesting a causative role . Additionally, virus-induced secondary bacterial infection has been reported in both experimental and naturally occurring exacerbations . We have previously reported that experimental RV challenge in patients with COPD is associated with increased frequency of secondary bacterial infection compared with healthy subjects , an effect that is related to virus loads. Here, we extend these findings to reveal that frequent exacerbators have higher bacterial loads at 2 wk following onset of virus-associated exacerbation, suggesting that this subgroup of COPD patients might be at greatest risk of developing secondary bacterial", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: Bacterial colonization and viral respiratory pathogens play important roles in exacerbations of chronic obstructive pulmonary disease , 1,2 especially in patients requiring hospitalization. 3 Viral and/or bacterial infections have been detected in up to 78% of patients with COPD exacerbations. 4 Although bacteria are considered the major cause of COPD exacerbations and antibiotics commonly used to treat exacerbations, 5 the importance of viral infections in COPD exacerbations was mentioned after the introduction and wide use of viral culture and real-time polymerase chain reaction . 6, 7 The link of viral infections to COPD has been emphasized in recent studies. COPD", "Title: Th17 profile in COPD exacerbations\nPassage: In the past, it was believed that only bacteria were capable of generating exacerbations in patients with COPD. 48, 52 However, the occurrence of these in the winter and symptoms similar to cold led to the belief that viruses were also associated with the complications of this obstructive pathology of the airways. 53 On the other hand, viral infections of the respiratory tract have been shown to influence the lung microbiome in patients with COPD, which indicates that both microorganisms can coexist and predispose to exacerbations. 54 The most prevalent viruses during acute exacerbations of COPD are rhinovirus, coronavirus, influenza," ]

[ [ "0a", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits" ], [ "0b", "Passage: In this study, the commonly identified viruses in patients with COPD exacerbations requiring ED visits were PIV3, Inf A virus, and human rhinovirus." ], [ "0c", "This result was similar to the finding of Cameron et al from a study in Australia in which the most frequently detected viral etiologies were Inf A, PIV3, and rhinovirus." ], [ "0d", "21 In a recent review of eight studies, picornavirus was the most common virus in western countries and influenza virus was most common in Asia." ], [ "0e", "7 H. influenzae was the most common bacterial pathogen in COPD exacerbations in a previous study." ], [ "0f", "4 Pseudomonas aeruginosa and Klebsiella pneumoniae" ] ]

[ "0b", "0c", "2c", "2d", "2e", "3c", "3d", "3e", "1c", "1d", "0e" ]

[ "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: In this study, the commonly identified viruses in patients with COPD exacerbations requiring ED visits were PIV3, Inf A virus, and human rhinovirus. This result was similar to the finding of Cameron et al from a study in Australia in which the most frequently detected viral etiologies were Inf A, PIV3, and rhinovirus. 21 In a recent review of eight studies, picornavirus was the most common virus in western countries and influenza virus was most common in Asia. 7 H. influenzae was the most common bacterial pathogen in COPD exacerbations in a previous study. 4 Pseudomonas aeruginosa and Klebsiella pneumoniae", "Title: Antiviral immunity is impaired in COPD patients with frequent exacerbations\nPassage: bacterial detection at exacerbation versus stable state, suggesting a causative role . Additionally, virus-induced secondary bacterial infection has been reported in both experimental and naturally occurring exacerbations . We have previously reported that experimental RV challenge in patients with COPD is associated with increased frequency of secondary bacterial infection compared with healthy subjects , an effect that is related to virus loads. Here, we extend these findings to reveal that frequent exacerbators have higher bacterial loads at 2 wk following onset of virus-associated exacerbation, suggesting that this subgroup of COPD patients might be at greatest risk of developing secondary bacterial", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: Bacterial colonization and viral respiratory pathogens play important roles in exacerbations of chronic obstructive pulmonary disease , 1,2 especially in patients requiring hospitalization. 3 Viral and/or bacterial infections have been detected in up to 78% of patients with COPD exacerbations. 4 Although bacteria are considered the major cause of COPD exacerbations and antibiotics commonly used to treat exacerbations, 5 the importance of viral infections in COPD exacerbations was mentioned after the introduction and wide use of viral culture and real-time polymerase chain reaction . 6, 7 The link of viral infections to COPD has been emphasized in recent studies. COPD", "Title: Th17 profile in COPD exacerbations\nPassage: In the past, it was believed that only bacteria were capable of generating exacerbations in patients with COPD. 48, 52 However, the occurrence of these in the winter and symptoms similar to cold led to the belief that viruses were also associated with the complications of this obstructive pathology of the airways. 53 On the other hand, viral infections of the respiratory tract have been shown to influence the lung microbiome in patients with COPD, which indicates that both microorganisms can coexist and predispose to exacerbations. 54 The most prevalent viruses during acute exacerbations of COPD are rhinovirus, coronavirus, influenza," ]

[ [ "1a", "Title: Antiviral immunity is impaired in COPD patients with frequent exacerbations" ], [ "1b", "Passage: bacterial detection at exacerbation versus stable state, suggesting a causative role ." ], [ "1c", "Additionally, virus-induced secondary bacterial infection has been reported in both experimental and naturally occurring exacerbations ." ], [ "1d", "We have previously reported that experimental RV challenge in patients with COPD is associated with increased frequency of secondary bacterial infection compared with healthy subjects , an effect that is related to virus loads." ], [ "1e", "Here, we extend these findings to reveal that frequent exacerbators have higher bacterial loads at 2 wk following onset of virus-associated exacerbation, suggesting that this subgroup of COPD patients might be at greatest risk of developing secondary bacterial" ] ]

[ "0b", "0c", "2c", "2d", "2e", "3c", "3d", "3e", "1c", "1d", "0e" ]

[ "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: In this study, the commonly identified viruses in patients with COPD exacerbations requiring ED visits were PIV3, Inf A virus, and human rhinovirus. This result was similar to the finding of Cameron et al from a study in Australia in which the most frequently detected viral etiologies were Inf A, PIV3, and rhinovirus. 21 In a recent review of eight studies, picornavirus was the most common virus in western countries and influenza virus was most common in Asia. 7 H. influenzae was the most common bacterial pathogen in COPD exacerbations in a previous study. 4 Pseudomonas aeruginosa and Klebsiella pneumoniae", "Title: Antiviral immunity is impaired in COPD patients with frequent exacerbations\nPassage: bacterial detection at exacerbation versus stable state, suggesting a causative role . Additionally, virus-induced secondary bacterial infection has been reported in both experimental and naturally occurring exacerbations . We have previously reported that experimental RV challenge in patients with COPD is associated with increased frequency of secondary bacterial infection compared with healthy subjects , an effect that is related to virus loads. Here, we extend these findings to reveal that frequent exacerbators have higher bacterial loads at 2 wk following onset of virus-associated exacerbation, suggesting that this subgroup of COPD patients might be at greatest risk of developing secondary bacterial", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: Bacterial colonization and viral respiratory pathogens play important roles in exacerbations of chronic obstructive pulmonary disease , 1,2 especially in patients requiring hospitalization. 3 Viral and/or bacterial infections have been detected in up to 78% of patients with COPD exacerbations. 4 Although bacteria are considered the major cause of COPD exacerbations and antibiotics commonly used to treat exacerbations, 5 the importance of viral infections in COPD exacerbations was mentioned after the introduction and wide use of viral culture and real-time polymerase chain reaction . 6, 7 The link of viral infections to COPD has been emphasized in recent studies. COPD", "Title: Th17 profile in COPD exacerbations\nPassage: In the past, it was believed that only bacteria were capable of generating exacerbations in patients with COPD. 48, 52 However, the occurrence of these in the winter and symptoms similar to cold led to the belief that viruses were also associated with the complications of this obstructive pathology of the airways. 53 On the other hand, viral infections of the respiratory tract have been shown to influence the lung microbiome in patients with COPD, which indicates that both microorganisms can coexist and predispose to exacerbations. 54 The most prevalent viruses during acute exacerbations of COPD are rhinovirus, coronavirus, influenza," ]

[ [ "2a", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits" ], [ "2b", "Passage: Bacterial colonization and viral respiratory pathogens play important roles in exacerbations of chronic obstructive pulmonary disease , 1,2 especially in patients requiring hospitalization." ], [ "2c", "3 Viral and/or bacterial infections have been detected in up to 78% of patients with COPD exacerbations." ], [ "2d", "4 Although bacteria are considered the major cause of COPD exacerbations and antibiotics commonly used to treat exacerbations, 5 the importance of viral infections in COPD exacerbations was mentioned after the introduction and wide use of viral culture and real-time polymerase chain reaction ." ], [ "2e", "6, 7 The link of viral infections to COPD has been emphasized in recent studies. COPD" ] ]

[ "0b", "0c", "2c", "2d", "2e", "3c", "3d", "3e", "1c", "1d", "0e" ]

[ "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: In this study, the commonly identified viruses in patients with COPD exacerbations requiring ED visits were PIV3, Inf A virus, and human rhinovirus. This result was similar to the finding of Cameron et al from a study in Australia in which the most frequently detected viral etiologies were Inf A, PIV3, and rhinovirus. 21 In a recent review of eight studies, picornavirus was the most common virus in western countries and influenza virus was most common in Asia. 7 H. influenzae was the most common bacterial pathogen in COPD exacerbations in a previous study. 4 Pseudomonas aeruginosa and Klebsiella pneumoniae", "Title: Antiviral immunity is impaired in COPD patients with frequent exacerbations\nPassage: bacterial detection at exacerbation versus stable state, suggesting a causative role . Additionally, virus-induced secondary bacterial infection has been reported in both experimental and naturally occurring exacerbations . We have previously reported that experimental RV challenge in patients with COPD is associated with increased frequency of secondary bacterial infection compared with healthy subjects , an effect that is related to virus loads. Here, we extend these findings to reveal that frequent exacerbators have higher bacterial loads at 2 wk following onset of virus-associated exacerbation, suggesting that this subgroup of COPD patients might be at greatest risk of developing secondary bacterial", "Title: Procalcitonin and C-reactive protein cannot differentiate bacterial or viral infection in COPD exacerbation requiring emergency department visits\nPassage: Bacterial colonization and viral respiratory pathogens play important roles in exacerbations of chronic obstructive pulmonary disease , 1,2 especially in patients requiring hospitalization. 3 Viral and/or bacterial infections have been detected in up to 78% of patients with COPD exacerbations. 4 Although bacteria are considered the major cause of COPD exacerbations and antibiotics commonly used to treat exacerbations, 5 the importance of viral infections in COPD exacerbations was mentioned after the introduction and wide use of viral culture and real-time polymerase chain reaction . 6, 7 The link of viral infections to COPD has been emphasized in recent studies. COPD", "Title: Th17 profile in COPD exacerbations\nPassage: In the past, it was believed that only bacteria were capable of generating exacerbations in patients with COPD. 48, 52 However, the occurrence of these in the winter and symptoms similar to cold led to the belief that viruses were also associated with the complications of this obstructive pathology of the airways. 53 On the other hand, viral infections of the respiratory tract have been shown to influence the lung microbiome in patients with COPD, which indicates that both microorganisms can coexist and predispose to exacerbations. 54 The most prevalent viruses during acute exacerbations of COPD are rhinovirus, coronavirus, influenza," ]

[ [ "3a", "Title: Th17 profile in COPD exacerbations" ], [ "3b", "Passage: In the past, it was believed that only bacteria were capable of generating exacerbations in patients with COPD." ], [ "3c", "48, 52 However, the occurrence of these in the winter and symptoms similar to cold led to the belief that viruses were also associated with the complications of this obstructive pathology of the airways." ], [ "3d", "53 On the other hand, viral infections of the respiratory tract have been shown to influence the lung microbiome in patients with COPD, which indicates that both microorganisms can coexist and predispose to exacerbations." ], [ "3e", "54 The most prevalent viruses during acute exacerbations of COPD are rhinovirus, coronavirus, influenza," ] ]

[ "0b", "0c", "2c", "2d", "2e", "3c", "3d", "3e", "1c", "1d", "0e" ]

[ "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas\nPassage: A major question related to the pathogenesis of MERS-CoV infection in camels, and of great relevance to vaccination strategies, is whether animals that have been infected are resistant to reinfection and virus shedding and, if so, for how long. Our experimentally infected animals were completely protected against rechallenge 70 days later, which suggests that sterilizing immunity can be achieved. However, the animals that were infected through contact shed infectious virus after reinfection, albeit at much lower levels than infected control animals .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Some sero-assays have bypassed the risks of working with infectious virus by creating transfected cells expressing recombinant portions of the MERS-CoV nucleocapsid and spike proteins , or using a recombinant lentivirus expressing MERS-CoV spike protein and luciferase . A pseudo particle neutralization assay has seen widespread used in animal studies and was at least as sensitive as the traditional microneutralization test. ] Studies using small sample numbers and ppNT found no evidence of MERS-CoV neutralizing antibody in sera from 158 children with LRT infections between May 2010 and May 2011, 110 sera from 19 to 52 year old male blood", "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas\nPassage: quantities of virus . Serum was collected weekly and tested for neutralizing antibodies against MERS-CoV. All 3 experimentally infected animals had detectable levels of antibodies beginning on day 14 . Although infectious virus was isolated only from 2 of the 3 co-housed animals, these 3 animals had neutralizing antibodies detected first on day 21 or day 28 .", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Various therapeutic options have been investigated for the treatment of MERS-CoV, but no therapy of proven value currently exists. The use of SC was associated with adverse outcome in SARS 69 and is not recommended for MERS-CoV. Many agents have shown inhibitory effects against MERS-CoV in cell culture including interferon +/À ribavirin, cyclosporine A, mycophenolic acid, chloroquine and lopinavir. 70 Interferons, lopinavir, mycophenolate, possibly alisporivir and combinations are reasonable choices for testing in controlled clinical trials. Exploratory post hoc metaanalysis of studies related to SARS and severe influenza has shown a significant reduction in mortality following convalescent plasma treatment compared" ]

[ [ "0a", "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas" ], [ "0b", "Passage: A major question related to the pathogenesis of MERS-CoV infection in camels, and of great relevance to vaccination strategies, is whether animals that have been infected are resistant to reinfection and virus shedding and, if so, for how long." ], [ "0c", "Our experimentally infected animals were completely protected against rechallenge 70 days later, which suggests that sterilizing immunity can be achieved." ], [ "0d", "However, the animals that were infected through contact shed infectious virus after reinfection, albeit at much lower levels than infected control animals ." ] ]

[ "0c", "2d" ]

[ "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas\nPassage: A major question related to the pathogenesis of MERS-CoV infection in camels, and of great relevance to vaccination strategies, is whether animals that have been infected are resistant to reinfection and virus shedding and, if so, for how long. Our experimentally infected animals were completely protected against rechallenge 70 days later, which suggests that sterilizing immunity can be achieved. However, the animals that were infected through contact shed infectious virus after reinfection, albeit at much lower levels than infected control animals .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Some sero-assays have bypassed the risks of working with infectious virus by creating transfected cells expressing recombinant portions of the MERS-CoV nucleocapsid and spike proteins , or using a recombinant lentivirus expressing MERS-CoV spike protein and luciferase . A pseudo particle neutralization assay has seen widespread used in animal studies and was at least as sensitive as the traditional microneutralization test. ] Studies using small sample numbers and ppNT found no evidence of MERS-CoV neutralizing antibody in sera from 158 children with LRT infections between May 2010 and May 2011, 110 sera from 19 to 52 year old male blood", "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas\nPassage: quantities of virus . Serum was collected weekly and tested for neutralizing antibodies against MERS-CoV. All 3 experimentally infected animals had detectable levels of antibodies beginning on day 14 . Although infectious virus was isolated only from 2 of the 3 co-housed animals, these 3 animals had neutralizing antibodies detected first on day 21 or day 28 .", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Various therapeutic options have been investigated for the treatment of MERS-CoV, but no therapy of proven value currently exists. The use of SC was associated with adverse outcome in SARS 69 and is not recommended for MERS-CoV. Many agents have shown inhibitory effects against MERS-CoV in cell culture including interferon +/À ribavirin, cyclosporine A, mycophenolic acid, chloroquine and lopinavir. 70 Interferons, lopinavir, mycophenolate, possibly alisporivir and combinations are reasonable choices for testing in controlled clinical trials. Exploratory post hoc metaanalysis of studies related to SARS and severe influenza has shown a significant reduction in mortality following convalescent plasma treatment compared" ]

[ [ "2a", "Title: Infection, Replication, and Transmission of Middle East Respiratory Syndrome Coronavirus in Alpacas" ], [ "2b", "Passage: quantities of virus ." ], [ "2c", "Serum was collected weekly and tested for neutralizing antibodies against MERS-CoV." ], [ "2d", "All 3 experimentally infected animals had detectable levels of antibodies beginning on day 14 ." ], [ "2e", "Although infectious virus was isolated only from 2 of the 3 co-housed animals, these 3 animals had neutralizing antibodies detected first on day 21 or day 28 ." ] ]

[ "0c", "2d" ]

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: The mouse-adapted SARS virus was generated by serial passage of an infectious wildtype SARS CoV clone in the respiratory tract of BALB/c mice. After 15 passages in mice, the SARS-CoV gained elevated replication and lung pathogenesis in aged mice , due to six coding genetic mutations associated with mouse adaptation. It is likely that MA15 is highly attenuated to replicate in human cells or patients due to the mouse adaptation.", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: aged mouse lungs, infection was attenuated, and less virus antigen was present in the airway epithelium as compared to SARS MA15, which causes lethal outcomes in aged mice .", "Title: Internal genes of a highly pathogenic H5N1 influenza virus determine high viral replication in myeloid cells and severe outcome of infection in mice\nPassage: lung homogenates was highest for mice infected with the 6:2 Eng/09 virus on both day 2 and day 7 post infection. Day 2 lung titres were similar between the other three viruses. At the later time point two mice surviving in the 6:2 Tky/05 infected group had cleared the virus from the lung but did not regain weight .", "Title: Internal genes of a highly pathogenic H5N1 influenza virus determine high viral replication in myeloid cells and severe outcome of infection in mice\nPassage: Six to eight week old BALB/c mice were infected with 10 4 or 10 5 PFU of either 6:2 Eng/09, or 6:2 Tky/05 virus intranasally. Two to three days post infection mice were culled; the lungs inflated with 1mL PBS, and placed in 4% PFA solution overnight. Lungs were embedded in paraffin, and mounted on slides by the Inflammation, Repair, and Development group, NHLI at Imperial College London." ]

[ [ "0a", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2" ], [ "0b", "Passage: The mouse-adapted SARS virus was generated by serial passage of an infectious wildtype SARS CoV clone in the respiratory tract of BALB/c mice." ], [ "0c", "After 15 passages in mice, the SARS-CoV gained elevated replication and lung pathogenesis in aged mice , due to six coding genetic mutations associated with mouse adaptation." ], [ "0d", "It is likely that MA15 is highly attenuated to replicate in human cells or patients due to the mouse adaptation." ] ]

[ "0a", "0c" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Individual human case studies report long periods of viral shedding, sometimes intermittently and not necessarily linked to the presence of disease symptoms. In one instance, a HCW shed viral RNA for 42 days in the absence of disease . It is an area of high priority to better understand whether such cases are able to infect others. Over three quarters of MERS cases shed viral RNA in their LRT specimens for at least 30 days, while only 30 % of contacts were still shedding RNA in their URT specimens .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The WHO recommends sampling from the LRT for MERS-CoV RT-rtPCR testing, especially when sample collection is delayed by a week or more after onset of symptoms. LRT samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists . Recommended sample types include bronchoalveolar lavage , tracheal/tracheobronchial aspirate, pleural fluid and sputum . Fresh samples yield better diagnostic results than refrigerated material and if delays in testing of ≥72 h are likely, samples should be frozen at −70°C . If available, lung biopsy or autopsy tissues can also be tested .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The URT is a less invasive and more convenient sampling site however, and an oropharyngeal and throat swab or a nasopharyngeal aspirate/wash are recommended when URT sampling is to be conducted . Paired sera, collected two to three weeks apart are preferable for serological testing while a single sample is suggested to be sufficient if collected two weeks after onset of disease or a single serum collected during the first 10-12 days if conducting RT-rtPCR . Human urine and stool have been found to contain MERS-CoV RNA 12 to 26 days after symptom onset and are listed as samples that", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In the only study to examine the effect of sample type on molecular analysis, 64 nasopharyngeal aspirates , 30 tracheal aspirates, 13 sputa and three BAL were examined. The tracheal aspirates and BAL returned the highest viral load values followed by NPA and sputum. Unsurprisingly, higher viral loads generally paralleled whole genome sequencing and culture success and, in NPA testing, were significantly correlated with severe disease and death . This study demonstrated the importance of LRT sampling for whole genome sequencing." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: Individual human case studies report long periods of viral shedding, sometimes intermittently and not necessarily linked to the presence of disease symptoms." ], [ "0c", "In one instance, a HCW shed viral RNA for 42 days in the absence of disease ." ], [ "0d", "It is an area of high priority to better understand whether such cases are able to infect others." ], [ "0e", "Over three quarters of MERS cases shed viral RNA in their LRT specimens for at least 30 days, while only 30 % of contacts were still shedding RNA in their URT specimens ." ] ]

