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[ "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: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: Five time periods that are useful for public health surveillance were evaluated. For the H5N1 group, with the exception of the median days from onset to antiviral treatment, there were differences between the fatalities and survivors in other median days, including days from onset to hospitalization vs. 5 days, p = 0.023]; days from onset to confirmation of infection Figure 4 ).", "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: In the H5N1 group, the CFR was statistically significantly higher in the index fatalities than in the secondary fatalities vs. 43.3% , respectively, p < 0.001], as was the number of people with comorbidities vs. 0.0% , respectively, p = 0.043]; however, there were no differences between H7N9 virus index and secondary fatalities in the CFR and underlying diseases ." ]

[ [ "2a", "Title: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses" ], [ "2b", "Passage: 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 ." ] ]

[ "0b", "0c", "1b", "1c", "2b", "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: Comparative Epidemiology of Human Fatal Infections with Novel, High (H5N6 and H5N1) and Low (H7N9 and H9N2) Pathogenicity Avian Influenza A Viruses\nPassage: Five time periods that are useful for public health surveillance were evaluated. For the H5N1 group, with the exception of the median days from onset to antiviral treatment, there were differences between the fatalities and survivors in other median days, including days from onset to hospitalization vs. 5 days, p = 0.023]; days from onset to confirmation of infection Figure 4 ).", "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: In the H5N1 group, the CFR was statistically significantly higher in the index fatalities than in the secondary fatalities vs. 43.3% , respectively, p < 0.001], as was the number of people with comorbidities vs. 0.0% , respectively, p = 0.043]; however, there were no differences between H7N9 virus index and secondary fatalities in the CFR and underlying diseases ." ]

[ [ "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: In the H5N1 group, the CFR was statistically significantly higher in the index fatalities than in the secondary fatalities vs. 43.3% , respectively, p < 0.001], as was the number of people with comorbidities vs. 0.0% , respectively, p = 0.043]; however, there were no differences between H7N9 virus index and secondary fatalities in the CFR and underlying diseases ." ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: and how these influence the process warrant a more in-depth examination.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed .", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The 21 Focus of Review topic areas were further broken down into 291 sub-topic categories. There were 34 sub-topics with no reviews available including: hormone replacement therapy, infertility, Norwalk virus, autism, and elder abuse, among others . The 21 Focus of Review topic areas that had sub-topics with no review included adult health, communicable disease/infection, dental health, environmental health, food safety and inspection, parenting, and senior health. The largest proportion of sub-topic with no review was observed within communicable disease/infection . Adult health was ranked sixth and communicable disease/ infection ranked tenth by registered users. Parenting was ranked as a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: As of April 1, 2011 there were 2, 175 systematic reviews evaluating the effectiveness of public health and health promotion interventions indexed in the health-evidence. ca registry. Table 3 provides an overview of the availability of reviews within each of the 21 Focus of Review topic areas. Figure 3 depicts the relationship between registered users' interests, visitor searches, and available reviews within each of the 21 topic areas." ]

[ [ "1a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature" ], [ "1b", "Passage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature." ], [ "1c", "Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified." ], [ "1d", "Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews." ], [ "1e", "Reviews that addressed multiple topics were accounted for within each topic area that they addressed ." ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: and how these influence the process warrant a more in-depth examination.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed .", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The 21 Focus of Review topic areas were further broken down into 291 sub-topic categories. There were 34 sub-topics with no reviews available including: hormone replacement therapy, infertility, Norwalk virus, autism, and elder abuse, among others . The 21 Focus of Review topic areas that had sub-topics with no review included adult health, communicable disease/infection, dental health, environmental health, food safety and inspection, parenting, and senior health. The largest proportion of sub-topic with no review was observed within communicable disease/infection . Adult health was ranked sixth and communicable disease/ infection ranked tenth by registered users. Parenting was ranked as a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: As of April 1, 2011 there were 2, 175 systematic reviews evaluating the effectiveness of public health and health promotion interventions indexed in the health-evidence. ca registry. Table 3 provides an overview of the availability of reviews within each of the 21 Focus of Review topic areas. Figure 3 depicts the relationship between registered users' interests, visitor searches, and available reviews within each of the 21 topic areas." ]

[ [ "2a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature" ], [ "2b", "Passage: The 21 Focus of Review topic areas were further broken down into 291 sub-topic categories." ], [ "2c", "There were 34 sub-topics with no reviews available including: hormone replacement therapy, infertility, Norwalk virus, autism, and elder abuse, among others ." ], [ "2d", "The 21 Focus of Review topic areas that had sub-topics with no review included adult health, communicable disease/infection, dental health, environmental health, food safety and inspection, parenting, and senior health." ], [ "2e", "The largest proportion of sub-topic with no review was observed within communicable disease/infection ." ], [ "2f", "Adult health was ranked sixth and communicable disease/ infection ranked tenth by registered users." ], [ "2g", "Parenting was ranked as a" ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: and how these influence the process warrant a more in-depth examination.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed .", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The 21 Focus of Review topic areas were further broken down into 291 sub-topic categories. There were 34 sub-topics with no reviews available including: hormone replacement therapy, infertility, Norwalk virus, autism, and elder abuse, among others . The 21 Focus of Review topic areas that had sub-topics with no review included adult health, communicable disease/infection, dental health, environmental health, food safety and inspection, parenting, and senior health. The largest proportion of sub-topic with no review was observed within communicable disease/infection . Adult health was ranked sixth and communicable disease/ infection ranked tenth by registered users. Parenting was ranked as a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: As of April 1, 2011 there were 2, 175 systematic reviews evaluating the effectiveness of public health and health promotion interventions indexed in the health-evidence. ca registry. Table 3 provides an overview of the availability of reviews within each of the 21 Focus of Review topic areas. Figure 3 depicts the relationship between registered users' interests, visitor searches, and available reviews within each of the 21 topic areas." ]

[ [ "3a", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature" ], [ "3b", "Passage: As of April 1, 2011 there were 2, 175 systematic reviews evaluating the effectiveness of public health and health promotion interventions indexed in the health-evidence. ca registry." ], [ "3c", "Table 3 provides an overview of the availability of reviews within each of the 21 Focus of Review topic areas." ], [ "3d", "Figure 3 depicts the relationship between registered users' interests, visitor searches, and available reviews within each of the 21 topic areas." ] ]

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

[ "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa .", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: The response by the US arguably began in March 2014 when CDC deployed personnel to investigate Ebola cases in Guinea, and further on July 9, 2014 with the activation of CDC's Emergency Operations Center. However, because EVD was largely out of the public's eye until the fall of 2014, its response was similarly delayed. That is, the peak number of EVD cases in Liberia was September 21, 2014; one week after President Obama's announcement to commit 3000 troops and provide additional aid to the Ebola response effort and one month after WHO declared it a public health emergency of international", "Title: Chinese Public Attention to the Outbreak of Ebola in West Africa: Evidence from the Online Big Data Platform\nPassage: This current Ebola outbreak started in Guéckédou and Macenta districts of Guinea during December 2013 , and WHO proclaimed the EVD outbreak on 23 March 2014. As the situation deteriorated, from all of the available evidence, Director-General Margaret Chan of WHO defined the epidemic to be a Public Health Emergency of International Concern. Figure 1", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: WHO declared the Ebola epidemic over on March 29, 2016 with 28,646 cases and 11,323 deaths across 10 countries and three continents. Of the three countries most widely affected, Liberia was first to successfully control the epidemic , which was before the key indicator data were collected . The epidemic in Sierra Leone and Guinea was largely controlled by April 2015, but experienced sustained transmission into November 2015." ]

[ [ "0a", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak" ], [ "0b", "Passage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa ." ] ]

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

[ "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa .", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: The response by the US arguably began in March 2014 when CDC deployed personnel to investigate Ebola cases in Guinea, and further on July 9, 2014 with the activation of CDC's Emergency Operations Center. However, because EVD was largely out of the public's eye until the fall of 2014, its response was similarly delayed. That is, the peak number of EVD cases in Liberia was September 21, 2014; one week after President Obama's announcement to commit 3000 troops and provide additional aid to the Ebola response effort and one month after WHO declared it a public health emergency of international", "Title: Chinese Public Attention to the Outbreak of Ebola in West Africa: Evidence from the Online Big Data Platform\nPassage: This current Ebola outbreak started in Guéckédou and Macenta districts of Guinea during December 2013 , and WHO proclaimed the EVD outbreak on 23 March 2014. As the situation deteriorated, from all of the available evidence, Director-General Margaret Chan of WHO defined the epidemic to be a Public Health Emergency of International Concern. Figure 1", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: WHO declared the Ebola epidemic over on March 29, 2016 with 28,646 cases and 11,323 deaths across 10 countries and three continents. Of the three countries most widely affected, Liberia was first to successfully control the epidemic , which was before the key indicator data were collected . The epidemic in Sierra Leone and Guinea was largely controlled by April 2015, but experienced sustained transmission into November 2015." ]

[ [ "1a", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak" ], [ "1b", "Passage: The response by the US arguably began in March 2014 when CDC deployed personnel to investigate Ebola cases in Guinea, and further on July 9, 2014 with the activation of CDC's Emergency Operations Center." ], [ "1c", "However, because EVD was largely out of the public's eye until the fall of 2014, its response was similarly delayed." ], [ "1d", "That is, the peak number of EVD cases in Liberia was September 21, 2014; one week after President Obama's announcement to commit 3000 troops and provide additional aid to the Ebola response effort and one month after WHO declared it a public health emergency of international" ] ]

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

[ "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa .", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: The response by the US arguably began in March 2014 when CDC deployed personnel to investigate Ebola cases in Guinea, and further on July 9, 2014 with the activation of CDC's Emergency Operations Center. However, because EVD was largely out of the public's eye until the fall of 2014, its response was similarly delayed. That is, the peak number of EVD cases in Liberia was September 21, 2014; one week after President Obama's announcement to commit 3000 troops and provide additional aid to the Ebola response effort and one month after WHO declared it a public health emergency of international", "Title: Chinese Public Attention to the Outbreak of Ebola in West Africa: Evidence from the Online Big Data Platform\nPassage: This current Ebola outbreak started in Guéckédou and Macenta districts of Guinea during December 2013 , and WHO proclaimed the EVD outbreak on 23 March 2014. As the situation deteriorated, from all of the available evidence, Director-General Margaret Chan of WHO defined the epidemic to be a Public Health Emergency of International Concern. Figure 1", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: WHO declared the Ebola epidemic over on March 29, 2016 with 28,646 cases and 11,323 deaths across 10 countries and three continents. Of the three countries most widely affected, Liberia was first to successfully control the epidemic , which was before the key indicator data were collected . The epidemic in Sierra Leone and Guinea was largely controlled by April 2015, but experienced sustained transmission into November 2015." ]

[ [ "2a", "Title: Chinese Public Attention to the Outbreak of Ebola in West Africa: Evidence from the Online Big Data Platform" ], [ "2b", "Passage: This current Ebola outbreak started in Guéckédou and Macenta districts of Guinea during December 2013 , and WHO proclaimed the EVD outbreak on 23 March 2014." ], [ "2c", "As the situation deteriorated, from all of the available evidence, Director-General Margaret Chan of WHO defined the epidemic to be a Public Health Emergency of International Concern. Figure 1" ] ]

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

[ "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa .", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: The response by the US arguably began in March 2014 when CDC deployed personnel to investigate Ebola cases in Guinea, and further on July 9, 2014 with the activation of CDC's Emergency Operations Center. However, because EVD was largely out of the public's eye until the fall of 2014, its response was similarly delayed. That is, the peak number of EVD cases in Liberia was September 21, 2014; one week after President Obama's announcement to commit 3000 troops and provide additional aid to the Ebola response effort and one month after WHO declared it a public health emergency of international", "Title: Chinese Public Attention to the Outbreak of Ebola in West Africa: Evidence from the Online Big Data Platform\nPassage: This current Ebola outbreak started in Guéckédou and Macenta districts of Guinea during December 2013 , and WHO proclaimed the EVD outbreak on 23 March 2014. As the situation deteriorated, from all of the available evidence, Director-General Margaret Chan of WHO defined the epidemic to be a Public Health Emergency of International Concern. Figure 1", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: WHO declared the Ebola epidemic over on March 29, 2016 with 28,646 cases and 11,323 deaths across 10 countries and three continents. Of the three countries most widely affected, Liberia was first to successfully control the epidemic , which was before the key indicator data were collected . The epidemic in Sierra Leone and Guinea was largely controlled by April 2015, but experienced sustained transmission into November 2015." ]

[ [ "3a", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak" ], [ "3b", "Passage: WHO declared the Ebola epidemic over on March 29, 2016 with 28,646 cases and 11,323 deaths across 10 countries and three continents." ], [ "3c", "Of the three countries most widely affected, Liberia was first to successfully control the epidemic , which was before the key indicator data were collected ." ], [ "3d", "The epidemic in Sierra Leone and Guinea was largely controlled by April 2015, but experienced sustained transmission into November 2015." ] ]

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

[ "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: A total of 23,646 of MERS-CoV suspected cases were included in this study, of which 52.3% were males and 47.7% were females . e age of individuals with suspected cases ranged between 0 to 92 years with a mean age of 43. 23 e adjusted odds of MERS-CoV remained significant among different age groups; the odds of patients aged between 20-40 years increased threefold , whereas in the age group of 41-60 years, it increased further to a risk that was six times higher", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: ese data agreed with a previous surveillance study, which stated that the majority of confirmed cases of MERS-CoV were reported among people aged 40 and above . In 2016, only 9 of 552 cases of MERS-CoV infection were found among pediatric patients. Moreover, the study which was conducted in King Fahad Medical City in Riyadh between January 2012 and December 2013 did not report any MERS-CoV cases among children . e study which was conducted across the Gulf countries for four years by Mahmoud Aly et al. between 2012 and 2016 suggests that the prevalence and distribution of MERS-CoV were", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: the highest-risk in elderly aged 60 years or above . Similar to our results, this study also reported the highest number of confirmed cases during the summer season ." ]

[ [ "0a", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory" ], [ "0b", "Passage: A total of 23,646 of MERS-CoV suspected cases were included in this study, of which 52.3% were males and 47.7% were females ." ], [ "0c", "e age of individuals with suspected cases ranged between 0 to 92 years with a mean age of 43." ], [ "0d", "23 e adjusted odds of MERS-CoV remained significant among different age groups; the odds of patients aged between 20-40 years increased threefold , whereas in the age group of 41-60 years, it increased further to a risk that was six times higher" ] ]

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

[ "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: A total of 23,646 of MERS-CoV suspected cases were included in this study, of which 52.3% were males and 47.7% were females . e age of individuals with suspected cases ranged between 0 to 92 years with a mean age of 43. 23 e adjusted odds of MERS-CoV remained significant among different age groups; the odds of patients aged between 20-40 years increased threefold , whereas in the age group of 41-60 years, it increased further to a risk that was six times higher", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: ese data agreed with a previous surveillance study, which stated that the majority of confirmed cases of MERS-CoV were reported among people aged 40 and above . In 2016, only 9 of 552 cases of MERS-CoV infection were found among pediatric patients. Moreover, the study which was conducted in King Fahad Medical City in Riyadh between January 2012 and December 2013 did not report any MERS-CoV cases among children . e study which was conducted across the Gulf countries for four years by Mahmoud Aly et al. between 2012 and 2016 suggests that the prevalence and distribution of MERS-CoV were", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: the highest-risk in elderly aged 60 years or above . Similar to our results, this study also reported the highest number of confirmed cases during the summer season ." ]

[ [ "1a", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management" ], [ "1b", "Passage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths." ], [ "1c", "62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47." ], [ "1d", "63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV." ], [ "1e", "65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals" ] ]

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

[ "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: A total of 23,646 of MERS-CoV suspected cases were included in this study, of which 52.3% were males and 47.7% were females . e age of individuals with suspected cases ranged between 0 to 92 years with a mean age of 43. 23 e adjusted odds of MERS-CoV remained significant among different age groups; the odds of patients aged between 20-40 years increased threefold , whereas in the age group of 41-60 years, it increased further to a risk that was six times higher", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: ese data agreed with a previous surveillance study, which stated that the majority of confirmed cases of MERS-CoV were reported among people aged 40 and above . In 2016, only 9 of 552 cases of MERS-CoV infection were found among pediatric patients. Moreover, the study which was conducted in King Fahad Medical City in Riyadh between January 2012 and December 2013 did not report any MERS-CoV cases among children . e study which was conducted across the Gulf countries for four years by Mahmoud Aly et al. between 2012 and 2016 suggests that the prevalence and distribution of MERS-CoV were", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: the highest-risk in elderly aged 60 years or above . Similar to our results, this study also reported the highest number of confirmed cases during the summer season ." ]

[ [ "2a", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory" ], [ "2b", "Passage: ese data agreed with a previous surveillance study, which stated that the majority of confirmed cases of MERS-CoV were reported among people aged 40 and above ." ], [ "2c", "In 2016, only 9 of 552 cases of MERS-CoV infection were found among pediatric patients." ], [ "2d", "Moreover, the study which was conducted in King Fahad Medical City in Riyadh between January 2012 and December 2013 did not report any MERS-CoV cases among children ." ], [ "2e", "e study which was conducted across the Gulf countries for four years by Mahmoud Aly et al. between 2012 and 2016 suggests that the prevalence and distribution of MERS-CoV were" ] ]

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

[ "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: A total of 23,646 of MERS-CoV suspected cases were included in this study, of which 52.3% were males and 47.7% were females . e age of individuals with suspected cases ranged between 0 to 92 years with a mean age of 43. 23 e adjusted odds of MERS-CoV remained significant among different age groups; the odds of patients aged between 20-40 years increased threefold , whereas in the age group of 41-60 years, it increased further to a risk that was six times higher", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: ese data agreed with a previous surveillance study, which stated that the majority of confirmed cases of MERS-CoV were reported among people aged 40 and above . In 2016, only 9 of 552 cases of MERS-CoV infection were found among pediatric patients. Moreover, the study which was conducted in King Fahad Medical City in Riyadh between January 2012 and December 2013 did not report any MERS-CoV cases among children . e study which was conducted across the Gulf countries for four years by Mahmoud Aly et al. between 2012 and 2016 suggests that the prevalence and distribution of MERS-CoV were", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: the highest-risk in elderly aged 60 years or above . Similar to our results, this study also reported the highest number of confirmed cases during the summer season ." ]

[ [ "3a", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory" ], [ "3b", "Passage: the highest-risk in elderly aged 60 years or above ." ], [ "3c", "Similar to our results, this study also reported the highest number of confirmed cases during the summer season ." ] ]

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

[ "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: It is interesting to note that on average, our simple rules yielded a PPV of 0.84 and an NPV of 0.75. This means that on average, rules will correctly predict an abnormal laboratory result 5 times out of 6 and correctly predict a normal result 3 times out of 4. While not good enough to replace testing , these observations raise the question of how much better prediction can get. Integration of information not considered in the present study, including vital signs, chief complaints, and physical findings, may improve prediction by these methods.", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: All tests had either two or three possible response values. For tests with three values, we performed two separate rule searches: one for high vs. not high-i.e., grouping normal and low-and one for low vs. not low.", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: We based our study on 10 years of records from the Beth Israel Deaconess Medical Center , a 585-bed tertiary care center in Boston, MA. We first anonymized records and reconciled test names . Informed consent was not obtained because patient records/ information was anonymized prior to analysis. Each blood test , over 69.4 million in all, was marked as an in-house test or a sendout . For each test, we compiled a list of all instances in which the test was ordered and performed. For each instance, we recorded the patient's age, gender, and any diagnoses or other blood-test", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: We used four types of input-age, gender, diagnoses , and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval or outside of it in a given direction , treating high and low results separately." ]

