Datasets:

param-bharat

/

ragbench-context-relevance-filtered

like 1

[ "Title: Unified feature association networks through integration of transcriptomic and proteomic data\nPassage: Network centrality in biological networks is an indicator of the importance of the node to the function of the network . Pathways with higher centrality in host response networks may be more important to the host response and/or may be more coordinated in terms of their activity. To that end, the centrality of features in KEGG pathways was compared between each network to identify functions that may have higher or lower centrality in an antibody vs. receptor-mediated network. We used betweenness, the number of paths through a network that pass through the gene in question, as a measure of centrality.", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: Multiple measures can improve the confidence in performance evaluation. We calculated five measures to evaluate the perfor-mance of features and TS prediction models from cross-validations. To compare the five measures, we computed the Pearson correlation and mutual information between every pair of the five measures across all 133 individual feature-based classifiers . Pearson correlation is only sensitive to a linear relationship between two variables while mutual information is capable of detecting non-linear relationships. We found that AUC and DD had the best concordance according to mutual information and the third best concordance according to the Pearson correlation. Both measures consider", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: Next, we were interested in testing the predictive power of sequence and structure features. The ''sequence features'' model contained features calculated from sequence information only, while the ''structure features'' model had features derived from the protein crystal structure. The ''all features'' model combined sequence and structure features. The performance of the ''all features'' model was slightly better than that of the ''structure features'' model, while the ''structure features'' model performed better than the ''sequence features'' model . This suggests that structure-based features have higher predictive power than sequence-based features in differentiating TS mutations from neutral mutations. Nevertheless, the results demonstrated", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: As shown in Figure 6A , the ROC curve of the ''all features'' model is biphasic. True positive rates are three-fold of false positive rates when applying thresholds greater than 0.5, while true positive rates are less than two-fold of false positive rates when applying thresholds less than 0.5. Although the AUC value is slightly lower than those of leave-one protein-out , the lower left portion of the ROC curve is comparable with those, suggesting our top-ranked predictions are particularly accurate. We further plotted precision-recall curves to evaluate the performance of the ''all features'' model . A 50% precision is" ]

[ [ "0a", "Title: Unified feature association networks through integration of transcriptomic and proteomic data" ], [ "0b", "Passage: Network centrality in biological networks is an indicator of the importance of the node to the function of the network ." ], [ "0c", "Pathways with higher centrality in host response networks may be more important to the host response and/or may be more coordinated in terms of their activity." ], [ "0d", "To that end, the centrality of features in KEGG pathways was compared between each network to identify functions that may have higher or lower centrality in an antibody vs. receptor-mediated network." ], [ "0e", "We used betweenness, the number of paths through a network that pass through the gene in question, as a measure of centrality." ] ]

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

[ "Title: Unified feature association networks through integration of transcriptomic and proteomic data\nPassage: Network centrality in biological networks is an indicator of the importance of the node to the function of the network . Pathways with higher centrality in host response networks may be more important to the host response and/or may be more coordinated in terms of their activity. To that end, the centrality of features in KEGG pathways was compared between each network to identify functions that may have higher or lower centrality in an antibody vs. receptor-mediated network. We used betweenness, the number of paths through a network that pass through the gene in question, as a measure of centrality.", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: Multiple measures can improve the confidence in performance evaluation. We calculated five measures to evaluate the perfor-mance of features and TS prediction models from cross-validations. To compare the five measures, we computed the Pearson correlation and mutual information between every pair of the five measures across all 133 individual feature-based classifiers . Pearson correlation is only sensitive to a linear relationship between two variables while mutual information is capable of detecting non-linear relationships. We found that AUC and DD had the best concordance according to mutual information and the third best concordance according to the Pearson correlation. Both measures consider", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: Next, we were interested in testing the predictive power of sequence and structure features. The ''sequence features'' model contained features calculated from sequence information only, while the ''structure features'' model had features derived from the protein crystal structure. The ''all features'' model combined sequence and structure features. The performance of the ''all features'' model was slightly better than that of the ''structure features'' model, while the ''structure features'' model performed better than the ''sequence features'' model . This suggests that structure-based features have higher predictive power than sequence-based features in differentiating TS mutations from neutral mutations. Nevertheless, the results demonstrated", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations\nPassage: As shown in Figure 6A , the ROC curve of the ''all features'' model is biphasic. True positive rates are three-fold of false positive rates when applying thresholds greater than 0.5, while true positive rates are less than two-fold of false positive rates when applying thresholds less than 0.5. Although the AUC value is slightly lower than those of leave-one protein-out , the lower left portion of the ROC curve is comparable with those, suggesting our top-ranked predictions are particularly accurate. We further plotted precision-recall curves to evaluate the performance of the ''all features'' model . A 50% precision is" ]

[ [ "1a", "Title: Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations" ], [ "1b", "Passage: Multiple measures can improve the confidence in performance evaluation." ], [ "1c", "We calculated five measures to evaluate the perfor-mance of features and TS prediction models from cross-validations." ], [ "1d", "To compare the five measures, we computed the Pearson correlation and mutual information between every pair of the five measures across all 133 individual feature-based classifiers ." ], [ "1e", "Pearson correlation is only sensitive to a linear relationship between two variables while mutual information is capable of detecting non-linear relationships." ], [ "1f", "We found that AUC and DD had the best concordance according to mutual information and the third best concordance according to the Pearson correlation." ], [ "1g", "Both measures consider" ] ]

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

[ "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Despite the availability of safe and effective antibiotics and vaccines for treatment and prevention, pneumonia is a leading cause of death worldwide and the leading infectious disease killer . Pneumonia is the single leading cause of death globally among children under 5 years of age accounting for approximately 2 million deaths annually . Children in developing countries have an estimated 0.29 episodes of pneumonia per person-year, compared with 0.05 episodes per person-year in developed countries .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: September 2009 . In addition, Hong Kong SAR recommends seasonal influenza vaccine use in high risk groups. Vaccine clinical trials in other countries have estimated that 21% of radiologically confirmed pneumonia is caused by Hib and 36% by pneumococcus ; over 10% of hospitalized pneumonia in children in nearby Thailand are due to influenza . Studies within China have suggested that Hib and pneumococcus are common causes of pneumonia in children , suggesting that widespread use of these two vaccines, as well as influenza vaccine, could reduce the incidence and mortality of pneumonia in China.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: A systematic review of etiology studies prior to availability of new conjugate vaccines confirmed S. pneumoniae and H. influenzae type B as the most important bacterial causes of pneumonia, with Staphylococcus aureus and Klebsiella pneumoniae associated with some severe cases. Respiratory syncytial virus was the leading viral cause, identified in 15-40% of pneumonia cases, followed by influenza A and B, parainfluenza, human metapneumovirus and adenovirus .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Better access to proven public health interventions, including vaccines, is needed in the public sector in China. Vaccines against Haemophilus influenzae type b , Streptococcus pneumoniae, and influenza are not part of routine childhood vaccination programs in many countries worldwide ; none of these vaccines are included in the routine childhood immunization schedule in mainland China. However, Hib and influenza vaccines are commonly available in many parts of China through vaccination clinics, and Hong Kong SAR is the first region in China, as well as Asia, where pneumococcal conjugate vaccine will be included in their routine childhood immunization program starting" ]

[ [ "1a", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008" ], [ "1b", "Passage: September 2009 ." ], [ "1c", "In addition, Hong Kong SAR recommends seasonal influenza vaccine use in high risk groups." ], [ "1d", "Vaccine clinical trials in other countries have estimated that 21% of radiologically confirmed pneumonia is caused by Hib and 36% by pneumococcus ; over 10% of hospitalized pneumonia in children in nearby Thailand are due to influenza ." ], [ "1e", "Studies within China have suggested that Hib and pneumococcus are common causes of pneumonia in children , suggesting that widespread use of these two vaccines, as well as influenza vaccine, could reduce the incidence and mortality of pneumonia in China." ] ]

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

[ "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Despite the availability of safe and effective antibiotics and vaccines for treatment and prevention, pneumonia is a leading cause of death worldwide and the leading infectious disease killer . Pneumonia is the single leading cause of death globally among children under 5 years of age accounting for approximately 2 million deaths annually . Children in developing countries have an estimated 0.29 episodes of pneumonia per person-year, compared with 0.05 episodes per person-year in developed countries .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: September 2009 . In addition, Hong Kong SAR recommends seasonal influenza vaccine use in high risk groups. Vaccine clinical trials in other countries have estimated that 21% of radiologically confirmed pneumonia is caused by Hib and 36% by pneumococcus ; over 10% of hospitalized pneumonia in children in nearby Thailand are due to influenza . Studies within China have suggested that Hib and pneumococcus are common causes of pneumonia in children , suggesting that widespread use of these two vaccines, as well as influenza vaccine, could reduce the incidence and mortality of pneumonia in China.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: A systematic review of etiology studies prior to availability of new conjugate vaccines confirmed S. pneumoniae and H. influenzae type B as the most important bacterial causes of pneumonia, with Staphylococcus aureus and Klebsiella pneumoniae associated with some severe cases. Respiratory syncytial virus was the leading viral cause, identified in 15-40% of pneumonia cases, followed by influenza A and B, parainfluenza, human metapneumovirus and adenovirus .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Better access to proven public health interventions, including vaccines, is needed in the public sector in China. Vaccines against Haemophilus influenzae type b , Streptococcus pneumoniae, and influenza are not part of routine childhood vaccination programs in many countries worldwide ; none of these vaccines are included in the routine childhood immunization schedule in mainland China. However, Hib and influenza vaccines are commonly available in many parts of China through vaccination clinics, and Hong Kong SAR is the first region in China, as well as Asia, where pneumococcal conjugate vaccine will be included in their routine childhood immunization program starting" ]

[ [ "2a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "2b", "Passage: A systematic review of etiology studies prior to availability of new conjugate vaccines confirmed S. pneumoniae and H. influenzae type B as the most important bacterial causes of pneumonia, with Staphylococcus aureus and Klebsiella pneumoniae associated with some severe cases." ], [ "2c", "Respiratory syncytial virus was the leading viral cause, identified in 15-40% of pneumonia cases, followed by influenza A and B, parainfluenza, human metapneumovirus and adenovirus ." ] ]

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

[ "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Despite the availability of safe and effective antibiotics and vaccines for treatment and prevention, pneumonia is a leading cause of death worldwide and the leading infectious disease killer . Pneumonia is the single leading cause of death globally among children under 5 years of age accounting for approximately 2 million deaths annually . Children in developing countries have an estimated 0.29 episodes of pneumonia per person-year, compared with 0.05 episodes per person-year in developed countries .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: September 2009 . In addition, Hong Kong SAR recommends seasonal influenza vaccine use in high risk groups. Vaccine clinical trials in other countries have estimated that 21% of radiologically confirmed pneumonia is caused by Hib and 36% by pneumococcus ; over 10% of hospitalized pneumonia in children in nearby Thailand are due to influenza . Studies within China have suggested that Hib and pneumococcus are common causes of pneumonia in children , suggesting that widespread use of these two vaccines, as well as influenza vaccine, could reduce the incidence and mortality of pneumonia in China.", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: A systematic review of etiology studies prior to availability of new conjugate vaccines confirmed S. pneumoniae and H. influenzae type B as the most important bacterial causes of pneumonia, with Staphylococcus aureus and Klebsiella pneumoniae associated with some severe cases. Respiratory syncytial virus was the leading viral cause, identified in 15-40% of pneumonia cases, followed by influenza A and B, parainfluenza, human metapneumovirus and adenovirus .", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008\nPassage: Better access to proven public health interventions, including vaccines, is needed in the public sector in China. Vaccines against Haemophilus influenzae type b , Streptococcus pneumoniae, and influenza are not part of routine childhood vaccination programs in many countries worldwide ; none of these vaccines are included in the routine childhood immunization schedule in mainland China. However, Hib and influenza vaccines are commonly available in many parts of China through vaccination clinics, and Hong Kong SAR is the first region in China, as well as Asia, where pneumococcal conjugate vaccine will be included in their routine childhood immunization program starting" ]

[ [ "3a", "Title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008" ], [ "3b", "Passage: Better access to proven public health interventions, including vaccines, is needed in the public sector in China." ], [ "3c", "Vaccines against Haemophilus influenzae type b , Streptococcus pneumoniae, and influenza are not part of routine childhood vaccination programs in many countries worldwide ; none of these vaccines are included in the routine childhood immunization schedule in mainland China." ], [ "3d", "However, Hib and influenza vaccines are commonly available in many parts of China through vaccination clinics, and Hong Kong SAR is the first region in China, as well as Asia, where pneumococcal conjugate vaccine will be included in their routine childhood immunization program starting" ] ]

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

[ "Title: Quantifying social distancing arising from pandemic influenza\nPassage: social distancing.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: thus discouraging people from getting out and circulating in the wider population .", "Title: Estimating the number of infections and the impact of non-\nPassage: Social distancing Avoid social interaction wherever possible", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: F waŝ RðFÞZ 0:95G0:04ðGs:e:Þ." ]

[ [ "1a", "Title: Quantifying social distancing arising from pandemic influenza" ], [ "1b", "Passage: thus discouraging people from getting out and circulating in the wider population ." ] ]

[ "1b", "2b" ]

[ "Title: Quantifying social distancing arising from pandemic influenza\nPassage: social distancing.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: thus discouraging people from getting out and circulating in the wider population .", "Title: Estimating the number of infections and the impact of non-\nPassage: Social distancing Avoid social interaction wherever possible", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: F waŝ RðFÞZ 0:95G0:04ðGs:e:Þ." ]

[ [ "2a", "Title: Estimating the number of infections and the impact of non-" ], [ "2b", "Passage: Social distancing Avoid social interaction wherever possible" ] ]

[ "1b", "2b" ]

[ "Title: Dating the time of viral subtype divergence\nPassage: The study here focuses on influenza, although the techniques are readily applied to other rapidly evolving organisms. Influenza has three types, A, B and C, classified based on serological analysis. To date, only type A sequences have been demonstrably associated with global pandemics . Since modern surveillance began in the 1930s, type B has only been responsible for mild epidemics while type C has been nearly asymptomatic in human infection. Several subtypes of A, notably H1N1 and H3N2, are currently co-circulating in the human population. As the H1N1 and H3N2 subtypes may be as divergent from each other as they", "Title: Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types\nPassage: At the conclusion of this analysis of all available HRV VP1 sequences, totals of 77 HRV-A types, 29 HRV-B and 51 HRV-C types have been listed in full in Tables S1 and S2). Novel strains of HRV were classified based on date of submission to the Picornaviridae Study Group, rather than the earliest isolated strain.", "Title: Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types\nPassage: As described above, their current classification can incorporate phylogenetic data and any available information on neutralization properties in addition to VP1 distances. Combined, these may potentially resolve any remaining uncertainties over type assignments.", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: There are 3 main types of circulating influenza viruses in the world: A, B, and C. Influenza viruses are enveloped negative-strand RNA viruses with segmented genomes . Of its two genera, one includes influenza A and B viruses, and the other influenza C virus. Type A influenza viruses are subtyped based on 16 known hemagglutinin and nine neuraminidase subtypes that exist in wild birds and provide a source of viral HA and NA subtypes antigenically novel to humans. The subtypes are further classified according to the combinations of virus surface proteins, abbreviated as H1-H16 and N1-N9 , starting with the" ]

[ [ "0a", "Title: Dating the time of viral subtype divergence" ], [ "0b", "Passage: The study here focuses on influenza, although the techniques are readily applied to other rapidly evolving organisms." ], [ "0c", "Influenza has three types, A, B and C, classified based on serological analysis." ], [ "0d", "To date, only type A sequences have been demonstrably associated with global pandemics ." ], [ "0e", "Since modern surveillance began in the 1930s, type B has only been responsible for mild epidemics while type C has been nearly asymptomatic in human infection." ], [ "0f", "Several subtypes of A, notably H1N1 and H3N2, are currently co-circulating in the human population." ], [ "0g", "As the H1N1 and H3N2 subtypes may be as divergent from each other as they" ] ]

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

[ "Title: Dating the time of viral subtype divergence\nPassage: The study here focuses on influenza, although the techniques are readily applied to other rapidly evolving organisms. Influenza has three types, A, B and C, classified based on serological analysis. To date, only type A sequences have been demonstrably associated with global pandemics . Since modern surveillance began in the 1930s, type B has only been responsible for mild epidemics while type C has been nearly asymptomatic in human infection. Several subtypes of A, notably H1N1 and H3N2, are currently co-circulating in the human population. As the H1N1 and H3N2 subtypes may be as divergent from each other as they", "Title: Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types\nPassage: At the conclusion of this analysis of all available HRV VP1 sequences, totals of 77 HRV-A types, 29 HRV-B and 51 HRV-C types have been listed in full in Tables S1 and S2). Novel strains of HRV were classified based on date of submission to the Picornaviridae Study Group, rather than the earliest isolated strain.", "Title: Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types\nPassage: As described above, their current classification can incorporate phylogenetic data and any available information on neutralization properties in addition to VP1 distances. Combined, these may potentially resolve any remaining uncertainties over type assignments.", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: There are 3 main types of circulating influenza viruses in the world: A, B, and C. Influenza viruses are enveloped negative-strand RNA viruses with segmented genomes . Of its two genera, one includes influenza A and B viruses, and the other influenza C virus. Type A influenza viruses are subtyped based on 16 known hemagglutinin and nine neuraminidase subtypes that exist in wild birds and provide a source of viral HA and NA subtypes antigenically novel to humans. The subtypes are further classified according to the combinations of virus surface proteins, abbreviated as H1-H16 and N1-N9 , starting with the" ]

[ [ "3a", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic" ], [ "3b", "Passage: There are 3 main types of circulating influenza viruses in the world: A, B, and C. Influenza viruses are enveloped negative-strand RNA viruses with segmented genomes ." ], [ "3c", "Of its two genera, one includes influenza A and B viruses, and the other influenza C virus." ], [ "3d", "Type A influenza viruses are subtyped based on 16 known hemagglutinin and nine neuraminidase subtypes that exist in wild birds and provide a source of viral HA and NA subtypes antigenically novel to humans." ], [ "3e", "The subtypes are further classified according to the combinations of virus surface proteins, abbreviated as H1-H16 and N1-N9 , starting with the" ] ]

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

[ "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: We found that daily air travel volume positively correlates with imported-and-reported case counts of SARS-CoV-2 infection among high surveillance locations . We noted that increasing flight volume by 31 passengers/day is associated with 1 additional expected imported-and-reported case. In addition, Singapore and India lie above the 95% PI in our model; Singapore had 12 more imported-and-reported cases than expected and India had 3 more than expected. Thailand has a relatively high air travel volume compared with other locations, but it lies below the 95% PI, reporting 16 fewer imported-and-reported cases than expected under the model. Indonesia lies below the PI", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: The model requires data on imported-and-reported cases of SARS-CoV-2 infection, daily air travel volume, and surveillance capacity. We obtained data on imported-and-reported cases aggregated by destination from the World Health Organization technical report issued February 4, 2020 . We assumed a case count of 0 for locations not listed. We used February 4 as the cutoff for cumulative imported-and-reported case counts because exported cases from Hubei Province dropped rapidly after this date , likely because of travel restrictions for the province implement on January 23. We defined imported-and-reported cases as those with known travel history from China; of those, 83%", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: Most cases imported to other locations have been linked to recent travel history from China , suggesting that air travel plays a major role in exportation of cases to locations outside of China. To prevent other cities and countries from becoming epicenters of the SARS-CoV-2 epidemic, substantial targeted public health interventions are required to detect cases and control local spread of the virus. We collected estimates of air travel volume from Wuhan to 194 international destinations. We then identified 49 countries that had a score of >49.2/100 on category 2, Early Detection and Reporting of Epidemics of Potential International Concern,", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: To identify locations reporting fewer than predicted imported SARS-CoV-2 infected cases, we fit a model to data from 49 locations outside mainland China with high surveillance capacity according to the GHS Index . Among these, 17 had high travel connectivity to Wuhan and 32 have low connectivity to Wuhan. We considered locations to be countries without any position on territorial claims. We performed a Poisson regression by using the cumulative number of imported-and-reported SARS-CoV-2 cases in these 49 countries and the estimated number of daily airline passengers from the Wuhan airport. We then compared predictions from this model with imported-and-reported" ]

[ [ "0a", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions," ], [ "0b", "Passage: We found that daily air travel volume positively correlates with imported-and-reported case counts of SARS-CoV-2 infection among high surveillance locations ." ], [ "0c", "We noted that increasing flight volume by 31 passengers/day is associated with 1 additional expected imported-and-reported case." ], [ "0d", "In addition, Singapore and India lie above the 95% PI in our model; Singapore had 12 more imported-and-reported cases than expected and India had 3 more than expected." ], [ "0e", "Thailand has a relatively high air travel volume compared with other locations, but it lies below the 95% PI, reporting 16 fewer imported-and-reported cases than expected under the model." ], [ "0f", "Indonesia lies below the PI" ] ]

[ "0b", "2b" ]

[ "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: We found that daily air travel volume positively correlates with imported-and-reported case counts of SARS-CoV-2 infection among high surveillance locations . We noted that increasing flight volume by 31 passengers/day is associated with 1 additional expected imported-and-reported case. In addition, Singapore and India lie above the 95% PI in our model; Singapore had 12 more imported-and-reported cases than expected and India had 3 more than expected. Thailand has a relatively high air travel volume compared with other locations, but it lies below the 95% PI, reporting 16 fewer imported-and-reported cases than expected under the model. Indonesia lies below the PI", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: The model requires data on imported-and-reported cases of SARS-CoV-2 infection, daily air travel volume, and surveillance capacity. We obtained data on imported-and-reported cases aggregated by destination from the World Health Organization technical report issued February 4, 2020 . We assumed a case count of 0 for locations not listed. We used February 4 as the cutoff for cumulative imported-and-reported case counts because exported cases from Hubei Province dropped rapidly after this date , likely because of travel restrictions for the province implement on January 23. We defined imported-and-reported cases as those with known travel history from China; of those, 83%", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: Most cases imported to other locations have been linked to recent travel history from China , suggesting that air travel plays a major role in exportation of cases to locations outside of China. To prevent other cities and countries from becoming epicenters of the SARS-CoV-2 epidemic, substantial targeted public health interventions are required to detect cases and control local spread of the virus. We collected estimates of air travel volume from Wuhan to 194 international destinations. We then identified 49 countries that had a score of >49.2/100 on category 2, Early Detection and Reporting of Epidemics of Potential International Concern,", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: To identify locations reporting fewer than predicted imported SARS-CoV-2 infected cases, we fit a model to data from 49 locations outside mainland China with high surveillance capacity according to the GHS Index . Among these, 17 had high travel connectivity to Wuhan and 32 have low connectivity to Wuhan. We considered locations to be countries without any position on territorial claims. We performed a Poisson regression by using the cumulative number of imported-and-reported SARS-CoV-2 cases in these 49 countries and the estimated number of daily airline passengers from the Wuhan airport. We then compared predictions from this model with imported-and-reported" ]

[ [ "2a", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions," ], [ "2b", "Passage: Most cases imported to other locations have been linked to recent travel history from China , suggesting that air travel plays a major role in exportation of cases to locations outside of China." ], [ "2c", "To prevent other cities and countries from becoming epicenters of the SARS-CoV-2 epidemic, substantial targeted public health interventions are required to detect cases and control local spread of the virus." ], [ "2d", "We collected estimates of air travel volume from Wuhan to 194 international destinations." ], [ "2e", "We then identified 49 countries that had a score of >49.2/100 on category 2, Early Detection and Reporting of Epidemics of Potential International Concern," ] ]

[ "0b", "2b" ]

[ "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: National preparedness to detect emerging or epidemic-prone diseases requires adequate financial resources and investment in public health systems. 16 The same is true of response: a large body of evidence points to a direct link between the adequacy of health financing and key metrics associated with effective response, including the quality of clinical care and health outcomes. 17 During acute public health emergencies, health ministries as well as local government units may be required to rapidly scale up surveillance and health provision activities. This can lead to rapidly mounting costs, especially for personnel and consumables such as personal protective equipment", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: Effective public health systems are vital for early detection, mitigation and management of infectious disease outbreaks. Early detection requires robust surveillance and effective outbreak investigation capabilities for rapidly identifying, characterising and tracking emerging infectious diseases. 10 This capacity requires effective health institutions with capacity to access and monitor the entirety of the geography and population. Once an epidemic is underway, the healthcare and public health systems must be able to identify, investigate, monitor and manage abrupt surges in cases through the mobilisation of personnel and resources. Health systems must be able to manage the clinical care for infected persons, and", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: A conceptual framework for epidemic preparedness and response Epidemic preparedness reflects the capacity of institutions-public health authorities, health systems and emergency response bodies-to detect, report and respond to outbreaks. Government institutions must detect and assess potentially consequential outbreak events, report outbreaks and their causes to relevant national and international organisations and networks, and respond with measures to reduce the health, societal and economic impacts of outbreaks. 5 7 While preparedness for public health emergencies is typically considered in terms of surveillance, response and health capacity, these functions in turn rely on a broader set of institutional, financial and infrastructural factors.", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: and vaccines, which can be difficult to sustain without adequate resources." ]