[ "0a", "0e" ]

[ "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: \"I've certainly thought about how would we get food, or how much food did we have in the house, if we were to get quarantined.\"", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: Leisure activities and hobbies may be tapped to generate environmental monitoring data that can help describe the effects of climate change. As of 2011, there were 47 million bird-watchers in the US; 102 this group has been engaged by Project FeederWatch, a citizen science project sponsored by the Cornell Lab of Ornithology, to tally and report the number of each bird species they see in their yards for two consecutive days each week. They also enter weather data . For the 2014-2015 season, over 12,000 birders across the US and Canada submitted checklists . It would not be possible to", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: how the characteristics of the field change over time will be interesting to see.", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: it might be worth considering how the proposed proximity data might relate to existing diary-based studies." ]

[ [ "2a", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis" ], [ "2b", "Passage: how the characteristics of the field change over time will be interesting to see." ] ]

[ "2b", "3b" ]

[ "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: \"I've certainly thought about how would we get food, or how much food did we have in the house, if we were to get quarantined.\"", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: Leisure activities and hobbies may be tapped to generate environmental monitoring data that can help describe the effects of climate change. As of 2011, there were 47 million bird-watchers in the US; 102 this group has been engaged by Project FeederWatch, a citizen science project sponsored by the Cornell Lab of Ornithology, to tally and report the number of each bird species they see in their yards for two consecutive days each week. They also enter weather data . For the 2014-2015 season, over 12,000 birders across the US and Canada submitted checklists . It would not be possible to", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: how the characteristics of the field change over time will be interesting to see.", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: it might be worth considering how the proposed proximity data might relate to existing diary-based studies." ]

[ [ "3a", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors" ], [ "3b", "Passage: it might be worth considering how the proposed proximity data might relate to existing diary-based studies." ] ]

[ "2b", "3b" ]

[ "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: Both CQ and HCQ are weak bases that are known to elevate the pH of acidic intracellular organelles, such as endosomes/lysosomes, essential for membrane fusion 5 . In addition, CQ could inhibit SARS-CoV entry through changing the glycosylation of ACE2 receptor and spike protein 6 . Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment . To further explore the detailed mechanism of action of CQ and HCQ in inhibiting virus entry, co-localization of virions with early endosomes or endolysosomes was analyzed by immunofluorescence", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: of the two potential drugs, CQ appears to be the drug of choice for large-scale use due to its availability, proven safety record, and a relatively low cost. In light of the preliminary clinical data, CQ has been added to the list of trial drugs in the Guidelines for the Diagnosis and Treatment of COVID-19 published by National Health Commission of the People's Republic of China. CQ -N1,N1-diethyl-1,4pentanediamine) has long been used to treat malaria and amebiasis. However, Plasmodium falciparum developed widespread resistance to it, and with the development of new antimalarials, it has become a choice for the prophylaxis", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: and mechanisms of acting as a weak base and immunomodulator, it is easy to conjure up the idea that HCQ may be a potent candidate to treat infection by SARS-CoV-2. Actually, as of February 23, 2020, seven clinical trial registries were found in Chinese Clinical Trial Registry for using HCQ to treat COVID-19. Whether HCQ is as efficacious as CQ in treating SARS-CoV-2 infection still lacks the experimental evidence.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro. First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ]

[ [ "0a", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro" ], [ "0b", "Passage: Both CQ and HCQ are weak bases that are known to elevate the pH of acidic intracellular organelles, such as endosomes/lysosomes, essential for membrane fusion 5 ." ], [ "0c", "In addition, CQ could inhibit SARS-CoV entry through changing the glycosylation of ACE2 receptor and spike protein 6 ." ], [ "0d", "Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment ." ], [ "0e", "To further explore the detailed mechanism of action of CQ and HCQ in inhibiting virus entry, co-localization of virions with early endosomes or endolysosomes was analyzed by immunofluorescence" ] ]

[ "0b", "0c", "0d", "0e", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: Both CQ and HCQ are weak bases that are known to elevate the pH of acidic intracellular organelles, such as endosomes/lysosomes, essential for membrane fusion 5 . In addition, CQ could inhibit SARS-CoV entry through changing the glycosylation of ACE2 receptor and spike protein 6 . Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment . To further explore the detailed mechanism of action of CQ and HCQ in inhibiting virus entry, co-localization of virions with early endosomes or endolysosomes was analyzed by immunofluorescence", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: of the two potential drugs, CQ appears to be the drug of choice for large-scale use due to its availability, proven safety record, and a relatively low cost. In light of the preliminary clinical data, CQ has been added to the list of trial drugs in the Guidelines for the Diagnosis and Treatment of COVID-19 published by National Health Commission of the People's Republic of China. CQ -N1,N1-diethyl-1,4pentanediamine) has long been used to treat malaria and amebiasis. However, Plasmodium falciparum developed widespread resistance to it, and with the development of new antimalarials, it has become a choice for the prophylaxis", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: and mechanisms of acting as a weak base and immunomodulator, it is easy to conjure up the idea that HCQ may be a potent candidate to treat infection by SARS-CoV-2. Actually, as of February 23, 2020, seven clinical trial registries were found in Chinese Clinical Trial Registry for using HCQ to treat COVID-19. Whether HCQ is as efficacious as CQ in treating SARS-CoV-2 infection still lacks the experimental evidence.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro. First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ]

[ [ "1a", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro" ], [ "1b", "Passage: of the two potential drugs, CQ appears to be the drug of choice for large-scale use due to its availability, proven safety record, and a relatively low cost." ], [ "1c", "In light of the preliminary clinical data, CQ has been added to the list of trial drugs in the Guidelines for the Diagnosis and Treatment of COVID-19 published by National Health Commission of the People's Republic of China." ], [ "1d", "CQ -N1,N1-diethyl-1,4pentanediamine) has long been used to treat malaria and amebiasis." ], [ "1e", "However, Plasmodium falciparum developed widespread resistance to it, and with the development of new antimalarials, it has become a choice for the prophylaxis" ] ]

[ "0b", "0c", "0d", "0e", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: Both CQ and HCQ are weak bases that are known to elevate the pH of acidic intracellular organelles, such as endosomes/lysosomes, essential for membrane fusion 5 . In addition, CQ could inhibit SARS-CoV entry through changing the glycosylation of ACE2 receptor and spike protein 6 . Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment . To further explore the detailed mechanism of action of CQ and HCQ in inhibiting virus entry, co-localization of virions with early endosomes or endolysosomes was analyzed by immunofluorescence", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: of the two potential drugs, CQ appears to be the drug of choice for large-scale use due to its availability, proven safety record, and a relatively low cost. In light of the preliminary clinical data, CQ has been added to the list of trial drugs in the Guidelines for the Diagnosis and Treatment of COVID-19 published by National Health Commission of the People's Republic of China. CQ -N1,N1-diethyl-1,4pentanediamine) has long been used to treat malaria and amebiasis. However, Plasmodium falciparum developed widespread resistance to it, and with the development of new antimalarials, it has become a choice for the prophylaxis", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: and mechanisms of acting as a weak base and immunomodulator, it is easy to conjure up the idea that HCQ may be a potent candidate to treat infection by SARS-CoV-2. Actually, as of February 23, 2020, seven clinical trial registries were found in Chinese Clinical Trial Registry for using HCQ to treat COVID-19. Whether HCQ is as efficacious as CQ in treating SARS-CoV-2 infection still lacks the experimental evidence.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro. First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ]

[ [ "2a", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro" ], [ "2b", "Passage: and mechanisms of acting as a weak base and immunomodulator, it is easy to conjure up the idea that HCQ may be a potent candidate to treat infection by SARS-CoV-2." ], [ "2c", "Actually, as of February 23, 2020, seven clinical trial registries were found in Chinese Clinical Trial Registry for using HCQ to treat COVID-19." ], [ "2d", "Whether HCQ is as efficacious as CQ in treating SARS-CoV-2 infection still lacks the experimental evidence." ] ]

[ "0b", "0c", "0d", "0e", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: Both CQ and HCQ are weak bases that are known to elevate the pH of acidic intracellular organelles, such as endosomes/lysosomes, essential for membrane fusion 5 . In addition, CQ could inhibit SARS-CoV entry through changing the glycosylation of ACE2 receptor and spike protein 6 . Time-of-addition experiment confirmed that HCQ effectively inhibited the entry step, as well as the post-entry stages of SARS-CoV-2, which was also found upon CQ treatment . To further explore the detailed mechanism of action of CQ and HCQ in inhibiting virus entry, co-localization of virions with early endosomes or endolysosomes was analyzed by immunofluorescence", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: of the two potential drugs, CQ appears to be the drug of choice for large-scale use due to its availability, proven safety record, and a relatively low cost. In light of the preliminary clinical data, CQ has been added to the list of trial drugs in the Guidelines for the Diagnosis and Treatment of COVID-19 published by National Health Commission of the People's Republic of China. CQ -N1,N1-diethyl-1,4pentanediamine) has long been used to treat malaria and amebiasis. However, Plasmodium falciparum developed widespread resistance to it, and with the development of new antimalarials, it has become a choice for the prophylaxis", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: and mechanisms of acting as a weak base and immunomodulator, it is easy to conjure up the idea that HCQ may be a potent candidate to treat infection by SARS-CoV-2. Actually, as of February 23, 2020, seven clinical trial registries were found in Chinese Clinical Trial Registry for using HCQ to treat COVID-19. Whether HCQ is as efficacious as CQ in treating SARS-CoV-2 infection still lacks the experimental evidence.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro. First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ]

[ [ "3a", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro" ], [ "3b", "Passage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro." ], [ "3c", "First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ] ]

[ "0b", "0c", "0d", "0e", "1c", "2b", "2c", "2d", "3b", "3c" ]

[ "Title: Exploratory Analysis of Methods for Automated Classification of Laboratory Test Orders into Syndromic Groups in Veterinary Medicine\nPassage: it is ''serum'' or ''blood''.", "Title: Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays\nPassage: of the same patient serum as shown in , and for a blood donor serum. All dilutions refer to the 50 µL of diluted serum which together with the 50 µL bead panel had a final volume of 100 µL. Thus, final dilutions were two times higher than the ones mentioned in the figure.", "Title: Investigation of serum protein profiles in scrapie infected sheep by means of SELDI-TOF-MS and multivariate data analysis\nPassage: Serum samples used in this work were drawn every two weeks from six weeks post infection until euthanasia in 2007 for the longitudinal study . Serum samples at time of euthanasia from both 2006 and 2007 were used for the end-stage study . Serum samples were allowed to clot at room temperature for a minimum of 30 minutes and maximum 60 minutes, and then processed. Serum was pipetted in aliquots and frozen at minus 80 degrees within two hours of sampling. All the samples were subjected to the same handling procedures throughout the experiment.", "Title: Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays\nPassage: A convalescent serum from a patient diagnosed with an uncertain filovirus infection was obtained with informed consent. Anonymous blood donor sera from the Uppsala Academic Hospital were used as negative controls. They were all used with informed consent according to the Swedish Biobank law which allows diagnostic patient samples to be used for similar purposes as the original sampling purpose." ]

[ [ "2a", "Title: Investigation of serum protein profiles in scrapie infected sheep by means of SELDI-TOF-MS and multivariate data analysis" ], [ "2b", "Passage: Serum samples used in this work were drawn every two weeks from six weeks post infection until euthanasia in 2007 for the longitudinal study ." ], [ "2c", "Serum samples at time of euthanasia from both 2006 and 2007 were used for the end-stage study ." ], [ "2d", "Serum samples were allowed to clot at room temperature for a minimum of 30 minutes and maximum 60 minutes, and then processed." ], [ "2e", "Serum was pipetted in aliquots and frozen at minus 80 degrees within two hours of sampling." ], [ "2f", "All the samples were subjected to the same handling procedures throughout the experiment." ] ]

[ "2b", "2c", "2d", "2e", "2f", "3a", "3c", "3d" ]

[ "Title: Exploratory Analysis of Methods for Automated Classification of Laboratory Test Orders into Syndromic Groups in Veterinary Medicine\nPassage: it is ''serum'' or ''blood''.", "Title: Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays\nPassage: of the same patient serum as shown in , and for a blood donor serum. All dilutions refer to the 50 µL of diluted serum which together with the 50 µL bead panel had a final volume of 100 µL. Thus, final dilutions were two times higher than the ones mentioned in the figure.", "Title: Investigation of serum protein profiles in scrapie infected sheep by means of SELDI-TOF-MS and multivariate data analysis\nPassage: Serum samples used in this work were drawn every two weeks from six weeks post infection until euthanasia in 2007 for the longitudinal study . Serum samples at time of euthanasia from both 2006 and 2007 were used for the end-stage study . Serum samples were allowed to clot at room temperature for a minimum of 30 minutes and maximum 60 minutes, and then processed. Serum was pipetted in aliquots and frozen at minus 80 degrees within two hours of sampling. All the samples were subjected to the same handling procedures throughout the experiment.", "Title: Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays\nPassage: A convalescent serum from a patient diagnosed with an uncertain filovirus infection was obtained with informed consent. Anonymous blood donor sera from the Uppsala Academic Hospital were used as negative controls. They were all used with informed consent according to the Swedish Biobank law which allows diagnostic patient samples to be used for similar purposes as the original sampling purpose." ]

[ [ "3a", "Title: Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays" ], [ "3b", "Passage: A convalescent serum from a patient diagnosed with an uncertain filovirus infection was obtained with informed consent." ], [ "3c", "Anonymous blood donor sera from the Uppsala Academic Hospital were used as negative controls." ], [ "3d", "They were all used with informed consent according to the Swedish Biobank law which allows diagnostic patient samples to be used for similar purposes as the original sampling purpose." ] ]

[ "2b", "2c", "2d", "2e", "2f", "3a", "3c", "3d" ]

[ "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: Whereas younger patients with asthma often suffer from allergic rhinitis complaints, elderly patients with asthma often suffer from sinus symptoms, including nasal obstruction, loss of smell and facial pain/headache. A recent Europe-wide epidemiologic study on the prevalence of chronic rhinosinusitis did confirm the well-known association between allergic rhinitis and early-onset asthma, but also demonstrated a clear increased risk to suffer from late-onset asthma in CRS patients . CRS may be phenotyped as CRS without and with nasal polyps , based on symptoms , nasal endoscopy and CT scanning. From those phenotypes, CRSwNP has a clearly increased risk of asthma comorbidity", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Additionally, in patients with asthma and patients with CRS with nasal polyp , viral infections such as RV and RSV promote a Type 2-biased immune response . This amplifies the basal type 2 inflammation resulting in a greater release of IL-4, IL-5, IL-13, RANTES and eotaxin and a further increase in eosinophilia, a key pathological driver of asthma and CRSwNP . Increased eosinophilia, in turn, worsens the classical symptoms of disease and may further lead to life-threatening conditions due to breathing difficulties. On the other hand, patients with COPD and patients with CRS without nasal polyp are more neutrophilic in", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: With regard to this, recent evidence indicates the potential roles of chronic rhinosinusitis in the asthma pathogenesis. The GA2LEN surveys found that late-onset adult asthma was independently associated with CRS irrespective of nasal allergies . Recent endotype approaches suggest the specific roles of Staphylococcal enterotoxin sensitization in the pathogenesis of CRS subtypes with nasal polyp and severe late-onset non-atopic adult asthma . These findings may also be quite relevant to the elderly population, as elderly asthma is a considerably late-onset disease.", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: in Caucasian populations , whereas CRSsNP does not significantly impact on asthma, but may be associated with other lower airway disease ." ]

[ [ "1a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "1b", "Passage: Additionally, in patients with asthma and patients with CRS with nasal polyp , viral infections such as RV and RSV promote a Type 2-biased immune response ." ], [ "1c", "This amplifies the basal type 2 inflammation resulting in a greater release of IL-4, IL-5, IL-13, RANTES and eotaxin and a further increase in eosinophilia, a key pathological driver of asthma and CRSwNP ." ], [ "1d", "Increased eosinophilia, in turn, worsens the classical symptoms of disease and may further lead to life-threatening conditions due to breathing difficulties." ], [ "1e", "On the other hand, patients with COPD and patients with CRS without nasal polyp are more neutrophilic in" ] ]

[ "1b", "1c", "1d", "2d" ]

[ "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: Whereas younger patients with asthma often suffer from allergic rhinitis complaints, elderly patients with asthma often suffer from sinus symptoms, including nasal obstruction, loss of smell and facial pain/headache. A recent Europe-wide epidemiologic study on the prevalence of chronic rhinosinusitis did confirm the well-known association between allergic rhinitis and early-onset asthma, but also demonstrated a clear increased risk to suffer from late-onset asthma in CRS patients . CRS may be phenotyped as CRS without and with nasal polyps , based on symptoms , nasal endoscopy and CT scanning. From those phenotypes, CRSwNP has a clearly increased risk of asthma comorbidity", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Additionally, in patients with asthma and patients with CRS with nasal polyp , viral infections such as RV and RSV promote a Type 2-biased immune response . This amplifies the basal type 2 inflammation resulting in a greater release of IL-4, IL-5, IL-13, RANTES and eotaxin and a further increase in eosinophilia, a key pathological driver of asthma and CRSwNP . Increased eosinophilia, in turn, worsens the classical symptoms of disease and may further lead to life-threatening conditions due to breathing difficulties. On the other hand, patients with COPD and patients with CRS without nasal polyp are more neutrophilic in", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: With regard to this, recent evidence indicates the potential roles of chronic rhinosinusitis in the asthma pathogenesis. The GA2LEN surveys found that late-onset adult asthma was independently associated with CRS irrespective of nasal allergies . Recent endotype approaches suggest the specific roles of Staphylococcal enterotoxin sensitization in the pathogenesis of CRS subtypes with nasal polyp and severe late-onset non-atopic adult asthma . These findings may also be quite relevant to the elderly population, as elderly asthma is a considerably late-onset disease.", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: in Caucasian populations , whereas CRSsNP does not significantly impact on asthma, but may be associated with other lower airway disease ." ]

[ [ "2a", "Title: Asthma in the elderly: what we know and what we have yet to know" ], [ "2b", "Passage: With regard to this, recent evidence indicates the potential roles of chronic rhinosinusitis in the asthma pathogenesis." ], [ "2c", "The GA2LEN surveys found that late-onset adult asthma was independently associated with CRS irrespective of nasal allergies ." ], [ "2d", "Recent endotype approaches suggest the specific roles of Staphylococcal enterotoxin sensitization in the pathogenesis of CRS subtypes with nasal polyp and severe late-onset non-atopic adult asthma ." ], [ "2e", "These findings may also be quite relevant to the elderly population, as elderly asthma is a considerably late-onset disease." ] ]

[ "1b", "1c", "1d", "2d" ]

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: abundantly in the microvascular endothelium. ANDV-infected hamsters fitted with physiologic monitoring devices exhibited diminished pulse pressures, tachycardia, and hypotension that appear to closely mimic the shock that is believed to be the proximate cause of demise in patients who succumb to HCPS .", "Title: Depletion of Alveolar Macrophages Does Not Prevent Hantavirus Disease Pathogenesis in Golden Syrian Hamsters\nPassage: Serial sections of lung tissue from these groups further revealed the presence of ANDV antigen colocalized to CD31-positive endothelial cells in both capillaries and larger vessels . Regardless of treatment, no differences were observed in the pathogenesis of HPS-like disease in ANDV-infected hamsters. Hamsters in all groups exhibited signs of mild to moderate inflam- mation, interstitial pneumonia, alveolar fibrin deposition, and edema characteristic of ANDV infection.", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: The ANDV-Syrian hamster model has a number of features in common with the human disease, as well as some differences. Unlike the neurologic diseases that have been possible to elicit with HTNV, the hamster model for HCPS appears to be caused by capillary leak that results in pulmonary edema and the production of a pleural effusion with exudative characteristics. Typically the hamsters die between 11 and 14-d post-inoculation, reflecting a slightly accelerated incubation period in comparison to human infections. As with human HCPS, the microscopic examination of the lung reveals abundant fibrin deposition, thickened alveolar septa, and viral antigen expressed", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Compared to the human disease, ANDV-infected hamsters exhibit exceptionally high titers of live ANDV in their tissues, with much of the viral replication occurring in hepatocytes, which are spared in the human disease. Titers of live ANDV in some cases exceed 10 8 /g, whereas hantavirus isolates from human tissues have been notoriously difficult to obtain. Despite the universal occurrence of mildly-elevated hepatic enzymes in patients with HCPS, hepatic enzymes do not appear to be present at elevated levels in the blood of diseased hamsters even immediately before death ." ]

