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[ "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: In conclusion, our study suggests that bacterial coinfection is not uncommon in H1N1 infected patients and laboratory investigations should go beyond establishing a viral cause alone. Bacterial coinfection was more frequently seen in the older age group and was associated with higher rates of complications. As adjunct to clinical findings, clinicians need to have a high index of suspicion if neutrophilia was identified on admission as it may denote bacterial coinfection. A larger scale study will be useful to further confirm our findings.", "Title: Severe novel influenza A (H1N1) infection in cancer patients\nPassage: In our study, we detected bacterial coinfection in seven of the eight patients. The CDC reported that 29% of fatal cases in the United States presented at least one bacterial coinfection . Mauad et al. found evidence of bacterial coinfection in 38% of fatal cases in Sao Paulo.", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: Forty-five patients had lower respiratory tract specimens sent for bacterial cultures. The 5 patients without these specimens were children who had difficulty in producing respiratory secretions, however, they appeared generally well with no evidence of pneumonia. Blood cultures were performed in 23 patients and Mycoplasma pneumoniae serology in 27 patients . Of the 50 H1N1 patients, 17 were coinfected with a second respiratory pathogen; 14 bacterial and only 3 viral. Mycoplasma pneumoniae was the commonest bacterial coinfection followed by Staphylococcus aureus , Klebsiella pneumoniae , Streptococcus pneumoniae , Moraxella catarrhalis , Pseudomonas aeruginosa , Streptococcus pyogenes and Streptococcus agalactiae .", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies . A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection . Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study." ]

[ [ "1a", "Title: Severe novel influenza A (H1N1) infection in cancer patients" ], [ "1b", "Passage: In our study, we detected bacterial coinfection in seven of the eight patients." ], [ "1c", "The CDC reported that 29% of fatal cases in the United States presented at least one bacterial coinfection ." ], [ "1d", "Mauad et al. found evidence of bacterial coinfection in 38% of fatal cases in Sao Paulo." ] ]

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

[ "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: In conclusion, our study suggests that bacterial coinfection is not uncommon in H1N1 infected patients and laboratory investigations should go beyond establishing a viral cause alone. Bacterial coinfection was more frequently seen in the older age group and was associated with higher rates of complications. As adjunct to clinical findings, clinicians need to have a high index of suspicion if neutrophilia was identified on admission as it may denote bacterial coinfection. A larger scale study will be useful to further confirm our findings.", "Title: Severe novel influenza A (H1N1) infection in cancer patients\nPassage: In our study, we detected bacterial coinfection in seven of the eight patients. The CDC reported that 29% of fatal cases in the United States presented at least one bacterial coinfection . Mauad et al. found evidence of bacterial coinfection in 38% of fatal cases in Sao Paulo.", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: Forty-five patients had lower respiratory tract specimens sent for bacterial cultures. The 5 patients without these specimens were children who had difficulty in producing respiratory secretions, however, they appeared generally well with no evidence of pneumonia. Blood cultures were performed in 23 patients and Mycoplasma pneumoniae serology in 27 patients . Of the 50 H1N1 patients, 17 were coinfected with a second respiratory pathogen; 14 bacterial and only 3 viral. Mycoplasma pneumoniae was the commonest bacterial coinfection followed by Staphylococcus aureus , Klebsiella pneumoniae , Streptococcus pneumoniae , Moraxella catarrhalis , Pseudomonas aeruginosa , Streptococcus pyogenes and Streptococcus agalactiae .", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies . A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection . Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study." ]

[ [ "2a", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection" ], [ "2b", "Passage: Forty-five patients had lower respiratory tract specimens sent for bacterial cultures." ], [ "2c", "The 5 patients without these specimens were children who had difficulty in producing respiratory secretions, however, they appeared generally well with no evidence of pneumonia." ], [ "2d", "Blood cultures were performed in 23 patients and Mycoplasma pneumoniae serology in 27 patients ." ], [ "2e", "Of the 50 H1N1 patients, 17 were coinfected with a second respiratory pathogen; 14 bacterial and only 3 viral." ], [ "2f", "Mycoplasma pneumoniae was the commonest bacterial coinfection followed by Staphylococcus aureus , Klebsiella pneumoniae , Streptococcus pneumoniae , Moraxella catarrhalis , Pseudomonas aeruginosa , Streptococcus pyogenes and Streptococcus agalactiae ." ] ]

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

[ "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: In conclusion, our study suggests that bacterial coinfection is not uncommon in H1N1 infected patients and laboratory investigations should go beyond establishing a viral cause alone. Bacterial coinfection was more frequently seen in the older age group and was associated with higher rates of complications. As adjunct to clinical findings, clinicians need to have a high index of suspicion if neutrophilia was identified on admission as it may denote bacterial coinfection. A larger scale study will be useful to further confirm our findings.", "Title: Severe novel influenza A (H1N1) infection in cancer patients\nPassage: In our study, we detected bacterial coinfection in seven of the eight patients. The CDC reported that 29% of fatal cases in the United States presented at least one bacterial coinfection . Mauad et al. found evidence of bacterial coinfection in 38% of fatal cases in Sao Paulo.", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: Forty-five patients had lower respiratory tract specimens sent for bacterial cultures. The 5 patients without these specimens were children who had difficulty in producing respiratory secretions, however, they appeared generally well with no evidence of pneumonia. Blood cultures were performed in 23 patients and Mycoplasma pneumoniae serology in 27 patients . Of the 50 H1N1 patients, 17 were coinfected with a second respiratory pathogen; 14 bacterial and only 3 viral. Mycoplasma pneumoniae was the commonest bacterial coinfection followed by Staphylococcus aureus , Klebsiella pneumoniae , Streptococcus pneumoniae , Moraxella catarrhalis , Pseudomonas aeruginosa , Streptococcus pyogenes and Streptococcus agalactiae .", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies . A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection . Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study." ]