[ [ "0a", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index" ], [ "0b", "Passage: National preparedness to detect emerging or epidemic-prone diseases requires adequate financial resources and investment in public health systems." ], [ "0c", "16 The same is true of response: a large body of evidence points to a direct link between the adequacy of health financing and key metrics associated with effective response, including the quality of clinical care and health outcomes." ], [ "0d", "17 During acute public health emergencies, health ministries as well as local government units may be required to rapidly scale up surveillance and health provision activities." ], [ "0e", "This can lead to rapidly mounting costs, especially for personnel and consumables such as personal protective equipment" ] ]

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

[ "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: National preparedness to detect emerging or epidemic-prone diseases requires adequate financial resources and investment in public health systems. 16 The same is true of response: a large body of evidence points to a direct link between the adequacy of health financing and key metrics associated with effective response, including the quality of clinical care and health outcomes. 17 During acute public health emergencies, health ministries as well as local government units may be required to rapidly scale up surveillance and health provision activities. This can lead to rapidly mounting costs, especially for personnel and consumables such as personal protective equipment", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: Effective public health systems are vital for early detection, mitigation and management of infectious disease outbreaks. Early detection requires robust surveillance and effective outbreak investigation capabilities for rapidly identifying, characterising and tracking emerging infectious diseases. 10 This capacity requires effective health institutions with capacity to access and monitor the entirety of the geography and population. Once an epidemic is underway, the healthcare and public health systems must be able to identify, investigate, monitor and manage abrupt surges in cases through the mobilisation of personnel and resources. Health systems must be able to manage the clinical care for infected persons, and", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: A conceptual framework for epidemic preparedness and response Epidemic preparedness reflects the capacity of institutions-public health authorities, health systems and emergency response bodies-to detect, report and respond to outbreaks. Government institutions must detect and assess potentially consequential outbreak events, report outbreaks and their causes to relevant national and international organisations and networks, and respond with measures to reduce the health, societal and economic impacts of outbreaks. 5 7 While preparedness for public health emergencies is typically considered in terms of surveillance, response and health capacity, these functions in turn rely on a broader set of institutional, financial and infrastructural factors.", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: and vaccines, which can be difficult to sustain without adequate resources." ]

[ [ "1a", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index" ], [ "1b", "Passage: Effective public health systems are vital for early detection, mitigation and management of infectious disease outbreaks." ], [ "1c", "Early detection requires robust surveillance and effective outbreak investigation capabilities for rapidly identifying, characterising and tracking emerging infectious diseases." ], [ "1d", "10 This capacity requires effective health institutions with capacity to access and monitor the entirety of the geography and population." ], [ "1e", "Once an epidemic is underway, the healthcare and public health systems must be able to identify, investigate, monitor and manage abrupt surges in cases through the mobilisation of personnel and resources." ], [ "1f", "Health systems must be able to manage the clinical care for infected persons, and" ] ]

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

[ "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: National preparedness to detect emerging or epidemic-prone diseases requires adequate financial resources and investment in public health systems. 16 The same is true of response: a large body of evidence points to a direct link between the adequacy of health financing and key metrics associated with effective response, including the quality of clinical care and health outcomes. 17 During acute public health emergencies, health ministries as well as local government units may be required to rapidly scale up surveillance and health provision activities. This can lead to rapidly mounting costs, especially for personnel and consumables such as personal protective equipment", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: Effective public health systems are vital for early detection, mitigation and management of infectious disease outbreaks. Early detection requires robust surveillance and effective outbreak investigation capabilities for rapidly identifying, characterising and tracking emerging infectious diseases. 10 This capacity requires effective health institutions with capacity to access and monitor the entirety of the geography and population. Once an epidemic is underway, the healthcare and public health systems must be able to identify, investigate, monitor and manage abrupt surges in cases through the mobilisation of personnel and resources. Health systems must be able to manage the clinical care for infected persons, and", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: A conceptual framework for epidemic preparedness and response Epidemic preparedness reflects the capacity of institutions-public health authorities, health systems and emergency response bodies-to detect, report and respond to outbreaks. Government institutions must detect and assess potentially consequential outbreak events, report outbreaks and their causes to relevant national and international organisations and networks, and respond with measures to reduce the health, societal and economic impacts of outbreaks. 5 7 While preparedness for public health emergencies is typically considered in terms of surveillance, response and health capacity, these functions in turn rely on a broader set of institutional, financial and infrastructural factors.", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index\nPassage: and vaccines, which can be difficult to sustain without adequate resources." ]

[ [ "2a", "Title: Assessing global preparedness for the next pandemic: development and application of an Epidemic Preparedness Index" ], [ "2b", "Passage: A conceptual framework for epidemic preparedness and response Epidemic preparedness reflects the capacity of institutions-public health authorities, health systems and emergency response bodies-to detect, report and respond to outbreaks." ], [ "2c", "Government institutions must detect and assess potentially consequential outbreak events, report outbreaks and their causes to relevant national and international organisations and networks, and respond with measures to reduce the health, societal and economic impacts of outbreaks." ], [ "2d", "5 7 While preparedness for public health emergencies is typically considered in terms of surveillance, response and health capacity, these functions in turn rely on a broader set of institutional, financial and infrastructural factors." ] ]

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

[ "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: The only positive sample to HPIV2 was collected during winter. HPIV1 and HPIV3 detection occurred mainly in late winter and spring. Similar results were reported showing this virus presence in samples collected in spring, autumn and winter. According to literature, HPIV3 are the most frequent viruses from this family, being type 1 and 2 viruses barely detected or even detected, which shows agreement with obtained results to literature data.", "Title: Seasonal distribution of active systemic lupus erythematosus and its correlation with meteorological factors\nPassage: low incidence in the summer.", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: This study was conducted at the Genomic Studies The total respiratory infections were detected mainly in winter, spring and summer of 2004, and autumn and winter of 2005, as showed in Figure 1A , which also demonstrate the seasonal distribution of the detected respiratory viruses.", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: FLUA and FLUB were detected in few samples; however, these samples were collected during autumn and winter, agreeing to previous studies that showed Inlfuenza outbreaks occurring between late summer and early winter ." ]

[ [ "1a", "Title: Seasonal distribution of active systemic lupus erythematosus and its correlation with meteorological factors" ], [ "1b", "Passage: low incidence in the summer." ] ]

[ "1b", "2b" ]

[ "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: The only positive sample to HPIV2 was collected during winter. HPIV1 and HPIV3 detection occurred mainly in late winter and spring. Similar results were reported showing this virus presence in samples collected in spring, autumn and winter. According to literature, HPIV3 are the most frequent viruses from this family, being type 1 and 2 viruses barely detected or even detected, which shows agreement with obtained results to literature data.", "Title: Seasonal distribution of active systemic lupus erythematosus and its correlation with meteorological factors\nPassage: low incidence in the summer.", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: This study was conducted at the Genomic Studies The total respiratory infections were detected mainly in winter, spring and summer of 2004, and autumn and winter of 2005, as showed in Figure 1A , which also demonstrate the seasonal distribution of the detected respiratory viruses.", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity\nPassage: FLUA and FLUB were detected in few samples; however, these samples were collected during autumn and winter, agreeing to previous studies that showed Inlfuenza outbreaks occurring between late summer and early winter ." ]

[ [ "2a", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity" ], [ "2b", "Passage: This study was conducted at the Genomic Studies The total respiratory infections were detected mainly in winter, spring and summer of 2004, and autumn and winter of 2005, as showed in Figure 1A , which also demonstrate the seasonal distribution of the detected respiratory viruses." ] ]

[ "1b", "2b" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "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", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human. Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan." ], [ "0c", "In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards ." ] ]

[ "0b", "1b" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "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", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human. Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "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." ], [ "1c", "The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia ." ], [ "1d", "Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels ." ], [ "1e", "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." ], [ "1f", "Precisely how virus transmits to humans remains unknown" ] ]

[ "0b", "1b" ]

[ "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: Researches showed that the R 0 of severe acute respiratory syndrome was about 2.7-3.4 or 2-4 in Hong Kong, China . Another research found that the R 0 of SARS was about 2.1 in Hong Kong, China, 2.7 in Singapore, and 3.8 in Beijing, China . Therefore, we believe that the commonly acceptable average value of the R 0 of SARS might be 2.9 . The transmissibility of the Middle East respiratory syndrome is much lower than SARS. The reported value of the R 0 of MERS was about 0.8-1.3 , with the inter-human transmissibility of the disease was about", "Title: The Failure of R (0)\nPassage: While the first factor may be fairly uniform across outbreaks, the second may depend significantly on context, varying both within and among populations. The problem with the SARS estimates stems from the mass-action assumption of compartmental models; that is, that all susceptible individuals are equally likely to become infected. When this assumption does not hold, the models may yield inaccurate estimates or estimates that do not apply to all populations. R 0 estimates for SARS in the field were based largely on outbreak data from a hospital and a crowded apartment building, with anomalously high rates of close contacts among", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes. But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures. R is the effectiive number and can include the impact of control measures.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: In this study, we used the R 0 to assess the transmissibility of the SARS-CoV-2. Commonly, R 0 was defined as the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population . If R 0 > 1, the outbreak will occur. If R 0 < 1, the outbreak will toward an end. In this study, R 0 was deduced from the RP model by the next generation matrix approach . The multiple of the transmissibility of A P to that of I P ." ]

[ [ "0a", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus" ], [ "0b", "Passage: Researches showed that the R 0 of severe acute respiratory syndrome was about 2.7-3.4 or 2-4 in Hong Kong, China ." ], [ "0c", "Another research found that the R 0 of SARS was about 2.1 in Hong Kong, China, 2.7 in Singapore, and 3.8 in Beijing, China ." ], [ "0d", "Therefore, we believe that the commonly acceptable average value of the R 0 of SARS might be 2.9 ." ], [ "0e", "The transmissibility of the Middle East respiratory syndrome is much lower than SARS." ], [ "0f", "The reported value of the R 0 of MERS was about 0.8-1.3 , with the inter-human transmissibility of the disease was about" ] ]

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

[ "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: Researches showed that the R 0 of severe acute respiratory syndrome was about 2.7-3.4 or 2-4 in Hong Kong, China . Another research found that the R 0 of SARS was about 2.1 in Hong Kong, China, 2.7 in Singapore, and 3.8 in Beijing, China . Therefore, we believe that the commonly acceptable average value of the R 0 of SARS might be 2.9 . The transmissibility of the Middle East respiratory syndrome is much lower than SARS. The reported value of the R 0 of MERS was about 0.8-1.3 , with the inter-human transmissibility of the disease was about", "Title: The Failure of R (0)\nPassage: While the first factor may be fairly uniform across outbreaks, the second may depend significantly on context, varying both within and among populations. The problem with the SARS estimates stems from the mass-action assumption of compartmental models; that is, that all susceptible individuals are equally likely to become infected. When this assumption does not hold, the models may yield inaccurate estimates or estimates that do not apply to all populations. R 0 estimates for SARS in the field were based largely on outbreak data from a hospital and a crowded apartment building, with anomalously high rates of close contacts among", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes. But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures. R is the effectiive number and can include the impact of control measures.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: In this study, we used the R 0 to assess the transmissibility of the SARS-CoV-2. Commonly, R 0 was defined as the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population . If R 0 > 1, the outbreak will occur. If R 0 < 1, the outbreak will toward an end. In this study, R 0 was deduced from the RP model by the next generation matrix approach . The multiple of the transmissibility of A P to that of I P ." ]

[ [ "1a", "Title: The Failure of R (0)" ], [ "1b", "Passage: While the first factor may be fairly uniform across outbreaks, the second may depend significantly on context, varying both within and among populations." ], [ "1c", "The problem with the SARS estimates stems from the mass-action assumption of compartmental models; that is, that all susceptible individuals are equally likely to become infected." ], [ "1d", "When this assumption does not hold, the models may yield inaccurate estimates or estimates that do not apply to all populations." ], [ "1e", "R 0 estimates for SARS in the field were based largely on outbreak data from a hospital and a crowded apartment building, with anomalously high rates of close contacts among" ] ]

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

[ "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Among the 148 swabs initially negative for influenza because not previously tested for any other viruses, the study found an etiology for 95 swabs. In total, only 53 swabs, representing 24% of the sample, remained without etiology with negative multiplex PCR results all along the year. Multiple hypotheses can explain this result: a poor quality of swabs, preventing from identifying a pathogen, noninfectious causes or other pathogens not included in the multiplex PCR. However, we couldn't test the negative swabs for RNAse P, a marker of human cells, which could provide a modicum of assurance that the swab contained human", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: Of the 29 swabs received, 18 had a corresponding research swab that was positive for a respiratory pathogen. Seven corresponding self-swabs were concordant with the positive research swabs for influenza, and eight corresponding self-swabs were concordant with the research swab for noninfluenza pathogens . The kappa statistic between research and self-swab was 0.84. There were no differences in demographic variables, including education level or days between drop-off and receipt of swabs, among participants whose self-and research-staff obtained swabs correlated versus those whose swabs did not correlate . Of the self-swab samples that had a corresponding positive research swab, the longest", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Among the 250 randomly-selected swabs, 26 were not available anymore as they were sent to Influenza Reference Center for confirmation and characterization of the pathogenic agent. According to the sensitivity of the assay two samples could be discordant results between Influenza PCR initially realized and Multiplex PCR. Thus they were deleted from the analysis: one is positive for Influenza in singleplex and negative for all tested pathogens in multiplex and one is positive for Influenza in singleplex and positive for PIV2 in multiplex. In total, 222 analyses were considered. Moreover, 53 samples were negative for all analyzed respiratory pathogens and", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: 2 than -5 laboratory results were not linked to symptoms reported. On the other hand, 272 sick reports could not be merged to nasal swabs. Apart from the same issue of timing, this fact might also be explained by certain symptoms reported. The absence of a nasal sample correlates well with the presence of vomiting and the absence of runny nose. Further details on specimen results can be found in our Eurosurveillance paper . Briefly, when analyzing the seasonality, we found that the peak in the number of returned swabs was reached in the last week of September 2011, but" ]

[ [ "0a", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012" ], [ "0b", "Passage: Among the 148 swabs initially negative for influenza because not previously tested for any other viruses, the study found an etiology for 95 swabs." ], [ "0c", "In total, only 53 swabs, representing 24% of the sample, remained without etiology with negative multiplex PCR results all along the year." ], [ "0d", "Multiple hypotheses can explain this result: a poor quality of swabs, preventing from identifying a pathogen, noninfectious causes or other pathogens not included in the multiplex PCR." ], [ "0e", "However, we couldn't test the negative swabs for RNAse P, a marker of human cells, which could provide a modicum of assurance that the swab contained human" ] ]

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

[ "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Among the 148 swabs initially negative for influenza because not previously tested for any other viruses, the study found an etiology for 95 swabs. In total, only 53 swabs, representing 24% of the sample, remained without etiology with negative multiplex PCR results all along the year. Multiple hypotheses can explain this result: a poor quality of swabs, preventing from identifying a pathogen, noninfectious causes or other pathogens not included in the multiplex PCR. However, we couldn't test the negative swabs for RNAse P, a marker of human cells, which could provide a modicum of assurance that the swab contained human", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: Of the 29 swabs received, 18 had a corresponding research swab that was positive for a respiratory pathogen. Seven corresponding self-swabs were concordant with the positive research swabs for influenza, and eight corresponding self-swabs were concordant with the research swab for noninfluenza pathogens . The kappa statistic between research and self-swab was 0.84. There were no differences in demographic variables, including education level or days between drop-off and receipt of swabs, among participants whose self-and research-staff obtained swabs correlated versus those whose swabs did not correlate . Of the self-swab samples that had a corresponding positive research swab, the longest", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Among the 250 randomly-selected swabs, 26 were not available anymore as they were sent to Influenza Reference Center for confirmation and characterization of the pathogenic agent. According to the sensitivity of the assay two samples could be discordant results between Influenza PCR initially realized and Multiplex PCR. Thus they were deleted from the analysis: one is positive for Influenza in singleplex and negative for all tested pathogens in multiplex and one is positive for Influenza in singleplex and positive for PIV2 in multiplex. In total, 222 analyses were considered. Moreover, 53 samples were negative for all analyzed respiratory pathogens and", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: 2 than -5 laboratory results were not linked to symptoms reported. On the other hand, 272 sick reports could not be merged to nasal swabs. Apart from the same issue of timing, this fact might also be explained by certain symptoms reported. The absence of a nasal sample correlates well with the presence of vomiting and the absence of runny nose. Further details on specimen results can be found in our Eurosurveillance paper . Briefly, when analyzing the seasonality, we found that the peak in the number of returned swabs was reached in the last week of September 2011, but" ]

[ [ "2a", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012" ], [ "2b", "Passage: Among the 250 randomly-selected swabs, 26 were not available anymore as they were sent to Influenza Reference Center for confirmation and characterization of the pathogenic agent." ], [ "2c", "According to the sensitivity of the assay two samples could be discordant results between Influenza PCR initially realized and Multiplex PCR." ], [ "2d", "Thus they were deleted from the analysis: one is positive for Influenza in singleplex and negative for all tested pathogens in multiplex and one is positive for Influenza in singleplex and positive for PIV2 in multiplex." ], [ "2e", "In total, 222 analyses were considered." ], [ "2f", "Moreover, 53 samples were negative for all analyzed respiratory pathogens and" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 ). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 , and 82% with human SARS-CoV BJ01 2003 and human SARS-CoV Tor2 . The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes were shown ). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: subunit of 2019-nCoV shares around 70% identity to that of the two bat SARS-like CoVs and human SARS-CoV ), the core domain of RBD are highly conserved ). Most of the amino acid differences of RBD are located in the external subdomain, which is responsible for the direct interaction with the host receptor. Further investigation of this soluble variable external subdomain region will reveal its receptor usage, interspecies transmission and pathogenesis. Unlike 2019-nCoV and human SARS-CoV, most known bat SARSr-CoVs have two stretches of deletions in the spike receptor binding domain when compared with that of human SARS-CoV. But some", "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." ]

[ [ "2a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "2b", "Passage: subunit of 2019-nCoV shares around 70% identity to that of the two bat SARS-like CoVs and human SARS-CoV ), the core domain of RBD are highly conserved )." ], [ "2c", "Most of the amino acid differences of RBD are located in the external subdomain, which is responsible for the direct interaction with the host receptor." ], [ "2d", "Further investigation of this soluble variable external subdomain region will reveal its receptor usage, interspecies transmission and pathogenesis." ], [ "2e", "Unlike 2019-nCoV and human SARS-CoV, most known bat SARSr-CoVs have two stretches of deletions in the spike receptor binding domain when compared with that of human SARS-CoV. But some" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first WHO case definition defined probable cases of MERS based on the presence of febrile illness, cough and requirement for hospitalization with suspicion of lower respiratory tract involvement. It also included roles for contact with a probable or confirmed case or for travel or residence within the Arabian Peninsula. If strictly adhered to, only the severe syndrome would be subject to laboratory testing, which was the paradigm early on . From July 2013, the revised WHO case definition included the importance of seeking out and understanding the role of asymptomatic cases and from June 2014, the WHO definition more", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: clearly stated that a confirmed case included any person whose sample was RT-PCR positive for MERS-CoV, or who produced a seroconversion, irrespective of clinical signs and symptoms. Apart from the WHO and the KSA Ministry of Health reports, asymptomatic or subclinical cases of MERS-CoV infection were documented in the scientific literature although not always as often as occurred early on . The KSA definition of a case became more strict on 13 th May 2014, relying on the presence of both clinical features and laboratory confirmation . Testing of asymptomatic people was recommended against from December 2014 , reinforced by", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: As a group, HCWs comprised 16 % of MERS cases in the KSA and South Korea. It is apparent that the weekly proportion of infected HCWs increases alongside each steep rise in overall detections . In May 2013, the WHO published guidelines for IPC during care of probable or confirmed cases of MERS-CoV infection in a healthcare setting . This is explainable because to date, each case rise has been intimately associated with healthcare-facility related outbreaks . These rises in MERS-CoV detections can decrease the average age during each event because HCWs are usually younger than inpatients with MERS. Healthcare", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: case detection and management. Data collected included demographics, history of recent travel to affected areas, close contact with a probable or confirmed COVID-19 case, underlying conditions, signs and symptoms of disease at onset, type of specimens from which the virus was detected, and clinical outcome. The WHO case definition was adopted for surveillance: a confirmed case was a person with laboratory confirmation of SARS-CoV-2 infection , irrespective of clinical signs and symptoms, whereas a probable case was a suspect case for whom testing for SARS-CoV-2 was inconclusive or positive using a pan-coronavirus assay . By 31 January 2020, 47 laboratories" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: The first WHO case definition defined probable cases of MERS based on the presence of febrile illness, cough and requirement for hospitalization with suspicion of lower respiratory tract involvement." ], [ "0c", "It also included roles for contact with a probable or confirmed case or for travel or residence within the Arabian Peninsula." ], [ "0d", "If strictly adhered to, only the severe syndrome would be subject to laboratory testing, which was the paradigm early on ." ], [ "0e", "From July 2013, the revised WHO case definition included the importance of seeking out and understanding the role of asymptomatic cases and from June 2014, the WHO definition more" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first WHO case definition defined probable cases of MERS based on the presence of febrile illness, cough and requirement for hospitalization with suspicion of lower respiratory tract involvement. It also included roles for contact with a probable or confirmed case or for travel or residence within the Arabian Peninsula. If strictly adhered to, only the severe syndrome would be subject to laboratory testing, which was the paradigm early on . From July 2013, the revised WHO case definition included the importance of seeking out and understanding the role of asymptomatic cases and from June 2014, the WHO definition more", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: clearly stated that a confirmed case included any person whose sample was RT-PCR positive for MERS-CoV, or who produced a seroconversion, irrespective of clinical signs and symptoms. Apart from the WHO and the KSA Ministry of Health reports, asymptomatic or subclinical cases of MERS-CoV infection were documented in the scientific literature although not always as often as occurred early on . The KSA definition of a case became more strict on 13 th May 2014, relying on the presence of both clinical features and laboratory confirmation . Testing of asymptomatic people was recommended against from December 2014 , reinforced by", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: As a group, HCWs comprised 16 % of MERS cases in the KSA and South Korea. It is apparent that the weekly proportion of infected HCWs increases alongside each steep rise in overall detections . In May 2013, the WHO published guidelines for IPC during care of probable or confirmed cases of MERS-CoV infection in a healthcare setting . This is explainable because to date, each case rise has been intimately associated with healthcare-facility related outbreaks . These rises in MERS-CoV detections can decrease the average age during each event because HCWs are usually younger than inpatients with MERS. Healthcare", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: case detection and management. Data collected included demographics, history of recent travel to affected areas, close contact with a probable or confirmed COVID-19 case, underlying conditions, signs and symptoms of disease at onset, type of specimens from which the virus was detected, and clinical outcome. The WHO case definition was adopted for surveillance: a confirmed case was a person with laboratory confirmation of SARS-CoV-2 infection , irrespective of clinical signs and symptoms, whereas a probable case was a suspect case for whom testing for SARS-CoV-2 was inconclusive or positive using a pan-coronavirus assay . By 31 January 2020, 47 laboratories" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: clearly stated that a confirmed case included any person whose sample was RT-PCR positive for MERS-CoV, or who produced a seroconversion, irrespective of clinical signs and symptoms." ], [ "1c", "Apart from the WHO and the KSA Ministry of Health reports, asymptomatic or subclinical cases of MERS-CoV infection were documented in the scientific literature although not always as often as occurred early on ." ], [ "1d", "The KSA definition of a case became more strict on 13 th May 2014, relying on the presence of both clinical features and laboratory confirmation ." ], [ "1e", "Testing of asymptomatic people was recommended against from December 2014 , reinforced by" ] ]

