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[ "Title: CDC Summary 21 MAR 2020,\nPassage: Highlights of CDC’s Response", "Title: CDC Summary 21 MAR 2020,\nPassage: Risk of exposure:", "Title: CDC Summary 21 MAR 2020,\nPassage: Updated March 21, 2020", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 Pandemic" ]

[ [ "0a", "Title: CDC Summary 21 MAR 2020," ], [ "0b", "Passage: Highlights of CDC’s Response" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: Highlights of CDC’s Response", "Title: CDC Summary 21 MAR 2020,\nPassage: Risk of exposure:", "Title: CDC Summary 21 MAR 2020,\nPassage: Updated March 21, 2020", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 Pandemic" ]

[ [ "1a", "Title: CDC Summary 21 MAR 2020," ], [ "1b", "Passage: Risk of exposure:" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: Highlights of CDC’s Response", "Title: CDC Summary 21 MAR 2020,\nPassage: Risk of exposure:", "Title: CDC Summary 21 MAR 2020,\nPassage: Updated March 21, 2020", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 Pandemic" ]

[ [ "2a", "Title: CDC Summary 21 MAR 2020," ], [ "2b", "Passage: Updated March 21, 2020" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: Highlights of CDC’s Response", "Title: CDC Summary 21 MAR 2020,\nPassage: Risk of exposure:", "Title: CDC Summary 21 MAR 2020,\nPassage: Updated March 21, 2020", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 Pandemic" ]

[ [ "3a", "Title: CDC Summary 21 MAR 2020," ], [ "3b", "Passage: COVID-19 Pandemic" ] ]

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

[ "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: estimation years. All of the sequences belonging to one particular lineage for each segment were used for regression analysis.", "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: The H3 Hb Thai isolates were estimated to have derived from a hypothetical common ancestor in 1976, which had acquired an H3 HA gene from a human-like H3N2 swine strain circulating in the early 1970s. Similar evolutional pattern was observed in the N2 tree . N2 gene of the H1N2 isolate, Sara13021, which HA gene was of classical swine origin, also belonged to the cluster Hb. The branch points of common ancestors for those clusters of N2 genes were estimated to be 1998 for Ha and 1976 for Hb respectively.", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study\nPassage: N2 viruses had circulated the previous years some degree of herd immunity against the new strain was expected. The H1N2 viruses were not associated with severe influenza illness that season. In 2002, a new lineage A/Fujian/411/02-like emerged in Asia and caused significant outbreaks on every continent .", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: The current outbreak of swine infl uenza that originated in Mexico in March 2009 has spread to more than 80 countries causing more than 3,99,232 laboratory confi rmed cases of pandemic infl uenza H1N1 globally and over 4735 deaths reported to World Health Organization as of 11 October 2009 . The WHO declared pandemic alert stage 6 on 11 June 2009, indicating an ongoing infl uenza pandemic . The 2009 swine fl u virus designated H1N1 A/swine/California/04/2009 is not zoonotic swine fl u and is not transmitted from pigs to humans, but rather from person to person and has higher" ]

[ [ "0a", "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand" ], [ "0b", "Passage: estimation years." ], [ "0c", "All of the sequences belonging to one particular lineage for each segment were used for regression analysis." ] ]

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

[ "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: estimation years. All of the sequences belonging to one particular lineage for each segment were used for regression analysis.", "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: The H3 Hb Thai isolates were estimated to have derived from a hypothetical common ancestor in 1976, which had acquired an H3 HA gene from a human-like H3N2 swine strain circulating in the early 1970s. Similar evolutional pattern was observed in the N2 tree . N2 gene of the H1N2 isolate, Sara13021, which HA gene was of classical swine origin, also belonged to the cluster Hb. The branch points of common ancestors for those clusters of N2 genes were estimated to be 1998 for Ha and 1976 for Hb respectively.", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study\nPassage: N2 viruses had circulated the previous years some degree of herd immunity against the new strain was expected. The H1N2 viruses were not associated with severe influenza illness that season. In 2002, a new lineage A/Fujian/411/02-like emerged in Asia and caused significant outbreaks on every continent .", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: The current outbreak of swine infl uenza that originated in Mexico in March 2009 has spread to more than 80 countries causing more than 3,99,232 laboratory confi rmed cases of pandemic infl uenza H1N1 globally and over 4735 deaths reported to World Health Organization as of 11 October 2009 . The WHO declared pandemic alert stage 6 on 11 June 2009, indicating an ongoing infl uenza pandemic . The 2009 swine fl u virus designated H1N1 A/swine/California/04/2009 is not zoonotic swine fl u and is not transmitted from pigs to humans, but rather from person to person and has higher" ]

[ [ "1a", "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand" ], [ "1b", "Passage: The H3 Hb Thai isolates were estimated to have derived from a hypothetical common ancestor in 1976, which had acquired an H3 HA gene from a human-like H3N2 swine strain circulating in the early 1970s." ], [ "1c", "Similar evolutional pattern was observed in the N2 tree ." ], [ "1d", "N2 gene of the H1N2 isolate, Sara13021, which HA gene was of classical swine origin, also belonged to the cluster Hb." ], [ "1e", "The branch points of common ancestors for those clusters of N2 genes were estimated to be 1998 for Ha and 1976 for Hb respectively." ] ]

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

[ "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: estimation years. All of the sequences belonging to one particular lineage for each segment were used for regression analysis.", "Title: Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand\nPassage: The H3 Hb Thai isolates were estimated to have derived from a hypothetical common ancestor in 1976, which had acquired an H3 HA gene from a human-like H3N2 swine strain circulating in the early 1970s. Similar evolutional pattern was observed in the N2 tree . N2 gene of the H1N2 isolate, Sara13021, which HA gene was of classical swine origin, also belonged to the cluster Hb. The branch points of common ancestors for those clusters of N2 genes were estimated to be 1998 for Ha and 1976 for Hb respectively.", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study\nPassage: N2 viruses had circulated the previous years some degree of herd immunity against the new strain was expected. The H1N2 viruses were not associated with severe influenza illness that season. In 2002, a new lineage A/Fujian/411/02-like emerged in Asia and caused significant outbreaks on every continent .", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: The current outbreak of swine infl uenza that originated in Mexico in March 2009 has spread to more than 80 countries causing more than 3,99,232 laboratory confi rmed cases of pandemic infl uenza H1N1 globally and over 4735 deaths reported to World Health Organization as of 11 October 2009 . The WHO declared pandemic alert stage 6 on 11 June 2009, indicating an ongoing infl uenza pandemic . The 2009 swine fl u virus designated H1N1 A/swine/California/04/2009 is not zoonotic swine fl u and is not transmitted from pigs to humans, but rather from person to person and has higher" ]

[ [ "2a", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study" ], [ "2b", "Passage: N2 viruses had circulated the previous years some degree of herd immunity against the new strain was expected." ], [ "2c", "The H1N2 viruses were not associated with severe influenza illness that season." ], [ "2d", "In 2002, a new lineage A/Fujian/411/02-like emerged in Asia and caused significant outbreaks on every continent ." ] ]

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

[ "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: Compared to the original search volume, which used 21 cities without sampling, the revised index represents the output of the combination of cities with the high-quality search volume and valuable information obtained from historical cases. Thus, the revised index can predict HFMD cases more reliably.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: In order to analyze the spatial distributions of different types of keywords across the province, the total search volume for each type of keyword was first determined at the city level. The results show that the search volumes of each type of keyword have a similar spatial distribution across the entire province. Cities suffering from more HFMD cases had a higher search volume for all types of keywords , while cities showing fewer HFMD cases had a lower search volume for all types of keywords. General keywords had a much higher search volume than keywords related to treatment and prevention.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: was found to be 0.8, but 10 cities showed a correlation of close to or larger than 0.8. When these cities were selected as sample cities to estimate the total search volume for the entire province via B-SHADE, the correlation improved from 0.8 to 0.864. Thus, the revised search volume was found to be more similar to the real cases.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: revised search volume to examine the predictive effects of the revised search volume." ]

[ [ "0a", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data" ], [ "0b", "Passage: Compared to the original search volume, which used 21 cities without sampling, the revised index represents the output of the combination of cities with the high-quality search volume and valuable information obtained from historical cases." ], [ "0c", "Thus, the revised index can predict HFMD cases more reliably." ] ]

[ "0c", "2d" ]

[ "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: Compared to the original search volume, which used 21 cities without sampling, the revised index represents the output of the combination of cities with the high-quality search volume and valuable information obtained from historical cases. Thus, the revised index can predict HFMD cases more reliably.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: In order to analyze the spatial distributions of different types of keywords across the province, the total search volume for each type of keyword was first determined at the city level. The results show that the search volumes of each type of keyword have a similar spatial distribution across the entire province. Cities suffering from more HFMD cases had a higher search volume for all types of keywords , while cities showing fewer HFMD cases had a lower search volume for all types of keywords. General keywords had a much higher search volume than keywords related to treatment and prevention.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: was found to be 0.8, but 10 cities showed a correlation of close to or larger than 0.8. When these cities were selected as sample cities to estimate the total search volume for the entire province via B-SHADE, the correlation improved from 0.8 to 0.864. Thus, the revised search volume was found to be more similar to the real cases.", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data\nPassage: revised search volume to examine the predictive effects of the revised search volume." ]

[ [ "2a", "Title: Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data" ], [ "2b", "Passage: was found to be 0.8, but 10 cities showed a correlation of close to or larger than 0.8." ], [ "2c", "When these cities were selected as sample cities to estimate the total search volume for the entire province via B-SHADE, the correlation improved from 0.8 to 0.864." ], [ "2d", "Thus, the revised search volume was found to be more similar to the real cases." ] ]

[ "0c", "2d" ]

[ "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Disease ecology and the global emergence of zoonotic pathogens\nPassage: It follows that for intervention to be globally effective, in addition to rebuilding public health infrastructure based on the comprehensive view of infectious disease ecology presented here, at least three elements are required:", "Title: Emerging zoonotic diseases: An opportunity to apply the concepts of nidality and one-medicine\nPassage: There is an overall lack of knowledge regarding the natural history and ecology of these zoonotic organisms . There is an abysmal lack of understanding among the general public and media of the natural occurrence of many biological organisms in the agricultural and animal industry setting as well as in free-ranging animal populations. The natural history, normal ecology, and epidemiology of potential agents of bioterrorism provide scenarios for explaining risk to the human population at large. Understanding the natural history of these organisms and their role in agriculture and free-ranging animal populations provides a context for health care providers to" ]

[ [ "0a", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats" ], [ "0b", "Passage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020." ], [ "0c", "Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'." ], [ "0d", "When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics." ], [ "0e", "These investigators and others suggest that surveillance efforts can be rationally focused both geographically" ] ]

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

[ "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Disease ecology and the global emergence of zoonotic pathogens\nPassage: It follows that for intervention to be globally effective, in addition to rebuilding public health infrastructure based on the comprehensive view of infectious disease ecology presented here, at least three elements are required:", "Title: Emerging zoonotic diseases: An opportunity to apply the concepts of nidality and one-medicine\nPassage: There is an overall lack of knowledge regarding the natural history and ecology of these zoonotic organisms . There is an abysmal lack of understanding among the general public and media of the natural occurrence of many biological organisms in the agricultural and animal industry setting as well as in free-ranging animal populations. The natural history, normal ecology, and epidemiology of potential agents of bioterrorism provide scenarios for explaining risk to the human population at large. Understanding the natural history of these organisms and their role in agriculture and free-ranging animal populations provides a context for health care providers to" ]

[ [ "1a", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats" ], [ "1b", "Passage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020." ], [ "1c", "Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'." ], [ "1d", "When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics." ], [ "1e", "These investigators and others suggest that surveillance efforts can be rationally focused both geographically" ] ]

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

[ "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Historical reviews Brown et al., 2008a; Jones et al., 2008) of emerging infectious disease events have shown that most are of zoonotic origin, among zoonotic EID events, most originated in wildlife and an estimated 10-40 new human viruses are expected to emerge by 2020. Jones et al. found that 'Wildlife host species richness is a significant predictor for the emergence of zoonotic EIDs with a wildlife origin'. When plotted on a global map, the areas at greatest risk for zoonotic pathogen emergence were the equatorial tropics. These investigators and others suggest that surveillance efforts can be rationally focused both geographically", "Title: Disease ecology and the global emergence of zoonotic pathogens\nPassage: It follows that for intervention to be globally effective, in addition to rebuilding public health infrastructure based on the comprehensive view of infectious disease ecology presented here, at least three elements are required:", "Title: Emerging zoonotic diseases: An opportunity to apply the concepts of nidality and one-medicine\nPassage: There is an overall lack of knowledge regarding the natural history and ecology of these zoonotic organisms . There is an abysmal lack of understanding among the general public and media of the natural occurrence of many biological organisms in the agricultural and animal industry setting as well as in free-ranging animal populations. The natural history, normal ecology, and epidemiology of potential agents of bioterrorism provide scenarios for explaining risk to the human population at large. Understanding the natural history of these organisms and their role in agriculture and free-ranging animal populations provides a context for health care providers to" ]

[ [ "3a", "Title: Emerging zoonotic diseases: An opportunity to apply the concepts of nidality and one-medicine" ], [ "3b", "Passage: There is an overall lack of knowledge regarding the natural history and ecology of these zoonotic organisms ." ], [ "3c", "There is an abysmal lack of understanding among the general public and media of the natural occurrence of many biological organisms in the agricultural and animal industry setting as well as in free-ranging animal populations." ], [ "3d", "The natural history, normal ecology, and epidemiology of potential agents of bioterrorism provide scenarios for explaining risk to the human population at large." ], [ "3e", "Understanding the natural history of these organisms and their role in agriculture and free-ranging animal populations provides a context for health care providers to" ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: setting activity and study objectives.", "Title: A Simulation Optimization Approach to Epidemic Forecasting\nPassage: study comparing the effects of different objective functions would be beneficial.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ]

[ [ "0a", "Title: Setting healthcare priorities in hospitals: a review of empirical studies" ], [ "0b", "Passage: setting activity and study objectives." ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: setting activity and study objectives.", "Title: A Simulation Optimization Approach to Epidemic Forecasting\nPassage: study comparing the effects of different objective functions would be beneficial.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ]

[ [ "1a", "Title: A Simulation Optimization Approach to Epidemic Forecasting" ], [ "1b", "Passage: study comparing the effects of different objective functions would be beneficial." ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: setting activity and study objectives.", "Title: A Simulation Optimization Approach to Epidemic Forecasting\nPassage: study comparing the effects of different objective functions would be beneficial.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ]

[ [ "2a", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households" ], [ "2b", "Passage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level." ], [ "2c", "Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions." ] ]

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

[ "Title: Setting healthcare priorities in hospitals: a review of empirical studies\nPassage: setting activity and study objectives.", "Title: A Simulation Optimization Approach to Epidemic Forecasting\nPassage: study comparing the effects of different objective functions would be beneficial.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ]

[ [ "3a", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study" ], [ "3b", "Passage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns." ], [ "3c", "The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ] ]

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

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: The emergence of a significant respiratory illness linked to a novel coronavirus represents a test of the global capacity to detect and mange emerging disease threats. Its emergence in China adds an additional dimension in the light of previous experience with SARS. The timing of the outbreak immediately before the Chinese Lunar New Year with its attendant population movements adds extra risk and urgency to the response." ]

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

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

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: The emergence of a significant respiratory illness linked to a novel coronavirus represents a test of the global capacity to detect and mange emerging disease threats. Its emergence in China adds an additional dimension in the light of previous experience with SARS. The timing of the outbreak immediately before the Chinese Lunar New Year with its attendant population movements adds extra risk and urgency to the response." ]

[ [ "1a", "Title: CDC Summary 21 MAR 2020," ], [ "1b", "Passage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV." ], [ "1c", "All three of these viruses have their origins in bats." ], [ "1d", "The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir." ] ]

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

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: The emergence of a significant respiratory illness linked to a novel coronavirus represents a test of the global capacity to detect and mange emerging disease threats. Its emergence in China adds an additional dimension in the light of previous experience with SARS. The timing of the outbreak immediately before the Chinese Lunar New Year with its attendant population movements adds extra risk and urgency to the response." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: MERS and SARS have some clinical similarities but they also diverge significantly ." ], [ "2c", "Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities." ], [ "2d", "For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV." ] ]

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

[ "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Species-specific evolution of immune receptor tyrosine based activation motif-containing CEACAM1-related immune receptors in the dog\nPassage: and 4. The cloned CEACAM25 splice variants also code for proteins with only one N domain followed by a transmembrane domain. Three out of four clones encode cytoplasmic domains which contain the predicted ITAM motif . In one clone, the absence of the 53 nucleotide cytoplasmic domain exon 1 leads to a frame shift and the usage of an alternative stop codon located in cytoplasmic domain exon3 . Using supposedly CEACAM28specific primers, two products were amplified which differ in their length by 276 bp. Cloning and sequencing revealed that the CEACAM28 gene codes for a protein with one N domain,", "Title: The Transmembrane Domain of CEACAM1-4S Is a Determinant of Anchorage Independent Growth and Tumorigenicity\nPassage: CEACAM1 is a member of the carcinoembryonic antigen gene family of Ig-like cell-cell adhesion molecules . Like other members of this family, CEACAM1 is a type I transmembrane protein with a heavily glycosylated extracellular region composed of four Ig-like domains, a transmembrane domain and a cytoplasmic tail . In the rat liver there are two allelic variants of CEACAM1 which differ by 16 amino acids in their N-terminal domains and two major splice variants, designated 4L and 4S, that are distinguished by differences in the length of their cytoplasmic tails of 70-72 amino acids and 10-12 amino acids, respectively ." ]

[ [ "0a", "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1" ], [ "0b", "Passage: Eleven CEACAM1 splice variants have been reported in humans 20 ." ], [ "0c", "CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail ." ], [ "0d", "The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail." ], [ "0e", "The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 ." ], [ "0f", "The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1" ] ]

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

[ "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Species-specific evolution of immune receptor tyrosine based activation motif-containing CEACAM1-related immune receptors in the dog\nPassage: and 4. The cloned CEACAM25 splice variants also code for proteins with only one N domain followed by a transmembrane domain. Three out of four clones encode cytoplasmic domains which contain the predicted ITAM motif . In one clone, the absence of the 53 nucleotide cytoplasmic domain exon 1 leads to a frame shift and the usage of an alternative stop codon located in cytoplasmic domain exon3 . Using supposedly CEACAM28specific primers, two products were amplified which differ in their length by 276 bp. Cloning and sequencing revealed that the CEACAM28 gene codes for a protein with one N domain,", "Title: The Transmembrane Domain of CEACAM1-4S Is a Determinant of Anchorage Independent Growth and Tumorigenicity\nPassage: CEACAM1 is a member of the carcinoembryonic antigen gene family of Ig-like cell-cell adhesion molecules . Like other members of this family, CEACAM1 is a type I transmembrane protein with a heavily glycosylated extracellular region composed of four Ig-like domains, a transmembrane domain and a cytoplasmic tail . In the rat liver there are two allelic variants of CEACAM1 which differ by 16 amino acids in their N-terminal domains and two major splice variants, designated 4L and 4S, that are distinguished by differences in the length of their cytoplasmic tails of 70-72 amino acids and 10-12 amino acids, respectively ." ]

[ [ "1a", "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1" ], [ "1b", "Passage: Eleven CEACAM1 splice variants have been reported in humans 20 ." ], [ "1c", "CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail ." ], [ "1d", "The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail." ], [ "1e", "The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 ." ], [ "1f", "The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1" ] ]

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

[ "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1\nPassage: Eleven CEACAM1 splice variants have been reported in humans 20 . CEACAM1 isoforms can differ in the number of immunoglobulin-like domains present, in the presence or absence of a transmembrane domain and/or the length of their cytoplasmic tail . The full-length human CEACAM1 protein consists of four extracellular domains domain and three immunoglobulin constant region 2-like domains), a transmembrane domain, and a long cytoplasmic tail. The long cytoplasmic tail contains two immunoreceptor tyrosine-based inhibitory motifs that are absent in the short form 20 . The most common isoforms expressed by human immune cells are CEACAM1-4L and CEACAM1-3L 21 . CEACAM1", "Title: Species-specific evolution of immune receptor tyrosine based activation motif-containing CEACAM1-related immune receptors in the dog\nPassage: and 4. The cloned CEACAM25 splice variants also code for proteins with only one N domain followed by a transmembrane domain. Three out of four clones encode cytoplasmic domains which contain the predicted ITAM motif . In one clone, the absence of the 53 nucleotide cytoplasmic domain exon 1 leads to a frame shift and the usage of an alternative stop codon located in cytoplasmic domain exon3 . Using supposedly CEACAM28specific primers, two products were amplified which differ in their length by 276 bp. Cloning and sequencing revealed that the CEACAM28 gene codes for a protein with one N domain,", "Title: The Transmembrane Domain of CEACAM1-4S Is a Determinant of Anchorage Independent Growth and Tumorigenicity\nPassage: CEACAM1 is a member of the carcinoembryonic antigen gene family of Ig-like cell-cell adhesion molecules . Like other members of this family, CEACAM1 is a type I transmembrane protein with a heavily glycosylated extracellular region composed of four Ig-like domains, a transmembrane domain and a cytoplasmic tail . In the rat liver there are two allelic variants of CEACAM1 which differ by 16 amino acids in their N-terminal domains and two major splice variants, designated 4L and 4S, that are distinguished by differences in the length of their cytoplasmic tails of 70-72 amino acids and 10-12 amino acids, respectively ." ]