[ [ "0a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "0b", "Passage: abundantly in the microvascular endothelium." ], [ "0c", "ANDV-infected hamsters fitted with physiologic monitoring devices exhibited diminished pulse pressures, tachycardia, and hypotension that appear to closely mimic the shock that is believed to be the proximate cause of demise in patients who succumb to HCPS ." ] ]

[ "0c" ]

[ "Title: Responding to the COVID-19 pandemic in complex humanitarian crises\nPassage: The Sphere Handbook, a collection of rights-based guidelines for humanitarian response, is the foremost authority on minimum standards for humanitarian assistance . However, despite the indisputable evidence for the efficacy of hand hygiene for reducing both bacterial and viral pathogen transmission, humanitarian WASH standards are based on evidence pertaining to the prevention of illnesses transmitted by the faecal-oral route, with the focus on hand hygiene proximate to latrines . And yet, latrines in crisis settings are often shared and distant from residential shelters, conferring a high risk of gender-based violence . Gender-based violence around latrines is an important deterrent for", "Title: The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks\nPassage: We then use the model to find the measures to keep R 0 v1. The necessary levels of latrine and bore hole coverages needed to eradicate the epidemic are both around 16 to 18%. Although the cost of construction of the required number of latrines is a one off cost, the benefits are large. Here we show what the benefits would have been in terms of protection against Hepatitis E. However, other diseases due to poor sanitation that have been reported in Uganda, such as cholera and dysentery, could be prevented in the same way . c Per capita rate", "Title: The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks\nPassage: Our model suggests that to eradicate the epidemic, the minimum number of additional latrines required is 3,47. The average cost of digging and constructing a basic pit latrine is approximately USD 250.00 Therefore, 3,477 would cost a total of USD 869,250.00. Thus, the cost per disability adjusted life year averted in Kitgum, in the case of Hepatitis E is 869,250/7,066 = USD 123.00. In addition to improving hygiene we should consider education. Let us now consider the case of education to the camp dwellers. Taking the simplest and cheapest scenario of hiring twenty guidance and counseling officials to educate the", "Title: The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks\nPassage: The number of latrines and boreholes that would have prevented the Hepatitis E outbreak in Kitgum are calculated using our results in preceding sections. First, it is assumed that if the people had the necessary and sufficient number of latrines in addition to safe drinking, then the outbreak would not have occurred. Then, the costs of constructing the required latrines and boreholes are computed. From the results, the cost of saving one life from Hepatitis E, for one year is determined." ]

[ [ "0a", "Title: Responding to the COVID-19 pandemic in complex humanitarian crises" ], [ "0b", "Passage: The Sphere Handbook, a collection of rights-based guidelines for humanitarian response, is the foremost authority on minimum standards for humanitarian assistance ." ], [ "0c", "However, despite the indisputable evidence for the efficacy of hand hygiene for reducing both bacterial and viral pathogen transmission, humanitarian WASH standards are based on evidence pertaining to the prevention of illnesses transmitted by the faecal-oral route, with the focus on hand hygiene proximate to latrines ." ], [ "0d", "And yet, latrines in crisis settings are often shared and distant from residential shelters, conferring a high risk of gender-based violence ." ], [ "0e", "Gender-based violence around latrines is an important deterrent for" ] ]

[ "0d", "0e" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers.", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: is is in agreement with the study done by Ahmad to estimate the survival rate in MERS-CoV globally prior to 26 January 2017; 86.9% were not health-care workers compared with 13.1% confirmed cases of healthcare workers . Similarly, other studies also reported a lower prevalence in healthcare workers .", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: the percentage of confirmed cases among males to be 66%, compared with 34% among females ." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks." ], [ "0c", "Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA." ], [ "0d", "The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die." ], [ "0e", "However the proportion of male deaths from total males with MERS is a similar figure to that for" ] ]

[ "0c" ]

[ "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: RANBP2, a nuclear pore protein, has numerous roles in the cell cycle. RANBP2 is associated with microtubules and mitochondria suggesting roles in intracellular protein trafficking or energy maintenance and homeostasis of neuronal cells. RANBP2 mutations have been reported in acute necrotizing encephalopathy which could present with coma, convulsions, and encephalopathy. The hallmark of ANE is multiple, symmetric brain lesions located in the thalami bilaterally, putamina, deep periventricular white matter, cerebellum, and brainstem. It could be triggered by a viral infection in previously healthy children .", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: A gene panel targeting inflammatory disorders and post-infectious necrotic encephalopathies found a heterozygous RANBP2 missense mutation . This mutation has not been previously reported in the HGMD database. This variant has been observed at a frequency of <0.01% across the entire Broad ExAC dataset of individuals without severe childhood onset disease . Analysis of amino acid conservation indicates that the wild-type amino acid Lys1665 is conserved in 59 of 60 mammals examined, including 12 of 12 primates, and in 25 of 34 nonmammalian vertebrates increasing the likelihood that a change at this position might not be tolerated. In silico tools", "Title: Human core duplicon gene families: game changers or game players?\nPassage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export . Hence, the RGPD gene family members may be modifiers of this function. Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus . It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition. The Ranbp2 knockout in mice is homozygous lethal.", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: Autosomal dominant mutations in RANBP2 have been associated with susceptibility to infectioninduced necrotizing encephalopathy . Previously healthy patients with pathogenic mutations in RANBP2 can present acutely with encephalopathy and convulsions in the context of an infection, with brain imaging revealing involvement of the brainstem, thalami, putamina, cerebellum and external capsules, and claustrum . Our patient has a similar presentation and imaging features as infection-induced necrotizing encephalopathy, including bilateral thalamic involvement. The rare heterozygous previously unreported variant we identified in RANBP2 affects a very conserved aminoacid and is predicted deleterious using in silico tools . It is possible that this variant" ]

[ [ "0a", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant" ], [ "0b", "Passage: RANBP2, a nuclear pore protein, has numerous roles in the cell cycle." ], [ "0c", "RANBP2 is associated with microtubules and mitochondria suggesting roles in intracellular protein trafficking or energy maintenance and homeostasis of neuronal cells." ], [ "0d", "RANBP2 mutations have been reported in acute necrotizing encephalopathy which could present with coma, convulsions, and encephalopathy." ], [ "0e", "The hallmark of ANE is multiple, symmetric brain lesions located in the thalami bilaterally, putamina, deep periventricular white matter, cerebellum, and brainstem." ], [ "0f", "It could be triggered by a viral infection in previously healthy children ." ] ]

[ "0b", "0c", "0d", "3b" ]

[ "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: RANBP2, a nuclear pore protein, has numerous roles in the cell cycle. RANBP2 is associated with microtubules and mitochondria suggesting roles in intracellular protein trafficking or energy maintenance and homeostasis of neuronal cells. RANBP2 mutations have been reported in acute necrotizing encephalopathy which could present with coma, convulsions, and encephalopathy. The hallmark of ANE is multiple, symmetric brain lesions located in the thalami bilaterally, putamina, deep periventricular white matter, cerebellum, and brainstem. It could be triggered by a viral infection in previously healthy children .", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: A gene panel targeting inflammatory disorders and post-infectious necrotic encephalopathies found a heterozygous RANBP2 missense mutation . This mutation has not been previously reported in the HGMD database. This variant has been observed at a frequency of <0.01% across the entire Broad ExAC dataset of individuals without severe childhood onset disease . Analysis of amino acid conservation indicates that the wild-type amino acid Lys1665 is conserved in 59 of 60 mammals examined, including 12 of 12 primates, and in 25 of 34 nonmammalian vertebrates increasing the likelihood that a change at this position might not be tolerated. In silico tools", "Title: Human core duplicon gene families: game changers or game players?\nPassage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export . Hence, the RGPD gene family members may be modifiers of this function. Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus . It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition. The Ranbp2 knockout in mice is homozygous lethal.", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: Autosomal dominant mutations in RANBP2 have been associated with susceptibility to infectioninduced necrotizing encephalopathy . Previously healthy patients with pathogenic mutations in RANBP2 can present acutely with encephalopathy and convulsions in the context of an infection, with brain imaging revealing involvement of the brainstem, thalami, putamina, cerebellum and external capsules, and claustrum . Our patient has a similar presentation and imaging features as infection-induced necrotizing encephalopathy, including bilateral thalamic involvement. The rare heterozygous previously unreported variant we identified in RANBP2 affects a very conserved aminoacid and is predicted deleterious using in silico tools . It is possible that this variant" ]

[ [ "3a", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant" ], [ "3b", "Passage: Autosomal dominant mutations in RANBP2 have been associated with susceptibility to infectioninduced necrotizing encephalopathy ." ], [ "3c", "Previously healthy patients with pathogenic mutations in RANBP2 can present acutely with encephalopathy and convulsions in the context of an infection, with brain imaging revealing involvement of the brainstem, thalami, putamina, cerebellum and external capsules, and claustrum ." ], [ "3d", "Our patient has a similar presentation and imaging features as infection-induced necrotizing encephalopathy, including bilateral thalamic involvement." ], [ "3e", "The rare heterozygous previously unreported variant we identified in RANBP2 affects a very conserved aminoacid and is predicted deleterious using in silico tools ." ], [ "3f", "It is possible that this variant" ] ]

[ "0b", "0c", "0d", "3b" ]

[ "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: . Several studies have reported that many genes have been found to be associated with Salmonella resistance in the chicken .", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: niche that provides easy access for the pathogen to colonize with limited restriction . This factor alone makes young chickens highly susceptible to enteric bacterial infections, such as Salmonella, which can result in different degrees of disease spectrum from a subclinical carrier state to a high mortality rate depending on the infecting bacterial serovar and host's susceptibility.", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: Salmonella enterica subsp. enterica serovar Enteritidis is a zoonotic enteric pathogen that is most frequently associated with diarrheal disease in humans while chickens serve as asymptotic carrier . Consumption of contaminated eggs produced by infected layer hens is one of the leading causes of Salmonella food poisoning in humans . In chickens, S. Enteritidis can be easily transmitted horizontally via the fecal-oral route as well as vertically via the reproductive tract, which can contaminate the egg . Additionally, chickens can also harbor S. Enteritidis asymptomatically and persist throughout their lifespan, which makes the identification of infected chickens and the eradication", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: The impact of genetic background on the composition of chicken gut microbiota has been mostly investigated in broilers due to the association of intestinal microbiota with performance of broiler chickens in terms of feed conversion efficiency . Studies in broiler chickens have indeed shown evidence that host genotype had significant impact on shaping the composition of the gut microbiota . Few studies had explored the relationship between the host genotype and its influence on microbiota composition in layer chickens, especially related to disease resistance. The host genetic background plays an important role in the resistance and susceptibility to Salmonella infection" ]

[ [ "1a", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks" ], [ "1b", "Passage: niche that provides easy access for the pathogen to colonize with limited restriction ." ], [ "1c", "This factor alone makes young chickens highly susceptible to enteric bacterial infections, such as Salmonella, which can result in different degrees of disease spectrum from a subclinical carrier state to a high mortality rate depending on the infecting bacterial serovar and host's susceptibility." ] ]

[ "1c", "2c", "2d", "2e", "2f", "3e" ]

[ "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: . Several studies have reported that many genes have been found to be associated with Salmonella resistance in the chicken .", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: niche that provides easy access for the pathogen to colonize with limited restriction . This factor alone makes young chickens highly susceptible to enteric bacterial infections, such as Salmonella, which can result in different degrees of disease spectrum from a subclinical carrier state to a high mortality rate depending on the infecting bacterial serovar and host's susceptibility.", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: Salmonella enterica subsp. enterica serovar Enteritidis is a zoonotic enteric pathogen that is most frequently associated with diarrheal disease in humans while chickens serve as asymptotic carrier . Consumption of contaminated eggs produced by infected layer hens is one of the leading causes of Salmonella food poisoning in humans . In chickens, S. Enteritidis can be easily transmitted horizontally via the fecal-oral route as well as vertically via the reproductive tract, which can contaminate the egg . Additionally, chickens can also harbor S. Enteritidis asymptomatically and persist throughout their lifespan, which makes the identification of infected chickens and the eradication", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: The impact of genetic background on the composition of chicken gut microbiota has been mostly investigated in broilers due to the association of intestinal microbiota with performance of broiler chickens in terms of feed conversion efficiency . Studies in broiler chickens have indeed shown evidence that host genotype had significant impact on shaping the composition of the gut microbiota . Few studies had explored the relationship between the host genotype and its influence on microbiota composition in layer chickens, especially related to disease resistance. The host genetic background plays an important role in the resistance and susceptibility to Salmonella infection" ]

[ [ "2a", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks" ], [ "2b", "Passage: Salmonella enterica subsp." ], [ "2c", "enterica serovar Enteritidis is a zoonotic enteric pathogen that is most frequently associated with diarrheal disease in humans while chickens serve as asymptotic carrier ." ], [ "2d", "Consumption of contaminated eggs produced by infected layer hens is one of the leading causes of Salmonella food poisoning in humans ." ], [ "2e", "In chickens, S. Enteritidis can be easily transmitted horizontally via the fecal-oral route as well as vertically via the reproductive tract, which can contaminate the egg ." ], [ "2f", "Additionally, chickens can also harbor S. Enteritidis asymptomatically and persist throughout their lifespan, which makes the identification of infected chickens and the eradication" ] ]

[ "1c", "2c", "2d", "2e", "2f", "3e" ]

[ "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: . Several studies have reported that many genes have been found to be associated with Salmonella resistance in the chicken .", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: niche that provides easy access for the pathogen to colonize with limited restriction . This factor alone makes young chickens highly susceptible to enteric bacterial infections, such as Salmonella, which can result in different degrees of disease spectrum from a subclinical carrier state to a high mortality rate depending on the infecting bacterial serovar and host's susceptibility.", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: Salmonella enterica subsp. enterica serovar Enteritidis is a zoonotic enteric pathogen that is most frequently associated with diarrheal disease in humans while chickens serve as asymptotic carrier . Consumption of contaminated eggs produced by infected layer hens is one of the leading causes of Salmonella food poisoning in humans . In chickens, S. Enteritidis can be easily transmitted horizontally via the fecal-oral route as well as vertically via the reproductive tract, which can contaminate the egg . Additionally, chickens can also harbor S. Enteritidis asymptomatically and persist throughout their lifespan, which makes the identification of infected chickens and the eradication", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks\nPassage: The impact of genetic background on the composition of chicken gut microbiota has been mostly investigated in broilers due to the association of intestinal microbiota with performance of broiler chickens in terms of feed conversion efficiency . Studies in broiler chickens have indeed shown evidence that host genotype had significant impact on shaping the composition of the gut microbiota . Few studies had explored the relationship between the host genotype and its influence on microbiota composition in layer chickens, especially related to disease resistance. The host genetic background plays an important role in the resistance and susceptibility to Salmonella infection" ]

[ [ "3a", "Title: Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks" ], [ "3b", "Passage: The impact of genetic background on the composition of chicken gut microbiota has been mostly investigated in broilers due to the association of intestinal microbiota with performance of broiler chickens in terms of feed conversion efficiency ." ], [ "3c", "Studies in broiler chickens have indeed shown evidence that host genotype had significant impact on shaping the composition of the gut microbiota ." ], [ "3d", "Few studies had explored the relationship between the host genotype and its influence on microbiota composition in layer chickens, especially related to disease resistance." ], [ "3e", "The host genetic background plays an important role in the resistance and susceptibility to Salmonella infection" ] ]

[ "1c", "2c", "2d", "2e", "2f", "3e" ]

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population. For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life . The low average age of infection with a swine variant form of H3N2 in North America is likely driven by reduced susceptibility in adults because of", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: For small host communities, the depletion of susceptible hosts can play a significant role in limiting an ongoing outbreak. What is the effect of a finite population size on these analytical results which assume an infinite host population? Figure 3A compares the simulated outbreak size distribution of different sized populations with our analytical predictions. Note that, for populations greater than 500, there is close agreement between numerical and analytical results. When considering populations of size 1,000 or more, we do not expect population size dependence to have a substantial effect.", "Title: Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence\nPassage: to the lack of sufficient host contact networks. This has resulted in a highly patchy distribution, characterized by sporadic and short-lived outbreaks in the United States, often confined to animal shelters , but a marked lack of sustained transmission in most dog populations that may be too small and sparse to support ongoing transmission. Hence, although a pathogen may possess all the mutations required to successfully infect a new host, whether it establishes itself is also dependent on the underlying population ecology. Interestingly, a new H3N2 CIV of avian origin has emerged in Asia and, more recently, in North America", "Title: Local risk perception enhances epidemic control\nPassage: Several studies suggest that immunizing or isolating interventions should target the most connected individuals in a population 52] . However, we rarely know the full contact network of a population. As proxies, we can target populations subgroups that tend to have high numbers of potentially disease-spreading contacts, such as young and school-aged children or health-care workers. We can also use biased sampling to identify highly connected individuals, such as the random acquaintance strategy in which random individuals are asked to name one of their social contact; individuals with more contacts are more likely to be named . In a sense," ]

[ [ "0a", "Title: Viral factors in influenza pandemic risk assessment" ], [ "0b", "Passage: pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population." ], [ "0c", "For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life ." ], [ "0d", "The low average age of infection with a swine variant form of H3N2 in North America is likely driven by reduced susceptibility in adults because of" ] ]

[ "0c", "1b", "2c", "3d" ]

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population. For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life . The low average age of infection with a swine variant form of H3N2 in North America is likely driven by reduced susceptibility in adults because of", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: For small host communities, the depletion of susceptible hosts can play a significant role in limiting an ongoing outbreak. What is the effect of a finite population size on these analytical results which assume an infinite host population? Figure 3A compares the simulated outbreak size distribution of different sized populations with our analytical predictions. Note that, for populations greater than 500, there is close agreement between numerical and analytical results. When considering populations of size 1,000 or more, we do not expect population size dependence to have a substantial effect.", "Title: Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence\nPassage: to the lack of sufficient host contact networks. This has resulted in a highly patchy distribution, characterized by sporadic and short-lived outbreaks in the United States, often confined to animal shelters , but a marked lack of sustained transmission in most dog populations that may be too small and sparse to support ongoing transmission. Hence, although a pathogen may possess all the mutations required to successfully infect a new host, whether it establishes itself is also dependent on the underlying population ecology. Interestingly, a new H3N2 CIV of avian origin has emerged in Asia and, more recently, in North America", "Title: Local risk perception enhances epidemic control\nPassage: Several studies suggest that immunizing or isolating interventions should target the most connected individuals in a population 52] . However, we rarely know the full contact network of a population. As proxies, we can target populations subgroups that tend to have high numbers of potentially disease-spreading contacts, such as young and school-aged children or health-care workers. We can also use biased sampling to identify highly connected individuals, such as the random acquaintance strategy in which random individuals are asked to name one of their social contact; individuals with more contacts are more likely to be named . In a sense," ]

[ [ "1a", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease" ], [ "1b", "Passage: For small host communities, the depletion of susceptible hosts can play a significant role in limiting an ongoing outbreak." ], [ "1c", "What is the effect of a finite population size on these analytical results which assume an infinite host population?" ], [ "1d", "Figure 3A compares the simulated outbreak size distribution of different sized populations with our analytical predictions." ], [ "1e", "Note that, for populations greater than 500, there is close agreement between numerical and analytical results." ], [ "1f", "When considering populations of size 1,000 or more, we do not expect population size dependence to have a substantial effect." ] ]

[ "0c", "1b", "2c", "3d" ]

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population. For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life . The low average age of infection with a swine variant form of H3N2 in North America is likely driven by reduced susceptibility in adults because of", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: For small host communities, the depletion of susceptible hosts can play a significant role in limiting an ongoing outbreak. What is the effect of a finite population size on these analytical results which assume an infinite host population? Figure 3A compares the simulated outbreak size distribution of different sized populations with our analytical predictions. Note that, for populations greater than 500, there is close agreement between numerical and analytical results. When considering populations of size 1,000 or more, we do not expect population size dependence to have a substantial effect.", "Title: Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence\nPassage: to the lack of sufficient host contact networks. This has resulted in a highly patchy distribution, characterized by sporadic and short-lived outbreaks in the United States, often confined to animal shelters , but a marked lack of sustained transmission in most dog populations that may be too small and sparse to support ongoing transmission. Hence, although a pathogen may possess all the mutations required to successfully infect a new host, whether it establishes itself is also dependent on the underlying population ecology. Interestingly, a new H3N2 CIV of avian origin has emerged in Asia and, more recently, in North America", "Title: Local risk perception enhances epidemic control\nPassage: Several studies suggest that immunizing or isolating interventions should target the most connected individuals in a population 52] . However, we rarely know the full contact network of a population. As proxies, we can target populations subgroups that tend to have high numbers of potentially disease-spreading contacts, such as young and school-aged children or health-care workers. We can also use biased sampling to identify highly connected individuals, such as the random acquaintance strategy in which random individuals are asked to name one of their social contact; individuals with more contacts are more likely to be named . In a sense," ]