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

[ "Title: Quantifying social distancing arising from pandemic influenza\nPassage: the build-up of herd immunity and possibly pre-existing immunity.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We have assumed an 'all or nothing' model of prior immunity, meaning that a fraction of individuals were totally protected from infection during the pandemic period. The main alternative model of prior immunity is that a fraction of the population is partially immune, having a lower risk of infection. Under some circumstances, there will be material differences between the behaviour of these prior immunity models: if R 0 is very large, all susceptibles, whether fully or partially immune, will inevitably be infected; alternatively, if there is assortative mixing between classes of susceptibles, fully susceptibles will be overrepresented during the early", "Title: Human mobility and the worldwide impact of intentional localized highly pathogenic virus release\nPassage: The case of 20% immunity in population as a result of the vaccination campaign that successfully eradicated smallpox in the late seventies, was also considered. The results for the UK and the top 20 affected countries in each scenario, 14 days after the attack, are summarized in Fig 9 and Fig 10 for the two seeding possibilities considered. As expected, in both cases, immunity is able to reduce both the number of cases within each country and the respective outbreak probability, but is not sufficient to prevent the infection from spreading into other countries.", "Title: Prolonging herd immunity to cholera via vaccination: Accounting for human mobility and waning vaccine effects\nPassage: Following mass vaccination with 100% coverage, population susceptibility, X, quickly increases over time in the presence of high migration rates and short-lived vaccine efficacy . Even with a hypothetical perfect vaccine that retains complete protection indefinitely, high migration rates can drive population susceptibility near 100% within 9-10 years . Between three primary drivers causing herd immunity to wane, namely migration, waning efficacy, and demographic turnover through births and deaths, we find that the first two are substantially more influential than either the birth or death rate, which are each typically much slower processes. As compared to rates of birth and" ]

[ [ "0a", "Title: Quantifying social distancing arising from pandemic influenza" ], [ "0b", "Passage: the build-up of herd immunity and possibly pre-existing immunity." ] ]

[ "0a", "1a", "3a" ]

[ "Title: Quantifying social distancing arising from pandemic influenza\nPassage: the build-up of herd immunity and possibly pre-existing immunity.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We have assumed an 'all or nothing' model of prior immunity, meaning that a fraction of individuals were totally protected from infection during the pandemic period. The main alternative model of prior immunity is that a fraction of the population is partially immune, having a lower risk of infection. Under some circumstances, there will be material differences between the behaviour of these prior immunity models: if R 0 is very large, all susceptibles, whether fully or partially immune, will inevitably be infected; alternatively, if there is assortative mixing between classes of susceptibles, fully susceptibles will be overrepresented during the early", "Title: Human mobility and the worldwide impact of intentional localized highly pathogenic virus release\nPassage: The case of 20% immunity in population as a result of the vaccination campaign that successfully eradicated smallpox in the late seventies, was also considered. The results for the UK and the top 20 affected countries in each scenario, 14 days after the attack, are summarized in Fig 9 and Fig 10 for the two seeding possibilities considered. As expected, in both cases, immunity is able to reduce both the number of cases within each country and the respective outbreak probability, but is not sufficient to prevent the infection from spreading into other countries.", "Title: Prolonging herd immunity to cholera via vaccination: Accounting for human mobility and waning vaccine effects\nPassage: Following mass vaccination with 100% coverage, population susceptibility, X, quickly increases over time in the presence of high migration rates and short-lived vaccine efficacy . Even with a hypothetical perfect vaccine that retains complete protection indefinitely, high migration rates can drive population susceptibility near 100% within 9-10 years . Between three primary drivers causing herd immunity to wane, namely migration, waning efficacy, and demographic turnover through births and deaths, we find that the first two are substantially more influential than either the birth or death rate, which are each typically much slower processes. As compared to rates of birth and" ]

[ [ "1a", "Title: Quantifying social distancing arising from pandemic influenza" ], [ "1b", "Passage: We have assumed an 'all or nothing' model of prior immunity, meaning that a fraction of individuals were totally protected from infection during the pandemic period." ], [ "1c", "The main alternative model of prior immunity is that a fraction of the population is partially immune, having a lower risk of infection." ], [ "1d", "Under some circumstances, there will be material differences between the behaviour of these prior immunity models: if R 0 is very large, all susceptibles, whether fully or partially immune, will inevitably be infected; alternatively, if there is assortative mixing between classes of susceptibles, fully susceptibles will be overrepresented during the early" ] ]

[ "0a", "1a", "3a" ]

[ "Title: Quantifying social distancing arising from pandemic influenza\nPassage: the build-up of herd immunity and possibly pre-existing immunity.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We have assumed an 'all or nothing' model of prior immunity, meaning that a fraction of individuals were totally protected from infection during the pandemic period. The main alternative model of prior immunity is that a fraction of the population is partially immune, having a lower risk of infection. Under some circumstances, there will be material differences between the behaviour of these prior immunity models: if R 0 is very large, all susceptibles, whether fully or partially immune, will inevitably be infected; alternatively, if there is assortative mixing between classes of susceptibles, fully susceptibles will be overrepresented during the early", "Title: Human mobility and the worldwide impact of intentional localized highly pathogenic virus release\nPassage: The case of 20% immunity in population as a result of the vaccination campaign that successfully eradicated smallpox in the late seventies, was also considered. The results for the UK and the top 20 affected countries in each scenario, 14 days after the attack, are summarized in Fig 9 and Fig 10 for the two seeding possibilities considered. As expected, in both cases, immunity is able to reduce both the number of cases within each country and the respective outbreak probability, but is not sufficient to prevent the infection from spreading into other countries.", "Title: Prolonging herd immunity to cholera via vaccination: Accounting for human mobility and waning vaccine effects\nPassage: Following mass vaccination with 100% coverage, population susceptibility, X, quickly increases over time in the presence of high migration rates and short-lived vaccine efficacy . Even with a hypothetical perfect vaccine that retains complete protection indefinitely, high migration rates can drive population susceptibility near 100% within 9-10 years . Between three primary drivers causing herd immunity to wane, namely migration, waning efficacy, and demographic turnover through births and deaths, we find that the first two are substantially more influential than either the birth or death rate, which are each typically much slower processes. As compared to rates of birth and" ]

[ [ "3a", "Title: Prolonging herd immunity to cholera via vaccination: Accounting for human mobility and waning vaccine effects" ], [ "3b", "Passage: Following mass vaccination with 100% coverage, population susceptibility, X, quickly increases over time in the presence of high migration rates and short-lived vaccine efficacy ." ], [ "3c", "Even with a hypothetical perfect vaccine that retains complete protection indefinitely, high migration rates can drive population susceptibility near 100% within 9-10 years ." ], [ "3d", "Between three primary drivers causing herd immunity to wane, namely migration, waning efficacy, and demographic turnover through births and deaths, we find that the first two are substantially more influential than either the birth or death rate, which are each typically much slower processes." ], [ "3e", "As compared to rates of birth and" ] ]

[ "0a", "1a", "3a" ]

[ "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: syndrome such as high blood pressure. Macrophage activation syndrome could also lead to acute necrotic brain injury. However, it is associated to high ferritin and low triglycerides at the time of the encephalopathy, other multisystemic injuries, typical neuropathological findings, and recurrence over time, which were not noted in our patient . Parvovirus B19 has been described to cause encephalopathy in sickle cell patients. It is associated with aplastic anemia. It caused punctate areas of hemorrhages in the basal ganglia, periventricular white matter, and mainly along the posterior parietal cortex. This was attributed to parvovirus B19-induced vasculitis . In our patient,", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: Several differential diagnoses of acute encephalopathy in a patient with sickle cell anemia can be considered. An infectious encephalitis, including herpes encephalitis, was ruled out by blood and CSF bacterial and viral cultures and negative HSV I/ II PCR. Nasopharyngeal aspirate was negative for viruses. Some infections have been previously associated with necrotizing encephalitis such as Influenza A . SCD patients are prone to ischemic or hemorrhagic strokes . Primary hemorrhagic stroke is uncommon in pediatric SCD. Most cases were from adults and have been described in the context of previous ischemic stroke, aneurysms, low hemoglobin, acute chest syndrome, and", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: there was no sign of aplasia or any neuroradiological finding of parvovirus B19 infection. Finally, acute encephalitis has been observed in SCD patients in the context of arterial hypoxemia from fat embolism, pulmonary embolism, sudden anemia, or acute chest syndrome due to pneumonia . This was ruled out as the patient did not have clinical or radiological signs of acute chest syndrome or embolism and there was no arterial hypoxemia.", "Title: MLKL Mediated Necroptosis Accelerates JEV-Induced Neuroinflammation in Mice\nPassage: Japanese encephalitis virus is the most prevalent cause of viral encephalitis worldwide. More than 67,900 cases of JE are reported annually, among which approximately 30% are fatal and 50% suffer from permanent neuropsychiatric sequelae . JEV infection causes devastating and fatal neuroinflammation characterized by neuronal destruction accompanied with intense microgliosis, strogliosis, and production of various inflammatory cytokines . Neurons can be destroyed directly by JEV infection and indirectly by inflammation mediated cytotoxicity . Then the massive neuronal death contributes to the progression and deterioration of Japanese encephalitis ." ]

[ [ "0a", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant" ], [ "0b", "Passage: syndrome such as high blood pressure." ], [ "0c", "Macrophage activation syndrome could also lead to acute necrotic brain injury." ], [ "0d", "However, it is associated to high ferritin and low triglycerides at the time of the encephalopathy, other multisystemic injuries, typical neuropathological findings, and recurrence over time, which were not noted in our patient ." ], [ "0e", "Parvovirus B19 has been described to cause encephalopathy in sickle cell patients." ], [ "0f", "It is associated with aplastic anemia." ], [ "0g", "It caused punctate areas of hemorrhages in the basal ganglia, periventricular white matter, and mainly along the posterior parietal cortex." ], [ "0h", "This was attributed to parvovirus B19-induced vasculitis ." ], [ "0i", "In our patient," ] ]

[ "0c", "0e", "0g", "0h", "1e", "1f", "2c" ]

[ "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: syndrome such as high blood pressure. Macrophage activation syndrome could also lead to acute necrotic brain injury. However, it is associated to high ferritin and low triglycerides at the time of the encephalopathy, other multisystemic injuries, typical neuropathological findings, and recurrence over time, which were not noted in our patient . Parvovirus B19 has been described to cause encephalopathy in sickle cell patients. It is associated with aplastic anemia. It caused punctate areas of hemorrhages in the basal ganglia, periventricular white matter, and mainly along the posterior parietal cortex. This was attributed to parvovirus B19-induced vasculitis . In our patient,", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: Several differential diagnoses of acute encephalopathy in a patient with sickle cell anemia can be considered. An infectious encephalitis, including herpes encephalitis, was ruled out by blood and CSF bacterial and viral cultures and negative HSV I/ II PCR. Nasopharyngeal aspirate was negative for viruses. Some infections have been previously associated with necrotizing encephalitis such as Influenza A . SCD patients are prone to ischemic or hemorrhagic strokes . Primary hemorrhagic stroke is uncommon in pediatric SCD. Most cases were from adults and have been described in the context of previous ischemic stroke, aneurysms, low hemoglobin, acute chest syndrome, and", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: there was no sign of aplasia or any neuroradiological finding of parvovirus B19 infection. Finally, acute encephalitis has been observed in SCD patients in the context of arterial hypoxemia from fat embolism, pulmonary embolism, sudden anemia, or acute chest syndrome due to pneumonia . This was ruled out as the patient did not have clinical or radiological signs of acute chest syndrome or embolism and there was no arterial hypoxemia.", "Title: MLKL Mediated Necroptosis Accelerates JEV-Induced Neuroinflammation in Mice\nPassage: Japanese encephalitis virus is the most prevalent cause of viral encephalitis worldwide. More than 67,900 cases of JE are reported annually, among which approximately 30% are fatal and 50% suffer from permanent neuropsychiatric sequelae . JEV infection causes devastating and fatal neuroinflammation characterized by neuronal destruction accompanied with intense microgliosis, strogliosis, and production of various inflammatory cytokines . Neurons can be destroyed directly by JEV infection and indirectly by inflammation mediated cytotoxicity . Then the massive neuronal death contributes to the progression and deterioration of Japanese encephalitis ." ]

[ [ "1a", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant" ], [ "1b", "Passage: Several differential diagnoses of acute encephalopathy in a patient with sickle cell anemia can be considered." ], [ "1c", "An infectious encephalitis, including herpes encephalitis, was ruled out by blood and CSF bacterial and viral cultures and negative HSV I/ II PCR." ], [ "1d", "Nasopharyngeal aspirate was negative for viruses." ], [ "1e", "Some infections have been previously associated with necrotizing encephalitis such as Influenza A ." ], [ "1f", "SCD patients are prone to ischemic or hemorrhagic strokes ." ], [ "1g", "Primary hemorrhagic stroke is uncommon in pediatric SCD." ], [ "1h", "Most cases were from adults and have been described in the context of previous ischemic stroke, aneurysms, low hemoglobin, acute chest syndrome, and" ] ]

[ "0c", "0e", "0g", "0h", "1e", "1f", "2c" ]

[ "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: syndrome such as high blood pressure. Macrophage activation syndrome could also lead to acute necrotic brain injury. However, it is associated to high ferritin and low triglycerides at the time of the encephalopathy, other multisystemic injuries, typical neuropathological findings, and recurrence over time, which were not noted in our patient . Parvovirus B19 has been described to cause encephalopathy in sickle cell patients. It is associated with aplastic anemia. It caused punctate areas of hemorrhages in the basal ganglia, periventricular white matter, and mainly along the posterior parietal cortex. This was attributed to parvovirus B19-induced vasculitis . In our patient,", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: Several differential diagnoses of acute encephalopathy in a patient with sickle cell anemia can be considered. An infectious encephalitis, including herpes encephalitis, was ruled out by blood and CSF bacterial and viral cultures and negative HSV I/ II PCR. Nasopharyngeal aspirate was negative for viruses. Some infections have been previously associated with necrotizing encephalitis such as Influenza A . SCD patients are prone to ischemic or hemorrhagic strokes . Primary hemorrhagic stroke is uncommon in pediatric SCD. Most cases were from adults and have been described in the context of previous ischemic stroke, aneurysms, low hemoglobin, acute chest syndrome, and", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: there was no sign of aplasia or any neuroradiological finding of parvovirus B19 infection. Finally, acute encephalitis has been observed in SCD patients in the context of arterial hypoxemia from fat embolism, pulmonary embolism, sudden anemia, or acute chest syndrome due to pneumonia . This was ruled out as the patient did not have clinical or radiological signs of acute chest syndrome or embolism and there was no arterial hypoxemia.", "Title: MLKL Mediated Necroptosis Accelerates JEV-Induced Neuroinflammation in Mice\nPassage: Japanese encephalitis virus is the most prevalent cause of viral encephalitis worldwide. More than 67,900 cases of JE are reported annually, among which approximately 30% are fatal and 50% suffer from permanent neuropsychiatric sequelae . JEV infection causes devastating and fatal neuroinflammation characterized by neuronal destruction accompanied with intense microgliosis, strogliosis, and production of various inflammatory cytokines . Neurons can be destroyed directly by JEV infection and indirectly by inflammation mediated cytotoxicity . Then the massive neuronal death contributes to the progression and deterioration of Japanese encephalitis ." ]

[ [ "2a", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant" ], [ "2b", "Passage: there was no sign of aplasia or any neuroradiological finding of parvovirus B19 infection." ], [ "2c", "Finally, acute encephalitis has been observed in SCD patients in the context of arterial hypoxemia from fat embolism, pulmonary embolism, sudden anemia, or acute chest syndrome due to pneumonia ." ], [ "2d", "This was ruled out as the patient did not have clinical or radiological signs of acute chest syndrome or embolism and there was no arterial hypoxemia." ] ]

[ "0c", "0e", "0g", "0h", "1e", "1f", "2c" ]

[ "Title: Early responses to H7N9 in southern Mainland China\nPassage: random number. Three thousand and fifty-four telephone numbers were dialled, of which 1082 gave interviews, and 1972 refused to participate . A further 32 gave incomplete responses , 39 were deleted as they had not heard of H7N9 or were out of the age quota group, leaving an eligible 1011 participants. Response rates compare positively to analogous public surveys on swine flu . Table 1 breaks down participants by age, sex and occupation, comparing these categories with wider Shanghai data .", "Title: Initial psychological responses to Influenza A, H1N1 (\"Swine flu\")\nPassage: Following ethical approval by the relevant University ethics boards in London and Malaysia, data was collected from a total of 328 respondents . A paper version of the questionnaire was distributed in Malaysia, with students recruiting 180 respondents from their own classes, and community members from residential areas and local offices in Kuala Lumpur , 59% female)). Response rate was generally good, with 180 out of 200 approached to participate completing the questionnaire. In Europe, data was collected between 30 th April and 6 th May 2009 from 158 respondents via an online questionnaire in English or Portuguese, linked to", "Title: Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study\nPassage: Sample size determination. We estimated that a sample of at least 500 was required to achieve 80% power at an a = 0.05 to reject a model of the specified complexity if the model fit index Root Mean Square Error of Approximation exceeded 0.08 . To allow for a response rate ,60% in the follow-up and the baseline surveys, we need to target at least 1,389 subjects in the baseline survey.", "Title: Phase 1 Study of Pandemic H1 DNA Vaccine in Healthy Adults\nPassage: binomial confidence interval of the true response rate will range from 0.057 to 0.437. Table 6 .1 gives the probabilities of observing 0 or at least 2 responses over a range of underlying response rates. For example, if the true response rate at a particular time point is 0.20, then there is a probability of 0.988 to observe at least one response and a probability of 0.931 to observe at least two responses among the 20 vaccinees." ]

[ [ "1a", "Title: Initial psychological responses to Influenza A, H1N1 (\"Swine flu\")" ], [ "1b", "Passage: Following ethical approval by the relevant University ethics boards in London and Malaysia, data was collected from a total of 328 respondents ." ], [ "1c", "A paper version of the questionnaire was distributed in Malaysia, with students recruiting 180 respondents from their own classes, and community members from residential areas and local offices in Kuala Lumpur , 59% female))." ], [ "1d", "Response rate was generally good, with 180 out of 200 approached to participate completing the questionnaire." ], [ "1e", "In Europe, data was collected between 30 th April and 6 th May 2009 from 158 respondents via an online questionnaire in English or Portuguese, linked to" ] ]

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

[ "Title: Early responses to H7N9 in southern Mainland China\nPassage: random number. Three thousand and fifty-four telephone numbers were dialled, of which 1082 gave interviews, and 1972 refused to participate . A further 32 gave incomplete responses , 39 were deleted as they had not heard of H7N9 or were out of the age quota group, leaving an eligible 1011 participants. Response rates compare positively to analogous public surveys on swine flu . Table 1 breaks down participants by age, sex and occupation, comparing these categories with wider Shanghai data .", "Title: Initial psychological responses to Influenza A, H1N1 (\"Swine flu\")\nPassage: Following ethical approval by the relevant University ethics boards in London and Malaysia, data was collected from a total of 328 respondents . A paper version of the questionnaire was distributed in Malaysia, with students recruiting 180 respondents from their own classes, and community members from residential areas and local offices in Kuala Lumpur , 59% female)). Response rate was generally good, with 180 out of 200 approached to participate completing the questionnaire. In Europe, data was collected between 30 th April and 6 th May 2009 from 158 respondents via an online questionnaire in English or Portuguese, linked to", "Title: Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study\nPassage: Sample size determination. We estimated that a sample of at least 500 was required to achieve 80% power at an a = 0.05 to reject a model of the specified complexity if the model fit index Root Mean Square Error of Approximation exceeded 0.08 . To allow for a response rate ,60% in the follow-up and the baseline surveys, we need to target at least 1,389 subjects in the baseline survey.", "Title: Phase 1 Study of Pandemic H1 DNA Vaccine in Healthy Adults\nPassage: binomial confidence interval of the true response rate will range from 0.057 to 0.437. Table 6 .1 gives the probabilities of observing 0 or at least 2 responses over a range of underlying response rates. For example, if the true response rate at a particular time point is 0.20, then there is a probability of 0.988 to observe at least one response and a probability of 0.931 to observe at least two responses among the 20 vaccinees." ]

[ [ "2a", "Title: Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study" ], [ "2b", "Passage: Sample size determination." ], [ "2c", "We estimated that a sample of at least 500 was required to achieve 80% power at an a = 0.05 to reject a model of the specified complexity if the model fit index Root Mean Square Error of Approximation exceeded 0.08 ." ], [ "2d", "To allow for a response rate ,60% in the follow-up and the baseline surveys, we need to target at least 1,389 subjects in the baseline survey." ] ]

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

[ "Title: Junín virus induces autophagy in human A549 cells\nPassage: the Candid#1 vaccine.", "Title: Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors\nPassage: Currently, the only clinically successful anti-arenaviral vaccine is the anti-JUNV Candid #1 strain, which is currently manufactured by the Argentinian government but is not being considered for large-scale use due to its limited target population as only Argentina is endemic for JUNV infection. To generate Candid #1, a human viral isolate was used to passage twice in guinea pigs followed by additional passages in suckling mice and cell cultures . A number of unique mutations in Candid #1 were originally thought to attenuate Candid #1 compared to its parental WT strain , and one such mutation was consistently found to", "Title: Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors\nPassage: of other arenaviral vaccines. However, they may be limited to the JUNV vaccine for several reasons. While the IFN1 pathway pathway and subsequent T-cell response have been found to be critical in controlling arenaviral infection in mice , arenaviral-associated immunosuppression results in limited T-cell responses . Furthermore, the JUNV GP has been found to contain fewer glycans than the GPs from other mammarenaviruses , and glycan residues on the glycan-rich LASV GP has been shown to promote neutralization antibody evasion . This is strengthened by recent observations that anti-JUNV antibodies from infected patients can neutralize other JUNV strains but cannot", "Title: In silico Design of a Multivalent Vaccine Against Candida albicans\nPassage: suffering from chronic vaginal yeast infections . It consists of a truncated recombinant secreted aspartic protease 2 , currently in clinical testing by Pevion BiotechAG 10 . NDV3 targets the recombinant N-terminal region of the hyphal protein agglutinin-like sequence three protein and is being developed by NovaDigm Therapeutics 12 . Another vaccination approach from Novartis Pharmaceuticals based on monoclonal antibody targeting the heat shock protein 90 progressed through to a Phase III clinical trial but was abandoned in later stages of development due to safety concerns 13 . Finally, a prophylactic and therapeutic IgM-monoclonal antibody by LigoCyte Pharmaceuticals that targeted" ]

[ [ "0a", "Title: Junín virus induces autophagy in human A549 cells" ], [ "0b", "Passage: the Candid#1 vaccine." ] ]

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

[ "Title: Junín virus induces autophagy in human A549 cells\nPassage: the Candid#1 vaccine.", "Title: Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors\nPassage: Currently, the only clinically successful anti-arenaviral vaccine is the anti-JUNV Candid #1 strain, which is currently manufactured by the Argentinian government but is not being considered for large-scale use due to its limited target population as only Argentina is endemic for JUNV infection. To generate Candid #1, a human viral isolate was used to passage twice in guinea pigs followed by additional passages in suckling mice and cell cultures . A number of unique mutations in Candid #1 were originally thought to attenuate Candid #1 compared to its parental WT strain , and one such mutation was consistently found to", "Title: Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors\nPassage: of other arenaviral vaccines. However, they may be limited to the JUNV vaccine for several reasons. While the IFN1 pathway pathway and subsequent T-cell response have been found to be critical in controlling arenaviral infection in mice , arenaviral-associated immunosuppression results in limited T-cell responses . Furthermore, the JUNV GP has been found to contain fewer glycans than the GPs from other mammarenaviruses , and glycan residues on the glycan-rich LASV GP has been shown to promote neutralization antibody evasion . This is strengthened by recent observations that anti-JUNV antibodies from infected patients can neutralize other JUNV strains but cannot", "Title: In silico Design of a Multivalent Vaccine Against Candida albicans\nPassage: suffering from chronic vaginal yeast infections . It consists of a truncated recombinant secreted aspartic protease 2 , currently in clinical testing by Pevion BiotechAG 10 . NDV3 targets the recombinant N-terminal region of the hyphal protein agglutinin-like sequence three protein and is being developed by NovaDigm Therapeutics 12 . Another vaccination approach from Novartis Pharmaceuticals based on monoclonal antibody targeting the heat shock protein 90 progressed through to a Phase III clinical trial but was abandoned in later stages of development due to safety concerns 13 . Finally, a prophylactic and therapeutic IgM-monoclonal antibody by LigoCyte Pharmaceuticals that targeted" ]

[ [ "1a", "Title: Hemorrhagic Fever-Causing Arenaviruses: Lethal Pathogens and Potent Immune Suppressors" ], [ "1b", "Passage: Currently, the only clinically successful anti-arenaviral vaccine is the anti-JUNV Candid #1 strain, which is currently manufactured by the Argentinian government but is not being considered for large-scale use due to its limited target population as only Argentina is endemic for JUNV infection." ], [ "1c", "To generate Candid #1, a human viral isolate was used to passage twice in guinea pigs followed by additional passages in suckling mice and cell cultures ." ], [ "1d", "A number of unique mutations in Candid #1 were originally thought to attenuate Candid #1 compared to its parental WT strain , and one such mutation was consistently found to" ] ]