[ [ "3a", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection" ], [ "3b", "Passage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies ." ], [ "3c", "A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection ." ], [ "3d", "Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study." ] ]

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

[ "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The intestinal epithelial barrier forms a selectively permeable immunologically tolerant but alert barrier between the sterile inside and microbe-laden lumen.", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: of this system is apparent with the identification of different types of Goblet cells, which synthesize and secrete the mucus along the crypt in the human colon. Indeed a \"sentinel\" Goblet cell has been identified, positioned at the top of each colonic crypt. Endocytosis of TLR generates MUC2 secretion, together with an intercellular gap junction signal, which induces MUC2 secretion in adjacent Goblet cells and thus regulates the entry of bacteria into the crypt .", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: The stability of the mucus barrier and the innate defense mechanisms rely on the secretion of intact, gel forming mucus and the availability of mucosal immune proteins, including immunoglobulins and the trefoil factor peptides. Together these factors normally ensure mucosal cell integrity and epithelial homeostasis through restitution and regeneration processes. Part of the risk is linked to the immature state of the mucosa at this very early stage of life. A role for the mucins in the pathogenesis of NEC is indicated by the depletion of Goblet cells seen in the mucosa of neonates with NEC and this is expected", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: homeostasis Similar to intestinal mucosal epithelial cells, lung epithelial cells have developed many defence mechanisms to deal with environmental exposures. Increasing evidence shows that the UPR pathways interact with the recognition and handling of exogenous threats, like viruses. 44 The continuous epithelium in the airways acts as a physical barrier to keep the underlying immune system separated from exogenous air-borne pathogens. Ciliated cells continuously clear inhaled matter trapped by the mucus layer. Respiratory goblet cells synthesise and secrete the mucins, MUC5B and MUC5AC rather than MUC2. MUC5B/AC, and their glycoforms contribute to the elasticity and viscous nature of the mucus" ]

[ [ "0a", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection" ], [ "0b", "Passage: The intestinal epithelial barrier forms a selectively permeable immunologically tolerant but alert barrier between the sterile inside and microbe-laden lumen." ] ]

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

[ "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The intestinal epithelial barrier forms a selectively permeable immunologically tolerant but alert barrier between the sterile inside and microbe-laden lumen.", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: of this system is apparent with the identification of different types of Goblet cells, which synthesize and secrete the mucus along the crypt in the human colon. Indeed a \"sentinel\" Goblet cell has been identified, positioned at the top of each colonic crypt. Endocytosis of TLR generates MUC2 secretion, together with an intercellular gap junction signal, which induces MUC2 secretion in adjacent Goblet cells and thus regulates the entry of bacteria into the crypt .", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: The stability of the mucus barrier and the innate defense mechanisms rely on the secretion of intact, gel forming mucus and the availability of mucosal immune proteins, including immunoglobulins and the trefoil factor peptides. Together these factors normally ensure mucosal cell integrity and epithelial homeostasis through restitution and regeneration processes. Part of the risk is linked to the immature state of the mucosa at this very early stage of life. A role for the mucins in the pathogenesis of NEC is indicated by the depletion of Goblet cells seen in the mucosa of neonates with NEC and this is expected", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: homeostasis Similar to intestinal mucosal epithelial cells, lung epithelial cells have developed many defence mechanisms to deal with environmental exposures. Increasing evidence shows that the UPR pathways interact with the recognition and handling of exogenous threats, like viruses. 44 The continuous epithelium in the airways acts as a physical barrier to keep the underlying immune system separated from exogenous air-borne pathogens. Ciliated cells continuously clear inhaled matter trapped by the mucus layer. Respiratory goblet cells synthesise and secrete the mucins, MUC5B and MUC5AC rather than MUC2. MUC5B/AC, and their glycoforms contribute to the elasticity and viscous nature of the mucus" ]

[ [ "1a", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human" ], [ "1b", "Passage: of this system is apparent with the identification of different types of Goblet cells, which synthesize and secrete the mucus along the crypt in the human colon." ], [ "1c", "Indeed a \"sentinel\" Goblet cell has been identified, positioned at the top of each colonic crypt." ], [ "1d", "Endocytosis of TLR generates MUC2 secretion, together with an intercellular gap junction signal, which induces MUC2 secretion in adjacent Goblet cells and thus regulates the entry of bacteria into the crypt ." ] ]