[ [ "2a", "Title: Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence" ], [ "2b", "Passage: to the lack of sufficient host contact networks." ], [ "2c", "This has resulted in a highly patchy distribution, characterized by sporadic and short-lived outbreaks in the United States, often confined to animal shelters , but a marked lack of sustained transmission in most dog populations that may be too small and sparse to support ongoing transmission." ], [ "2d", "Hence, although a pathogen may possess all the mutations required to successfully infect a new host, whether it establishes itself is also dependent on the underlying population ecology." ], [ "2e", "Interestingly, a new H3N2 CIV of avian origin has emerged in Asia and, more recently, in North America" ] ]

[ "0c", "1b", "2c", "3d" ]

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population. For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life . The low average age of infection with a swine variant form of H3N2 in North America is likely driven by reduced susceptibility in adults because of", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: For small host communities, the depletion of susceptible hosts can play a significant role in limiting an ongoing outbreak. What is the effect of a finite population size on these analytical results which assume an infinite host population? Figure 3A compares the simulated outbreak size distribution of different sized populations with our analytical predictions. Note that, for populations greater than 500, there is close agreement between numerical and analytical results. When considering populations of size 1,000 or more, we do not expect population size dependence to have a substantial effect.", "Title: Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence\nPassage: to the lack of sufficient host contact networks. This has resulted in a highly patchy distribution, characterized by sporadic and short-lived outbreaks in the United States, often confined to animal shelters , but a marked lack of sustained transmission in most dog populations that may be too small and sparse to support ongoing transmission. Hence, although a pathogen may possess all the mutations required to successfully infect a new host, whether it establishes itself is also dependent on the underlying population ecology. Interestingly, a new H3N2 CIV of avian origin has emerged in Asia and, more recently, in North America", "Title: Local risk perception enhances epidemic control\nPassage: Several studies suggest that immunizing or isolating interventions should target the most connected individuals in a population 52] . However, we rarely know the full contact network of a population. As proxies, we can target populations subgroups that tend to have high numbers of potentially disease-spreading contacts, such as young and school-aged children or health-care workers. We can also use biased sampling to identify highly connected individuals, such as the random acquaintance strategy in which random individuals are asked to name one of their social contact; individuals with more contacts are more likely to be named . In a sense," ]

[ [ "3a", "Title: Local risk perception enhances epidemic control" ], [ "3b", "Passage: Several studies suggest that immunizing or isolating interventions should target the most connected individuals in a population 52] ." ], [ "3c", "However, we rarely know the full contact network of a population." ], [ "3d", "As proxies, we can target populations subgroups that tend to have high numbers of potentially disease-spreading contacts, such as young and school-aged children or health-care workers." ], [ "3e", "We can also use biased sampling to identify highly connected individuals, such as the random acquaintance strategy in which random individuals are asked to name one of their social contact; individuals with more contacts are more likely to be named ." ], [ "3f", "In a sense," ] ]

[ "0c", "1b", "2c", "3d" ]

[ "Title: Monitoring Influenza Epidemics in China with Search Query from Baidu\nPassage: area in that, the keyword selection and composition approach presented is more economical in terms of computational resources and cost compared to the original method by Ginsberg et al . Unlike the United States, in China alternative search engines such as Baidu are more widely used than Google. The market share of Google in China is less than 20%, while that for Baidu is more than 80% . The wide use of Baidu in China makes it a more representative search query source for this analysis.", "Title: A Multi-Method Approach to Curriculum Development for In-Service Training in China’s Newly Established Health Emergency Response Offices\nPassage: The outbreak of severe acute respiratory syndrome in 2003 was a watershed moment for China . It triggered major health reforms and led to an increase in public health funding of about 100% by 2007, accounting for a rise in spending from 0.75% to 0.89% of the gross domestic product . Subsequent emergencies that echoed the imperative for reforms included the outbreaks of influenza H5N1 in birds and humans , melamine contamination of milk formula that affected over 294,000 Chinese children , and the earthquake in Sichuan that resulted in over 69 000 deaths, displaced about 15 million people and", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: This study was performed in seven urban regions and two rural areas of China with over one million people in each region. Regarding the urban sites, Beijing as the capital of China locates in the northeast; Shanghai is a municipality in the east of China; Wuhan and Zhengzhou are both in the centre of China; Xi'an in the northwest of China is the provincial capital of Shanxi province; and Shenzhen of the Guangdong province is in the southeast of China. As for the rural sites, Jingzhou county and Zhengzhou county, from Hubei and Henan provinces, respectively, both locate in the", "Title: A Multi-Method Approach to Curriculum Development for In-Service Training in China’s Newly Established Health Emergency Response Offices\nPassage: The proportion of the 1606 respondents who expressed a high level of need for these modules are shown in Table 3 ." ]

[ [ "0a", "Title: Monitoring Influenza Epidemics in China with Search Query from Baidu" ], [ "0b", "Passage: area in that, the keyword selection and composition approach presented is more economical in terms of computational resources and cost compared to the original method by Ginsberg et al ." ], [ "0c", "Unlike the United States, in China alternative search engines such as Baidu are more widely used than Google." ], [ "0d", "The market share of Google in China is less than 20%, while that for Baidu is more than 80% ." ], [ "0e", "The wide use of Baidu in China makes it a more representative search query source for this analysis." ] ]

[ "0b", "0c", "0d", "0e" ]

[ "Title: Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability\nPassage: The indicated ZUFSP HALO-Tag fusion proteins were coupled to HALO Link beads and incubated with di-, tri-, tetra-, or penta-K63Ub. The last well shows competitive pull down with di-, tri-, tetra-and penta-Ub mixed together. Bound material was analysed as in . U2-OS/iGFP-ZUFSP *siR wild type or U2-OS/iGFP-ZUFSP *siR C360S cells were transfected with ZUFSP siRNA for 72 h with or without addition of doxycycline. Cells were fixed and processed for immunostaining with the indicated antibodies.", "Title: TRAF molecules in cell signaling and in human diseases\nPassage: in TLR3 signaling . In contrast, K48-linked polyubiquitination of Regulators of mRNA stability Tristetraprolin TRAF2 TNF-R1 Autophagy proteins Beclin 1 TRAF6 TLR4-, IL-1R-induced autophagy NDP52 TRAF6 TLR3-induced autophagy Regulators of ROS production ECSIT TRAF6 TLR1, 2, 4-induced ROS production TRAFs results in degradation of TRAF proteins by the 26S proteasome. K48-linked E3 ligases of TRAFs include cIAP1/2, Triad3A, AWP1, SOCS2, Siva-1, Numbl and CHIP. For example, upon viral infection, Triad3A is upregulated, and induces K48-linked ubiquitination and degradation of TRAF3, thereby forming a negative feedback loop to halt RIG-I signaling and type I IFN production . Thus, K48-linked ubiquitination and", "Title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus\nPassage: promoted the dissociation of the 19S subunit from the 20S proteasome, followed by the distinct enrichment of the 19S-like complex in nuclear extracts together with the Tat-mediated recruitment of the 19S subunits to the HIV-1 promoter, which facilitated its transcriptional elongation . We also quantified UBA1 , the E3 ubiquitin-protein ligase UHRF1 , UBC and two Ubiquitinspecific-peptidases, USP30 and USP20 .", "Title: A Method to Identify p62's UBA Domain Interacting Proteins\nPassage: vitro ubiquitination . TRAF6 was chosen as an E3 in this in vitro ubiquitination assay due to its RING domain, a common feature of E3 ligases, and the observation that p62 is a scaffold for TRAF6 interaction . Therefore, in vitro ubiquitination assays using the E1-E2-E3 system were performed in the presence of either ubiquitin wild type or ubiquitin mutants . If one lysine mutant blocks the ubiquitination of HSP70, it would suggest that the ubiquitination of HSP70 utilizes that specific lysine linkage." ]

[ [ "1a", "Title: TRAF molecules in cell signaling and in human diseases" ], [ "1b", "Passage: in TLR3 signaling ." ], [ "1c", "In contrast, K48-linked polyubiquitination of Regulators of mRNA stability Tristetraprolin TRAF2 TNF-R1 Autophagy proteins Beclin 1 TRAF6 TLR4-, IL-1R-induced autophagy NDP52 TRAF6 TLR3-induced autophagy Regulators of ROS production ECSIT TRAF6 TLR1, 2, 4-induced ROS production TRAFs results in degradation of TRAF proteins by the 26S proteasome." ], [ "1d", "K48-linked E3 ligases of TRAFs include cIAP1/2, Triad3A, AWP1, SOCS2, Siva-1, Numbl and CHIP." ], [ "1e", "For example, upon viral infection, Triad3A is upregulated, and induces K48-linked ubiquitination and degradation of TRAF3, thereby forming a negative feedback loop to halt RIG-I signaling and type I IFN production ." ], [ "1f", "Thus, K48-linked ubiquitination and" ] ]

[ "1c" ]

[ "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: of a nose and throat swab as the gold standard.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: throat swab as the gold standard. See also 7.", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: A classic human study found that, in donors lacking neutralizing antibodies, pre-existing cytotoxic T-cell levels against influenza correlated with reduced virus shedding but not reduced symptoms after influenza virus challenge . Epidemiological studies of the 1957 pandemic, an H1N1 to H2N2 shift, suggested cross-protection, but these studies were too small for statistical significance or lacked laboratory confirmation of self-reported symptoms . A human challenge study found a correlation of CD4 memory with reduced illness duration, viral shedding, and symptom severity .", "Title: Monitoring Influenza Activity in the United States: A Comparison of Traditional Surveillance Systems with Google Flu Trends\nPassage: Correlations among influenza surveillance systems differed by influenza season. The correlation coefficient describing the association between Google Flu Trends and CDC Virus surveillance ranged from 0.67 during the 2003-04 influenza season to 0.94 during the 2004-05 influenza season . The mean correlation coefficient for these comparisons was 0.79 . The correlation between CDC ILI Surveillance and CDC Virus Surveillance ranged from 0.79 during the 2005-06 influenza season to 0.94 during the 2004-05 influenza season. The mean correlation coefficient for these comparisons was 0.86 ." ]

[ [ "2a", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic" ], [ "2b", "Passage: A classic human study found that, in donors lacking neutralizing antibodies, pre-existing cytotoxic T-cell levels against influenza correlated with reduced virus shedding but not reduced symptoms after influenza virus challenge ." ], [ "2c", "Epidemiological studies of the 1957 pandemic, an H1N1 to H2N2 shift, suggested cross-protection, but these studies were too small for statistical significance or lacked laboratory confirmation of self-reported symptoms ." ], [ "2d", "A human challenge study found a correlation of CD4 memory with reduced illness duration, viral shedding, and symptom severity ." ] ]

[ "2b", "2d" ]

[ "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: The grey bands correspond to the mass of the different peptides found and to which part of the amino acid sequence it corresponds to. When the intensity of the MS signal was strong enough, MS/MS analysis was performed and is displayed by the red marks. The MS sequence coverage was greater than 95%.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Within the primate sub-clade, three separate clusters of IFITM1, IFITM2, and IFITM3 were observed. The IFITM1 cluster contains the sequences from all analyzed primates, excluding marmoset and orangutan, and is located at the basal position of the primate sub-clade, indicating that IFITM1 separated earlier than other IR-IFITM genes, including IFITM2 and IFITM3, during the primate evolution. The IFITM2 and IFITM3 clusters only contain sequences from three hominids , indicating that IFITM2 and IFITM3 originated prior to the separation of these three hominids.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Primate and rodent IFITM1, IFITM2 and IFITM3 have similar functions , but do not form a monophyletic cluster , indicating that they do not share the most recent common ancestor and moreover suggesting convergent evolution of IFITM1, IFITM2 and IFITM3 in primates and rodents. Convergently evolved amino acids between primates and rodents were found in the C-terminus of IFITM2 and IFITM3 , a crucial region for antiviral activity, supporting the association between viral infections and the evolution of IR-IFITM genes.", "Title: Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes\nPassage: Here our RNA-seq analysis of the ENA dataset shows that chIFITM1 basal expression levels are very low compared to chIFITM2 and chIFITM3. The analysis of the samples in presence of IFNα, H5N2, H5N1, H5N3, IBDV, IRF7, ALV, Lipopolysaccharide or in heat-stress induced conditions, also shows that higher expression levels can be observed for chIFITM3 and chIFITM2 suggesting a key role for these two proteins as antiviral IFITMs compared to chIFITM1, expression of which is only in the intestinal tract and in the testis. Although immunofluorescence staining seems to suggest that chIFITM2 is analogous to hIFITM1 the genome organisation supported by" ]

[ [ "1a", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates" ], [ "1b", "Passage: Within the primate sub-clade, three separate clusters of IFITM1, IFITM2, and IFITM3 were observed." ], [ "1c", "The IFITM1 cluster contains the sequences from all analyzed primates, excluding marmoset and orangutan, and is located at the basal position of the primate sub-clade, indicating that IFITM1 separated earlier than other IR-IFITM genes, including IFITM2 and IFITM3, during the primate evolution." ], [ "1d", "The IFITM2 and IFITM3 clusters only contain sequences from three hominids , indicating that IFITM2 and IFITM3 originated prior to the separation of these three hominids." ] ]

[ "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: The grey bands correspond to the mass of the different peptides found and to which part of the amino acid sequence it corresponds to. When the intensity of the MS signal was strong enough, MS/MS analysis was performed and is displayed by the red marks. The MS sequence coverage was greater than 95%.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Within the primate sub-clade, three separate clusters of IFITM1, IFITM2, and IFITM3 were observed. The IFITM1 cluster contains the sequences from all analyzed primates, excluding marmoset and orangutan, and is located at the basal position of the primate sub-clade, indicating that IFITM1 separated earlier than other IR-IFITM genes, including IFITM2 and IFITM3, during the primate evolution. The IFITM2 and IFITM3 clusters only contain sequences from three hominids , indicating that IFITM2 and IFITM3 originated prior to the separation of these three hominids.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Primate and rodent IFITM1, IFITM2 and IFITM3 have similar functions , but do not form a monophyletic cluster , indicating that they do not share the most recent common ancestor and moreover suggesting convergent evolution of IFITM1, IFITM2 and IFITM3 in primates and rodents. Convergently evolved amino acids between primates and rodents were found in the C-terminus of IFITM2 and IFITM3 , a crucial region for antiviral activity, supporting the association between viral infections and the evolution of IR-IFITM genes.", "Title: Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes\nPassage: Here our RNA-seq analysis of the ENA dataset shows that chIFITM1 basal expression levels are very low compared to chIFITM2 and chIFITM3. The analysis of the samples in presence of IFNα, H5N2, H5N1, H5N3, IBDV, IRF7, ALV, Lipopolysaccharide or in heat-stress induced conditions, also shows that higher expression levels can be observed for chIFITM3 and chIFITM2 suggesting a key role for these two proteins as antiviral IFITMs compared to chIFITM1, expression of which is only in the intestinal tract and in the testis. Although immunofluorescence staining seems to suggest that chIFITM2 is analogous to hIFITM1 the genome organisation supported by" ]

[ [ "2a", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates" ], [ "2b", "Passage: Primate and rodent IFITM1, IFITM2 and IFITM3 have similar functions , but do not form a monophyletic cluster , indicating that they do not share the most recent common ancestor and moreover suggesting convergent evolution of IFITM1, IFITM2 and IFITM3 in primates and rodents." ], [ "2c", "Convergently evolved amino acids between primates and rodents were found in the C-terminus of IFITM2 and IFITM3 , a crucial region for antiviral activity, supporting the association between viral infections and the evolution of IR-IFITM genes." ] ]

[ "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: The grey bands correspond to the mass of the different peptides found and to which part of the amino acid sequence it corresponds to. When the intensity of the MS signal was strong enough, MS/MS analysis was performed and is displayed by the red marks. The MS sequence coverage was greater than 95%.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Within the primate sub-clade, three separate clusters of IFITM1, IFITM2, and IFITM3 were observed. The IFITM1 cluster contains the sequences from all analyzed primates, excluding marmoset and orangutan, and is located at the basal position of the primate sub-clade, indicating that IFITM1 separated earlier than other IR-IFITM genes, including IFITM2 and IFITM3, during the primate evolution. The IFITM2 and IFITM3 clusters only contain sequences from three hominids , indicating that IFITM2 and IFITM3 originated prior to the separation of these three hominids.", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: Primate and rodent IFITM1, IFITM2 and IFITM3 have similar functions , but do not form a monophyletic cluster , indicating that they do not share the most recent common ancestor and moreover suggesting convergent evolution of IFITM1, IFITM2 and IFITM3 in primates and rodents. Convergently evolved amino acids between primates and rodents were found in the C-terminus of IFITM2 and IFITM3 , a crucial region for antiviral activity, supporting the association between viral infections and the evolution of IR-IFITM genes.", "Title: Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes\nPassage: Here our RNA-seq analysis of the ENA dataset shows that chIFITM1 basal expression levels are very low compared to chIFITM2 and chIFITM3. The analysis of the samples in presence of IFNα, H5N2, H5N1, H5N3, IBDV, IRF7, ALV, Lipopolysaccharide or in heat-stress induced conditions, also shows that higher expression levels can be observed for chIFITM3 and chIFITM2 suggesting a key role for these two proteins as antiviral IFITMs compared to chIFITM1, expression of which is only in the intestinal tract and in the testis. Although immunofluorescence staining seems to suggest that chIFITM2 is analogous to hIFITM1 the genome organisation supported by" ]

[ [ "3a", "Title: Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes" ], [ "3b", "Passage: Here our RNA-seq analysis of the ENA dataset shows that chIFITM1 basal expression levels are very low compared to chIFITM2 and chIFITM3." ], [ "3c", "The analysis of the samples in presence of IFNα, H5N2, H5N1, H5N3, IBDV, IRF7, ALV, Lipopolysaccharide or in heat-stress induced conditions, also shows that higher expression levels can be observed for chIFITM3 and chIFITM2 suggesting a key role for these two proteins as antiviral IFITMs compared to chIFITM1, expression of which is only in the intestinal tract and in the testis." ], [ "3d", "Although immunofluorescence staining seems to suggest that chIFITM2 is analogous to hIFITM1 the genome organisation supported by" ] ]

[ "1b", "1c", "1d", "2b", "2c", "3b", "3c" ]

[ "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: could be affected by 2019-nCoV.", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes\nPassage: We quickly identified the etiological agent, termed 2019-nCoV . The newly identified virus is an SARS-related virus but shares only 74.5% genome identity to SARS-CoV . We developed molecular detection tools based on viral spike genes. Our previous studies indicate that qPCR method can be used for the detection of 2019-nCoV in oral swabs or in bronchoalveolar lavage fluid .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: can however be found in up to 30% ofpatients negative for influenza viruses . Chinese scientists in Wuhan, who had to deal with an increasing number of acute respiratory tract diseases resembling viral pneumonia, performed deep sequencing analysis from samples taken from the lower respiratory tract and found a \"novel\" coronavirus. The sequence of the complete genome was made public. At the same time, however, the notice from Wuhan brought to mind the SARS- and MERS-epidemics. The measures taken by the Chinese- and WHO-authorities are now well known.", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: 9." ]

[ [ "1a", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes" ], [ "1b", "Passage: We quickly identified the etiological agent, termed 2019-nCoV ." ], [ "1c", "The newly identified virus is an SARS-related virus but shares only 74.5% genome identity to SARS-CoV ." ], [ "1d", "We developed molecular detection tools based on viral spike genes." ], [ "1e", "Our previous studies indicate that qPCR method can be used for the detection of 2019-nCoV in oral swabs or in bronchoalveolar lavage fluid ." ] ]

[ "1e", "2b", "2c" ]

[ "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: could be affected by 2019-nCoV.", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes\nPassage: We quickly identified the etiological agent, termed 2019-nCoV . The newly identified virus is an SARS-related virus but shares only 74.5% genome identity to SARS-CoV . We developed molecular detection tools based on viral spike genes. Our previous studies indicate that qPCR method can be used for the detection of 2019-nCoV in oral swabs or in bronchoalveolar lavage fluid .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: can however be found in up to 30% ofpatients negative for influenza viruses . Chinese scientists in Wuhan, who had to deal with an increasing number of acute respiratory tract diseases resembling viral pneumonia, performed deep sequencing analysis from samples taken from the lower respiratory tract and found a \"novel\" coronavirus. The sequence of the complete genome was made public. At the same time, however, the notice from Wuhan brought to mind the SARS- and MERS-epidemics. The measures taken by the Chinese- and WHO-authorities are now well known.", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: 9." ]

[ [ "2a", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus" ], [ "2b", "Passage: can however be found in up to 30% ofpatients negative for influenza viruses ." ], [ "2c", "Chinese scientists in Wuhan, who had to deal with an increasing number of acute respiratory tract diseases resembling viral pneumonia, performed deep sequencing analysis from samples taken from the lower respiratory tract and found a \"novel\" coronavirus." ], [ "2d", "The sequence of the complete genome was made public." ], [ "2e", "At the same time, however, the notice from Wuhan brought to mind the SARS- and MERS-epidemics." ], [ "2f", "The measures taken by the Chinese- and WHO-authorities are now well known." ] ]