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

[ "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: should also stimulate further studies of mechanisms of the different pathogenicity among human adenovirus serotypes.", "Title: A review of Phase I trials of Ebola virus vaccines: what can we learn from the race to develop novel vaccines?\nPassage: Recombinant human serotype 5 adenovirus vectors encoding GP have been evaluated in single-dose studies and have shown very acceptable safety profiles. Unfortunately, AdHu5-seropositive volunteers demonstrated statistically significantly lower GP-specific IgG titres . Increasing the administered dose of vaccine appears to overcome pre-existing immunity to this serotype; however, this is associated with increased reactogenicity . Unfounded concerns also still persist about a potential increase in HIV-1 infection rates among AdHu5-seropositive vaccinees, based on data from two Phase II studies of the Merck rAd5 HIV-1 gag/pol/nef vaccine . Use of rarer serotypes of human adenoviruses, such as Ad26 and AdHu35, can bypass", "Title: Germinal Center B Cell and T Follicular Helper Cell Responses to Viral Vector and Protein-in-Adjuvant Vaccines\nPassage: Adenovirus is probably the leading viral vector platform for Ab response induction, having reached clinical trials for a variety of major diseases and attracted the interest of leading pharmaceutical companies. To represent this approach, we used human adenovirus serotype 5 expressing the model Ag OVA. AdHu5 is the most widely studied adenovirus vaccine vector, and although its use in humans is limited by the prevalence of anti-AdHu5 neutralizing Abs, it is among the most immunogenic adenovectors in mice and primates . There are a variety of differences between and within adenovirus species: as a member of adenovirus species C, AdHu5", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Currently, replication-deficient human adenovirus serotype 5 vaccines are being evaluated against several pathogens. Several candidates have been shown to induce protective immune responses against emerging or re-emerging infectious pathogens such as Ebola and avian influenza viruses Complete protection and long-term memory responses have also been reported in different animal models ; however, the final development of AdHu5-based vector to approved human vaccines has been hampered by the presence of natural preexisting immunity to AdHu5 which is present in a large fraction of the human population. Neutralizing antibody to porcine adenovirus 3 was not detected from pooled immune globulin representing 10" ]

[ [ "1a", "Title: A review of Phase I trials of Ebola virus vaccines: what can we learn from the race to develop novel vaccines?" ], [ "1b", "Passage: Recombinant human serotype 5 adenovirus vectors encoding GP have been evaluated in single-dose studies and have shown very acceptable safety profiles." ], [ "1c", "Unfortunately, AdHu5-seropositive volunteers demonstrated statistically significantly lower GP-specific IgG titres ." ], [ "1d", "Increasing the administered dose of vaccine appears to overcome pre-existing immunity to this serotype; however, this is associated with increased reactogenicity ." ], [ "1e", "Unfounded concerns also still persist about a potential increase in HIV-1 infection rates among AdHu5-seropositive vaccinees, based on data from two Phase II studies of the Merck rAd5 HIV-1 gag/pol/nef vaccine ." ], [ "1f", "Use of rarer serotypes of human adenoviruses, such as Ad26 and AdHu35, can bypass" ] ]

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

[ "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: should also stimulate further studies of mechanisms of the different pathogenicity among human adenovirus serotypes.", "Title: A review of Phase I trials of Ebola virus vaccines: what can we learn from the race to develop novel vaccines?\nPassage: Recombinant human serotype 5 adenovirus vectors encoding GP have been evaluated in single-dose studies and have shown very acceptable safety profiles. Unfortunately, AdHu5-seropositive volunteers demonstrated statistically significantly lower GP-specific IgG titres . Increasing the administered dose of vaccine appears to overcome pre-existing immunity to this serotype; however, this is associated with increased reactogenicity . Unfounded concerns also still persist about a potential increase in HIV-1 infection rates among AdHu5-seropositive vaccinees, based on data from two Phase II studies of the Merck rAd5 HIV-1 gag/pol/nef vaccine . Use of rarer serotypes of human adenoviruses, such as Ad26 and AdHu35, can bypass", "Title: Germinal Center B Cell and T Follicular Helper Cell Responses to Viral Vector and Protein-in-Adjuvant Vaccines\nPassage: Adenovirus is probably the leading viral vector platform for Ab response induction, having reached clinical trials for a variety of major diseases and attracted the interest of leading pharmaceutical companies. To represent this approach, we used human adenovirus serotype 5 expressing the model Ag OVA. AdHu5 is the most widely studied adenovirus vaccine vector, and although its use in humans is limited by the prevalence of anti-AdHu5 neutralizing Abs, it is among the most immunogenic adenovectors in mice and primates . There are a variety of differences between and within adenovirus species: as a member of adenovirus species C, AdHu5", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Currently, replication-deficient human adenovirus serotype 5 vaccines are being evaluated against several pathogens. Several candidates have been shown to induce protective immune responses against emerging or re-emerging infectious pathogens such as Ebola and avian influenza viruses Complete protection and long-term memory responses have also been reported in different animal models ; however, the final development of AdHu5-based vector to approved human vaccines has been hampered by the presence of natural preexisting immunity to AdHu5 which is present in a large fraction of the human population. Neutralizing antibody to porcine adenovirus 3 was not detected from pooled immune globulin representing 10" ]

[ [ "2a", "Title: Germinal Center B Cell and T Follicular Helper Cell Responses to Viral Vector and Protein-in-Adjuvant Vaccines" ], [ "2b", "Passage: Adenovirus is probably the leading viral vector platform for Ab response induction, having reached clinical trials for a variety of major diseases and attracted the interest of leading pharmaceutical companies." ], [ "2c", "To represent this approach, we used human adenovirus serotype 5 expressing the model Ag OVA." ], [ "2d", "AdHu5 is the most widely studied adenovirus vaccine vector, and although its use in humans is limited by the prevalence of anti-AdHu5 neutralizing Abs, it is among the most immunogenic adenovectors in mice and primates ." ], [ "2e", "There are a variety of differences between and within adenovirus species: as a member of adenovirus species C, AdHu5" ] ]

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

[ "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: should also stimulate further studies of mechanisms of the different pathogenicity among human adenovirus serotypes.", "Title: A review of Phase I trials of Ebola virus vaccines: what can we learn from the race to develop novel vaccines?\nPassage: Recombinant human serotype 5 adenovirus vectors encoding GP have been evaluated in single-dose studies and have shown very acceptable safety profiles. Unfortunately, AdHu5-seropositive volunteers demonstrated statistically significantly lower GP-specific IgG titres . Increasing the administered dose of vaccine appears to overcome pre-existing immunity to this serotype; however, this is associated with increased reactogenicity . Unfounded concerns also still persist about a potential increase in HIV-1 infection rates among AdHu5-seropositive vaccinees, based on data from two Phase II studies of the Merck rAd5 HIV-1 gag/pol/nef vaccine . Use of rarer serotypes of human adenoviruses, such as Ad26 and AdHu35, can bypass", "Title: Germinal Center B Cell and T Follicular Helper Cell Responses to Viral Vector and Protein-in-Adjuvant Vaccines\nPassage: Adenovirus is probably the leading viral vector platform for Ab response induction, having reached clinical trials for a variety of major diseases and attracted the interest of leading pharmaceutical companies. To represent this approach, we used human adenovirus serotype 5 expressing the model Ag OVA. AdHu5 is the most widely studied adenovirus vaccine vector, and although its use in humans is limited by the prevalence of anti-AdHu5 neutralizing Abs, it is among the most immunogenic adenovectors in mice and primates . There are a variety of differences between and within adenovirus species: as a member of adenovirus species C, AdHu5", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Currently, replication-deficient human adenovirus serotype 5 vaccines are being evaluated against several pathogens. Several candidates have been shown to induce protective immune responses against emerging or re-emerging infectious pathogens such as Ebola and avian influenza viruses Complete protection and long-term memory responses have also been reported in different animal models ; however, the final development of AdHu5-based vector to approved human vaccines has been hampered by the presence of natural preexisting immunity to AdHu5 which is present in a large fraction of the human population. Neutralizing antibody to porcine adenovirus 3 was not detected from pooled immune globulin representing 10" ]

[ [ "3a", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model" ], [ "3b", "Passage: Currently, replication-deficient human adenovirus serotype 5 vaccines are being evaluated against several pathogens." ], [ "3c", "Several candidates have been shown to induce protective immune responses against emerging or re-emerging infectious pathogens such as Ebola and avian influenza viruses Complete protection and long-term memory responses have also been reported in different animal models ; however, the final development of AdHu5-based vector to approved human vaccines has been hampered by the presence of natural preexisting immunity to AdHu5 which is present in a large fraction of the human population." ], [ "3d", "Neutralizing antibody to porcine adenovirus 3 was not detected from pooled immune globulin representing 10" ] ]

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

[ "Title: National intensive care unit bed capacity and ICU patient characteristics in a low income country\nPassage: Limitations of this study include its retrospective nature with the consequence that it could not provide the same level of evidence as a prospective survey. Furthermore, due to the concise format of medical records, only limited data could be retrieved for this audit. For example, information on whether patients received mechanical ventilation; the volume of fluids; and drugs was not available. According to anecdotal evidence, 99% of all admissions are mechanically ventilated; however, the lack of data to support this precludes us stating this as a fact. Other ICU-relevant data would have allowed better description of the study population. More", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: The lack of inclusion of relevant factors in the methods was the most common limitation acknowledged by the authors. These included: spatial and socio-economic heterogeneity, seasonality, changing immunity, and other environmental drivers. In almost 20% of papers, the authors identified reporting bias as a key limitation. Examples of reporting bias were: sample collections not properly designed ; voluntary internetbased survey reflecting survey respondents' idiosyncrasies; and health-seeking behaviours and socio-economic factors affecting access to health facilities.", "Title: Early and dynamic alterations of Th2/Th1 in previously immunocompetent patients with community-acquired severe sepsis: a prospective observational study\nPassage: There are several potential limitations. This was a single-centre study. Data collection was limited to variables available during usual care and resulted in an imbalance between groups. Besides, among 338 severe sepsis patients admitted to our centre during 2-year study period, most were excluded for hospital-acquired sepsis, diagnosis of tumour and receipt of chemotherapy or corticosteroid, resulting in enrolling 71 patients, which might bring enrolment bias. Another limitation of this study is that the exact time of severe sepsis onset could not be precisely determined, though we have defined the onset to be the time recordable manifestation or laboratory findings", "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: A limitation to this study is that only SHCLCI cases were recorded during the study period. This unables global hospitalization burden estimates caused by seasonal influenza nor the estimation of seasonal differences in vaccine effectiveness to prevent severity and death. The system identifies the epidemiological and virological characteristics of severe forms of influenza that show changes in their virulence, but comparison between severe and non-severe cases is not feasible. The proportion of SHCLCI cases admitted to ICU and CFRs are potentially higher than other surveillance systems that monitor all hospitalised cases of confirmed influenza. This is particularly evident with regard" ]

[ [ "3a", "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)" ], [ "3b", "Passage: A limitation to this study is that only SHCLCI cases were recorded during the study period." ], [ "3c", "This unables global hospitalization burden estimates caused by seasonal influenza nor the estimation of seasonal differences in vaccine effectiveness to prevent severity and death." ], [ "3d", "The system identifies the epidemiological and virological characteristics of severe forms of influenza that show changes in their virulence, but comparison between severe and non-severe cases is not feasible." ], [ "3e", "The proportion of SHCLCI cases admitted to ICU and CFRs are potentially higher than other surveillance systems that monitor all hospitalised cases of confirmed influenza." ], [ "3f", "This is particularly evident with regard" ] ]

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

[ "Title: Passive immunization of macaques with polyclonal anti-SHIV IgG against a heterologous tier 2 SHIV: outcome depends on IgG dose\nPassage: the difference was statistically significant. The higher HIV-1 infection rate of HIVIGLOB-treated infants persisted throughout six months of follow-up, although differences at later time points were not statistically significant. In essence, passive immunization with HIVIGLOB did not prevent HIV-1 acquisition in any infants born to infected mothers, and may have enhanced in utero HIV-1 transmission.", "Title: Treatment with hyperimmune equine immunoglobulin or immunoglobulin fragments completely protects rodents from Ebola virus infection\nPassage: survived , with an average weight loss of 12.3% and a MTD of 6.6 ± 0.6 dpi . Comparing groups with equal treatment times, there was no statistical difference between F 2 at 1 or 2 dpi . However, given that multiple administrations of F 2 were required to achieve similar protection levels demonstrated by a single injection of antisera, the results suggest that equine antisera is a superior product to F 2 in terms of efficacy, possibly due to a longer in vivo half-life of equine antiseras.", "Title: Evaluation of Mucosal and Systemic Immune Responses Elicited by GPI-0100- Adjuvanted Influenza Vaccine Delivered by Different Immunization Strategies\nPassage: Calibration plates for IgG1 and IgG2a assay were coated with 0.1 µg goat anti-mouse IgG . Increasing concentrations of purified mouse IgG1 or IgG2a were added to the plates. IgG1 and IgG2a responses detected from individual sample are given as concentration of H1N1-specific IgG1 and IgG2a.", "Title: Generation of Human Antigen-Specific Monoclonal IgM Antibodies Using Vaccinated “Human Immune System” Mice\nPassage: IgG response . This suggests that repeated vaccination leads to enhanced antigen-specific antibody production. The responder mice exhibited higher total IgM and total IgG concentrations in their plasma, as compared to PBS-injected and non-responder vaccinated animals ." ]

[ [ "0a", "Title: Passive immunization of macaques with polyclonal anti-SHIV IgG against a heterologous tier 2 SHIV: outcome depends on IgG dose" ], [ "0b", "Passage: the difference was statistically significant." ], [ "0c", "The higher HIV-1 infection rate of HIVIGLOB-treated infants persisted throughout six months of follow-up, although differences at later time points were not statistically significant." ], [ "0d", "In essence, passive immunization with HIVIGLOB did not prevent HIV-1 acquisition in any infants born to infected mothers, and may have enhanced in utero HIV-1 transmission." ] ]

[ "0a", "0d" ]

[ "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China\nPassage: 2019-nCoV patients should be admitted to singlebedded, negative pressure rooms in isolated units with intensive care and monitoring . Clinical engineering should have plans to reconstruct standard rooms . Retrofitting the rooms with externally exhausted HEPA filters may be an expedient solution. Also, the general hospital may consider procedures such as suspending elective surgeries, canceling ambulatory clinics and outpatient diagnostic procedures, transferring patients to other institutions, and restricting hospital visitors . More importantly, because the hospitals' ability to respond to the outbreak largely depends on their available ICU beds, the plan to increase ICU bed capacity needs to be determined.", "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China\nPassage: > 3 weeks according to some literature and our unpublished data . Healthcare providers and those in contact with infected patients should utilize contact, droplet, and airborne precautions with N95 respirator. Strict infection prevention and control practices have been implemented and audited in our units following the infection prevention and control plan published by China's National Health Committee . In addition, wellequipped fever clinic as triage station with trained staff knowing 2019-nCoV case definitions is established. For suspected 2019-nCoV infection, several key points are crucial procedures: recording a detailed history, standardizing pneumonia workup, obtaining lower respiratory tract specimens , and", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: hospitals be needed, and social media be employed.", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: and DR examination rooms, should be implemented properly." ]

[ [ "0a", "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China" ], [ "0b", "Passage: 2019-nCoV patients should be admitted to singlebedded, negative pressure rooms in isolated units with intensive care and monitoring ." ], [ "0c", "Clinical engineering should have plans to reconstruct standard rooms ." ], [ "0d", "Retrofitting the rooms with externally exhausted HEPA filters may be an expedient solution." ], [ "0e", "Also, the general hospital may consider procedures such as suspending elective surgeries, canceling ambulatory clinics and outpatient diagnostic procedures, transferring patients to other institutions, and restricting hospital visitors ." ], [ "0f", "More importantly, because the hospitals' ability to respond to the outbreak largely depends on their available ICU beds, the plan to increase ICU bed capacity needs to be determined." ] ]

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

[ "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China\nPassage: 2019-nCoV patients should be admitted to singlebedded, negative pressure rooms in isolated units with intensive care and monitoring . Clinical engineering should have plans to reconstruct standard rooms . Retrofitting the rooms with externally exhausted HEPA filters may be an expedient solution. Also, the general hospital may consider procedures such as suspending elective surgeries, canceling ambulatory clinics and outpatient diagnostic procedures, transferring patients to other institutions, and restricting hospital visitors . More importantly, because the hospitals' ability to respond to the outbreak largely depends on their available ICU beds, the plan to increase ICU bed capacity needs to be determined.", "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China\nPassage: > 3 weeks according to some literature and our unpublished data . Healthcare providers and those in contact with infected patients should utilize contact, droplet, and airborne precautions with N95 respirator. Strict infection prevention and control practices have been implemented and audited in our units following the infection prevention and control plan published by China's National Health Committee . In addition, wellequipped fever clinic as triage station with trained staff knowing 2019-nCoV case definitions is established. For suspected 2019-nCoV infection, several key points are crucial procedures: recording a detailed history, standardizing pneumonia workup, obtaining lower respiratory tract specimens , and", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: hospitals be needed, and social media be employed.", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: and DR examination rooms, should be implemented properly." ]

[ [ "1a", "Title: Critical care response to a hospital outbreak of the 2019-nCoV infection in Shenzhen, China" ], [ "1b", "Passage: > 3 weeks according to some literature and our unpublished data ." ], [ "1c", "Healthcare providers and those in contact with infected patients should utilize contact, droplet, and airborne precautions with N95 respirator." ], [ "1d", "Strict infection prevention and control practices have been implemented and audited in our units following the infection prevention and control plan published by China's National Health Committee ." ], [ "1e", "In addition, wellequipped fever clinic as triage station with trained staff knowing 2019-nCoV case definitions is established." ], [ "1f", "For suspected 2019-nCoV infection, several key points are crucial procedures: recording a detailed history, standardizing pneumonia workup, obtaining lower respiratory tract specimens , and" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "0a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "0b", "Passage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute ." ], [ "0c", "Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 ." ], [ "0d", "White blood cell counts were low or in the normal range." ], [ "0e", "All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase ." ], [ "0f", "At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range." ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "1a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "1b", "Passage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute ." ], [ "1c", "Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 ." ], [ "1d", "White blood cell counts were low or in the normal range." ], [ "1e", "All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase ." ], [ "1f", "At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range." ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: tachypnea when admitted to the ICU, with a mean rate of 43 breaths per minute . Arterial blood gas analysis at ICU admission revealed profound hypoxia, with a mean PaO 2 /FiO 2 of 58.1 . White blood cell counts were low or in the normal range. All patients had elevated serum aspartate aminotransferase , lactate dehydrogenase and hydroxybutyrate dehydrogenase . At admission, all patients' levels of immunoglobulin and components C3 and C4 were in the normal range.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "2a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "2b", "Passage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included." ], [ "2c", "All five patients were immunocompetent young men with a median age of 32 years." ], [ "2d", "The mean time from onset to dyspnea was 5 days." ], [ "2e", "Arterial blood gas analysis at ICU admission revealed profound hypoxia." ], [ "2f", "Mean partial oxygen pressure/fraction of inspired oxygen was 58.1." ], [ "2g", "Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively." ], [ "2h", "The viral load was higher than 1 × 10 copies in three patients and was" ] ]

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

[ "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Home caregivers 1 Clean and disinfect hands after contact with the patient, before leaving patient's room or the house, before and after eating, after using the toilet and after entering house from outside .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Persons with close contacts and suspicious exposure should be advised to have a 14-day health observation period, which starts from the last day of contact with the 2019-nCoV infected patients or suspicious environmental exposure. Once they display any symptoms, especially fever, respiratory symptoms such as coughing, shortness of breath, or diarrhea, they should reach out for medical attention immediately . Contact surveillance should be carried out for those who had exposed to accidental contact, low-level exposure to suspected or confirmed patients, i.e. checking any potential symptoms when carrying out daily activities . See Table 3 for details .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: If they had travelled to Hubei Province in the past 14 days and is in fever, cough or difficulty in breathing, they should: see a doctor immediately; call the doctor about his/her recent trips and symptoms before going to the doctor's office or emergency room; avoid contact with others; not to travel around; cover mouth and nose with a tissue or sleeve when coughing or sneezing; and wash hands with soap and water for at least 20 s. If soap and water are not available, use alcohol-based hand sanitizers ." ]

[ [ "0a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "0b", "Passage: Home caregivers 1 Clean and disinfect hands after contact with the patient, before leaving patient's room or the house, before and after eating, after using the toilet and after entering house from outside ." ] ]

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

[ "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Home caregivers 1 Clean and disinfect hands after contact with the patient, before leaving patient's room or the house, before and after eating, after using the toilet and after entering house from outside .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Persons with close contacts and suspicious exposure should be advised to have a 14-day health observation period, which starts from the last day of contact with the 2019-nCoV infected patients or suspicious environmental exposure. Once they display any symptoms, especially fever, respiratory symptoms such as coughing, shortness of breath, or diarrhea, they should reach out for medical attention immediately . Contact surveillance should be carried out for those who had exposed to accidental contact, low-level exposure to suspected or confirmed patients, i.e. checking any potential symptoms when carrying out daily activities . See Table 3 for details .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: If they had travelled to Hubei Province in the past 14 days and is in fever, cough or difficulty in breathing, they should: see a doctor immediately; call the doctor about his/her recent trips and symptoms before going to the doctor's office or emergency room; avoid contact with others; not to travel around; cover mouth and nose with a tissue or sleeve when coughing or sneezing; and wash hands with soap and water for at least 20 s. If soap and water are not available, use alcohol-based hand sanitizers ." ]

[ [ "1a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "1b", "Passage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted ." ] ]

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

[ "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Home caregivers 1 Clean and disinfect hands after contact with the patient, before leaving patient's room or the house, before and after eating, after using the toilet and after entering house from outside .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Persons with close contacts and suspicious exposure should be advised to have a 14-day health observation period, which starts from the last day of contact with the 2019-nCoV infected patients or suspicious environmental exposure. Once they display any symptoms, especially fever, respiratory symptoms such as coughing, shortness of breath, or diarrhea, they should reach out for medical attention immediately . Contact surveillance should be carried out for those who had exposed to accidental contact, low-level exposure to suspected or confirmed patients, i.e. checking any potential symptoms when carrying out daily activities . See Table 3 for details .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: If they had travelled to Hubei Province in the past 14 days and is in fever, cough or difficulty in breathing, they should: see a doctor immediately; call the doctor about his/her recent trips and symptoms before going to the doctor's office or emergency room; avoid contact with others; not to travel around; cover mouth and nose with a tissue or sleeve when coughing or sneezing; and wash hands with soap and water for at least 20 s. If soap and water are not available, use alcohol-based hand sanitizers ." ]

[ [ "2a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "2b", "Passage: Persons with close contacts and suspicious exposure should be advised to have a 14-day health observation period, which starts from the last day of contact with the 2019-nCoV infected patients or suspicious environmental exposure." ], [ "2c", "Once they display any symptoms, especially fever, respiratory symptoms such as coughing, shortness of breath, or diarrhea, they should reach out for medical attention immediately ." ], [ "2d", "Contact surveillance should be carried out for those who had exposed to accidental contact, low-level exposure to suspected or confirmed patients, i.e. checking any potential symptoms when carrying out daily activities ." ], [ "2e", "See Table 3 for details ." ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants . Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants . Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: of improved or altered binding, roughly mimicking the somatic evolution strategy of the immune system . However, other in vitro display systems, such as yeast display, have important advantages over the filamentous phage for affinity maturation , and regardless of the display method, selection of \"improved\" variants can be slow and cumbersome. Iterative methods have been developed to combine computationally designed mutations and circumvent the screening of combinatorial libraries, but these have had limited success to date.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: of improved or altered binding, roughly mimicking the somatic evolution strategy of the immune system . However, other in vitro display systems, such as yeast display, have important advantages over the filamentous phage for affinity maturation , and regardless of the display method, selection of \"improved\" variants can be slow and cumbersome. Iterative methods have been developed to combine computationally designed mutations and circumvent the screening of combinatorial libraries, but these have had limited success to date." ]

[ [ "0a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "0b", "Passage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants ." ], [ "0c", "Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells." ] ]

[ "0b", "1b" ]