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

[ "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: The intestinal epithelial barrier forms a selectively permeable immunologically tolerant but alert barrier between the sterile inside and microbe-laden lumen.", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: of this system is apparent with the identification of different types of Goblet cells, which synthesize and secrete the mucus along the crypt in the human colon. Indeed a \"sentinel\" Goblet cell has been identified, positioned at the top of each colonic crypt. Endocytosis of TLR generates MUC2 secretion, together with an intercellular gap junction signal, which induces MUC2 secretion in adjacent Goblet cells and thus regulates the entry of bacteria into the crypt .", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human\nPassage: The stability of the mucus barrier and the innate defense mechanisms rely on the secretion of intact, gel forming mucus and the availability of mucosal immune proteins, including immunoglobulins and the trefoil factor peptides. Together these factors normally ensure mucosal cell integrity and epithelial homeostasis through restitution and regeneration processes. Part of the risk is linked to the immature state of the mucosa at this very early stage of life. A role for the mucins in the pathogenesis of NEC is indicated by the depletion of Goblet cells seen in the mucosa of neonates with NEC and this is expected", "Title: Immune regulation of the unfolded protein response at the mucosal barrier in viral infection\nPassage: homeostasis Similar to intestinal mucosal epithelial cells, lung epithelial cells have developed many defence mechanisms to deal with environmental exposures. Increasing evidence shows that the UPR pathways interact with the recognition and handling of exogenous threats, like viruses. 44 The continuous epithelium in the airways acts as a physical barrier to keep the underlying immune system separated from exogenous air-borne pathogens. Ciliated cells continuously clear inhaled matter trapped by the mucus layer. Respiratory goblet cells synthesise and secrete the mucins, MUC5B and MUC5AC rather than MUC2. MUC5B/AC, and their glycoforms contribute to the elasticity and viscous nature of the mucus" ]

[ [ "2a", "Title: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human" ], [ "2b", "Passage: The stability of the mucus barrier and the innate defense mechanisms rely on the secretion of intact, gel forming mucus and the availability of mucosal immune proteins, including immunoglobulins and the trefoil factor peptides." ], [ "2c", "Together these factors normally ensure mucosal cell integrity and epithelial homeostasis through restitution and regeneration processes." ], [ "2d", "Part of the risk is linked to the immature state of the mucosa at this very early stage of life." ], [ "2e", "A role for the mucins in the pathogenesis of NEC is indicated by the depletion of Goblet cells seen in the mucosa of neonates with NEC and this is expected" ] ]

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

[ "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The analysis of the focus group data was undertaken by a single researcher who was neither present at the focus groups nor had read any preliminary findings. This work was verified by the focus group facilitators to ensure that any \"contextual richness\" had not been missed in the data. Thematic analysis was used to identify themes and concepts across the entire data set to \"identify repeated patterns of meaning\" . The process involved working through the six phases of thematic analyses as identified by Braun and Clarke .", "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.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The study was part of a rapid response initiative; therefore focus groups were selected as the most efficient means of data collection in the time available. Eight semi-structured focus groups were recruited between May and July 2010 comprising 7 to 13 participants each and lasting approximately 1 hour. Separate focus groups were conducted for each of the target groups with a total of 80 participants representative of five target populations groups identified in consultation with Ministry of Health staff: Māori, Pacific Peoples, children , general population, and vulnerable people with chronic conditions (defined as those who are eligible for subsidised", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large. It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate. Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender. Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's" ]

[ [ "1a", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study" ], [ "1b", "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." ], [ "1c", "The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns." ] ]

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

[ "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The analysis of the focus group data was undertaken by a single researcher who was neither present at the focus groups nor had read any preliminary findings. This work was verified by the focus group facilitators to ensure that any \"contextual richness\" had not been missed in the data. Thematic analysis was used to identify themes and concepts across the entire data set to \"identify repeated patterns of meaning\" . The process involved working through the six phases of thematic analyses as identified by Braun and Clarke .", "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.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The study was part of a rapid response initiative; therefore focus groups were selected as the most efficient means of data collection in the time available. Eight semi-structured focus groups were recruited between May and July 2010 comprising 7 to 13 participants each and lasting approximately 1 hour. Separate focus groups were conducted for each of the target groups with a total of 80 participants representative of five target populations groups identified in consultation with Ministry of Health staff: Māori, Pacific Peoples, children , general population, and vulnerable people with chronic conditions (defined as those who are eligible for subsidised", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large. It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate. Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender. Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's" ]