[ [ "3a", "Title: The Transmembrane Domain of CEACAM1-4S Is a Determinant of Anchorage Independent Growth and Tumorigenicity" ], [ "3b", "Passage: CEACAM1 is a member of the carcinoembryonic antigen gene family of Ig-like cell-cell adhesion molecules ." ], [ "3c", "Like other members of this family, CEACAM1 is a type I transmembrane protein with a heavily glycosylated extracellular region composed of four Ig-like domains, a transmembrane domain and a cytoplasmic tail ." ], [ "3d", "In the rat liver there are two allelic variants of CEACAM1 which differ by 16 amino acids in their N-terminal domains and two major splice variants, designated 4L and 4S, that are distinguished by differences in the length of their cytoplasmic tails of 70-72 amino acids and 10-12 amino acids, respectively ." ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: testing rAd5 vectors expressing the HA genes from avian viruses of the A, A and A subtype 199, 206 combinations thereof) showed that mice could be protected from homologous challenge infection. Heterosubtypic immunite was never observed, however it was shown that simultaneous vaccination with 5 different rAd5-HA vaccines was feasible and protected from challenge infection with viruses of all subtypes under investigation. 207 Comparable to expressing modified influenza antigens in other vectors with the goal of inducing universal influenza immunity , a rAd expressing a modified HA gene was constructed. This HA gene was modified to shield the immunodominant head", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: mice with this construct induced robust neutralizing antibody responses and protected mice from challenge with a heterologous virus, A/Hong Kong/1/1968 . Replication defective rAd5 vaccines expressing influenza HA have also been tested in humans. A rAd5-HA expressing the HA from A/Puerto Rico/8/1934 was delivered to humans epicutaneously or intranasally and assayed for safety and immunogenicity. The vaccine was well tolerated and induced seroconversion with the intranasal administration had a higher conversion rate and higher geometric meant HI titers . While clinical trials with rAd vectors have overall been successful, demonstrating safety and some level of efficacy, rAd5 as a vector", "Title: An in vivo system for directed experimental evolution of rabbit haemorrhagic disease virus\nPassage: RHDV serum diluted 1/5,000 in standard carbonate buffer. After incubation at 37˚C for 1 hour, plates were washed and incubated with a mixture of the mabs 1H3, 5D11 and 2B4 at 37˚C for 1 hour. Finally, horseradish peroxidase-labelled rabbit anti-mouse IgG was used to detect the binding of the mabs to the virus. For each virus, the OD 492 value obtained with the non-binding mab 5F5 was set as 0% inhibition. RHDV Bs89 was used as the reference strain for the mabs 2B4, 2G3, 1H8, 2A10 and 1H3, while the antigenic variant RHDVa Pv97 was the reference strain for the", "Title: A Single Residue Substitution in the Receptor-Binding Domain of H5N1 Hemagglutinin Is Critical for Packaging into Pseudotyped Lentiviral Particles\nPassage: 293T cells transfected with H5 HA were detached with and resuspended in PBS, blocked in 10% horse serum and then labelled with a polyclonal rabbit anti-H5N1 antibody at a 1:400 dilution for 1 hr at 4uC. Unbound antibodies were removed by washing three times with cold PBS, followed by staining with a phycoerythrin -conjugated, donkey-anti-goat secondary antibody for 30 min at 4uC. Data were collected from at least 5000 cells on an LSRII flow cytometer and post-acquisition analyses of cell surface expression of H5-HA was performed using FlowJo software ." ]

[ [ "0a", "Title: Viral vector-based influenza vaccines" ], [ "0b", "Passage: testing rAd5 vectors expressing the HA genes from avian viruses of the A, A and A subtype 199, 206 combinations thereof) showed that mice could be protected from homologous challenge infection." ], [ "0c", "Heterosubtypic immunite was never observed, however it was shown that simultaneous vaccination with 5 different rAd5-HA vaccines was feasible and protected from challenge infection with viruses of all subtypes under investigation." ], [ "0d", "207 Comparable to expressing modified influenza antigens in other vectors with the goal of inducing universal influenza immunity , a rAd expressing a modified HA gene was constructed." ], [ "0e", "This HA gene was modified to shield the immunodominant head" ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: testing rAd5 vectors expressing the HA genes from avian viruses of the A, A and A subtype 199, 206 combinations thereof) showed that mice could be protected from homologous challenge infection. Heterosubtypic immunite was never observed, however it was shown that simultaneous vaccination with 5 different rAd5-HA vaccines was feasible and protected from challenge infection with viruses of all subtypes under investigation. 207 Comparable to expressing modified influenza antigens in other vectors with the goal of inducing universal influenza immunity , a rAd expressing a modified HA gene was constructed. This HA gene was modified to shield the immunodominant head", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: mice with this construct induced robust neutralizing antibody responses and protected mice from challenge with a heterologous virus, A/Hong Kong/1/1968 . Replication defective rAd5 vaccines expressing influenza HA have also been tested in humans. A rAd5-HA expressing the HA from A/Puerto Rico/8/1934 was delivered to humans epicutaneously or intranasally and assayed for safety and immunogenicity. The vaccine was well tolerated and induced seroconversion with the intranasal administration had a higher conversion rate and higher geometric meant HI titers . While clinical trials with rAd vectors have overall been successful, demonstrating safety and some level of efficacy, rAd5 as a vector", "Title: An in vivo system for directed experimental evolution of rabbit haemorrhagic disease virus\nPassage: RHDV serum diluted 1/5,000 in standard carbonate buffer. After incubation at 37˚C for 1 hour, plates were washed and incubated with a mixture of the mabs 1H3, 5D11 and 2B4 at 37˚C for 1 hour. Finally, horseradish peroxidase-labelled rabbit anti-mouse IgG was used to detect the binding of the mabs to the virus. For each virus, the OD 492 value obtained with the non-binding mab 5F5 was set as 0% inhibition. RHDV Bs89 was used as the reference strain for the mabs 2B4, 2G3, 1H8, 2A10 and 1H3, while the antigenic variant RHDVa Pv97 was the reference strain for the", "Title: A Single Residue Substitution in the Receptor-Binding Domain of H5N1 Hemagglutinin Is Critical for Packaging into Pseudotyped Lentiviral Particles\nPassage: 293T cells transfected with H5 HA were detached with and resuspended in PBS, blocked in 10% horse serum and then labelled with a polyclonal rabbit anti-H5N1 antibody at a 1:400 dilution for 1 hr at 4uC. Unbound antibodies were removed by washing three times with cold PBS, followed by staining with a phycoerythrin -conjugated, donkey-anti-goat secondary antibody for 30 min at 4uC. Data were collected from at least 5000 cells on an LSRII flow cytometer and post-acquisition analyses of cell surface expression of H5-HA was performed using FlowJo software ." ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: mice with this construct induced robust neutralizing antibody responses and protected mice from challenge with a heterologous virus, A/Hong Kong/1/1968 ." ], [ "1c", "Replication defective rAd5 vaccines expressing influenza HA have also been tested in humans." ], [ "1d", "A rAd5-HA expressing the HA from A/Puerto Rico/8/1934 was delivered to humans epicutaneously or intranasally and assayed for safety and immunogenicity." ], [ "1e", "The vaccine was well tolerated and induced seroconversion with the intranasal administration had a higher conversion rate and higher geometric meant HI titers ." ], [ "1f", "While clinical trials with rAd vectors have overall been successful, demonstrating safety and some level of efficacy, rAd5 as a vector" ] ]

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

[ "Title: Consequences of delays and imperfect implementation of isolation in epidemic control\nPassage: Roughly 400 infectious diseases have been identified since 1940. New pathogens are emerging at higher rates, despite the increase in awareness and vigilance. A grave public health concern is when and how the next outbreak will occur 1 ; threats of imminent global outbreaks are real 2 . The 1917 Spanish influenza, which killed 50 million people, was the worst-ever pandemic on record -and that was back at a time when travel by ship was the fastest means of transportation around the globe. In today's tightly connected world, an epidemic can potentially travel at jet-speed. Indeed, Swine flu was first", "Title: European Monitoring Systems and Data for Assessing Environmental and Climate Impacts on Human Infectious Diseases\nPassage: outbreaks has already been examined . Both heavy rainfall and periods of sustained low rainfall appear to be associated with outbreaks. Similarly, cholera outbreaks have been analysed to examine global differences in seasonality .", "Title: Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease\nPassage: Bovine Spongiform Encephalopathy, Bluetongue or Foot and Mouth disease , and diseases of wildlife-potentially white-nose syndrome in bats . In the USA, many other wildlife diseases and zoonoses have been linked to live animal imports . Trade and travel affect the likelihood that pathogens are spread internationally by altering the number and variety of infectious-susceptible contacts Jones et al. 2008; Suhrcke et al. 2011; Daszak 2012; Kilpatrick and Randolph 2012) . In the same way, the decisions people make to engage with others in their own community affect the spread of disease nationally. Since people take account of potential disease", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: will have an increasingly important role as a driver of changes in the ecology of these diseases, influencing both disease incidence and distribution. Severe storms, heat waves, and weather patterns have been linked to outbreaks of many environmentally-sensitive infectious diseases. West Nile Virus transmission intensity has been associated with warmer than normal summer temperatures. 48 Rift Valley Fever outbreaks in East Africa have been correlated with ENSO events. 49 Plague transmission in the Southwest and Rocky Mountain region has been linked to temperature and rainfall patterns leading to increases in wild rodent populations. 50 Waterborne disease outbreaks have been associated" ]

[ [ "0a", "Title: Consequences of delays and imperfect implementation of isolation in epidemic control" ], [ "0b", "Passage: Roughly 400 infectious diseases have been identified since 1940." ], [ "0c", "New pathogens are emerging at higher rates, despite the increase in awareness and vigilance." ], [ "0d", "A grave public health concern is when and how the next outbreak will occur 1 ; threats of imminent global outbreaks are real 2 ." ], [ "0e", "The 1917 Spanish influenza, which killed 50 million people, was the worst-ever pandemic on record -and that was back at a time when travel by ship was the fastest means of transportation around the globe." ], [ "0f", "In today's tightly connected world, an epidemic can potentially travel at jet-speed." ], [ "0g", "Indeed, Swine flu was first" ] ]

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

[ "Title: Consequences of delays and imperfect implementation of isolation in epidemic control\nPassage: Roughly 400 infectious diseases have been identified since 1940. New pathogens are emerging at higher rates, despite the increase in awareness and vigilance. A grave public health concern is when and how the next outbreak will occur 1 ; threats of imminent global outbreaks are real 2 . The 1917 Spanish influenza, which killed 50 million people, was the worst-ever pandemic on record -and that was back at a time when travel by ship was the fastest means of transportation around the globe. In today's tightly connected world, an epidemic can potentially travel at jet-speed. Indeed, Swine flu was first", "Title: European Monitoring Systems and Data for Assessing Environmental and Climate Impacts on Human Infectious Diseases\nPassage: outbreaks has already been examined . Both heavy rainfall and periods of sustained low rainfall appear to be associated with outbreaks. Similarly, cholera outbreaks have been analysed to examine global differences in seasonality .", "Title: Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease\nPassage: Bovine Spongiform Encephalopathy, Bluetongue or Foot and Mouth disease , and diseases of wildlife-potentially white-nose syndrome in bats . In the USA, many other wildlife diseases and zoonoses have been linked to live animal imports . Trade and travel affect the likelihood that pathogens are spread internationally by altering the number and variety of infectious-susceptible contacts Jones et al. 2008; Suhrcke et al. 2011; Daszak 2012; Kilpatrick and Randolph 2012) . In the same way, the decisions people make to engage with others in their own community affect the spread of disease nationally. Since people take account of potential disease", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: will have an increasingly important role as a driver of changes in the ecology of these diseases, influencing both disease incidence and distribution. Severe storms, heat waves, and weather patterns have been linked to outbreaks of many environmentally-sensitive infectious diseases. West Nile Virus transmission intensity has been associated with warmer than normal summer temperatures. 48 Rift Valley Fever outbreaks in East Africa have been correlated with ENSO events. 49 Plague transmission in the Southwest and Rocky Mountain region has been linked to temperature and rainfall patterns leading to increases in wild rodent populations. 50 Waterborne disease outbreaks have been associated" ]

[ [ "1a", "Title: European Monitoring Systems and Data for Assessing Environmental and Climate Impacts on Human Infectious Diseases" ], [ "1b", "Passage: outbreaks has already been examined ." ], [ "1c", "Both heavy rainfall and periods of sustained low rainfall appear to be associated with outbreaks." ], [ "1d", "Similarly, cholera outbreaks have been analysed to examine global differences in seasonality ." ] ]

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

[ "Title: Consequences of delays and imperfect implementation of isolation in epidemic control\nPassage: Roughly 400 infectious diseases have been identified since 1940. New pathogens are emerging at higher rates, despite the increase in awareness and vigilance. A grave public health concern is when and how the next outbreak will occur 1 ; threats of imminent global outbreaks are real 2 . The 1917 Spanish influenza, which killed 50 million people, was the worst-ever pandemic on record -and that was back at a time when travel by ship was the fastest means of transportation around the globe. In today's tightly connected world, an epidemic can potentially travel at jet-speed. Indeed, Swine flu was first", "Title: European Monitoring Systems and Data for Assessing Environmental and Climate Impacts on Human Infectious Diseases\nPassage: outbreaks has already been examined . Both heavy rainfall and periods of sustained low rainfall appear to be associated with outbreaks. Similarly, cholera outbreaks have been analysed to examine global differences in seasonality .", "Title: Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease\nPassage: Bovine Spongiform Encephalopathy, Bluetongue or Foot and Mouth disease , and diseases of wildlife-potentially white-nose syndrome in bats . In the USA, many other wildlife diseases and zoonoses have been linked to live animal imports . Trade and travel affect the likelihood that pathogens are spread internationally by altering the number and variety of infectious-susceptible contacts Jones et al. 2008; Suhrcke et al. 2011; Daszak 2012; Kilpatrick and Randolph 2012) . In the same way, the decisions people make to engage with others in their own community affect the spread of disease nationally. Since people take account of potential disease", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: will have an increasingly important role as a driver of changes in the ecology of these diseases, influencing both disease incidence and distribution. Severe storms, heat waves, and weather patterns have been linked to outbreaks of many environmentally-sensitive infectious diseases. West Nile Virus transmission intensity has been associated with warmer than normal summer temperatures. 48 Rift Valley Fever outbreaks in East Africa have been correlated with ENSO events. 49 Plague transmission in the Southwest and Rocky Mountain region has been linked to temperature and rainfall patterns leading to increases in wild rodent populations. 50 Waterborne disease outbreaks have been associated" ]

[ [ "2a", "Title: Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease" ], [ "2b", "Passage: Bovine Spongiform Encephalopathy, Bluetongue or Foot and Mouth disease , and diseases of wildlife-potentially white-nose syndrome in bats ." ], [ "2c", "In the USA, many other wildlife diseases and zoonoses have been linked to live animal imports ." ], [ "2d", "Trade and travel affect the likelihood that pathogens are spread internationally by altering the number and variety of infectious-susceptible contacts Jones et al. 2008; Suhrcke et al. 2011; Daszak 2012; Kilpatrick and Randolph 2012) ." ], [ "2e", "In the same way, the decisions people make to engage with others in their own community affect the spread of disease nationally." ], [ "2f", "Since people take account of potential disease" ] ]

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

[ "Title: Consequences of delays and imperfect implementation of isolation in epidemic control\nPassage: Roughly 400 infectious diseases have been identified since 1940. New pathogens are emerging at higher rates, despite the increase in awareness and vigilance. A grave public health concern is when and how the next outbreak will occur 1 ; threats of imminent global outbreaks are real 2 . The 1917 Spanish influenza, which killed 50 million people, was the worst-ever pandemic on record -and that was back at a time when travel by ship was the fastest means of transportation around the globe. In today's tightly connected world, an epidemic can potentially travel at jet-speed. Indeed, Swine flu was first", "Title: European Monitoring Systems and Data for Assessing Environmental and Climate Impacts on Human Infectious Diseases\nPassage: outbreaks has already been examined . Both heavy rainfall and periods of sustained low rainfall appear to be associated with outbreaks. Similarly, cholera outbreaks have been analysed to examine global differences in seasonality .", "Title: Merging Economics and Epidemiology to Improve the Prediction and Management of Infectious Disease\nPassage: Bovine Spongiform Encephalopathy, Bluetongue or Foot and Mouth disease , and diseases of wildlife-potentially white-nose syndrome in bats . In the USA, many other wildlife diseases and zoonoses have been linked to live animal imports . Trade and travel affect the likelihood that pathogens are spread internationally by altering the number and variety of infectious-susceptible contacts Jones et al. 2008; Suhrcke et al. 2011; Daszak 2012; Kilpatrick and Randolph 2012) . In the same way, the decisions people make to engage with others in their own community affect the spread of disease nationally. Since people take account of potential disease", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities\nPassage: will have an increasingly important role as a driver of changes in the ecology of these diseases, influencing both disease incidence and distribution. Severe storms, heat waves, and weather patterns have been linked to outbreaks of many environmentally-sensitive infectious diseases. West Nile Virus transmission intensity has been associated with warmer than normal summer temperatures. 48 Rift Valley Fever outbreaks in East Africa have been correlated with ENSO events. 49 Plague transmission in the Southwest and Rocky Mountain region has been linked to temperature and rainfall patterns leading to increases in wild rodent populations. 50 Waterborne disease outbreaks have been associated" ]

[ [ "3a", "Title: Exposure science in an age of rapidly changing climate: challenges and opportunities" ], [ "3b", "Passage: will have an increasingly important role as a driver of changes in the ecology of these diseases, influencing both disease incidence and distribution." ], [ "3c", "Severe storms, heat waves, and weather patterns have been linked to outbreaks of many environmentally-sensitive infectious diseases." ], [ "3d", "West Nile Virus transmission intensity has been associated with warmer than normal summer temperatures." ], [ "3e", "48 Rift Valley Fever outbreaks in East Africa have been correlated with ENSO events." ], [ "3f", "49 Plague transmission in the Southwest and Rocky Mountain region has been linked to temperature and rainfall patterns leading to increases in wild rodent populations." ], [ "3g", "50 Waterborne disease outbreaks have been associated" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: infection may also alter the nutrient profile in the airway through release of previously inaccessible nutrients that will alter bacterial growth . Furthermore, the destabilization is further compounded by impaired bacterial immune response, either from direct viral influences, or use of corticosteroids to suppress the exacerbation symptoms . All these may gradually lead to more far reaching effect when normal flora is replaced with opportunistic pathogens, altering the inflammatory profiles . These changes may in turn result in more severe and frequent acute exacerbations due to the interplay between virus and pathogenic bacteria in exacerbating chronic airway inflammatory diseases .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: eosinophilic infiltration in the asthmatic airway. The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway." ]

[ [ "0a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "0b", "Passage: infection may also alter the nutrient profile in the airway through release of previously inaccessible nutrients that will alter bacterial growth ." ], [ "0c", "Furthermore, the destabilization is further compounded by impaired bacterial immune response, either from direct viral influences, or use of corticosteroids to suppress the exacerbation symptoms ." ], [ "0d", "All these may gradually lead to more far reaching effect when normal flora is replaced with opportunistic pathogens, altering the inflammatory profiles ." ], [ "0e", "These changes may in turn result in more severe and frequent acute exacerbations due to the interplay between virus and pathogenic bacteria in exacerbating chronic airway inflammatory diseases ." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: infection may also alter the nutrient profile in the airway through release of previously inaccessible nutrients that will alter bacterial growth . Furthermore, the destabilization is further compounded by impaired bacterial immune response, either from direct viral influences, or use of corticosteroids to suppress the exacerbation symptoms . All these may gradually lead to more far reaching effect when normal flora is replaced with opportunistic pathogens, altering the inflammatory profiles . These changes may in turn result in more severe and frequent acute exacerbations due to the interplay between virus and pathogenic bacteria in exacerbating chronic airway inflammatory diseases .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: eosinophilic infiltration in the asthmatic airway. The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway." ]

[ [ "1a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "1b", "Passage: of the classical symptoms of chronic airway inflammatory diseases ." ], [ "1c", "In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) ." ], [ "1d", "These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: infection may also alter the nutrient profile in the airway through release of previously inaccessible nutrients that will alter bacterial growth . Furthermore, the destabilization is further compounded by impaired bacterial immune response, either from direct viral influences, or use of corticosteroids to suppress the exacerbation symptoms . All these may gradually lead to more far reaching effect when normal flora is replaced with opportunistic pathogens, altering the inflammatory profiles . These changes may in turn result in more severe and frequent acute exacerbations due to the interplay between virus and pathogenic bacteria in exacerbating chronic airway inflammatory diseases .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: eosinophilic infiltration in the asthmatic airway. The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway." ]

[ [ "2a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "2b", "Passage: Respiratory viruses primarily infect and replicate within airway epithelial cells ." ], [ "2c", "During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche ." ], [ "2d", "In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells." ], [ "2e", "This eventually results in the resolution of the inflammatory response and clearance of the viral infection ." ], [ "2f", "However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: infection may also alter the nutrient profile in the airway through release of previously inaccessible nutrients that will alter bacterial growth . Furthermore, the destabilization is further compounded by impaired bacterial immune response, either from direct viral influences, or use of corticosteroids to suppress the exacerbation symptoms . All these may gradually lead to more far reaching effect when normal flora is replaced with opportunistic pathogens, altering the inflammatory profiles . These changes may in turn result in more severe and frequent acute exacerbations due to the interplay between virus and pathogenic bacteria in exacerbating chronic airway inflammatory diseases .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: eosinophilic infiltration in the asthmatic airway. The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway." ]