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants . Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants . Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: of improved or altered binding, roughly mimicking the somatic evolution strategy of the immune system . However, other in vitro display systems, such as yeast display, have important advantages over the filamentous phage for affinity maturation , and regardless of the display method, selection of \"improved\" variants can be slow and cumbersome. Iterative methods have been developed to combine computationally designed mutations and circumvent the screening of combinatorial libraries, but these have had limited success to date.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: of improved or altered binding, roughly mimicking the somatic evolution strategy of the immune system . However, other in vitro display systems, such as yeast display, have important advantages over the filamentous phage for affinity maturation , and regardless of the display method, selection of \"improved\" variants can be slow and cumbersome. Iterative methods have been developed to combine computationally designed mutations and circumvent the screening of combinatorial libraries, but these have had limited success to date." ]

[ [ "1a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "1b", "Passage: surface , and the term \"phage-displayed library\" to refer to a diverse pool of recombinant filamentous phage displaying an array of polypeptide variants ." ], [ "1c", "Such libraries are typically screened by iterative cycles of panning against an immobilized protein of interest followed by amplification of the bound phage in E. coli cells." ] ]

[ "0b", "1b" ]

[ "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: pathway commonly known as the unfolded protein response . The UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells\nPassage: load of new proteins through transcriptional induction of secretory pathway components and general translational attenuation. One of the key players in the UPR is Ire1 , a conserved transmembrane protein with a luminal domain that senses protein misfolding in the ER.", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The UPR pathways trigger a complex network of signals via three ER transmembrane stress sensors: inositol-requiring enzyme 1 a/b , PKR-like ER kinase and activating transcription factor 6 , depicted schematically in Figure 1 . Under homeostatic condition, the ER luminal domains of these sensor proteins are inactive, due to association with glucose regulating protein 78 . GRP78 has a high affinity for misfolded and unfolded proteins: when luminal load of misfolded protein increases, GRP78 is released from the ER stress sensors, which are then free to initiate downstream signalling outside the ER." ]

[ [ "0a", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors" ], [ "0b", "Passage: pathway commonly known as the unfolded protein response ." ], [ "0c", "The UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery." ], [ "0d", "The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins ." ], [ "0e", "Finally, the UPR reduces protein load through the attenuation of protein translation ." ], [ "0f", "If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death." ] ]

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

[ "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: pathway commonly known as the unfolded protein response . The UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells\nPassage: load of new proteins through transcriptional induction of secretory pathway components and general translational attenuation. One of the key players in the UPR is Ire1 , a conserved transmembrane protein with a luminal domain that senses protein misfolding in the ER.", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The UPR pathways trigger a complex network of signals via three ER transmembrane stress sensors: inositol-requiring enzyme 1 a/b , PKR-like ER kinase and activating transcription factor 6 , depicted schematically in Figure 1 . Under homeostatic condition, the ER luminal domains of these sensor proteins are inactive, due to association with glucose regulating protein 78 . GRP78 has a high affinity for misfolded and unfolded proteins: when luminal load of misfolded protein increases, GRP78 is released from the ER stress sensors, which are then free to initiate downstream signalling outside the ER." ]

[ [ "1a", "Title: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells" ], [ "1b", "Passage: load of new proteins through transcriptional induction of secretory pathway components and general translational attenuation." ], [ "1c", "One of the key players in the UPR is Ire1 , a conserved transmembrane protein with a luminal domain that senses protein misfolding in the ER." ] ]

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

[ "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: pathway commonly known as the unfolded protein response . The UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells\nPassage: load of new proteins through transcriptional induction of secretory pathway components and general translational attenuation. One of the key players in the UPR is Ire1 , a conserved transmembrane protein with a luminal domain that senses protein misfolding in the ER.", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The UPR pathways trigger a complex network of signals via three ER transmembrane stress sensors: inositol-requiring enzyme 1 a/b , PKR-like ER kinase and activating transcription factor 6 , depicted schematically in Figure 1 . Under homeostatic condition, the ER luminal domains of these sensor proteins are inactive, due to association with glucose regulating protein 78 . GRP78 has a high affinity for misfolded and unfolded proteins: when luminal load of misfolded protein increases, GRP78 is released from the ER stress sensors, which are then free to initiate downstream signalling outside the ER." ]

[ [ "2a", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors" ], [ "2b", "Passage: UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery." ], [ "2c", "The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins ." ], [ "2d", "Finally, the UPR reduces protein load through the attenuation of protein translation ." ], [ "2e", "If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death." ] ]

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

[ "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: pathway commonly known as the unfolded protein response . The UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells\nPassage: load of new proteins through transcriptional induction of secretory pathway components and general translational attenuation. One of the key players in the UPR is Ire1 , a conserved transmembrane protein with a luminal domain that senses protein misfolding in the ER.", "Title: Transcriptional regulation of secretory capacity by bZip transcription factors\nPassage: UPR alleviates ER stress by increasing transcription of the chaperone proteins and lipids that increase folding capacity in the ER, as well as upregulating other components of the secretory machinery. The UPR also decreases protein load by increasing production of the ERAD machinery that degrades misfolded proteins . Finally, the UPR reduces protein load through the attenuation of protein translation . If ER homeostasis is not restored, the UPR then triggers the execution of cytotoxic programs leading to cell death.", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The UPR pathways trigger a complex network of signals via three ER transmembrane stress sensors: inositol-requiring enzyme 1 a/b , PKR-like ER kinase and activating transcription factor 6 , depicted schematically in Figure 1 . Under homeostatic condition, the ER luminal domains of these sensor proteins are inactive, due to association with glucose regulating protein 78 . GRP78 has a high affinity for misfolded and unfolded proteins: when luminal load of misfolded protein increases, GRP78 is released from the ER stress sensors, which are then free to initiate downstream signalling outside the ER." ]

[ [ "3a", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection" ], [ "3b", "Passage: The UPR pathways trigger a complex network of signals via three ER transmembrane stress sensors: inositol-requiring enzyme 1 a/b , PKR-like ER kinase and activating transcription factor 6 , depicted schematically in Figure 1 ." ], [ "3c", "Under homeostatic condition, the ER luminal domains of these sensor proteins are inactive, due to association with glucose regulating protein 78 ." ], [ "3d", "GRP78 has a high affinity for misfolded and unfolded proteins: when luminal load of misfolded protein increases, GRP78 is released from the ER stress sensors, which are then free to initiate downstream signalling outside the ER." ] ]

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

[ "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: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "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: 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: but close and lengthy exposure appears to be a requirement." ], [ "0c", "The KSA is the focal point of MERS, with the majority of human cases." ], [ "0d", "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." ], [ "0e", "However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms." ], [ "0f", "Older males most obviously suffer severe disease and MERS patients often have comorbidities." ], [ "0g", "Compared to severe acute" ] ]

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

[ "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: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "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: 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" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: a case definition released by the KSA Ministry of Health in June 2015 ." ], [ "1c", "The KSA has been the source of 79 % of human cases." ], [ "1d", "Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions ." ], [ "1e", "Interestingly in June 2015, an outbreak in South Korea followed a similar distribution ." ], [ "1f", "Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia ." ], [ "1g", "Patients often present to a hospital with pneumonia," ] ]

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

[ "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: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "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: 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: In humans, overt disease was given the name Middle East respiratory syndrome, with the acronym MERS." ], [ "2c", "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." ], [ "2d", "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 ." ] ]

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

[ "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: The cardiac glycoside ouabain is an inhibitor of ATP1A1 that has been used to treat congestive heart failure in European countries . The PHB inhibitor rocaglamide is a flavagline from an Aglaia tree used in traditional Chinese medicine that has potent anticancer activity . To examine whether pharmacological inhibition of ATP1A1 or PHB inhibited LCMV multiplication, we pretreated human , nonhuman primate , and rodent cells with ouabain or rocaglamide and infected them with rLCMV/eGFP . Ouabain treatment resulted in a strong dosedependent inhibition of eGFP expression in infected human-and nonhuman primate cells, but did not affect eGFP expression intensity", "Title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus\nPassage: secondary matrix protein VP24-apart from its role in the evasion of host immune response, nucleocapsid formation, and regulation of replication-has an important role in viral budding and egress. Na + /K + -ATPase ATP1A1 is detected to have a close interaction with VP24 of EBOV during replication. Ouabain, at a non-cytotoxic concentration of 20nM, is able to suppress the replication of the EBOV in human MRC-5 cells . Among the three cardiac glycosides that may include digoxin, digitoxin, and ouabain, only digoxin is commonly used in clinical practice. Ouabain, because of its poor oral availability, is used primarily as a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: anti-LCMV activity of ouabain . Nevertheless, ATP1A1-mediated Src signaling could plausibly contribute to the inhibitory effect of ouabain on JUNV multiplication as similarly to that observed with MHV. Moreover, cell entry of JUNV occurs also by clathrin-mediated endocytosis , a process affected by Src signaling. Ouabain has been clinically used in several European countries for the management of congestive heart failure, whereas bufalin has been tested in clinical trials for cancer treatments , and the CST digoxin has been FDA-approved since 1997 to treat heart failure and atrial fibrillation. Hence, opportunities for the repurposing CSTs have potential as therapeutics to", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: fresh cell monolayer and identified infected cells based on ZsGreen expression. To assess the effect of ouabain on de novo assembly of infectious progeny we determined normalized ratios of ZsGreen + cells . The second experiment involved infection of cells with WT LCMV, and 48 h later we washed infected cells three times to remove the extracellular infectious progeny produced during the first 48 h of infection. Then, fresh media containing ouabain or DMSO vehicle control were added, and 24 h later we determined virus titers in TCS . Results from both experiments consistently showed that ouabain did not inhibit" ]

[ [ "0a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses" ], [ "0b", "Passage: The cardiac glycoside ouabain is an inhibitor of ATP1A1 that has been used to treat congestive heart failure in European countries ." ], [ "0c", "The PHB inhibitor rocaglamide is a flavagline from an Aglaia tree used in traditional Chinese medicine that has potent anticancer activity ." ], [ "0d", "To examine whether pharmacological inhibition of ATP1A1 or PHB inhibited LCMV multiplication, we pretreated human , nonhuman primate , and rodent cells with ouabain or rocaglamide and infected them with rLCMV/eGFP ." ], [ "0e", "Ouabain treatment resulted in a strong dosedependent inhibition of eGFP expression in infected human-and nonhuman primate cells, but did not affect eGFP expression intensity" ] ]

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

[ "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: The cardiac glycoside ouabain is an inhibitor of ATP1A1 that has been used to treat congestive heart failure in European countries . The PHB inhibitor rocaglamide is a flavagline from an Aglaia tree used in traditional Chinese medicine that has potent anticancer activity . To examine whether pharmacological inhibition of ATP1A1 or PHB inhibited LCMV multiplication, we pretreated human , nonhuman primate , and rodent cells with ouabain or rocaglamide and infected them with rLCMV/eGFP . Ouabain treatment resulted in a strong dosedependent inhibition of eGFP expression in infected human-and nonhuman primate cells, but did not affect eGFP expression intensity", "Title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus\nPassage: secondary matrix protein VP24-apart from its role in the evasion of host immune response, nucleocapsid formation, and regulation of replication-has an important role in viral budding and egress. Na + /K + -ATPase ATP1A1 is detected to have a close interaction with VP24 of EBOV during replication. Ouabain, at a non-cytotoxic concentration of 20nM, is able to suppress the replication of the EBOV in human MRC-5 cells . Among the three cardiac glycosides that may include digoxin, digitoxin, and ouabain, only digoxin is commonly used in clinical practice. Ouabain, because of its poor oral availability, is used primarily as a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: anti-LCMV activity of ouabain . Nevertheless, ATP1A1-mediated Src signaling could plausibly contribute to the inhibitory effect of ouabain on JUNV multiplication as similarly to that observed with MHV. Moreover, cell entry of JUNV occurs also by clathrin-mediated endocytosis , a process affected by Src signaling. Ouabain has been clinically used in several European countries for the management of congestive heart failure, whereas bufalin has been tested in clinical trials for cancer treatments , and the CST digoxin has been FDA-approved since 1997 to treat heart failure and atrial fibrillation. Hence, opportunities for the repurposing CSTs have potential as therapeutics to", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: fresh cell monolayer and identified infected cells based on ZsGreen expression. To assess the effect of ouabain on de novo assembly of infectious progeny we determined normalized ratios of ZsGreen + cells . The second experiment involved infection of cells with WT LCMV, and 48 h later we washed infected cells three times to remove the extracellular infectious progeny produced during the first 48 h of infection. Then, fresh media containing ouabain or DMSO vehicle control were added, and 24 h later we determined virus titers in TCS . Results from both experiments consistently showed that ouabain did not inhibit" ]

[ [ "1a", "Title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus" ], [ "1b", "Passage: secondary matrix protein VP24-apart from its role in the evasion of host immune response, nucleocapsid formation, and regulation of replication-has an important role in viral budding and egress." ], [ "1c", "Na + /K + -ATPase ATP1A1 is detected to have a close interaction with VP24 of EBOV during replication." ], [ "1d", "Ouabain, at a non-cytotoxic concentration of 20nM, is able to suppress the replication of the EBOV in human MRC-5 cells ." ], [ "1e", "Among the three cardiac glycosides that may include digoxin, digitoxin, and ouabain, only digoxin is commonly used in clinical practice." ], [ "1f", "Ouabain, because of its poor oral availability, is used primarily as a" ] ]

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

[ "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: The cardiac glycoside ouabain is an inhibitor of ATP1A1 that has been used to treat congestive heart failure in European countries . The PHB inhibitor rocaglamide is a flavagline from an Aglaia tree used in traditional Chinese medicine that has potent anticancer activity . To examine whether pharmacological inhibition of ATP1A1 or PHB inhibited LCMV multiplication, we pretreated human , nonhuman primate , and rodent cells with ouabain or rocaglamide and infected them with rLCMV/eGFP . Ouabain treatment resulted in a strong dosedependent inhibition of eGFP expression in infected human-and nonhuman primate cells, but did not affect eGFP expression intensity", "Title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus\nPassage: secondary matrix protein VP24-apart from its role in the evasion of host immune response, nucleocapsid formation, and regulation of replication-has an important role in viral budding and egress. Na + /K + -ATPase ATP1A1 is detected to have a close interaction with VP24 of EBOV during replication. Ouabain, at a non-cytotoxic concentration of 20nM, is able to suppress the replication of the EBOV in human MRC-5 cells . Among the three cardiac glycosides that may include digoxin, digitoxin, and ouabain, only digoxin is commonly used in clinical practice. Ouabain, because of its poor oral availability, is used primarily as a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: anti-LCMV activity of ouabain . Nevertheless, ATP1A1-mediated Src signaling could plausibly contribute to the inhibitory effect of ouabain on JUNV multiplication as similarly to that observed with MHV. Moreover, cell entry of JUNV occurs also by clathrin-mediated endocytosis , a process affected by Src signaling. Ouabain has been clinically used in several European countries for the management of congestive heart failure, whereas bufalin has been tested in clinical trials for cancer treatments , and the CST digoxin has been FDA-approved since 1997 to treat heart failure and atrial fibrillation. Hence, opportunities for the repurposing CSTs have potential as therapeutics to", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: fresh cell monolayer and identified infected cells based on ZsGreen expression. To assess the effect of ouabain on de novo assembly of infectious progeny we determined normalized ratios of ZsGreen + cells . The second experiment involved infection of cells with WT LCMV, and 48 h later we washed infected cells three times to remove the extracellular infectious progeny produced during the first 48 h of infection. Then, fresh media containing ouabain or DMSO vehicle control were added, and 24 h later we determined virus titers in TCS . Results from both experiments consistently showed that ouabain did not inhibit" ]

[ [ "2a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses" ], [ "2b", "Passage: anti-LCMV activity of ouabain ." ], [ "2c", "Nevertheless, ATP1A1-mediated Src signaling could plausibly contribute to the inhibitory effect of ouabain on JUNV multiplication as similarly to that observed with MHV." ], [ "2d", "Moreover, cell entry of JUNV occurs also by clathrin-mediated endocytosis , a process affected by Src signaling." ], [ "2e", "Ouabain has been clinically used in several European countries for the management of congestive heart failure, whereas bufalin has been tested in clinical trials for cancer treatments , and the CST digoxin has been FDA-approved since 1997 to treat heart failure and atrial fibrillation." ], [ "2f", "Hence, opportunities for the repurposing CSTs have potential as therapeutics to" ] ]

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

[ "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: The cardiac glycoside ouabain is an inhibitor of ATP1A1 that has been used to treat congestive heart failure in European countries . The PHB inhibitor rocaglamide is a flavagline from an Aglaia tree used in traditional Chinese medicine that has potent anticancer activity . To examine whether pharmacological inhibition of ATP1A1 or PHB inhibited LCMV multiplication, we pretreated human , nonhuman primate , and rodent cells with ouabain or rocaglamide and infected them with rLCMV/eGFP . Ouabain treatment resulted in a strong dosedependent inhibition of eGFP expression in infected human-and nonhuman primate cells, but did not affect eGFP expression intensity", "Title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus\nPassage: secondary matrix protein VP24-apart from its role in the evasion of host immune response, nucleocapsid formation, and regulation of replication-has an important role in viral budding and egress. Na + /K + -ATPase ATP1A1 is detected to have a close interaction with VP24 of EBOV during replication. Ouabain, at a non-cytotoxic concentration of 20nM, is able to suppress the replication of the EBOV in human MRC-5 cells . Among the three cardiac glycosides that may include digoxin, digitoxin, and ouabain, only digoxin is commonly used in clinical practice. Ouabain, because of its poor oral availability, is used primarily as a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: anti-LCMV activity of ouabain . Nevertheless, ATP1A1-mediated Src signaling could plausibly contribute to the inhibitory effect of ouabain on JUNV multiplication as similarly to that observed with MHV. Moreover, cell entry of JUNV occurs also by clathrin-mediated endocytosis , a process affected by Src signaling. Ouabain has been clinically used in several European countries for the management of congestive heart failure, whereas bufalin has been tested in clinical trials for cancer treatments , and the CST digoxin has been FDA-approved since 1997 to treat heart failure and atrial fibrillation. Hence, opportunities for the repurposing CSTs have potential as therapeutics to", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses\nPassage: fresh cell monolayer and identified infected cells based on ZsGreen expression. To assess the effect of ouabain on de novo assembly of infectious progeny we determined normalized ratios of ZsGreen + cells . The second experiment involved infection of cells with WT LCMV, and 48 h later we washed infected cells three times to remove the extracellular infectious progeny produced during the first 48 h of infection. Then, fresh media containing ouabain or DMSO vehicle control were added, and 24 h later we determined virus titers in TCS . Results from both experiments consistently showed that ouabain did not inhibit" ]

[ [ "3a", "Title: Interactome analysis of the lymphocytic choriomeningitis virus nucleoprotein in infected cells reveals ATPase Na(+)/K(+) transporting subunit Alpha 1 and prohibitin as host-cell factors involved in the life cycle of mammarenaviruses" ], [ "3b", "Passage: fresh cell monolayer and identified infected cells based on ZsGreen expression." ], [ "3c", "To assess the effect of ouabain on de novo assembly of infectious progeny we determined normalized ratios of ZsGreen + cells ." ], [ "3d", "The second experiment involved infection of cells with WT LCMV, and 48 h later we washed infected cells three times to remove the extracellular infectious progeny produced during the first 48 h of infection." ], [ "3e", "Then, fresh media containing ouabain or DMSO vehicle control were added, and 24 h later we determined virus titers in TCS ." ], [ "3f", "Results from both experiments consistently showed that ouabain did not inhibit" ] ]

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

[ "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: RTIs are a major cause of morbidity and mortality worldwide. Acute RTI is most common in children under five years of age, and represents 30-50% of the paediatric medical admissions, as well as 20-40% of hospitalizations in children. Respiratory infections cluster during winter and early spring months. The leading viral agents include respiratory syncytial virus , influenza A and B viruses, parainfluenza viruses , and human adenoviruses . In addition, there is a continuously increasing list of new respiratory viruses that contribute significantly to the burden of acute respiratory infections, such as the recently identified human metapneumovirus and human Bocavirus", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Text: Viral Respiratory tract infections represent a major public health problem because of their world-wide occurrence, ease of transmission and considerable morbidity and mortality effecting people of all ages. Children are on average infected two to three times more frequently than adults, with acute RTIs being the most common infection in childhood . Illnesses caused by respiratory viruses include, among others, common colds, pharyngitis, croup, bronchiolitis, viral pneumonia and otitis media. Rapid diagnosis is important not only for timely therapeutic intervention but also for the identification of a beginning influenza epidemic and the avoidance of unnecessary antibiotic treatment .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: The most common viruses detected were RSV and rhinovirus accounting for almost 60% of all cases. Both viruses were reported previously by others as the major aetiology for respiratory viral infections in young children with rhinoviruses being recognized increasingly for their role in lower respiratory tract infections .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Acute RTIs are classified as upper and lower RTI , according to the involved anatomic localization. URTIs cause non-severe but widespread epidemics that are responsible for continuous circulation of pathogens in the community. LRTIs have been classified as frank pneumonia and bronchiolitis with clinical, radiological and etiological features that usually overlap . Viruses are again the foremost agents of LRTIs often misdiagnosed as bacterial in origin and hence treated with antibiotics unnecessarily ." ]

[ [ "0a", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus" ], [ "0b", "Passage: RTIs are a major cause of morbidity and mortality worldwide." ], [ "0c", "Acute RTI is most common in children under five years of age, and represents 30-50% of the paediatric medical admissions, as well as 20-40% of hospitalizations in children." ], [ "0d", "Respiratory infections cluster during winter and early spring months." ], [ "0e", "The leading viral agents include respiratory syncytial virus , influenza A and B viruses, parainfluenza viruses , and human adenoviruses ." ], [ "0f", "In addition, there is a continuously increasing list of new respiratory viruses that contribute significantly to the burden of acute respiratory infections, such as the recently identified human metapneumovirus and human Bocavirus" ] ]

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

[ "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: RTIs are a major cause of morbidity and mortality worldwide. Acute RTI is most common in children under five years of age, and represents 30-50% of the paediatric medical admissions, as well as 20-40% of hospitalizations in children. Respiratory infections cluster during winter and early spring months. The leading viral agents include respiratory syncytial virus , influenza A and B viruses, parainfluenza viruses , and human adenoviruses . In addition, there is a continuously increasing list of new respiratory viruses that contribute significantly to the burden of acute respiratory infections, such as the recently identified human metapneumovirus and human Bocavirus", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Text: Viral Respiratory tract infections represent a major public health problem because of their world-wide occurrence, ease of transmission and considerable morbidity and mortality effecting people of all ages. Children are on average infected two to three times more frequently than adults, with acute RTIs being the most common infection in childhood . Illnesses caused by respiratory viruses include, among others, common colds, pharyngitis, croup, bronchiolitis, viral pneumonia and otitis media. Rapid diagnosis is important not only for timely therapeutic intervention but also for the identification of a beginning influenza epidemic and the avoidance of unnecessary antibiotic treatment .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: The most common viruses detected were RSV and rhinovirus accounting for almost 60% of all cases. Both viruses were reported previously by others as the major aetiology for respiratory viral infections in young children with rhinoviruses being recognized increasingly for their role in lower respiratory tract infections .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Acute RTIs are classified as upper and lower RTI , according to the involved anatomic localization. URTIs cause non-severe but widespread epidemics that are responsible for continuous circulation of pathogens in the community. LRTIs have been classified as frank pneumonia and bronchiolitis with clinical, radiological and etiological features that usually overlap . Viruses are again the foremost agents of LRTIs often misdiagnosed as bacterial in origin and hence treated with antibiotics unnecessarily ." ]

[ [ "1a", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus" ], [ "1b", "Passage: Text: Viral Respiratory tract infections represent a major public health problem because of their world-wide occurrence, ease of transmission and considerable morbidity and mortality effecting people of all ages." ], [ "1c", "Children are on average infected two to three times more frequently than adults, with acute RTIs being the most common infection in childhood ." ], [ "1d", "Illnesses caused by respiratory viruses include, among others, common colds, pharyngitis, croup, bronchiolitis, viral pneumonia and otitis media." ], [ "1e", "Rapid diagnosis is important not only for timely therapeutic intervention but also for the identification of a beginning influenza epidemic and the avoidance of unnecessary antibiotic treatment ." ] ]