[ [ "0a", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data" ], [ "0b", "Passage: It is interesting to note that on average, our simple rules yielded a PPV of 0.84 and an NPV of 0.75." ], [ "0c", "This means that on average, rules will correctly predict an abnormal laboratory result 5 times out of 6 and correctly predict a normal result 3 times out of 4." ], [ "0d", "While not good enough to replace testing , these observations raise the question of how much better prediction can get." ], [ "0e", "Integration of information not considered in the present study, including vital signs, chief complaints, and physical findings, may improve prediction by these methods." ] ]

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

[ "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: It is interesting to note that on average, our simple rules yielded a PPV of 0.84 and an NPV of 0.75. This means that on average, rules will correctly predict an abnormal laboratory result 5 times out of 6 and correctly predict a normal result 3 times out of 4. While not good enough to replace testing , these observations raise the question of how much better prediction can get. Integration of information not considered in the present study, including vital signs, chief complaints, and physical findings, may improve prediction by these methods.", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: All tests had either two or three possible response values. For tests with three values, we performed two separate rule searches: one for high vs. not high-i.e., grouping normal and low-and one for low vs. not low.", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: We based our study on 10 years of records from the Beth Israel Deaconess Medical Center , a 585-bed tertiary care center in Boston, MA. We first anonymized records and reconciled test names . Informed consent was not obtained because patient records/ information was anonymized prior to analysis. Each blood test , over 69.4 million in all, was marked as an in-house test or a sendout . For each test, we compiled a list of all instances in which the test was ordered and performed. For each instance, we recorded the patient's age, gender, and any diagnoses or other blood-test", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: We used four types of input-age, gender, diagnoses , and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval or outside of it in a given direction , treating high and low results separately." ]

[ [ "3a", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data" ], [ "3b", "Passage: We used four types of input-age, gender, diagnoses , and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval or outside of it in a given direction , treating high and low results separately." ] ]

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

[ "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The field of 'virus dynamics' was first developed to describe the mechanistic underpinnings of long-term patterns of steady-state viral load exhibited by patients in chronic phase infections with HIV, who appeared to produce and clear virus at equivalent rates . Models of simple target cell depletion, in which viral load is dictated by a bottom-eLife digest Bats can carry viruses that are deadly to other mammals without themselves showing serious symptoms. In fact, bats are natural reservoirs for viruses that have some of the highest fatality rates of any viruses that people acquire from wild animals -including rabies, Ebola and", "Title: Computational Approaches and Challenges to Developing Universal Influenza Vaccines\nPassage: was introduced in 2004 to study \"how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies\" . Dynamics of influenza virus infections and transmissions at individual-level , population-level , or ecology-level have been studied . Specially, phylodynamics have been used to study factors of interest on some viral phenotypes, including virulence, viral transmissibility, cell or tissue tropism, and antigenic phenotypes that can facilitate immune escape, etc. . Details of methods and examined significant factors can be found in these reviews .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats. up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: a spatially-explicit, stochastic reconstruction of our mean field model. In spatial simulations, rates of antiviral acquisition were fixed at fitted values for r and \" derived from mean field estimates, while transmission rates were fixed at values ten times greater than those estimated under mean field conditions, accounting for the intensification of parameter thresholds permitting pathogen invasion in local spatial interactions . In immune capable time series, spatial antiviral cells acted as 'refugia' which protected live cells from infection as each initial epidemic wave 'washed' across a cell monolayer. Eventual birth of new susceptibles from these living refugia allowed for" ]

[ [ "0a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "0b", "Passage: The field of 'virus dynamics' was first developed to describe the mechanistic underpinnings of long-term patterns of steady-state viral load exhibited by patients in chronic phase infections with HIV, who appeared to produce and clear virus at equivalent rates ." ], [ "0c", "Models of simple target cell depletion, in which viral load is dictated by a bottom-eLife digest Bats can carry viruses that are deadly to other mammals without themselves showing serious symptoms." ], [ "0d", "In fact, bats are natural reservoirs for viruses that have some of the highest fatality rates of any viruses that people acquire from wild animals -including rabies, Ebola and" ] ]

[ "0b" ]

[ "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: of the three assays.", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: The correlation between viral load and quantitative proinflammatory factors profile was analyzed by Pearson's correlation test using Instat software . Differences were considered significant at p,0.05. Figure S1 The distribution of viral load in selected tissue samples. The viral HA gene and b-actin gene copies in tissues were determined by quantified real-time RT-PCR. The ratios between HA and b-actin gene copies which was showed by logarithm presented the viral-load level in different tissue. Found at: doi:10.1371/journal.pone.0013315.s001", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: To ascertain the involvement of cellular factors in TGEV RNA synthesis, TGEV 3' and 5' genome ends were used as baits for RNA affinity protein purification . Of the ten cellular proteins pulled down with either genome end, poly-binding protein , hnRNP Q, and glutamyl-prolyl-tRNA synthetase were confirmed to enhance TGEV infection through their respective interactions with the TGEV 3' end, while glyceraldehyde 3-phosphate dehydrogenase -originally employed as a control-was discovered, surprisingly, to have a diminishing effect on TGEV infection instead .", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: Another study showed that the relationship between viral loads and multiple virus infections is virus specific . The limited sample size of our study did not allow us to further explore viral load in relation to each different virus, which might explain why we did not see an overall change in influenza or RSV viral loads in cases of viral coinfection." ]

[ [ "0a", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR" ], [ "0b", "Passage: of the three assays." ] ]

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

[ "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: of the three assays.", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: The correlation between viral load and quantitative proinflammatory factors profile was analyzed by Pearson's correlation test using Instat software . Differences were considered significant at p,0.05. Figure S1 The distribution of viral load in selected tissue samples. The viral HA gene and b-actin gene copies in tissues were determined by quantified real-time RT-PCR. The ratios between HA and b-actin gene copies which was showed by logarithm presented the viral-load level in different tissue. Found at: doi:10.1371/journal.pone.0013315.s001", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: To ascertain the involvement of cellular factors in TGEV RNA synthesis, TGEV 3' and 5' genome ends were used as baits for RNA affinity protein purification . Of the ten cellular proteins pulled down with either genome end, poly-binding protein , hnRNP Q, and glutamyl-prolyl-tRNA synthetase were confirmed to enhance TGEV infection through their respective interactions with the TGEV 3' end, while glyceraldehyde 3-phosphate dehydrogenase -originally employed as a control-was discovered, surprisingly, to have a diminishing effect on TGEV infection instead .", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: Another study showed that the relationship between viral loads and multiple virus infections is virus specific . The limited sample size of our study did not allow us to further explore viral load in relation to each different virus, which might explain why we did not see an overall change in influenza or RSV viral loads in cases of viral coinfection." ]

[ [ "1a", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case" ], [ "1b", "Passage: The correlation between viral load and quantitative proinflammatory factors profile was analyzed by Pearson's correlation test using Instat software ." ], [ "1c", "Differences were considered significant at p,0.05." ], [ "1d", "Figure S1 The distribution of viral load in selected tissue samples." ], [ "1e", "The viral HA gene and b-actin gene copies in tissues were determined by quantified real-time RT-PCR." ], [ "1f", "The ratios between HA and b-actin gene copies which was showed by logarithm presented the viral-load level in different tissue." ], [ "1g", "Found at: doi:10.1371/journal.pone.0013315.s001" ] ]

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

[ "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: of the three assays.", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: The correlation between viral load and quantitative proinflammatory factors profile was analyzed by Pearson's correlation test using Instat software . Differences were considered significant at p,0.05. Figure S1 The distribution of viral load in selected tissue samples. The viral HA gene and b-actin gene copies in tissues were determined by quantified real-time RT-PCR. The ratios between HA and b-actin gene copies which was showed by logarithm presented the viral-load level in different tissue. Found at: doi:10.1371/journal.pone.0013315.s001", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: To ascertain the involvement of cellular factors in TGEV RNA synthesis, TGEV 3' and 5' genome ends were used as baits for RNA affinity protein purification . Of the ten cellular proteins pulled down with either genome end, poly-binding protein , hnRNP Q, and glutamyl-prolyl-tRNA synthetase were confirmed to enhance TGEV infection through their respective interactions with the TGEV 3' end, while glyceraldehyde 3-phosphate dehydrogenase -originally employed as a control-was discovered, surprisingly, to have a diminishing effect on TGEV infection instead .", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: Another study showed that the relationship between viral loads and multiple virus infections is virus specific . The limited sample size of our study did not allow us to further explore viral load in relation to each different virus, which might explain why we did not see an overall change in influenza or RSV viral loads in cases of viral coinfection." ]

[ [ "2a", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions" ], [ "2b", "Passage: To ascertain the involvement of cellular factors in TGEV RNA synthesis, TGEV 3' and 5' genome ends were used as baits for RNA affinity protein purification ." ], [ "2c", "Of the ten cellular proteins pulled down with either genome end, poly-binding protein , hnRNP Q, and glutamyl-prolyl-tRNA synthetase were confirmed to enhance TGEV infection through their respective interactions with the TGEV 3' end, while glyceraldehyde 3-phosphate dehydrogenase -originally employed as a control-was discovered, surprisingly, to have a diminishing effect on TGEV infection instead ." ] ]

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

[ "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: of the three assays.", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: The correlation between viral load and quantitative proinflammatory factors profile was analyzed by Pearson's correlation test using Instat software . Differences were considered significant at p,0.05. Figure S1 The distribution of viral load in selected tissue samples. The viral HA gene and b-actin gene copies in tissues were determined by quantified real-time RT-PCR. The ratios between HA and b-actin gene copies which was showed by logarithm presented the viral-load level in different tissue. Found at: doi:10.1371/journal.pone.0013315.s001", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: To ascertain the involvement of cellular factors in TGEV RNA synthesis, TGEV 3' and 5' genome ends were used as baits for RNA affinity protein purification . Of the ten cellular proteins pulled down with either genome end, poly-binding protein , hnRNP Q, and glutamyl-prolyl-tRNA synthetase were confirmed to enhance TGEV infection through their respective interactions with the TGEV 3' end, while glyceraldehyde 3-phosphate dehydrogenase -originally employed as a control-was discovered, surprisingly, to have a diminishing effect on TGEV infection instead .", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: Another study showed that the relationship between viral loads and multiple virus infections is virus specific . The limited sample size of our study did not allow us to further explore viral load in relation to each different virus, which might explain why we did not see an overall change in influenza or RSV viral loads in cases of viral coinfection." ]

[ [ "3a", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR" ], [ "3b", "Passage: Another study showed that the relationship between viral loads and multiple virus infections is virus specific ." ], [ "3c", "The limited sample size of our study did not allow us to further explore viral load in relation to each different virus, which might explain why we did not see an overall change in influenza or RSV viral loads in cases of viral coinfection." ] ]

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

[ "Title: Human core duplicon gene families: game changers or game players?\nPassage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export . Hence, the RGPD gene family members may be modifiers of this function. Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus . It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition. The Ranbp2 knockout in mice is homozygous lethal.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: As summarized in Table 1 , RanBP2 seems to be generally important for nuclear import of HIV-1 and HIV-2, but so far there is less evidence that it is important for SIVs from monkeys. We next tested whether great ape SIVs are dependent on RanBP2 for optimal entry. We used a lentiviral shRNA system to knockdown RanBP2 in 293T cells . The knockdown of RanBP2 is known to be toxic to cells , so we tested three different RanBP2 shRNA constructs for their general effect on cell proliferation using an MTT assay . Compared to a non-targeting shRNA control, the", "Title: RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders\nPassage: Similarly, it should be established whether repeat binding proteins, such as MBNL, which are known to localize in both the nucleus and cytoplasm , play a role in RAN translation. The question of whether these proteins participate directly in the initiation event or facilitate recruitment of key initiation factors to the expanded repeats still needs to be answered.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: Introduction RanBP2 is the major constituent of the cytoplasmic filaments extruding from the mammalian nuclear pore complex, where it mediates cargo import and export . Depletion of RanBP2 negatively affects HIV-1 and HIV-2 infection and nuclear import . Although HIV-1 can use other redundant pathways for import, pathways not involving RanBP2 lead to suboptimal chromosomal integration sites for the HIV-1 genome . The interaction between RanBP2 and HIV-1 may not occur strictly at the nuclear pore. It was recently reported that the Kinesin-1 motor, KIF5B, relocalizes RanBP2 to the cytoplasm during infection . As summarized in Table 1 , RanBP2" ]

[ [ "0a", "Title: Human core duplicon gene families: game changers or game players?" ], [ "0b", "Passage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export ." ], [ "0c", "Hence, the RGPD gene family members may be modifiers of this function." ], [ "0d", "Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus ." ], [ "0e", "It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition." ], [ "0f", "The Ranbp2 knockout in mice is homozygous lethal." ] ]

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

[ "Title: Human core duplicon gene families: game changers or game players?\nPassage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export . Hence, the RGPD gene family members may be modifiers of this function. Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus . It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition. The Ranbp2 knockout in mice is homozygous lethal.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: As summarized in Table 1 , RanBP2 seems to be generally important for nuclear import of HIV-1 and HIV-2, but so far there is less evidence that it is important for SIVs from monkeys. We next tested whether great ape SIVs are dependent on RanBP2 for optimal entry. We used a lentiviral shRNA system to knockdown RanBP2 in 293T cells . The knockdown of RanBP2 is known to be toxic to cells , so we tested three different RanBP2 shRNA constructs for their general effect on cell proliferation using an MTT assay . Compared to a non-targeting shRNA control, the", "Title: RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders\nPassage: Similarly, it should be established whether repeat binding proteins, such as MBNL, which are known to localize in both the nucleus and cytoplasm , play a role in RAN translation. The question of whether these proteins participate directly in the initiation event or facilitate recruitment of key initiation factors to the expanded repeats still needs to be answered.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: Introduction RanBP2 is the major constituent of the cytoplasmic filaments extruding from the mammalian nuclear pore complex, where it mediates cargo import and export . Depletion of RanBP2 negatively affects HIV-1 and HIV-2 infection and nuclear import . Although HIV-1 can use other redundant pathways for import, pathways not involving RanBP2 lead to suboptimal chromosomal integration sites for the HIV-1 genome . The interaction between RanBP2 and HIV-1 may not occur strictly at the nuclear pore. It was recently reported that the Kinesin-1 motor, KIF5B, relocalizes RanBP2 to the cytoplasm during infection . As summarized in Table 1 , RanBP2" ]

[ [ "1a", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes" ], [ "1b", "Passage: As summarized in Table 1 , RanBP2 seems to be generally important for nuclear import of HIV-1 and HIV-2, but so far there is less evidence that it is important for SIVs from monkeys." ], [ "1c", "We next tested whether great ape SIVs are dependent on RanBP2 for optimal entry." ], [ "1d", "We used a lentiviral shRNA system to knockdown RanBP2 in 293T cells ." ], [ "1e", "The knockdown of RanBP2 is known to be toxic to cells , so we tested three different RanBP2 shRNA constructs for their general effect on cell proliferation using an MTT assay ." ], [ "1f", "Compared to a non-targeting shRNA control, the" ] ]

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

[ "Title: Human core duplicon gene families: game changers or game players?\nPassage: The RANBP2 protein encoded by the progenitor gene is primarily localized within the periphery of the nuclear envelope and is thought to be required for cargo import and export . Hence, the RGPD gene family members may be modifiers of this function. Interestingly, RANBP2 was also shown to be involved in resistance against Simian Immunodeficiency Virus . It is thus possible that the expansion of RGPD genes is the result of an arms race between virus evolution and host resistance acquisition. The Ranbp2 knockout in mice is homozygous lethal.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: As summarized in Table 1 , RanBP2 seems to be generally important for nuclear import of HIV-1 and HIV-2, but so far there is less evidence that it is important for SIVs from monkeys. We next tested whether great ape SIVs are dependent on RanBP2 for optimal entry. We used a lentiviral shRNA system to knockdown RanBP2 in 293T cells . The knockdown of RanBP2 is known to be toxic to cells , so we tested three different RanBP2 shRNA constructs for their general effect on cell proliferation using an MTT assay . Compared to a non-targeting shRNA control, the", "Title: RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders\nPassage: Similarly, it should be established whether repeat binding proteins, such as MBNL, which are known to localize in both the nucleus and cytoplasm , play a role in RAN translation. The question of whether these proteins participate directly in the initiation event or facilitate recruitment of key initiation factors to the expanded repeats still needs to be answered.", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes\nPassage: Introduction RanBP2 is the major constituent of the cytoplasmic filaments extruding from the mammalian nuclear pore complex, where it mediates cargo import and export . Depletion of RanBP2 negatively affects HIV-1 and HIV-2 infection and nuclear import . Although HIV-1 can use other redundant pathways for import, pathways not involving RanBP2 lead to suboptimal chromosomal integration sites for the HIV-1 genome . The interaction between RanBP2 and HIV-1 may not occur strictly at the nuclear pore. It was recently reported that the Kinesin-1 motor, KIF5B, relocalizes RanBP2 to the cytoplasm during infection . As summarized in Table 1 , RanBP2" ]

[ [ "3a", "Title: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes" ], [ "3b", "Passage: Introduction RanBP2 is the major constituent of the cytoplasmic filaments extruding from the mammalian nuclear pore complex, where it mediates cargo import and export ." ], [ "3c", "Depletion of RanBP2 negatively affects HIV-1 and HIV-2 infection and nuclear import ." ], [ "3d", "Although HIV-1 can use other redundant pathways for import, pathways not involving RanBP2 lead to suboptimal chromosomal integration sites for the HIV-1 genome ." ], [ "3e", "The interaction between RanBP2 and HIV-1 may not occur strictly at the nuclear pore." ], [ "3f", "It was recently reported that the Kinesin-1 motor, KIF5B, relocalizes RanBP2 to the cytoplasm during infection ." ], [ "3g", "As summarized in Table 1 , RanBP2" ] ]

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

[ "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", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Another notable change is the sharp decline of the proportion of sputum positive cases, which accounted for 30.5% of all cases in the 2000 survey but was reduced to 6.6% in the 2010 survey. The proportion of notified sputum cases out of all TB cases in Shandong also declined from 80.9% in 2005 to 64.6% in 2010 .", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Three sputum specimens of all suspected cases were collected and sent for smear microscopy and culture. RESULTS: Adjusted prevalence rate of bacteriologically confirmed cases was 34 per 100,000 for adults in Shandong in 2010. Compared to the 2000 survey, TB prevalence has declined by 80%. 53% of bacteriologically confirmed cases did not present persistent cough. The yield of bacteriologically confirmed cases was 47% by symptom screening and 95% by CXRAY. Over 50% of TB cases were among over 65’s. CONCLUSIONS: The prevalence rate of bacteriologically confirmed cases was significantly reduced compared with 2000. The survey raised challenges to identify TB", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: This study has shown that the prevalence of bacteriologically confirmed TB in Shandong has reduced substantially over the last decade. Importantly, the majority of these cases did not present with persistent cough and the proportion of sputum positive cases has declined sharply. Further studies are recommended to assess the feasibility of adopting CXRAY in the existing health care services to detect TB cases and the cost effectiveness of such intervention." ]

[ [ "0a", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China" ], [ "0b", "Passage: 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 ." ], [ "0c", "The adjusted prevalence rates of the whole population in Shandong were17.8 , 27.8 and 239.4 per 100,000 in 2010." ], [ "0d", "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 ." ], [ "0e", "Large declines were observed in males between 40 and 65 years old, and in females over 60 years" ] ]