[ "1e", "2b", "2c" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Baculovirus has been extensively used to produce recombinant proteins. Recently, a baculovirus-derived recombinant HA vaccine was approved for human use and was first available for use in the United States for the 2013-2014 influenza season . Baculoviruses have also been explored as vaccine vectors. Baculoviruses have a number of advantages as vaccine vectors. The viruses have been extensively studied for protein expression and for pesticide use and so are readily manipulated. The vectors can accommodate large gene insertions, show limited cytopathic effect in mammalian cells, and have been shown to infect and express genes of interest in a spectrum of", "Title: Viral vector-based influenza vaccines\nPassage: Baculoviruses are extensively used as tool to express and produce influenza virus proteins. Currently, a recombinant HA protein vaccine produced in baculoviruses was approved for human use in the United States. However, baculoviruses have also been explored as live vaccine vectors. Since baculoviruses can readily be manipulated to express foreign antigens and can infect mammalian cells without causing cytopathic effect they are potentially promising vaccine vectors for influenza . 171 Initially, it was reported that vaccination with recombinant baculovirus expressing the HA gene of influenza virus could induce complete protection from homologous challenge infection. 172 Interestingly, in this study the", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is growing data on the potential use of baculovirus or pseudotyped baculovirus as a vaccine vector, efficacy data in mammalian animal models other than mice is lacking. There is also no data on the safety in humans, reducing enthusiasm for baculovirus as a vaccine vector for influenza at this time.", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Besides the extra peace of mind that baculovirus-expressed vaccines have over inactivated vaccines, no large-scale bio-containments are required during the manufacturing of baculovirus-expressed vaccines, since baculovirus does not cause harm to human beings and its handling only requires biosafety class 1 practices . In contrast, large bio-containments are required for inactivated vaccine production, especially when handling the pathogens before and during the inactivation process. As no bio-containments or extra safety equipment are required, this would translate to a much lower production cost for baculovirus-expressed vaccines as compared to the cost of producing inactivated vaccines." ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: Baculovirus has been extensively used to produce recombinant proteins." ], [ "0c", "Recently, a baculovirus-derived recombinant HA vaccine was approved for human use and was first available for use in the United States for the 2013-2014 influenza season ." ], [ "0d", "Baculoviruses have also been explored as vaccine vectors." ], [ "0e", "Baculoviruses have a number of advantages as vaccine vectors." ], [ "0f", "The viruses have been extensively studied for protein expression and for pesticide use and so are readily manipulated." ], [ "0g", "The vectors can accommodate large gene insertions, show limited cytopathic effect in mammalian cells, and have been shown to infect and express genes of interest in a spectrum of" ] ]

[ "0c", "1c" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Baculovirus has been extensively used to produce recombinant proteins. Recently, a baculovirus-derived recombinant HA vaccine was approved for human use and was first available for use in the United States for the 2013-2014 influenza season . Baculoviruses have also been explored as vaccine vectors. Baculoviruses have a number of advantages as vaccine vectors. The viruses have been extensively studied for protein expression and for pesticide use and so are readily manipulated. The vectors can accommodate large gene insertions, show limited cytopathic effect in mammalian cells, and have been shown to infect and express genes of interest in a spectrum of", "Title: Viral vector-based influenza vaccines\nPassage: Baculoviruses are extensively used as tool to express and produce influenza virus proteins. Currently, a recombinant HA protein vaccine produced in baculoviruses was approved for human use in the United States. However, baculoviruses have also been explored as live vaccine vectors. Since baculoviruses can readily be manipulated to express foreign antigens and can infect mammalian cells without causing cytopathic effect they are potentially promising vaccine vectors for influenza . 171 Initially, it was reported that vaccination with recombinant baculovirus expressing the HA gene of influenza virus could induce complete protection from homologous challenge infection. 172 Interestingly, in this study the", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is growing data on the potential use of baculovirus or pseudotyped baculovirus as a vaccine vector, efficacy data in mammalian animal models other than mice is lacking. There is also no data on the safety in humans, reducing enthusiasm for baculovirus as a vaccine vector for influenza at this time.", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Besides the extra peace of mind that baculovirus-expressed vaccines have over inactivated vaccines, no large-scale bio-containments are required during the manufacturing of baculovirus-expressed vaccines, since baculovirus does not cause harm to human beings and its handling only requires biosafety class 1 practices . In contrast, large bio-containments are required for inactivated vaccine production, especially when handling the pathogens before and during the inactivation process. As no bio-containments or extra safety equipment are required, this would translate to a much lower production cost for baculovirus-expressed vaccines as compared to the cost of producing inactivated vaccines." ]

[ [ "1a", "Title: Viral vector-based influenza vaccines" ], [ "1b", "Passage: Baculoviruses are extensively used as tool to express and produce influenza virus proteins." ], [ "1c", "Currently, a recombinant HA protein vaccine produced in baculoviruses was approved for human use in the United States." ], [ "1d", "However, baculoviruses have also been explored as live vaccine vectors." ], [ "1e", "Since baculoviruses can readily be manipulated to express foreign antigens and can infect mammalian cells without causing cytopathic effect they are potentially promising vaccine vectors for influenza ." ], [ "1f", "171 Initially, it was reported that vaccination with recombinant baculovirus expressing the HA gene of influenza virus could induce complete protection from homologous challenge infection." ], [ "1g", "172 Interestingly, in this study the" ] ]

[ "0c", "1c" ]

[ "Title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919\nPassage: suppression of important antiviral immune responses . In addition, other influenza strains, such as fatal H5N1 infections in humans, have also been associated with the deleterious consequences of an excessive inflammatory response . Ultimately, the case fatality rate was so severe in young adults during the 1918-1919 pandemic that the average life expectancy rate in the US dropped by~12 years .", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide . In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality . This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 . However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the", "Title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919\nPassage: Although mortality rates were low, the pandemic would ultimately claim between 500,000 and 2 million lives . In April 2009, the 2009-2010 swine flu pandemic, subtype H1N1, began with nearly simultaneous outbreaks in Mexico and the US, before spreading globally over the next 6 weeks. While the 2009-2010 pandemic had a low associated case fatality rate, resulting in 284,000 deaths worldwide, it had devastating effects on global economies and healthcare networks . Conventionally, influenza pandemics result in the extinction of previously circulating virus strains; however, this view was complicated by events in 1977. Although H1N1 was replaced by H2N2 as", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Spain experienced one of the highest excess mortality rates during the 1918 influenza pandemic in Europe , although this country did not take part in World War I. Perhaps this pandemic outcome is associated with the fact that Spain was going through a demographic transition and experiencing elevated death rates that were only comparable to those of eastern Europe. Of note, the life expectancy in Spain was 41 years in 1910 and 40 years in 1920 ." ]

[ [ "0a", "Title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919" ], [ "0b", "Passage: suppression of important antiviral immune responses ." ], [ "0c", "In addition, other influenza strains, such as fatal H5N1 infections in humans, have also been associated with the deleterious consequences of an excessive inflammatory response ." ], [ "0d", "Ultimately, the case fatality rate was so severe in young adults during the 1918-1919 pandemic that the average life expectancy rate in the US dropped by~12 years ." ] ]

[ "0d", "1b", "1d" ]

[ "Title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919\nPassage: suppression of important antiviral immune responses . In addition, other influenza strains, such as fatal H5N1 infections in humans, have also been associated with the deleterious consequences of an excessive inflammatory response . Ultimately, the case fatality rate was so severe in young adults during the 1918-1919 pandemic that the average life expectancy rate in the US dropped by~12 years .", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide . In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality . This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 . However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the", "Title: A year of terror and a century of reflection: perspectives on the great influenza pandemic of 1918–1919\nPassage: Although mortality rates were low, the pandemic would ultimately claim between 500,000 and 2 million lives . In April 2009, the 2009-2010 swine flu pandemic, subtype H1N1, began with nearly simultaneous outbreaks in Mexico and the US, before spreading globally over the next 6 weeks. While the 2009-2010 pandemic had a low associated case fatality rate, resulting in 284,000 deaths worldwide, it had devastating effects on global economies and healthcare networks . Conventionally, influenza pandemics result in the extinction of previously circulating virus strains; however, this view was complicated by events in 1977. Although H1N1 was replaced by H2N2 as", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Spain experienced one of the highest excess mortality rates during the 1918 influenza pandemic in Europe , although this country did not take part in World War I. Perhaps this pandemic outcome is associated with the fact that Spain was going through a demographic transition and experiencing elevated death rates that were only comparable to those of eastern Europe. Of note, the life expectancy in Spain was 41 years in 1910 and 40 years in 1920 ." ]

[ [ "1a", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain" ], [ "1b", "Passage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide ." ], [ "1c", "In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality ." ], [ "1d", "This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 ." ], [ "1e", "However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the" ] ]

[ "0d", "1b", "1d" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases , which result in frequent mutations and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics . However, sensitive, validated reverse transcriptase real-time polymerase chain reaction -based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations . Subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase 4 ; that MERS-CoV has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than SARS-CoV; is widespread in DCs; has the potential to infect other animals and that MERS kills" ]

[ [ "0a", "Title: Host resilience to emerging coronaviruses" ], [ "0b", "Passage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity." ], [ "0c", "The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect." ], [ "0d", "SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 ." ], [ "0e", "Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure ." ], [ "0f", "SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it" ] ]

[ "0d", "1d", "2c", "3d" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases , which result in frequent mutations and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics . However, sensitive, validated reverse transcriptase real-time polymerase chain reaction -based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations . Subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase 4 ; that MERS-CoV has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than SARS-CoV; is widespread in DCs; has the potential to infect other animals and that MERS kills" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: MERS and SARS have some clinical similarities but they also diverge significantly ." ], [ "1c", "Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities." ], [ "1d", "For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV." ] ]

[ "0d", "1d", "2c", "3d" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases , which result in frequent mutations and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics . However, sensitive, validated reverse transcriptase real-time polymerase chain reaction -based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations . Subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase 4 ; that MERS-CoV has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than SARS-CoV; is widespread in DCs; has the potential to infect other animals and that MERS kills" ]

[ [ "2a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "2b", "Passage: Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered." ], [ "2c", "ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV ." ], [ "2d", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases." ], [ "2e", "In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems ." ], [ "2f", "Coronaviruses have error-prone RNA-dependent RNA polymerases , which result in frequent mutations and" ] ]

[ "0d", "1d", "2c", "3d" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases , which result in frequent mutations and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics . However, sensitive, validated reverse transcriptase real-time polymerase chain reaction -based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations . Subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase 4 ; that MERS-CoV has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than SARS-CoV; is widespread in DCs; has the potential to infect other animals and that MERS kills" ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: The first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics ." ], [ "3c", "However, sensitive, validated reverse transcriptase real-time polymerase chain reaction -based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations ." ], [ "3d", "Subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase 4 ; that MERS-CoV has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than SARS-CoV; is widespread in DCs; has the potential to infect other animals and that MERS kills" ] ]

[ "0d", "1d", "2c", "3d" ]

[ "Title: Discovery and Genomic Characterization of a Novel Bat Sapovirus with Unusual Genomic Features and Phylogenetic Position\nPassage: the seasonality of its detection or its host specificity. To address these limitations, long-term follow-up studies would be required to identify sufficient positive samples with associated clinical data. Increasing the scale of surveillance would also help, though there are practical geographical and logistic constraints in our locality.", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: The pathogenicity of these viruses is typically species-dependent, as is the severity of infection; they infect mainly their natural hosts and/or species that are closely related. Certain virus infections, however, can cross the species barrier, with the prime example being the zoonotic SARS-CoV, a novel coronavirus that is thought to have originated from bats before it adapted to its intermediate host, civet cats, and finally to humans . Bat colonies, which are scattered worldwide, are widely known to play host to a variety of coronaviral and adenoviral pathogens while acting as natural wildlife reservoirs of these viruses .", "Title: Finding and identifying the viral needle in the metagenomic haystack: trends and challenges\nPassage: approaches is overspecificity, which makes classification of unknown sequences problematic. This limitation can be particularly acute given the known very high intraspecific variability existing in some viral species or higher order taxa. For example, current criteria of the International Committee for the taxonomy of viruses tolerate up to 28% of nucleotide sequence divergence for the polymerase or capsid protein genes for isolates of a same species in the Betaflexiviridae family and a similar level of divergence at the whole genome level in the Potyviridae family .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first open reading frames have become a key diagnostic and taxonomic target for CoV species identification. With less than 80 % identity between the amino acid sequence of MERS ORF 1ab and betacoronavirus relatives, Tylonycteris bat HKU4 and Pipistrellus bat HKU5, it can be concluded that it is a novel and distinct virus. MERS-CoV is predicted to encode ten open reading frames with 5' and 3' untranslated regions . The structural proteins include the spike , envelope , membrane and nucleocapsid . The products of ORF1a and ORF1b are predicted to encode nonstructural proteins." ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: The first open reading frames have become a key diagnostic and taxonomic target for CoV species identification." ], [ "3c", "With less than 80 % identity between the amino acid sequence of MERS ORF 1ab and betacoronavirus relatives, Tylonycteris bat HKU4 and Pipistrellus bat HKU5, it can be concluded that it is a novel and distinct virus." ], [ "3d", "MERS-CoV is predicted to encode ten open reading frames with 5' and 3' untranslated regions ." ], [ "3e", "The structural proteins include the spike , envelope , membrane and nucleocapsid ." ], [ "3f", "The products of ORF1a and ORF1b are predicted to encode nonstructural proteins." ] ]

[ "3b" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In humans, overt disease was given the name Middle East respiratory syndrome, with the acronym MERS. From intermittent animal-to-human spill-over events, the MERS-CoV spreads sporadically among people, causing more severe disease among older adults, especially males, with pre-existing diseases. The spread of MERS-CoV among humans has often been associated with outbreaks in hospitals, with around 20 % of all cases to date involving healthcare workers .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Qatar for care . The new virus was initially called novel coronavirus and subsequentlty entitled the Middle East respiratoy syndrome coronavirus . As of 2 nd of September 2015, there have been 1,493 detections of viral RNA or virus-specific antibodies across 26 countries confirmed by the World Health Organization , with over a third of the positive people dying .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: In humans, overt disease was given the name Middle East respiratory syndrome, with the acronym MERS." ], [ "0c", "From intermittent animal-to-human spill-over events, the MERS-CoV spreads sporadically among people, causing more severe disease among older adults, especially males, with pre-existing diseases." ], [ "0d", "The spread of MERS-CoV among humans has often been associated with outbreaks in hospitals, with around 20 % of all cases to date involving healthcare workers ." ] ]

[ "0b", "2c", "3a" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In humans, overt disease was given the name Middle East respiratory syndrome, with the acronym MERS. From intermittent animal-to-human spill-over events, the MERS-CoV spreads sporadically among people, causing more severe disease among older adults, especially males, with pre-existing diseases. The spread of MERS-CoV among humans has often been associated with outbreaks in hospitals, with around 20 % of all cases to date involving healthcare workers .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Qatar for care . The new virus was initially called novel coronavirus and subsequentlty entitled the Middle East respiratoy syndrome coronavirus . As of 2 nd of September 2015, there have been 1,493 detections of viral RNA or virus-specific antibodies across 26 countries confirmed by the World Health Organization , with over a third of the positive people dying .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: Qatar for care ." ], [ "2c", "The new virus was initially called novel coronavirus and subsequentlty entitled the Middle East respiratoy syndrome coronavirus ." ], [ "2d", "As of 2 nd of September 2015, there have been 1,493 detections of viral RNA or virus-specific antibodies across 26 countries confirmed by the World Health Organization , with over a third of the positive people dying ." ] ]

[ "0b", "2c", "3a" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In humans, overt disease was given the name Middle East respiratory syndrome, with the acronym MERS. From intermittent animal-to-human spill-over events, the MERS-CoV spreads sporadically among people, causing more severe disease among older adults, especially males, with pre-existing diseases. The spread of MERS-CoV among humans has often been associated with outbreaks in hospitals, with around 20 % of all cases to date involving healthcare workers .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Qatar for care . The new virus was initially called novel coronavirus and subsequentlty entitled the Middle East respiratoy syndrome coronavirus . As of 2 nd of September 2015, there have been 1,493 detections of viral RNA or virus-specific antibodies across 26 countries confirmed by the World Health Organization , with over a third of the positive people dying .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown" ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively." ], [ "3c", "The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia ." ], [ "3d", "Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels ." ], [ "3e", "MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections." ], [ "3f", "Precisely how virus transmits to humans remains unknown" ] ]

[ "0b", "2c", "3a" ]

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: It is Unlikely That Influenza Viruses Will Cause a Pandemic Again Like What Happened in 1918 and 1919\nPassage: Additionally, a significant number of viruses can cause influenza-like syndromes, such as rhinovirus, parainfluenza virus, adenovirus, coronavirus, respiratory syncytial virus, Coxsackie B virus, echovirus, and metapneumovirus . Some of the above-mentioned viruses like adenovirus and mutated coronavirus could cause problems that are comparable to influenza viruses ." ]

[ [ "0a", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2" ], [ "0b", "Passage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV." ], [ "0c", "The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity ." ] ]

[ "0b", "0c", "1c", "1d", "2b", "2c" ]

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: It is Unlikely That Influenza Viruses Will Cause a Pandemic Again Like What Happened in 1918 and 1919\nPassage: Additionally, a significant number of viruses can cause influenza-like syndromes, such as rhinovirus, parainfluenza virus, adenovirus, coronavirus, respiratory syncytial virus, Coxsackie B virus, echovirus, and metapneumovirus . Some of the above-mentioned viruses like adenovirus and mutated coronavirus could cause problems that are comparable to influenza viruses ." ]

[ [ "1a", "Title: CDC Summary 21 MAR 2020," ], [ "1b", "Passage: COVID-19 is caused by a coronavirus." ], [ "1c", "Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats." ], [ "1d", "Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus ." ] ]

[ "0b", "0c", "1c", "1d", "2b", "2c" ]

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: It is Unlikely That Influenza Viruses Will Cause a Pandemic Again Like What Happened in 1918 and 1919\nPassage: Additionally, a significant number of viruses can cause influenza-like syndromes, such as rhinovirus, parainfluenza virus, adenovirus, coronavirus, respiratory syncytial virus, Coxsackie B virus, echovirus, and metapneumovirus . Some of the above-mentioned viruses like adenovirus and mutated coronavirus could cause problems that are comparable to influenza viruses ." ]

[ [ "2a", "Title: CDC Summary 21 MAR 2020," ], [ "2b", "Passage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV." ], [ "2c", "All three of these viruses have their origins in bats." ], [ "2d", "The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir." ] ]

[ "0b", "0c", "1c", "1d", "2b", "2c" ]

[ "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests . The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups . The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups .", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: decade and it has been reported to protect young individuals better than IIV . Importantly, recent studies showed that LAIV can pre-sensitize the population and, subsequently, synergistically boost the efficacy of IIV . It should be noted that the use of LAIV in poultry requires strict safety standards due to concerns about the possibility that wild type strains may circulate in domestic poultry without apparent clinical symptoms, undergo genetic reassortment with the vaccine virus, and produce novel virulent strains . An ideal poultry LAIV should not be able to revert to wild type virus or undergo reassortment with field strains.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: protective efficacy of LAIV in 1-day-old chickens.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: One of the perceived risks of vaccinating commercial poultry against influenza is the possibility of the vaccine protecting birds from disease without preventing replication and spread of the virus. We have demonstrated that a single dose of LAIV is able to induce stronger innate and mucosal IgA responses and protect young immunologically immature chickens better than a single dose of conventional IIV. Most importantly, priming with LAIV led to a synergistic serum antibody induction by IIV and enhancement of antibody cross-reactivity, thereby increasing the chance of protection from distantly related strains. Our prime-boost vaccine strategy requires further improvements to address" ]

[ [ "0a", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens" ], [ "0b", "Passage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests ." ], [ "0c", "The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups ." ], [ "0d", "The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups ." ] ]

[ "0b", "0c", "0d", "1b", "1c", "3c", "3d" ]

[ "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests . The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups . The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups .", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: decade and it has been reported to protect young individuals better than IIV . Importantly, recent studies showed that LAIV can pre-sensitize the population and, subsequently, synergistically boost the efficacy of IIV . It should be noted that the use of LAIV in poultry requires strict safety standards due to concerns about the possibility that wild type strains may circulate in domestic poultry without apparent clinical symptoms, undergo genetic reassortment with the vaccine virus, and produce novel virulent strains . An ideal poultry LAIV should not be able to revert to wild type virus or undergo reassortment with field strains.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: protective efficacy of LAIV in 1-day-old chickens.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: One of the perceived risks of vaccinating commercial poultry against influenza is the possibility of the vaccine protecting birds from disease without preventing replication and spread of the virus. We have demonstrated that a single dose of LAIV is able to induce stronger innate and mucosal IgA responses and protect young immunologically immature chickens better than a single dose of conventional IIV. Most importantly, priming with LAIV led to a synergistic serum antibody induction by IIV and enhancement of antibody cross-reactivity, thereby increasing the chance of protection from distantly related strains. Our prime-boost vaccine strategy requires further improvements to address" ]