[ [ "3a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "3b", "Passage: eosinophilic infiltration in the asthmatic airway." ], [ "3c", "The effect is also further compounded by the participation of Th1 and ILC1 cells in the COPD airway; and Th2 and ILC2 cells in the asthmatic airway." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: 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: Date: 2020-03-05", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068164/" ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "Passage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia." ], [ "0c", "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 ." ], [ "0d", "As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region ." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: 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: Date: 2020-03-05", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068164/" ]

[ [ "1a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "1b", "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 ." ], [ "1c", "Data on 38 of these cases are included in this analysis." ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Nasal swabs were collected from the subjects and stored in DNA/RNA shield . Collected samples were spinned and the swab removed. Residues containing the nasal samples were stored at -20 °C prior to molecular analysis.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ]

[ [ "1a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "1b", "Passage: We also compared and contrasted the clinical and community results." ], [ "1c", "Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample." ], [ "1d", "These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community." ], [ "1e", "Together they infected 94% of clinical subjects, and 7% in the community ." ], [ "1f", "The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples." ], [ "1g", "However a different strain, coronavirus OC 229" ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Nasal swabs were collected from the subjects and stored in DNA/RNA shield . Collected samples were spinned and the swab removed. Residues containing the nasal samples were stored at -20 °C prior to molecular analysis.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ]

[ [ "2a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "2b", "Passage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria." ], [ "2c", "RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria." ], [ "2d", "Nasal swabs were collected and tested using polymerase chain reaction." ], [ "2e", "The majority of subjects were under 6 years old, of whom 46 were infected ." ], [ "2f", "A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Nasal swabs were collected from the subjects and stored in DNA/RNA shield . Collected samples were spinned and the swab removed. Residues containing the nasal samples were stored at -20 °C prior to molecular analysis.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ]

[ [ "3a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "3b", "Passage: and 5 of quadruple." ], [ "3c", "Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects ." ], [ "3d", "Coronavirus OC43 was the most common virus detected in community members ." ], [ "3e", "A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community." ], [ "3f", "This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ] ]

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

[ "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: cytotoxicity caused by the test compound . Viability and cytotox-icity data can therefore help reconcile aberrant data points or explain decreases in genetic reporter signals due to cell death.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: Cytotoxicity in mock infected cell plates was measured 48 or 72 h after treatment with compounds using the CellTiter Glo luminescent cell viability assay kit according to the manufacturer's instructions . Luminescence was read on the Infinite 1 M1000 Tecan plate reader .", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: A host of new assays have been described and utilized which measure biomarkers of cellular stress or specific signaling events more proximal to initial cytotoxic insult . These methods offer early indication of potential cytotoxicity, but are typically relegated to secondary screening because they are more difficult to employ as endpoint assays due to the transient nature of the biomarker and kinetic differences associated with cell death progression . Therefore assay chemistries predicated upon the detection of changes in membrane integrity remain the gold standard for in vitro cytotoxicity testing.", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: Depending upon the goals of the screen, either viability or true cytotoxicity assay chemistries can be employed. Cytotoxicity assays based on membrane integrity changes are positive-readout assays most typically indicated for shorterterm exposure models . These assays may not always accurately estimate the absolute degree of early or late stage cytotoxicity due to the kinetics of biomarker emergence or degradation. Viability assays measure the level of biomarker activity inversely correlated with cytotoxicity and therefore may be used at any endpoint during a compound/cell incubation period." ]

[ [ "0a", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening" ], [ "0b", "Passage: cytotoxicity caused by the test compound ." ], [ "0c", "Viability and cytotox-icity data can therefore help reconcile aberrant data points or explain decreases in genetic reporter signals due to cell death." ] ]

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

[ "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: cytotoxicity caused by the test compound . Viability and cytotox-icity data can therefore help reconcile aberrant data points or explain decreases in genetic reporter signals due to cell death.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: Cytotoxicity in mock infected cell plates was measured 48 or 72 h after treatment with compounds using the CellTiter Glo luminescent cell viability assay kit according to the manufacturer's instructions . Luminescence was read on the Infinite 1 M1000 Tecan plate reader .", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: A host of new assays have been described and utilized which measure biomarkers of cellular stress or specific signaling events more proximal to initial cytotoxic insult . These methods offer early indication of potential cytotoxicity, but are typically relegated to secondary screening because they are more difficult to employ as endpoint assays due to the transient nature of the biomarker and kinetic differences associated with cell death progression . Therefore assay chemistries predicated upon the detection of changes in membrane integrity remain the gold standard for in vitro cytotoxicity testing.", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: Depending upon the goals of the screen, either viability or true cytotoxicity assay chemistries can be employed. Cytotoxicity assays based on membrane integrity changes are positive-readout assays most typically indicated for shorterterm exposure models . These assays may not always accurately estimate the absolute degree of early or late stage cytotoxicity due to the kinetics of biomarker emergence or degradation. Viability assays measure the level of biomarker activity inversely correlated with cytotoxicity and therefore may be used at any endpoint during a compound/cell incubation period." ]

[ [ "2a", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening" ], [ "2b", "Passage: A host of new assays have been described and utilized which measure biomarkers of cellular stress or specific signaling events more proximal to initial cytotoxic insult ." ], [ "2c", "These methods offer early indication of potential cytotoxicity, but are typically relegated to secondary screening because they are more difficult to employ as endpoint assays due to the transient nature of the biomarker and kinetic differences associated with cell death progression ." ], [ "2d", "Therefore assay chemistries predicated upon the detection of changes in membrane integrity remain the gold standard for in vitro cytotoxicity testing." ] ]

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

[ "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: cytotoxicity caused by the test compound . Viability and cytotox-icity data can therefore help reconcile aberrant data points or explain decreases in genetic reporter signals due to cell death.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: Cytotoxicity in mock infected cell plates was measured 48 or 72 h after treatment with compounds using the CellTiter Glo luminescent cell viability assay kit according to the manufacturer's instructions . Luminescence was read on the Infinite 1 M1000 Tecan plate reader .", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: A host of new assays have been described and utilized which measure biomarkers of cellular stress or specific signaling events more proximal to initial cytotoxic insult . These methods offer early indication of potential cytotoxicity, but are typically relegated to secondary screening because they are more difficult to employ as endpoint assays due to the transient nature of the biomarker and kinetic differences associated with cell death progression . Therefore assay chemistries predicated upon the detection of changes in membrane integrity remain the gold standard for in vitro cytotoxicity testing.", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening\nPassage: Depending upon the goals of the screen, either viability or true cytotoxicity assay chemistries can be employed. Cytotoxicity assays based on membrane integrity changes are positive-readout assays most typically indicated for shorterterm exposure models . These assays may not always accurately estimate the absolute degree of early or late stage cytotoxicity due to the kinetics of biomarker emergence or degradation. Viability assays measure the level of biomarker activity inversely correlated with cytotoxicity and therefore may be used at any endpoint during a compound/cell incubation period." ]

[ [ "3a", "Title: In Vitro Viability and Cytotoxicity Testing and Same-Well Multi-Parametric Combinations for High Throughput Screening" ], [ "3b", "Passage: Depending upon the goals of the screen, either viability or true cytotoxicity assay chemistries can be employed." ], [ "3c", "Cytotoxicity assays based on membrane integrity changes are positive-readout assays most typically indicated for shorterterm exposure models ." ], [ "3d", "These assays may not always accurately estimate the absolute degree of early or late stage cytotoxicity due to the kinetics of biomarker emergence or degradation." ], [ "3e", "Viability assays measure the level of biomarker activity inversely correlated with cytotoxicity and therefore may be used at any endpoint during a compound/cell incubation period." ] ]

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Notwithstanding this progress, there remains a disproportionate burden of disease in low-and middle-income countries, where more than 90% of pneumonia cases and deaths occur. The incidence in high-income countries is estimated at 0.015 episodes per child year, compared to 0.22 episodes per child year in low-and middle-income countries . On average, 1 in 66 children in high-income countries is affected by pneumonia per year, compared to 1 in 5 children in low-and middle-income countries. Even within low-and middleincome countries there are regional inequities and challenges with access to health care services: up to 81% of severe pneumonia deaths occur outside", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: a hospital . In addition to a higher incidence of pneumonia, the case fatality rate is estimated to be almost 10-fold higher in low-and middle-income countries as compared to high-income countries .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: odds of severe pneumonia by 2.7 times in low-and middle-income countries and 1.3 times in highincome countries. Markers of undernutrition are strong risk factors for pneumonia in low-and middle-income countries only, with highly significant odds ratios for underweight for age , stunting and wasting . Household crowding has uniform risk, with odds ratios between 1.9 and 2.3 in both low-and middle-income countries and high-income countries. Indoor air pollution from use of solid or biomass fuels increases odds of pneumonia by 1.6 times; lack of measles vaccination by the end of the first year of age increases odds of pneumonia by", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: that the mortality rate was 119 per 100,000 and the case-fatality rate was 5% for pneumococcal pneumonia; however, for pneumococcal meningitis, the case-fatality rate was as high as 59% despite the mortality rate of 10 per 100,000. Within the European region identified by WHO, the mortality rate was 25 per 100,000 and the case-fatality rate was 5% for pneumococcal pneumonia, whereas these rates were 3 per 100,000 and 38% , respectively, for pneumococcal meningitis. The differences in quality and accessibility of healthcare services may create differences between countries." ]

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

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Notwithstanding this progress, there remains a disproportionate burden of disease in low-and middle-income countries, where more than 90% of pneumonia cases and deaths occur. The incidence in high-income countries is estimated at 0.015 episodes per child year, compared to 0.22 episodes per child year in low-and middle-income countries . On average, 1 in 66 children in high-income countries is affected by pneumonia per year, compared to 1 in 5 children in low-and middle-income countries. Even within low-and middleincome countries there are regional inequities and challenges with access to health care services: up to 81% of severe pneumonia deaths occur outside", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: a hospital . In addition to a higher incidence of pneumonia, the case fatality rate is estimated to be almost 10-fold higher in low-and middle-income countries as compared to high-income countries .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: odds of severe pneumonia by 2.7 times in low-and middle-income countries and 1.3 times in highincome countries. Markers of undernutrition are strong risk factors for pneumonia in low-and middle-income countries only, with highly significant odds ratios for underweight for age , stunting and wasting . Household crowding has uniform risk, with odds ratios between 1.9 and 2.3 in both low-and middle-income countries and high-income countries. Indoor air pollution from use of solid or biomass fuels increases odds of pneumonia by 1.6 times; lack of measles vaccination by the end of the first year of age increases odds of pneumonia by", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: that the mortality rate was 119 per 100,000 and the case-fatality rate was 5% for pneumococcal pneumonia; however, for pneumococcal meningitis, the case-fatality rate was as high as 59% despite the mortality rate of 10 per 100,000. Within the European region identified by WHO, the mortality rate was 25 per 100,000 and the case-fatality rate was 5% for pneumococcal pneumonia, whereas these rates were 3 per 100,000 and 38% , respectively, for pneumococcal meningitis. The differences in quality and accessibility of healthcare services may create differences between countries." ]

[ [ "1a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "1b", "Passage: a hospital ." ], [ "1c", "In addition to a higher incidence of pneumonia, the case fatality rate is estimated to be almost 10-fold higher in low-and middle-income countries as compared to high-income countries ." ] ]

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

[ "Title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy\nPassage: CHC was classically treated with recombinant PEG-IFNalpha in combination with Ribavirin . The treatment duration was long and wearing, with PEG-IFN-alpha being administered 3 times a week, severe side effects occurring frequently, and still only approximately half of the patients being cured. Since 2014 HCV therapy improved drastically, as several direct acting antivirals targeting HCV NS3/4A protease, NS5A, or NS5B RNA-polymerase were approved. These inhibitors, either alone or in combination with RBV, now heal over 90% of patients treated. Direct acting antivirals are more effective than PEG-IFN-alpha in eliminating HCV, but also treatment duration is shorter , they can be", "Title: Advanced Molecular Surveillance of Hepatitis C Virus\nPassage: The arrival of the second generation of direct-acting antivirals in 2011 resulted in improved SVR and a revolution in the field of anti-HCV therapy. Despite the development of drug resistance, the initial NS3-4A protease inhibitors telaprevir and boceprevir undoubtedly possessed advantages over dual IFN/RBV treatment . The success of both drugs was subsequently eclipsed by the licensing of simeprevir and sofosbuvir . The field of HCV therapy is rapidly evolving, and as a result, a large number of new antiviral drugs are currently being evaluated in advanced clinical trials .", "Title: Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus\nPassage: There are approximately 71 million people globally who are chronically infected with hepatitis C virus . A significant number of those with chronic infection will develop cirrhosis, hepatocellular carcinoma or liver failure, resulting in approximately 400,000 deaths each year . Recently approved combination regimens of DAAs, such as sofosbuvir plus ledipasvir or velpatasvir and glecaprevir plus pibrentasvir, have not only drastically improved efficacy outcomes, but have decreased treatment side effects compared to the interferon-containing regimens of the past . Indeed, these regimens have produced sustained virologic response rates greater than 90%, and with treatment duration of 8-12 weeks, depending on", "Title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection\nPassage: Hepatitis C virus is a positive-stranded RNA virus in the family Flaviviridae, and it is estimated 130-170 million people are infected with HCV worldwide . Acute HCV infection is spontaneously cured in 20%-30% of patients, but the majority of infected patients fail to clear the virus and develop chronic persistent infection . In addition to a combination regimen of pegylated interferon -α and ribavirin, direct acting antiviral drugs against HCV have been developed, and a high rate of sustained virological response has been achieved by using these antiviral drugs . However, the high cost of these drugs results in limited" ]

[ [ "0a", "Title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy" ], [ "0b", "Passage: CHC was classically treated with recombinant PEG-IFNalpha in combination with Ribavirin ." ], [ "0c", "The treatment duration was long and wearing, with PEG-IFN-alpha being administered 3 times a week, severe side effects occurring frequently, and still only approximately half of the patients being cured." ], [ "0d", "Since 2014 HCV therapy improved drastically, as several direct acting antivirals targeting HCV NS3/4A protease, NS5A, or NS5B RNA-polymerase were approved." ], [ "0e", "These inhibitors, either alone or in combination with RBV, now heal over 90% of patients treated." ], [ "0f", "Direct acting antivirals are more effective than PEG-IFN-alpha in eliminating HCV, but also treatment duration is shorter , they can be" ] ]

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

[ "Title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy\nPassage: CHC was classically treated with recombinant PEG-IFNalpha in combination with Ribavirin . The treatment duration was long and wearing, with PEG-IFN-alpha being administered 3 times a week, severe side effects occurring frequently, and still only approximately half of the patients being cured. Since 2014 HCV therapy improved drastically, as several direct acting antivirals targeting HCV NS3/4A protease, NS5A, or NS5B RNA-polymerase were approved. These inhibitors, either alone or in combination with RBV, now heal over 90% of patients treated. Direct acting antivirals are more effective than PEG-IFN-alpha in eliminating HCV, but also treatment duration is shorter , they can be", "Title: Advanced Molecular Surveillance of Hepatitis C Virus\nPassage: The arrival of the second generation of direct-acting antivirals in 2011 resulted in improved SVR and a revolution in the field of anti-HCV therapy. Despite the development of drug resistance, the initial NS3-4A protease inhibitors telaprevir and boceprevir undoubtedly possessed advantages over dual IFN/RBV treatment . The success of both drugs was subsequently eclipsed by the licensing of simeprevir and sofosbuvir . The field of HCV therapy is rapidly evolving, and as a result, a large number of new antiviral drugs are currently being evaluated in advanced clinical trials .", "Title: Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus\nPassage: There are approximately 71 million people globally who are chronically infected with hepatitis C virus . A significant number of those with chronic infection will develop cirrhosis, hepatocellular carcinoma or liver failure, resulting in approximately 400,000 deaths each year . Recently approved combination regimens of DAAs, such as sofosbuvir plus ledipasvir or velpatasvir and glecaprevir plus pibrentasvir, have not only drastically improved efficacy outcomes, but have decreased treatment side effects compared to the interferon-containing regimens of the past . Indeed, these regimens have produced sustained virologic response rates greater than 90%, and with treatment duration of 8-12 weeks, depending on", "Title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection\nPassage: Hepatitis C virus is a positive-stranded RNA virus in the family Flaviviridae, and it is estimated 130-170 million people are infected with HCV worldwide . Acute HCV infection is spontaneously cured in 20%-30% of patients, but the majority of infected patients fail to clear the virus and develop chronic persistent infection . In addition to a combination regimen of pegylated interferon -α and ribavirin, direct acting antiviral drugs against HCV have been developed, and a high rate of sustained virological response has been achieved by using these antiviral drugs . However, the high cost of these drugs results in limited" ]

[ [ "1a", "Title: Advanced Molecular Surveillance of Hepatitis C Virus" ], [ "1b", "Passage: The arrival of the second generation of direct-acting antivirals in 2011 resulted in improved SVR and a revolution in the field of anti-HCV therapy." ], [ "1c", "Despite the development of drug resistance, the initial NS3-4A protease inhibitors telaprevir and boceprevir undoubtedly possessed advantages over dual IFN/RBV treatment ." ], [ "1d", "The success of both drugs was subsequently eclipsed by the licensing of simeprevir and sofosbuvir ." ], [ "1e", "The field of HCV therapy is rapidly evolving, and as a result, a large number of new antiviral drugs are currently being evaluated in advanced clinical trials ." ] ]

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

[ "Title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy\nPassage: CHC was classically treated with recombinant PEG-IFNalpha in combination with Ribavirin . The treatment duration was long and wearing, with PEG-IFN-alpha being administered 3 times a week, severe side effects occurring frequently, and still only approximately half of the patients being cured. Since 2014 HCV therapy improved drastically, as several direct acting antivirals targeting HCV NS3/4A protease, NS5A, or NS5B RNA-polymerase were approved. These inhibitors, either alone or in combination with RBV, now heal over 90% of patients treated. Direct acting antivirals are more effective than PEG-IFN-alpha in eliminating HCV, but also treatment duration is shorter , they can be", "Title: Advanced Molecular Surveillance of Hepatitis C Virus\nPassage: The arrival of the second generation of direct-acting antivirals in 2011 resulted in improved SVR and a revolution in the field of anti-HCV therapy. Despite the development of drug resistance, the initial NS3-4A protease inhibitors telaprevir and boceprevir undoubtedly possessed advantages over dual IFN/RBV treatment . The success of both drugs was subsequently eclipsed by the licensing of simeprevir and sofosbuvir . The field of HCV therapy is rapidly evolving, and as a result, a large number of new antiviral drugs are currently being evaluated in advanced clinical trials .", "Title: Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus\nPassage: There are approximately 71 million people globally who are chronically infected with hepatitis C virus . A significant number of those with chronic infection will develop cirrhosis, hepatocellular carcinoma or liver failure, resulting in approximately 400,000 deaths each year . Recently approved combination regimens of DAAs, such as sofosbuvir plus ledipasvir or velpatasvir and glecaprevir plus pibrentasvir, have not only drastically improved efficacy outcomes, but have decreased treatment side effects compared to the interferon-containing regimens of the past . Indeed, these regimens have produced sustained virologic response rates greater than 90%, and with treatment duration of 8-12 weeks, depending on", "Title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection\nPassage: Hepatitis C virus is a positive-stranded RNA virus in the family Flaviviridae, and it is estimated 130-170 million people are infected with HCV worldwide . Acute HCV infection is spontaneously cured in 20%-30% of patients, but the majority of infected patients fail to clear the virus and develop chronic persistent infection . In addition to a combination regimen of pegylated interferon -α and ribavirin, direct acting antiviral drugs against HCV have been developed, and a high rate of sustained virological response has been achieved by using these antiviral drugs . However, the high cost of these drugs results in limited" ]

[ [ "2a", "Title: Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus" ], [ "2b", "Passage: There are approximately 71 million people globally who are chronically infected with hepatitis C virus ." ], [ "2c", "A significant number of those with chronic infection will develop cirrhosis, hepatocellular carcinoma or liver failure, resulting in approximately 400,000 deaths each year ." ], [ "2d", "Recently approved combination regimens of DAAs, such as sofosbuvir plus ledipasvir or velpatasvir and glecaprevir plus pibrentasvir, have not only drastically improved efficacy outcomes, but have decreased treatment side effects compared to the interferon-containing regimens of the past ." ], [ "2e", "Indeed, these regimens have produced sustained virologic response rates greater than 90%, and with treatment duration of 8-12 weeks, depending on" ] ]