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

[ "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", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Another notable change is the sharp decline of the proportion of sputum positive cases, which accounted for 30.5% of all cases in the 2000 survey but was reduced to 6.6% in the 2010 survey. The proportion of notified sputum cases out of all TB cases in Shandong also declined from 80.9% in 2005 to 64.6% in 2010 .", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Three sputum specimens of all suspected cases were collected and sent for smear microscopy and culture. RESULTS: Adjusted prevalence rate of bacteriologically confirmed cases was 34 per 100,000 for adults in Shandong in 2010. Compared to the 2000 survey, TB prevalence has declined by 80%. 53% of bacteriologically confirmed cases did not present persistent cough. The yield of bacteriologically confirmed cases was 47% by symptom screening and 95% by CXRAY. Over 50% of TB cases were among over 65’s. CONCLUSIONS: The prevalence rate of bacteriologically confirmed cases was significantly reduced compared with 2000. The survey raised challenges to identify TB", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: This study has shown that the prevalence of bacteriologically confirmed TB in Shandong has reduced substantially over the last decade. Importantly, the majority of these cases did not present with persistent cough and the proportion of sputum positive cases has declined sharply. Further studies are recommended to assess the feasibility of adopting CXRAY in the existing health care services to detect TB cases and the cost effectiveness of such intervention." ]

[ [ "1a", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China" ], [ "1b", "Passage: Another notable change is the sharp decline of the proportion of sputum positive cases, which accounted for 30.5% of all cases in the 2000 survey but was reduced to 6.6% in the 2010 survey." ], [ "1c", "The proportion of notified sputum cases out of all TB cases in Shandong also declined from 80.9% in 2005 to 64.6% in 2010 ." ] ]

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

[ "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", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Another notable change is the sharp decline of the proportion of sputum positive cases, which accounted for 30.5% of all cases in the 2000 survey but was reduced to 6.6% in the 2010 survey. The proportion of notified sputum cases out of all TB cases in Shandong also declined from 80.9% in 2005 to 64.6% in 2010 .", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: Three sputum specimens of all suspected cases were collected and sent for smear microscopy and culture. RESULTS: Adjusted prevalence rate of bacteriologically confirmed cases was 34 per 100,000 for adults in Shandong in 2010. Compared to the 2000 survey, TB prevalence has declined by 80%. 53% of bacteriologically confirmed cases did not present persistent cough. The yield of bacteriologically confirmed cases was 47% by symptom screening and 95% by CXRAY. Over 50% of TB cases were among over 65’s. CONCLUSIONS: The prevalence rate of bacteriologically confirmed cases was significantly reduced compared with 2000. The survey raised challenges to identify TB", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China\nPassage: This study has shown that the prevalence of bacteriologically confirmed TB in Shandong has reduced substantially over the last decade. Importantly, the majority of these cases did not present with persistent cough and the proportion of sputum positive cases has declined sharply. Further studies are recommended to assess the feasibility of adopting CXRAY in the existing health care services to detect TB cases and the cost effectiveness of such intervention." ]

[ [ "3a", "Title: Changes in pulmonary tuberculosis prevalence: evidence from the 2010 population survey in a populous province of China" ], [ "3b", "Passage: This study has shown that the prevalence of bacteriologically confirmed TB in Shandong has reduced substantially over the last decade." ], [ "3c", "Importantly, the majority of these cases did not present with persistent cough and the proportion of sputum positive cases has declined sharply." ], [ "3d", "Further studies are recommended to assess the feasibility of adopting CXRAY in the existing health care services to detect TB cases and the cost effectiveness of such intervention." ] ]

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

[ "Title: Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells\nPassage: The arthropod-borne SINV is a small, enveloped, positive, single-stranded RNA virus and is the prototype for the alphavirus genus. Alphaviruses represent a group of widely distributed human and animal pathogens, which pose a serious public health threat . Some of them induce febrile and arthritogenic diseases, while others can cause highly debilitating diseases, such as encephalitis. The SINV genomic RNA is capped and polyadenylated and is infectious as naked RNA. Upon entry into the cytoplasm by endocytosis, the host translational machinery recognizes the genomic RNA, and four nonstructural proteins are produced . Their expression is sufficient for the establishment of", "Title: Host and viral traits predict zoonotic spillover from mammals\nPassage: highest for Bunya-, Flavi-and Arenaviruses in rodents; Flavi-, Bunyaand Rhabdoviruses in bats; and Herpesviruses in non-human primates . Of 586 mammalian viruses in our dataset, 263 have been detected in humans, 75 of which are exclusively human and 188 zoonotic-defined operationally here as viruses detected at least once in humans and at least once in another mammal species . The proportion of zoonotic viruses is higher for RNA than DNA viruses. The observed number of viruses per wild host species was comparable when averaged across orders, but bats, primates, and rodents had a higher proportion of observed zoonotic viruses compared", "Title: Determining the molecular drivers of species-specific interferon-stimulated gene product 15 interactions with nairovirus ovarian tumor domain proteases\nPassage: In addition to infecting humans, many nairoviruses have been directly associated with other vertebrate hosts. CCHFV, for example, is reported to infect a wide array of mammalian species , however disease is restricted to humans. Importantly, CCHFV maintenance and transmission relies on asymptomatic circulation among a number of hosts, including small mammals, reptiles, and livestock . NSDV and DUGV also infect livestock, with NSDV causing severe gastroenteritis in sheep and goats. Nairoviruses have been isolated from bats , and are often detected in vertebrate associated ectoparasites; Kupe virus , for example, was isolated from ticks infesting cattle, sheep, and goats,", "Title: Distribution and characteristics of rodent picornaviruses in China\nPassage: Increasing attention focused on rodents as the natural hosts of many important zoonotic virus. Firth et al. 25 identified a wide range of known and novel viruses from groups that include important human pathogens, including sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses carried by commensal Rattus norvegicus in New York city 25 . The role of rodent picornaviruses in the evolution, transmission, and biology of picornaviruses remains unclear. Drexler et al. 11 conducted a targeted search for hepatoviruses in 15,987 specimens of 209 small mammal species, and ancestral-state reconstructions suggested a hepatovirus origin in small insectivorous mammals, and a rodent" ]

[ [ "3a", "Title: Distribution and characteristics of rodent picornaviruses in China" ], [ "3b", "Passage: Increasing attention focused on rodents as the natural hosts of many important zoonotic virus." ], [ "3c", "Firth et al. 25 identified a wide range of known and novel viruses from groups that include important human pathogens, including sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses carried by commensal Rattus norvegicus in New York city 25 ." ], [ "3d", "The role of rodent picornaviruses in the evolution, transmission, and biology of picornaviruses remains unclear." ], [ "3e", "Drexler et al. 11 conducted a targeted search for hepatoviruses in 15,987 specimens of 209 small mammal species, and ancestral-state reconstructions suggested a hepatovirus origin in small insectivorous mammals, and a rodent" ] ]

[ "3b", "3c" ]

[ "Title: Multi-criteria decision analysis as an innovative approach to managing zoonoses: results from a study on Lyme disease in Canada\nPassage: the validity of analysis.", "Title: Outcomes of Influenza A(H1N1)pdm09 Virus Infection: Results from Two International Cohort Studies\nPassage: of imputation were used to obtain the ORs. The imputation had little effect on the univariable analyses, therefore summary statistics from these analyses are based on the observed data. In a sensitivity analysis, a complete case analysis was performed and adjusted ORs were estimated for all of the baseline variables excluding BMI. Estimates similar to those based on multiple imputation were obtained .", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: As proof of principle for GLM, we first tested it on the anion gap, a result calculated by subtracting the serum concentrations of the anions chloride and bicarbonate from those of the cations sodium and potassium, and confirmed that our methods found a rule for elevated anion gap based on these four items.", "Title: The Screening Research of NF-κB Inhibitors from Moutan Cortex Based on Bioactivity-Integrated UPLC-Q/TOF-MS\nPassage: Analysis. The test results were represented with mean ± SEM. And t-test was used for comparison of significant differences among different groups. SPSS v.18.0 statistical analysis software was used for statistical analysis. Results with values of P < 0.05 were considered statistically significant." ]

[ [ "1a", "Title: Outcomes of Influenza A(H1N1)pdm09 Virus Infection: Results from Two International Cohort Studies" ], [ "1b", "Passage: of imputation were used to obtain the ORs." ], [ "1c", "The imputation had little effect on the univariable analyses, therefore summary statistics from these analyses are based on the observed data." ], [ "1d", "In a sensitivity analysis, a complete case analysis was performed and adjusted ORs were estimated for all of the baseline variables excluding BMI." ], [ "1e", "Estimates similar to those based on multiple imputation were obtained ." ] ]

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

[ "Title: Multi-criteria decision analysis as an innovative approach to managing zoonoses: results from a study on Lyme disease in Canada\nPassage: the validity of analysis.", "Title: Outcomes of Influenza A(H1N1)pdm09 Virus Infection: Results from Two International Cohort Studies\nPassage: of imputation were used to obtain the ORs. The imputation had little effect on the univariable analyses, therefore summary statistics from these analyses are based on the observed data. In a sensitivity analysis, a complete case analysis was performed and adjusted ORs were estimated for all of the baseline variables excluding BMI. Estimates similar to those based on multiple imputation were obtained .", "Title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data\nPassage: As proof of principle for GLM, we first tested it on the anion gap, a result calculated by subtracting the serum concentrations of the anions chloride and bicarbonate from those of the cations sodium and potassium, and confirmed that our methods found a rule for elevated anion gap based on these four items.", "Title: The Screening Research of NF-κB Inhibitors from Moutan Cortex Based on Bioactivity-Integrated UPLC-Q/TOF-MS\nPassage: Analysis. The test results were represented with mean ± SEM. And t-test was used for comparison of significant differences among different groups. SPSS v.18.0 statistical analysis software was used for statistical analysis. Results with values of P < 0.05 were considered statistically significant." ]

[ [ "3a", "Title: The Screening Research of NF-κB Inhibitors from Moutan Cortex Based on Bioactivity-Integrated UPLC-Q/TOF-MS Passage: Analysis." ], [ "3b", "The test results were represented with mean ± SEM." ], [ "3c", "And t-test was used for comparison of significant differences among different groups." ], [ "3d", "SPSS v.18.0 statistical analysis software was used for statistical analysis." ], [ "3e", "Results with values of P < 0.05 were considered statistically significant." ] ]

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

[ "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: where N  is the total number of the interactive NR-drug pairs investigated while N   the number of the interactive NR-drug pairs incorrectly predicted as the non-interactive NR-drug pairs; N  the total number of the non-interactive NR-drug pairs investigated while N   the number of the non-interactive NR-drug pairs incorrectly predicted as the interactive NR-drug pairs.", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: where N  is the total number of the interactive NR-drug pairs investigated while N   the number of the interactive NR-drug pairs incorrectly predicted as the non-interactive NR-drug pairs; N  the total number of the non-interactive NR-drug pairs investigated while N   the number of the non-interactive NR-drug pairs incorrectly predicted as the interactive NR-drug pairs.", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell. Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences . N is also reported to interact with actin microfilaments, and the SUMO-1 protein . Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: It has also been observed that the N protein of several coronaviruses can localize in the nucleolus where it may perturb cell cycle activities of the host cell for the benefit of viral mRNA synthesis . IBV N, for example, appears to target CDK2, cyclins A and D1 for proteasomemediated degradation and cause the accumulation of hypophosphorylated retinoblastoma , resulting in the downregulation of CDK1, cyclins E and B1 ." ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell." ], [ "2c", "Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences ." ], [ "2d", "N is also reported to interact with actin microfilaments, and the SUMO-1 protein ." ], [ "2e", "Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in" ] ]

[ "2d" ]

[ "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The simultaneous outbreaks of influenza in humans and pigs during the 1918 pandemic naturally raised questions about whether the virus had transmitted from pigs to humans, or humans to pigs. At the time, Koen noted that the flu outbreaks appeared to represent a novel disease in pigs, whereas humans had a long history of influenza pandemics, which suggested that humanto-swine transmission was more likely. Almost a century later, the reconstruction of a 1918 virus from human tissues preserved in Alaskan permafrost and autopsy blocks indicated that the virus's genes appeared to have avian origins . But this did not end", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian .", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: coincidence if not suggesting a close relation between the two conditions\" . Confirmation that influenza was circulating in US swine was achieved in 1931 when Richard Shope isolated the first influenza virus from pigs . Two years later, the H1N1 virus was isolated from humans . It was later demonstrated that sera from humans infected with the 1918 pandemic virus could neutralize the swine virus ." ]

[ [ "0a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "0b", "Passage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine." ] ]

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

[ "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The simultaneous outbreaks of influenza in humans and pigs during the 1918 pandemic naturally raised questions about whether the virus had transmitted from pigs to humans, or humans to pigs. At the time, Koen noted that the flu outbreaks appeared to represent a novel disease in pigs, whereas humans had a long history of influenza pandemics, which suggested that humanto-swine transmission was more likely. Almost a century later, the reconstruction of a 1918 virus from human tissues preserved in Alaskan permafrost and autopsy blocks indicated that the virus's genes appeared to have avian origins . But this did not end", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian .", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: coincidence if not suggesting a close relation between the two conditions\" . Confirmation that influenza was circulating in US swine was achieved in 1931 when Richard Shope isolated the first influenza virus from pigs . Two years later, the H1N1 virus was isolated from humans . It was later demonstrated that sera from humans infected with the 1918 pandemic virus could neutralize the swine virus ." ]

[ [ "1a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "1b", "Passage: The simultaneous outbreaks of influenza in humans and pigs during the 1918 pandemic naturally raised questions about whether the virus had transmitted from pigs to humans, or humans to pigs." ], [ "1c", "At the time, Koen noted that the flu outbreaks appeared to represent a novel disease in pigs, whereas humans had a long history of influenza pandemics, which suggested that humanto-swine transmission was more likely." ], [ "1d", "Almost a century later, the reconstruction of a 1918 virus from human tissues preserved in Alaskan permafrost and autopsy blocks indicated that the virus's genes appeared to have avian origins ." ], [ "1e", "But this did not end" ] ]

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

[ "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The simultaneous outbreaks of influenza in humans and pigs during the 1918 pandemic naturally raised questions about whether the virus had transmitted from pigs to humans, or humans to pigs. At the time, Koen noted that the flu outbreaks appeared to represent a novel disease in pigs, whereas humans had a long history of influenza pandemics, which suggested that humanto-swine transmission was more likely. Almost a century later, the reconstruction of a 1918 virus from human tissues preserved in Alaskan permafrost and autopsy blocks indicated that the virus's genes appeared to have avian origins . But this did not end", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian .", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: coincidence if not suggesting a close relation between the two conditions\" . Confirmation that influenza was circulating in US swine was achieved in 1931 when Richard Shope isolated the first influenza virus from pigs . Two years later, the H1N1 virus was isolated from humans . It was later demonstrated that sera from humans infected with the 1918 pandemic virus could neutralize the swine virus ." ]

[ [ "2a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "2b", "Passage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic ." ], [ "2c", "In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian ." ] ]

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

[ "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The simultaneous outbreaks of influenza in humans and pigs during the 1918 pandemic naturally raised questions about whether the virus had transmitted from pigs to humans, or humans to pigs. At the time, Koen noted that the flu outbreaks appeared to represent a novel disease in pigs, whereas humans had a long history of influenza pandemics, which suggested that humanto-swine transmission was more likely. Almost a century later, the reconstruction of a 1918 virus from human tissues preserved in Alaskan permafrost and autopsy blocks indicated that the virus's genes appeared to have avian origins . But this did not end", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian .", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: coincidence if not suggesting a close relation between the two conditions\" . Confirmation that influenza was circulating in US swine was achieved in 1931 when Richard Shope isolated the first influenza virus from pigs . Two years later, the H1N1 virus was isolated from humans . It was later demonstrated that sera from humans infected with the 1918 pandemic virus could neutralize the swine virus ." ]

[ [ "3a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "3b", "Passage: coincidence if not suggesting a close relation between the two conditions\" ." ], [ "3c", "Confirmation that influenza was circulating in US swine was achieved in 1931 when Richard Shope isolated the first influenza virus from pigs ." ], [ "3d", "Two years later, the H1N1 virus was isolated from humans ." ], [ "3e", "It was later demonstrated that sera from humans infected with the 1918 pandemic virus could neutralize the swine virus ." ] ]

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: Identification of pneumonia and influenza deaths using the death certificate pipeline\nPassage: Pneumonia and influenza are serious public health threats and are a cause of substantial morbidity and mortality worldwide; for instance, the World Health Organization estimates seasonal influenza causes between 250,000 to 500,000 deaths worldwide each year while pneumonia kills more than 4 million people worldwide every year . Worldwide, the morbidity and mortality of influenza and pneumonia have a considerable economic impact in the form of hospital and other health care costs. Each year in the United States approximately 3 million persons acquire pneumonia and, depending on the severity of the influenza season, 15 to 61 million people in the" ]

[ [ "0a", "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)" ], [ "0b", "Passage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide." ], [ "0c", "Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually." ], [ "0d", "In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza." ], [ "0e", "However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly ." ], [ "0f", "Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to" ] ]

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: Identification of pneumonia and influenza deaths using the death certificate pipeline\nPassage: Pneumonia and influenza are serious public health threats and are a cause of substantial morbidity and mortality worldwide; for instance, the World Health Organization estimates seasonal influenza causes between 250,000 to 500,000 deaths worldwide each year while pneumonia kills more than 4 million people worldwide every year . Worldwide, the morbidity and mortality of influenza and pneumonia have a considerable economic impact in the form of hospital and other health care costs. Each year in the United States approximately 3 million persons acquire pneumonia and, depending on the severity of the influenza season, 15 to 61 million people in the" ]

[ [ "1a", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics" ], [ "1b", "Passage: Seasonal influenza remains an important infectious cause of morbidity and mortality ." ], [ "1c", "In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths ." ] ]

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: Identification of pneumonia and influenza deaths using the death certificate pipeline\nPassage: Pneumonia and influenza are serious public health threats and are a cause of substantial morbidity and mortality worldwide; for instance, the World Health Organization estimates seasonal influenza causes between 250,000 to 500,000 deaths worldwide each year while pneumonia kills more than 4 million people worldwide every year . Worldwide, the morbidity and mortality of influenza and pneumonia have a considerable economic impact in the form of hospital and other health care costs. Each year in the United States approximately 3 million persons acquire pneumonia and, depending on the severity of the influenza season, 15 to 61 million people in the" ]

[ [ "2a", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia" ], [ "2b", "Passage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year ." ], [ "2c", "The result is a significant public health and economic burden for the U.S. population ." ] ]

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: Identification of pneumonia and influenza deaths using the death certificate pipeline\nPassage: Pneumonia and influenza are serious public health threats and are a cause of substantial morbidity and mortality worldwide; for instance, the World Health Organization estimates seasonal influenza causes between 250,000 to 500,000 deaths worldwide each year while pneumonia kills more than 4 million people worldwide every year . Worldwide, the morbidity and mortality of influenza and pneumonia have a considerable economic impact in the form of hospital and other health care costs. Each year in the United States approximately 3 million persons acquire pneumonia and, depending on the severity of the influenza season, 15 to 61 million people in the" ]