[ [ "2a", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study" ], [ "2b", "Passage: The study was part of a rapid response initiative; therefore focus groups were selected as the most efficient means of data collection in the time available." ], [ "2c", "Eight semi-structured focus groups were recruited between May and July 2010 comprising 7 to 13 participants each and lasting approximately 1 hour." ], [ "2d", "Separate focus groups were conducted for each of the target groups with a total of 80 participants representative of five target populations groups identified in consultation with Ministry of Health staff: Māori, Pacific Peoples, children , general population, and vulnerable people with chronic conditions (defined as those who are eligible for subsidised" ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Immunogenicity and Safety of an AS03-Adjuvanted H7N9 Pandemic Influenza Vaccine in a Randomized Trial in Healthy Adults\nPassage: increase . The coprimary safety objective was to describe the safety and reactogenicity of the vaccines up to day 42.", "Title: Safety of Tdap vaccine in pregnant women: an observational study\nPassage: SAEs were also reported to the Marketing Authorisation Holder as part of global drug safety surveillance.", "Title: The promise of mRNA vaccines: a biotech and industrial perspective\nPassage: As the field accrues more data from early-phase human studies, the focus of mRNA vaccines will shift from documenting local and systemic tolerability to capturing potential long-term safety. Unfortunately detecting safety signals for uncommon adverse events requires thousands of subjects. As with novel adjuvants, an adequate safety database to assure safety for candidate mRNA vaccines is likely to be in the tens of thousands range. Given that different manufacturers are pursuing different strategies to optimize their candidate vaccines, conclusions from one candidate may not be generalizable. Therefore, it is likely that each candidate vaccine will have to independently prove its" ]

[ [ "0a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "0b", "Passage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria." ], [ "0c", "Safety is a major concern, as even a low level of toxicity is unacceptable ." ], [ "0d", "Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries ." ], [ "0e", "Similar constraints apply to veterinary vaccines, with cost often an even more important consideration." ], [ "0f", "Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose ." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Immunogenicity and Safety of an AS03-Adjuvanted H7N9 Pandemic Influenza Vaccine in a Randomized Trial in Healthy Adults\nPassage: increase . The coprimary safety objective was to describe the safety and reactogenicity of the vaccines up to day 42.", "Title: Safety of Tdap vaccine in pregnant women: an observational study\nPassage: SAEs were also reported to the Marketing Authorisation Holder as part of global drug safety surveillance.", "Title: The promise of mRNA vaccines: a biotech and industrial perspective\nPassage: As the field accrues more data from early-phase human studies, the focus of mRNA vaccines will shift from documenting local and systemic tolerability to capturing potential long-term safety. Unfortunately detecting safety signals for uncommon adverse events requires thousands of subjects. As with novel adjuvants, an adequate safety database to assure safety for candidate mRNA vaccines is likely to be in the tens of thousands range. Given that different manufacturers are pursuing different strategies to optimize their candidate vaccines, conclusions from one candidate may not be generalizable. Therefore, it is likely that each candidate vaccine will have to independently prove its" ]

[ [ "1a", "Title: Immunogenicity and Safety of an AS03-Adjuvanted H7N9 Pandemic Influenza Vaccine in a Randomized Trial in Healthy Adults" ], [ "1b", "Passage: increase ." ], [ "1c", "The coprimary safety objective was to describe the safety and reactogenicity of the vaccines up to day 42." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Immunogenicity and Safety of an AS03-Adjuvanted H7N9 Pandemic Influenza Vaccine in a Randomized Trial in Healthy Adults\nPassage: increase . The coprimary safety objective was to describe the safety and reactogenicity of the vaccines up to day 42.", "Title: Safety of Tdap vaccine in pregnant women: an observational study\nPassage: SAEs were also reported to the Marketing Authorisation Holder as part of global drug safety surveillance.", "Title: The promise of mRNA vaccines: a biotech and industrial perspective\nPassage: As the field accrues more data from early-phase human studies, the focus of mRNA vaccines will shift from documenting local and systemic tolerability to capturing potential long-term safety. Unfortunately detecting safety signals for uncommon adverse events requires thousands of subjects. As with novel adjuvants, an adequate safety database to assure safety for candidate mRNA vaccines is likely to be in the tens of thousands range. Given that different manufacturers are pursuing different strategies to optimize their candidate vaccines, conclusions from one candidate may not be generalizable. Therefore, it is likely that each candidate vaccine will have to independently prove its" ]

[ [ "3a", "Title: The promise of mRNA vaccines: a biotech and industrial perspective" ], [ "3b", "Passage: As the field accrues more data from early-phase human studies, the focus of mRNA vaccines will shift from documenting local and systemic tolerability to capturing potential long-term safety." ], [ "3c", "Unfortunately detecting safety signals for uncommon adverse events requires thousands of subjects." ], [ "3d", "As with novel adjuvants, an adequate safety database to assure safety for candidate mRNA vaccines is likely to be in the tens of thousands range." ], [ "3e", "Given that different manufacturers are pursuing different strategies to optimize their candidate vaccines, conclusions from one candidate may not be generalizable." ], [ "3f", "Therefore, it is likely that each candidate vaccine will have to independently prove its" ] ]