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

[ "Title: The Role of Type III Interferons in Hepatitis C Virus Infection and Therapy\nPassage: CHC was classically treated with recombinant PEG-IFNalpha in combination with Ribavirin . The treatment duration was long and wearing, with PEG-IFN-alpha being administered 3 times a week, severe side effects occurring frequently, and still only approximately half of the patients being cured. Since 2014 HCV therapy improved drastically, as several direct acting antivirals targeting HCV NS3/4A protease, NS5A, or NS5B RNA-polymerase were approved. These inhibitors, either alone or in combination with RBV, now heal over 90% of patients treated. Direct acting antivirals are more effective than PEG-IFN-alpha in eliminating HCV, but also treatment duration is shorter , they can be", "Title: Advanced Molecular Surveillance of Hepatitis C Virus\nPassage: The arrival of the second generation of direct-acting antivirals in 2011 resulted in improved SVR and a revolution in the field of anti-HCV therapy. Despite the development of drug resistance, the initial NS3-4A protease inhibitors telaprevir and boceprevir undoubtedly possessed advantages over dual IFN/RBV treatment . The success of both drugs was subsequently eclipsed by the licensing of simeprevir and sofosbuvir . The field of HCV therapy is rapidly evolving, and as a result, a large number of new antiviral drugs are currently being evaluated in advanced clinical trials .", "Title: Preclinical evaluation of AT-527, a novel guanosine nucleotide prodrug with potent, pan-genotypic activity against hepatitis C virus\nPassage: There are approximately 71 million people globally who are chronically infected with hepatitis C virus . A significant number of those with chronic infection will develop cirrhosis, hepatocellular carcinoma or liver failure, resulting in approximately 400,000 deaths each year . Recently approved combination regimens of DAAs, such as sofosbuvir plus ledipasvir or velpatasvir and glecaprevir plus pibrentasvir, have not only drastically improved efficacy outcomes, but have decreased treatment side effects compared to the interferon-containing regimens of the past . Indeed, these regimens have produced sustained virologic response rates greater than 90%, and with treatment duration of 8-12 weeks, depending on", "Title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection\nPassage: Hepatitis C virus is a positive-stranded RNA virus in the family Flaviviridae, and it is estimated 130-170 million people are infected with HCV worldwide . Acute HCV infection is spontaneously cured in 20%-30% of patients, but the majority of infected patients fail to clear the virus and develop chronic persistent infection . In addition to a combination regimen of pegylated interferon -α and ribavirin, direct acting antiviral drugs against HCV have been developed, and a high rate of sustained virological response has been achieved by using these antiviral drugs . However, the high cost of these drugs results in limited" ]

[ [ "3a", "Title: Interferon Response in Hepatitis C Virus (HCV) Infection: Lessons from Cell Culture Systems of HCV Infection" ], [ "3b", "Passage: Hepatitis C virus is a positive-stranded RNA virus in the family Flaviviridae, and it is estimated 130-170 million people are infected with HCV worldwide ." ], [ "3c", "Acute HCV infection is spontaneously cured in 20%-30% of patients, but the majority of infected patients fail to clear the virus and develop chronic persistent infection ." ], [ "3d", "In addition to a combination regimen of pegylated interferon -α and ribavirin, direct acting antiviral drugs against HCV have been developed, and a high rate of sustained virological response has been achieved by using these antiviral drugs ." ], [ "3e", "However, the high cost of these drugs results in limited" ] ]

[ "0b", "0d", "0e", "1b", "1c", "1d", "2d", "2e", "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: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes .", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes ." ]

[ [ "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" ] ]

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

[ "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: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes .", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes ." ]

[ [ "2a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "2b", "Passage: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy." ], [ "2c", "It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes ." ] ]

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

[ "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: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes .", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus\nPassage: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy. It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes ." ]

[ [ "3a", "Title: Identification and characterisation of the CD40-ligand of Sigmodon hispidus" ], [ "3b", "Passage: enhance antigen affinity, and lastly, the formation of long-lived plasma cells and memory B cells .Various studies have been conducted to utilize gene delivery of CD40L to DCs and tumor cells for tumor immunotherapy." ], [ "3c", "It was found that expression of CD40L in a small proportion of tumor cells was sufficient to generate a long-lasting systemic anti-tumor immune response in mice that was shown to be dependent on cytotoxic T lymphocytes ." ] ]

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

[ "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: shedding was low or missed by swab timing. These 7 cases are termed \"pH1N1+ILI. \" Donors with ILI symptoms but negative PCR and no seroconversion are termed \"non-pH1N1 febrile illness. \" Six pH1N1 infections were detected by seroconversion in donors asymptomatic or reporting symptoms milder than ILI. They are termed \"mild/asymptomatic. \"", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: Responses of 153 donors are shown in Figure 1A ; To assess linkage to reduction in symptoms, baseline T-cell results were compared for donors later infected with pH1N1 who had ILI versus those with mild/ asymptomatic infections . There was a trend toward greater T-cell responses in the mild/asymptomatic group, but the difference was not statistically significant. We also compared our 2 small groups of infected donors for IFN-γ responses to the peptides with which other investigators found T-cell differences: NP pools only rather than total ELISPOT in the case of Hayward et al , and NP, M, PB1 9-mer", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic\nPassage: of a certain human leukocyte antigen -B family react to this peptide, but not all donors. Thus, this marker could not be used alone for screening purposes but perhaps as part of a group of markers. We describe it as an interesting case study and proof-of-concept for this type of testing. ). One hundred thirty-seven donor sera were tested; each circle represents 1 donor. The solid red circles represent values above a 3% threshold considered positive. Open black circles are considered negative. Values <0 reflect more binding to untransfected cells than to transfected cells , which is presumably nonspecific.", "Title: Pandemic influenza A/H1N1 virus infection and TNF, LTA, IL1B, IL6, IL8, and CCL polymorphisms in Mexican population: a case–control study\nPassage: The patients were separated into two groups depending whether they were positive or negative for influenza A/H1N1, thereby forming the groups, influenza A/H1N1 and ILI, respectively. In both the A/H1N1 and ILI groups, the majority was male , whereas in the AHC group, 61.93% were female. The mean age of the A/H1N1 and ILI groups was <45 years , compared to that of the AHC group, 56.82% of who were 45-64 years of age." ]

[ [ "0a", "Title: Surveillance Study of Influenza Occurrence and Immunity in a Wisconsin Cohort During the 2009 Pandemic" ], [ "0b", "Passage: shedding was low or missed by swab timing." ], [ "0c", "These 7 cases are termed \"pH1N1+ILI. \"" ], [ "0d", "Donors with ILI symptoms but negative PCR and no seroconversion are termed \"non-pH1N1 febrile illness. \"" ], [ "0e", "Six pH1N1 infections were detected by seroconversion in donors asymptomatic or reporting symptoms milder than ILI." ], [ "0f", "They are termed \"mild/asymptomatic. \"" ] ]

[ "0d" ]

[ "Title: Pandemic A/H1N1v influenza 2009 in hospitalized children: a multicenter Belgian survey\nPassage: least 17700 deaths worldwide and the Centers for Disease Control and Prevention reported 59 millions infected people in the USA ).", "Title: Low-Cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR\nPassage: It is estimated that 33.2 million people were infected with HIV-1 at the end of 2007; 2.5 million were children under 15 years of age, the majority of whom acquired infection through mother-tochild transmission ). Antiretroviral therapy is effective at blocking MTCT and can markedly improve the outcome of pediatric HIV-1 infection. However, efforts to provide widespread access to ART have been hampered by the limited availability of infant diagnostic methods. Methods to diagnose and monitor HIV-1 infection in resource-poor settings are usually limited to serologic assays and CD4/CD8 counts. However, antibody based assays can reliably guide diagnosis and management", "Title: HIV/AIDS prevention in China: A challenge for the new millennium\nPassage: about 30,000 HIV cases nationwide, although their official count was later revised 25-fold upwards to 840,000. By 2003 the United Nations had estimated that the number of cases was closer to 1.5 million . In the first half of 2001 alone, China's HIV incidence rate increased by 67% , and at least 80,000 people now have full-blown AIDS . The Chinese Academy of Preventive Medicine finally acknowledged in 2001 that they may soon have the largest HIV infected population in the world, possibly 6 million cases by 2005 . With infection rates now rising at about 30% per year, the", "Title: Worldwide circulation of HSV-2 × HSV-1 recombinant strains\nPassage: America, and Africa, with a few from Asia or of unknown origin. Men comprised 38% of the cohort with 50% women and 12% unknown, while 44% were HIV-1 infected, 45% HIV-1 uninfected, and 11% unknown." ]

[ [ "1a", "Title: Low-Cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR" ], [ "1b", "Passage: It is estimated that 33.2 million people were infected with HIV-1 at the end of 2007; 2.5 million were children under 15 years of age, the majority of whom acquired infection through mother-tochild transmission )." ], [ "1c", "Antiretroviral therapy is effective at blocking MTCT and can markedly improve the outcome of pediatric HIV-1 infection." ], [ "1d", "However, efforts to provide widespread access to ART have been hampered by the limited availability of infant diagnostic methods." ], [ "1e", "Methods to diagnose and monitor HIV-1 infection in resource-poor settings are usually limited to serologic assays and CD4/CD8 counts." ], [ "1f", "However, antibody based assays can reliably guide diagnosis and management" ] ]

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

[ "Title: Pandemic A/H1N1v influenza 2009 in hospitalized children: a multicenter Belgian survey\nPassage: least 17700 deaths worldwide and the Centers for Disease Control and Prevention reported 59 millions infected people in the USA ).", "Title: Low-Cost HIV-1 Diagnosis and Quantification in Dried Blood Spots by Real Time PCR\nPassage: It is estimated that 33.2 million people were infected with HIV-1 at the end of 2007; 2.5 million were children under 15 years of age, the majority of whom acquired infection through mother-tochild transmission ). Antiretroviral therapy is effective at blocking MTCT and can markedly improve the outcome of pediatric HIV-1 infection. However, efforts to provide widespread access to ART have been hampered by the limited availability of infant diagnostic methods. Methods to diagnose and monitor HIV-1 infection in resource-poor settings are usually limited to serologic assays and CD4/CD8 counts. However, antibody based assays can reliably guide diagnosis and management", "Title: HIV/AIDS prevention in China: A challenge for the new millennium\nPassage: about 30,000 HIV cases nationwide, although their official count was later revised 25-fold upwards to 840,000. By 2003 the United Nations had estimated that the number of cases was closer to 1.5 million . In the first half of 2001 alone, China's HIV incidence rate increased by 67% , and at least 80,000 people now have full-blown AIDS . The Chinese Academy of Preventive Medicine finally acknowledged in 2001 that they may soon have the largest HIV infected population in the world, possibly 6 million cases by 2005 . With infection rates now rising at about 30% per year, the", "Title: Worldwide circulation of HSV-2 × HSV-1 recombinant strains\nPassage: America, and Africa, with a few from Asia or of unknown origin. Men comprised 38% of the cohort with 50% women and 12% unknown, while 44% were HIV-1 infected, 45% HIV-1 uninfected, and 11% unknown." ]

[ [ "2a", "Title: HIV/AIDS prevention in China: A challenge for the new millennium" ], [ "2b", "Passage: about 30,000 HIV cases nationwide, although their official count was later revised 25-fold upwards to 840,000." ], [ "2c", "By 2003 the United Nations had estimated that the number of cases was closer to 1.5 million ." ], [ "2d", "In the first half of 2001 alone, China's HIV incidence rate increased by 67% , and at least 80,000 people now have full-blown AIDS ." ], [ "2e", "The Chinese Academy of Preventive Medicine finally acknowledged in 2001 that they may soon have the largest HIV infected population in the world, possibly 6 million cases by 2005 ." ], [ "2f", "With infection rates now rising at about 30% per year, the" ] ]

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

[ "Title: Nearly Complete Genome Sequence of an Echovirus 30 Strain from a Cluster of Aseptic Meningitis Cases in California, September 2017\nPassage: According to the California Code of Regulations, meningitis cases are reportable to the California Department of Public Health within 1 day of identification of etiology . In the fall of 2017, a cluster of aseptic meningitis cases from a northern California high school were reported to the CDPH. The Viral and Rickettsial Disease Laboratory at the CDPH detected EV from 19 of 30 patients by real-time reverse transcription-PCR , as previously described . We generated and analyzed partial capsid ) sequences using methods developed by Minnaar et al. . Fifteen of 19 EV-positive patients were confirmed to have echovirus 30", "Title: The combination of decoy receptor 3 and soluble triggering receptor expressed on myeloid cells-1 for the diagnosis of nosocomial bacterial meningitis\nPassage: Diagnosis of bacterial meningitis was based on a positive result of CSF culture. Nosocomial meningitis was defined as negative bacterial infection when the patient was admitted to the hospital, clinical evidence of an infection was found after 48 hours on admission or within one month after discharge from the hospital where the patient had received an invasive neurosurgical procedure. Otherwise, the patient was considered to have community-acquired meningitis . External ventricular drain-related meningitis was diagnosed with bacterial infection being found within 7 days of external ventricular drain removal .", "Title: Description of two measles outbreaks in the Lazio Region, Italy (2006-2007). Importance of pockets of low vaccine coverage in sustaining the infection\nPassage: In Italy, measles is a disease subject to mandatory notification, and according to the routine procedure, physicians must report suspected measles cases to their LHU within 48 hours of diagnosis. The local health authorities then report confirmed measles cases to the ASP monthly. At the beginning of the outbreaks this procedure was modified and physicians were asked to report suspected measles cases to both the local health authorities and ASP offices within 24 hours of diagnosis. Personnel of the LHUs performed epidemiological investigation of suspected cases including laboratory investigation and contact tracing.", "Title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China\nPassage: before the onset of any symptom. The epidemiological investigations were performed through direct contacts in the relevant village, community, or school, or through direct contacts for mass gathering events. The clinically confirmed and laboratory-confirmed cases were both regarded as cases, and reporting personnel were required to report such cases to the NIDMIS within 6 hours." ]

[ [ "0a", "Title: Nearly Complete Genome Sequence of an Echovirus 30 Strain from a Cluster of Aseptic Meningitis Cases in California, September 2017" ], [ "0b", "Passage: According to the California Code of Regulations, meningitis cases are reportable to the California Department of Public Health within 1 day of identification of etiology ." ], [ "0c", "In the fall of 2017, a cluster of aseptic meningitis cases from a northern California high school were reported to the CDPH." ], [ "0d", "The Viral and Rickettsial Disease Laboratory at the CDPH detected EV from 19 of 30 patients by real-time reverse transcription-PCR , as previously described ." ], [ "0e", "We generated and analyzed partial capsid ) sequences using methods developed by Minnaar et al. ." ], [ "0f", "Fifteen of 19 EV-positive patients were confirmed to have echovirus 30" ] ]

[ "0b" ]

[ "Title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity\nPassage: transduction, cell differentiation, and development to cell cycle control and metabolism. Enzymes and receptors can be switched \"on\" and \"off \" by phosphorylation and dephosphorylation. It was estimated that 10-50% of proteins are phosphorylated. Phosphorylation often occurs on serine, threonine, and tyrosine residues in eukaryotic proteins . Analysis of the entire cellular phosphoproteome has been an attractive study subject since the discovery of phosphorylation as a key regulatory mechanism of cell life. Unfortunately, phosphoproteins analysis is not straightforward for five main reasons. First, the stoichiometry of phosphorylation is generally relatively low, because only a small fraction of the available intracellular", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: CK2 inhibitors were found to depress GH-induced activation of STAT5, consistent with CK2 playing a role in GH signaling. With kinases like CK2 that are constitutively active, the regulation of ligand-dependent signaling likely requires a change in the conformation of protein substrates or altered subcellular localization of substrates or kinases to permit phosphorylation. Therefore, for potential substrates of CK2, it may be informative to determine whether any GH-dependent changes in subcellular localization of the substrates can be detected.", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: ACLY is the primary enzyme responsible for the synthesis of cytosolic acetyl-coenzyme A in many tissues. Phosphorylation of ACLY Ser455 by Akt has been shown to activate ACLY .", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: To gain insight into the reliability of the identification of the novel GH-dependent phosphosites, we performed immunoblotting with phosphospecific antibodies. Sites with available antibodies included three sites in proteins associated with the mTOR pathway , one site identified in a protein in the insulin and focal adhesion categories , and one site identified in a protein involved in regulation of actin cytoskeleton . Of these, PRAS40 Thr247 and NHE1 Ser707 fell into the category of Akt/PKA substrate sites. We also tested for phosphorylation at two additional Akt/PKA substrate consensus sites, NDRG1 Ser330 and ACLY Ser455. All of these sites were" ]

[ [ "1a", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics" ], [ "1b", "Passage: CK2 inhibitors were found to depress GH-induced activation of STAT5, consistent with CK2 playing a role in GH signaling." ], [ "1c", "With kinases like CK2 that are constitutively active, the regulation of ligand-dependent signaling likely requires a change in the conformation of protein substrates or altered subcellular localization of substrates or kinases to permit phosphorylation." ], [ "1d", "Therefore, for potential substrates of CK2, it may be informative to determine whether any GH-dependent changes in subcellular localization of the substrates can be detected." ] ]

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

[ "Title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity\nPassage: transduction, cell differentiation, and development to cell cycle control and metabolism. Enzymes and receptors can be switched \"on\" and \"off \" by phosphorylation and dephosphorylation. It was estimated that 10-50% of proteins are phosphorylated. Phosphorylation often occurs on serine, threonine, and tyrosine residues in eukaryotic proteins . Analysis of the entire cellular phosphoproteome has been an attractive study subject since the discovery of phosphorylation as a key regulatory mechanism of cell life. Unfortunately, phosphoproteins analysis is not straightforward for five main reasons. First, the stoichiometry of phosphorylation is generally relatively low, because only a small fraction of the available intracellular", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: CK2 inhibitors were found to depress GH-induced activation of STAT5, consistent with CK2 playing a role in GH signaling. With kinases like CK2 that are constitutively active, the regulation of ligand-dependent signaling likely requires a change in the conformation of protein substrates or altered subcellular localization of substrates or kinases to permit phosphorylation. Therefore, for potential substrates of CK2, it may be informative to determine whether any GH-dependent changes in subcellular localization of the substrates can be detected.", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: ACLY is the primary enzyme responsible for the synthesis of cytosolic acetyl-coenzyme A in many tissues. Phosphorylation of ACLY Ser455 by Akt has been shown to activate ACLY .", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: To gain insight into the reliability of the identification of the novel GH-dependent phosphosites, we performed immunoblotting with phosphospecific antibodies. Sites with available antibodies included three sites in proteins associated with the mTOR pathway , one site identified in a protein in the insulin and focal adhesion categories , and one site identified in a protein involved in regulation of actin cytoskeleton . Of these, PRAS40 Thr247 and NHE1 Ser707 fell into the category of Akt/PKA substrate sites. We also tested for phosphorylation at two additional Akt/PKA substrate consensus sites, NDRG1 Ser330 and ACLY Ser455. All of these sites were" ]

[ [ "2a", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics" ], [ "2b", "Passage: ACLY is the primary enzyme responsible for the synthesis of cytosolic acetyl-coenzyme A in many tissues." ], [ "2c", "Phosphorylation of ACLY Ser455 by Akt has been shown to activate ACLY ." ] ]

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

[ "Title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity\nPassage: transduction, cell differentiation, and development to cell cycle control and metabolism. Enzymes and receptors can be switched \"on\" and \"off \" by phosphorylation and dephosphorylation. It was estimated that 10-50% of proteins are phosphorylated. Phosphorylation often occurs on serine, threonine, and tyrosine residues in eukaryotic proteins . Analysis of the entire cellular phosphoproteome has been an attractive study subject since the discovery of phosphorylation as a key regulatory mechanism of cell life. Unfortunately, phosphoproteins analysis is not straightforward for five main reasons. First, the stoichiometry of phosphorylation is generally relatively low, because only a small fraction of the available intracellular", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: CK2 inhibitors were found to depress GH-induced activation of STAT5, consistent with CK2 playing a role in GH signaling. With kinases like CK2 that are constitutively active, the regulation of ligand-dependent signaling likely requires a change in the conformation of protein substrates or altered subcellular localization of substrates or kinases to permit phosphorylation. Therefore, for potential substrates of CK2, it may be informative to determine whether any GH-dependent changes in subcellular localization of the substrates can be detected.", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: ACLY is the primary enzyme responsible for the synthesis of cytosolic acetyl-coenzyme A in many tissues. Phosphorylation of ACLY Ser455 by Akt has been shown to activate ACLY .", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: To gain insight into the reliability of the identification of the novel GH-dependent phosphosites, we performed immunoblotting with phosphospecific antibodies. Sites with available antibodies included three sites in proteins associated with the mTOR pathway , one site identified in a protein in the insulin and focal adhesion categories , and one site identified in a protein involved in regulation of actin cytoskeleton . Of these, PRAS40 Thr247 and NHE1 Ser707 fell into the category of Akt/PKA substrate sites. We also tested for phosphorylation at two additional Akt/PKA substrate consensus sites, NDRG1 Ser330 and ACLY Ser455. All of these sites were" ]

[ [ "3a", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics" ], [ "3b", "Passage: To gain insight into the reliability of the identification of the novel GH-dependent phosphosites, we performed immunoblotting with phosphospecific antibodies." ], [ "3c", "Sites with available antibodies included three sites in proteins associated with the mTOR pathway , one site identified in a protein in the insulin and focal adhesion categories , and one site identified in a protein involved in regulation of actin cytoskeleton ." ], [ "3d", "Of these, PRAS40 Thr247 and NHE1 Ser707 fell into the category of Akt/PKA substrate sites." ], [ "3e", "We also tested for phosphorylation at two additional Akt/PKA substrate consensus sites, NDRG1 Ser330 and ACLY Ser455." ], [ "3f", "All of these sites were" ] ]