[ [ "3a", "Title: Identification of pneumonia and influenza deaths using the death certificate pipeline" ], [ "3b", "Passage: Pneumonia and influenza are serious public health threats and are a cause of substantial morbidity and mortality worldwide; for instance, the World Health Organization estimates seasonal influenza causes between 250,000 to 500,000 deaths worldwide each year while pneumonia kills more than 4 million people worldwide every year ." ], [ "3c", "Worldwide, the morbidity and mortality of influenza and pneumonia have a considerable economic impact in the form of hospital and other health care costs." ], [ "3d", "Each year in the United States approximately 3 million persons acquire pneumonia and, depending on the severity of the influenza season, 15 to 61 million people in the" ] ]

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

[ "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: Non-influenza related upper respiratory infections are universally experienced illnesses that, despite their typically selflimited nature, lead to billions of dollars of lost income, and predispose to serious illnesses including pneumonia. When influenza is responsible, pandemics can result and cause millions of deaths. In 2009, a novel H1N1 influenza virus emerged and rapidly spread worldwide, causing excess mortality in children and young adults. Although the global estimate of deaths has been lower than seen in several previous pandemics, the number of life years lost is estimated to be five times higher than those lost to seasonal H1N1 viruses and comparable to", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: All subjects provided written, voluntary informed consent in the presence of an ombudsman. The study was approved by Wilford Hall Medical Center/Brooke Army Medical Center Institutional Review Board . Gender and ethnicity were self-reported. Per Department of Defense Directive 3216.02, for purposes of legal capacity to participate in DoD-conducted or -supported research involving human subjects, all active duty service members in a federal duty status are considered to be adults. The participation of such members is not subject to requirements regarding research involving children or minors. When service members are under 18 years of age, students at service academies, or", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: Febrile Respiratory Illness Surveillance Update show a rate of febrile respiratory infection that increased in December of 2009, 82% of which was associated with adenovirus, with no influenza virus detected. Additionally, the use of oseltamivir, both for prophylaxis and for treatment, would have impacted both epidemiology and severity of illness. Finally, without inclusion of asymptomatic or minimally symptomatic individuals, conclusions can only be drawn about the scarcity of coinfections with individuals at the point of presentation to care.", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: In summary, this epidemiologic survey of young adults in military training presenting with fever and URI demonstrated significant differences in 2009 H1N1 vs. adenovirus in terms of gender predilection and presenting symptoms. In addition, coinfections with 2009 H1N1 and adenovirus were rare despite high endemicity of adenovirus before and during the 2009 H1N1 epidemic, and, beyond a higher temperature on presentation, coinfections were not associated with increased clinical severity compared with adenovirus alone." ]

[ [ "0a", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection" ], [ "0b", "Passage: Non-influenza related upper respiratory infections are universally experienced illnesses that, despite their typically selflimited nature, lead to billions of dollars of lost income, and predispose to serious illnesses including pneumonia." ], [ "0c", "When influenza is responsible, pandemics can result and cause millions of deaths." ], [ "0d", "In 2009, a novel H1N1 influenza virus emerged and rapidly spread worldwide, causing excess mortality in children and young adults." ], [ "0e", "Although the global estimate of deaths has been lower than seen in several previous pandemics, the number of life years lost is estimated to be five times higher than those lost to seasonal H1N1 viruses and comparable to" ] ]

[ "0b", "2b" ]

[ "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: Non-influenza related upper respiratory infections are universally experienced illnesses that, despite their typically selflimited nature, lead to billions of dollars of lost income, and predispose to serious illnesses including pneumonia. When influenza is responsible, pandemics can result and cause millions of deaths. In 2009, a novel H1N1 influenza virus emerged and rapidly spread worldwide, causing excess mortality in children and young adults. Although the global estimate of deaths has been lower than seen in several previous pandemics, the number of life years lost is estimated to be five times higher than those lost to seasonal H1N1 viruses and comparable to", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: All subjects provided written, voluntary informed consent in the presence of an ombudsman. The study was approved by Wilford Hall Medical Center/Brooke Army Medical Center Institutional Review Board . Gender and ethnicity were self-reported. Per Department of Defense Directive 3216.02, for purposes of legal capacity to participate in DoD-conducted or -supported research involving human subjects, all active duty service members in a federal duty status are considered to be adults. The participation of such members is not subject to requirements regarding research involving children or minors. When service members are under 18 years of age, students at service academies, or", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: Febrile Respiratory Illness Surveillance Update show a rate of febrile respiratory infection that increased in December of 2009, 82% of which was associated with adenovirus, with no influenza virus detected. Additionally, the use of oseltamivir, both for prophylaxis and for treatment, would have impacted both epidemiology and severity of illness. Finally, without inclusion of asymptomatic or minimally symptomatic individuals, conclusions can only be drawn about the scarcity of coinfections with individuals at the point of presentation to care.", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection\nPassage: In summary, this epidemiologic survey of young adults in military training presenting with fever and URI demonstrated significant differences in 2009 H1N1 vs. adenovirus in terms of gender predilection and presenting symptoms. In addition, coinfections with 2009 H1N1 and adenovirus were rare despite high endemicity of adenovirus before and during the 2009 H1N1 epidemic, and, beyond a higher temperature on presentation, coinfections were not associated with increased clinical severity compared with adenovirus alone." ]

[ [ "2a", "Title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection" ], [ "2b", "Passage: Febrile Respiratory Illness Surveillance Update show a rate of febrile respiratory infection that increased in December of 2009, 82% of which was associated with adenovirus, with no influenza virus detected." ], [ "2c", "Additionally, the use of oseltamivir, both for prophylaxis and for treatment, would have impacted both epidemiology and severity of illness." ], [ "2d", "Finally, without inclusion of asymptomatic or minimally symptomatic individuals, conclusions can only be drawn about the scarcity of coinfections with individuals at the point of presentation to care." ] ]

[ "0b", "2b" ]

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly" ]

[ [ "0a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "0b", "Passage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy." ], [ "0c", "Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations." ], [ "0d", "For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes ." ], [ "0e", "Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development." ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly" ]

[ [ "1a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "1b", "Passage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy." ], [ "1c", "Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations." ], [ "1d", "For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes ." ], [ "1e", "Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development." ] ]

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

[ "Title: School closures during the 2009 influenza pandemic: national and local experiences\nPassage: In the early phase of the pandemic, HK implemented aggressive strategies to attempt to contain and later on to mitigate the spread the virus. Once the first case due to indigenous transmission was confirmed on 10 June 2009, they moved from a \"containment phase\" to a \"mitigation phase\" designed to relieve disease burden and mortality, primarily based on NPI . The mitigation phase included: public health campaigns , medical resource mobilization, opening of eight designated fever clinics , and antiviral treatment of confirmed cases. In addition, there was an immediate proactive closure of kindergarten/primary schools for at least 2 weeks", "Title: Breaking the Waves: Modelling the Potential Impact of Public Health Measures to Defer the Epidemic Peak of Novel Influenza A/H1N1\nPassage: It has been shown before that so called targeted layered containment strategies, a combination of antiviral prophylaxis and non-pharmaceutical interventions, can be effective in reducing the transmission of pandemic influenza . We extended this approach by analyzing the effect of a more intensive phase including contact tracing, identification and management of contacts outside of the household , followed by household centred measures .", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: measures are a combination of early diagnosis, case isolation, contact precaution, awareness campaigns, and sanitary burial practices. Identifying infected people quickly by the polymerase chain reaction assay and isolating them to break chains of EVD transmission may be effective to control the outbreak. The effect of reducing the time between symptoms onset and diagnosis with rapid testing has also been investigated in the literature .", "Title: Logistics of community smallpox control through contact tracing and ring vaccination: a stochastic network model\nPassage: Finally, scenario e demonstrates that containment is still possible even when the vaccine is completely ineffective in everyone -because of case isolation and isolation of contacts . Here, with 40 contact tracings possible per day, 55% of the replications nevertheless exhibited containment even with a vaccine which offered no protection whatever. With 90 contact tracings possible per day, all replications exhibited containment even assuming no vaccine protection." ]

[ [ "0a", "Title: School closures during the 2009 influenza pandemic: national and local experiences" ], [ "0b", "Passage: In the early phase of the pandemic, HK implemented aggressive strategies to attempt to contain and later on to mitigate the spread the virus." ], [ "0c", "Once the first case due to indigenous transmission was confirmed on 10 June 2009, they moved from a \"containment phase\" to a \"mitigation phase\" designed to relieve disease burden and mortality, primarily based on NPI ." ], [ "0d", "The mitigation phase included: public health campaigns , medical resource mobilization, opening of eight designated fever clinics , and antiviral treatment of confirmed cases." ], [ "0e", "In addition, there was an immediate proactive closure of kindergarten/primary schools for at least 2 weeks" ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: expressing tetC, induced much lower anti-tetC responses than mice that had not been primed. This argues strongly that prior immunological immunity to the vector can seriously dampen subsequent antigen-specific humoral responses. Whether the same is true for cellular responses was not evaluated.", "Title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus\nPassage: to EBOVGP when part of the mucin-rich region was deleted, possibly as a result of altered proteosomal processing of EBOVGP or direct deletion of T-cell epitopes. After decay of the primary cell-mediated immune response, a second vaccine dose boosted ELISpot responses to levels seen after primary vaccination; however, there was still no detectable cell-mediated immune response elicited by vectors expressing EBOVGP from position 3 and 6, indicating the requirement for higher EBOVGP levels in infected cells to generate detectable EBOVGP-specific cell-mediated immune responses." ]

[ [ "0a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "0b", "Passage: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response." ], [ "0c", "Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses." ], [ "0d", "This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes ." ], [ "0e", "As these authors conclude, it will be possible to utilize such vectors only" ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: expressing tetC, induced much lower anti-tetC responses than mice that had not been primed. This argues strongly that prior immunological immunity to the vector can seriously dampen subsequent antigen-specific humoral responses. Whether the same is true for cellular responses was not evaluated.", "Title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus\nPassage: to EBOVGP when part of the mucin-rich region was deleted, possibly as a result of altered proteosomal processing of EBOVGP or direct deletion of T-cell epitopes. After decay of the primary cell-mediated immune response, a second vaccine dose boosted ELISpot responses to levels seen after primary vaccination; however, there was still no detectable cell-mediated immune response elicited by vectors expressing EBOVGP from position 3 and 6, indicating the requirement for higher EBOVGP levels in infected cells to generate detectable EBOVGP-specific cell-mediated immune responses." ]

[ [ "1a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "1b", "Passage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens ." ], [ "1c", "However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time." ], [ "1d", "Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen." ], [ "1e", "Of course, such repeated vaccination may not be practicable in real-world situations." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: expressing tetC, induced much lower anti-tetC responses than mice that had not been primed. This argues strongly that prior immunological immunity to the vector can seriously dampen subsequent antigen-specific humoral responses. Whether the same is true for cellular responses was not evaluated.", "Title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus\nPassage: to EBOVGP when part of the mucin-rich region was deleted, possibly as a result of altered proteosomal processing of EBOVGP or direct deletion of T-cell epitopes. After decay of the primary cell-mediated immune response, a second vaccine dose boosted ELISpot responses to levels seen after primary vaccination; however, there was still no detectable cell-mediated immune response elicited by vectors expressing EBOVGP from position 3 and 6, indicating the requirement for higher EBOVGP levels in infected cells to generate detectable EBOVGP-specific cell-mediated immune responses." ]

[ [ "2a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "2b", "Passage: expressing tetC, induced much lower anti-tetC responses than mice that had not been primed." ], [ "2c", "This argues strongly that prior immunological immunity to the vector can seriously dampen subsequent antigen-specific humoral responses." ], [ "2d", "Whether the same is true for cellular responses was not evaluated." ] ]

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

[ "Title: Investments in respiratory infectious disease research 1997–2010: a systematic analysis of UK funding\nPassage: Tuberculosis also represents a substantial challenge to global health, accounting for 2.2% of all-cause DALYs lost world-wide, 1 and an estimated 1.4 million deaths in 2011. 3 The target of the WHO Global TB Plan is to reduce tuberculosis deaths to half of those recorded in 1990 by 2015, but it is thought that both Europe and Africa will fail to meet these goals. Control efforts are hampered by limited vaccine effectiveness, coinfection with HIV, insufficient diagnostic capacity in low income settings, prolonged treatment courses and the emergence of drug resistant strains. 3, 4 Globally an estimated 500,000 deaths annually", "Title: Mortality among patients with tuberculosis requiring intensive care: a retrospective cohort study\nPassage: Across the world tuberculosis remains an important public health problem, especially in developing countries. One third of the world's population is infected with Mycobacterium tuberculosis. Brazil is ranking 15 th among the 22 high-burden countries that collectively account for 80% of TB cases globally. The incidence of TB was of 50 cases/100,000 population/yr in 2006, and recently reached approximately 100 cases/ 100,000 population in the city of Porto Alegre . Every year, almost 2 million people die of TB, most of them in low-and middle-income countries. The annual death rate from TB in Brazil was estimated at 4.0/100,000 population/yr in", "Title: Investments in respiratory infectious disease research 1997–2010: a systematic analysis of UK funding\nPassage: 1 and an estimated 1.4 million deaths in 2011. 3 The target of the WHO Global TB Plan is to reduce tuberculosis deaths to half of those recorded in 1990 by 2015, but it is thought that both Europe and Africa will fail to meet these goals. Control efforts are hampered by limited vaccine effectiveness, co-infection with HIV, insufficient diagnostic capacity in low income settings, prolonged treatment courses and the emergence of drug resistant strains. 3, 4 Globally an estimated 500,000 deaths annually are attributable to influenza. 5 1 2 3 4 5 6 7 8 9 10 11 12", "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: Tuberculosis remains a serious public health issue worldwide. Even in the era of effective chemotherapy, TB still accounts for a substantial number of deaths annually. Early diagnosis is challenging, even in areas with abundant medical resources . In 2012, there were an estimated 12 million TB cases globally, including 8.6 million new cases, and 1.3 million fatal cases . The global case-fatality rates are reported to be between 7% and 35% , and risk factors for death may include noninfective comorbidities, human immunodeficiency virus infection and multidrug-resistant TB . Since the World Health Organization defined TB deaths as the number" ]

[ [ "1a", "Title: Mortality among patients with tuberculosis requiring intensive care: a retrospective cohort study" ], [ "1b", "Passage: Across the world tuberculosis remains an important public health problem, especially in developing countries." ], [ "1c", "One third of the world's population is infected with Mycobacterium tuberculosis." ], [ "1d", "Brazil is ranking 15 th among the 22 high-burden countries that collectively account for 80% of TB cases globally." ], [ "1e", "The incidence of TB was of 50 cases/100,000 population/yr in 2006, and recently reached approximately 100 cases/ 100,000 population in the city of Porto Alegre ." ], [ "1f", "Every year, almost 2 million people die of TB, most of them in low-and middle-income countries." ], [ "1g", "The annual death rate from TB in Brazil was estimated at 4.0/100,000 population/yr in" ] ]

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

[ "Title: Investments in respiratory infectious disease research 1997–2010: a systematic analysis of UK funding\nPassage: Tuberculosis also represents a substantial challenge to global health, accounting for 2.2% of all-cause DALYs lost world-wide, 1 and an estimated 1.4 million deaths in 2011. 3 The target of the WHO Global TB Plan is to reduce tuberculosis deaths to half of those recorded in 1990 by 2015, but it is thought that both Europe and Africa will fail to meet these goals. Control efforts are hampered by limited vaccine effectiveness, coinfection with HIV, insufficient diagnostic capacity in low income settings, prolonged treatment courses and the emergence of drug resistant strains. 3, 4 Globally an estimated 500,000 deaths annually", "Title: Mortality among patients with tuberculosis requiring intensive care: a retrospective cohort study\nPassage: Across the world tuberculosis remains an important public health problem, especially in developing countries. One third of the world's population is infected with Mycobacterium tuberculosis. Brazil is ranking 15 th among the 22 high-burden countries that collectively account for 80% of TB cases globally. The incidence of TB was of 50 cases/100,000 population/yr in 2006, and recently reached approximately 100 cases/ 100,000 population in the city of Porto Alegre . Every year, almost 2 million people die of TB, most of them in low-and middle-income countries. The annual death rate from TB in Brazil was estimated at 4.0/100,000 population/yr in", "Title: Investments in respiratory infectious disease research 1997–2010: a systematic analysis of UK funding\nPassage: 1 and an estimated 1.4 million deaths in 2011. 3 The target of the WHO Global TB Plan is to reduce tuberculosis deaths to half of those recorded in 1990 by 2015, but it is thought that both Europe and Africa will fail to meet these goals. Control efforts are hampered by limited vaccine effectiveness, co-infection with HIV, insufficient diagnostic capacity in low income settings, prolonged treatment courses and the emergence of drug resistant strains. 3, 4 Globally an estimated 500,000 deaths annually are attributable to influenza. 5 1 2 3 4 5 6 7 8 9 10 11 12", "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: Tuberculosis remains a serious public health issue worldwide. Even in the era of effective chemotherapy, TB still accounts for a substantial number of deaths annually. Early diagnosis is challenging, even in areas with abundant medical resources . In 2012, there were an estimated 12 million TB cases globally, including 8.6 million new cases, and 1.3 million fatal cases . The global case-fatality rates are reported to be between 7% and 35% , and risk factors for death may include noninfective comorbidities, human immunodeficiency virus infection and multidrug-resistant TB . Since the World Health Organization defined TB deaths as the number" ]

[ [ "3a", "Title: Tuberculosis mortality: patient characteristics and causes" ], [ "3b", "Passage: Tuberculosis remains a serious public health issue worldwide." ], [ "3c", "Even in the era of effective chemotherapy, TB still accounts for a substantial number of deaths annually." ], [ "3d", "Early diagnosis is challenging, even in areas with abundant medical resources ." ], [ "3e", "In 2012, there were an estimated 12 million TB cases globally, including 8.6 million new cases, and 1.3 million fatal cases ." ], [ "3f", "The global case-fatality rates are reported to be between 7% and 35% , and risk factors for death may include noninfective comorbidities, human immunodeficiency virus infection and multidrug-resistant TB ." ], [ "3g", "Since the World Health Organization defined TB deaths as the number" ] ]

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

[ "Title: Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis\nPassage: Patients commonly showing swelling of the affected jaw bones and the lymph nodes in the neck, and jaws are rapidly enlarged without tenderness . In the sporadic cases of this lymphoma, abdominal and pelvic organs are usually involved with the other abdominal and glandular tissues seen affected in some cases but to a lesser extent . Patients of BL are commonly presented to the Gastroenterology clinics with abdominal pain, ascites, abdominal distension and signs of intestinal obstruction. BL has also been observed to occur as a consequence of immunodeficiency, mostly in people with HIV/AIDS infections where it accounts for 30%", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: There is a substantial amount of evidence that HPAI H5N1 virus can infect extrapulmonary organ tissues 27] and precede other clinical manifestation . Our results presented that the viral antigens or viral RNA can be found in trachea, lung, brain, intestines, liver, spleen, lymph-node and kidney which were reported as same before , as well as in aortopulmonary vessel and ureter which were not reported before. Notably, the virus can be found in tissues of lower gastrointestinal tract including small intestine and large intestine but in stomach and duodenum. The origin of infection in the extrapulmonary organs could be blood-borne,", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: There is much diversity among the manifestations of pulmonary strongyloidiasis. However, it is likely most patients present with one or more of the three most common complications; bacterial pneumonia, alveolar hemorrhage and allergic/eosinophilic manifestation from larvae . In patients with HS/DS, the number of larvae in the host is continuously multiplying . As this happens, many larvae pass through the alveolar membranes causing, sometimes, Abbreviations: HTLV-1 = human T-cell leukemia virus type 1, a mean was used for these values, b total 13 cases were tested serum albumin, c total 14 cases were tested HTLV-1 Acute exacerbation of interstitial pneumonia", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: Meanwhile, fifteen of the sixteen cases had pulmonary manifestations . Acute respiratory distress syndrome was the most common manifestation , bacterial pneumonia and respiratory hemorrhage including pulmonary alveolar hemorrhage and hemoptysis followed. Acute respiratory failure was a common indication for pulmonary manifestations . In cases with bacterial pneumonia, pathogens detected were always enteric bacteria; 2 Klebsiella pneumoniae, 1 Escherichia coli, 1 Acinetobacter baumannii, 1 Citrobacter koseri ." ]