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

[ "Title: Timing and causes of death in septic shock\nPassage: ICU also directly resulted from end-of-life decisions in 36 patients with fixed multiple organ failure for whom the treating physicians were convinced that meaningful recovery was not possible. Therefore, extensive diagnostic procedures were not carried out in such settings of exclusive palliative care. Besides, most early-onset deaths were directly related to the primary infection through intractable shock and multiple organ failure . In addition, 6.4 % of early decedents were diagnosed with mesenteric ischemia likely to act as a consequence or a contributor of multiple organ failure. Most late deaths were related to ICU-acquired complications such as nosocomial infections and", "Title: Epidemiology and outcome of severe pneumococcal pneumonia admitted to intensive care unit: a multicenter study\nPassage: a high rate of fatality, with more than one fourth of the patients dying in hospital. The highest proportion of death occurs early in the course of the disease, despite an excellent proportion of initial adequate antibiotherapy . This is considered to be related to the early inflammatory process, which is overwhelming host defences. In a recent study, Garcia-Vidal et al. investigated independent factors associated with early deaths in CAP and demonstrated that age, altered mental status, multilobar pneumonia, shock, bacteraemia and inadequate empiric antibiotic therapy were predictors of death within 48 hours . The small number of patient dying", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Local elaboration of inflammatory and chemotactic mediators is considered to be a requirement for the development of systemic disease symptoms, with those abnormalities sometimes culminating in shock and death. Yet it is not hypoxemia, due to the prominent pulmonary edema, that leads to death in most fatal cases of HCPS, but rather intoxication of the heart by as-yet-undefined mediators that leads to the low cardiac output state and the associated shock syndrome . It is tempting to speculate that mediators produced in the lung in connection with the inflammatory infiltrate can percolate through the coronary circulation with minimal dilution in", "Title: Timing and causes of death in septic shock\nPassage: failure, the development of , digestive perforation . Others : myocardial infarction , lymphoma-related tumor lysis syndrome , extensive limb ischemia , acute liver failure . Iatrogenic complications related to chest tube insertion , catheter insertion , accidental removal of tracheostomy , and cardiac arrest at the start of hemodialysis . MOF multiple organ failure, ICU intensive care unit, ARDS acute respiratory distress syndrome sepsis-induced immunosuppression in patients that survive the primary insult may favor the development of secondary infections in addition to other common risk factors related to severity and requirements for invasive procedures . Ventilator-associated pneumonia remains the" ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: Local elaboration of inflammatory and chemotactic mediators is considered to be a requirement for the development of systemic disease symptoms, with those abnormalities sometimes culminating in shock and death." ], [ "2c", "Yet it is not hypoxemia, due to the prominent pulmonary edema, that leads to death in most fatal cases of HCPS, but rather intoxication of the heart by as-yet-undefined mediators that leads to the low cardiac output state and the associated shock syndrome ." ], [ "2d", "It is tempting to speculate that mediators produced in the lung in connection with the inflammatory infiltrate can percolate through the coronary circulation with minimal dilution in" ] ]

[ "2b", "2c" ]

[ "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: HIV infectivity by increasing the viral mutation frequency . In a follow up study, Clouser et al. further reported the antiviral effect of gemcitabine against HIV-related retrovirus, murine leukemia virus , in vitro and even in murine AIDS model . A significant antiviral effect of gemcitabine on IAVs was also reported for RPE cells by Denisova et al. . They also tested whether gemcitabine had an antiviral effect on several other viruses of different families and found its strong inhibitory effect on Sindbis virus and herpes simplex virus-1 but relatively weak effects on Semliki forest virus and human echovirus 6,", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: and minimal effects on Bunyamwera virus, measles virus , and vaccinia virus . The antiviral effect of gemcitabine on EVs, initially performed on Coxsackievirus B3 , was found from screening FDA-approved drugs in CVB3 replicon-harboring Vero cells by our group . Its broad-spectrum antiviral activity on EVs was further identified by observing a similar inhibitory effect on enterovirus 71 and human rhinoviruses . In the case of HRV, the antiviral effect of gemcitabine was further confirmed in a virus-infected mouse model . In this study, intranasal administration of gemcitabine significantly lowered the pulmonary viral load and inflammation by decreasing proinflammatory", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: can infect pregnant women and cause congenital abnormalities such as microcephaly in infants, which has attracted increasing public attention as well as extensive research and development into possible treatments. Effective antiviral activities of gemcitabine were also found for the replication of HCV in Huh-7 cells and the infection of HIV in U373-MAGI-CXCR4 CEM cells, with estimated EC 50 s of 12 nM and 16.3 nM, respectively , which were lower concentrations than those used in cancer therapy . In the case of HIV, the combination of gemcitabine with decitabine, another nucleoside analog in clinical use for cancer therapy, synergistically reduced", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: Most studies regarding the antiviral activity of gemcitabine lack experimental evidence of the mode of action. However, our group has recently reported that gemcitabine had an anti-EV effect by targeting the salvage pathway of pyrimidine biosynthesis . Moreover, gemcitabine strongly induced the expression of several ISGs including CXCL10, IRF7, IRF9, IFIT1, and DDX58, which were the major effectors in the innate immunity that defended the host against the virus infection. These results were consistent with a previous report that gemcitabine stimulated the production of IFN-β and IFN-γ in IAV-infected RPE cells . Importantly, the activation of ISGs was well-correlated with" ]

[ [ "0a", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity" ], [ "0b", "Passage: HIV infectivity by increasing the viral mutation frequency ." ], [ "0c", "In a follow up study, Clouser et al. further reported the antiviral effect of gemcitabine against HIV-related retrovirus, murine leukemia virus , in vitro and even in murine AIDS model ." ], [ "0d", "A significant antiviral effect of gemcitabine on IAVs was also reported for RPE cells by Denisova et al. ." ], [ "0e", "They also tested whether gemcitabine had an antiviral effect on several other viruses of different families and found its strong inhibitory effect on Sindbis virus and herpes simplex virus-1 but relatively weak effects on Semliki forest virus and human echovirus 6," ] ]