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

[ "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1\nPassage: spillover . In humans, VEEV causes a febrile illness typified by fever, malaise, and vomiting. In some cases, infection progresses to the central nervous system and neurological symptoms, such as confusion, ataxia, and seizures, manifest. The mortality rate among cases with neurological symptoms can be as high as 35% in children and 10% in adults, with long-term neurological deficits often being seen in survivors . In 1995, an outbreak of VEEV in Colombia and Venezuela resulted in over 100,000 human cases . In addition to natural outbreaks, VEEV is also a concern from a bioterrorism perspective, as it can be", "Title: Treatment of Neuroterrorism\nPassage: Diseases caused by alphaviruses are mainly neurological and include Venezuelan equine encephalomyelitis and Eastern and Western equine encephalomyelitis. This disease occurs naturally in North, Central, or South America, but human illness is rare, and most infections result in nonspecific symptoms of fever, headache, and myalgia. Less than 6% of infected adults or children will develop encephalitis, however the mortality rate of those can be as high as 50 to 75% for Eastern equine encephalitis , which is the most severe of these infections, and survivors frequently have neurological sequelae .", "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 ." ]

[ [ "0a", "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1" ], [ "0b", "Passage: spillover ." ], [ "0c", "In humans, VEEV causes a febrile illness typified by fever, malaise, and vomiting." ], [ "0d", "In some cases, infection progresses to the central nervous system and neurological symptoms, such as confusion, ataxia, and seizures, manifest." ], [ "0e", "The mortality rate among cases with neurological symptoms can be as high as 35% in children and 10% in adults, with long-term neurological deficits often being seen in survivors ." ], [ "0f", "In 1995, an outbreak of VEEV in Colombia and Venezuela resulted in over 100,000 human cases ." ], [ "0g", "In addition to natural outbreaks, VEEV is also a concern from a bioterrorism perspective, as it can be" ] ]

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

[ "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1\nPassage: spillover . In humans, VEEV causes a febrile illness typified by fever, malaise, and vomiting. In some cases, infection progresses to the central nervous system and neurological symptoms, such as confusion, ataxia, and seizures, manifest. The mortality rate among cases with neurological symptoms can be as high as 35% in children and 10% in adults, with long-term neurological deficits often being seen in survivors . In 1995, an outbreak of VEEV in Colombia and Venezuela resulted in over 100,000 human cases . In addition to natural outbreaks, VEEV is also a concern from a bioterrorism perspective, as it can be", "Title: Treatment of Neuroterrorism\nPassage: Diseases caused by alphaviruses are mainly neurological and include Venezuelan equine encephalomyelitis and Eastern and Western equine encephalomyelitis. This disease occurs naturally in North, Central, or South America, but human illness is rare, and most infections result in nonspecific symptoms of fever, headache, and myalgia. Less than 6% of infected adults or children will develop encephalitis, however the mortality rate of those can be as high as 50 to 75% for Eastern equine encephalitis , which is the most severe of these infections, and survivors frequently have neurological sequelae .", "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 ." ]

[ [ "1a", "Title: Treatment of Neuroterrorism" ], [ "1b", "Passage: Diseases caused by alphaviruses are mainly neurological and include Venezuelan equine encephalomyelitis and Eastern and Western equine encephalomyelitis." ], [ "1c", "This disease occurs naturally in North, Central, or South America, but human illness is rare, and most infections result in nonspecific symptoms of fever, headache, and myalgia." ], [ "1d", "Less than 6% of infected adults or children will develop encephalitis, however the mortality rate of those can be as high as 50 to 75% for Eastern equine encephalitis , which is the most severe of these infections, and survivors frequently have neurological sequelae ." ] ]

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

[ "Title: Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1\nPassage: spillover . In humans, VEEV causes a febrile illness typified by fever, malaise, and vomiting. In some cases, infection progresses to the central nervous system and neurological symptoms, such as confusion, ataxia, and seizures, manifest. The mortality rate among cases with neurological symptoms can be as high as 35% in children and 10% in adults, with long-term neurological deficits often being seen in survivors . In 1995, an outbreak of VEEV in Colombia and Venezuela resulted in over 100,000 human cases . In addition to natural outbreaks, VEEV is also a concern from a bioterrorism perspective, as it can be", "Title: Treatment of Neuroterrorism\nPassage: Diseases caused by alphaviruses are mainly neurological and include Venezuelan equine encephalomyelitis and Eastern and Western equine encephalomyelitis. This disease occurs naturally in North, Central, or South America, but human illness is rare, and most infections result in nonspecific symptoms of fever, headache, and myalgia. Less than 6% of infected adults or children will develop encephalitis, however the mortality rate of those can be as high as 50 to 75% for Eastern equine encephalitis , which is the most severe of these infections, and survivors frequently have neurological sequelae .", "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 ." ]

[ [ "2a", "Title: Treatment of Neuroterrorism" ], [ "2b", "Passage: Venezuelan equine encephalitis virus is an alphavirus that is most commonly found in Central and South America." ], [ "2c", "It is transmitted to humans by mosquitoes." ], [ "2d", "In case of a bioterrorist attack, the distribution would be made through aerosols ." ], [ "2e", "The virus usually leads to an initial severe febrile illness in nearly everyone exposed at 1 to 6 days after exposure." ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Ninety-five percent of infected adults are symptomatic after infection, and of these, most become disabled for weeks to months as a result of decreased dexterity, loss of mobility, and delayed reaction. Eighteen months after disease onset, 40% of patients are found to still have anti-CHIKV IgM . The chronic stage of CHIKF is characterized by polyarthralgia that can last from weeks to years beyond the acute stage . CHIKV has been shown to attack fibroblasts, explaining the involvement of muscles, joints, and skin connective tissues. The high number of nociceptive nerve endings found within the joints and muscle connective tissues", "Title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses\nPassage: rashes, arthralgia and myalgia. The typical clinical sign of the disease is poly-arthralgia, which is a very painful condition affecting joints and may persist for several months to years in some cases . Being an arthropodborne virus, the mode of transmission is the mosquitoes of the Aedes spp. It is generally accepted that CHIKV originated from Africa, where it is primarily maintained in a yellow fever-like zoonotic sylvatic cycle and depends upon non-human primates and arboreal, peridomestic mosquitoes as reservoir hosts. However, the spread of CHIKV in Asia and urban endemics are associated with a dengue-like ''human-mosquito-human'' direct transmission cycle,", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: can explain pain associated with CHIKF ." ]

[ [ "0a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "0b", "Passage: Ninety-five percent of infected adults are symptomatic after infection, and of these, most become disabled for weeks to months as a result of decreased dexterity, loss of mobility, and delayed reaction." ], [ "0c", "Eighteen months after disease onset, 40% of patients are found to still have anti-CHIKV IgM ." ], [ "0d", "The chronic stage of CHIKF is characterized by polyarthralgia that can last from weeks to years beyond the acute stage ." ], [ "0e", "CHIKV has been shown to attack fibroblasts, explaining the involvement of muscles, joints, and skin connective tissues." ], [ "0f", "The high number of nociceptive nerve endings found within the joints and muscle connective tissues" ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Ninety-five percent of infected adults are symptomatic after infection, and of these, most become disabled for weeks to months as a result of decreased dexterity, loss of mobility, and delayed reaction. Eighteen months after disease onset, 40% of patients are found to still have anti-CHIKV IgM . The chronic stage of CHIKF is characterized by polyarthralgia that can last from weeks to years beyond the acute stage . CHIKV has been shown to attack fibroblasts, explaining the involvement of muscles, joints, and skin connective tissues. The high number of nociceptive nerve endings found within the joints and muscle connective tissues", "Title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses\nPassage: rashes, arthralgia and myalgia. The typical clinical sign of the disease is poly-arthralgia, which is a very painful condition affecting joints and may persist for several months to years in some cases . Being an arthropodborne virus, the mode of transmission is the mosquitoes of the Aedes spp. It is generally accepted that CHIKV originated from Africa, where it is primarily maintained in a yellow fever-like zoonotic sylvatic cycle and depends upon non-human primates and arboreal, peridomestic mosquitoes as reservoir hosts. However, the spread of CHIKV in Asia and urban endemics are associated with a dengue-like ''human-mosquito-human'' direct transmission cycle,", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: can explain pain associated with CHIKF ." ]

[ [ "1a", "Title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses" ], [ "1b", "Passage: rashes, arthralgia and myalgia." ], [ "1c", "The typical clinical sign of the disease is poly-arthralgia, which is a very painful condition affecting joints and may persist for several months to years in some cases ." ], [ "1d", "Being an arthropodborne virus, the mode of transmission is the mosquitoes of the Aedes spp." ], [ "1e", "It is generally accepted that CHIKV originated from Africa, where it is primarily maintained in a yellow fever-like zoonotic sylvatic cycle and depends upon non-human primates and arboreal, peridomestic mosquitoes as reservoir hosts." ], [ "1f", "However, the spread of CHIKV in Asia and urban endemics are associated with a dengue-like ''human-mosquito-human'' direct transmission cycle," ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Ninety-five percent of infected adults are symptomatic after infection, and of these, most become disabled for weeks to months as a result of decreased dexterity, loss of mobility, and delayed reaction. Eighteen months after disease onset, 40% of patients are found to still have anti-CHIKV IgM . The chronic stage of CHIKF is characterized by polyarthralgia that can last from weeks to years beyond the acute stage . CHIKV has been shown to attack fibroblasts, explaining the involvement of muscles, joints, and skin connective tissues. The high number of nociceptive nerve endings found within the joints and muscle connective tissues", "Title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses\nPassage: rashes, arthralgia and myalgia. The typical clinical sign of the disease is poly-arthralgia, which is a very painful condition affecting joints and may persist for several months to years in some cases . Being an arthropodborne virus, the mode of transmission is the mosquitoes of the Aedes spp. It is generally accepted that CHIKV originated from Africa, where it is primarily maintained in a yellow fever-like zoonotic sylvatic cycle and depends upon non-human primates and arboreal, peridomestic mosquitoes as reservoir hosts. However, the spread of CHIKV in Asia and urban endemics are associated with a dengue-like ''human-mosquito-human'' direct transmission cycle,", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: can explain pain associated with CHIKF ." ]

[ [ "2a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "2b", "Passage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times ." ], [ "2c", "CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator ." ], [ "2d", "CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures ." ], [ "2e", "The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends" ] ]

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

[ "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: Endothelial cells create a physical barrier on the luminal surface of blood and lymphatic vessels. This barrier must be traversed by blood-borne pathogens and immune cells trafficking between tissues and the bloodstream. Many herpesviruses require systemic spread for persistence within a host, and therefore must cross such an endothelial cell barrier. To date, herpesviruses have been implicated as potential initiators of arterial injury, endothelial dysfunction, and local inflammation, possibly contributing to the pathogenesis of atherosclerosis . Human cytomegalovirus , a betaherpesvirus, infects endothelial cells in vivo. Studies have shown that infected endothelial cells play a role in HCMV dissemination and", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: Endothelial cells serve as a natural site of infection and possible viral reservoir of HCMV , suggesting a role for HCMVinfected endothelial cells in viral spread and persistence. Additionally, recent reports implicate circulating endothelial progenitor cells as potential reservoirs of KSHV and possible precursors of KS spindle cells . However, the specific mechanisms by which infected endothelial cells contribute to the pathogenesis of these human viruses remains unclear. Murine cHV68 pathogenesis involves dissemination from the lung to lymph nodes, spleen, and peritoneum . In light of this systemic spread, cHV68 likely encounters an endothelial cell barrier.", "Title: The Battle Between Influenza and the Innate Immune Response in the Human Respiratory Tract\nPassage: Endothelial cells in the past were considered as collateral damage when the process of DAD was initiated as a loss of the endothelial integrity with subsequent microvascular leakage was a key feature in bacterial sepsis and in viral infection such as H5N1 . In the 2009 pandemic autopsy studies demonstrated viral antigen in endothelial cells and if the same can be demonstrated in H5N1 infection this may explain the extrapulmonary dissemination of virus in these infections . It has also been shown that polarized endothelial cells can be infected in vitro . Intriguingly recent publications have shown that endothelial cells", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: infection." ]

[ [ "0a", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection" ], [ "0b", "Passage: Endothelial cells create a physical barrier on the luminal surface of blood and lymphatic vessels." ], [ "0c", "This barrier must be traversed by blood-borne pathogens and immune cells trafficking between tissues and the bloodstream." ], [ "0d", "Many herpesviruses require systemic spread for persistence within a host, and therefore must cross such an endothelial cell barrier." ], [ "0e", "To date, herpesviruses have been implicated as potential initiators of arterial injury, endothelial dysfunction, and local inflammation, possibly contributing to the pathogenesis of atherosclerosis ." ], [ "0f", "Human cytomegalovirus , a betaherpesvirus, infects endothelial cells in vivo." ], [ "0g", "Studies have shown that infected endothelial cells play a role in HCMV dissemination and" ] ]

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

[ "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: Endothelial cells create a physical barrier on the luminal surface of blood and lymphatic vessels. This barrier must be traversed by blood-borne pathogens and immune cells trafficking between tissues and the bloodstream. Many herpesviruses require systemic spread for persistence within a host, and therefore must cross such an endothelial cell barrier. To date, herpesviruses have been implicated as potential initiators of arterial injury, endothelial dysfunction, and local inflammation, possibly contributing to the pathogenesis of atherosclerosis . Human cytomegalovirus , a betaherpesvirus, infects endothelial cells in vivo. Studies have shown that infected endothelial cells play a role in HCMV dissemination and", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: Endothelial cells serve as a natural site of infection and possible viral reservoir of HCMV , suggesting a role for HCMVinfected endothelial cells in viral spread and persistence. Additionally, recent reports implicate circulating endothelial progenitor cells as potential reservoirs of KSHV and possible precursors of KS spindle cells . However, the specific mechanisms by which infected endothelial cells contribute to the pathogenesis of these human viruses remains unclear. Murine cHV68 pathogenesis involves dissemination from the lung to lymph nodes, spleen, and peritoneum . In light of this systemic spread, cHV68 likely encounters an endothelial cell barrier.", "Title: The Battle Between Influenza and the Innate Immune Response in the Human Respiratory Tract\nPassage: Endothelial cells in the past were considered as collateral damage when the process of DAD was initiated as a loss of the endothelial integrity with subsequent microvascular leakage was a key feature in bacterial sepsis and in viral infection such as H5N1 . In the 2009 pandemic autopsy studies demonstrated viral antigen in endothelial cells and if the same can be demonstrated in H5N1 infection this may explain the extrapulmonary dissemination of virus in these infections . It has also been shown that polarized endothelial cells can be infected in vitro . Intriguingly recent publications have shown that endothelial cells", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection\nPassage: infection." ]

[ [ "1a", "Title: Endothelial Cells Support Persistent Gammaherpesvirus 68 Infection" ], [ "1b", "Passage: Endothelial cells serve as a natural site of infection and possible viral reservoir of HCMV , suggesting a role for HCMVinfected endothelial cells in viral spread and persistence." ], [ "1c", "Additionally, recent reports implicate circulating endothelial progenitor cells as potential reservoirs of KSHV and possible precursors of KS spindle cells ." ], [ "1d", "However, the specific mechanisms by which infected endothelial cells contribute to the pathogenesis of these human viruses remains unclear." ], [ "1e", "Murine cHV68 pathogenesis involves dissemination from the lung to lymph nodes, spleen, and peritoneum ." ], [ "1f", "In light of this systemic spread, cHV68 likely encounters an endothelial cell barrier." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Text: The prevalence of chronic airway inflammatory disease is increasing worldwide especially in developed nations . This disease is characterized by airway inflammation leading to complications such as coughing, wheezing and shortness of breath. The disease can manifest in both the upper airway and lower airway which greatly affect the patients' quality of life . Treatment and management vary greatly in efficacy due to the complexity and heterogeneity of the disease. This is further complicated by the effect of episodic exacerbations of the disease, defined as worsening of disease symptoms including wheeze, cough, breathlessness and chest tightness . Such exacerbations", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of tight junction increasing the leakiness further augments the inflammation and exacerbations. In addition, viral infections are usually accompanied with oxidative stress which will further increase the local inflammation in the airway. The dysregulation of inflammation can be further compounded by modulation of miRNAs and epigenetic modification such as DNA methylation and histone modifications that promote dysregulation in inflammation. Finally, the change in the local airway environment and inflammation promotes growth of pathogenic bacteria that may replace the airway microbiome. Furthermore, the inflammatory environment may also disperse upper airway commensals into the lower airway, further causing inflammation and alteration of", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another recent area of interest is the relationship between asthma and COPD exacerbations and their association with the airway microbiome. The development of chronic airway inflammatory diseases is usually linked to specific bacterial species in the microbiome which may thrive in the inflamed airway environment . In the event of a viral infection such as RV infection, the effect induced by the virus may destabilize the equilibrium of the microbiome present . In addition, viral infection may disrupt biofilm colonies in the upper airway microbiome to be release into the lower airway and worsening the inflammation . Moreover, a viral" ]

[ [ "3a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "3b", "Passage: Another recent area of interest is the relationship between asthma and COPD exacerbations and their association with the airway microbiome." ], [ "3c", "The development of chronic airway inflammatory diseases is usually linked to specific bacterial species in the microbiome which may thrive in the inflamed airway environment ." ], [ "3d", "In the event of a viral infection such as RV infection, the effect induced by the virus may destabilize the equilibrium of the microbiome present ." ], [ "3e", "In addition, viral infection may disrupt biofilm colonies in the upper airway microbiome to be release into the lower airway and worsening the inflammation ." ], [ "3f", "Moreover, a viral" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: is is in agreement with the study done by Ahmad to estimate the survival rate in MERS-CoV globally prior to 26 January 2017; 86.9% were not health-care workers compared with 13.1% confirmed cases of healthcare workers . Similarly, other studies also reported a lower prevalence in healthcare workers .", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: virus is usually described by the media as 'deadly' and although this is true in the sense that it has caused deaths, the nuances of uncertain case fatality rates in the early stages of an outbreak are not being communicated. The current estimated case fatality rate seems to be around 3% which is significant but not comparable to the 10% rate for SARS or 34% reported for MERS. These misperceptions are still driving public anxiety.", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers." ]

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

[ "0c", "2c" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: is is in agreement with the study done by Ahmad to estimate the survival rate in MERS-CoV globally prior to 26 January 2017; 86.9% were not health-care workers compared with 13.1% confirmed cases of healthcare workers . Similarly, other studies also reported a lower prevalence in healthcare workers .", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: virus is usually described by the media as 'deadly' and although this is true in the sense that it has caused deaths, the nuances of uncertain case fatality rates in the early stages of an outbreak are not being communicated. The current estimated case fatality rate seems to be around 3% which is significant but not comparable to the 10% rate for SARS or 34% reported for MERS. These misperceptions are still driving public anxiety.", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers." ]

[ [ "2a", "Title: SARS to novel coronavirus – old lessons and new lessons" ], [ "2b", "Passage: virus is usually described by the media as 'deadly' and although this is true in the sense that it has caused deaths, the nuances of uncertain case fatality rates in the early stages of an outbreak are not being communicated." ], [ "2c", "The current estimated case fatality rate seems to be around 3% which is significant but not comparable to the 10% rate for SARS or 34% reported for MERS." ], [ "2d", "These misperceptions are still driving public anxiety." ] ]

[ "0c", "2c" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In the only study to examine the effect of sample type on molecular analysis, 64 nasopharyngeal aspirates , 30 tracheal aspirates, 13 sputa and three BAL were examined. The tracheal aspirates and BAL returned the highest viral load values followed by NPA and sputum. Unsurprisingly, higher viral loads generally paralleled whole genome sequencing and culture success and, in NPA testing, were significantly correlated with severe disease and death . This study demonstrated the importance of LRT sampling for whole genome sequencing.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: absent or non-productive or because the viral load is low . Despite this both the largest human MERS-CoV studies and smaller ones , use samples from the URT. It is then noteworthy that one study reported an association between higher loads in the URT and worse clinical outcome including intensive care and death . At writing, no human data exist to define whether the virus replicates solely or preferentially in the LRT or URT, or replicates in other human tissues in vivo although MERS-CoV RNA has been detected from both the URT and LRT in a macaque monkey model .The", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The WHO recommends sampling from the LRT for MERS-CoV RT-rtPCR testing, especially when sample collection is delayed by a week or more after onset of symptoms. LRT samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists . Recommended sample types include bronchoalveolar lavage , tracheal/tracheobronchial aspirate, pleural fluid and sputum . Fresh samples yield better diagnostic results than refrigerated material and if delays in testing of ≥72 h are likely, samples should be frozen at −70°C . If available, lung biopsy or autopsy tissues can also be tested ." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: In the only study to examine the effect of sample type on molecular analysis, 64 nasopharyngeal aspirates , 30 tracheal aspirates, 13 sputa and three BAL were examined." ], [ "0c", "The tracheal aspirates and BAL returned the highest viral load values followed by NPA and sputum." ], [ "0d", "Unsurprisingly, higher viral loads generally paralleled whole genome sequencing and culture success and, in NPA testing, were significantly correlated with severe disease and death ." ], [ "0e", "This study demonstrated the importance of LRT sampling for whole genome sequencing." ] ]