[ [ "0a", "Title: Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis" ], [ "0b", "Passage: Patients commonly showing swelling of the affected jaw bones and the lymph nodes in the neck, and jaws are rapidly enlarged without tenderness ." ], [ "0c", "In the sporadic cases of this lymphoma, abdominal and pelvic organs are usually involved with the other abdominal and glandular tissues seen affected in some cases but to a lesser extent ." ], [ "0d", "Patients of BL are commonly presented to the Gastroenterology clinics with abdominal pain, ascites, abdominal distension and signs of intestinal obstruction." ], [ "0e", "BL has also been observed to occur as a consequence of immunodeficiency, mostly in people with HIV/AIDS infections where it accounts for 30%" ] ]

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

[ "Title: Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis\nPassage: Patients commonly showing swelling of the affected jaw bones and the lymph nodes in the neck, and jaws are rapidly enlarged without tenderness . In the sporadic cases of this lymphoma, abdominal and pelvic organs are usually involved with the other abdominal and glandular tissues seen affected in some cases but to a lesser extent . Patients of BL are commonly presented to the Gastroenterology clinics with abdominal pain, ascites, abdominal distension and signs of intestinal obstruction. BL has also been observed to occur as a consequence of immunodeficiency, mostly in people with HIV/AIDS infections where it accounts for 30%", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: There is a substantial amount of evidence that HPAI H5N1 virus can infect extrapulmonary organ tissues 27] and precede other clinical manifestation . Our results presented that the viral antigens or viral RNA can be found in trachea, lung, brain, intestines, liver, spleen, lymph-node and kidney which were reported as same before , as well as in aortopulmonary vessel and ureter which were not reported before. Notably, the virus can be found in tissues of lower gastrointestinal tract including small intestine and large intestine but in stomach and duodenum. The origin of infection in the extrapulmonary organs could be blood-borne,", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: There is much diversity among the manifestations of pulmonary strongyloidiasis. However, it is likely most patients present with one or more of the three most common complications; bacterial pneumonia, alveolar hemorrhage and allergic/eosinophilic manifestation from larvae . In patients with HS/DS, the number of larvae in the host is continuously multiplying . As this happens, many larvae pass through the alveolar membranes causing, sometimes, Abbreviations: HTLV-1 = human T-cell leukemia virus type 1, a mean was used for these values, b total 13 cases were tested serum albumin, c total 14 cases were tested HTLV-1 Acute exacerbation of interstitial pneumonia", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: Meanwhile, fifteen of the sixteen cases had pulmonary manifestations . Acute respiratory distress syndrome was the most common manifestation , bacterial pneumonia and respiratory hemorrhage including pulmonary alveolar hemorrhage and hemoptysis followed. Acute respiratory failure was a common indication for pulmonary manifestations . In cases with bacterial pneumonia, pathogens detected were always enteric bacteria; 2 Klebsiella pneumoniae, 1 Escherichia coli, 1 Acinetobacter baumannii, 1 Citrobacter koseri ." ]

[ [ "1a", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case" ], [ "1b", "Passage: There is a substantial amount of evidence that HPAI H5N1 virus can infect extrapulmonary organ tissues 27] and precede other clinical manifestation ." ], [ "1c", "Our results presented that the viral antigens or viral RNA can be found in trachea, lung, brain, intestines, liver, spleen, lymph-node and kidney which were reported as same before , as well as in aortopulmonary vessel and ureter which were not reported before." ], [ "1d", "Notably, the virus can be found in tissues of lower gastrointestinal tract including small intestine and large intestine but in stomach and duodenum." ], [ "1e", "The origin of infection in the extrapulmonary organs could be blood-borne," ] ]

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

[ "Title: Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis\nPassage: Patients commonly showing swelling of the affected jaw bones and the lymph nodes in the neck, and jaws are rapidly enlarged without tenderness . In the sporadic cases of this lymphoma, abdominal and pelvic organs are usually involved with the other abdominal and glandular tissues seen affected in some cases but to a lesser extent . Patients of BL are commonly presented to the Gastroenterology clinics with abdominal pain, ascites, abdominal distension and signs of intestinal obstruction. BL has also been observed to occur as a consequence of immunodeficiency, mostly in people with HIV/AIDS infections where it accounts for 30%", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: There is a substantial amount of evidence that HPAI H5N1 virus can infect extrapulmonary organ tissues 27] and precede other clinical manifestation . Our results presented that the viral antigens or viral RNA can be found in trachea, lung, brain, intestines, liver, spleen, lymph-node and kidney which were reported as same before , as well as in aortopulmonary vessel and ureter which were not reported before. Notably, the virus can be found in tissues of lower gastrointestinal tract including small intestine and large intestine but in stomach and duodenum. The origin of infection in the extrapulmonary organs could be blood-borne,", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: There is much diversity among the manifestations of pulmonary strongyloidiasis. However, it is likely most patients present with one or more of the three most common complications; bacterial pneumonia, alveolar hemorrhage and allergic/eosinophilic manifestation from larvae . In patients with HS/DS, the number of larvae in the host is continuously multiplying . As this happens, many larvae pass through the alveolar membranes causing, sometimes, Abbreviations: HTLV-1 = human T-cell leukemia virus type 1, a mean was used for these values, b total 13 cases were tested serum albumin, c total 14 cases were tested HTLV-1 Acute exacerbation of interstitial pneumonia", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: Meanwhile, fifteen of the sixteen cases had pulmonary manifestations . Acute respiratory distress syndrome was the most common manifestation , bacterial pneumonia and respiratory hemorrhage including pulmonary alveolar hemorrhage and hemoptysis followed. Acute respiratory failure was a common indication for pulmonary manifestations . In cases with bacterial pneumonia, pathogens detected were always enteric bacteria; 2 Klebsiella pneumoniae, 1 Escherichia coli, 1 Acinetobacter baumannii, 1 Citrobacter koseri ." ]

[ [ "2a", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases" ], [ "2b", "Passage: There is much diversity among the manifestations of pulmonary strongyloidiasis." ], [ "2c", "However, it is likely most patients present with one or more of the three most common complications; bacterial pneumonia, alveolar hemorrhage and allergic/eosinophilic manifestation from larvae ." ], [ "2d", "In patients with HS/DS, the number of larvae in the host is continuously multiplying ." ], [ "2e", "As this happens, many larvae pass through the alveolar membranes causing, sometimes, Abbreviations: HTLV-1 = human T-cell leukemia virus type 1, a mean was used for these values, b total 13 cases were tested serum albumin, c total 14 cases were tested HTLV-1 Acute exacerbation of interstitial pneumonia" ] ]

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

[ "Title: Epstein- Barr Virus: Clinical and Epidemiological Revisits and Genetic Basis of Oncogenesis\nPassage: Patients commonly showing swelling of the affected jaw bones and the lymph nodes in the neck, and jaws are rapidly enlarged without tenderness . In the sporadic cases of this lymphoma, abdominal and pelvic organs are usually involved with the other abdominal and glandular tissues seen affected in some cases but to a lesser extent . Patients of BL are commonly presented to the Gastroenterology clinics with abdominal pain, ascites, abdominal distension and signs of intestinal obstruction. BL has also been observed to occur as a consequence of immunodeficiency, mostly in people with HIV/AIDS infections where it accounts for 30%", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: There is a substantial amount of evidence that HPAI H5N1 virus can infect extrapulmonary organ tissues 27] and precede other clinical manifestation . Our results presented that the viral antigens or viral RNA can be found in trachea, lung, brain, intestines, liver, spleen, lymph-node and kidney which were reported as same before , as well as in aortopulmonary vessel and ureter which were not reported before. Notably, the virus can be found in tissues of lower gastrointestinal tract including small intestine and large intestine but in stomach and duodenum. The origin of infection in the extrapulmonary organs could be blood-borne,", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: There is much diversity among the manifestations of pulmonary strongyloidiasis. However, it is likely most patients present with one or more of the three most common complications; bacterial pneumonia, alveolar hemorrhage and allergic/eosinophilic manifestation from larvae . In patients with HS/DS, the number of larvae in the host is continuously multiplying . As this happens, many larvae pass through the alveolar membranes causing, sometimes, Abbreviations: HTLV-1 = human T-cell leukemia virus type 1, a mean was used for these values, b total 13 cases were tested serum albumin, c total 14 cases were tested HTLV-1 Acute exacerbation of interstitial pneumonia", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases\nPassage: Meanwhile, fifteen of the sixteen cases had pulmonary manifestations . Acute respiratory distress syndrome was the most common manifestation , bacterial pneumonia and respiratory hemorrhage including pulmonary alveolar hemorrhage and hemoptysis followed. Acute respiratory failure was a common indication for pulmonary manifestations . In cases with bacterial pneumonia, pathogens detected were always enteric bacteria; 2 Klebsiella pneumoniae, 1 Escherichia coli, 1 Acinetobacter baumannii, 1 Citrobacter koseri ." ]

[ [ "3a", "Title: Pulmonary strongyloidiasis: assessment between manifestation and radiological findings in 16 severe strongyloidiasis cases" ], [ "3b", "Passage: Meanwhile, fifteen of the sixteen cases had pulmonary manifestations ." ], [ "3c", "Acute respiratory distress syndrome was the most common manifestation , bacterial pneumonia and respiratory hemorrhage including pulmonary alveolar hemorrhage and hemoptysis followed." ], [ "3d", "Acute respiratory failure was a common indication for pulmonary manifestations ." ], [ "3e", "In cases with bacterial pneumonia, pathogens detected were always enteric bacteria; 2 Klebsiella pneumoniae, 1 Escherichia coli, 1 Acinetobacter baumannii, 1 Citrobacter koseri ." ] ]

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

[ "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: reported. On January 15, 2020, the Centers for Disease Control and Prevention confirmed the first known imported case of 2019-nCoV in the US state of Washington. The patient had recently returned from Wuhan City, where he likely contracted the disease. Chicago health authorities reported a second US case on January 24, 2020. This was quickly followed by additional imported cases reported in Orange and Los Angeles Counties, California on January 26, 2020. Additional suspected cases continue to be evaluated. On January 30, 2020, the CDC reported the first local transmission in the US between members in a household. On the", "Title: CDC Summary 21 MAR 2020,\nPassage: Twenty-seven U.S. states are reporting some community spread of COVID-19.", "Title: CDC Summary 21 MAR 2020,\nPassage: More cases of COVID-19 are likely to be identified in the United States in the coming days, including more instances of community spread. CDC expects that widespread transmission of COVID-19 in the United States will occur. In the coming months, most of the U.S. population will be exposed to this virus.", "Title: CDC Summary 21 MAR 2020,\nPassage: All 50 states have reported cases of COVID-19 to CDC." ]

[ [ "0a", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus Passage: reported." ], [ "0b", "On January 15, 2020, the Centers for Disease Control and Prevention confirmed the first known imported case of 2019-nCoV in the US state of Washington." ], [ "0c", "The patient had recently returned from Wuhan City, where he likely contracted the disease." ], [ "0d", "Chicago health authorities reported a second US case on January 24, 2020." ], [ "0e", "This was quickly followed by additional imported cases reported in Orange and Los Angeles Counties, California on January 26, 2020." ], [ "0f", "Additional suspected cases continue to be evaluated." ], [ "0g", "On January 30, 2020, the CDC reported the first local transmission in the US between members in a household. On the" ] ]

[ "0a", "0b", "0c", "0d", "0e", "0f", "0g" ]

[ "Title: Focus on Translation Initiation of the HIV-1 mRNAs\nPassage: could also be involved in both mechanisms. This opened question has to be resolved.", "Title: Focus on Translation Initiation of the HIV-1 mRNAs\nPassage: alternative initiation mechanism that remains to be determined.", "Title: Lost in Translation (LiT)\nPassage: Drug discovery over the last 60 years has had cyclical ups and downs and has become accustomed to the great majority of projects failing. Almost all the major developments have been based on strong basic science, credible clinical evidence and advances in technology, but with single molecule targets. Many of the current major developments in basic and clinical science are based on applying very large data sets, GWAS, ENCODE, omics to complex pathways in biological control, disease aetiology and pathogenesis. The assumption is that many, perhaps most, of these will require multiple points of intervention, not single targets. Can translational", "Title: Lost in Translation (LiT)\nPassage: may be a pathway or a control system, not a single molecule. The concept that translational medicine starts when the pre-clinical teams offers a molecule for testing for the first time in human and ends when it is marketed as no longer appropriate. Translational medicine in the LiT3 era begins with the choice of target, not with FTIH and does not end until many years later when both physicians and patients have understood how to use it safely and effectively in the real world." ]

[ [ "2a", "Title: Lost in Translation (LiT)" ], [ "2b", "Passage: Drug discovery over the last 60 years has had cyclical ups and downs and has become accustomed to the great majority of projects failing." ], [ "2c", "Almost all the major developments have been based on strong basic science, credible clinical evidence and advances in technology, but with single molecule targets." ], [ "2d", "Many of the current major developments in basic and clinical science are based on applying very large data sets, GWAS, ENCODE, omics to complex pathways in biological control, disease aetiology and pathogenesis." ], [ "2e", "The assumption is that many, perhaps most, of these will require multiple points of intervention, not single targets. Can translational" ] ]

[ "2d", "3d" ]

[ "Title: Focus on Translation Initiation of the HIV-1 mRNAs\nPassage: could also be involved in both mechanisms. This opened question has to be resolved.", "Title: Focus on Translation Initiation of the HIV-1 mRNAs\nPassage: alternative initiation mechanism that remains to be determined.", "Title: Lost in Translation (LiT)\nPassage: Drug discovery over the last 60 years has had cyclical ups and downs and has become accustomed to the great majority of projects failing. Almost all the major developments have been based on strong basic science, credible clinical evidence and advances in technology, but with single molecule targets. Many of the current major developments in basic and clinical science are based on applying very large data sets, GWAS, ENCODE, omics to complex pathways in biological control, disease aetiology and pathogenesis. The assumption is that many, perhaps most, of these will require multiple points of intervention, not single targets. Can translational", "Title: Lost in Translation (LiT)\nPassage: may be a pathway or a control system, not a single molecule. The concept that translational medicine starts when the pre-clinical teams offers a molecule for testing for the first time in human and ends when it is marketed as no longer appropriate. Translational medicine in the LiT3 era begins with the choice of target, not with FTIH and does not end until many years later when both physicians and patients have understood how to use it safely and effectively in the real world." ]

[ [ "3a", "Title: Lost in Translation (LiT)" ], [ "3b", "Passage: may be a pathway or a control system, not a single molecule." ], [ "3c", "The concept that translational medicine starts when the pre-clinical teams offers a molecule for testing for the first time in human and ends when it is marketed as no longer appropriate." ], [ "3d", "Translational medicine in the LiT3 era begins with the choice of target, not with FTIH and does not end until many years later when both physicians and patients have understood how to use it safely and effectively in the real world." ] ]

[ "2d", "3d" ]

[ "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Beyond processes of deliberative democracy, furthermore, carefully designed social research will be important for shedding light on people's ultimate values, value weightings, levels of risk aversion, and risk-taking strategies etc. that policy should aim to reflect.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: were published in 2012. Advocates of these studies/publications argued that they would improve surveillance of H5N1 in nature and facilitate development of vaccines that might be needed to protect against pandemic strains of the virus. Critics questioned the validity of claims about such benefits and argued that the studies might facilitate creation of biological weapons agents that could kill millions, or possibly even billions, of people.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: at issue.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Conceived as a scalar moral desideratum the point of this principle is that, in cases where the research poses serious risks, its evaluation should partly be based on the importance of the research question it aims to address. Some research questions are obviously more important than others. The more important any given target research question, the more ethically acceptable it would be to fund/conduct/publish a study posing a given magnitude of risk . The less important any given research question would be, the less ethically acceptable it would be to fund/conduct/publish a study posing the same magnitude of risk ." ]

[ [ "1a", "Title: Gain-of-Function Research: Ethical Analysis" ], [ "1b", "Passage: were published in 2012." ], [ "1c", "Advocates of these studies/publications argued that they would improve surveillance of H5N1 in nature and facilitate development of vaccines that might be needed to protect against pandemic strains of the virus." ], [ "1d", "Critics questioned the validity of claims about such benefits and argued that the studies might facilitate creation of biological weapons agents that could kill millions, or possibly even billions, of people." ] ]

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

[ "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Beyond processes of deliberative democracy, furthermore, carefully designed social research will be important for shedding light on people's ultimate values, value weightings, levels of risk aversion, and risk-taking strategies etc. that policy should aim to reflect.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: were published in 2012. Advocates of these studies/publications argued that they would improve surveillance of H5N1 in nature and facilitate development of vaccines that might be needed to protect against pandemic strains of the virus. Critics questioned the validity of claims about such benefits and argued that the studies might facilitate creation of biological weapons agents that could kill millions, or possibly even billions, of people.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: at issue.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Conceived as a scalar moral desideratum the point of this principle is that, in cases where the research poses serious risks, its evaluation should partly be based on the importance of the research question it aims to address. Some research questions are obviously more important than others. The more important any given target research question, the more ethically acceptable it would be to fund/conduct/publish a study posing a given magnitude of risk . The less important any given research question would be, the less ethically acceptable it would be to fund/conduct/publish a study posing the same magnitude of risk ." ]

[ [ "3a", "Title: Gain-of-Function Research: Ethical Analysis" ], [ "3b", "Passage: Conceived as a scalar moral desideratum the point of this principle is that, in cases where the research poses serious risks, its evaluation should partly be based on the importance of the research question it aims to address." ], [ "3c", "Some research questions are obviously more important than others." ], [ "3d", "The more important any given target research question, the more ethically acceptable it would be to fund/conduct/publish a study posing a given magnitude of risk ." ], [ "3e", "The less important any given research question would be, the less ethically acceptable it would be to fund/conduct/publish a study posing the same magnitude of risk ." ] ]

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

[ "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1\nPassage: grown to high titers, requires a low infectious dose, and contains multiple serotypes. Both the former Soviet Union and the United States previously weaponized the virus, producing large quantities for their now defunct offensive bioweapons programs . Currently, vaccine strain TC83 is used in horses and for high-risk personnel; however, due to the low rate of seroconversion achieved with this vaccine and its reliance on two single attenuating mutations , it is considered unfit for mass distribution . To date there are no FDA-approved therapeutics for VEEV infection, and further studies are required for clarification of the mechanisms associated with", "Title: Treatment of Neuroterrorism\nPassage: Venezuelan equine encephalitis virus is an alphavirus that is most commonly found in Central and South America. It is transmitted to humans by mosquitoes. In case of a bioterrorist attack, the distribution would be made through aerosols . The virus usually leads to an initial severe febrile illness in nearly everyone exposed at 1 to 6 days after exposure.", "Title: Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas\nPassage: within the VEE subtype, subtype II Everglades virus , which is found only in Florida, can cause neurologic disease in humans and equids . Subtype IIIA, Mucambo virus, also causes febrile disease in humans .", "Title: Advances in Designing and Developing Vaccines, Drugs, and Therapies to Counter Ebola Virus\nPassage: not formed. Viruses such as Venezuelan equine encephalitis virus can be used for production of EBOV antigen instead of structural proteins for the replicon vector. Thus, such vaccines are also quite safe . The gene inserted is typically GP, the main target of neutralizing antibodies. VRPs expressing EBOV VP24, VP30, VP35, and VP40 have been evaluated for their protective efficacy in a mouse model, but these were found not to be as protective as EBOV GP and NP antigens. VEEV replicons containing GPs from both EBOV and SUDV showed promising results in cynomolgus macaques after administration of a single dose." ]