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

[ "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: HIV infectivity by increasing the viral mutation frequency . In a follow up study, Clouser et al. further reported the antiviral effect of gemcitabine against HIV-related retrovirus, murine leukemia virus , in vitro and even in murine AIDS model . A significant antiviral effect of gemcitabine on IAVs was also reported for RPE cells by Denisova et al. . They also tested whether gemcitabine had an antiviral effect on several other viruses of different families and found its strong inhibitory effect on Sindbis virus and herpes simplex virus-1 but relatively weak effects on Semliki forest virus and human echovirus 6,", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: and minimal effects on Bunyamwera virus, measles virus , and vaccinia virus . The antiviral effect of gemcitabine on EVs, initially performed on Coxsackievirus B3 , was found from screening FDA-approved drugs in CVB3 replicon-harboring Vero cells by our group . Its broad-spectrum antiviral activity on EVs was further identified by observing a similar inhibitory effect on enterovirus 71 and human rhinoviruses . In the case of HRV, the antiviral effect of gemcitabine was further confirmed in a virus-infected mouse model . In this study, intranasal administration of gemcitabine significantly lowered the pulmonary viral load and inflammation by decreasing proinflammatory", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: can infect pregnant women and cause congenital abnormalities such as microcephaly in infants, which has attracted increasing public attention as well as extensive research and development into possible treatments. Effective antiviral activities of gemcitabine were also found for the replication of HCV in Huh-7 cells and the infection of HIV in U373-MAGI-CXCR4 CEM cells, with estimated EC 50 s of 12 nM and 16.3 nM, respectively , which were lower concentrations than those used in cancer therapy . In the case of HIV, the combination of gemcitabine with decitabine, another nucleoside analog in clinical use for cancer therapy, synergistically reduced", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: Most studies regarding the antiviral activity of gemcitabine lack experimental evidence of the mode of action. However, our group has recently reported that gemcitabine had an anti-EV effect by targeting the salvage pathway of pyrimidine biosynthesis . Moreover, gemcitabine strongly induced the expression of several ISGs including CXCL10, IRF7, IRF9, IFIT1, and DDX58, which were the major effectors in the innate immunity that defended the host against the virus infection. These results were consistent with a previous report that gemcitabine stimulated the production of IFN-β and IFN-γ in IAV-infected RPE cells . Importantly, the activation of ISGs was well-correlated with" ]

[ [ "1a", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity" ], [ "1b", "Passage: and minimal effects on Bunyamwera virus, measles virus , and vaccinia virus ." ], [ "1c", "The antiviral effect of gemcitabine on EVs, initially performed on Coxsackievirus B3 , was found from screening FDA-approved drugs in CVB3 replicon-harboring Vero cells by our group ." ], [ "1d", "Its broad-spectrum antiviral activity on EVs was further identified by observing a similar inhibitory effect on enterovirus 71 and human rhinoviruses ." ], [ "1e", "In the case of HRV, the antiviral effect of gemcitabine was further confirmed in a virus-infected mouse model ." ], [ "1f", "In this study, intranasal administration of gemcitabine significantly lowered the pulmonary viral load and inflammation by decreasing proinflammatory" ] ]

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

[ "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: HIV infectivity by increasing the viral mutation frequency . In a follow up study, Clouser et al. further reported the antiviral effect of gemcitabine against HIV-related retrovirus, murine leukemia virus , in vitro and even in murine AIDS model . A significant antiviral effect of gemcitabine on IAVs was also reported for RPE cells by Denisova et al. . They also tested whether gemcitabine had an antiviral effect on several other viruses of different families and found its strong inhibitory effect on Sindbis virus and herpes simplex virus-1 but relatively weak effects on Semliki forest virus and human echovirus 6,", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: and minimal effects on Bunyamwera virus, measles virus , and vaccinia virus . The antiviral effect of gemcitabine on EVs, initially performed on Coxsackievirus B3 , was found from screening FDA-approved drugs in CVB3 replicon-harboring Vero cells by our group . Its broad-spectrum antiviral activity on EVs was further identified by observing a similar inhibitory effect on enterovirus 71 and human rhinoviruses . In the case of HRV, the antiviral effect of gemcitabine was further confirmed in a virus-infected mouse model . In this study, intranasal administration of gemcitabine significantly lowered the pulmonary viral load and inflammation by decreasing proinflammatory", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: can infect pregnant women and cause congenital abnormalities such as microcephaly in infants, which has attracted increasing public attention as well as extensive research and development into possible treatments. Effective antiviral activities of gemcitabine were also found for the replication of HCV in Huh-7 cells and the infection of HIV in U373-MAGI-CXCR4 CEM cells, with estimated EC 50 s of 12 nM and 16.3 nM, respectively , which were lower concentrations than those used in cancer therapy . In the case of HIV, the combination of gemcitabine with decitabine, another nucleoside analog in clinical use for cancer therapy, synergistically reduced", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: Most studies regarding the antiviral activity of gemcitabine lack experimental evidence of the mode of action. However, our group has recently reported that gemcitabine had an anti-EV effect by targeting the salvage pathway of pyrimidine biosynthesis . Moreover, gemcitabine strongly induced the expression of several ISGs including CXCL10, IRF7, IRF9, IFIT1, and DDX58, which were the major effectors in the innate immunity that defended the host against the virus infection. These results were consistent with a previous report that gemcitabine stimulated the production of IFN-β and IFN-γ in IAV-infected RPE cells . Importantly, the activation of ISGs was well-correlated with" ]