[ "0c", "3d" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In the only study to examine the effect of sample type on molecular analysis, 64 nasopharyngeal aspirates , 30 tracheal aspirates, 13 sputa and three BAL were examined. The tracheal aspirates and BAL returned the highest viral load values followed by NPA and sputum. Unsurprisingly, higher viral loads generally paralleled whole genome sequencing and culture success and, in NPA testing, were significantly correlated with severe disease and death . This study demonstrated the importance of LRT sampling for whole genome sequencing.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: absent or non-productive or because the viral load is low . Despite this both the largest human MERS-CoV studies and smaller ones , use samples from the URT. It is then noteworthy that one study reported an association between higher loads in the URT and worse clinical outcome including intensive care and death . At writing, no human data exist to define whether the virus replicates solely or preferentially in the LRT or URT, or replicates in other human tissues in vivo although MERS-CoV RNA has been detected from both the URT and LRT in a macaque monkey model .The", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The WHO recommends sampling from the LRT for MERS-CoV RT-rtPCR testing, especially when sample collection is delayed by a week or more after onset of symptoms. LRT samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists . Recommended sample types include bronchoalveolar lavage , tracheal/tracheobronchial aspirate, pleural fluid and sputum . Fresh samples yield better diagnostic results than refrigerated material and if delays in testing of ≥72 h are likely, samples should be frozen at −70°C . If available, lung biopsy or autopsy tissues can also be tested ." ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: The WHO recommends sampling from the LRT for MERS-CoV RT-rtPCR testing, especially when sample collection is delayed by a week or more after onset of symptoms." ], [ "3c", "LRT samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists ." ], [ "3d", "Recommended sample types include bronchoalveolar lavage , tracheal/tracheobronchial aspirate, pleural fluid and sputum ." ], [ "3e", "Fresh samples yield better diagnostic results than refrigerated material and if delays in testing of ≥72 h are likely, samples should be frozen at −70°C ." ], [ "3f", "If available, lung biopsy or autopsy tissues can also be tested ." ] ]

[ "0c", "3d" ]

[ "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: In general, there are several advantages of baculovirus-expressed vaccines, such as baculovirus-expressed virus-like particles and baculovirus surface display, over inactivated vaccines. One advantage of baculovirus-expressed vaccines is the complete elimination of any fear that may arise from the incomplete inactivation of the highly pathogenic viruses during the manufacturing process of inactivated vaccines, which is a concern that inactivated vaccines hold. Such extra peace of mind is attributed to two facts, namely no EV71 virus genomic material is present in baculovirus-expressed vaccines; and baculoviruses are harmless, largely owing to their non-replicable nature in mammalian cells .", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Baculoviruses are a group of insect-specific pathogens, with each species and/or strain targeting a very limited host range . A particular strain of this virus, namely Baculovirus Autographa californica nuclear polyhedrosis virus , capable of infecting a broad range of lepidopteran hosts, was isolated, and eventually formed the basis for modern day recombinant baculovirus vectors, which are widely used for protein expression . The baculovirus expression system has been widely exploited in modern-day research for protein expression due to its superiority over the traditional expression systems, in particular the E. coli expression system . Such superiority of BVES could be", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Firstly, live wild-type baculoviruses alone are proven to induce immune responses, both innate and cell-mediated immunity, upon their inoculation into the body . Hence, displaying the antigens on the baculovirus surface and using such recombinant baculoviruses live may reduce the need for adjuvants. Secondly, although baculoviruses are unable to replicate within mammalian host cells, they are capable of transducing them . Lastly, the Ie1 promoter used to regulate the expression of foreign genes in the baculovirus surface display is an active promoter not just in insect cells, but also in mammalian cells .", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: Since its inception more than 30 years ago, the baculovirus expression vector system has been widely used to express heterologous foreign proteins . Autographa californica nucleopolyhedrovirus -Sf9 and Bombyx mori nucleopolyhedrovirus -silkworm are two typical BEVSs . The BmNPV-silkworm offers several advantages in comparison with the AcMNPV-Sf9 system ." ]

[ [ "0a", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines" ], [ "0b", "Passage: In general, there are several advantages of baculovirus-expressed vaccines, such as baculovirus-expressed virus-like particles and baculovirus surface display, over inactivated vaccines." ], [ "0c", "One advantage of baculovirus-expressed vaccines is the complete elimination of any fear that may arise from the incomplete inactivation of the highly pathogenic viruses during the manufacturing process of inactivated vaccines, which is a concern that inactivated vaccines hold." ], [ "0d", "Such extra peace of mind is attributed to two facts, namely no EV71 virus genomic material is present in baculovirus-expressed vaccines; and baculoviruses are harmless, largely owing to their non-replicable nature in mammalian cells ." ] ]

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

[ "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: In general, there are several advantages of baculovirus-expressed vaccines, such as baculovirus-expressed virus-like particles and baculovirus surface display, over inactivated vaccines. One advantage of baculovirus-expressed vaccines is the complete elimination of any fear that may arise from the incomplete inactivation of the highly pathogenic viruses during the manufacturing process of inactivated vaccines, which is a concern that inactivated vaccines hold. Such extra peace of mind is attributed to two facts, namely no EV71 virus genomic material is present in baculovirus-expressed vaccines; and baculoviruses are harmless, largely owing to their non-replicable nature in mammalian cells .", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Baculoviruses are a group of insect-specific pathogens, with each species and/or strain targeting a very limited host range . A particular strain of this virus, namely Baculovirus Autographa californica nuclear polyhedrosis virus , capable of infecting a broad range of lepidopteran hosts, was isolated, and eventually formed the basis for modern day recombinant baculovirus vectors, which are widely used for protein expression . The baculovirus expression system has been widely exploited in modern-day research for protein expression due to its superiority over the traditional expression systems, in particular the E. coli expression system . Such superiority of BVES could be", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Firstly, live wild-type baculoviruses alone are proven to induce immune responses, both innate and cell-mediated immunity, upon their inoculation into the body . Hence, displaying the antigens on the baculovirus surface and using such recombinant baculoviruses live may reduce the need for adjuvants. Secondly, although baculoviruses are unable to replicate within mammalian host cells, they are capable of transducing them . Lastly, the Ie1 promoter used to regulate the expression of foreign genes in the baculovirus surface display is an active promoter not just in insect cells, but also in mammalian cells .", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: Since its inception more than 30 years ago, the baculovirus expression vector system has been widely used to express heterologous foreign proteins . Autographa californica nucleopolyhedrovirus -Sf9 and Bombyx mori nucleopolyhedrovirus -silkworm are two typical BEVSs . The BmNPV-silkworm offers several advantages in comparison with the AcMNPV-Sf9 system ." ]

[ [ "1a", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines" ], [ "1b", "Passage: Baculoviruses are a group of insect-specific pathogens, with each species and/or strain targeting a very limited host range ." ], [ "1c", "A particular strain of this virus, namely Baculovirus Autographa californica nuclear polyhedrosis virus , capable of infecting a broad range of lepidopteran hosts, was isolated, and eventually formed the basis for modern day recombinant baculovirus vectors, which are widely used for protein expression ." ], [ "1d", "The baculovirus expression system has been widely exploited in modern-day research for protein expression due to its superiority over the traditional expression systems, in particular the E. coli expression system ." ], [ "1e", "Such superiority of BVES could be" ] ]

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

[ "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: In general, there are several advantages of baculovirus-expressed vaccines, such as baculovirus-expressed virus-like particles and baculovirus surface display, over inactivated vaccines. One advantage of baculovirus-expressed vaccines is the complete elimination of any fear that may arise from the incomplete inactivation of the highly pathogenic viruses during the manufacturing process of inactivated vaccines, which is a concern that inactivated vaccines hold. Such extra peace of mind is attributed to two facts, namely no EV71 virus genomic material is present in baculovirus-expressed vaccines; and baculoviruses are harmless, largely owing to their non-replicable nature in mammalian cells .", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Baculoviruses are a group of insect-specific pathogens, with each species and/or strain targeting a very limited host range . A particular strain of this virus, namely Baculovirus Autographa californica nuclear polyhedrosis virus , capable of infecting a broad range of lepidopteran hosts, was isolated, and eventually formed the basis for modern day recombinant baculovirus vectors, which are widely used for protein expression . The baculovirus expression system has been widely exploited in modern-day research for protein expression due to its superiority over the traditional expression systems, in particular the E. coli expression system . Such superiority of BVES could be", "Title: Recent Progress towards Novel EV71 Anti-Therapeutics and Vaccines\nPassage: Firstly, live wild-type baculoviruses alone are proven to induce immune responses, both innate and cell-mediated immunity, upon their inoculation into the body . Hence, displaying the antigens on the baculovirus surface and using such recombinant baculoviruses live may reduce the need for adjuvants. Secondly, although baculoviruses are unable to replicate within mammalian host cells, they are capable of transducing them . Lastly, the Ie1 promoter used to regulate the expression of foreign genes in the baculovirus surface display is an active promoter not just in insect cells, but also in mammalian cells .", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: Since its inception more than 30 years ago, the baculovirus expression vector system has been widely used to express heterologous foreign proteins . Autographa californica nucleopolyhedrovirus -Sf9 and Bombyx mori nucleopolyhedrovirus -silkworm are two typical BEVSs . The BmNPV-silkworm offers several advantages in comparison with the AcMNPV-Sf9 system ." ]

[ [ "3a", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus" ], [ "3b", "Passage: Since its inception more than 30 years ago, the baculovirus expression vector system has been widely used to express heterologous foreign proteins ." ], [ "3c", "Autographa californica nucleopolyhedrovirus -Sf9 and Bombyx mori nucleopolyhedrovirus -silkworm are two typical BEVSs ." ], [ "3d", "The BmNPV-silkworm offers several advantages in comparison with the AcMNPV-Sf9 system ." ] ]

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

[ "Title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus\nPassage: To identify the most-effective rVSV/EBOV vector design for induction of EBOVGP-specific immune responses, the vectors outlined in Figure 1A were compared for their ability to elicit EBOVGP-specific cell-mediated immune and binding antibody responses in mice . Groups of BALB/c mice were immunized intramuscularly at study week 0 . Ten days after primary immunizations, splenocytes were collected from 5 mice/group and tested for EBOVGP-specific IFN-γ secretion by ELISpot assay. The remaining 5 mice/ group were boosted intramuscularly at study week 3 with 10 7 PFU of each rVSV/EBOV vector. Ten days after boosting, splenocytes were collected and tested as described above.", "Title: BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge\nPassage: with B6R alone. Nevertheless, our studies reveal that protection can be afforded even when a small number of mice are used. Further studies should be considered that increase the dose of vector administered to the mice. Also, since the combination of all 3 vectors gave 80% protection against mortality and morbidity, various vector permutations should be considered to elucidate the most efficacious combination and ratio of vectors.", "Title: Viral vector-based influenza vaccines\nPassage: were capable of inducing protective immunity against infection with homologous viruses in mice. Although recombinant baculovirus vector vaccines were tested in mice, efficacy data in other animal models is still lacking. Short-term production of baculovirus-based influenza virus vaccines for use in clinical trials is therefore not likely.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Baculovirus vectors have been tested as influenza vaccines, with the first reported vaccine using Autographa californica nuclear polyhedrosis virus expressing the HA of PR8 under control of the CAG promoter . Intramuscular, intranasal, intradermal, and intraperitoneal immunization or mice with AcCAG-HA elicited HA-specific antibody responses, however only intranasal immunization provided protection from lethal challenge. Interestingly, intranasal immunization with the wild type AcNPV also resulted in protection from PR8 challenge. The robust innate immune response to the baculovirus provided non-specific protection from subsequent influenza virus infection . While these studies did not demonstrate specific protection, there were antigen-specific immune responses and" ]

[ [ "2a", "Title: Viral vector-based influenza vaccines" ], [ "2b", "Passage: were capable of inducing protective immunity against infection with homologous viruses in mice." ], [ "2c", "Although recombinant baculovirus vector vaccines were tested in mice, efficacy data in other animal models is still lacking." ], [ "2d", "Short-term production of baculovirus-based influenza virus vaccines for use in clinical trials is therefore not likely." ] ]

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

[ "Title: Vaccination With a Highly Attenuated Recombinant Vesicular Stomatitis Virus Vector Protects Against Challenge With a Lethal Dose of Ebola Virus\nPassage: To identify the most-effective rVSV/EBOV vector design for induction of EBOVGP-specific immune responses, the vectors outlined in Figure 1A were compared for their ability to elicit EBOVGP-specific cell-mediated immune and binding antibody responses in mice . Groups of BALB/c mice were immunized intramuscularly at study week 0 . Ten days after primary immunizations, splenocytes were collected from 5 mice/group and tested for EBOVGP-specific IFN-γ secretion by ELISpot assay. The remaining 5 mice/ group were boosted intramuscularly at study week 3 with 10 7 PFU of each rVSV/EBOV vector. Ten days after boosting, splenocytes were collected and tested as described above.", "Title: BoHV-4-Based Vector Single Heterologous Antigen Delivery Protects STAT1((-/-)) Mice from Monkeypoxvirus Lethal Challenge\nPassage: with B6R alone. Nevertheless, our studies reveal that protection can be afforded even when a small number of mice are used. Further studies should be considered that increase the dose of vector administered to the mice. Also, since the combination of all 3 vectors gave 80% protection against mortality and morbidity, various vector permutations should be considered to elucidate the most efficacious combination and ratio of vectors.", "Title: Viral vector-based influenza vaccines\nPassage: were capable of inducing protective immunity against infection with homologous viruses in mice. Although recombinant baculovirus vector vaccines were tested in mice, efficacy data in other animal models is still lacking. Short-term production of baculovirus-based influenza virus vaccines for use in clinical trials is therefore not likely.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Baculovirus vectors have been tested as influenza vaccines, with the first reported vaccine using Autographa californica nuclear polyhedrosis virus expressing the HA of PR8 under control of the CAG promoter . Intramuscular, intranasal, intradermal, and intraperitoneal immunization or mice with AcCAG-HA elicited HA-specific antibody responses, however only intranasal immunization provided protection from lethal challenge. Interestingly, intranasal immunization with the wild type AcNPV also resulted in protection from PR8 challenge. The robust innate immune response to the baculovirus provided non-specific protection from subsequent influenza virus infection . While these studies did not demonstrate specific protection, there were antigen-specific immune responses and" ]

[ [ "3a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "3b", "Passage: Baculovirus vectors have been tested as influenza vaccines, with the first reported vaccine using Autographa californica nuclear polyhedrosis virus expressing the HA of PR8 under control of the CAG promoter ." ], [ "3c", "Intramuscular, intranasal, intradermal, and intraperitoneal immunization or mice with AcCAG-HA elicited HA-specific antibody responses, however only intranasal immunization provided protection from lethal challenge." ], [ "3d", "Interestingly, intranasal immunization with the wild type AcNPV also resulted in protection from PR8 challenge." ], [ "3e", "The robust innate immune response to the baculovirus provided non-specific protection from subsequent influenza virus infection ." ], [ "3f", "While these studies did not demonstrate specific protection, there were antigen-specific immune responses and" ] ]

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

[ "Title: Nanorobot Hardware Architecture for Medical Defense\nPassage: Time for incubation of pandemic syndromes may vary from one contagious plague to another, and first symptoms can be predicted given clinical information and previous historic occurrences, using statistical models. The size of an outbreak is directly correlated and influenced by the delay for recognition about the contaminated area. The incubation period of disease is the time from exposure to the infectious agent to the onset of disease, and depending on the infection dose of influenza, it can vary about 2 to 5 days . For influenza, the contamination can happens through inhalation, ingestion, or direct contact through hand shaking", "Title: Introducing the Outbreak Threshold in Epidemiology\nPassage: as the fact that the incubation period is around 5 days, by which point it had easily caused more secondary cases. However, in subsequent outbreaks super-spreaders might not be infected early on, allowing more time to contain the spread.", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Astrovirus, rotavirus, and caliciviruses are important causes of healthcare associated infections and institutional outbreaks . The incubation period is important for accurate surveillance for healthcare associated infections and implementation of effective outbreak control measures . The incubation period is frequently used to determine the infecting exposure in foodborne outbreaks and can assist in diagnosis when laboratory resources are unavailable. Kaplan's criteria were developed and are frequently employed to determine whether an outbreak was caused by norovirus; the incubation period is one of the key elements of these criteria. Other applications of a precisely described incubation period include predictive models that", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Despite its importance, the incubation periods of enteric viruses are not well characterized in the medical literature. Statements of the incubation period tend to be a single number ) or a poorly defined range ). It is difficult to translate these statements of incubation period into the realities of prevention and control. The single number estimate could represent the mean, median, upper limit, or some other measure of the incubation period. The range could represent an exhaustive range of all observations, or some unspecified quantile . Furthermore, the strength of the evidence behind these estimates is often unclear. Statements of" ]

[ [ "0a", "Title: Nanorobot Hardware Architecture for Medical Defense" ], [ "0b", "Passage: Time for incubation of pandemic syndromes may vary from one contagious plague to another, and first symptoms can be predicted given clinical information and previous historic occurrences, using statistical models." ], [ "0c", "The size of an outbreak is directly correlated and influenced by the delay for recognition about the contaminated area." ], [ "0d", "The incubation period of disease is the time from exposure to the infectious agent to the onset of disease, and depending on the infection dose of influenza, it can vary about 2 to 5 days ." ], [ "0e", "For influenza, the contamination can happens through inhalation, ingestion, or direct contact through hand shaking" ] ]

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

[ "Title: Nanorobot Hardware Architecture for Medical Defense\nPassage: Time for incubation of pandemic syndromes may vary from one contagious plague to another, and first symptoms can be predicted given clinical information and previous historic occurrences, using statistical models. The size of an outbreak is directly correlated and influenced by the delay for recognition about the contaminated area. The incubation period of disease is the time from exposure to the infectious agent to the onset of disease, and depending on the infection dose of influenza, it can vary about 2 to 5 days . For influenza, the contamination can happens through inhalation, ingestion, or direct contact through hand shaking", "Title: Introducing the Outbreak Threshold in Epidemiology\nPassage: as the fact that the incubation period is around 5 days, by which point it had easily caused more secondary cases. However, in subsequent outbreaks super-spreaders might not be infected early on, allowing more time to contain the spread.", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Astrovirus, rotavirus, and caliciviruses are important causes of healthcare associated infections and institutional outbreaks . The incubation period is important for accurate surveillance for healthcare associated infections and implementation of effective outbreak control measures . The incubation period is frequently used to determine the infecting exposure in foodborne outbreaks and can assist in diagnosis when laboratory resources are unavailable. Kaplan's criteria were developed and are frequently employed to determine whether an outbreak was caused by norovirus; the incubation period is one of the key elements of these criteria. Other applications of a precisely described incubation period include predictive models that", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Despite its importance, the incubation periods of enteric viruses are not well characterized in the medical literature. Statements of the incubation period tend to be a single number ) or a poorly defined range ). It is difficult to translate these statements of incubation period into the realities of prevention and control. The single number estimate could represent the mean, median, upper limit, or some other measure of the incubation period. The range could represent an exhaustive range of all observations, or some unspecified quantile . Furthermore, the strength of the evidence behind these estimates is often unclear. Statements of" ]

[ [ "2a", "Title: Incubation periods of viral gastroenteritis: a systematic review" ], [ "2b", "Passage: Astrovirus, rotavirus, and caliciviruses are important causes of healthcare associated infections and institutional outbreaks ." ], [ "2c", "The incubation period is important for accurate surveillance for healthcare associated infections and implementation of effective outbreak control measures ." ], [ "2d", "The incubation period is frequently used to determine the infecting exposure in foodborne outbreaks and can assist in diagnosis when laboratory resources are unavailable." ], [ "2e", "Kaplan's criteria were developed and are frequently employed to determine whether an outbreak was caused by norovirus; the incubation period is one of the key elements of these criteria." ], [ "2f", "Other applications of a precisely described incubation period include predictive models that" ] ]

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

[ "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Computed tomography can play a role in both diagnosing and categorizing", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: CT: computed tomography", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Our diagnostic process is limited as chest CT along is not diagnostic of COVID-19", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: scanning can reduce the radiation damage to patients." ]

[ [ "0a", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management" ], [ "0b", "Passage: Computed tomography can play a role in both diagnosing and categorizing" ] ]

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

[ "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Computed tomography can play a role in both diagnosing and categorizing", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: CT: computed tomography", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Our diagnostic process is limited as chest CT along is not diagnostic of COVID-19", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: scanning can reduce the radiation damage to patients." ]

[ [ "2a", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management" ], [ "2b", "Passage: Our diagnostic process is limited as chest CT along is not diagnostic of COVID-19" ] ]

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

[ "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Computed tomography can play a role in both diagnosing and categorizing", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: CT: computed tomography", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: Our diagnostic process is limited as chest CT along is not diagnostic of COVID-19", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: scanning can reduce the radiation damage to patients." ]

[ [ "3a", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management" ], [ "3b", "Passage: scanning can reduce the radiation damage to patients." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: contrast, the combination therapies led to 50% and 90% survival, depending on the Zanamivir concentration. Statistical analysis showed that the Zanamivir mono-therapy 1 mg/kg BW/day did not show a significant benefit , whereas the mono-therapy with 3 mg/kg BW/day significantly increased the survival rate compared with placebo treated mice . Both Zanamivir concentrations experienced significant benefit in survival by the combination with carrageenan . Similarly, the combination therapies resulted in remarkably increased survival when compared to the carrageenan mono-therapy. No statistically significant difference was observed between the combination containing 3 mg/kg BW/day Zanamivir and that containing 1 mg/kg BW/day .", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: Two virus strains were selected for those experiments, one being the most sensitive to carrageenan pdm) and one being the least sensitive . In both cases the isobolograms show a synergistic interaction of carrageenan and Zanamivir . Thus, it was shown that Zanamivir and carrageenan target individual influenza viruses with different efficiencies, most probably due to their different antiviral strategies. As a result, the combination provides synergistic activity with higher protection against a broader spectrum of influenza virus strains than the individual compounds.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model." ]