[ [ "0a", "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1" ], [ "0b", "Passage: grown to high titers, requires a low infectious dose, and contains multiple serotypes." ], [ "0c", "Both the former Soviet Union and the United States previously weaponized the virus, producing large quantities for their now defunct offensive bioweapons programs ." ], [ "0d", "Currently, vaccine strain TC83 is used in horses and for high-risk personnel; however, due to the low rate of seroconversion achieved with this vaccine and its reliance on two single attenuating mutations , it is considered unfit for mass distribution ." ], [ "0e", "To date there are no FDA-approved therapeutics for VEEV infection, and further studies are required for clarification of the mechanisms associated with" ] ]

[ "0a", "0d", "1a" ]

[ "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1\nPassage: grown to high titers, requires a low infectious dose, and contains multiple serotypes. Both the former Soviet Union and the United States previously weaponized the virus, producing large quantities for their now defunct offensive bioweapons programs . Currently, vaccine strain TC83 is used in horses and for high-risk personnel; however, due to the low rate of seroconversion achieved with this vaccine and its reliance on two single attenuating mutations , it is considered unfit for mass distribution . To date there are no FDA-approved therapeutics for VEEV infection, and further studies are required for clarification of the mechanisms associated with", "Title: Treatment of Neuroterrorism\nPassage: Venezuelan equine encephalitis virus is an alphavirus that is most commonly found in Central and South America. It is transmitted to humans by mosquitoes. In case of a bioterrorist attack, the distribution would be made through aerosols . The virus usually leads to an initial severe febrile illness in nearly everyone exposed at 1 to 6 days after exposure.", "Title: Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas\nPassage: within the VEE subtype, subtype II Everglades virus , which is found only in Florida, can cause neurologic disease in humans and equids . Subtype IIIA, Mucambo virus, also causes febrile disease in humans .", "Title: Advances in Designing and Developing Vaccines, Drugs, and Therapies to Counter Ebola Virus\nPassage: not formed. Viruses such as Venezuelan equine encephalitis virus can be used for production of EBOV antigen instead of structural proteins for the replicon vector. Thus, such vaccines are also quite safe . The gene inserted is typically GP, the main target of neutralizing antibodies. VRPs expressing EBOV VP24, VP30, VP35, and VP40 have been evaluated for their protective efficacy in a mouse model, but these were found not to be as protective as EBOV GP and NP antigens. VEEV replicons containing GPs from both EBOV and SUDV showed promising results in cynomolgus macaques after administration of a single dose." ]

[ [ "1a", "Title: Treatment of Neuroterrorism" ], [ "1b", "Passage: Venezuelan equine encephalitis virus is an alphavirus that is most commonly found in Central and South America." ], [ "1c", "It is transmitted to humans by mosquitoes." ], [ "1d", "In case of a bioterrorist attack, the distribution would be made through aerosols ." ], [ "1e", "The virus usually leads to an initial severe febrile illness in nearly everyone exposed at 1 to 6 days after exposure." ] ]

[ "0a", "0d", "1a" ]

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: During the 7 d preceding birth, no human mother has been reported to transmit the disease vertically. However, about 50% of newborns delivered while the mother was infected with CHIKV contracted the disease from their mother, despite the method of delivery. Furthermore, there have been instances of CHIKV transmission from mother to fetus causing congenital illness and fetal death .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: According to Payne et al. , epidemiologic investigation of the 2012 MERS outbreak in Zarqa, Jordan, revealed that a 2nd trimester stillbirth had occurred as a result of maternal exposure to MERS-CoV. The mother experienced fever, fatigue, headache and cough, concurrently with vaginal bleeding and abdominal pain. On the 7th day of symptoms, she had a fetal death. The mother was confirmed to have antibody to MERS-CoV, and she self-reported having had unprotected contact with family members who later tested positive for the virus. This was the first documented occurrence of stillbirth during maternal infection with MERS-CoV.", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: MTCT of HIV-1 can occur during pregnancy , at delivery and via breastfeeding . HIV-1 can cross the placental barrier in utero either by microtransfusion or by transcytosis across the trophoblast cell layer . IP transmission may occur through direct contact between infant mucosa and HIV-1 infected maternal blood and/ or cervico-vaginal secretions . Finally, HIV-1 in breast milk may result in PP infection of the newborn through mucosal exposure . High maternal viral loads in serum and breast milk and low CD4 cell count as well as obstetric factors such as preterm delivery, vaginal delivery, and prolonged membrane rupture", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: And according to Dr. Paul Hunter, Professor of Medicine at the University of East Anglia , \"As far as I am aware there is currently no evidence that the novel coronavirus can be transmitted in the womb. When a baby is born vaginally it is exposed to the mother's gut microbiome, therefore if a baby does get infected with coronavirus a few days after birth we currently cannot tell if the baby was infected in the womb or during birth.\"" ]

[ [ "0a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "0b", "Passage: During the 7 d preceding birth, no human mother has been reported to transmit the disease vertically." ], [ "0c", "However, about 50% of newborns delivered while the mother was infected with CHIKV contracted the disease from their mother, despite the method of delivery." ], [ "0d", "Furthermore, there have been instances of CHIKV transmission from mother to fetus causing congenital illness and fetal death ." ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: During the 7 d preceding birth, no human mother has been reported to transmit the disease vertically. However, about 50% of newborns delivered while the mother was infected with CHIKV contracted the disease from their mother, despite the method of delivery. Furthermore, there have been instances of CHIKV transmission from mother to fetus causing congenital illness and fetal death .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: According to Payne et al. , epidemiologic investigation of the 2012 MERS outbreak in Zarqa, Jordan, revealed that a 2nd trimester stillbirth had occurred as a result of maternal exposure to MERS-CoV. The mother experienced fever, fatigue, headache and cough, concurrently with vaginal bleeding and abdominal pain. On the 7th day of symptoms, she had a fetal death. The mother was confirmed to have antibody to MERS-CoV, and she self-reported having had unprotected contact with family members who later tested positive for the virus. This was the first documented occurrence of stillbirth during maternal infection with MERS-CoV.", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: MTCT of HIV-1 can occur during pregnancy , at delivery and via breastfeeding . HIV-1 can cross the placental barrier in utero either by microtransfusion or by transcytosis across the trophoblast cell layer . IP transmission may occur through direct contact between infant mucosa and HIV-1 infected maternal blood and/ or cervico-vaginal secretions . Finally, HIV-1 in breast milk may result in PP infection of the newborn through mucosal exposure . High maternal viral loads in serum and breast milk and low CD4 cell count as well as obstetric factors such as preterm delivery, vaginal delivery, and prolonged membrane rupture", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: And according to Dr. Paul Hunter, Professor of Medicine at the University of East Anglia , \"As far as I am aware there is currently no evidence that the novel coronavirus can be transmitted in the womb. When a baby is born vaginally it is exposed to the mother's gut microbiome, therefore if a baby does get infected with coronavirus a few days after birth we currently cannot tell if the baby was infected in the womb or during birth.\"" ]

[ [ "1a", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections" ], [ "1b", "Passage: According to Payne et al. , epidemiologic investigation of the 2012 MERS outbreak in Zarqa, Jordan, revealed that a 2nd trimester stillbirth had occurred as a result of maternal exposure to MERS-CoV." ], [ "1c", "The mother experienced fever, fatigue, headache and cough, concurrently with vaginal bleeding and abdominal pain." ], [ "1d", "On the 7th day of symptoms, she had a fetal death." ], [ "1e", "The mother was confirmed to have antibody to MERS-CoV, and she self-reported having had unprotected contact with family members who later tested positive for the virus." ], [ "1f", "This was the first documented occurrence of stillbirth during maternal infection with MERS-CoV." ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: During the 7 d preceding birth, no human mother has been reported to transmit the disease vertically. However, about 50% of newborns delivered while the mother was infected with CHIKV contracted the disease from their mother, despite the method of delivery. Furthermore, there have been instances of CHIKV transmission from mother to fetus causing congenital illness and fetal death .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: According to Payne et al. , epidemiologic investigation of the 2012 MERS outbreak in Zarqa, Jordan, revealed that a 2nd trimester stillbirth had occurred as a result of maternal exposure to MERS-CoV. The mother experienced fever, fatigue, headache and cough, concurrently with vaginal bleeding and abdominal pain. On the 7th day of symptoms, she had a fetal death. The mother was confirmed to have antibody to MERS-CoV, and she self-reported having had unprotected contact with family members who later tested positive for the virus. This was the first documented occurrence of stillbirth during maternal infection with MERS-CoV.", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: MTCT of HIV-1 can occur during pregnancy , at delivery and via breastfeeding . HIV-1 can cross the placental barrier in utero either by microtransfusion or by transcytosis across the trophoblast cell layer . IP transmission may occur through direct contact between infant mucosa and HIV-1 infected maternal blood and/ or cervico-vaginal secretions . Finally, HIV-1 in breast milk may result in PP infection of the newborn through mucosal exposure . High maternal viral loads in serum and breast milk and low CD4 cell count as well as obstetric factors such as preterm delivery, vaginal delivery, and prolonged membrane rupture", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: And according to Dr. Paul Hunter, Professor of Medicine at the University of East Anglia , \"As far as I am aware there is currently no evidence that the novel coronavirus can be transmitted in the womb. When a baby is born vaginally it is exposed to the mother's gut microbiome, therefore if a baby does get infected with coronavirus a few days after birth we currently cannot tell if the baby was infected in the womb or during birth.\"" ]

[ [ "2a", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission" ], [ "2b", "Passage: MTCT of HIV-1 can occur during pregnancy , at delivery and via breastfeeding ." ], [ "2c", "HIV-1 can cross the placental barrier in utero either by microtransfusion or by transcytosis across the trophoblast cell layer ." ], [ "2d", "IP transmission may occur through direct contact between infant mucosa and HIV-1 infected maternal blood and/ or cervico-vaginal secretions ." ], [ "2e", "Finally, HIV-1 in breast milk may result in PP infection of the newborn through mucosal exposure ." ], [ "2f", "High maternal viral loads in serum and breast milk and low CD4 cell count as well as obstetric factors such as preterm delivery, vaginal delivery, and prolonged membrane rupture" ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Abstract: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters’ index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters' index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February 2020, 47 confirmed cases of COVID-19 were reported in the WHO European Region and one of these cases had died . Data on 38 of these cases are included in this analysis.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "Passage: Abstract: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020." ], [ "0c", "We detail the first European cases." ], [ "0d", "As at 21 February, nine European countries reported 47 cases." ], [ "0e", "Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China." ], [ "0f", "Median case age was 42 years; 25 were male." ], [ "0g", "Late detection of the clusters’ index cases delayed isolation of further local cases." ], [ "0h", "As at 5 March, there were 4,250 cases." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Abstract: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters’ index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters' index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February 2020, 47 confirmed cases of COVID-19 were reported in the WHO European Region and one of these cases had died . Data on 38 of these cases are included in this analysis.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ]

[ [ "1a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "1b", "Passage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020." ], [ "1c", "We detail the first European cases." ], [ "1d", "As at 21 February, nine European countries reported 47 cases." ], [ "1e", "Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China." ], [ "1f", "Median case age was 42 years; 25 were male." ], [ "1g", "Late detection of the clusters' index cases delayed isolation of further local cases." ], [ "1h", "As at 5 March, there were 4,250 cases." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Abstract: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters’ index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters' index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February 2020, 47 confirmed cases of COVID-19 were reported in the WHO European Region and one of these cases had died . Data on 38 of these cases are included in this analysis.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ]

[ [ "2a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "2b", "Passage: As at 09:00 on 21 February 2020, 47 confirmed cases of COVID-19 were reported in the WHO European Region and one of these cases had died ." ], [ "2c", "Data on 38 of these cases are included in this analysis." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Abstract: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters’ index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020. We detail the first European cases. As at 21 February, nine European countries reported 47 cases. Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China. Median case age was 42 years; 25 were male. Late detection of the clusters' index cases delayed isolation of further local cases. As at 5 March, there were 4,250 cases.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February 2020, 47 confirmed cases of COVID-19 were reported in the WHO European Region and one of these cases had died . Data on 38 of these cases are included in this analysis.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ]

[ [ "3a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "3b", "Passage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia." ], [ "3c", "However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths ." ], [ "3d", "As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ] ]

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

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ]

[ [ "0a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "0b", "Passage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera." ], [ "0c", "Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region." ] ]

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

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ]

[ [ "1a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "1b", "Passage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera." ], [ "1c", "Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region." ] ]

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

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ]

[ [ "2a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "2b", "Passage: able to enhance the anti-HIV-1 activity of AP3." ], [ "2c", "Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 ." ], [ "2d", "We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ] ]

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

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: the present study showed significant decrease of anti-HIV-1 activity in the presence of patients' sera. Instead, the antiviral activity of AP3 increased in the presence of antisera from HIV-1-infected patients , suggesting that anti-HIV-1 antibodies actually enhanced the anti-HIV-1 activity of AP3, possibly because the binding of the antibodies to some sites in gp120 or gp41 promote the interaction of AP3 with viral gp41 NHR region.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: able to enhance the anti-HIV-1 activity of AP3. Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 . We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ]

[ [ "3a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "3b", "Passage: able to enhance the anti-HIV-1 activity of AP3." ], [ "3c", "Our recent study has demonstrated that T20's anti-HIV-1 activity is enhanced by a non-neutralizing antibody directed against the NHR domain of the HIV-1 gp41 46 ." ], [ "3d", "We thus hypothesize that some of the anti-gp41 antibodies in HIV/AIDS patients may bind to a site in NHR domain adjacent to the AP3's binding region, resulting in increased interaction between AP3 and NHR-trimer and enhanced antiviral activity of AP3." ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern. Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population. While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains. This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Poxvirus vaccines have a long history and the notable hallmark of being responsible for eradication of smallpox. The termination of the smallpox virus vaccination program has resulted in a large population of poxvirus-naï ve individuals that provides the opportunity for the use of poxviruses as vectors without preexisting immunity concerns . Poxvirus-vectored vaccines were first proposed for use in 1982 with two reports of recombinant vaccinia viruses encoding and expressing functional thymidine kinase gene from herpes virus . Within a year, a vaccinia virus encoding the HA of an H2N2 virus was shown to express a functional HA protein and", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While poxvirus-vectored vaccines have not yet been approved for use in humans, there is a growing list of licensed poxvirus for veterinary use that include fowlpox-and canarypox-vectored vaccines for avian and equine influenza viruses, respectively . The fowlpox-vectored vaccine expressing the avian influenza virus HA antigen has the added benefit of providing protection against fowlpox infection. Currently, at least ten poxvirus-vectored vaccines have been licensed for veterinary use . These poxvirus vectors have the potential for use as vaccine vectors in humans, similar to the first use of cowpox for vaccination against smallpox . The availability of these non-human poxvirus", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose ." ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern." ], [ "0c", "Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population." ], [ "0d", "While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains." ], [ "0e", "This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern. Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population. While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains. This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Poxvirus vaccines have a long history and the notable hallmark of being responsible for eradication of smallpox. The termination of the smallpox virus vaccination program has resulted in a large population of poxvirus-naï ve individuals that provides the opportunity for the use of poxviruses as vectors without preexisting immunity concerns . Poxvirus-vectored vaccines were first proposed for use in 1982 with two reports of recombinant vaccinia viruses encoding and expressing functional thymidine kinase gene from herpes virus . Within a year, a vaccinia virus encoding the HA of an H2N2 virus was shown to express a functional HA protein and", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While poxvirus-vectored vaccines have not yet been approved for use in humans, there is a growing list of licensed poxvirus for veterinary use that include fowlpox-and canarypox-vectored vaccines for avian and equine influenza viruses, respectively . The fowlpox-vectored vaccine expressing the avian influenza virus HA antigen has the added benefit of providing protection against fowlpox infection. Currently, at least ten poxvirus-vectored vaccines have been licensed for veterinary use . These poxvirus vectors have the potential for use as vaccine vectors in humans, similar to the first use of cowpox for vaccination against smallpox . The availability of these non-human poxvirus", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose ." ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: Poxvirus vaccines have a long history and the notable hallmark of being responsible for eradication of smallpox." ], [ "1c", "The termination of the smallpox virus vaccination program has resulted in a large population of poxvirus-naï ve individuals that provides the opportunity for the use of poxviruses as vectors without preexisting immunity concerns ." ], [ "1d", "Poxvirus-vectored vaccines were first proposed for use in 1982 with two reports of recombinant vaccinia viruses encoding and expressing functional thymidine kinase gene from herpes virus ." ], [ "1e", "Within a year, a vaccinia virus encoding the HA of an H2N2 virus was shown to express a functional HA protein and" ] ]

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

[ "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: For the simulated daily number of cases , see Figure 1d , we found that ε i matched the observed daily number after 17 January 2020, but was significantly larger than the observations from 1 to 17 January 2020. This finding implied that under-reporting was likely to have occurred in the first half of January 2020. We estimated that the reporting rate after 17 January 2020 increased 21-fold compared to the situation from 1 to 17 January 2020 on average. One of the possible reasons was that the official diagnostic protocol was released by WHO on 17 January 2020 ,", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: and the diagnosis and reporting efforts of 2019-nCoV infections probably increased. Thereafter, the daily number of newly reported cases started increasing rapidly after 17 January 2020, see Figure 1d . We conducted additional sensitivity analysis by varying the starting date of the under-reporting time window, e.g., 1 January 2020 in the main results, from 2 December 2019 to 3 January 2020, and we report our estimates largely hold. The exact value of the reporting rate was difficult to determine due to lack of serological surveillance data. The reporting rate can be determined if serological surveillance data are available for a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: Under-reporting was likely to have occurred and resulted in 469 unreported cases from 1 to 15 January 2020. The reporting rate after 17 January 2020 was likely to have increased 21-fold compared with the situation from 1 to 17 January 2020 on average, and it should be considered in future investigation. We estimated the R 0 at 2019-nCoV to be 2.56 .", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: population; we would know who was infected and who was not , with high confidence. The reporting rate is the ratio of reported cases over the number of seropositive individuals. It was statistically evident that increasing in reporting was likely, and thus it should be considered in the future investigation of this outbreak." ]

[ [ "0a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak" ], [ "0b", "Passage: For the simulated daily number of cases , see Figure 1d , we found that ε i matched the observed daily number after 17 January 2020, but was significantly larger than the observations from 1 to 17 January 2020." ], [ "0c", "This finding implied that under-reporting was likely to have occurred in the first half of January 2020." ], [ "0d", "We estimated that the reporting rate after 17 January 2020 increased 21-fold compared to the situation from 1 to 17 January 2020 on average." ], [ "0e", "One of the possible reasons was that the official diagnostic protocol was released by WHO on 17 January 2020 ," ] ]