[ [ "1a", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens" ], [ "1b", "Passage: decade and it has been reported to protect young individuals better than IIV ." ], [ "1c", "Importantly, recent studies showed that LAIV can pre-sensitize the population and, subsequently, synergistically boost the efficacy of IIV ." ], [ "1d", "It should be noted that the use of LAIV in poultry requires strict safety standards due to concerns about the possibility that wild type strains may circulate in domestic poultry without apparent clinical symptoms, undergo genetic reassortment with the vaccine virus, and produce novel virulent strains ." ], [ "1e", "An ideal poultry LAIV should not be able to revert to wild type virus or undergo reassortment with field strains." ] ]

[ "0b", "0c", "0d", "1b", "1c", "3c", "3d" ]

[ "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests . The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups . The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups .", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: decade and it has been reported to protect young individuals better than IIV . Importantly, recent studies showed that LAIV can pre-sensitize the population and, subsequently, synergistically boost the efficacy of IIV . It should be noted that the use of LAIV in poultry requires strict safety standards due to concerns about the possibility that wild type strains may circulate in domestic poultry without apparent clinical symptoms, undergo genetic reassortment with the vaccine virus, and produce novel virulent strains . An ideal poultry LAIV should not be able to revert to wild type virus or undergo reassortment with field strains.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: protective efficacy of LAIV in 1-day-old chickens.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: One of the perceived risks of vaccinating commercial poultry against influenza is the possibility of the vaccine protecting birds from disease without preventing replication and spread of the virus. We have demonstrated that a single dose of LAIV is able to induce stronger innate and mucosal IgA responses and protect young immunologically immature chickens better than a single dose of conventional IIV. Most importantly, priming with LAIV led to a synergistic serum antibody induction by IIV and enhancement of antibody cross-reactivity, thereby increasing the chance of protection from distantly related strains. Our prime-boost vaccine strategy requires further improvements to address" ]

[ [ "3a", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens" ], [ "3b", "Passage: One of the perceived risks of vaccinating commercial poultry against influenza is the possibility of the vaccine protecting birds from disease without preventing replication and spread of the virus." ], [ "3c", "We have demonstrated that a single dose of LAIV is able to induce stronger innate and mucosal IgA responses and protect young immunologically immature chickens better than a single dose of conventional IIV." ], [ "3d", "Most importantly, priming with LAIV led to a synergistic serum antibody induction by IIV and enhancement of antibody cross-reactivity, thereby increasing the chance of protection from distantly related strains." ], [ "3e", "Our prime-boost vaccine strategy requires further improvements to address" ] ]

[ "0b", "0c", "0d", "1b", "1c", "3c", "3d" ]

[ "Title: Estimating the number of infections and the impact of non-\nPassage: Case-based", "Title: Estimating the number of infections and the impact of non-\nPassage: Case-based", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: staff to undertake personal measures to reduce infection, such as wearing masks at all instances", "Title: Estimating the number of infections and the impact of non-\nPassage: and in some examples have implemented these interventions all on a single day." ]

[ [ "3a", "Title: Estimating the number of infections and the impact of non-" ], [ "3b", "Passage: and in some examples have implemented these interventions all on a single day." ] ]

[ "3b" ]

[ "Title: Estimating the number of infections and the impact of non-\nPassage: Austria 1.1%", "Title: Estimating the number of infections and the impact of non-\nPassage: Austria measures Implemented at lockdown.22 16/3/2020", "Title: Estimating the number of infections and the impact of non-\nPassage: infected as of March 28th, giving an attack rate of 9.8% of the population . Spain", "Title: Estimating the number of infections and the impact of non-\nPassage: Table l: Posterior model estimates of percentage of total population infected as of 28th March 2020." ]

[ [ "0a", "Title: Estimating the number of infections and the impact of non-" ], [ "0b", "Passage: Austria 1.1%" ] ]

[ "0b" ]

[ "Title: Zika virus-induced acute myelitis and motor deficits in adult interferon αβ/γ receptor knockout mice\nPassage: The fact that relative CMAP amplitude after spinal cord stimulation did not statistically correlate with VPS score suggests that damage upstream of spinal motor neurons may contribute to the hindlimb deficits. For example, CMAP amplitude was not reduced in two infected mice with overt paralysis . Paralysis in these animals could be caused by motor cortex, cerebellum, or brainstem dysfunction, as extensive infection was observed in these areas of the brain. While upper motor neuron disease is associated with rigid, rather than flaccid paralysis, we occasionally saw symptoms that could be interpreted as rigidity, such as walking with high haunches", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: We defined disability as the inability to independently carry out one or more activities of daily living, which included getting in or out of bed, walking across a room, bathing or showering, using the toilet, dressing, cutting food and eating. This definition of disability captures individuals who have difficulty maintaining independence and require supportive care.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: The most common causes of disability globally are adult-onset hearing loss and refractive errors. Mental disorders such as depression, alcohol use disorders and psychoses are also among the 20 leading causes of disability . The pattern differs between the highincome countries and the low-and middle-income countries. In the lower income countries, many more people are disabled due to preventable causes such as unintentional injuries and infertility arising from unsafe abortion and maternal sepsis. The data also demonstrate the lack of interventions for easily treated conditions such as hearing loss, refractive errors and cataracts in low-income countries. Disability due to mental", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: Dementia was defined on the basis of the coexistence of cognitive impairment and disability, or a report of a doctor diagnosis of dementia by the participant or caregiver. Cognitive impairment was defined as an impairment in two or more functional tests or a score higher than 3.6 on the Informant Questionnaire on Cognitive Decline ." ]

[ [ "0a", "Title: Zika virus-induced acute myelitis and motor deficits in adult interferon αβ/γ receptor knockout mice" ], [ "0b", "Passage: The fact that relative CMAP amplitude after spinal cord stimulation did not statistically correlate with VPS score suggests that damage upstream of spinal motor neurons may contribute to the hindlimb deficits." ], [ "0c", "For example, CMAP amplitude was not reduced in two infected mice with overt paralysis ." ], [ "0d", "Paralysis in these animals could be caused by motor cortex, cerebellum, or brainstem dysfunction, as extensive infection was observed in these areas of the brain." ], [ "0e", "While upper motor neuron disease is associated with rigid, rather than flaccid paralysis, we occasionally saw symptoms that could be interpreted as rigidity, such as walking with high haunches" ] ]

[ "0b", "0d", "1a", "1c", "2b", "2c", "2e", "3b", "3c" ]

[ "Title: Zika virus-induced acute myelitis and motor deficits in adult interferon αβ/γ receptor knockout mice\nPassage: The fact that relative CMAP amplitude after spinal cord stimulation did not statistically correlate with VPS score suggests that damage upstream of spinal motor neurons may contribute to the hindlimb deficits. For example, CMAP amplitude was not reduced in two infected mice with overt paralysis . Paralysis in these animals could be caused by motor cortex, cerebellum, or brainstem dysfunction, as extensive infection was observed in these areas of the brain. While upper motor neuron disease is associated with rigid, rather than flaccid paralysis, we occasionally saw symptoms that could be interpreted as rigidity, such as walking with high haunches", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: We defined disability as the inability to independently carry out one or more activities of daily living, which included getting in or out of bed, walking across a room, bathing or showering, using the toilet, dressing, cutting food and eating. This definition of disability captures individuals who have difficulty maintaining independence and require supportive care.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: The most common causes of disability globally are adult-onset hearing loss and refractive errors. Mental disorders such as depression, alcohol use disorders and psychoses are also among the 20 leading causes of disability . The pattern differs between the highincome countries and the low-and middle-income countries. In the lower income countries, many more people are disabled due to preventable causes such as unintentional injuries and infertility arising from unsafe abortion and maternal sepsis. The data also demonstrate the lack of interventions for easily treated conditions such as hearing loss, refractive errors and cataracts in low-income countries. Disability due to mental", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: Dementia was defined on the basis of the coexistence of cognitive impairment and disability, or a report of a doctor diagnosis of dementia by the participant or caregiver. Cognitive impairment was defined as an impairment in two or more functional tests or a score higher than 3.6 on the Informant Questionnaire on Cognitive Decline ." ]

[ [ "1a", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study" ], [ "1b", "Passage: We defined disability as the inability to independently carry out one or more activities of daily living, which included getting in or out of bed, walking across a room, bathing or showering, using the toilet, dressing, cutting food and eating." ], [ "1c", "This definition of disability captures individuals who have difficulty maintaining independence and require supportive care." ] ]

[ "0b", "0d", "1a", "1c", "2b", "2c", "2e", "3b", "3c" ]

[ "Title: Zika virus-induced acute myelitis and motor deficits in adult interferon αβ/γ receptor knockout mice\nPassage: The fact that relative CMAP amplitude after spinal cord stimulation did not statistically correlate with VPS score suggests that damage upstream of spinal motor neurons may contribute to the hindlimb deficits. For example, CMAP amplitude was not reduced in two infected mice with overt paralysis . Paralysis in these animals could be caused by motor cortex, cerebellum, or brainstem dysfunction, as extensive infection was observed in these areas of the brain. While upper motor neuron disease is associated with rigid, rather than flaccid paralysis, we occasionally saw symptoms that could be interpreted as rigidity, such as walking with high haunches", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: We defined disability as the inability to independently carry out one or more activities of daily living, which included getting in or out of bed, walking across a room, bathing or showering, using the toilet, dressing, cutting food and eating. This definition of disability captures individuals who have difficulty maintaining independence and require supportive care.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: The most common causes of disability globally are adult-onset hearing loss and refractive errors. Mental disorders such as depression, alcohol use disorders and psychoses are also among the 20 leading causes of disability . The pattern differs between the highincome countries and the low-and middle-income countries. In the lower income countries, many more people are disabled due to preventable causes such as unintentional injuries and infertility arising from unsafe abortion and maternal sepsis. The data also demonstrate the lack of interventions for easily treated conditions such as hearing loss, refractive errors and cataracts in low-income countries. Disability due to mental", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: Dementia was defined on the basis of the coexistence of cognitive impairment and disability, or a report of a doctor diagnosis of dementia by the participant or caregiver. Cognitive impairment was defined as an impairment in two or more functional tests or a score higher than 3.6 on the Informant Questionnaire on Cognitive Decline ." ]

[ [ "2a", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response" ], [ "2b", "Passage: The most common causes of disability globally are adult-onset hearing loss and refractive errors." ], [ "2c", "Mental disorders such as depression, alcohol use disorders and psychoses are also among the 20 leading causes of disability ." ], [ "2d", "The pattern differs between the highincome countries and the low-and middle-income countries." ], [ "2e", "In the lower income countries, many more people are disabled due to preventable causes such as unintentional injuries and infertility arising from unsafe abortion and maternal sepsis." ], [ "2f", "The data also demonstrate the lack of interventions for easily treated conditions such as hearing loss, refractive errors and cataracts in low-income countries." ], [ "2g", "Disability due to mental" ] ]

[ "0b", "0d", "1a", "1c", "2b", "2c", "2e", "3b", "3c" ]

[ "Title: Zika virus-induced acute myelitis and motor deficits in adult interferon αβ/γ receptor knockout mice\nPassage: The fact that relative CMAP amplitude after spinal cord stimulation did not statistically correlate with VPS score suggests that damage upstream of spinal motor neurons may contribute to the hindlimb deficits. For example, CMAP amplitude was not reduced in two infected mice with overt paralysis . Paralysis in these animals could be caused by motor cortex, cerebellum, or brainstem dysfunction, as extensive infection was observed in these areas of the brain. While upper motor neuron disease is associated with rigid, rather than flaccid paralysis, we occasionally saw symptoms that could be interpreted as rigidity, such as walking with high haunches", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: We defined disability as the inability to independently carry out one or more activities of daily living, which included getting in or out of bed, walking across a room, bathing or showering, using the toilet, dressing, cutting food and eating. This definition of disability captures individuals who have difficulty maintaining independence and require supportive care.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: The most common causes of disability globally are adult-onset hearing loss and refractive errors. Mental disorders such as depression, alcohol use disorders and psychoses are also among the 20 leading causes of disability . The pattern differs between the highincome countries and the low-and middle-income countries. In the lower income countries, many more people are disabled due to preventable causes such as unintentional injuries and infertility arising from unsafe abortion and maternal sepsis. The data also demonstrate the lack of interventions for easily treated conditions such as hearing loss, refractive errors and cataracts in low-income countries. Disability due to mental", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study\nPassage: Dementia was defined on the basis of the coexistence of cognitive impairment and disability, or a report of a doctor diagnosis of dementia by the participant or caregiver. Cognitive impairment was defined as an impairment in two or more functional tests or a score higher than 3.6 on the Informant Questionnaire on Cognitive Decline ." ]

[ [ "3a", "Title: Potential impact of diabetes prevention on mortality and future burden of dementia and disability: a modelling study" ], [ "3b", "Passage: Dementia was defined on the basis of the coexistence of cognitive impairment and disability, or a report of a doctor diagnosis of dementia by the participant or caregiver." ], [ "3c", "Cognitive impairment was defined as an impairment in two or more functional tests or a score higher than 3.6 on the Informant Questionnaire on Cognitive Decline ." ] ]

[ "0b", "0d", "1a", "1c", "2b", "2c", "2e", "3b", "3c" ]

[ "Title: Variation in RNA Virus Mutation Rates across Host Cells\nPassage: genetic andmetabolic alterations in addition to p53 inactivation. To check the potential effects of these changes, we performed fluctuation tests in CT26 cells from an undifferentiated grade IV colon adenocarcinoma of a BALB/c mouse , but we found no significant differences with primary MEFs . Of note, BHK-21 are also tumor-forming cells, and the mutation rate was similar to the rate observed in MEFs or CT26 cells . This homogeneity in the VSV mutation rate was not an obvious a priori, because metabolic and mitotic activity should alter the availability of NTPs and hence could impact RNA replication fidelity, although", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: Propidium iodide staining was used for cell cycle analysis of primary TCs and TCs SV40 as described in manufacturer. In brief, cells were collected and fixed in 75% ethanol at 4 °C for overnight. After centrifuging and washing, staining buffer with 0.5 ml PI/RNase was added to each tube for 15 min at room temperature. Samples were examined with a fluorescence-activated cell sorting flow cytometer and DNA histograms were analyzed with Flowjo 7.6.1 software. Each test was repeated thrice.", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: , where cell nuclei were stained with DAPI. Dynamic alterations of TCs SV40 at 2, 5, 10, 20, 30, 50, or 60 generations were recorded automatically each 30 min for 48 h and cell morphological phenomes were presented each 12 h, respectively, in Additional file 1: Figure S1 . Figure 3 demonstrated that immuno-positive staining of the vimentin labeled with particle diameter at 10 nm, CD34 at18 nm, platelet-derived growth factor receptor α at 25 nm, or ckit at 40 nm in lung TCs SV40 under transmission electronic microscopy. Tomography of TCs was taken immediately after transfer with SV40 tomography,", "Title: Evaluation of Ultra-Microscopic Changes and Proliferation of Apoptotic Glioblastoma Multiforme Cells Induced by Velogenic Strain of Newcastle Disease Virus AF2240\nPassage: 12 x 75 Falcon tubes and the cell cycle was analyzed by flow cytometer . Each experiment was assayed three times ." ]

[ [ "1a", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation" ], [ "1b", "Passage: Propidium iodide staining was used for cell cycle analysis of primary TCs and TCs SV40 as described in manufacturer." ], [ "1c", "In brief, cells were collected and fixed in 75% ethanol at 4 °C for overnight." ], [ "1d", "After centrifuging and washing, staining buffer with 0.5 ml PI/RNase was added to each tube for 15 min at room temperature." ], [ "1e", "Samples were examined with a fluorescence-activated cell sorting flow cytometer and DNA histograms were analyzed with Flowjo 7.6.1 software." ], [ "1f", "Each test was repeated thrice." ] ]

[ "1b", "2b", "2c", "3b" ]

[ "Title: Variation in RNA Virus Mutation Rates across Host Cells\nPassage: genetic andmetabolic alterations in addition to p53 inactivation. To check the potential effects of these changes, we performed fluctuation tests in CT26 cells from an undifferentiated grade IV colon adenocarcinoma of a BALB/c mouse , but we found no significant differences with primary MEFs . Of note, BHK-21 are also tumor-forming cells, and the mutation rate was similar to the rate observed in MEFs or CT26 cells . This homogeneity in the VSV mutation rate was not an obvious a priori, because metabolic and mitotic activity should alter the availability of NTPs and hence could impact RNA replication fidelity, although", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: Propidium iodide staining was used for cell cycle analysis of primary TCs and TCs SV40 as described in manufacturer. In brief, cells were collected and fixed in 75% ethanol at 4 °C for overnight. After centrifuging and washing, staining buffer with 0.5 ml PI/RNase was added to each tube for 15 min at room temperature. Samples were examined with a fluorescence-activated cell sorting flow cytometer and DNA histograms were analyzed with Flowjo 7.6.1 software. Each test was repeated thrice.", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: , where cell nuclei were stained with DAPI. Dynamic alterations of TCs SV40 at 2, 5, 10, 20, 30, 50, or 60 generations were recorded automatically each 30 min for 48 h and cell morphological phenomes were presented each 12 h, respectively, in Additional file 1: Figure S1 . Figure 3 demonstrated that immuno-positive staining of the vimentin labeled with particle diameter at 10 nm, CD34 at18 nm, platelet-derived growth factor receptor α at 25 nm, or ckit at 40 nm in lung TCs SV40 under transmission electronic microscopy. Tomography of TCs was taken immediately after transfer with SV40 tomography,", "Title: Evaluation of Ultra-Microscopic Changes and Proliferation of Apoptotic Glioblastoma Multiforme Cells Induced by Velogenic Strain of Newcastle Disease Virus AF2240\nPassage: 12 x 75 Falcon tubes and the cell cycle was analyzed by flow cytometer . Each experiment was assayed three times ." ]

[ [ "2a", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation" ], [ "2b", "Passage: , where cell nuclei were stained with DAPI." ], [ "2c", "Dynamic alterations of TCs SV40 at 2, 5, 10, 20, 30, 50, or 60 generations were recorded automatically each 30 min for 48 h and cell morphological phenomes were presented each 12 h, respectively, in Additional file 1: Figure S1 ." ], [ "2d", "Figure 3 demonstrated that immuno-positive staining of the vimentin labeled with particle diameter at 10 nm, CD34 at18 nm, platelet-derived growth factor receptor α at 25 nm, or ckit at 40 nm in lung TCs SV40 under transmission electronic microscopy." ], [ "2e", "Tomography of TCs was taken immediately after transfer with SV40 tomography," ] ]

[ "1b", "2b", "2c", "3b" ]

[ "Title: Variation in RNA Virus Mutation Rates across Host Cells\nPassage: genetic andmetabolic alterations in addition to p53 inactivation. To check the potential effects of these changes, we performed fluctuation tests in CT26 cells from an undifferentiated grade IV colon adenocarcinoma of a BALB/c mouse , but we found no significant differences with primary MEFs . Of note, BHK-21 are also tumor-forming cells, and the mutation rate was similar to the rate observed in MEFs or CT26 cells . This homogeneity in the VSV mutation rate was not an obvious a priori, because metabolic and mitotic activity should alter the availability of NTPs and hence could impact RNA replication fidelity, although", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: Propidium iodide staining was used for cell cycle analysis of primary TCs and TCs SV40 as described in manufacturer. In brief, cells were collected and fixed in 75% ethanol at 4 °C for overnight. After centrifuging and washing, staining buffer with 0.5 ml PI/RNase was added to each tube for 15 min at room temperature. Samples were examined with a fluorescence-activated cell sorting flow cytometer and DNA histograms were analyzed with Flowjo 7.6.1 software. Each test was repeated thrice.", "Title: Influence of gene modification in biological behaviors and responses of mouse lung telocytes to inflammation\nPassage: , where cell nuclei were stained with DAPI. Dynamic alterations of TCs SV40 at 2, 5, 10, 20, 30, 50, or 60 generations were recorded automatically each 30 min for 48 h and cell morphological phenomes were presented each 12 h, respectively, in Additional file 1: Figure S1 . Figure 3 demonstrated that immuno-positive staining of the vimentin labeled with particle diameter at 10 nm, CD34 at18 nm, platelet-derived growth factor receptor α at 25 nm, or ckit at 40 nm in lung TCs SV40 under transmission electronic microscopy. Tomography of TCs was taken immediately after transfer with SV40 tomography,", "Title: Evaluation of Ultra-Microscopic Changes and Proliferation of Apoptotic Glioblastoma Multiforme Cells Induced by Velogenic Strain of Newcastle Disease Virus AF2240\nPassage: 12 x 75 Falcon tubes and the cell cycle was analyzed by flow cytometer . Each experiment was assayed three times ." ]