[ [ "0a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "0b", "Passage: contrast, the combination therapies led to 50% and 90% survival, depending on the Zanamivir concentration." ], [ "0c", "Statistical analysis showed that the Zanamivir mono-therapy 1 mg/kg BW/day did not show a significant benefit , whereas the mono-therapy with 3 mg/kg BW/day significantly increased the survival rate compared with placebo treated mice ." ], [ "0d", "Both Zanamivir concentrations experienced significant benefit in survival by the combination with carrageenan ." ], [ "0e", "Similarly, the combination therapies resulted in remarkably increased survival when compared to the carrageenan mono-therapy." ], [ "0f", "No statistically significant difference was observed between the combination containing 3 mg/kg BW/day Zanamivir and that containing 1 mg/kg BW/day ." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: contrast, the combination therapies led to 50% and 90% survival, depending on the Zanamivir concentration. Statistical analysis showed that the Zanamivir mono-therapy 1 mg/kg BW/day did not show a significant benefit , whereas the mono-therapy with 3 mg/kg BW/day significantly increased the survival rate compared with placebo treated mice . Both Zanamivir concentrations experienced significant benefit in survival by the combination with carrageenan . Similarly, the combination therapies resulted in remarkably increased survival when compared to the carrageenan mono-therapy. No statistically significant difference was observed between the combination containing 3 mg/kg BW/day Zanamivir and that containing 1 mg/kg BW/day .", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: Two virus strains were selected for those experiments, one being the most sensitive to carrageenan pdm) and one being the least sensitive . In both cases the isobolograms show a synergistic interaction of carrageenan and Zanamivir . Thus, it was shown that Zanamivir and carrageenan target individual influenza viruses with different efficiencies, most probably due to their different antiviral strategies. As a result, the combination provides synergistic activity with higher protection against a broader spectrum of influenza virus strains than the individual compounds.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model." ]

[ [ "1a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "1b", "Passage: Two virus strains were selected for those experiments, one being the most sensitive to carrageenan pdm) and one being the least sensitive ." ], [ "1c", "In both cases the isobolograms show a synergistic interaction of carrageenan and Zanamivir ." ], [ "1d", "Thus, it was shown that Zanamivir and carrageenan target individual influenza viruses with different efficiencies, most probably due to their different antiviral strategies." ], [ "1e", "As a result, the combination provides synergistic activity with higher protection against a broader spectrum of influenza virus strains than the individual compounds." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: contrast, the combination therapies led to 50% and 90% survival, depending on the Zanamivir concentration. Statistical analysis showed that the Zanamivir mono-therapy 1 mg/kg BW/day did not show a significant benefit , whereas the mono-therapy with 3 mg/kg BW/day significantly increased the survival rate compared with placebo treated mice . Both Zanamivir concentrations experienced significant benefit in survival by the combination with carrageenan . Similarly, the combination therapies resulted in remarkably increased survival when compared to the carrageenan mono-therapy. No statistically significant difference was observed between the combination containing 3 mg/kg BW/day Zanamivir and that containing 1 mg/kg BW/day .", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: Two virus strains were selected for those experiments, one being the most sensitive to carrageenan pdm) and one being the least sensitive . In both cases the isobolograms show a synergistic interaction of carrageenan and Zanamivir . Thus, it was shown that Zanamivir and carrageenan target individual influenza viruses with different efficiencies, most probably due to their different antiviral strategies. As a result, the combination provides synergistic activity with higher protection against a broader spectrum of influenza virus strains than the individual compounds.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model." ]

[ [ "2a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "2b", "Passage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies ." ], [ "2c", "The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi." ], [ "2d", "Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi." ], [ "2e", "This is a remarkable finding since NIs are normally not effective when applied 72 hpi." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Ltd), scheduled for administration at 6, 10, and 14 weeks, is received with significant delays . These data support the WHO's recommendation that countries using whole cell pertussis vaccine continue to do so given that the majority of outbreaks have been concentrated in countries using the acellular pertussis vaccine . Recent studies suggest that protection from acellular pertussis vaccine is not as strong or long lasting as that conferred by the whole cell pertussis vaccine .", "Title: Neonatal Pertussis, an Under-Recognized Health Burden and Rationale for Maternal Immunization: A Systematic Review of South and South-East Asian Countries\nPassage: In 2011, the Tdap vaccine was recommended in unvaccinated pregnant women by the US Advisory Committee on Immunization Practice . The WHO recommended that national programs consider the vaccination of pregnant women with one dose of Tdap when infant morbidity or mortality from pertussis is high or increasing . Pertussis vaccination practices differ across the Asia-Pacific region, with only some countries recommending booster dosing. Countries usually adapt their recommendations from the WHO based on local information about risk groups, disease burden and cost-effectiveness, but these data are limited in low-or middleincome countries .", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: In conclusion, prevention of pertussis with currently available vaccines reaching high vaccination coverage rates remains a priority, including the vaccination of pregnant women . Several different aP vaccines are available, but it has yet to be determined which of them confers the highest and the most-prolonged protection. Further studies are needed to evaluate the importance of individual antigens included in aP vaccines in conferring protection against disease, colonization, and transmission. However, present knowledge seems to indicate that pertussis toxin, particularly if genetically detoxified, represents the main antigen that ensures protection from disease even if not from infection. The optimal pertussis", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: Pertussis Pertussis cases and deaths were based on a natural history model using vaccine coverage and age-specific case fatality rates from community-based studies . Updated estimates for 2004 were prepared by the WHO Department of Immunization, Vaccines and Biologicals using WHO-United Nations Children's Fund estimates for vaccine coverage in 2004, interpolated for missing data ." ]

[ [ "0a", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal" ], [ "0b", "Passage: Ltd), scheduled for administration at 6, 10, and 14 weeks, is received with significant delays ." ], [ "0c", "These data support the WHO's recommendation that countries using whole cell pertussis vaccine continue to do so given that the majority of outbreaks have been concentrated in countries using the acellular pertussis vaccine ." ], [ "0d", "Recent studies suggest that protection from acellular pertussis vaccine is not as strong or long lasting as that conferred by the whole cell pertussis vaccine ." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Ltd), scheduled for administration at 6, 10, and 14 weeks, is received with significant delays . These data support the WHO's recommendation that countries using whole cell pertussis vaccine continue to do so given that the majority of outbreaks have been concentrated in countries using the acellular pertussis vaccine . Recent studies suggest that protection from acellular pertussis vaccine is not as strong or long lasting as that conferred by the whole cell pertussis vaccine .", "Title: Neonatal Pertussis, an Under-Recognized Health Burden and Rationale for Maternal Immunization: A Systematic Review of South and South-East Asian Countries\nPassage: In 2011, the Tdap vaccine was recommended in unvaccinated pregnant women by the US Advisory Committee on Immunization Practice . The WHO recommended that national programs consider the vaccination of pregnant women with one dose of Tdap when infant morbidity or mortality from pertussis is high or increasing . Pertussis vaccination practices differ across the Asia-Pacific region, with only some countries recommending booster dosing. Countries usually adapt their recommendations from the WHO based on local information about risk groups, disease burden and cost-effectiveness, but these data are limited in low-or middleincome countries .", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: In conclusion, prevention of pertussis with currently available vaccines reaching high vaccination coverage rates remains a priority, including the vaccination of pregnant women . Several different aP vaccines are available, but it has yet to be determined which of them confers the highest and the most-prolonged protection. Further studies are needed to evaluate the importance of individual antigens included in aP vaccines in conferring protection against disease, colonization, and transmission. However, present knowledge seems to indicate that pertussis toxin, particularly if genetically detoxified, represents the main antigen that ensures protection from disease even if not from infection. The optimal pertussis", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: Pertussis Pertussis cases and deaths were based on a natural history model using vaccine coverage and age-specific case fatality rates from community-based studies . Updated estimates for 2004 were prepared by the WHO Department of Immunization, Vaccines and Biologicals using WHO-United Nations Children's Fund estimates for vaccine coverage in 2004, interpolated for missing data ." ]

[ [ "1a", "Title: Neonatal Pertussis, an Under-Recognized Health Burden and Rationale for Maternal Immunization: A Systematic Review of South and South-East Asian Countries" ], [ "1b", "Passage: In 2011, the Tdap vaccine was recommended in unvaccinated pregnant women by the US Advisory Committee on Immunization Practice ." ], [ "1c", "The WHO recommended that national programs consider the vaccination of pregnant women with one dose of Tdap when infant morbidity or mortality from pertussis is high or increasing ." ], [ "1d", "Pertussis vaccination practices differ across the Asia-Pacific region, with only some countries recommending booster dosing." ], [ "1e", "Countries usually adapt their recommendations from the WHO based on local information about risk groups, disease burden and cost-effectiveness, but these data are limited in low-or middleincome countries ." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Ltd), scheduled for administration at 6, 10, and 14 weeks, is received with significant delays . These data support the WHO's recommendation that countries using whole cell pertussis vaccine continue to do so given that the majority of outbreaks have been concentrated in countries using the acellular pertussis vaccine . Recent studies suggest that protection from acellular pertussis vaccine is not as strong or long lasting as that conferred by the whole cell pertussis vaccine .", "Title: Neonatal Pertussis, an Under-Recognized Health Burden and Rationale for Maternal Immunization: A Systematic Review of South and South-East Asian Countries\nPassage: In 2011, the Tdap vaccine was recommended in unvaccinated pregnant women by the US Advisory Committee on Immunization Practice . The WHO recommended that national programs consider the vaccination of pregnant women with one dose of Tdap when infant morbidity or mortality from pertussis is high or increasing . Pertussis vaccination practices differ across the Asia-Pacific region, with only some countries recommending booster dosing. Countries usually adapt their recommendations from the WHO based on local information about risk groups, disease burden and cost-effectiveness, but these data are limited in low-or middleincome countries .", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: In conclusion, prevention of pertussis with currently available vaccines reaching high vaccination coverage rates remains a priority, including the vaccination of pregnant women . Several different aP vaccines are available, but it has yet to be determined which of them confers the highest and the most-prolonged protection. Further studies are needed to evaluate the importance of individual antigens included in aP vaccines in conferring protection against disease, colonization, and transmission. However, present knowledge seems to indicate that pertussis toxin, particularly if genetically detoxified, represents the main antigen that ensures protection from disease even if not from infection. The optimal pertussis", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: Pertussis Pertussis cases and deaths were based on a natural history model using vaccine coverage and age-specific case fatality rates from community-based studies . Updated estimates for 2004 were prepared by the WHO Department of Immunization, Vaccines and Biologicals using WHO-United Nations Children's Fund estimates for vaccine coverage in 2004, interpolated for missing data ." ]

[ [ "2a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "2b", "Passage: In conclusion, prevention of pertussis with currently available vaccines reaching high vaccination coverage rates remains a priority, including the vaccination of pregnant women ." ], [ "2c", "Several different aP vaccines are available, but it has yet to be determined which of them confers the highest and the most-prolonged protection." ], [ "2d", "Further studies are needed to evaluate the importance of individual antigens included in aP vaccines in conferring protection against disease, colonization, and transmission." ], [ "2e", "However, present knowledge seems to indicate that pertussis toxin, particularly if genetically detoxified, represents the main antigen that ensures protection from disease even if not from infection." ], [ "2f", "The optimal pertussis" ] ]

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

[ "Title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus\nPassage: in the mixed nucleolar fraction. Of note, nucleolin was equally distributed between the nuclear and cytoplasmic fractions. This distribution pattern for nucleolin appears to be specific for Jurkat T-cells as show previously . The nuclear protein PARP-1 was present in the nuclear and nucleoplasmic fraction but was depleted in the nucleolar fraction. Alpha-tubulin was highly abundant in the cytoplasmic fraction and weakly detected in the nuclear fractions. Collectively, these results confirmed that our methods produced a highly enriched nucleolar fraction without significant cross contamination.", "Title: Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription\nPassage: EGFP-TARG1 was reported to be predominantly nuclear 9 , and our proteomics data set contained a high number of nuclear and in particular nucleolar proteins, also reflected by GO analyses for cellular component . Therefore, we analyzed the sub-cellular localization of TARG1 in greater detail. EGFP-TARG1 expressed in U2OS cells accumulated in nucleoli in living cells, while EGFP alone was excluded from nucleoli . mCherry-tagged Histone H2B was used to define the nucleoplasm 28 .", "Title: Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton\nPassage: Microtubules are polarized filaments formed by tubulins and microtubule-associated proteins. In many eukaryotic cell types, the minus-ends are located near the cell center and plus-ends point to the plasma membrane . In addition to maintaining the structure of the cells and providing the framework for cell division, microtubules serve as tracks for the intracellular transport of organelles, proteins, and RNA-protein complexes . Microtubules support long range virion transport at µm/s speed. The role of microtubules in virus entry and egress from infected cells has been extensively reviewed . Microtubules are composed of different isotypes of alpha and beta tubulin, which", "Title: Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells\nPassage: To investigate whether these bortezomib-induced changes in the tubulin polymerization were mediated by phosphorylation of stathmin, we examined the tubulin polymerization in stable U266 clones that overexpressing WT stathmin and the phosphorylation site-deficient stathmin mutants S16A, S25A and S38A. As shown in Figure 5C , by comparing with U266 cells, overexpression of WT stathmin and phosphorylation site-deficient mutants resulted in a significant decrease in the percent of polymerized tubulin following treatment with bortezomib ." ]

[ [ "0a", "Title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus" ], [ "0b", "Passage: in the mixed nucleolar fraction." ], [ "0c", "Of note, nucleolin was equally distributed between the nuclear and cytoplasmic fractions." ], [ "0d", "This distribution pattern for nucleolin appears to be specific for Jurkat T-cells as show previously ." ], [ "0e", "The nuclear protein PARP-1 was present in the nuclear and nucleoplasmic fraction but was depleted in the nucleolar fraction." ], [ "0f", "Alpha-tubulin was highly abundant in the cytoplasmic fraction and weakly detected in the nuclear fractions." ], [ "0g", "Collectively, these results confirmed that our methods produced a highly enriched nucleolar fraction without significant cross contamination." ] ]

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

[ "Title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus\nPassage: in the mixed nucleolar fraction. Of note, nucleolin was equally distributed between the nuclear and cytoplasmic fractions. This distribution pattern for nucleolin appears to be specific for Jurkat T-cells as show previously . The nuclear protein PARP-1 was present in the nuclear and nucleoplasmic fraction but was depleted in the nucleolar fraction. Alpha-tubulin was highly abundant in the cytoplasmic fraction and weakly detected in the nuclear fractions. Collectively, these results confirmed that our methods produced a highly enriched nucleolar fraction without significant cross contamination.", "Title: Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription\nPassage: EGFP-TARG1 was reported to be predominantly nuclear 9 , and our proteomics data set contained a high number of nuclear and in particular nucleolar proteins, also reflected by GO analyses for cellular component . Therefore, we analyzed the sub-cellular localization of TARG1 in greater detail. EGFP-TARG1 expressed in U2OS cells accumulated in nucleoli in living cells, while EGFP alone was excluded from nucleoli . mCherry-tagged Histone H2B was used to define the nucleoplasm 28 .", "Title: Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton\nPassage: Microtubules are polarized filaments formed by tubulins and microtubule-associated proteins. In many eukaryotic cell types, the minus-ends are located near the cell center and plus-ends point to the plasma membrane . In addition to maintaining the structure of the cells and providing the framework for cell division, microtubules serve as tracks for the intracellular transport of organelles, proteins, and RNA-protein complexes . Microtubules support long range virion transport at µm/s speed. The role of microtubules in virus entry and egress from infected cells has been extensively reviewed . Microtubules are composed of different isotypes of alpha and beta tubulin, which", "Title: Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells\nPassage: To investigate whether these bortezomib-induced changes in the tubulin polymerization were mediated by phosphorylation of stathmin, we examined the tubulin polymerization in stable U266 clones that overexpressing WT stathmin and the phosphorylation site-deficient stathmin mutants S16A, S25A and S38A. As shown in Figure 5C , by comparing with U266 cells, overexpression of WT stathmin and phosphorylation site-deficient mutants resulted in a significant decrease in the percent of polymerized tubulin following treatment with bortezomib ." ]

[ [ "2a", "Title: Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton" ], [ "2b", "Passage: Microtubules are polarized filaments formed by tubulins and microtubule-associated proteins." ], [ "2c", "In many eukaryotic cell types, the minus-ends are located near the cell center and plus-ends point to the plasma membrane ." ], [ "2d", "In addition to maintaining the structure of the cells and providing the framework for cell division, microtubules serve as tracks for the intracellular transport of organelles, proteins, and RNA-protein complexes ." ], [ "2e", "Microtubules support long range virion transport at µm/s speed." ], [ "2f", "The role of microtubules in virus entry and egress from infected cells has been extensively reviewed ." ], [ "2g", "Microtubules are composed of different isotypes of alpha and beta tubulin, which" ] ]

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

[ "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: groups who are vulnerable because of social disadvantage. Nor does it note the need for explicit attention to vulnerable social subgroups, for example, low-wage workers in prioritized occupational fi elds and low-income and minority pregnant women, infants, and toddlers. We are not questioning the rationality of defi ning major priority groups according to occupation or of using biological criteria to further prioritize within the general population. Rather, our concern is with the absence of attention to both biological and social risk factors, which must be addressed to overcome the many social barriers to equal opportunity for vaccination.", "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: On a US government website for pandemic infl uenza , a question asks which groups would be especially vulnerable during an infl uenza pandemic. The answer notes that people may be vulnerable for a variety of reasons, including limited access to healthcare; limited profi ciency in English; or being disabled, homeless, economically disadvantaged, or a single parent. The response calls for faith-based and community-based organizations to develop plans \"to care for dependent populations\" and to \"provide fi nancial aid to the poor who are unable to work and are in need of emergency income for housing, medicine, or other essential", "Title: Existing health inequalities in India: informing preparedness planning for an influenza pandemic\nPassage: Experience suggests that younger, weaker and politically marginalized sections of society suffer disproportionately in disasters and crises. For example, during the Indian Ocean tsunami of 2004, mortality was higher among females, among those below 15 years of age and among those with no education compared with those with at least 1 year of education . In a cohort study of the population affected by an earthquake in Taiwan in 1999, poor pre-quake mental and physical health status and lower monthly wage were associated with higher risk of mortality .", "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: Crowding, an established risk factor for many infectious diseases, can increase the likelihood of pathogen transmission. In the United States, urban poverty and Hispanic and Asian ethnicity are correlated with domestic crowding; even at higher income levels, Hispanic and Asian households are relatively more crowded than white and African-American households . In addition, in the United States, low-income persons, African Americans, and nonwhite Hispanics are more likely than persons in other groups to obtain regular medical care at emergency departments and publicly funded clinics , where airborne transmission of infectious agents has been documented. Because these locations typically do not" ]

[ [ "2a", "Title: Existing health inequalities in India: informing preparedness planning for an influenza pandemic" ], [ "2b", "Passage: Experience suggests that younger, weaker and politically marginalized sections of society suffer disproportionately in disasters and crises." ], [ "2c", "For example, during the Indian Ocean tsunami of 2004, mortality was higher among females, among those below 15 years of age and among those with no education compared with those with at least 1 year of education ." ], [ "2d", "In a cohort study of the population affected by an earthquake in Taiwan in 1999, poor pre-quake mental and physical health status and lower monthly wage were associated with higher risk of mortality ." ] ]

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

[ "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: groups who are vulnerable because of social disadvantage. Nor does it note the need for explicit attention to vulnerable social subgroups, for example, low-wage workers in prioritized occupational fi elds and low-income and minority pregnant women, infants, and toddlers. We are not questioning the rationality of defi ning major priority groups according to occupation or of using biological criteria to further prioritize within the general population. Rather, our concern is with the absence of attention to both biological and social risk factors, which must be addressed to overcome the many social barriers to equal opportunity for vaccination.", "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: On a US government website for pandemic infl uenza , a question asks which groups would be especially vulnerable during an infl uenza pandemic. The answer notes that people may be vulnerable for a variety of reasons, including limited access to healthcare; limited profi ciency in English; or being disabled, homeless, economically disadvantaged, or a single parent. The response calls for faith-based and community-based organizations to develop plans \"to care for dependent populations\" and to \"provide fi nancial aid to the poor who are unable to work and are in need of emergency income for housing, medicine, or other essential", "Title: Existing health inequalities in India: informing preparedness planning for an influenza pandemic\nPassage: Experience suggests that younger, weaker and politically marginalized sections of society suffer disproportionately in disasters and crises. For example, during the Indian Ocean tsunami of 2004, mortality was higher among females, among those below 15 years of age and among those with no education compared with those with at least 1 year of education . In a cohort study of the population affected by an earthquake in Taiwan in 1999, poor pre-quake mental and physical health status and lower monthly wage were associated with higher risk of mortality .", "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective\nPassage: Crowding, an established risk factor for many infectious diseases, can increase the likelihood of pathogen transmission. In the United States, urban poverty and Hispanic and Asian ethnicity are correlated with domestic crowding; even at higher income levels, Hispanic and Asian households are relatively more crowded than white and African-American households . In addition, in the United States, low-income persons, African Americans, and nonwhite Hispanics are more likely than persons in other groups to obtain regular medical care at emergency departments and publicly funded clinics , where airborne transmission of infectious agents has been documented. Because these locations typically do not" ]