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

[ "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: RTIs are a major cause of morbidity and mortality worldwide. Acute RTI is most common in children under five years of age, and represents 30-50% of the paediatric medical admissions, as well as 20-40% of hospitalizations in children. Respiratory infections cluster during winter and early spring months. The leading viral agents include respiratory syncytial virus , influenza A and B viruses, parainfluenza viruses , and human adenoviruses . In addition, there is a continuously increasing list of new respiratory viruses that contribute significantly to the burden of acute respiratory infections, such as the recently identified human metapneumovirus and human Bocavirus", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Text: Viral Respiratory tract infections represent a major public health problem because of their world-wide occurrence, ease of transmission and considerable morbidity and mortality effecting people of all ages. Children are on average infected two to three times more frequently than adults, with acute RTIs being the most common infection in childhood . Illnesses caused by respiratory viruses include, among others, common colds, pharyngitis, croup, bronchiolitis, viral pneumonia and otitis media. Rapid diagnosis is important not only for timely therapeutic intervention but also for the identification of a beginning influenza epidemic and the avoidance of unnecessary antibiotic treatment .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: The most common viruses detected were RSV and rhinovirus accounting for almost 60% of all cases. Both viruses were reported previously by others as the major aetiology for respiratory viral infections in young children with rhinoviruses being recognized increasingly for their role in lower respiratory tract infections .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Acute RTIs are classified as upper and lower RTI , according to the involved anatomic localization. URTIs cause non-severe but widespread epidemics that are responsible for continuous circulation of pathogens in the community. LRTIs have been classified as frank pneumonia and bronchiolitis with clinical, radiological and etiological features that usually overlap . Viruses are again the foremost agents of LRTIs often misdiagnosed as bacterial in origin and hence treated with antibiotics unnecessarily ." ]

[ [ "2a", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus" ], [ "2b", "Passage: The most common viruses detected were RSV and rhinovirus accounting for almost 60% of all cases." ], [ "2c", "Both viruses were reported previously by others as the major aetiology for respiratory viral infections in young children with rhinoviruses being recognized increasingly for their role in lower respiratory tract infections ." ] ]

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

[ "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: RTIs are a major cause of morbidity and mortality worldwide. Acute RTI is most common in children under five years of age, and represents 30-50% of the paediatric medical admissions, as well as 20-40% of hospitalizations in children. Respiratory infections cluster during winter and early spring months. The leading viral agents include respiratory syncytial virus , influenza A and B viruses, parainfluenza viruses , and human adenoviruses . In addition, there is a continuously increasing list of new respiratory viruses that contribute significantly to the burden of acute respiratory infections, such as the recently identified human metapneumovirus and human Bocavirus", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Text: Viral Respiratory tract infections represent a major public health problem because of their world-wide occurrence, ease of transmission and considerable morbidity and mortality effecting people of all ages. Children are on average infected two to three times more frequently than adults, with acute RTIs being the most common infection in childhood . Illnesses caused by respiratory viruses include, among others, common colds, pharyngitis, croup, bronchiolitis, viral pneumonia and otitis media. Rapid diagnosis is important not only for timely therapeutic intervention but also for the identification of a beginning influenza epidemic and the avoidance of unnecessary antibiotic treatment .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: The most common viruses detected were RSV and rhinovirus accounting for almost 60% of all cases. Both viruses were reported previously by others as the major aetiology for respiratory viral infections in young children with rhinoviruses being recognized increasingly for their role in lower respiratory tract infections .", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus\nPassage: Acute RTIs are classified as upper and lower RTI , according to the involved anatomic localization. URTIs cause non-severe but widespread epidemics that are responsible for continuous circulation of pathogens in the community. LRTIs have been classified as frank pneumonia and bronchiolitis with clinical, radiological and etiological features that usually overlap . Viruses are again the foremost agents of LRTIs often misdiagnosed as bacterial in origin and hence treated with antibiotics unnecessarily ." ]

[ [ "3a", "Title: Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus" ], [ "3b", "Passage: Acute RTIs are classified as upper and lower RTI , according to the involved anatomic localization." ], [ "3c", "URTIs cause non-severe but widespread epidemics that are responsible for continuous circulation of pathogens in the community." ], [ "3d", "LRTIs have been classified as frank pneumonia and bronchiolitis with clinical, radiological and etiological features that usually overlap ." ], [ "3e", "Viruses are again the foremost agents of LRTIs often misdiagnosed as bacterial in origin and hence treated with antibiotics unnecessarily ." ] ]

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

[ "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: The survey revealed that over half of the TB patients were 65 years and older in Shandong, while the over 65's were more likely to present with abnormal CXRAY and persistent cough. Similar trends have been documented in other developed cities such as Hong Kong and Singapore . These high rates may reflect the higher TB rates in the past and decline in immunity in the over 65's. How to treat elders with TB and other complications such as diabetes remains an ongoing challenge in China and similar settings.", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: from people 65 years or older. The ratio between over 65's and 15 to 64 years old was 8.4 in sputum positive cases and 5.9 in bacteriologically confirmed cases. The ratio between rural and urban areas was 2.7 in sputum positive cases and 4.8 in bacteriologically confirmed cases.", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: the yields were higher in over 65's compared with the general Table 2 Prevalence rates of sputum positive TB cases, bacteriologically confirmed TB cases and all cases in Shandong, China, 2010 No population. Although using CXRAY to examine everyone is not feasible, it can be used in routine elder physical examinations. The China public health package now covers free CXRAY for elders, as well annual employee body examinations provided free CXRAY.", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: The crude prevalence rate in Shandong in 2010 of sputum positive cases was 22.1 , bacteriologically confirmed cases was 36.8 , and all cases were 337.1 per 100,000 in adult population . The adjusted prevalence rates of the whole population in Shandong were17.8 , 27.8 and 239.4 per 100,000 in 2010. A remarkable decline of 82.0%, 80.2% and 31.4% was observed in TB prevalence rates of sputum positive, bacteriologically confirmed, and all cases, respectively, compared to the adjusted rates in 2000 . Large declines were observed in males between 40 and 65 years old, and in females over 60 years" ]

[ [ "0a", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China" ], [ "0b", "Passage: The survey revealed that over half of the TB patients were 65 years and older in Shandong, while the over 65's were more likely to present with abnormal CXRAY and persistent cough." ], [ "0c", "Similar trends have been documented in other developed cities such as Hong Kong and Singapore ." ], [ "0d", "These high rates may reflect the higher TB rates in the past and decline in immunity in the over 65's." ], [ "0e", "How to treat elders with TB and other complications such as diabetes remains an ongoing challenge in China and similar settings." ] ]

[ "0b" ]

[ "Title: Temporal trends in the discovery of human viruses\nPassage: We confirmed that our model reproduced the observed slight downward trend in the rate of discovery since 1954 and the observed variance in the data from 1954 to 2006 . The distribution of the number of virus species discovered per year shows slight overdispersion which falls within the predicted range . Together, these results support our choice of model, even though we do not explicitly consider heterogeneity in the probability of discovering a given species in any one year or temporal variation in sampling effort, detection techniques and reporting.", "Title: Temporal trends in the discovery of human viruses\nPassage: yield useful estimates of the additional parameters required.", "Title: Temporal trends in the discovery of human viruses\nPassage: We used piecewise linear regression to test for changes in the slope of the discovery curve. The results suggested upswings in 1930 and 1954 (1953 -1956 . We therefore restricted detailed analysis to the period 1954-2006.", "Title: Temporal trends in the discovery of human viruses\nPassage: is therefore of considerable interest." ]

[ [ "0a", "Title: Temporal trends in the discovery of human viruses" ], [ "0b", "Passage: We confirmed that our model reproduced the observed slight downward trend in the rate of discovery since 1954 and the observed variance in the data from 1954 to 2006 ." ], [ "0c", "The distribution of the number of virus species discovered per year shows slight overdispersion which falls within the predicted range ." ], [ "0d", "Together, these results support our choice of model, even though we do not explicitly consider heterogeneity in the probability of discovering a given species in any one year or temporal variation in sampling effort, detection techniques and reporting." ] ]

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

[ "Title: Temporal trends in the discovery of human viruses\nPassage: We confirmed that our model reproduced the observed slight downward trend in the rate of discovery since 1954 and the observed variance in the data from 1954 to 2006 . The distribution of the number of virus species discovered per year shows slight overdispersion which falls within the predicted range . Together, these results support our choice of model, even though we do not explicitly consider heterogeneity in the probability of discovering a given species in any one year or temporal variation in sampling effort, detection techniques and reporting.", "Title: Temporal trends in the discovery of human viruses\nPassage: yield useful estimates of the additional parameters required.", "Title: Temporal trends in the discovery of human viruses\nPassage: We used piecewise linear regression to test for changes in the slope of the discovery curve. The results suggested upswings in 1930 and 1954 (1953 -1956 . We therefore restricted detailed analysis to the period 1954-2006.", "Title: Temporal trends in the discovery of human viruses\nPassage: is therefore of considerable interest." ]

[ [ "2a", "Title: Temporal trends in the discovery of human viruses" ], [ "2b", "Passage: We used piecewise linear regression to test for changes in the slope of the discovery curve." ], [ "2c", "The results suggested upswings in 1930 and 1954 (1953 -1956 ." ], [ "2d", "We therefore restricted detailed analysis to the period 1954-2006." ] ]

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

[ "Title: Studying copy number variations using a nanofluidic platform\nPassage: A real-time PCR reaction was also performed on these 48 samples. Twenty-four replicates were used for each sample. Although the average copy numbers were close to the digital array data, large fluctuations were observed in the 24 reactions of each sample. Studies on other genes showed that real-time PCR does not always produce accurate results .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: In addition, the intra and inter-assay reproducibility of quantification for all primer sets was evaluated using three replicates of each standard dilution in each of three real-time PCR assay runs. The coefficient of variation for the C values was #3.3% and #6.7% for intra-and inter-assay, respectively. All the data depicting mean C , standard deviation , and CV for each primer set selected for the real-time PCR array with each standard concentration are shown in Table S2 .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: The developed analytical standards were used to calculate the intra and inter-assay reproducibility of quantification for each virus-specific primer set. Mean C values, standard deviation and coefficient of variation were calculated from the data obtained in three replicates of each standard dilution for the intraassay reproducibility, and in three real-time PCR assays consisted of three replicates each for the inter-assay reproducibility. CV was calculated as SD/Mean C * 100%.", "Title: A cost effective real-time PCR for the detection of adenovirus from viral swabs\nPassage: were observed that spanned eight orders of magnitude with Cp values ranging from 14 to 40 . The intra-and inter-assay reproducibility of the real-time PCR following homogenization and heat treatment ranged from 0.03 to 4.80%, and 1.45 to 3.79%, respectively. Similarly, intra-and inter-assay reproducibility of following the nucleic acid extraction protocol ranged from 0.2 to 2.15% and 0.85 to 3.15%. As expected, the highest %CV values observed for both methods were with virus dilutions near the LoD." ]

[ [ "0a", "Title: Studying copy number variations using a nanofluidic platform" ], [ "0b", "Passage: A real-time PCR reaction was also performed on these 48 samples." ], [ "0c", "Twenty-four replicates were used for each sample." ], [ "0d", "Although the average copy numbers were close to the digital array data, large fluctuations were observed in the 24 reactions of each sample." ], [ "0e", "Studies on other genes showed that real-time PCR does not always produce accurate results ." ] ]

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

[ "Title: Studying copy number variations using a nanofluidic platform\nPassage: A real-time PCR reaction was also performed on these 48 samples. Twenty-four replicates were used for each sample. Although the average copy numbers were close to the digital array data, large fluctuations were observed in the 24 reactions of each sample. Studies on other genes showed that real-time PCR does not always produce accurate results .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: In addition, the intra and inter-assay reproducibility of quantification for all primer sets was evaluated using three replicates of each standard dilution in each of three real-time PCR assay runs. The coefficient of variation for the C values was #3.3% and #6.7% for intra-and inter-assay, respectively. All the data depicting mean C , standard deviation , and CV for each primer set selected for the real-time PCR array with each standard concentration are shown in Table S2 .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: The developed analytical standards were used to calculate the intra and inter-assay reproducibility of quantification for each virus-specific primer set. Mean C values, standard deviation and coefficient of variation were calculated from the data obtained in three replicates of each standard dilution for the intraassay reproducibility, and in three real-time PCR assays consisted of three replicates each for the inter-assay reproducibility. CV was calculated as SD/Mean C * 100%.", "Title: A cost effective real-time PCR for the detection of adenovirus from viral swabs\nPassage: were observed that spanned eight orders of magnitude with Cp values ranging from 14 to 40 . The intra-and inter-assay reproducibility of the real-time PCR following homogenization and heat treatment ranged from 0.03 to 4.80%, and 1.45 to 3.79%, respectively. Similarly, intra-and inter-assay reproducibility of following the nucleic acid extraction protocol ranged from 0.2 to 2.15% and 0.85 to 3.15%. As expected, the highest %CV values observed for both methods were with virus dilutions near the LoD." ]

[ [ "1a", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens" ], [ "1b", "Passage: In addition, the intra and inter-assay reproducibility of quantification for all primer sets was evaluated using three replicates of each standard dilution in each of three real-time PCR assay runs." ], [ "1c", "The coefficient of variation for the C values was #3.3% and #6.7% for intra-and inter-assay, respectively." ], [ "1d", "All the data depicting mean C , standard deviation , and CV for each primer set selected for the real-time PCR array with each standard concentration are shown in Table S2 ." ] ]

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

[ "Title: Studying copy number variations using a nanofluidic platform\nPassage: A real-time PCR reaction was also performed on these 48 samples. Twenty-four replicates were used for each sample. Although the average copy numbers were close to the digital array data, large fluctuations were observed in the 24 reactions of each sample. Studies on other genes showed that real-time PCR does not always produce accurate results .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: In addition, the intra and inter-assay reproducibility of quantification for all primer sets was evaluated using three replicates of each standard dilution in each of three real-time PCR assay runs. The coefficient of variation for the C values was #3.3% and #6.7% for intra-and inter-assay, respectively. All the data depicting mean C , standard deviation , and CV for each primer set selected for the real-time PCR array with each standard concentration are shown in Table S2 .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: The developed analytical standards were used to calculate the intra and inter-assay reproducibility of quantification for each virus-specific primer set. Mean C values, standard deviation and coefficient of variation were calculated from the data obtained in three replicates of each standard dilution for the intraassay reproducibility, and in three real-time PCR assays consisted of three replicates each for the inter-assay reproducibility. CV was calculated as SD/Mean C * 100%.", "Title: A cost effective real-time PCR for the detection of adenovirus from viral swabs\nPassage: were observed that spanned eight orders of magnitude with Cp values ranging from 14 to 40 . The intra-and inter-assay reproducibility of the real-time PCR following homogenization and heat treatment ranged from 0.03 to 4.80%, and 1.45 to 3.79%, respectively. Similarly, intra-and inter-assay reproducibility of following the nucleic acid extraction protocol ranged from 0.2 to 2.15% and 0.85 to 3.15%. As expected, the highest %CV values observed for both methods were with virus dilutions near the LoD." ]

[ [ "2a", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens" ], [ "2b", "Passage: The developed analytical standards were used to calculate the intra and inter-assay reproducibility of quantification for each virus-specific primer set." ], [ "2c", "Mean C values, standard deviation and coefficient of variation were calculated from the data obtained in three replicates of each standard dilution for the intraassay reproducibility, and in three real-time PCR assays consisted of three replicates each for the inter-assay reproducibility." ], [ "2d", "CV was calculated as SD/Mean C * 100%." ] ]

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

[ "Title: Studying copy number variations using a nanofluidic platform\nPassage: A real-time PCR reaction was also performed on these 48 samples. Twenty-four replicates were used for each sample. Although the average copy numbers were close to the digital array data, large fluctuations were observed in the 24 reactions of each sample. Studies on other genes showed that real-time PCR does not always produce accurate results .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: In addition, the intra and inter-assay reproducibility of quantification for all primer sets was evaluated using three replicates of each standard dilution in each of three real-time PCR assay runs. The coefficient of variation for the C values was #3.3% and #6.7% for intra-and inter-assay, respectively. All the data depicting mean C , standard deviation , and CV for each primer set selected for the real-time PCR array with each standard concentration are shown in Table S2 .", "Title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens\nPassage: The developed analytical standards were used to calculate the intra and inter-assay reproducibility of quantification for each virus-specific primer set. Mean C values, standard deviation and coefficient of variation were calculated from the data obtained in three replicates of each standard dilution for the intraassay reproducibility, and in three real-time PCR assays consisted of three replicates each for the inter-assay reproducibility. CV was calculated as SD/Mean C * 100%.", "Title: A cost effective real-time PCR for the detection of adenovirus from viral swabs\nPassage: were observed that spanned eight orders of magnitude with Cp values ranging from 14 to 40 . The intra-and inter-assay reproducibility of the real-time PCR following homogenization and heat treatment ranged from 0.03 to 4.80%, and 1.45 to 3.79%, respectively. Similarly, intra-and inter-assay reproducibility of following the nucleic acid extraction protocol ranged from 0.2 to 2.15% and 0.85 to 3.15%. As expected, the highest %CV values observed for both methods were with virus dilutions near the LoD." ]

[ [ "3a", "Title: A cost effective real-time PCR for the detection of adenovirus from viral swabs" ], [ "3b", "Passage: were observed that spanned eight orders of magnitude with Cp values ranging from 14 to 40 ." ], [ "3c", "The intra-and inter-assay reproducibility of the real-time PCR following homogenization and heat treatment ranged from 0.03 to 4.80%, and 1.45 to 3.79%, respectively." ], [ "3d", "Similarly, intra-and inter-assay reproducibility of following the nucleic acid extraction protocol ranged from 0.2 to 2.15% and 0.85 to 3.15%." ], [ "3e", "As expected, the highest %CV values observed for both methods were with virus dilutions near the LoD." ] ]

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

[ "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained. A single amino acid substitution in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence. CONCLUSIONS: These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: of ZIKV strain FSS13025 was used to amplify the DNA template for in vitro transcription of ZIKV 5 0 end RNA. JEV UFS mutants were generated by site-directed mutagenesis, the resultant plasmids were utilized to amplify the DNA templates for in vitro transcription of the corresponding JEV 5 0 RNA mutants.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: Site-directed mutagenesis method was employed for the generation of ZIKV fragments containing the desired UFS mutations, the generated Not I-Avr II restriction fragments were then subcloned into the infectious clone of ZIKV strain FSS13025 , which was kindly provided by Professor Pei-Yong Shi.", "Title: Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles\nPassage: For example, RdRp mutator variants of chikungunya virus and Sindbis virus are attenuated in fruit flies and mice . The attenuation observed in vivo has been directly correlated with the increased mutation rates that would presumably result in higher frequencies of lethal mutations. Indeed, mutator strains of RNA viruses present mutation frequency profiles similar to those of wild-type-like viruses whose mutation rates are extrinsically increased by treatment with RNA mutagens in studies evaluating lethal mutagenesis as an antiviral strategy . However, while many determinants that alter RdRp fidelity have been identified, the enzymatic mechanisms or dynamics by which this occurs" ]

[ [ "0a", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA" ], [ "0b", "Passage: passages within bacteria." ], [ "0c", "The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained." ], [ "0d", "A single amino acid substitution in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence." ], [ "0e", "CONCLUSIONS: These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses." ] ]

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

[ "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained. A single amino acid substitution in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence. CONCLUSIONS: These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: of ZIKV strain FSS13025 was used to amplify the DNA template for in vitro transcription of ZIKV 5 0 end RNA. JEV UFS mutants were generated by site-directed mutagenesis, the resultant plasmids were utilized to amplify the DNA templates for in vitro transcription of the corresponding JEV 5 0 RNA mutants.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: Site-directed mutagenesis method was employed for the generation of ZIKV fragments containing the desired UFS mutations, the generated Not I-Avr II restriction fragments were then subcloned into the infectious clone of ZIKV strain FSS13025 , which was kindly provided by Professor Pei-Yong Shi.", "Title: Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles\nPassage: For example, RdRp mutator variants of chikungunya virus and Sindbis virus are attenuated in fruit flies and mice . The attenuation observed in vivo has been directly correlated with the increased mutation rates that would presumably result in higher frequencies of lethal mutations. Indeed, mutator strains of RNA viruses present mutation frequency profiles similar to those of wild-type-like viruses whose mutation rates are extrinsically increased by treatment with RNA mutagens in studies evaluating lethal mutagenesis as an antiviral strategy . However, while many determinants that alter RdRp fidelity have been identified, the enzymatic mechanisms or dynamics by which this occurs" ]

[ [ "1a", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization" ], [ "1b", "Passage: of ZIKV strain FSS13025 was used to amplify the DNA template for in vitro transcription of ZIKV 5 0 end RNA." ], [ "1c", "JEV UFS mutants were generated by site-directed mutagenesis, the resultant plasmids were utilized to amplify the DNA templates for in vitro transcription of the corresponding JEV 5 0 RNA mutants." ] ]

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

[ "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that modifications in the E2 protein coding sequence were stably maintained. A single amino acid substitution in the RNA dependent RNA polymerase was observed in the rescued viruses vR26_E2gif and vR26, which was reversion to the parental Riems sequence. CONCLUSIONS: These results show that targeted recombination-mediated mutagenesis provides a powerful tool for expediting the construction of novel RNA genomes and should be applicable to the manipulation of other RNA viruses.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: of ZIKV strain FSS13025 was used to amplify the DNA template for in vitro transcription of ZIKV 5 0 end RNA. JEV UFS mutants were generated by site-directed mutagenesis, the resultant plasmids were utilized to amplify the DNA templates for in vitro transcription of the corresponding JEV 5 0 RNA mutants.", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization\nPassage: Site-directed mutagenesis method was employed for the generation of ZIKV fragments containing the desired UFS mutations, the generated Not I-Avr II restriction fragments were then subcloned into the infectious clone of ZIKV strain FSS13025 , which was kindly provided by Professor Pei-Yong Shi.", "Title: Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles\nPassage: For example, RdRp mutator variants of chikungunya virus and Sindbis virus are attenuated in fruit flies and mice . The attenuation observed in vivo has been directly correlated with the increased mutation rates that would presumably result in higher frequencies of lethal mutations. Indeed, mutator strains of RNA viruses present mutation frequency profiles similar to those of wild-type-like viruses whose mutation rates are extrinsically increased by treatment with RNA mutagens in studies evaluating lethal mutagenesis as an antiviral strategy . However, while many determinants that alter RdRp fidelity have been identified, the enzymatic mechanisms or dynamics by which this occurs" ]

[ [ "2a", "Title: Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization" ], [ "2b", "Passage: Site-directed mutagenesis method was employed for the generation of ZIKV fragments containing the desired UFS mutations, the generated Not I-Avr II restriction fragments were then subcloned into the infectious clone of ZIKV strain FSS13025 , which was kindly provided by Professor Pei-Yong Shi." ] ]

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

[ "Title: Globalization and emerging governance modalities\nPassage: becomes impossible.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: and a higher standard across the board.", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Achieving these changes would require the institutions that demand internationally comparable data from international organisationsmostly UN member states and their development organisations but also private foundations and multilateral health fundsto recognise that socially robust processes may result in slightly lower frequency and even somewhat less standardised measures, even as they lead to more use of data to guide service provision locally and nationally. We note that many richer nations do not themselves report health data in the formats required of most lowand middle-income nations, so they should have little difficulty understanding the utility of local variation.", "Title: On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management\nPassage: The above improvements in the healthcare sector can only be achieved if different smart city products are fashioned to support standardized protocols that would allow for seamless communication between themselves. Weber and Podnar Žarko suggest that IoT devices in use should support open protocols, and at the same time, the device provider should ensure that those fashioned uphold data integrity and safety during communication and transmission. Unfortunately, this has not been the case and, as Vermesan and Friess explain, most smart city products use proprietary solutions that are only understood by the service providers. This situation often creates unnecessary fragmentation" ]

[ [ "2a", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust" ], [ "2b", "Passage: Achieving these changes would require the institutions that demand internationally comparable data from international organisationsmostly UN member states and their development organisations but also private foundations and multilateral health fundsto recognise that socially robust processes may result in slightly lower frequency and even somewhat less standardised measures, even as they lead to more use of data to guide service provision locally and nationally." ], [ "2c", "We note that many richer nations do not themselves report health data in the formats required of most lowand middle-income nations, so they should have little difficulty understanding the utility of local variation." ] ]

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

[ "Title: Globalization and emerging governance modalities\nPassage: becomes impossible.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: and a higher standard across the board.", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Achieving these changes would require the institutions that demand internationally comparable data from international organisationsmostly UN member states and their development organisations but also private foundations and multilateral health fundsto recognise that socially robust processes may result in slightly lower frequency and even somewhat less standardised measures, even as they lead to more use of data to guide service provision locally and nationally. We note that many richer nations do not themselves report health data in the formats required of most lowand middle-income nations, so they should have little difficulty understanding the utility of local variation.", "Title: On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management\nPassage: The above improvements in the healthcare sector can only be achieved if different smart city products are fashioned to support standardized protocols that would allow for seamless communication between themselves. Weber and Podnar Žarko suggest that IoT devices in use should support open protocols, and at the same time, the device provider should ensure that those fashioned uphold data integrity and safety during communication and transmission. Unfortunately, this has not been the case and, as Vermesan and Friess explain, most smart city products use proprietary solutions that are only understood by the service providers. This situation often creates unnecessary fragmentation" ]