[ [ "3a", "Title: Evaluation of Ultra-Microscopic Changes and Proliferation of Apoptotic Glioblastoma Multiforme Cells Induced by Velogenic Strain of Newcastle Disease Virus AF2240" ], [ "3b", "Passage: 12 x 75 Falcon tubes and the cell cycle was analyzed by flow cytometer ." ], [ "3c", "Each experiment was assayed three times ." ] ]

[ "1b", "2b", "2c", "3b" ]

[ "Title: Pandemic (H1N1) 2009 Risk for Frontline Health Care Workers\nPassage: The risk for pandemic 2009 virus infection increased with the number of children <18 years of age living in the participant's household, which has previously been reported as a risk factor . In Victoria, the median age of persons with reported pandemic 2009 virus infection was 15 years, with 67% of all notifi ed casepatients being 5-17 years of age . Miller et al. also found that children were predominantly infected . This fi nding, coupled with the diffi culties of maintaining good respiratory etiquette in young children, is a plausible explanation for the effect of child number on infection", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: hospitalized children with influenza than in adults.", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: Of all 971 positive children, 890 were 4 years old or younger. The positive rate in this age group was significantly higher than that in children more than 4 years old . Children under 6 months were the most susceptible to respiratory viral pathogens with a positive rate of 14Á8% .", "Title: Host susceptibility to severe influenza A virus infection\nPassage: Extremes of age are well-recognised risk factors for severe disease. Children under the age of 5 years, and particularly those under 2 years, have consistently been found to be at high risk for severe disease and serious complications following IAV infection . Functional immaturity of the immune system, together with a failure to recognise IAV-related antigens, may largely explain this effect." ]

[ [ "0a", "Title: Pandemic (H1N1) 2009 Risk for Frontline Health Care Workers" ], [ "0b", "Passage: The risk for pandemic 2009 virus infection increased with the number of children <18 years of age living in the participant's household, which has previously been reported as a risk factor ." ], [ "0c", "In Victoria, the median age of persons with reported pandemic 2009 virus infection was 15 years, with 67% of all notifi ed casepatients being 5-17 years of age ." ], [ "0d", "Miller et al. also found that children were predominantly infected ." ], [ "0e", "This fi nding, coupled with the diffi culties of maintaining good respiratory etiquette in young children, is a plausible explanation for the effect of child number on infection" ] ]

[ "0b", "0c", "0d", "0e", "2b", "2c", "2d", "3b", "3c", "3d" ]

[ "Title: Pandemic (H1N1) 2009 Risk for Frontline Health Care Workers\nPassage: The risk for pandemic 2009 virus infection increased with the number of children <18 years of age living in the participant's household, which has previously been reported as a risk factor . In Victoria, the median age of persons with reported pandemic 2009 virus infection was 15 years, with 67% of all notifi ed casepatients being 5-17 years of age . Miller et al. also found that children were predominantly infected . This fi nding, coupled with the diffi culties of maintaining good respiratory etiquette in young children, is a plausible explanation for the effect of child number on infection", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: hospitalized children with influenza than in adults.", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: Of all 971 positive children, 890 were 4 years old or younger. The positive rate in this age group was significantly higher than that in children more than 4 years old . Children under 6 months were the most susceptible to respiratory viral pathogens with a positive rate of 14Á8% .", "Title: Host susceptibility to severe influenza A virus infection\nPassage: Extremes of age are well-recognised risk factors for severe disease. Children under the age of 5 years, and particularly those under 2 years, have consistently been found to be at high risk for severe disease and serious complications following IAV infection . Functional immaturity of the immune system, together with a failure to recognise IAV-related antigens, may largely explain this effect." ]

[ [ "2a", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China" ], [ "2b", "Passage: Of all 971 positive children, 890 were 4 years old or younger." ], [ "2c", "The positive rate in this age group was significantly higher than that in children more than 4 years old ." ], [ "2d", "Children under 6 months were the most susceptible to respiratory viral pathogens with a positive rate of 14Á8% ." ] ]

[ "0b", "0c", "0d", "0e", "2b", "2c", "2d", "3b", "3c", "3d" ]

[ "Title: Pandemic (H1N1) 2009 Risk for Frontline Health Care Workers\nPassage: The risk for pandemic 2009 virus infection increased with the number of children <18 years of age living in the participant's household, which has previously been reported as a risk factor . In Victoria, the median age of persons with reported pandemic 2009 virus infection was 15 years, with 67% of all notifi ed casepatients being 5-17 years of age . Miller et al. also found that children were predominantly infected . This fi nding, coupled with the diffi culties of maintaining good respiratory etiquette in young children, is a plausible explanation for the effect of child number on infection", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: hospitalized children with influenza than in adults.", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: Of all 971 positive children, 890 were 4 years old or younger. The positive rate in this age group was significantly higher than that in children more than 4 years old . Children under 6 months were the most susceptible to respiratory viral pathogens with a positive rate of 14Á8% .", "Title: Host susceptibility to severe influenza A virus infection\nPassage: Extremes of age are well-recognised risk factors for severe disease. Children under the age of 5 years, and particularly those under 2 years, have consistently been found to be at high risk for severe disease and serious complications following IAV infection . Functional immaturity of the immune system, together with a failure to recognise IAV-related antigens, may largely explain this effect." ]

[ [ "3a", "Title: Host susceptibility to severe influenza A virus infection" ], [ "3b", "Passage: Extremes of age are well-recognised risk factors for severe disease." ], [ "3c", "Children under the age of 5 years, and particularly those under 2 years, have consistently been found to be at high risk for severe disease and serious complications following IAV infection ." ], [ "3d", "Functional immaturity of the immune system, together with a failure to recognise IAV-related antigens, may largely explain this effect." ] ]

[ "0b", "0c", "0d", "0e", "2b", "2c", "2d", "3b", "3c", "3d" ]

[ "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: is worthy of note that Enterococcus and Enterobacter have been reported to play crucial roles of the gastrointestinal tract infections, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, endocarditis, CNS infections, septic arthritis, intra-abdominal infections, and ophthalmic infections 21, 22 .", "Title: Secretome of Intestinal Bacilli: A Natural Guard against Pathologies\nPassage: major role in the development of GALT -gut lymphoid tissue associated with the gastrointestinal mucosa -and in the diversity of the primary antibody population in rabbits . Bacillus spp. like other strains isolated from human stool were able to bind the human norovirus strains, the cause of acute viral gastroenteritis and foodborne diseases, around the outer cell surfaces and pili structures . The interaction between virus and bacteria is hypothesized to help the host immune system to better recognize infectious particles.", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: Remarkably, chronic complex diseases have been associated with gut microbiota. Although the intestinal microbiota is generally stable in healthy individuals over long periods of time, antibiotics can significantly reshape the gut microbiota, allowing exogenous microbes to outgrow commensal bacteria and cause permanent changes in varying states of disease 6, 11, 12 . Probiotic agents, which beneficially affect the host by improving the gut microbial balance, have been used for the prevention and treatment of respiratory tract diseases to avoid bacterial translocation 13, 14 . It is noteworthy that gastrointestinal distress symptoms were observed in some of our recently reported cases", "Title: Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention\nPassage: Changes are likely occurring also in the microbiota of the human gastrointestinal tract, which can itself be considered infectiousi.e., acquired from the environment. Gut microbial populations have been shown to impact a variety of metabolic processes including inflammation, angiogenesis, immunity, and insulin resistance . They may have an important role in growth, as relative proportions of bacterial phyla have been shown to be responsive to weight change . Thus, childhood infectious conditions, some of which dramatically impact the gut microbiota at least in the short term, may well have long-term effects on the microbiota and as such may well play" ]

[ [ "0a", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota" ], [ "0b", "Passage: is worthy of note that Enterococcus and Enterobacter have been reported to play crucial roles of the gastrointestinal tract infections, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, endocarditis, CNS infections, septic arthritis, intra-abdominal infections, and ophthalmic infections 21, 22 ." ] ]

[ "0b", "1a", "1c", "2b", "2c", "2d", "2e", "3b", "3c", "3e" ]

[ "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: is worthy of note that Enterococcus and Enterobacter have been reported to play crucial roles of the gastrointestinal tract infections, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, endocarditis, CNS infections, septic arthritis, intra-abdominal infections, and ophthalmic infections 21, 22 .", "Title: Secretome of Intestinal Bacilli: A Natural Guard against Pathologies\nPassage: major role in the development of GALT -gut lymphoid tissue associated with the gastrointestinal mucosa -and in the diversity of the primary antibody population in rabbits . Bacillus spp. like other strains isolated from human stool were able to bind the human norovirus strains, the cause of acute viral gastroenteritis and foodborne diseases, around the outer cell surfaces and pili structures . The interaction between virus and bacteria is hypothesized to help the host immune system to better recognize infectious particles.", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: Remarkably, chronic complex diseases have been associated with gut microbiota. Although the intestinal microbiota is generally stable in healthy individuals over long periods of time, antibiotics can significantly reshape the gut microbiota, allowing exogenous microbes to outgrow commensal bacteria and cause permanent changes in varying states of disease 6, 11, 12 . Probiotic agents, which beneficially affect the host by improving the gut microbial balance, have been used for the prevention and treatment of respiratory tract diseases to avoid bacterial translocation 13, 14 . It is noteworthy that gastrointestinal distress symptoms were observed in some of our recently reported cases", "Title: Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention\nPassage: Changes are likely occurring also in the microbiota of the human gastrointestinal tract, which can itself be considered infectiousi.e., acquired from the environment. Gut microbial populations have been shown to impact a variety of metabolic processes including inflammation, angiogenesis, immunity, and insulin resistance . They may have an important role in growth, as relative proportions of bacterial phyla have been shown to be responsive to weight change . Thus, childhood infectious conditions, some of which dramatically impact the gut microbiota at least in the short term, may well have long-term effects on the microbiota and as such may well play" ]

[ [ "1a", "Title: Secretome of Intestinal Bacilli: A Natural Guard against Pathologies" ], [ "1b", "Passage: major role in the development of GALT -gut lymphoid tissue associated with the gastrointestinal mucosa -and in the diversity of the primary antibody population in rabbits . Bacillus spp." ], [ "1c", "like other strains isolated from human stool were able to bind the human norovirus strains, the cause of acute viral gastroenteritis and foodborne diseases, around the outer cell surfaces and pili structures ." ], [ "1d", "The interaction between virus and bacteria is hypothesized to help the host immune system to better recognize infectious particles." ] ]

[ "0b", "1a", "1c", "2b", "2c", "2d", "2e", "3b", "3c", "3e" ]

[ "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: is worthy of note that Enterococcus and Enterobacter have been reported to play crucial roles of the gastrointestinal tract infections, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, endocarditis, CNS infections, septic arthritis, intra-abdominal infections, and ophthalmic infections 21, 22 .", "Title: Secretome of Intestinal Bacilli: A Natural Guard against Pathologies\nPassage: major role in the development of GALT -gut lymphoid tissue associated with the gastrointestinal mucosa -and in the diversity of the primary antibody population in rabbits . Bacillus spp. like other strains isolated from human stool were able to bind the human norovirus strains, the cause of acute viral gastroenteritis and foodborne diseases, around the outer cell surfaces and pili structures . The interaction between virus and bacteria is hypothesized to help the host immune system to better recognize infectious particles.", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: Remarkably, chronic complex diseases have been associated with gut microbiota. Although the intestinal microbiota is generally stable in healthy individuals over long periods of time, antibiotics can significantly reshape the gut microbiota, allowing exogenous microbes to outgrow commensal bacteria and cause permanent changes in varying states of disease 6, 11, 12 . Probiotic agents, which beneficially affect the host by improving the gut microbial balance, have been used for the prevention and treatment of respiratory tract diseases to avoid bacterial translocation 13, 14 . It is noteworthy that gastrointestinal distress symptoms were observed in some of our recently reported cases", "Title: Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention\nPassage: Changes are likely occurring also in the microbiota of the human gastrointestinal tract, which can itself be considered infectiousi.e., acquired from the environment. Gut microbial populations have been shown to impact a variety of metabolic processes including inflammation, angiogenesis, immunity, and insulin resistance . They may have an important role in growth, as relative proportions of bacterial phyla have been shown to be responsive to weight change . Thus, childhood infectious conditions, some of which dramatically impact the gut microbiota at least in the short term, may well have long-term effects on the microbiota and as such may well play" ]

[ [ "2a", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota" ], [ "2b", "Passage: Remarkably, chronic complex diseases have been associated with gut microbiota." ], [ "2c", "Although the intestinal microbiota is generally stable in healthy individuals over long periods of time, antibiotics can significantly reshape the gut microbiota, allowing exogenous microbes to outgrow commensal bacteria and cause permanent changes in varying states of disease 6, 11, 12 ." ], [ "2d", "Probiotic agents, which beneficially affect the host by improving the gut microbial balance, have been used for the prevention and treatment of respiratory tract diseases to avoid bacterial translocation 13, 14 ." ], [ "2e", "It is noteworthy that gastrointestinal distress symptoms were observed in some of our recently reported cases" ] ]

[ "0b", "1a", "1c", "2b", "2c", "2d", "2e", "3b", "3c", "3e" ]

[ "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: is worthy of note that Enterococcus and Enterobacter have been reported to play crucial roles of the gastrointestinal tract infections, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, endocarditis, CNS infections, septic arthritis, intra-abdominal infections, and ophthalmic infections 21, 22 .", "Title: Secretome of Intestinal Bacilli: A Natural Guard against Pathologies\nPassage: major role in the development of GALT -gut lymphoid tissue associated with the gastrointestinal mucosa -and in the diversity of the primary antibody population in rabbits . Bacillus spp. like other strains isolated from human stool were able to bind the human norovirus strains, the cause of acute viral gastroenteritis and foodborne diseases, around the outer cell surfaces and pili structures . The interaction between virus and bacteria is hypothesized to help the host immune system to better recognize infectious particles.", "Title: Influence of H7N9 virus infection and associated treatment on human gut microbiota\nPassage: Remarkably, chronic complex diseases have been associated with gut microbiota. Although the intestinal microbiota is generally stable in healthy individuals over long periods of time, antibiotics can significantly reshape the gut microbiota, allowing exogenous microbes to outgrow commensal bacteria and cause permanent changes in varying states of disease 6, 11, 12 . Probiotic agents, which beneficially affect the host by improving the gut microbial balance, have been used for the prevention and treatment of respiratory tract diseases to avoid bacterial translocation 13, 14 . It is noteworthy that gastrointestinal distress symptoms were observed in some of our recently reported cases", "Title: Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention\nPassage: Changes are likely occurring also in the microbiota of the human gastrointestinal tract, which can itself be considered infectiousi.e., acquired from the environment. Gut microbial populations have been shown to impact a variety of metabolic processes including inflammation, angiogenesis, immunity, and insulin resistance . They may have an important role in growth, as relative proportions of bacterial phyla have been shown to be responsive to weight change . Thus, childhood infectious conditions, some of which dramatically impact the gut microbiota at least in the short term, may well have long-term effects on the microbiota and as such may well play" ]

[ [ "3a", "Title: Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention" ], [ "3b", "Passage: Changes are likely occurring also in the microbiota of the human gastrointestinal tract, which can itself be considered infectiousi.e., acquired from the environment." ], [ "3c", "Gut microbial populations have been shown to impact a variety of metabolic processes including inflammation, angiogenesis, immunity, and insulin resistance ." ], [ "3d", "They may have an important role in growth, as relative proportions of bacterial phyla have been shown to be responsive to weight change ." ], [ "3e", "Thus, childhood infectious conditions, some of which dramatically impact the gut microbiota at least in the short term, may well have long-term effects on the microbiota and as such may well play" ] ]

[ "0b", "1a", "1c", "2b", "2c", "2d", "2e", "3b", "3c", "3e" ]

[ "Title: Interest of a simple on-line screening registry for measuring ICU burden related to an influenza pandemic\nPassage: Three hundred ninety-one patients with A were admitted from 26 September 2009 to 10 February 2010 in the 69 ICUs participating in the screening registry and were included in this study. Among them, 349 had a confirmed influenza A infection. This subset of 391 patients represents 36.7% of the whole cohort of French influenza-infected adult ICU patients ; they had the same overall characteristics, except for a higher rate of immunosuppression . Tables 2 and 3 show the baseline characteristics and main risk factors for flu recorded in these patients according to survival or to the intensity of ventilatory support.", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study\nPassage: Of the 200 enrolled in this study, 25 patients were excluded from the analysis of the data. Of these, 21 patients had incomplete sampling and four patients met exclusion criteria. The characteristics on admission of the 175 patients included in our analysis study group are presented in Table 1 . Mean age was 62 years; roughly one-third had CAP, one-third had HAP, and one-third had VAP. The median hospital and ICU lengths of stay prior to enrolment were six days and nine days , respectively.", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: In the period of the study, 1789 patients were admitted to the ICU and 13 PGWH patients were included. There were 10 male patients and 3 female , with a mean age of 30 years . There were no self-inflicted lesions . Glasgow Coma Scale at admission was 8 or less in 10 patients. On admission, 7 patients were anisocoric, 8 presenting shock, 5 had associated body lesions from another gunshot wound . Mean SAPS 3 was 67 and mean Apache II, 26 . The CT scan findings were: midline shift in 8 patients, 7 single lobe haemorrhages , and", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: Results: A total of 116 patients were enrolled from April 2014 to September 2015. Fifty-two patients were assigned to IABP group and 64 patients to control group. The mean age was 64 ± 8 years in the IABP group and 67 ± 9 years in the control group . The median LVEF was 40 % in the IABP group and 40 % in the control group and the median EuroSCORE was 6 vs. 6 , P = 0.873, respectively. The primary outcome was observed in 40.4 % in the IABP group and 37.5 % in the control group after cardiovascular" ]

[ [ "0a", "Title: Interest of a simple on-line screening registry for measuring ICU burden related to an influenza pandemic" ], [ "0b", "Passage: Three hundred ninety-one patients with A were admitted from 26 September 2009 to 10 February 2010 in the 69 ICUs participating in the screening registry and were included in this study." ], [ "0c", "Among them, 349 had a confirmed influenza A infection." ], [ "0d", "This subset of 391 patients represents 36.7% of the whole cohort of French influenza-infected adult ICU patients ; they had the same overall characteristics, except for a higher rate of immunosuppression ." ], [ "0e", "Tables 2 and 3 show the baseline characteristics and main risk factors for flu recorded in these patients according to survival or to the intensity of ventilatory support." ] ]

[ "0b", "1b", "2c", "3c" ]

[ "Title: Interest of a simple on-line screening registry for measuring ICU burden related to an influenza pandemic\nPassage: Three hundred ninety-one patients with A were admitted from 26 September 2009 to 10 February 2010 in the 69 ICUs participating in the screening registry and were included in this study. Among them, 349 had a confirmed influenza A infection. This subset of 391 patients represents 36.7% of the whole cohort of French influenza-infected adult ICU patients ; they had the same overall characteristics, except for a higher rate of immunosuppression . Tables 2 and 3 show the baseline characteristics and main risk factors for flu recorded in these patients according to survival or to the intensity of ventilatory support.", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study\nPassage: Of the 200 enrolled in this study, 25 patients were excluded from the analysis of the data. Of these, 21 patients had incomplete sampling and four patients met exclusion criteria. The characteristics on admission of the 175 patients included in our analysis study group are presented in Table 1 . Mean age was 62 years; roughly one-third had CAP, one-third had HAP, and one-third had VAP. The median hospital and ICU lengths of stay prior to enrolment were six days and nine days , respectively.", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: In the period of the study, 1789 patients were admitted to the ICU and 13 PGWH patients were included. There were 10 male patients and 3 female , with a mean age of 30 years . There were no self-inflicted lesions . Glasgow Coma Scale at admission was 8 or less in 10 patients. On admission, 7 patients were anisocoric, 8 presenting shock, 5 had associated body lesions from another gunshot wound . Mean SAPS 3 was 67 and mean Apache II, 26 . The CT scan findings were: midline shift in 8 patients, 7 single lobe haemorrhages , and", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: Results: A total of 116 patients were enrolled from April 2014 to September 2015. Fifty-two patients were assigned to IABP group and 64 patients to control group. The mean age was 64 ± 8 years in the IABP group and 67 ± 9 years in the control group . The median LVEF was 40 % in the IABP group and 40 % in the control group and the median EuroSCORE was 6 vs. 6 , P = 0.873, respectively. The primary outcome was observed in 40.4 % in the IABP group and 37.5 % in the control group after cardiovascular" ]

[ [ "1a", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study" ], [ "1b", "Passage: Of the 200 enrolled in this study, 25 patients were excluded from the analysis of the data." ], [ "1c", "Of these, 21 patients had incomplete sampling and four patients met exclusion criteria." ], [ "1d", "The characteristics on admission of the 175 patients included in our analysis study group are presented in Table 1 ." ], [ "1e", "Mean age was 62 years; roughly one-third had CAP, one-third had HAP, and one-third had VAP." ], [ "1f", "The median hospital and ICU lengths of stay prior to enrolment were six days and nine days , respectively." ] ]