[ [ "3a", "Title: Pandemic Influenza Planning in the United States from a Health Disparities Perspective" ], [ "3b", "Passage: Crowding, an established risk factor for many infectious diseases, can increase the likelihood of pathogen transmission." ], [ "3c", "In the United States, urban poverty and Hispanic and Asian ethnicity are correlated with domestic crowding; even at higher income levels, Hispanic and Asian households are relatively more crowded than white and African-American households ." ], [ "3d", "In addition, in the United States, low-income persons, African Americans, and nonwhite Hispanics are more likely than persons in other groups to obtain regular medical care at emergency departments and publicly funded clinics , where airborne transmission of infectious agents has been documented." ], [ "3e", "Because these locations typically do not" ] ]

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

[ "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: SILAC was achieved by growing 3T3-F442A preadipocytes in DMEM containing 5% dialyzed fetal bovine serum, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25 g/ml amphotericin, and either Lys and Arg or Lys and Arg for at least seven cell doublings. For the cells grown in Lys and Arg, heavy isotope incorporation was evaluated by running a pilot digestion of the heavy isotope labeled cell extract followed by LC-MSMS analysis. The heavy isotope-labeled amino acids were incorporated into more than 99% of the cellular protein. Cells were washed and incubated in DMEM containing 1% BSA, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25", "Title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity\nPassage: 18O Stable Isotope Labeling. Differential 16O/18O coding relies on the 18O exchange that takes place at the Cterminal carboxyl group of proteolytic fragments, where two 16O atoms are typically replaced by two 18O atoms by enzyme-catalyzed oxygen exchange in the presence of H218O . The resulting mass shift between differentially labeled peptide ions permits identification, characterization, and quantitation of proteins from which the peptides are proteolytically generated. In contrast to ICAT, 18O labeling does not favor peptides containing certain amino acids , nor does it require an additional affinity step to enrich for these peptides . Unlike iTRAQ, 16O/18O labeling", "Title: Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target\nPassage: SILAC labeling and preparation of cell extracts. Five biological replicates of the phosphoproteomic experiment were performed using SILAC-labeled A549 cells. For each replicate, two T150 flasks of cells labeled with each of the following conditions were used: L , where A549 cells were grown in normal DMEM; M , where A549 cells were grown in DMEM containing 4,4,5,5-D 4 lysine and 13 C 6 arginine; and H , where A549 cells were grown in DMEM containing 13 C 6 15 N 2 lysine and 13 C 6 15 N 4 arginine. Incorporation of the different isotopes was confirmed by LC-MS/MS.", "Title: Kinetic Modelling of Infection Tracers [(18)F]FDG, [(68)Ga]Ga-Citrate, [(11)C]Methionine, and [(11)C]Donepezil in a Porcine Osteomyelitis Model\nPassage: Methionine is a naturally occurring essential amino acid. It can be labelled with the positron-emitter 11 C to obtain the chemically identical PET tracer methionine. Methionine is transported into cells via the Ltype amino acid transporter 1. It is crucial for the formation of proteins and is involved in the synthesis of phospholipids. The accumulation of methionine therefore reflects amino acid transport and protein synthesis. During cell replication, the demand for essential amino acids increases, as do protein and phospholipid synthesis. Although primarily used to detect malignant tumours , methionine is known from brain studies to accumulate in inflammatory tissue" ]

[ [ "0a", "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics" ], [ "0b", "Passage: SILAC was achieved by growing 3T3-F442A preadipocytes in DMEM containing 5% dialyzed fetal bovine serum, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25 g/ml amphotericin, and either Lys and Arg or Lys and Arg for at least seven cell doublings." ], [ "0c", "For the cells grown in Lys and Arg, heavy isotope incorporation was evaluated by running a pilot digestion of the heavy isotope labeled cell extract followed by LC-MSMS analysis." ], [ "0d", "The heavy isotope-labeled amino acids were incorporated into more than 99% of the cellular protein." ], [ "0e", "Cells were washed and incubated in DMEM containing 1% BSA, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25" ] ]

[ "0b", "2d" ]

[ "Title: Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics\nPassage: SILAC was achieved by growing 3T3-F442A preadipocytes in DMEM containing 5% dialyzed fetal bovine serum, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25 g/ml amphotericin, and either Lys and Arg or Lys and Arg for at least seven cell doublings. For the cells grown in Lys and Arg, heavy isotope incorporation was evaluated by running a pilot digestion of the heavy isotope labeled cell extract followed by LC-MSMS analysis. The heavy isotope-labeled amino acids were incorporated into more than 99% of the cellular protein. Cells were washed and incubated in DMEM containing 1% BSA, 100 U/ml penicillin, 100 g/ml streptomycin, 0.25", "Title: Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity\nPassage: 18O Stable Isotope Labeling. Differential 16O/18O coding relies on the 18O exchange that takes place at the Cterminal carboxyl group of proteolytic fragments, where two 16O atoms are typically replaced by two 18O atoms by enzyme-catalyzed oxygen exchange in the presence of H218O . The resulting mass shift between differentially labeled peptide ions permits identification, characterization, and quantitation of proteins from which the peptides are proteolytically generated. In contrast to ICAT, 18O labeling does not favor peptides containing certain amino acids , nor does it require an additional affinity step to enrich for these peptides . Unlike iTRAQ, 16O/18O labeling", "Title: Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target\nPassage: SILAC labeling and preparation of cell extracts. Five biological replicates of the phosphoproteomic experiment were performed using SILAC-labeled A549 cells. For each replicate, two T150 flasks of cells labeled with each of the following conditions were used: L , where A549 cells were grown in normal DMEM; M , where A549 cells were grown in DMEM containing 4,4,5,5-D 4 lysine and 13 C 6 arginine; and H , where A549 cells were grown in DMEM containing 13 C 6 15 N 2 lysine and 13 C 6 15 N 4 arginine. Incorporation of the different isotopes was confirmed by LC-MS/MS.", "Title: Kinetic Modelling of Infection Tracers [(18)F]FDG, [(68)Ga]Ga-Citrate, [(11)C]Methionine, and [(11)C]Donepezil in a Porcine Osteomyelitis Model\nPassage: Methionine is a naturally occurring essential amino acid. It can be labelled with the positron-emitter 11 C to obtain the chemically identical PET tracer methionine. Methionine is transported into cells via the Ltype amino acid transporter 1. It is crucial for the formation of proteins and is involved in the synthesis of phospholipids. The accumulation of methionine therefore reflects amino acid transport and protein synthesis. During cell replication, the demand for essential amino acids increases, as do protein and phospholipid synthesis. Although primarily used to detect malignant tumours , methionine is known from brain studies to accumulate in inflammatory tissue" ]

[ [ "2a", "Title: Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target" ], [ "2b", "Passage: SILAC labeling and preparation of cell extracts." ], [ "2c", "Five biological replicates of the phosphoproteomic experiment were performed using SILAC-labeled A549 cells." ], [ "2d", "For each replicate, two T150 flasks of cells labeled with each of the following conditions were used: L , where A549 cells were grown in normal DMEM; M , where A549 cells were grown in DMEM containing 4,4,5,5-D 4 lysine and 13 C 6 arginine; and H , where A549 cells were grown in DMEM containing 13 C 6 15 N 2 lysine and 13 C 6 15 N 4 arginine." ], [ "2e", "Incorporation of the different isotopes was confirmed by LC-MS/MS." ] ]

[ "0b", "2d" ]

[ "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: 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: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: 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." ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "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 ." ], [ "0c", "Data on 38 of these cases are included in this analysis." ] ]

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

[ "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: 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: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: 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." ]

[ [ "1a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "1b", "Passage: Abstract: 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." ] ]

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

[ "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: 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: As at 09:00 on 21 February, few COVID-19 cases had been detected in Europe compared with Asia. However the situation is rapidly developing, with a large outbreak recently identified in northern Italy, with transmission in several municipalities and at least two deaths . As at 5 March 2020, there are 4,250 cases including 113 deaths reported among 38 countries in the WHO European region .", "Title: 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." ]

[ [ "3a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "3b", "Passage: Text: In the WHO European Region, COVID-19 surveillance was implemented 27 January 2020." ], [ "3c", "We detail the first European cases." ], [ "3d", "As at 21 February, nine European countries reported 47 cases." ], [ "3e", "Among 38 cases studied, 21 were linked to two clusters in Germany and France, 14 were infected in China." ], [ "3f", "Median case age was 42 years; 25 were male." ], [ "3g", "Late detection of the clusters' index cases delayed isolation of further local cases." ], [ "3h", "As at 5 March, there were 4,250 cases." ] ]

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

[ "Title: Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015): Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015\nPassage: Breast cancer is the most common type of cancer among women worldwide. It ranks first amongst cancer in Saudi females with an incidence of 19.8 % . Few studies have shown that the knowledge, awareness, and protective measures against this disease are very low in Saudi females . Objective of this study was to assess the level of awareness, knowledge, and practices of breast cancer among Saudi females living in Jeddah.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: the leading cause in four of the seven regions, second in two regions and fifth in the Western Pacific Region. Stomach cancer is the main cause of cancer death among women in that Region, followed by lung cancer and liver cancer. Cervix uteri cancer is the number one cause of cancer deaths in the South-East Asia Region and the African Region. Other cancers of the female reproductive system are the eighth and thirteenth leading causes of cancer deaths globally. • acute respiratory infections, mainly pneumonia", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: hepatitis B virus in the case of liver cancer. Globally, lung cancer is the most common cancer , followed by breast cancer, then colon and rectum cancer, and stomach cancer. Lung cancer is also the leading cancer in the Western Pacific Region, but is less common than colon and rectum cancers or breast cancers in most other regions. Cervix cancer is the cancer with the highest incidence in the African and South-East Asia regions, even though it occurs only in women.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: is the second leading cause of cancer death in the African Region. Colon and rectum cancers are the fourth leading cause and oesophagus cancer the fifth leading cause globally. Prostate cancer is sixth globally, but is the leading cause of cancer deaths in the African Region and in the low-and middle-income countries of the Region of the Americas. In the South-East Asia Region, For women, 15 cancers are ranked for each of the regions. The most common cancer at the global level is breast cancer, followed by cancers of the trachea, bronchus and lung, and stomach cancer. Breast cancer is" ]

[ [ "0a", "Title: Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015): Jeddah, Kingdom of Saudi Arabia." ], [ "0b", "30 November - 3 December 2015" ], [ "0c", "Passage: Breast cancer is the most common type of cancer among women worldwide." ], [ "0d", "It ranks first amongst cancer in Saudi females with an incidence of 19.8 % ." ], [ "0e", "Few studies have shown that the knowledge, awareness, and protective measures against this disease are very low in Saudi females ." ], [ "0f", "Objective of this study was to assess the level of awareness, knowledge, and practices of breast cancer among Saudi females living in Jeddah." ] ]

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

[ "Title: Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015): Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015\nPassage: Breast cancer is the most common type of cancer among women worldwide. It ranks first amongst cancer in Saudi females with an incidence of 19.8 % . Few studies have shown that the knowledge, awareness, and protective measures against this disease are very low in Saudi females . Objective of this study was to assess the level of awareness, knowledge, and practices of breast cancer among Saudi females living in Jeddah.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: the leading cause in four of the seven regions, second in two regions and fifth in the Western Pacific Region. Stomach cancer is the main cause of cancer death among women in that Region, followed by lung cancer and liver cancer. Cervix uteri cancer is the number one cause of cancer deaths in the South-East Asia Region and the African Region. Other cancers of the female reproductive system are the eighth and thirteenth leading causes of cancer deaths globally. • acute respiratory infections, mainly pneumonia", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: hepatitis B virus in the case of liver cancer. Globally, lung cancer is the most common cancer , followed by breast cancer, then colon and rectum cancer, and stomach cancer. Lung cancer is also the leading cancer in the Western Pacific Region, but is less common than colon and rectum cancers or breast cancers in most other regions. Cervix cancer is the cancer with the highest incidence in the African and South-East Asia regions, even though it occurs only in women.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: is the second leading cause of cancer death in the African Region. Colon and rectum cancers are the fourth leading cause and oesophagus cancer the fifth leading cause globally. Prostate cancer is sixth globally, but is the leading cause of cancer deaths in the African Region and in the low-and middle-income countries of the Region of the Americas. In the South-East Asia Region, For women, 15 cancers are ranked for each of the regions. The most common cancer at the global level is breast cancer, followed by cancers of the trachea, bronchus and lung, and stomach cancer. Breast cancer is" ]

[ [ "1a", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response" ], [ "1b", "Passage: the leading cause in four of the seven regions, second in two regions and fifth in the Western Pacific Region." ], [ "1c", "Stomach cancer is the main cause of cancer death among women in that Region, followed by lung cancer and liver cancer." ], [ "1d", "Cervix uteri cancer is the number one cause of cancer deaths in the South-East Asia Region and the African Region." ], [ "1e", "Other cancers of the female reproductive system are the eighth and thirteenth leading causes of cancer deaths globally." ], [ "1f", "• acute respiratory infections, mainly pneumonia" ] ]

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

[ "Title: Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015): Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015\nPassage: Breast cancer is the most common type of cancer among women worldwide. It ranks first amongst cancer in Saudi females with an incidence of 19.8 % . Few studies have shown that the knowledge, awareness, and protective measures against this disease are very low in Saudi females . Objective of this study was to assess the level of awareness, knowledge, and practices of breast cancer among Saudi females living in Jeddah.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: the leading cause in four of the seven regions, second in two regions and fifth in the Western Pacific Region. Stomach cancer is the main cause of cancer death among women in that Region, followed by lung cancer and liver cancer. Cervix uteri cancer is the number one cause of cancer deaths in the South-East Asia Region and the African Region. Other cancers of the female reproductive system are the eighth and thirteenth leading causes of cancer deaths globally. • acute respiratory infections, mainly pneumonia", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: hepatitis B virus in the case of liver cancer. Globally, lung cancer is the most common cancer , followed by breast cancer, then colon and rectum cancer, and stomach cancer. Lung cancer is also the leading cancer in the Western Pacific Region, but is less common than colon and rectum cancers or breast cancers in most other regions. Cervix cancer is the cancer with the highest incidence in the African and South-East Asia regions, even though it occurs only in women.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: is the second leading cause of cancer death in the African Region. Colon and rectum cancers are the fourth leading cause and oesophagus cancer the fifth leading cause globally. Prostate cancer is sixth globally, but is the leading cause of cancer deaths in the African Region and in the low-and middle-income countries of the Region of the Americas. In the South-East Asia Region, For women, 15 cancers are ranked for each of the regions. The most common cancer at the global level is breast cancer, followed by cancers of the trachea, bronchus and lung, and stomach cancer. Breast cancer is" ]

[ [ "2a", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response" ], [ "2b", "Passage: hepatitis B virus in the case of liver cancer." ], [ "2c", "Globally, lung cancer is the most common cancer , followed by breast cancer, then colon and rectum cancer, and stomach cancer." ], [ "2d", "Lung cancer is also the leading cancer in the Western Pacific Region, but is less common than colon and rectum cancers or breast cancers in most other regions." ], [ "2e", "Cervix cancer is the cancer with the highest incidence in the African and South-East Asia regions, even though it occurs only in women." ] ]

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

[ "Title: Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015): Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015\nPassage: Breast cancer is the most common type of cancer among women worldwide. It ranks first amongst cancer in Saudi females with an incidence of 19.8 % . Few studies have shown that the knowledge, awareness, and protective measures against this disease are very low in Saudi females . Objective of this study was to assess the level of awareness, knowledge, and practices of breast cancer among Saudi females living in Jeddah.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: the leading cause in four of the seven regions, second in two regions and fifth in the Western Pacific Region. Stomach cancer is the main cause of cancer death among women in that Region, followed by lung cancer and liver cancer. Cervix uteri cancer is the number one cause of cancer deaths in the South-East Asia Region and the African Region. Other cancers of the female reproductive system are the eighth and thirteenth leading causes of cancer deaths globally. • acute respiratory infections, mainly pneumonia", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: hepatitis B virus in the case of liver cancer. Globally, lung cancer is the most common cancer , followed by breast cancer, then colon and rectum cancer, and stomach cancer. Lung cancer is also the leading cancer in the Western Pacific Region, but is less common than colon and rectum cancers or breast cancers in most other regions. Cervix cancer is the cancer with the highest incidence in the African and South-East Asia regions, even though it occurs only in women.", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response\nPassage: is the second leading cause of cancer death in the African Region. Colon and rectum cancers are the fourth leading cause and oesophagus cancer the fifth leading cause globally. Prostate cancer is sixth globally, but is the leading cause of cancer deaths in the African Region and in the low-and middle-income countries of the Region of the Americas. In the South-East Asia Region, For women, 15 cancers are ranked for each of the regions. The most common cancer at the global level is breast cancer, followed by cancers of the trachea, bronchus and lung, and stomach cancer. Breast cancer is" ]

[ [ "3a", "Title: Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response" ], [ "3b", "Passage: is the second leading cause of cancer death in the African Region." ], [ "3c", "Colon and rectum cancers are the fourth leading cause and oesophagus cancer the fifth leading cause globally." ], [ "3d", "Prostate cancer is sixth globally, but is the leading cause of cancer deaths in the African Region and in the low-and middle-income countries of the Region of the Americas." ], [ "3e", "In the South-East Asia Region, For women, 15 cancers are ranked for each of the regions." ], [ "3f", "The most common cancer at the global level is breast cancer, followed by cancers of the trachea, bronchus and lung, and stomach cancer." ], [ "3g", "Breast cancer is" ] ]

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

[ "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: on chest radiograph, and were treated as having bacterial pneumonia; 4) they were often older patients with underlying comorbidity and a high risk of developing adverse drug effects, so physicians may not start empirical anti-TB treatment even when TB is highly suspected.", "Title: Identification of antigens presented by MHC for vaccines against tuberculosis\nPassage: Mycobacterium tuberculosis , the etiologic agent of tuberculosis is the largest cause of death by an infectious disease worldwide. M. africanum, M. canettii, M. microtti, and M. bovis, share 99.9% similarity at the nucleotide level and are grouped in the Mycobacterium tuberculosis complex , the mycobacteria causing TB disease. According to the last World Health Organization report, 1.6 million people died of TB, 300,000 of which were co-infected with HIV, in 2017 1 With the emergence of multi-drug and extensively-drug resistant strains, as well as co-infection with HIV, new tools to control this epidemic are urgently required. The currently available", "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: All of the authors declare no financial, professional, or otherwise personal interest of any nature or kind in any related product, service, and/or company.", "Title: Clonal Expansions of CD8(+) T Cells with IL-10 Secreting Capacity Occur during Chronic Mycobacterium tuberculosis Infection\nPassage: Following aerogenic infection of CBA/J and C57BL/6 mice with Mtb we observed a gradual accumulation of CD4 + T cells in the lungs of C57BL/6 mice and significantly fewer CD4 + T cells within the lungs of CBA/J mice , as we have previously described . In contrast to the reduced number of CD4 + T cells, CBA/J mice demonstrated a significant late accumulation of CD8 + T cells within the lungs as Mtb infection progressed , eventually reaching or surpassing the number of pulmonary CD8 + T cells observed in C57BL/6 mice. This late accumulation was absent from C57BL/6" ]

[ [ "1a", "Title: Identification of antigens presented by MHC for vaccines against tuberculosis" ], [ "1b", "Passage: Mycobacterium tuberculosis , the etiologic agent of tuberculosis is the largest cause of death by an infectious disease worldwide." ], [ "1c", "M. africanum, M. canettii, M. microtti, and M. bovis, share 99.9% similarity at the nucleotide level and are grouped in the Mycobacterium tuberculosis complex , the mycobacteria causing TB disease." ], [ "1d", "According to the last World Health Organization report, 1.6 million people died of TB, 300,000 of which were co-infected with HIV, in 2017 1 With the emergence of multi-drug and extensively-drug resistant strains, as well as co-infection with HIV, new tools to control this epidemic are urgently required." ], [ "1e", "The currently available" ] ]

[ "1a", "1c" ]

[ "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: Why language matters: insights and challenges in applying a social determination of health approach in a North-South collaborative research program\nPassage: serve as outcome to measure quantitatively. We therefore set out to build the infrastructural capacity, while promoting the use of the material, leaving rigorous evaluation to a future date. Traditional epidemiology would consider this study a failure; however, the research process itself brought together communities, non-governmental organizations, national government and international agencies, serving to raise the level of awareness and conferring some empowerment to serve as a basis for future challenges to detrimental social processes. Table 3 assessed this collaborative research project with respect to the 4 S framework.", "Title: Globalization and Health: developing the journal to advance the field\nPassage: review of all the articles that have been published to date. The purpose of this review was to identify strengths, trends and current gaps in research; highlight opportunities for strengthening existing research; and to propose upcoming areas of research, projected to be of increasing importance over the next ten years.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Some argued that publishing studies like these in full detail provided ''recipes'' for especially dangerous potential biological weapons agents to would-be bioterrorists. Many who acknowledged such potential dangers, on the other hand, argued that benefits of publication outweighed risks involved." ]

[ [ "0a", "Title: Gain-of-Function Research: Ethical Analysis" ], [ "0b", "Passage: were published in 2012." ], [ "0c", "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." ], [ "0d", "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." ] ]

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