[ [ "3a", "Title: On the Coronavirus (COVID-19) Outbreak and the Smart City Network: Universal Data Sharing Standards Coupled with Artificial Intelligence (AI) to Benefit Urban Health Monitoring and Management" ], [ "3b", "Passage: The above improvements in the healthcare sector can only be achieved if different smart city products are fashioned to support standardized protocols that would allow for seamless communication between themselves." ], [ "3c", "Weber and Podnar Žarko suggest that IoT devices in use should support open protocols, and at the same time, the device provider should ensure that those fashioned uphold data integrity and safety during communication and transmission." ], [ "3d", "Unfortunately, this has not been the case and, as Vermesan and Friess explain, most smart city products use proprietary solutions that are only understood by the service providers." ], [ "3e", "This situation often creates unnecessary fragmentation" ] ]

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

[ "Title: Long term outcomes in survivors of epidemic Influenza A (H7N9) virus infection\nPassage: function before and post infection of H7N9. In particular, this group of patients had pre-existing conditions, which may also have affected the HRQoL results. Patients who had suffered acute pathologies reported significant decreases in quality of life, whereas other patients with pre-existing conditions reported significant improvements in terms of reduced BP and improved MH, VT and SF scores 21 . In our study, H7N9 survivors had significantly higher VT and MH scores than the population norms. Thus, those scores may have been higher at baseline, i.e., prior to admission. Finally, after discharge from the hospital, there was no significant improvement;", "Title: Long term outcomes in survivors of epidemic Influenza A (H7N9) virus infection\nPassage: however, whether improvements in physical and mental health would have been detected had the follow-up duration been longer is unknown. Thus, further expanded research is needed.", "Title: Fast-track surgery improves postoperative clinical recovery and cellular and humoral immunity after esophagectomy for esophageal cancer\nPassage: All analyses were performed with the statistical package SPSS . A P value of <0.05 was considered significant.", "Title: Immunomodulatory Activity and Protective Effects of Polysaccharide from Eupatorium adenophorum Leaf Extract on Highly Pathogenic H5N1 Influenza Infection\nPassage: To test whether EAP could protect H5N1 infected mice, mice were treated with EAP at a dose of 5, 10, 25, or 50 mg/kg body weight intranasally once daily for 5 days prior to viral challenge with 120 PFU. Ten mice per group were monitored for 14 days for the survival rate. As shown in Figure 2 , all mice receiving PBS died at day 11. Mice administrated 25 mg/kg EAP had a survival rate of 50% at day 14, which was significantly higher than those receiving PBS . EAP treatment of 10 mg/kg and 50 mg/kg also appeared to" ]

[ [ "3a", "Title: Immunomodulatory Activity and Protective Effects of Polysaccharide from Eupatorium adenophorum Leaf Extract on Highly Pathogenic H5N1 Influenza Infection" ], [ "3b", "Passage: To test whether EAP could protect H5N1 infected mice, mice were treated with EAP at a dose of 5, 10, 25, or 50 mg/kg body weight intranasally once daily for 5 days prior to viral challenge with 120 PFU." ], [ "3c", "Ten mice per group were monitored for 14 days for the survival rate." ], [ "3d", "As shown in Figure 2 , all mice receiving PBS died at day 11." ], [ "3e", "Mice administrated 25 mg/kg EAP had a survival rate of 50% at day 14, which was significantly higher than those receiving PBS ." ], [ "3f", "EAP treatment of 10 mg/kg and 50 mg/kg also appeared to" ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: Tan and colleagues specifically focused on the newly-emerged MERS-CoV. The virus was identified in 2012 in the Middle East with some exported cases to Europe. In 2013 the virus has been re-emerging and expanding its borders to more European countries. In the initial diagnosis, the pan-coronavirus real-time reverse transcription polymerase chain reaction assay played a very important role for the identification of the causative agents. By using this method, scientists detected an expected-size PCR fragment for the corresponding conserved region of ORF1b of the replicase gene of a coronavirus. This is another example that molecular biology methods played for the", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: Zoonotic emergence of novel human infections poses a significant risk to global public health. For example, the 'Spanish flu' pandemic of 1918 probably originated in birds and caused millions of deaths worldwide . While much less virulent, the subsequent influenza pandemics of 1957, 1968 and 2009 are potent reminders of the capacity of the influenza virus to cross the species barrier into humans. Many other pathogens share this capacity: the SARS outbreak of 2003 has been linked to bats and palm civets . In 2008, a novel arenavirus which killed four out of five patients in South Africa was linked", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Text: Emerging pathogens cause new or previously unrecognized diseases, and among them, emerging zoonotic diseases are a major concern among scientists studying infectious diseases at different spatial and temporal scales . Changes in biotic and abiotic conditions may alter population disease dynamics and lead to the emergence of zoonotic infections . During the last decades, several outbreaks of emerging and re-emerging viral pathogens have occurred, affecting both purely-local and worldwide/pandemic involvement of human populations. Among the conspicuous examples are influenza A, Ebola virus, hepatitis C virus, severe adult respiratory distress , coronavirus, and human immunodeficiency virus, which challenge prevention and", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: With respect to their significance to the economy, vaccines have also been developed for many of these viruses in a bid to prevent localized infections from progressing into serious outbreaks. This has, however, proven to be a hard battle as the vaccines are unable to provide complete cross-protection among the various serotypes of each virus ." ]

[ [ "0a", "Title: Haunted with and hunting for viruses" ], [ "0b", "Passage: Tan and colleagues specifically focused on the newly-emerged MERS-CoV." ], [ "0c", "The virus was identified in 2012 in the Middle East with some exported cases to Europe." ], [ "0d", "In 2013 the virus has been re-emerging and expanding its borders to more European countries." ], [ "0e", "In the initial diagnosis, the pan-coronavirus real-time reverse transcription polymerase chain reaction assay played a very important role for the identification of the causative agents." ], [ "0f", "By using this method, scientists detected an expected-size PCR fragment for the corresponding conserved region of ORF1b of the replicase gene of a coronavirus." ], [ "0g", "This is another example that molecular biology methods played for the" ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: Tan and colleagues specifically focused on the newly-emerged MERS-CoV. The virus was identified in 2012 in the Middle East with some exported cases to Europe. In 2013 the virus has been re-emerging and expanding its borders to more European countries. In the initial diagnosis, the pan-coronavirus real-time reverse transcription polymerase chain reaction assay played a very important role for the identification of the causative agents. By using this method, scientists detected an expected-size PCR fragment for the corresponding conserved region of ORF1b of the replicase gene of a coronavirus. This is another example that molecular biology methods played for the", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: Zoonotic emergence of novel human infections poses a significant risk to global public health. For example, the 'Spanish flu' pandemic of 1918 probably originated in birds and caused millions of deaths worldwide . While much less virulent, the subsequent influenza pandemics of 1957, 1968 and 2009 are potent reminders of the capacity of the influenza virus to cross the species barrier into humans. Many other pathogens share this capacity: the SARS outbreak of 2003 has been linked to bats and palm civets . In 2008, a novel arenavirus which killed four out of five patients in South Africa was linked", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Text: Emerging pathogens cause new or previously unrecognized diseases, and among them, emerging zoonotic diseases are a major concern among scientists studying infectious diseases at different spatial and temporal scales . Changes in biotic and abiotic conditions may alter population disease dynamics and lead to the emergence of zoonotic infections . During the last decades, several outbreaks of emerging and re-emerging viral pathogens have occurred, affecting both purely-local and worldwide/pandemic involvement of human populations. Among the conspicuous examples are influenza A, Ebola virus, hepatitis C virus, severe adult respiratory distress , coronavirus, and human immunodeficiency virus, which challenge prevention and", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: With respect to their significance to the economy, vaccines have also been developed for many of these viruses in a bid to prevent localized infections from progressing into serious outbreaks. This has, however, proven to be a hard battle as the vaccines are unable to provide complete cross-protection among the various serotypes of each virus ." ]

[ [ "1a", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease" ], [ "1b", "Passage: Zoonotic emergence of novel human infections poses a significant risk to global public health." ], [ "1c", "For example, the 'Spanish flu' pandemic of 1918 probably originated in birds and caused millions of deaths worldwide ." ], [ "1d", "While much less virulent, the subsequent influenza pandemics of 1957, 1968 and 2009 are potent reminders of the capacity of the influenza virus to cross the species barrier into humans." ], [ "1e", "Many other pathogens share this capacity: the SARS outbreak of 2003 has been linked to bats and palm civets ." ], [ "1f", "In 2008, a novel arenavirus which killed four out of five patients in South Africa was linked" ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: Tan and colleagues specifically focused on the newly-emerged MERS-CoV. The virus was identified in 2012 in the Middle East with some exported cases to Europe. In 2013 the virus has been re-emerging and expanding its borders to more European countries. In the initial diagnosis, the pan-coronavirus real-time reverse transcription polymerase chain reaction assay played a very important role for the identification of the causative agents. By using this method, scientists detected an expected-size PCR fragment for the corresponding conserved region of ORF1b of the replicase gene of a coronavirus. This is another example that molecular biology methods played for the", "Title: Insights into the Evolution and Emergence of a Novel Infectious Disease\nPassage: Zoonotic emergence of novel human infections poses a significant risk to global public health. For example, the 'Spanish flu' pandemic of 1918 probably originated in birds and caused millions of deaths worldwide . While much less virulent, the subsequent influenza pandemics of 1957, 1968 and 2009 are potent reminders of the capacity of the influenza virus to cross the species barrier into humans. Many other pathogens share this capacity: the SARS outbreak of 2003 has been linked to bats and palm civets . In 2008, a novel arenavirus which killed four out of five patients in South Africa was linked", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Text: Emerging pathogens cause new or previously unrecognized diseases, and among them, emerging zoonotic diseases are a major concern among scientists studying infectious diseases at different spatial and temporal scales . Changes in biotic and abiotic conditions may alter population disease dynamics and lead to the emergence of zoonotic infections . During the last decades, several outbreaks of emerging and re-emerging viral pathogens have occurred, affecting both purely-local and worldwide/pandemic involvement of human populations. Among the conspicuous examples are influenza A, Ebola virus, hepatitis C virus, severe adult respiratory distress , coronavirus, and human immunodeficiency virus, which challenge prevention and", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: With respect to their significance to the economy, vaccines have also been developed for many of these viruses in a bid to prevent localized infections from progressing into serious outbreaks. This has, however, proven to be a hard battle as the vaccines are unable to provide complete cross-protection among the various serotypes of each virus ." ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: Text: Emerging pathogens cause new or previously unrecognized diseases, and among them, emerging zoonotic diseases are a major concern among scientists studying infectious diseases at different spatial and temporal scales ." ], [ "2c", "Changes in biotic and abiotic conditions may alter population disease dynamics and lead to the emergence of zoonotic infections ." ], [ "2d", "During the last decades, several outbreaks of emerging and re-emerging viral pathogens have occurred, affecting both purely-local and worldwide/pandemic involvement of human populations." ], [ "2e", "Among the conspicuous examples are influenza A, Ebola virus, hepatitis C virus, severe adult respiratory distress , coronavirus, and human immunodeficiency virus, which challenge prevention and" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Infectious MERS-CoV added to DC, goat or cow milk and stored at 4°C could be recovered at least 72 h later and, if stored at 22°C, recovery was possible for up to 48 h . MERS-CoV titre decreased somewhat when recovered from milk at 22°C but pasteurization completely ablated MERS-CoV infectivity . In a subsequent study, MERS-CoV RNA was identified in the milk, nasal secretion and faeces of DCs from Qatar .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations . What role maternal camel antibody might play in delaying infection of calves remains unknown . Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection. In contrast to earlier results, slaughterhouse workers who kill both younger and older", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: is an animal of ritual significance after the Hajj pilgrimage . However, MERS-CoV infection frequency is reportedly much lower than is the widespread and frequent habit of eating, drinking and preparing DC products. Daily ingestion of fresh unpasteurized DC milk is common among the desert Bedouin and many others in the KSA. DC urine is also consumed or used for supposed health benefits. Despite camel butchery being a local occupation, neither butchers nor other at-risk groups are identifiable among MERS cases; this may simply be a reporting issue rather than an unexplainable absence of MERS. A small case-control study published", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: positive DC had been infected by a variant of the same virus, harbouring the same distinct pattern of nucleotide polymorphisms. All nine DC in the owner's herd, serially sampled, reacted in a recombinant S1 antigen ELISA, with the two animals that had been RT-rtPCR positive showing a small, verifiable rise in antibody titre . A rise in titre theoretically begins 10 to 21 days after DC infection . The authors suggested that the rise in titre in DC sera which occurred alongside a declining RNA load, while the patient was actively ill and hospitalized, indicated that the DCs were infected" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: Infectious MERS-CoV added to DC, goat or cow milk and stored at 4°C could be recovered at least 72 h later and, if stored at 22°C, recovery was possible for up to 48 h ." ], [ "0c", "MERS-CoV titre decreased somewhat when recovered from milk at 22°C but pasteurization completely ablated MERS-CoV infectivity ." ], [ "0d", "In a subsequent study, MERS-CoV RNA was identified in the milk, nasal secretion and faeces of DCs from Qatar ." ] ]

[ "0b" ]

[ "Title: Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA\nPassage: al. 17 and Furuse et al. 26 Since M1 protein plays an important role in virus assembly and budding, any change in M1 can have deleterious effect on virus survival, whereas M2 protein is integral membrane protein forming pH-gated channels in the viral lipid membrane. 23 More sites in the M2 protein under positive selection are located in the extracellular domain, which is recognized by the host immune response system. Thus, to evade host immune response, M2 protein is more susceptible to mutations. 26, 39, 40 Also, higher rate of amino acid variations in M1 and M2 proteins was observed", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Protection against homo and hetero-subtypic influenza A virus by optimized M2e DNA vaccine\nPassage: Influenza virus M2 protein is an integral membrane protein expressed on the viral surface in low quantities, while being abundantly present on the surface of infected cells . This expression pattern plays an important role in viral replication. The M2 protein consists of an N-terminal extracellular region , transmembrane region, and C-terminal cytoplasmic tail region. The M2e is composed of 24 amino acids and is highly conserved among different influenza A subtypes . Thus, this region may be a good candidate epitope for the preparation of a universal vaccine. However, in its natural state, viral M2e has low immunogenicity and" ]

[ [ "0a", "Title: Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA Passage: al. 17 and Furuse et al. 26 Since M1 protein plays an important role in virus assembly and budding, any change in M1 can have deleterious effect on virus survival, whereas M2 protein is integral membrane protein forming pH-gated channels in the viral lipid membrane." ], [ "0b", "23 More sites in the M2 protein under positive selection are located in the extracellular domain, which is recognized by the host immune response system." ], [ "0c", "Thus, to evade host immune response, M2 protein is more susceptible to mutations." ], [ "0d", "26, 39, 40 Also, higher rate of amino acid variations in M1 and M2 proteins was observed" ] ]

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

[ "Title: Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA\nPassage: al. 17 and Furuse et al. 26 Since M1 protein plays an important role in virus assembly and budding, any change in M1 can have deleterious effect on virus survival, whereas M2 protein is integral membrane protein forming pH-gated channels in the viral lipid membrane. 23 More sites in the M2 protein under positive selection are located in the extracellular domain, which is recognized by the host immune response system. Thus, to evade host immune response, M2 protein is more susceptible to mutations. 26, 39, 40 Also, higher rate of amino acid variations in M1 and M2 proteins was observed", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Protection against homo and hetero-subtypic influenza A virus by optimized M2e DNA vaccine\nPassage: Influenza virus M2 protein is an integral membrane protein expressed on the viral surface in low quantities, while being abundantly present on the surface of infected cells . This expression pattern plays an important role in viral replication. The M2 protein consists of an N-terminal extracellular region , transmembrane region, and C-terminal cytoplasmic tail region. The M2e is composed of 24 amino acids and is highly conserved among different influenza A subtypes . Thus, this region may be a good candidate epitope for the preparation of a universal vaccine. However, in its natural state, viral M2e has low immunogenicity and" ]

[ [ "1a", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice" ], [ "1b", "Passage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine ." ], [ "1c", "In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice." ], [ "1d", "However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections." ], [ "1e", "Therefore, many strategies have been applied focusing on" ] ]

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

[ "Title: Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA\nPassage: al. 17 and Furuse et al. 26 Since M1 protein plays an important role in virus assembly and budding, any change in M1 can have deleterious effect on virus survival, whereas M2 protein is integral membrane protein forming pH-gated channels in the viral lipid membrane. 23 More sites in the M2 protein under positive selection are located in the extracellular domain, which is recognized by the host immune response system. Thus, to evade host immune response, M2 protein is more susceptible to mutations. 26, 39, 40 Also, higher rate of amino acid variations in M1 and M2 proteins was observed", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Protection against homo and hetero-subtypic influenza A virus by optimized M2e DNA vaccine\nPassage: Influenza virus M2 protein is an integral membrane protein expressed on the viral surface in low quantities, while being abundantly present on the surface of infected cells . This expression pattern plays an important role in viral replication. The M2 protein consists of an N-terminal extracellular region , transmembrane region, and C-terminal cytoplasmic tail region. The M2e is composed of 24 amino acids and is highly conserved among different influenza A subtypes . Thus, this region may be a good candidate epitope for the preparation of a universal vaccine. However, in its natural state, viral M2e has low immunogenicity and" ]

[ [ "2a", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice" ], [ "2b", "Passage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine ." ], [ "2c", "In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice." ], [ "2d", "However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections." ], [ "2e", "Therefore, many strategies have been applied focusing on" ] ]

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

[ "Title: Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA\nPassage: al. 17 and Furuse et al. 26 Since M1 protein plays an important role in virus assembly and budding, any change in M1 can have deleterious effect on virus survival, whereas M2 protein is integral membrane protein forming pH-gated channels in the viral lipid membrane. 23 More sites in the M2 protein under positive selection are located in the extracellular domain, which is recognized by the host immune response system. Thus, to evade host immune response, M2 protein is more susceptible to mutations. 26, 39, 40 Also, higher rate of amino acid variations in M1 and M2 proteins was observed", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Mucosal Vaccination with Recombinant Lactobacillus casei-Displayed CTA1-Conjugated Consensus Matrix Protein-2 (sM2) Induces Broad Protection against Divergent Influenza Subtypes in BALB/c Mice\nPassage: Matrix protein 2 is highly conserved among influenza A virus strains, indicating that M2 is an attractive target for developing a universal vaccine . In previous studies, various constructs of the M2 vaccine have been developed and tested, including recombinant Escherichia coli expressing M2 fusion protein, adenoviral vectors expressing the M2 protein, plasmid DNA encoding M2 and peptides encoding M2e , each of which was able to elicit protective immune responses in mice. However, the drawback of these M2-based vaccines is their low immunogenicity; additionally, most of them would require intramuscular injections. Therefore, many strategies have been applied focusing on", "Title: Protection against homo and hetero-subtypic influenza A virus by optimized M2e DNA vaccine\nPassage: Influenza virus M2 protein is an integral membrane protein expressed on the viral surface in low quantities, while being abundantly present on the surface of infected cells . This expression pattern plays an important role in viral replication. The M2 protein consists of an N-terminal extracellular region , transmembrane region, and C-terminal cytoplasmic tail region. The M2e is composed of 24 amino acids and is highly conserved among different influenza A subtypes . Thus, this region may be a good candidate epitope for the preparation of a universal vaccine. However, in its natural state, viral M2e has low immunogenicity and" ]

[ [ "3a", "Title: Protection against homo and hetero-subtypic influenza A virus by optimized M2e DNA vaccine" ], [ "3b", "Passage: Influenza virus M2 protein is an integral membrane protein expressed on the viral surface in low quantities, while being abundantly present on the surface of infected cells ." ], [ "3c", "This expression pattern plays an important role in viral replication." ], [ "3d", "The M2 protein consists of an N-terminal extracellular region , transmembrane region, and C-terminal cytoplasmic tail region." ], [ "3e", "The M2e is composed of 24 amino acids and is highly conserved among different influenza A subtypes ." ], [ "3f", "Thus, this region may be a good candidate epitope for the preparation of a universal vaccine." ], [ "3g", "However, in its natural state, viral M2e has low immunogenicity and" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: There are eleven studies that focus on SARS-CoV diagnostic testing . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity .", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: There is no perfect test for the diagnosis of infl uenza. Virus culture, the present 'gold-standard test' is not 100% sensitive and does not provide results in a time-frame that allows optimal use of potentially effective antiviral treatment. Although rapid diagnostic tests provide results in less than 30 minutes, they are signifi cantly less sensitive and do not differentiate between different subtypes of infl uenza A virus. Rapid testing is only offered after the fi rst culture-confi rmed cases of infl uenza are reported from the community. Molecular assays; reverse transcriptase polymerase chain reaction and real-time RT-PCR targeting conserved regions" ]

[ [ "0a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: There are eleven studies that focus on SARS-CoV diagnostic testing ." ], [ "0c", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis." ], [ "0d", "Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity." ], [ "0e", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis." ], [ "0f", "Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity ." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: There are eleven studies that focus on SARS-CoV diagnostic testing . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity .", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: There is no perfect test for the diagnosis of infl uenza. Virus culture, the present 'gold-standard test' is not 100% sensitive and does not provide results in a time-frame that allows optimal use of potentially effective antiviral treatment. Although rapid diagnostic tests provide results in less than 30 minutes, they are signifi cantly less sensitive and do not differentiate between different subtypes of infl uenza A virus. Rapid testing is only offered after the fi rst culture-confi rmed cases of infl uenza are reported from the community. Molecular assays; reverse transcriptase polymerase chain reaction and real-time RT-PCR targeting conserved regions" ]

[ [ "1a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "1b", "Passage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate." ], [ "1c", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens." ], [ "1d", "There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset ." ], [ "1e", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load." ], [ "1f", "Hence, serological diagnoses are likely used when nucleic amplification tests are" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: There are eleven studies that focus on SARS-CoV diagnostic testing . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity .", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: There is no perfect test for the diagnosis of infl uenza. Virus culture, the present 'gold-standard test' is not 100% sensitive and does not provide results in a time-frame that allows optimal use of potentially effective antiviral treatment. Although rapid diagnostic tests provide results in less than 30 minutes, they are signifi cantly less sensitive and do not differentiate between different subtypes of infl uenza A virus. Rapid testing is only offered after the fi rst culture-confi rmed cases of infl uenza are reported from the community. Molecular assays; reverse transcriptase polymerase chain reaction and real-time RT-PCR targeting conserved regions" ]

[ [ "2a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "2b", "Passage: The first validated diagnostic test was designed in Germany." ], [ "2c", "Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like." ], [ "2d", "Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment." ], [ "2e", "Two assays were used for the RNA dependent RNA polymerase gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing." ], [ "2f", "All assays were highly sensitive and specific in that they did" ] ]

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

[ "Title: Reverse Genetics Approaches for the Development of Influenza Vaccines\nPassage: Adjuvants have been shown to enhance the immune response elicited by an antigen and could be used to improve the immunogenicity of IIV . The use of adjuvants could also reduce vaccine dose, stretching antigen and vaccine supplies. Currently, FDA-licensed adjuvants for influenza vaccine usage include aluminum salt and the squalene oil-in-water emulsion systems MF59 ) and AS03 . However, most of the current IIVs do not contain any type of adjuvant, but many are under investigation.", "Title: Adjuvants and the vaccine response to the DS-Cav1-stabilized fusion glycoprotein of respiratory syncytial virus\nPassage: , and monophosphoryl lipid A have achieved widespread human use. Most adjuvants either activate pattern recognition receptors ) in the innate immune system or improve the delivery of antigens to the immune system. The most common adjuvant, alum, comprised of aluminum salts, has been used in humans since 1932, is approved for human use by the FDA, and is a component of numerous licensed vaccines such as Diphtheria, Tetanus and Pertussis vaccines, and hepatitis B vaccines. MPLA with Alum is used for the hepatitis B vaccine, Fendrix, and the human papillomavirus vaccine, Cervarix, and has extensive human safety data in", "Title: Safety, Reactogenicity, and Immunogenicity of Inactivated Monovalent Influenza A(H5N1) Virus Vaccine Administered With or Without AS03 Adjuvant\nPassage: In summary, we demonstrated the feasibility of a strategy in which proprietary adjuvants available in the US National Prepandemic Influenza Vaccine Stockpile could be combined with pandemic avian antigens produced by other manufacturers . This approach has the potential to substantially increase the supply of effective vaccine and to add flexibility and speed to the responses available for controlling an emerging influenza pandemic.", "Title: Oil-in-water emulsion adjuvants for pediatric influenza vaccines: a systematic review and meta-analysis\nPassage: stimulates the local inflammatory response at the injection site and thus increases the uptake of antigen by activated dendritic cells 43 . Similarly, AS03 facilities a stronger antibody response by inducing a local cytokine and chemokine response at the injection site to enhance antigen uptake 43 . Studies in young children also showed that MF59-adjuvanted influenza vaccines produced a stronger and more homogeneous innate transcription response like that of adults, thus resulting in significantly higher HI titers than those elicited by non-adjuvanted vaccines 22 ." ]