[ "0b", "1b", "2c", "3c" ]

[ "Title: Interest of a simple on-line screening registry for measuring ICU burden related to an influenza pandemic\nPassage: Three hundred ninety-one patients with A were admitted from 26 September 2009 to 10 February 2010 in the 69 ICUs participating in the screening registry and were included in this study. Among them, 349 had a confirmed influenza A infection. This subset of 391 patients represents 36.7% of the whole cohort of French influenza-infected adult ICU patients ; they had the same overall characteristics, except for a higher rate of immunosuppression . Tables 2 and 3 show the baseline characteristics and main risk factors for flu recorded in these patients according to survival or to the intensity of ventilatory support.", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study\nPassage: Of the 200 enrolled in this study, 25 patients were excluded from the analysis of the data. Of these, 21 patients had incomplete sampling and four patients met exclusion criteria. The characteristics on admission of the 175 patients included in our analysis study group are presented in Table 1 . Mean age was 62 years; roughly one-third had CAP, one-third had HAP, and one-third had VAP. The median hospital and ICU lengths of stay prior to enrolment were six days and nine days , respectively.", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: In the period of the study, 1789 patients were admitted to the ICU and 13 PGWH patients were included. There were 10 male patients and 3 female , with a mean age of 30 years . There were no self-inflicted lesions . Glasgow Coma Scale at admission was 8 or less in 10 patients. On admission, 7 patients were anisocoric, 8 presenting shock, 5 had associated body lesions from another gunshot wound . Mean SAPS 3 was 67 and mean Apache II, 26 . The CT scan findings were: midline shift in 8 patients, 7 single lobe haemorrhages , and", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: Results: A total of 116 patients were enrolled from April 2014 to September 2015. Fifty-two patients were assigned to IABP group and 64 patients to control group. The mean age was 64 ± 8 years in the IABP group and 67 ± 9 years in the control group . The median LVEF was 40 % in the IABP group and 40 % in the control group and the median EuroSCORE was 6 vs. 6 , P = 0.873, respectively. The primary outcome was observed in 40.4 % in the IABP group and 37.5 % in the control group after cardiovascular" ]

[ [ "2a", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium." ], [ "2b", "15-18 March 2016" ], [ "2c", "Passage: In the period of the study, 1789 patients were admitted to the ICU and 13 PGWH patients were included." ], [ "2d", "There were 10 male patients and 3 female , with a mean age of 30 years ." ], [ "2e", "There were no self-inflicted lesions ." ], [ "2f", "Glasgow Coma Scale at admission was 8 or less in 10 patients." ], [ "2g", "On admission, 7 patients were anisocoric, 8 presenting shock, 5 had associated body lesions from another gunshot wound ." ], [ "2h", "Mean SAPS 3 was 67 and mean Apache II, 26 ." ], [ "2i", "The CT scan findings were: midline shift in 8 patients, 7 single lobe haemorrhages , and" ] ]

[ "0b", "1b", "2c", "3c" ]

[ "Title: Interest of a simple on-line screening registry for measuring ICU burden related to an influenza pandemic\nPassage: Three hundred ninety-one patients with A were admitted from 26 September 2009 to 10 February 2010 in the 69 ICUs participating in the screening registry and were included in this study. Among them, 349 had a confirmed influenza A infection. This subset of 391 patients represents 36.7% of the whole cohort of French influenza-infected adult ICU patients ; they had the same overall characteristics, except for a higher rate of immunosuppression . Tables 2 and 3 show the baseline characteristics and main risk factors for flu recorded in these patients according to survival or to the intensity of ventilatory support.", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study\nPassage: Of the 200 enrolled in this study, 25 patients were excluded from the analysis of the data. Of these, 21 patients had incomplete sampling and four patients met exclusion criteria. The characteristics on admission of the 175 patients included in our analysis study group are presented in Table 1 . Mean age was 62 years; roughly one-third had CAP, one-third had HAP, and one-third had VAP. The median hospital and ICU lengths of stay prior to enrolment were six days and nine days , respectively.", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: In the period of the study, 1789 patients were admitted to the ICU and 13 PGWH patients were included. There were 10 male patients and 3 female , with a mean age of 30 years . There were no self-inflicted lesions . Glasgow Coma Scale at admission was 8 or less in 10 patients. On admission, 7 patients were anisocoric, 8 presenting shock, 5 had associated body lesions from another gunshot wound . Mean SAPS 3 was 67 and mean Apache II, 26 . The CT scan findings were: midline shift in 8 patients, 7 single lobe haemorrhages , and", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: Results: A total of 116 patients were enrolled from April 2014 to September 2015. Fifty-two patients were assigned to IABP group and 64 patients to control group. The mean age was 64 ± 8 years in the IABP group and 67 ± 9 years in the control group . The median LVEF was 40 % in the IABP group and 40 % in the control group and the median EuroSCORE was 6 vs. 6 , P = 0.873, respectively. The primary outcome was observed in 40.4 % in the IABP group and 37.5 % in the control group after cardiovascular" ]

[ [ "3a", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium." ], [ "3b", "15-18 March 2016" ], [ "3c", "Passage: Results: A total of 116 patients were enrolled from April 2014 to September 2015." ], [ "3d", "Fifty-two patients were assigned to IABP group and 64 patients to control group." ], [ "3e", "The mean age was 64 ± 8 years in the IABP group and 67 ± 9 years in the control group ." ], [ "3f", "The median LVEF was 40 % in the IABP group and 40 % in the control group and the median EuroSCORE was 6 vs. 6 , P = 0.873, respectively." ], [ "3g", "The primary outcome was observed in 40.4 % in the IABP group and 37.5 % in the control group after cardiovascular" ] ]

[ "0b", "1b", "2c", "3c" ]

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: All hospitalised cases had a benign clinical evolution except four, two reported in Italy and two reported in France, all of whom developed viral pneumonia. All three cases who were aged 65 years or over were admitted to intensive care and required respiratory support and one French case died. The case who died was hospitalised for 21 days and required intensive care and mechanical ventilation for 19 days. The duration of hospitalisation was reported for 16 cases with a median of 13 days . As at 21 February 2020, four cases were still hospitalised.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: 2 days to be hospitalised.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: The total population size of Sydney was NZ810 700, of which at least 14 130 were admitted to hospital and approximately 3500 died as a result of influenza infection . Based on a survey of 600 establishments covering 106 923 employees, the proportion of workers that were absent from duty as a result of influenza was 36.6% . This was considered as an unbiased estimate of the clinical attack rate, although we argue that the serological attack rate may have differed.", "Title: Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016\nPassage: Of the 1722 patients, 96 were admitted to a hospital for a reason other than acute respiratory infection and developed ILI symptoms ≥48 h after admission and were classified as nosocomial influenza. Of these 96 cases, 35 were aged 18-64 years, 22 were aged 64-74 years, 39 ≥ 75 years and 43 were female. Eighty patients presented ≥1 influenza risk factor and 36 had received the influenza vaccine ." ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "Passage: All hospitalised cases had a benign clinical evolution except four, two reported in Italy and two reported in France, all of whom developed viral pneumonia." ], [ "0c", "All three cases who were aged 65 years or over were admitted to intensive care and required respiratory support and one French case died." ], [ "0d", "The case who died was hospitalised for 21 days and required intensive care and mechanical ventilation for 19 days." ], [ "0e", "The duration of hospitalisation was reported for 16 cases with a median of 13 days ." ], [ "0f", "As at 21 February 2020, four cases were still hospitalised." ] ]

[ "0b", "0c", "0e", "0f", "2b", "3b" ]

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: All hospitalised cases had a benign clinical evolution except four, two reported in Italy and two reported in France, all of whom developed viral pneumonia. All three cases who were aged 65 years or over were admitted to intensive care and required respiratory support and one French case died. The case who died was hospitalised for 21 days and required intensive care and mechanical ventilation for 19 days. The duration of hospitalisation was reported for 16 cases with a median of 13 days . As at 21 February 2020, four cases were still hospitalised.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: 2 days to be hospitalised.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: The total population size of Sydney was NZ810 700, of which at least 14 130 were admitted to hospital and approximately 3500 died as a result of influenza infection . Based on a survey of 600 establishments covering 106 923 employees, the proportion of workers that were absent from duty as a result of influenza was 36.6% . This was considered as an unbiased estimate of the clinical attack rate, although we argue that the serological attack rate may have differed.", "Title: Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016\nPassage: Of the 1722 patients, 96 were admitted to a hospital for a reason other than acute respiratory infection and developed ILI symptoms ≥48 h after admission and were classified as nosocomial influenza. Of these 96 cases, 35 were aged 18-64 years, 22 were aged 64-74 years, 39 ≥ 75 years and 43 were female. Eighty patients presented ≥1 influenza risk factor and 36 had received the influenza vaccine ." ]

[ [ "2a", "Title: Quantifying social distancing arising from pandemic influenza" ], [ "2b", "Passage: The total population size of Sydney was NZ810 700, of which at least 14 130 were admitted to hospital and approximately 3500 died as a result of influenza infection ." ], [ "2c", "Based on a survey of 600 establishments covering 106 923 employees, the proportion of workers that were absent from duty as a result of influenza was 36.6% ." ], [ "2d", "This was considered as an unbiased estimate of the clinical attack rate, although we argue that the serological attack rate may have differed." ] ]

[ "0b", "0c", "0e", "0f", "2b", "3b" ]

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: All hospitalised cases had a benign clinical evolution except four, two reported in Italy and two reported in France, all of whom developed viral pneumonia. All three cases who were aged 65 years or over were admitted to intensive care and required respiratory support and one French case died. The case who died was hospitalised for 21 days and required intensive care and mechanical ventilation for 19 days. The duration of hospitalisation was reported for 16 cases with a median of 13 days . As at 21 February 2020, four cases were still hospitalised.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: 2 days to be hospitalised.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: The total population size of Sydney was NZ810 700, of which at least 14 130 were admitted to hospital and approximately 3500 died as a result of influenza infection . Based on a survey of 600 establishments covering 106 923 employees, the proportion of workers that were absent from duty as a result of influenza was 36.6% . This was considered as an unbiased estimate of the clinical attack rate, although we argue that the serological attack rate may have differed.", "Title: Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016\nPassage: Of the 1722 patients, 96 were admitted to a hospital for a reason other than acute respiratory infection and developed ILI symptoms ≥48 h after admission and were classified as nosocomial influenza. Of these 96 cases, 35 were aged 18-64 years, 22 were aged 64-74 years, 39 ≥ 75 years and 43 were female. Eighty patients presented ≥1 influenza risk factor and 36 had received the influenza vaccine ." ]

[ [ "3a", "Title: Hospital-acquired influenza infections detected by a surveillance system over six seasons, from 2010/2011 to 2015/2016" ], [ "3b", "Passage: Of the 1722 patients, 96 were admitted to a hospital for a reason other than acute respiratory infection and developed ILI symptoms ≥48 h after admission and were classified as nosocomial influenza." ], [ "3c", "Of these 96 cases, 35 were aged 18-64 years, 22 were aged 64-74 years, 39 ≥ 75 years and 43 were female." ], [ "3d", "Eighty patients presented ≥1 influenza risk factor and 36 had received the influenza vaccine ." ] ]

[ "0b", "0c", "0e", "0f", "2b", "3b" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: in humans . Currently, NA-specific antibody responses are not considered a correlate of protection . LAIV is administered as a nasal spray and contains the same three or four influenza virus strains as inactivated vaccines but on an attenuated vaccine backbone . LAIV are temperature-sensitive and cold-adapted so they do not replicate effectively at core body temperature, but replicate in the mucosa of the nasopharynx . LAIV immunization induces serum antibody responses, mucosal antibody responses , and T cell responses. While robust serum antibody and nasal wash antibody responses are associated with protection from infection, other immune responses, such as", "Title: Current and Novel Approaches in Influenza Management\nPassage: LAIV viruses in the nasopharynx elicit immune response that epitomizes a natural influenza infection. For this reason, LAIV has shown some superiority over the IIV in terms of the induction of mucosal immunity via secreted immunoglobulin A . Use of the LAIV has proven to be safe in children and immunocompromised persons . The most spelt-out advantage is the \"non-invasive\" capacity of the attenuated viruses and this had made it suitable to use for all categories of vaccines, although LAIVs are not recommended for people with underlying chronic medical conditions . A typical setback to the use of the LAIV", "Title: La Crosse virus infectivity, pathogenesis, and immunogenicity in mice and monkeys\nPassage: the lymph nodes and major organs, with subsequent infection of the upper respiratory tract followed by infection of the brain and eventually the spinal cord. By day six, mice began to succumb to infection in the high dose group showing signs of paralysis whereas mice in the low dose group failed to show clinical signs at this time, but would have succumbed later in infection. These results indicate that LACV replicates to low to moderate levels in peripheral tissues in weanling mice, with the nasal turbinates rather than striated muscle being the major site of replication.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests . The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups . The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups ." ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: in humans ." ], [ "0c", "Currently, NA-specific antibody responses are not considered a correlate of protection ." ], [ "0d", "LAIV is administered as a nasal spray and contains the same three or four influenza virus strains as inactivated vaccines but on an attenuated vaccine backbone ." ], [ "0e", "LAIV are temperature-sensitive and cold-adapted so they do not replicate effectively at core body temperature, but replicate in the mucosa of the nasopharynx ." ], [ "0f", "LAIV immunization induces serum antibody responses, mucosal antibody responses , and T cell responses." ], [ "0g", "While robust serum antibody and nasal wash antibody responses are associated with protection from infection, other immune responses, such as" ] ]

[ "0e", "1b" ]

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: in humans . Currently, NA-specific antibody responses are not considered a correlate of protection . LAIV is administered as a nasal spray and contains the same three or four influenza virus strains as inactivated vaccines but on an attenuated vaccine backbone . LAIV are temperature-sensitive and cold-adapted so they do not replicate effectively at core body temperature, but replicate in the mucosa of the nasopharynx . LAIV immunization induces serum antibody responses, mucosal antibody responses , and T cell responses. While robust serum antibody and nasal wash antibody responses are associated with protection from infection, other immune responses, such as", "Title: Current and Novel Approaches in Influenza Management\nPassage: LAIV viruses in the nasopharynx elicit immune response that epitomizes a natural influenza infection. For this reason, LAIV has shown some superiority over the IIV in terms of the induction of mucosal immunity via secreted immunoglobulin A . Use of the LAIV has proven to be safe in children and immunocompromised persons . The most spelt-out advantage is the \"non-invasive\" capacity of the attenuated viruses and this had made it suitable to use for all categories of vaccines, although LAIVs are not recommended for people with underlying chronic medical conditions . A typical setback to the use of the LAIV", "Title: La Crosse virus infectivity, pathogenesis, and immunogenicity in mice and monkeys\nPassage: the lymph nodes and major organs, with subsequent infection of the upper respiratory tract followed by infection of the brain and eventually the spinal cord. By day six, mice began to succumb to infection in the high dose group showing signs of paralysis whereas mice in the low dose group failed to show clinical signs at this time, but would have succumbed later in infection. These results indicate that LACV replicates to low to moderate levels in peripheral tissues in weanling mice, with the nasal turbinates rather than striated muscle being the major site of replication.", "Title: Efficacy and synergy of live-attenuated and inactivated influenza vaccines in young chickens\nPassage: Overall, birds in the LAIV-LAIV group showed consistently high mucosal antibody responses across all three ELISA tests . The LAIV-IIV group also showed a good level of antibody response that was somewhat biased toward IgG response despite the fact that the IgA response observed in this group was not significantly different from the LAIV vaccinated groups . The single vaccination regimens administered at 3 weeks of age showed a trend that was similar to the 1-day-old vaccination result: no differences in anti-NP or IgG antibodies and higher IgA responses in LAIV groups compared with IIV groups ." ]

[ [ "1a", "Title: Current and Novel Approaches in Influenza Management" ], [ "1b", "Passage: LAIV viruses in the nasopharynx elicit immune response that epitomizes a natural influenza infection." ], [ "1c", "For this reason, LAIV has shown some superiority over the IIV in terms of the induction of mucosal immunity via secreted immunoglobulin A ." ], [ "1d", "Use of the LAIV has proven to be safe in children and immunocompromised persons ." ], [ "1e", "The most spelt-out advantage is the \"non-invasive\" capacity of the attenuated viruses and this had made it suitable to use for all categories of vaccines, although LAIVs are not recommended for people with underlying chronic medical conditions ." ], [ "1f", "A typical setback to the use of the LAIV" ] ]

[ "0e", "1b" ]

[ "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: required for potential growth of pathogen population in the environment, exposure dynamics, incubation period, and delays in reporting.", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: Infections are typically revealed after the incubation period, t inc , ; which is associated with patient's physiology, whose distribution depends on the type of infection ). After symptoms start, only a proportion of the infected individuals seeks medical assistance , and for only a proportion of these cases further diagnostic testing will be conducted and recorded in the public health system. This introduces a further time lag, t det , between the time when infected individual approaches the health system and the actual appropriate laboratory detection with diagnosis . Even in a simple scenario, the temporal lag between the", "Title: Environmental factors preceding illness onset differ in phenotypes of the juvenile idiopathic inflammatory myopathies\nPassage: The physician questionnaire contained three questions about environmental exposures that had been previously suggested to be possibly associated with the onset of JDM . These included whether the patient had any documented infections, received any immunizations or took any medications within 6 months before illness onset. The questionnaire also included an additional open-ended question about other environmental exposures within 6 months before illness onset relating to other possible triggers of disease and to specify these and when they occurred. Stressful life events were categorized as major vs minor and as One hundred and twenty-one patients were tested by IP immunoblotting.", "Title: Development of a Symptom Score for Clinical Studies to Identify Children With a Documented Viral Upper Respiratory Tract Infection\nPassage: Although it may seem surprising that a viral etiology was not identified in Ͼ40% of children with cold symptoms using the most sensitive molecular techniques currently available, the definition of a \"cold\" is actually somewhat nebulous . In one study of 215 adults who reported they were developing a cold, only 54% had at least one respiratory symptom and only 17% met Jackson criteria for a cold . Thus, the use of a \"clinical cold\" as the entry criterion for clinical trials on the efficacy of a potential viral URI treatment includes participants with heterogeneous clinical conditions and may bias" ]

[ [ "1a", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review" ], [ "1b", "Passage: Infections are typically revealed after the incubation period, t inc , ; which is associated with patient's physiology, whose distribution depends on the type of infection )." ], [ "1c", "After symptoms start, only a proportion of the infected individuals seeks medical assistance , and for only a proportion of these cases further diagnostic testing will be conducted and recorded in the public health system." ], [ "1d", "This introduces a further time lag, t det , between the time when infected individual approaches the health system and the actual appropriate laboratory detection with diagnosis ." ], [ "1e", "Even in a simple scenario, the temporal lag between the" ] ]

[ "1b", "1c" ]

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Notwithstanding this progress, there remains a disproportionate burden of disease in low-and middle-income countries, where more than 90% of pneumonia cases and deaths occur. The incidence in high-income countries is estimated at 0.015 episodes per child year, compared to 0.22 episodes per child year in low-and middle-income countries . On average, 1 in 66 children in high-income countries is affected by pneumonia per year, compared to 1 in 5 children in low-and middle-income countries. Even within low-and middleincome countries there are regional inequities and challenges with access to health care services: up to 81% of severe pneumonia deaths occur outside", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: odds of severe pneumonia by 2.7 times in low-and middle-income countries and 1.3 times in highincome countries. Markers of undernutrition are strong risk factors for pneumonia in low-and middle-income countries only, with highly significant odds ratios for underweight for age , stunting and wasting . Household crowding has uniform risk, with odds ratios between 1.9 and 2.3 in both low-and middle-income countries and high-income countries. Indoor air pollution from use of solid or biomass fuels increases odds of pneumonia by 1.6 times; lack of measles vaccination by the end of the first year of age increases odds of pneumonia by", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: 1.8 times . It is estimated that the prevalence of these critical risk factors in low-and middle-income countries decreased by 25% between 2000 and 2010, contributing to reductions in pneumonia incidence and mortality in low-and middle-income countries, even in countries where conjugate vaccines have not been available .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: a hospital . In addition to a higher incidence of pneumonia, the case fatality rate is estimated to be almost 10-fold higher in low-and middle-income countries as compared to high-income countries ." ]

[ [ "0a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "0b", "Passage: Notwithstanding this progress, there remains a disproportionate burden of disease in low-and middle-income countries, where more than 90% of pneumonia cases and deaths occur." ], [ "0c", "The incidence in high-income countries is estimated at 0.015 episodes per child year, compared to 0.22 episodes per child year in low-and middle-income countries ." ], [ "0d", "On average, 1 in 66 children in high-income countries is affected by pneumonia per year, compared to 1 in 5 children in low-and middle-income countries." ], [ "0e", "Even within low-and middleincome countries there are regional inequities and challenges with access to health care services: up to 81% of severe pneumonia deaths occur outside" ] ]

[ "0e" ]