[ [ "3a", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity" ], [ "3b", "Passage: Most studies regarding the antiviral activity of gemcitabine lack experimental evidence of the mode of action." ], [ "3c", "However, our group has recently reported that gemcitabine had an anti-EV effect by targeting the salvage pathway of pyrimidine biosynthesis ." ], [ "3d", "Moreover, gemcitabine strongly induced the expression of several ISGs including CXCL10, IRF7, IRF9, IFIT1, and DDX58, which were the major effectors in the innate immunity that defended the host against the virus infection." ], [ "3e", "These results were consistent with a previous report that gemcitabine stimulated the production of IFN-β and IFN-γ in IAV-infected RPE cells ." ], [ "3f", "Importantly, the activation of ISGs was well-correlated with" ] ]

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

[ "Title: Enhanced Hygiene Measures and Norovirus Transmission during an Outbreak\nPassage: Third, the decline in reproduction number could be because many infections were asymptomatic and many symptomatic cases were not reported. The request to report any symptoms might not have reached all participants because of the event's large size and because participants came from many different countries. During norovirus outbreaks, asymptomatic cases occur; in almost half of the outbreaks in the Netherlands during 2002, stool samples from >1 healthy persons tested positive for norovirus . Volunteer and outbreak studies demonstrate that 30% of collected stool specimens of exposed, asymptomatic persons were positive for norovirus . However, both the proportion of asymptomatic", "Title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan\nPassage: the number of people in each category for each outbreak, genotyping results were obtained. Figure 1 summarizes the survey results, and the coded data are given in eTable 1. It should be noted that the number of asymptomatic and virusnegative individuals includes both uninfected individuals and infected cases without virus shedding. The abovementioned study 31 has been very rigorous, in that all individuals involved in each food-borne outbreak were fully surveyed, which has been extremely rare and not routinely attainable. In addition, such a study must employ the highly sensitive real-time RT-PCR, a condition that was also satisfied by the", "Title: Reporting errors in infectious disease outbreaks, with an application to Pandemic Influenza A/H1N1\nPassage: initial cases could arise from individuals who are asymptomatic, but still carrying and transmitting the virus or from others whose illness was not sufficiently acute to warrant seeking medical attention. To our knowledge, the issue of the impact of this misspecification of the number of cases on the estimation of epidemic parameters has not been well-studied.", "Title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan\nPassage: It should be noted that q was assumed as independent of symptoms because the RT-PCR testing employed was highly sensitive and the cut-off value must have allowed q to be comparable between symptomatic and asymptomatic infected individuals. 8, 26 Sensitivity analysis was conducted to address potential difference of q between symptomatic and asymptomatic infection . It should also be noted that the parameter p should have ideally reflected the demographic stochasticity of the data generating process, but p is a mixture of food-borne and human-to-human transmissions and we do not have a sufficient dataset to characterize the distribution. Thus, the" ]

[ [ "0a", "Title: Enhanced Hygiene Measures and Norovirus Transmission during an Outbreak" ], [ "0b", "Passage: Third, the decline in reproduction number could be because many infections were asymptomatic and many symptomatic cases were not reported." ], [ "0c", "The request to report any symptoms might not have reached all participants because of the event's large size and because participants came from many different countries." ], [ "0d", "During norovirus outbreaks, asymptomatic cases occur; in almost half of the outbreaks in the Netherlands during 2002, stool samples from >1 healthy persons tested positive for norovirus ." ], [ "0e", "Volunteer and outbreak studies demonstrate that 30% of collected stool specimens of exposed, asymptomatic persons were positive for norovirus ." ], [ "0f", "However, both the proportion of asymptomatic" ] ]