[ [ "0a", "Title: Reverse Genetics Approaches for the Development of Influenza Vaccines" ], [ "0b", "Passage: Adjuvants have been shown to enhance the immune response elicited by an antigen and could be used to improve the immunogenicity of IIV ." ], [ "0c", "The use of adjuvants could also reduce vaccine dose, stretching antigen and vaccine supplies." ], [ "0d", "Currently, FDA-licensed adjuvants for influenza vaccine usage include aluminum salt and the squalene oil-in-water emulsion systems MF59 ) and AS03 ." ], [ "0e", "However, most of the current IIVs do not contain any type of adjuvant, but many are under investigation." ] ]

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

[ "Title: Reverse Genetics Approaches for the Development of Influenza Vaccines\nPassage: Adjuvants have been shown to enhance the immune response elicited by an antigen and could be used to improve the immunogenicity of IIV . The use of adjuvants could also reduce vaccine dose, stretching antigen and vaccine supplies. Currently, FDA-licensed adjuvants for influenza vaccine usage include aluminum salt and the squalene oil-in-water emulsion systems MF59 ) and AS03 . However, most of the current IIVs do not contain any type of adjuvant, but many are under investigation.", "Title: Adjuvants and the vaccine response to the DS-Cav1-stabilized fusion glycoprotein of respiratory syncytial virus\nPassage: , and monophosphoryl lipid A have achieved widespread human use. Most adjuvants either activate pattern recognition receptors ) in the innate immune system or improve the delivery of antigens to the immune system. The most common adjuvant, alum, comprised of aluminum salts, has been used in humans since 1932, is approved for human use by the FDA, and is a component of numerous licensed vaccines such as Diphtheria, Tetanus and Pertussis vaccines, and hepatitis B vaccines. MPLA with Alum is used for the hepatitis B vaccine, Fendrix, and the human papillomavirus vaccine, Cervarix, and has extensive human safety data in", "Title: Safety, Reactogenicity, and Immunogenicity of Inactivated Monovalent Influenza A(H5N1) Virus Vaccine Administered With or Without AS03 Adjuvant\nPassage: In summary, we demonstrated the feasibility of a strategy in which proprietary adjuvants available in the US National Prepandemic Influenza Vaccine Stockpile could be combined with pandemic avian antigens produced by other manufacturers . This approach has the potential to substantially increase the supply of effective vaccine and to add flexibility and speed to the responses available for controlling an emerging influenza pandemic.", "Title: Oil-in-water emulsion adjuvants for pediatric influenza vaccines: a systematic review and meta-analysis\nPassage: stimulates the local inflammatory response at the injection site and thus increases the uptake of antigen by activated dendritic cells 43 . Similarly, AS03 facilities a stronger antibody response by inducing a local cytokine and chemokine response at the injection site to enhance antigen uptake 43 . Studies in young children also showed that MF59-adjuvanted influenza vaccines produced a stronger and more homogeneous innate transcription response like that of adults, thus resulting in significantly higher HI titers than those elicited by non-adjuvanted vaccines 22 ." ]

[ [ "2a", "Title: Safety, Reactogenicity, and Immunogenicity of Inactivated Monovalent Influenza A(H5N1) Virus Vaccine Administered With or Without AS03 Adjuvant" ], [ "2b", "Passage: In summary, we demonstrated the feasibility of a strategy in which proprietary adjuvants available in the US National Prepandemic Influenza Vaccine Stockpile could be combined with pandemic avian antigens produced by other manufacturers ." ], [ "2c", "This approach has the potential to substantially increase the supply of effective vaccine and to add flexibility and speed to the responses available for controlling an emerging influenza pandemic." ] ]

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

[ "Title: Reverse Genetics Approaches for the Development of Influenza Vaccines\nPassage: Adjuvants have been shown to enhance the immune response elicited by an antigen and could be used to improve the immunogenicity of IIV . The use of adjuvants could also reduce vaccine dose, stretching antigen and vaccine supplies. Currently, FDA-licensed adjuvants for influenza vaccine usage include aluminum salt and the squalene oil-in-water emulsion systems MF59 ) and AS03 . However, most of the current IIVs do not contain any type of adjuvant, but many are under investigation.", "Title: Adjuvants and the vaccine response to the DS-Cav1-stabilized fusion glycoprotein of respiratory syncytial virus\nPassage: , and monophosphoryl lipid A have achieved widespread human use. Most adjuvants either activate pattern recognition receptors ) in the innate immune system or improve the delivery of antigens to the immune system. The most common adjuvant, alum, comprised of aluminum salts, has been used in humans since 1932, is approved for human use by the FDA, and is a component of numerous licensed vaccines such as Diphtheria, Tetanus and Pertussis vaccines, and hepatitis B vaccines. MPLA with Alum is used for the hepatitis B vaccine, Fendrix, and the human papillomavirus vaccine, Cervarix, and has extensive human safety data in", "Title: Safety, Reactogenicity, and Immunogenicity of Inactivated Monovalent Influenza A(H5N1) Virus Vaccine Administered With or Without AS03 Adjuvant\nPassage: In summary, we demonstrated the feasibility of a strategy in which proprietary adjuvants available in the US National Prepandemic Influenza Vaccine Stockpile could be combined with pandemic avian antigens produced by other manufacturers . This approach has the potential to substantially increase the supply of effective vaccine and to add flexibility and speed to the responses available for controlling an emerging influenza pandemic.", "Title: Oil-in-water emulsion adjuvants for pediatric influenza vaccines: a systematic review and meta-analysis\nPassage: stimulates the local inflammatory response at the injection site and thus increases the uptake of antigen by activated dendritic cells 43 . Similarly, AS03 facilities a stronger antibody response by inducing a local cytokine and chemokine response at the injection site to enhance antigen uptake 43 . Studies in young children also showed that MF59-adjuvanted influenza vaccines produced a stronger and more homogeneous innate transcription response like that of adults, thus resulting in significantly higher HI titers than those elicited by non-adjuvanted vaccines 22 ." ]

[ [ "3a", "Title: Oil-in-water emulsion adjuvants for pediatric influenza vaccines: a systematic review and meta-analysis" ], [ "3b", "Passage: stimulates the local inflammatory response at the injection site and thus increases the uptake of antigen by activated dendritic cells 43 ." ], [ "3c", "Similarly, AS03 facilities a stronger antibody response by inducing a local cytokine and chemokine response at the injection site to enhance antigen uptake 43 ." ], [ "3d", "Studies in young children also showed that MF59-adjuvanted influenza vaccines produced a stronger and more homogeneous innate transcription response like that of adults, thus resulting in significantly higher HI titers than those elicited by non-adjuvanted vaccines 22 ." ] ]

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

[ "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: We were also aware that the clinical studies we analysed differed with respect to which comorbidities or identifiable causes for exacerbations were reported. Most patients were elderly and therefore were more likely to be suffering from one or more co-existing diseases such as asthma or cardiovascular disease. Such co-morbidity makes interpretation of our findings more difficult with respect to the true causes of exacerbations. If their aetiology could be determined, then susceptible patients such as those in Level I could be identified and new treatments developed to help prevent their onset and related hospital costs.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: are due to the effect of enhanced acute airway inflammation impacting upon and worsening the symptoms of the existing disease . These acute exacerbations are the main cause of morbidity and sometimes mortality in patients, as well as resulting in major economic burdens worldwide. However, due to the complex interactions between the host and the exacerbation agents, the mechanisms of exacerbation may vary considerably in different individuals under various triggers. Acute exacerbations are usually due to the presence of environmental factors such as allergens, pollutants, smoke, cold or dry air and pathogenic microbes in the airway . These agents elicit", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Finally, the compatibility between the studies of COPD exacerbation that we analysed may have been limited by substantial variations in the time and location of studies. Exacerbations are more likely in summer but many studies failed to report the time of year or the time period for study implementation. Thus, seasonal effects, combined with the low incidence of exacerbations per patient, could represent an inherent bias. In addition, different institutions probably had different standards with respect to diagnosis and management of COPD exacerbations when these studies were performed. Such variations may also explain any observed inconsistencies in our findings. However,", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Lastly, our findings were obtained from COPD patients that had experienced at least one exacerbation during the study assessment period. In the same studies, there were also patients who did not experience an exacerbation. This indicates that a fraction of COPD patients may be regarded as being susceptible to an exacerbation whereas another fraction is 'exacerbation-free'. It would be interesting to determine how the variables we identified in our study change in the latter patient group according to FEV 1 . Some published studies have stratified COPD patients on the basis of exacerbation frequency; this is generally done by categorising" ]

[ [ "1a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "1b", "Passage: are due to the effect of enhanced acute airway inflammation impacting upon and worsening the symptoms of the existing disease ." ], [ "1c", "These acute exacerbations are the main cause of morbidity and sometimes mortality in patients, as well as resulting in major economic burdens worldwide." ], [ "1d", "However, due to the complex interactions between the host and the exacerbation agents, the mechanisms of exacerbation may vary considerably in different individuals under various triggers." ], [ "1e", "Acute exacerbations are usually due to the presence of environmental factors such as allergens, pollutants, smoke, cold or dry air and pathogenic microbes in the airway ." ], [ "1f", "These agents elicit" ] ]

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

[ "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: We were also aware that the clinical studies we analysed differed with respect to which comorbidities or identifiable causes for exacerbations were reported. Most patients were elderly and therefore were more likely to be suffering from one or more co-existing diseases such as asthma or cardiovascular disease. Such co-morbidity makes interpretation of our findings more difficult with respect to the true causes of exacerbations. If their aetiology could be determined, then susceptible patients such as those in Level I could be identified and new treatments developed to help prevent their onset and related hospital costs.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: are due to the effect of enhanced acute airway inflammation impacting upon and worsening the symptoms of the existing disease . These acute exacerbations are the main cause of morbidity and sometimes mortality in patients, as well as resulting in major economic burdens worldwide. However, due to the complex interactions between the host and the exacerbation agents, the mechanisms of exacerbation may vary considerably in different individuals under various triggers. Acute exacerbations are usually due to the presence of environmental factors such as allergens, pollutants, smoke, cold or dry air and pathogenic microbes in the airway . These agents elicit", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Finally, the compatibility between the studies of COPD exacerbation that we analysed may have been limited by substantial variations in the time and location of studies. Exacerbations are more likely in summer but many studies failed to report the time of year or the time period for study implementation. Thus, seasonal effects, combined with the low incidence of exacerbations per patient, could represent an inherent bias. In addition, different institutions probably had different standards with respect to diagnosis and management of COPD exacerbations when these studies were performed. Such variations may also explain any observed inconsistencies in our findings. However,", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Lastly, our findings were obtained from COPD patients that had experienced at least one exacerbation during the study assessment period. In the same studies, there were also patients who did not experience an exacerbation. This indicates that a fraction of COPD patients may be regarded as being susceptible to an exacerbation whereas another fraction is 'exacerbation-free'. It would be interesting to determine how the variables we identified in our study change in the latter patient group according to FEV 1 . Some published studies have stratified COPD patients on the basis of exacerbation frequency; this is generally done by categorising" ]

[ [ "2a", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease" ], [ "2b", "Passage: Finally, the compatibility between the studies of COPD exacerbation that we analysed may have been limited by substantial variations in the time and location of studies." ], [ "2c", "Exacerbations are more likely in summer but many studies failed to report the time of year or the time period for study implementation." ], [ "2d", "Thus, seasonal effects, combined with the low incidence of exacerbations per patient, could represent an inherent bias." ], [ "2e", "In addition, different institutions probably had different standards with respect to diagnosis and management of COPD exacerbations when these studies were performed." ], [ "2f", "Such variations may also explain any observed inconsistencies in our findings. However," ] ]

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

[ "Title: Advances in Directly Amplifying Nucleic Acids from Complex Samples\nPassage: Saliva and sputum are abundant and easy to obtain, and are thus attractive samples for diagnostics. Saliva flows into the oral cavities through salivary glands, where blood vessels secrete the same protein and nucleic acid biomarkers as in peripheral blood. In contrast with blood-based samples, saliva sampling does not require trained technicians, presents fewer antigen-associated risks, and can be more easily purified . Sputum, a necessary sample for respiratory infections, is mucus from the lower airways. Unfortunately, saliva and sputum are very heterogeneous with respect to the distribution of organisms, chemical composition, and the presence of outside contaminants such as", "Title: Selection of key recommendations for quality indicators describing good quality outbreak response\nPassage: Two researchers performed the extraction of recommendations independently on a sample consisting of 25% of all selected sources . The researchers extracted good quality response recommendations from the selected literature. Discrepancies between the two researchers were discussed until consensus was reached. After reaching consensus on this 25% sample, one researcher continued to extract recommendations from the remaining selected literature . The two researchers examined the total set of recommendations to remove identical recommendations.", "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: Near-Patient Sampling to Assist Infection Control—A Case Report and Discussion\nPassage: The other related, practical issue is then to define what the clinically relevant threshold should be for the limit of detection of any molecular assay used to test such air samples. The following example illustrates some of these issues. Note that the figures discussed are for illustrative purposes only but the methods and equipment are based on some of the authors' current experiments." ]

[ [ "0a", "Title: Advances in Directly Amplifying Nucleic Acids from Complex Samples" ], [ "0b", "Passage: Saliva and sputum are abundant and easy to obtain, and are thus attractive samples for diagnostics." ], [ "0c", "Saliva flows into the oral cavities through salivary glands, where blood vessels secrete the same protein and nucleic acid biomarkers as in peripheral blood." ], [ "0d", "In contrast with blood-based samples, saliva sampling does not require trained technicians, presents fewer antigen-associated risks, and can be more easily purified ." ], [ "0e", "Sputum, a necessary sample for respiratory infections, is mucus from the lower airways." ], [ "0f", "Unfortunately, saliva and sputum are very heterogeneous with respect to the distribution of organisms, chemical composition, and the presence of outside contaminants such as" ] ]

[ "0b", "0e", "2d", "2f" ]

[ "Title: Advances in Directly Amplifying Nucleic Acids from Complex Samples\nPassage: Saliva and sputum are abundant and easy to obtain, and are thus attractive samples for diagnostics. Saliva flows into the oral cavities through salivary glands, where blood vessels secrete the same protein and nucleic acid biomarkers as in peripheral blood. In contrast with blood-based samples, saliva sampling does not require trained technicians, presents fewer antigen-associated risks, and can be more easily purified . Sputum, a necessary sample for respiratory infections, is mucus from the lower airways. Unfortunately, saliva and sputum are very heterogeneous with respect to the distribution of organisms, chemical composition, and the presence of outside contaminants such as", "Title: Selection of key recommendations for quality indicators describing good quality outbreak response\nPassage: Two researchers performed the extraction of recommendations independently on a sample consisting of 25% of all selected sources . The researchers extracted good quality response recommendations from the selected literature. Discrepancies between the two researchers were discussed until consensus was reached. After reaching consensus on this 25% sample, one researcher continued to extract recommendations from the remaining selected literature . The two researchers examined the total set of recommendations to remove identical recommendations.", "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: Near-Patient Sampling to Assist Infection Control—A Case Report and Discussion\nPassage: The other related, practical issue is then to define what the clinically relevant threshold should be for the limit of detection of any molecular assay used to test such air samples. The following example illustrates some of these issues. Note that the figures discussed are for illustrative purposes only but the methods and equipment are based on some of the authors' current experiments." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: 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." ], [ "2c", "LRT samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists ." ], [ "2d", "Recommended sample types include bronchoalveolar lavage , tracheal/tracheobronchial aspirate, pleural fluid and sputum ." ], [ "2e", "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 ." ], [ "2f", "If available, lung biopsy or autopsy tissues can also be tested ." ] ]

[ "0b", "0e", "2d", "2f" ]

[ "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: ranged from 36%-60% overall, which is alarmingly high compared with all previous outbreaks of human cases of seasonal influenza in the United States, for which the CFR has ranged from 0.04%-1.0% . This high level of illness severity and high mortality rate was unexpected and increased disease burden, resulting in concern among clinicians and public health officials; however, the risk factors that are most highly associated with the deaths from avian influenza were not clear.", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China\nPassage: of cases were men and the median age was 61 years . Forty-four died resulting in a case fatality proportion of 33% .", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: For the H7N9 group, the median number of days from onset to confirmation of infection in the fatality groups was slightly longer than that of survivors vs. 8 days, p = 0.011]; however, the median number of days from onset to outcome vs. 31 days, p < 0.001] and number of hospitalization days vs. 25 days, p < 0.001] in the fatality groups was slightly less than those relating to survivors, respectively .", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: The ratio of comorbidity was much higher in the H5N1 and H7N9 virus fatalities than in the survivors vs. 8.33% , p = 0.046 for H5N1; 58.6% vs. 34.8% , p < 0.001 for H7N9]. Only two H5N6 survivors were found to have underlying conditions, one of which was pregnancy, while only 22.2% of the H9N2 survivors had comorbidities. In total, the rate of comorbidities in the H7N9 fatality and survivor groups was slightly higher than that of the H5N1 groups ." ]

[ [ "1a", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China" ], [ "1b", "Passage: of cases were men and the median age was 61 years ." ], [ "1c", "Forty-four died resulting in a case fatality proportion of 33% ." ] ]

[ "1c", "3b" ]

[ "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: ranged from 36%-60% overall, which is alarmingly high compared with all previous outbreaks of human cases of seasonal influenza in the United States, for which the CFR has ranged from 0.04%-1.0% . This high level of illness severity and high mortality rate was unexpected and increased disease burden, resulting in concern among clinicians and public health officials; however, the risk factors that are most highly associated with the deaths from avian influenza were not clear.", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China\nPassage: of cases were men and the median age was 61 years . Forty-four died resulting in a case fatality proportion of 33% .", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: For the H7N9 group, the median number of days from onset to confirmation of infection in the fatality groups was slightly longer than that of survivors vs. 8 days, p = 0.011]; however, the median number of days from onset to outcome vs. 31 days, p < 0.001] and number of hospitalization days vs. 25 days, p < 0.001] in the fatality groups was slightly less than those relating to survivors, respectively .", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: The ratio of comorbidity was much higher in the H5N1 and H7N9 virus fatalities than in the survivors vs. 8.33% , p = 0.046 for H5N1; 58.6% vs. 34.8% , p < 0.001 for H7N9]. Only two H5N6 survivors were found to have underlying conditions, one of which was pregnancy, while only 22.2% of the H9N2 survivors had comorbidities. In total, the rate of comorbidities in the H7N9 fatality and survivor groups was slightly higher than that of the H5N1 groups ." ]

[ [ "3a", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses" ], [ "3b", "Passage: The ratio of comorbidity was much higher in the H5N1 and H7N9 virus fatalities than in the survivors vs. 8.33% , p = 0.046 for H5N1; 58.6% vs. 34.8% , p < 0.001 for H7N9]." ], [ "3c", "Only two H5N6 survivors were found to have underlying conditions, one of which was pregnancy, while only 22.2% of the H9N2 survivors had comorbidities." ], [ "3d", "In total, the rate of comorbidities in the H7N9 fatality and survivor groups was slightly higher than that of the H5N1 groups ." ] ]

[ "1c", "3b" ]

[ "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database\nPassage: away from hospitals . The subjects for this investigation were randomly selected and unfiltered. The time period of each group was consistent and was evenly distributed in two weeks. We made further inquiries 189 amicable interviewees who were willing to take the SMP tests about their background, as well as the privacy protection in SMP data. The patients were fully informed before the voluntary agreements for SMP tests were signed. The researchers obtained the respective remaining samples from nurses after the ordinary blood tests were performed. No extra sampling of blood was performed in this study.", "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database\nPassage: room for blood sampling. Our researchers were permitted to wait in the room and give the patients suggestions to permit the additional SMP tests accompanied by their original blood tests. The data acquisition was performed in a passive way, i.e., the participators were randomly involved in. We orally interviewed the patients, doctors and nurses regarding their attitude towards the SMP test. The investigators for survey studies were divided into two groups: one group interviewed the people who will get their blood tested in the blood-collection room of hospitals, whereas the other group randomly interviewed the pedestrians in city streets far", "Title: A simple novel device for air sampling by electrokinetic capture\nPassage: Authors' contributions JG contributed to experimental design, performed the air sampling and mold spore data reduction, and had primary responsibility for drafting the manuscript. PG contributed to the experimental design and reviewing of the manuscript. GS performed the atomic force microscopy and interpretation of the results therefrom. AF performed the PCR and amplicon analysis and wrote that part of the methods section. JH-M was responsible for the PCR and amplicon analysis experimental design and data reduction and contributed to the manuscript writing. JAG contributed to the experimental design and manuscript review and writing. All authors read and approved the final", "Title: Near-Patient Sampling to Assist Infection Control—A Case Report and Discussion\nPassage: After discussion with our local institutional review board it was agreed that this air sampling constituted environmental sampling and therefore did not require a formal ethics approval." ]

[ [ "0a", "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database" ], [ "0b", "Passage: away from hospitals ." ], [ "0c", "The subjects for this investigation were randomly selected and unfiltered." ], [ "0d", "The time period of each group was consistent and was evenly distributed in two weeks." ], [ "0e", "We made further inquiries 189 amicable interviewees who were willing to take the SMP tests about their background, as well as the privacy protection in SMP data." ], [ "0f", "The patients were fully informed before the voluntary agreements for SMP tests were signed." ], [ "0g", "The researchers obtained the respective remaining samples from nurses after the ordinary blood tests were performed." ], [ "0h", "No extra sampling of blood was performed in this study." ] ]

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

[ "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database\nPassage: away from hospitals . The subjects for this investigation were randomly selected and unfiltered. The time period of each group was consistent and was evenly distributed in two weeks. We made further inquiries 189 amicable interviewees who were willing to take the SMP tests about their background, as well as the privacy protection in SMP data. The patients were fully informed before the voluntary agreements for SMP tests were signed. The researchers obtained the respective remaining samples from nurses after the ordinary blood tests were performed. No extra sampling of blood was performed in this study.", "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database\nPassage: room for blood sampling. Our researchers were permitted to wait in the room and give the patients suggestions to permit the additional SMP tests accompanied by their original blood tests. The data acquisition was performed in a passive way, i.e., the participators were randomly involved in. We orally interviewed the patients, doctors and nurses regarding their attitude towards the SMP test. The investigators for survey studies were divided into two groups: one group interviewed the people who will get their blood tested in the blood-collection room of hospitals, whereas the other group randomly interviewed the pedestrians in city streets far", "Title: A simple novel device for air sampling by electrokinetic capture\nPassage: Authors' contributions JG contributed to experimental design, performed the air sampling and mold spore data reduction, and had primary responsibility for drafting the manuscript. PG contributed to the experimental design and reviewing of the manuscript. GS performed the atomic force microscopy and interpretation of the results therefrom. AF performed the PCR and amplicon analysis and wrote that part of the methods section. JH-M was responsible for the PCR and amplicon analysis experimental design and data reduction and contributed to the manuscript writing. JAG contributed to the experimental design and manuscript review and writing. All authors read and approved the final", "Title: Near-Patient Sampling to Assist Infection Control—A Case Report and Discussion\nPassage: After discussion with our local institutional review board it was agreed that this air sampling constituted environmental sampling and therefore did not require a formal ethics approval." ]

[ [ "1a", "Title: Design and Experimental Approach to the Construction of a Human Signal-Molecule-Profiling Database" ], [ "1b", "Passage: room for blood sampling." ], [ "1c", "Our researchers were permitted to wait in the room and give the patients suggestions to permit the additional SMP tests accompanied by their original blood tests." ], [ "1d", "The data acquisition was performed in a passive way, i.e., the participators were randomly involved in." ], [ "1e", "We orally interviewed the patients, doctors and nurses regarding their attitude towards the SMP test." ], [ "1f", "The investigators for survey studies were divided into two groups: one group interviewed the people who will get their blood tested in the blood-collection room of hospitals, whereas the other group randomly interviewed the pedestrians in city streets far" ] ]

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