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

[ "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: For the simulated daily number of cases , see Figure 1d , we found that ε i matched the observed daily number after 17 January 2020, but was significantly larger than the observations from 1 to 17 January 2020. This finding implied that under-reporting was likely to have occurred in the first half of January 2020. We estimated that the reporting rate after 17 January 2020 increased 21-fold compared to the situation from 1 to 17 January 2020 on average. One of the possible reasons was that the official diagnostic protocol was released by WHO on 17 January 2020 ,", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: and the diagnosis and reporting efforts of 2019-nCoV infections probably increased. Thereafter, the daily number of newly reported cases started increasing rapidly after 17 January 2020, see Figure 1d . We conducted additional sensitivity analysis by varying the starting date of the under-reporting time window, e.g., 1 January 2020 in the main results, from 2 December 2019 to 3 January 2020, and we report our estimates largely hold. The exact value of the reporting rate was difficult to determine due to lack of serological surveillance data. The reporting rate can be determined if serological surveillance data are available for a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: Under-reporting was likely to have occurred and resulted in 469 unreported cases from 1 to 15 January 2020. The reporting rate after 17 January 2020 was likely to have increased 21-fold compared with the situation from 1 to 17 January 2020 on average, and it should be considered in future investigation. We estimated the R 0 at 2019-nCoV to be 2.56 .", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: population; we would know who was infected and who was not , with high confidence. The reporting rate is the ratio of reported cases over the number of seropositive individuals. It was statistically evident that increasing in reporting was likely, and thus it should be considered in the future investigation of this outbreak." ]

[ [ "1a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak" ], [ "1b", "Passage: and the diagnosis and reporting efforts of 2019-nCoV infections probably increased." ], [ "1c", "Thereafter, the daily number of newly reported cases started increasing rapidly after 17 January 2020, see Figure 1d ." ], [ "1d", "We conducted additional sensitivity analysis by varying the starting date of the under-reporting time window, e.g., 1 January 2020 in the main results, from 2 December 2019 to 3 January 2020, and we report our estimates largely hold." ], [ "1e", "The exact value of the reporting rate was difficult to determine due to lack of serological surveillance data." ], [ "1f", "The reporting rate can be determined if serological surveillance data are available for a" ] ]

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

[ "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: For the simulated daily number of cases , see Figure 1d , we found that ε i matched the observed daily number after 17 January 2020, but was significantly larger than the observations from 1 to 17 January 2020. This finding implied that under-reporting was likely to have occurred in the first half of January 2020. We estimated that the reporting rate after 17 January 2020 increased 21-fold compared to the situation from 1 to 17 January 2020 on average. One of the possible reasons was that the official diagnostic protocol was released by WHO on 17 January 2020 ,", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: and the diagnosis and reporting efforts of 2019-nCoV infections probably increased. Thereafter, the daily number of newly reported cases started increasing rapidly after 17 January 2020, see Figure 1d . We conducted additional sensitivity analysis by varying the starting date of the under-reporting time window, e.g., 1 January 2020 in the main results, from 2 December 2019 to 3 January 2020, and we report our estimates largely hold. The exact value of the reporting rate was difficult to determine due to lack of serological surveillance data. The reporting rate can be determined if serological surveillance data are available for a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: Under-reporting was likely to have occurred and resulted in 469 unreported cases from 1 to 15 January 2020. The reporting rate after 17 January 2020 was likely to have increased 21-fold compared with the situation from 1 to 17 January 2020 on average, and it should be considered in future investigation. We estimated the R 0 at 2019-nCoV to be 2.56 .", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak\nPassage: population; we would know who was infected and who was not , with high confidence. The reporting rate is the ratio of reported cases over the number of seropositive individuals. It was statistically evident that increasing in reporting was likely, and thus it should be considered in the future investigation of this outbreak." ]

[ [ "2a", "Title: Estimating the Unreported Number of Novel Coronavirus (2019-nCoV) Cases in China in the First Half of January 2020: A Data-Driven Modelling Analysis of the Early Outbreak" ], [ "2b", "Passage: Under-reporting was likely to have occurred and resulted in 469 unreported cases from 1 to 15 January 2020." ], [ "2c", "The reporting rate after 17 January 2020 was likely to have increased 21-fold compared with the situation from 1 to 17 January 2020 on average, and it should be considered in future investigation." ], [ "2d", "We estimated the R 0 at 2019-nCoV to be 2.56 ." ] ]

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

[ "Title: The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts\nPassage: When vaccines do not prevent infection or are not given, the last step in preventing morbidity and mortality in influenza is therapeutic treatment, of which antivirals are the current gold standard. The prevalence of antiviral drug resistance found in this and other studies is a warning that should not be ignored. Consistent with recent observations, all influenza viruses identified in this study were resistant to at least one class of antiviral. In this group of patients, 4% of viruses were resistant to both major classes of antivirals including some isolates of H3N2 and Apdm09. The majority of these viruses were", "Title: ICU-treated influenza A(H1N1) pdm09 infections more severe post pandemic than during 2009 pandemic: a retrospective analysis\nPassage: The benefits of antiviral treatment are controversial in the literature. A recent systematic analysis of influenza patients found only small benefits for either oseltamavir or zanamavir in the prophylaxis or treatment of influenza . However, they did not perform a subgroup analysis of neuraminidase inhibitor treatment of critically ill patients . Muthuri et al. reported that early versus later neuraminidase inhibitor treatment reduced the likelihood of mortality and the need for ventilator support in influenza patients with documented pneumonia . Our results, which suggest an association between early initiation of antiviral treatment and good outcome, support the active use of", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Chloroquine is effective against influenza A virus in vitro but not in vivo\nPassage: Despite the availability of effective antiviral drugs, 1 influenza causes 3-5 million severe illnesses and 250 000-500 000 deaths in the industrialized world annually. 2 There are two classes of drugs currently licensed for use against influenza. The adamantanes, amantadine and rimantadine, target the M2 ion channel, and the neuraminidase inhibitors target the viral sialidase. The adamantane class of drugs has limited effectiveness against currently circulating strains of influenza due to the emergence of resistance. 3 Resistance to the NAIs is not as widespread but is becoming a concern in populations where use is frequent 4 and in the treatment" ]

[ [ "0a", "Title: The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts" ], [ "0b", "Passage: When vaccines do not prevent infection or are not given, the last step in preventing morbidity and mortality in influenza is therapeutic treatment, of which antivirals are the current gold standard." ], [ "0c", "The prevalence of antiviral drug resistance found in this and other studies is a warning that should not be ignored." ], [ "0d", "Consistent with recent observations, all influenza viruses identified in this study were resistant to at least one class of antiviral." ], [ "0e", "In this group of patients, 4% of viruses were resistant to both major classes of antivirals including some isolates of H3N2 and Apdm09." ], [ "0f", "The majority of these viruses were" ] ]

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

[ "Title: The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts\nPassage: When vaccines do not prevent infection or are not given, the last step in preventing morbidity and mortality in influenza is therapeutic treatment, of which antivirals are the current gold standard. The prevalence of antiviral drug resistance found in this and other studies is a warning that should not be ignored. Consistent with recent observations, all influenza viruses identified in this study were resistant to at least one class of antiviral. In this group of patients, 4% of viruses were resistant to both major classes of antivirals including some isolates of H3N2 and Apdm09. The majority of these viruses were", "Title: ICU-treated influenza A(H1N1) pdm09 infections more severe post pandemic than during 2009 pandemic: a retrospective analysis\nPassage: The benefits of antiviral treatment are controversial in the literature. A recent systematic analysis of influenza patients found only small benefits for either oseltamavir or zanamavir in the prophylaxis or treatment of influenza . However, they did not perform a subgroup analysis of neuraminidase inhibitor treatment of critically ill patients . Muthuri et al. reported that early versus later neuraminidase inhibitor treatment reduced the likelihood of mortality and the need for ventilator support in influenza patients with documented pneumonia . Our results, which suggest an association between early initiation of antiviral treatment and good outcome, support the active use of", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Chloroquine is effective against influenza A virus in vitro but not in vivo\nPassage: Despite the availability of effective antiviral drugs, 1 influenza causes 3-5 million severe illnesses and 250 000-500 000 deaths in the industrialized world annually. 2 There are two classes of drugs currently licensed for use against influenza. The adamantanes, amantadine and rimantadine, target the M2 ion channel, and the neuraminidase inhibitors target the viral sialidase. The adamantane class of drugs has limited effectiveness against currently circulating strains of influenza due to the emergence of resistance. 3 Resistance to the NAIs is not as widespread but is becoming a concern in populations where use is frequent 4 and in the treatment" ]

[ [ "1a", "Title: ICU-treated influenza A(H1N1) pdm09 infections more severe post pandemic than during 2009 pandemic: a retrospective analysis" ], [ "1b", "Passage: The benefits of antiviral treatment are controversial in the literature." ], [ "1c", "A recent systematic analysis of influenza patients found only small benefits for either oseltamavir or zanamavir in the prophylaxis or treatment of influenza ." ], [ "1d", "However, they did not perform a subgroup analysis of neuraminidase inhibitor treatment of critically ill patients ." ], [ "1e", "Muthuri et al. reported that early versus later neuraminidase inhibitor treatment reduced the likelihood of mortality and the need for ventilator support in influenza patients with documented pneumonia ." ], [ "1f", "Our results, which suggest an association between early initiation of antiviral treatment and good outcome, support the active use of" ] ]

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

[ "Title: The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts\nPassage: When vaccines do not prevent infection or are not given, the last step in preventing morbidity and mortality in influenza is therapeutic treatment, of which antivirals are the current gold standard. The prevalence of antiviral drug resistance found in this and other studies is a warning that should not be ignored. Consistent with recent observations, all influenza viruses identified in this study were resistant to at least one class of antiviral. In this group of patients, 4% of viruses were resistant to both major classes of antivirals including some isolates of H3N2 and Apdm09. The majority of these viruses were", "Title: ICU-treated influenza A(H1N1) pdm09 infections more severe post pandemic than during 2009 pandemic: a retrospective analysis\nPassage: The benefits of antiviral treatment are controversial in the literature. A recent systematic analysis of influenza patients found only small benefits for either oseltamavir or zanamavir in the prophylaxis or treatment of influenza . However, they did not perform a subgroup analysis of neuraminidase inhibitor treatment of critically ill patients . Muthuri et al. reported that early versus later neuraminidase inhibitor treatment reduced the likelihood of mortality and the need for ventilator support in influenza patients with documented pneumonia . Our results, which suggest an association between early initiation of antiviral treatment and good outcome, support the active use of", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Chloroquine is effective against influenza A virus in vitro but not in vivo\nPassage: Despite the availability of effective antiviral drugs, 1 influenza causes 3-5 million severe illnesses and 250 000-500 000 deaths in the industrialized world annually. 2 There are two classes of drugs currently licensed for use against influenza. The adamantanes, amantadine and rimantadine, target the M2 ion channel, and the neuraminidase inhibitors target the viral sialidase. The adamantane class of drugs has limited effectiveness against currently circulating strains of influenza due to the emergence of resistance. 3 Resistance to the NAIs is not as widespread but is becoming a concern in populations where use is frequent 4 and in the treatment" ]

[ [ "2a", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment" ], [ "2b", "Passage: Treatment of severe influenza presents multiple challenges." ], [ "2c", "The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset ." ], [ "2d", "Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes ." ], [ "2e", "NAIs and baloxavir have activity against both influenza A and B viruses." ], [ "2f", "Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses." ], [ "2g", "Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated" ] ]

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

[ "Title: The Natural History of Influenza Infection in the Severely Immunocompromised vs Nonimmunocompromised Hosts\nPassage: When vaccines do not prevent infection or are not given, the last step in preventing morbidity and mortality in influenza is therapeutic treatment, of which antivirals are the current gold standard. The prevalence of antiviral drug resistance found in this and other studies is a warning that should not be ignored. Consistent with recent observations, all influenza viruses identified in this study were resistant to at least one class of antiviral. In this group of patients, 4% of viruses were resistant to both major classes of antivirals including some isolates of H3N2 and Apdm09. The majority of these viruses were", "Title: ICU-treated influenza A(H1N1) pdm09 infections more severe post pandemic than during 2009 pandemic: a retrospective analysis\nPassage: The benefits of antiviral treatment are controversial in the literature. A recent systematic analysis of influenza patients found only small benefits for either oseltamavir or zanamavir in the prophylaxis or treatment of influenza . However, they did not perform a subgroup analysis of neuraminidase inhibitor treatment of critically ill patients . Muthuri et al. reported that early versus later neuraminidase inhibitor treatment reduced the likelihood of mortality and the need for ventilator support in influenza patients with documented pneumonia . Our results, which suggest an association between early initiation of antiviral treatment and good outcome, support the active use of", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Chloroquine is effective against influenza A virus in vitro but not in vivo\nPassage: Despite the availability of effective antiviral drugs, 1 influenza causes 3-5 million severe illnesses and 250 000-500 000 deaths in the industrialized world annually. 2 There are two classes of drugs currently licensed for use against influenza. The adamantanes, amantadine and rimantadine, target the M2 ion channel, and the neuraminidase inhibitors target the viral sialidase. The adamantane class of drugs has limited effectiveness against currently circulating strains of influenza due to the emergence of resistance. 3 Resistance to the NAIs is not as widespread but is becoming a concern in populations where use is frequent 4 and in the treatment" ]

[ [ "3a", "Title: Chloroquine is effective against influenza A virus in vitro but not in vivo" ], [ "3b", "Passage: Despite the availability of effective antiviral drugs, 1 influenza causes 3-5 million severe illnesses and 250 000-500 000 deaths in the industrialized world annually." ], [ "3c", "2 There are two classes of drugs currently licensed for use against influenza." ], [ "3d", "The adamantanes, amantadine and rimantadine, target the M2 ion channel, and the neuraminidase inhibitors target the viral sialidase." ], [ "3e", "The adamantane class of drugs has limited effectiveness against currently circulating strains of influenza due to the emergence of resistance." ], [ "3f", "3 Resistance to the NAIs is not as widespread but is becoming a concern in populations where use is frequent 4 and in the treatment" ] ]

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

[ "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: Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article\nPassage: viruses were more frequently detected in spring and winter, and RSV was more common in autumn. The variation pattern of influenza viruses was generally consistent. However, our study showed that RSV was more common in winter and spring, which was different from that reported in Saraya's study. Their study was conducted in adult patients with asthma, which might be responsible for the difference. In another study conducted from the year 2002 to 2014 involving 5102 samples, RSV was most frequently detected from December to March, influenza viruses from November to March, and HRV from December to June. Yang et al's", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Analyses showed that some viruses are possibly seasonal and were circulating during a specific period of the year. They are detected only in summer for Human Metapneumovirus, RSV A and B, and influenza Apdm09. For the latter, it is specific to the studied period since the influenza Apdm09 virus reappeared in Réunion Island in October 2012 and was no longer circulating since late 2010. On the opposite, Parainfluenza 1,2 and 4 viruses were identified only in winter. For other pathogens, no specific period of detection was observed.", "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." ]

[ [ "0a", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity" ], [ "0b", "Passage: The only positive sample to HPIV2 was collected during winter." ], [ "0c", "HPIV1 and HPIV3 detection occurred mainly in late winter and spring." ], [ "0d", "Similar results were reported showing this virus presence in samples collected in spring, autumn and winter." ], [ "0e", "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." ] ]

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

[ "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: Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article\nPassage: viruses were more frequently detected in spring and winter, and RSV was more common in autumn. The variation pattern of influenza viruses was generally consistent. However, our study showed that RSV was more common in winter and spring, which was different from that reported in Saraya's study. Their study was conducted in adult patients with asthma, which might be responsible for the difference. In another study conducted from the year 2002 to 2014 involving 5102 samples, RSV was most frequently detected from December to March, influenza viruses from November to March, and HRV from December to June. Yang et al's", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Analyses showed that some viruses are possibly seasonal and were circulating during a specific period of the year. They are detected only in summer for Human Metapneumovirus, RSV A and B, and influenza Apdm09. For the latter, it is specific to the studied period since the influenza Apdm09 virus reappeared in Réunion Island in October 2012 and was no longer circulating since late 2010. On the opposite, Parainfluenza 1,2 and 4 viruses were identified only in winter. For other pathogens, no specific period of detection was observed.", "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." ]

[ [ "1a", "Title: Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article" ], [ "1b", "Passage: viruses were more frequently detected in spring and winter, and RSV was more common in autumn." ], [ "1c", "The variation pattern of influenza viruses was generally consistent." ], [ "1d", "However, our study showed that RSV was more common in winter and spring, which was different from that reported in Saraya's study." ], [ "1e", "Their study was conducted in adult patients with asthma, which might be responsible for the difference." ], [ "1f", "In another study conducted from the year 2002 to 2014 involving 5102 samples, RSV was most frequently detected from December to March, influenza viruses from November to March, and HRV from December to June." ], [ "1g", "Yang et al's" ] ]

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

[ "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: Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article\nPassage: viruses were more frequently detected in spring and winter, and RSV was more common in autumn. The variation pattern of influenza viruses was generally consistent. However, our study showed that RSV was more common in winter and spring, which was different from that reported in Saraya's study. Their study was conducted in adult patients with asthma, which might be responsible for the difference. In another study conducted from the year 2002 to 2014 involving 5102 samples, RSV was most frequently detected from December to March, influenza viruses from November to March, and HRV from December to June. Yang et al's", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Analyses showed that some viruses are possibly seasonal and were circulating during a specific period of the year. They are detected only in summer for Human Metapneumovirus, RSV A and B, and influenza Apdm09. For the latter, it is specific to the studied period since the influenza Apdm09 virus reappeared in Réunion Island in October 2012 and was no longer circulating since late 2010. On the opposite, Parainfluenza 1,2 and 4 viruses were identified only in winter. For other pathogens, no specific period of detection was observed.", "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." ]

[ [ "2a", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012" ], [ "2b", "Passage: Analyses showed that some viruses are possibly seasonal and were circulating during a specific period of the year." ], [ "2c", "They are detected only in summer for Human Metapneumovirus, RSV A and B, and influenza Apdm09." ], [ "2d", "For the latter, it is specific to the studied period since the influenza Apdm09 virus reappeared in Réunion Island in October 2012 and was no longer circulating since late 2010." ], [ "2e", "On the opposite, Parainfluenza 1,2 and 4 viruses were identified only in winter." ], [ "2f", "For other pathogens, no specific period of detection was observed." ] ]

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

[ "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: Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article\nPassage: viruses were more frequently detected in spring and winter, and RSV was more common in autumn. The variation pattern of influenza viruses was generally consistent. However, our study showed that RSV was more common in winter and spring, which was different from that reported in Saraya's study. Their study was conducted in adult patients with asthma, which might be responsible for the difference. In another study conducted from the year 2002 to 2014 involving 5102 samples, RSV was most frequently detected from December to March, influenza viruses from November to March, and HRV from December to June. Yang et al's", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Analyses showed that some viruses are possibly seasonal and were circulating during a specific period of the year. They are detected only in summer for Human Metapneumovirus, RSV A and B, and influenza Apdm09. For the latter, it is specific to the studied period since the influenza Apdm09 virus reappeared in Réunion Island in October 2012 and was no longer circulating since late 2010. On the opposite, Parainfluenza 1,2 and 4 viruses were identified only in winter. For other pathogens, no specific period of detection was observed.", "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." ]

[ [ "3a", "Title: Seasonality of viral respiratory infections in southeast of Brazil: the influence of temperature and air humidity" ], [ "3b", "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." ] ]

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

[ "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: Text: An outbreak of novel coronavirus disease has occurred on a cruise ship, the Diamond Princess . The primary case remains unknown, but the index case, defined as the first identified case, is a passenger who started coughing from 19 January 2020 on board, disembarking the ship in Hong Kong on 25 January. As the case was diagnosed on 1 February, the ship was requested to remain in the ocean near Yokohama from 3 February onwards. Subsequently, the movement of all passengers was restricted on board from 5 February, for a matter of 14 days of quarantine. Out of a", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: A large outbreak of COVID-19 occurred on a cruise ship. Estimating the incidence, the peak time of infection was shown to have been from 2 to 4 February, and the incidence abruptly declined afterwards. The estimated number of new infections among passengers without close contact was very small from 5 February, on which the movement restriction policy was imposed, and at most there was, on average, one case of infection per day from 8 to 10 February. Other than continued exposure among crew members, the estimated incidence in this study indicates that the movement restriction policy from 5 February 2020", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: total of 3711 persons , 199 symptomatic cases have been diagnosed on board as of 24 February, and additional asymptomatic infections and symptomatic cases after disembarkation have also been reported.", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: Date: 2020" ]

[ [ "0a", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess" ], [ "0b", "Passage: Text: An outbreak of novel coronavirus disease has occurred on a cruise ship, the Diamond Princess ." ], [ "0c", "The primary case remains unknown, but the index case, defined as the first identified case, is a passenger who started coughing from 19 January 2020 on board, disembarking the ship in Hong Kong on 25 January." ], [ "0d", "As the case was diagnosed on 1 February, the ship was requested to remain in the ocean near Yokohama from 3 February onwards." ], [ "0e", "Subsequently, the movement of all passengers was restricted on board from 5 February, for a matter of 14 days of quarantine." ], [ "0f", "Out of a" ] ]

[ "0d" ]

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver. Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone . Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention . Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens . Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is bound to plasma alpha-2 macroglobulin . Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain. Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine. In addition, a part of hepcidin is cleansed through degradation along with ferritin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is effective on iron transfer from macrophages. In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell. In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron. After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: the regulation of iron hemostasis. This peptide prevents iron absorption from the small intestine and releases iron from reticuloendothelial cells. In infectious diseases, macrophages and bacteria compete to absorb iron . Macrophages interfere with the absorption of iron by bacteria. Eventually, the pathogen does not grow and replenish. Factors that cause hepcidin production are increased in bone marrow and anemia. Other factors that increase the production of hepcidin are iron accumulation and inflammation ." ]

[ [ "0a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "0b", "Passage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver." ], [ "0c", "Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone ." ], [ "0d", "Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention ." ], [ "0e", "Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens ." ], [ "0f", "Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via" ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver. Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone . Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention . Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens . Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is bound to plasma alpha-2 macroglobulin . Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain. Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine. In addition, a part of hepcidin is cleansed through degradation along with ferritin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is effective on iron transfer from macrophages. In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell. In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron. After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: the regulation of iron hemostasis. This peptide prevents iron absorption from the small intestine and releases iron from reticuloendothelial cells. In infectious diseases, macrophages and bacteria compete to absorb iron . Macrophages interfere with the absorption of iron by bacteria. Eventually, the pathogen does not grow and replenish. Factors that cause hepcidin production are increased in bone marrow and anemia. Other factors that increase the production of hepcidin are iron accumulation and inflammation ." ]

[ [ "1a", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells" ], [ "1b", "Passage: Hepcidin is bound to plasma alpha-2 macroglobulin ." ], [ "1c", "Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain." ], [ "1d", "Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine." ], [ "1e", "In addition, a part of hepcidin is cleansed through degradation along with ferritin ." ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver. Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone . Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention . Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens . Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is bound to plasma alpha-2 macroglobulin . Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain. Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine. In addition, a part of hepcidin is cleansed through degradation along with ferritin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is effective on iron transfer from macrophages. In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell. In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron. After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: the regulation of iron hemostasis. This peptide prevents iron absorption from the small intestine and releases iron from reticuloendothelial cells. In infectious diseases, macrophages and bacteria compete to absorb iron . Macrophages interfere with the absorption of iron by bacteria. Eventually, the pathogen does not grow and replenish. Factors that cause hepcidin production are increased in bone marrow and anemia. Other factors that increase the production of hepcidin are iron accumulation and inflammation ." ]

[ [ "2a", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells" ], [ "2b", "Passage: Hepcidin is effective on iron transfer from macrophages." ], [ "2c", "In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell." ], [ "2d", "In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron." ], [ "2e", "After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin ." ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver. Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone . Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention . Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens . Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is bound to plasma alpha-2 macroglobulin . Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain. Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine. In addition, a part of hepcidin is cleansed through degradation along with ferritin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is effective on iron transfer from macrophages. In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell. In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron. After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin .", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: the regulation of iron hemostasis. This peptide prevents iron absorption from the small intestine and releases iron from reticuloendothelial cells. In infectious diseases, macrophages and bacteria compete to absorb iron . Macrophages interfere with the absorption of iron by bacteria. Eventually, the pathogen does not grow and replenish. Factors that cause hepcidin production are increased in bone marrow and anemia. Other factors that increase the production of hepcidin are iron accumulation and inflammation ." ]

[ [ "3a", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells" ], [ "3b", "Passage: the regulation of iron hemostasis." ], [ "3c", "This peptide prevents iron absorption from the small intestine and releases iron from reticuloendothelial cells." ], [ "3d", "In infectious diseases, macrophages and bacteria compete to absorb iron ." ], [ "3e", "Macrophages interfere with the absorption of iron by bacteria." ], [ "3f", "Eventually, the pathogen does not grow and replenish." ], [ "3g", "Factors that cause hepcidin production are increased in bone marrow and anemia." ], [ "3h", "Other factors that increase the production of hepcidin are iron accumulation and inflammation ." ] ]

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

[ "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression\nPassage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation. This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis . Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease . Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far,", "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression\nPassage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation. This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis . Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease . Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far,", "Title: Contact pathway of coagulation and inflammation\nPassage: human factor XII to this plasma restored the increase in VIIc. In FIX-deficient or FXI-deficient plasma, the stearateinduced increase in VIIc was greatly reduced, indicating that in the presence of contact surface the activation of contact system results in the activation of FVII . In another in vitro study in which a FXI-dependent effect on clot formation initiated by tissue factor, FXI increased prothrombin activation and the fibrin formation rate, revealing a role for factor XI in the propagation of clot growth after tissue factor-dependent initiation .", "Title: Contact pathway of coagulation and inflammation\nPassage: in the downregulation of fibrinolysis . In consistence with this hypothesis, systemic incorporation of anti-factor XI antibodies resulted in an almost twofold increase in endogenous fibrinolysis compared with a control antibody, indicating a novel role for the intrinsic pathway of coagulation . In a static in-vitro coagulation model in which clotting is initiated in recalcified citrated plasma by tissue factor coated on the bottom of microtiter plates, when larger clots were formed, FXI not only increased prothrombin activation and the fibrin formation rate but also inhibited fibrinolysis. Thus, in addition to enhancement of tissue factor-initiated coagulation, FXI inhibits fibrinolysis to" ]

[ [ "0a", "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression" ], [ "0b", "Passage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation." ], [ "0c", "This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis ." ], [ "0d", "Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease ." ], [ "0e", "Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far," ] ]

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

[ "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression\nPassage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation. This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis . Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease . Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far,", "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression\nPassage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation. This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis . Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease . Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far,", "Title: Contact pathway of coagulation and inflammation\nPassage: human factor XII to this plasma restored the increase in VIIc. In FIX-deficient or FXI-deficient plasma, the stearateinduced increase in VIIc was greatly reduced, indicating that in the presence of contact surface the activation of contact system results in the activation of FVII . In another in vitro study in which a FXI-dependent effect on clot formation initiated by tissue factor, FXI increased prothrombin activation and the fibrin formation rate, revealing a role for factor XI in the propagation of clot growth after tissue factor-dependent initiation .", "Title: Contact pathway of coagulation and inflammation\nPassage: in the downregulation of fibrinolysis . In consistence with this hypothesis, systemic incorporation of anti-factor XI antibodies resulted in an almost twofold increase in endogenous fibrinolysis compared with a control antibody, indicating a novel role for the intrinsic pathway of coagulation . In a static in-vitro coagulation model in which clotting is initiated in recalcified citrated plasma by tissue factor coated on the bottom of microtiter plates, when larger clots were formed, FXI not only increased prothrombin activation and the fibrin formation rate but also inhibited fibrinolysis. Thus, in addition to enhancement of tissue factor-initiated coagulation, FXI inhibits fibrinolysis to" ]

[ [ "1a", "Title: Clara Cell 10 kDa Protein Alleviates Murine Hepatitis Virus Strain 3-Induced Fulminant Hepatitis by Inhibiting Fibrinogen-Like Protein 2 Expression" ], [ "1b", "Passage: Prothrombinase Fgl2 belongs to the fibrinogen superfamily and is produced by activated macrophages or endothelial cells, transforming prothrombin directly into thrombin, so as to quickly initiate the process of coagulation." ], [ "1c", "This promotes the conversion of fibrinogen into fibrin, resulting in thrombosis ." ], [ "1d", "Our study found that Fgl2 was highly expressed in peripheral blood mononuclear cells and in liver tissue of humans or mice with severe viral hepatitis, and was positively related to the severity of the disease ." ], [ "1e", "Gene therapy targeting Fgl2 silencing showed that the survival rate of fulminant hepatitis mice increased from 0 to 33.3% . Thus far," ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: 2 Results", "Title: Outcomes of Influenza A(H1N1)pdm09 Virus Infection: Results from Two International Cohort Studies\nPassage: FLU003.", "Title: Outcome of paediatric intensive care survivors\nPassage: and, therefore, strong conclusive statements difficult.", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: There were four potential limitations to our study. First, we only conducted a cross-sectional study in Study 3, whereas it would be preferable to measure Chikui likelihood earlier and then track the material and mental benefit of our participants years later. In the absence of a longitudinal study, our findings are suggestive but do not prove causality, and the following two questions therefore remain unaddressed: we are unable to confirm whether the correlation found in Study 2 means that it is the belief that boosts both financial and psychological well-being, rather than the reverse . Only a longitudinal study can" ]

[ [ "0a", "Title: Estimating the number of infections and the impact of non-" ], [ "0b", "Passage: 2 Results" ] ]

[ "0b", "3d" ]

[ "Title: Estimating the number of infections and the impact of non-\nPassage: 2 Results", "Title: Outcomes of Influenza A(H1N1)pdm09 Virus Infection: Results from Two International Cohort Studies\nPassage: FLU003.", "Title: Outcome of paediatric intensive care survivors\nPassage: and, therefore, strong conclusive statements difficult.", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: There were four potential limitations to our study. First, we only conducted a cross-sectional study in Study 3, whereas it would be preferable to measure Chikui likelihood earlier and then track the material and mental benefit of our participants years later. In the absence of a longitudinal study, our findings are suggestive but do not prove causality, and the following two questions therefore remain unaddressed: we are unable to confirm whether the correlation found in Study 2 means that it is the belief that boosts both financial and psychological well-being, rather than the reverse . Only a longitudinal study can" ]

[ [ "3a", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?" ], [ "3b", "Passage: There were four potential limitations to our study." ], [ "3c", "First, we only conducted a cross-sectional study in Study 3, whereas it would be preferable to measure Chikui likelihood earlier and then track the material and mental benefit of our participants years later." ], [ "3d", "In the absence of a longitudinal study, our findings are suggestive but do not prove causality, and the following two questions therefore remain unaddressed: we are unable to confirm whether the correlation found in Study 2 means that it is the belief that boosts both financial and psychological well-being, rather than the reverse ." ], [ "3e", "Only a longitudinal study can" ] ]

[ "0b", "3d" ]

[ "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of" ]

[ [ "0a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "0b", "Passage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems." ], [ "0c", "Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells." ], [ "0d", "When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to" ] ]

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

[ "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of" ]

[ [ "1a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "1b", "Passage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems." ], [ "1c", "Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells." ], [ "1d", "When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to" ] ]

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

[ "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of" ]

[ [ "2a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "2b", "Passage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells ." ], [ "2c", "In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated ." ], [ "2d", "Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L ." ], [ "2e", "Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L ." ], [ "2f", "When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used ." ], [ "2g", "CD11c was down regulated in both median flouresence intensity and the percentage of" ] ]

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

[ "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: It has been shown that upon interacting with its receptor, CD40, CD40L induces profound effects on T cells, DCs, B cells, endothelial cells, as well as many cells of the hematopoietic and non-hematopoietic systems. Moreover, when CD40L engages CD40 on the surface of DCs, it promotes cytokine production, the induction of cell surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells , enabling DCs to mature and effectively induce the activation and differentiation of T cells. When CD40L engages CD40 on the surface of B cells, it promotes germinal center formation, immunoglobulin isotype switching, somatic hypermutation to", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells . In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated . Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L . Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L . When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used . CD11c was down regulated in both median flouresence intensity and the percentage of" ]

[ [ "3a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "3b", "Passage: surface co-stimulatory molecules, and facilitates the cross-presentation of antigen by these cells ." ], [ "3c", "In addition, CD11c is a DC integrin marker and upon stimulation, is down-regulated ." ], [ "3d", "Intracellular adhesion marker CD54, along with co-stimulatory markers CD40, CD80, and CD86 are all upregulated upon stimulation with CD40L ." ], [ "3e", "Moreover, mouse I-A d major histocompatibility complex is also up-regulated upon stimulation with CD40L ." ], [ "3f", "When our recombinant crCD40L was used to stimulate immature murine bone marrow DCs, we observed similar results to that when murine CD40L is used ." ], [ "3g", "CD11c was down regulated in both median flouresence intensity and the percentage of" ] ]

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

[ "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: For the 143 HMPV genomes, we checked sequence conservation at transcriptional control regions, at the termini of each gene, as well as the lengths of intergenic sequences between gene boundaries. The length of the F-M2 intergenic region was different between group A and B viruses, that is, 13 nt and 2 nt, respectively. The SH-G and G-L intergenic regions were the longest, up to 125 nt and to 190 nt, respectively. Consensus nucleotides at the putative start and end regions flanking the ORF of the viral genes are shown in Fig. 1 . The gene-start and -end regions of N", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: For the 143 HMPV genomes, we checked sequence conservation at transcriptional control regions, at the termini of each gene, as well as the lengths of intergenic sequences between gene boundaries. The length of the F-M2 intergenic region was different between group A and B viruses, that is, 13 nt and 2 nt, respectively. The SH-G and G-L intergenic regions were the longest, up to 125 nt and to 190 nt, respectively. Consensus nucleotides at the putative start and end regions flanking the ORF of the viral genes are shown in Fig. 1 . The gene-start and -end regions of N", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions. The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%. Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B. Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity.", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions. The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%. Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B. Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity." ]

[ [ "2a", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia" ], [ "2b", "Passage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions." ], [ "2c", "The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%." ], [ "2d", "Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B." ], [ "2e", "Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity." ] ]

[ "2b", "3b" ]

[ "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: For the 143 HMPV genomes, we checked sequence conservation at transcriptional control regions, at the termini of each gene, as well as the lengths of intergenic sequences between gene boundaries. The length of the F-M2 intergenic region was different between group A and B viruses, that is, 13 nt and 2 nt, respectively. The SH-G and G-L intergenic regions were the longest, up to 125 nt and to 190 nt, respectively. Consensus nucleotides at the putative start and end regions flanking the ORF of the viral genes are shown in Fig. 1 . The gene-start and -end regions of N", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: For the 143 HMPV genomes, we checked sequence conservation at transcriptional control regions, at the termini of each gene, as well as the lengths of intergenic sequences between gene boundaries. The length of the F-M2 intergenic region was different between group A and B viruses, that is, 13 nt and 2 nt, respectively. The SH-G and G-L intergenic regions were the longest, up to 125 nt and to 190 nt, respectively. Consensus nucleotides at the putative start and end regions flanking the ORF of the viral genes are shown in Fig. 1 . The gene-start and -end regions of N", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions. The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%. Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B. Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity.", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia\nPassage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions. The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%. Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B. Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity." ]

[ [ "3a", "Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia" ], [ "3b", "Passage: Sequence annotation of the full-length genomes using Geneious R8.1.5 identified the expected eight coding ORFs and non-coding genomic regions." ], [ "3c", "The overall nucleotide identity between all 143 genome sequences analyzed was 58.2%." ], [ "3d", "Nucleotide sequence identity was 71.3% within HMPV-A and 80% within HMPV-B." ], [ "3e", "Intrasubgroup, A1, A2, B1 and B2 genomes shared 92.1% , 76.8% , 91% and 89.6% amino acid sequence identity." ] ]

[ "2b", "3b" ]

[ "Title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico\nPassage: Fifty randomly selected cases were asked to participate in the study from which 42 accepted participation. All approached controls agreed to participate. In total 126 individuals were recruited. Our drop-out rate was lower than 1% since one participant did not finish the follow-up due to the loss of the assigned GPS logger. Table 1 describes the main characteristics of the subjects in each group. No statistically significant differences were observed in most of variables except in age, since cases were significantly younger than the intradomestic or population controls .", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: We originally hoped to study T-cell cross-protection that might reduce symptom severity, but we also measured a variety of other parameters of pre-existing immunity . For statistical comparison of so many variables, we performed exploratory principal component and discriminant analyses. These analyses did not reveal any significant relationships of antibody or T-cell parameters at baseline with occurrence of pH1N1 infection or with symptom severity.", "Title: The Trojan Chicken Study, Minnesota\nPassage: This study was reviewed and approved by the University of Iowa's Institutional Review Board and Animal Use and Care Committee. The investigators participated in online human and animal subjects training. Informed consent was sought from participants before they were enrolled.", "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening." ]

[ [ "0a", "Title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico" ], [ "0b", "Passage: Fifty randomly selected cases were asked to participate in the study from which 42 accepted participation." ], [ "0c", "All approached controls agreed to participate." ], [ "0d", "In total 126 individuals were recruited." ], [ "0e", "Our drop-out rate was lower than 1% since one participant did not finish the follow-up due to the loss of the assigned GPS logger." ], [ "0f", "Table 1 describes the main characteristics of the subjects in each group." ], [ "0g", "No statistically significant differences were observed in most of variables except in age, since cases were significantly younger than the intradomestic or population controls ." ] ]

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

[ "Title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico\nPassage: Fifty randomly selected cases were asked to participate in the study from which 42 accepted participation. All approached controls agreed to participate. In total 126 individuals were recruited. Our drop-out rate was lower than 1% since one participant did not finish the follow-up due to the loss of the assigned GPS logger. Table 1 describes the main characteristics of the subjects in each group. No statistically significant differences were observed in most of variables except in age, since cases were significantly younger than the intradomestic or population controls .", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: We originally hoped to study T-cell cross-protection that might reduce symptom severity, but we also measured a variety of other parameters of pre-existing immunity . For statistical comparison of so many variables, we performed exploratory principal component and discriminant analyses. These analyses did not reveal any significant relationships of antibody or T-cell parameters at baseline with occurrence of pH1N1 infection or with symptom severity.", "Title: The Trojan Chicken Study, Minnesota\nPassage: This study was reviewed and approved by the University of Iowa's Institutional Review Board and Animal Use and Care Committee. The investigators participated in online human and animal subjects training. Informed consent was sought from participants before they were enrolled.", "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening." ]

[ [ "1a", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic" ], [ "1b", "Passage: We originally hoped to study T-cell cross-protection that might reduce symptom severity, but we also measured a variety of other parameters of pre-existing immunity ." ], [ "1c", "For statistical comparison of so many variables, we performed exploratory principal component and discriminant analyses." ], [ "1d", "These analyses did not reveal any significant relationships of antibody or T-cell parameters at baseline with occurrence of pH1N1 infection or with symptom severity." ] ]

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