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

[ "Title: Enhanced Hygiene Measures and Norovirus Transmission during an Outbreak\nPassage: Third, the decline in reproduction number could be because many infections were asymptomatic and many symptomatic cases were not reported. The request to report any symptoms might not have reached all participants because of the event's large size and because participants came from many different countries. During norovirus outbreaks, asymptomatic cases occur; in almost half of the outbreaks in the Netherlands during 2002, stool samples from >1 healthy persons tested positive for norovirus . Volunteer and outbreak studies demonstrate that 30% of collected stool specimens of exposed, asymptomatic persons were positive for norovirus . However, both the proportion of asymptomatic", "Title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan\nPassage: the number of people in each category for each outbreak, genotyping results were obtained. Figure 1 summarizes the survey results, and the coded data are given in eTable 1. It should be noted that the number of asymptomatic and virusnegative individuals includes both uninfected individuals and infected cases without virus shedding. The abovementioned study 31 has been very rigorous, in that all individuals involved in each food-borne outbreak were fully surveyed, which has been extremely rare and not routinely attainable. In addition, such a study must employ the highly sensitive real-time RT-PCR, a condition that was also satisfied by the", "Title: Reporting errors in infectious disease outbreaks, with an application to Pandemic Influenza A/H1N1\nPassage: initial cases could arise from individuals who are asymptomatic, but still carrying and transmitting the virus or from others whose illness was not sufficiently acute to warrant seeking medical attention. To our knowledge, the issue of the impact of this misspecification of the number of cases on the estimation of epidemic parameters has not been well-studied.", "Title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan\nPassage: It should be noted that q was assumed as independent of symptoms because the RT-PCR testing employed was highly sensitive and the cut-off value must have allowed q to be comparable between symptomatic and asymptomatic infected individuals. 8, 26 Sensitivity analysis was conducted to address potential difference of q between symptomatic and asymptomatic infection . It should also be noted that the parameter p should have ideally reflected the demographic stochasticity of the data generating process, but p is a mixture of food-borne and human-to-human transmissions and we do not have a sufficient dataset to characterize the distribution. Thus, the" ]

[ [ "1a", "Title: Estimating the Asymptomatic Ratio of Norovirus Infection During Foodborne Outbreaks With Laboratory Testing in Japan" ], [ "1b", "Passage: the number of people in each category for each outbreak, genotyping results were obtained." ], [ "1c", "Figure 1 summarizes the survey results, and the coded data are given in eTable 1." ], [ "1d", "It should be noted that the number of asymptomatic and virusnegative individuals includes both uninfected individuals and infected cases without virus shedding." ], [ "1e", "The abovementioned study 31 has been very rigorous, in that all individuals involved in each food-borne outbreak were fully surveyed, which has been extremely rare and not routinely attainable." ], [ "1f", "In addition, such a study must employ the highly sensitive real-time RT-PCR, a condition that was also satisfied by the" ] ]

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

[ "Title: High Throughput Screening for Small Molecule Enhancers of the Interferon Signaling Pathway to Drive Next-Generation Antiviral Drug Discovery\nPassage: To achieve simultaneous treatment of cells with IFN-b and various compound concentrations and to avoid reagent degradation over time, the screen was run in a modular manner with a precise timeline . The first step included production of plates with appropriate concentrations of compound and IFN-b and then storage at 4uC. A separate plate was made for each of the four compound concentrations . The Twister II, Sciclone, Orca, and Liconic cold storage incubator handled this step. For the second step, cells were plated at 8000 cells per well in 384-well assay plates . This step was accomplished in seven", "Title: High Throughput Screening for Small Molecule Enhancers of the Interferon Signaling Pathway to Drive Next-Generation Antiviral Drug Discovery\nPassage: concentrationresponse were rejected. Compounds with a consistent increase or decrease in response with increasing drug concentration or good efficacy at any concentration were included for further validation. This approach led to selection of 64 compounds for further validation, including compounds with the 20 highest z-scores.", "Title: High Throughput Screening for Small Molecule Enhancers of the Interferon Signaling Pathway to Drive Next-Generation Antiviral Drug Discovery\nPassage: Thereafter, to reach a smaller and tractable set of hits to validate experimentally, we took advantage of testing each compound at four concentrations. Specifically, we used self-organizing maps analysis to cluster hit compounds by shape of the dose-response curve. The significance of change from dose to dose was also analyzed using linear models and moderated F-statistics as implemented in the limma package in Bioconductor . The concentration-response curves for each compound were then visually inspected, using scatter plots generated in TIBCO Spotfire DecisionSite , with respect to the shape of the curve and reproducibility between replicates. Compounds showing an erratic", "Title: Identification of Novel Compounds Inhibiting Chikungunya Virus-Induced Cell Death by High Throughput Screening of a Kinase Inhibitor Library\nPassage: High-throughput screening is a technology widely used in today's drug discovery programs that aims to speed up the identification of potentially active substances against various diseases. By using high-throughput assays, a large collection of substances, from small molecules to natural products, can be evaluated for antiviral activity in a relatively short amount of time . The work reported here describes the development of a simple, cell-based high-throughput assay to screen potential CHIKV antivirals. The assay uses resazurin, an oxidized, nonfluorescent blue dye that is converted to the reduced, and highly fluorescent pink-colored resorufin through oxidation-reduction reaction, to measure cellular metabolic" ]

[ [ "3a", "Title: Identification of Novel Compounds Inhibiting Chikungunya Virus-Induced Cell Death by High Throughput Screening of a Kinase Inhibitor Library" ], [ "3b", "Passage: High-throughput screening is a technology widely used in today's drug discovery programs that aims to speed up the identification of potentially active substances against various diseases." ], [ "3c", "By using high-throughput assays, a large collection of substances, from small molecules to natural products, can be evaluated for antiviral activity in a relatively short amount of time ." ], [ "3d", "The work reported here describes the development of a simple, cell-based high-throughput assay to screen potential CHIKV antivirals." ], [ "3e", "The assay uses resazurin, an oxidized, nonfluorescent blue dye that is converted to the reduced, and highly fluorescent pink-colored resorufin through oxidation-reduction reaction, to measure cellular metabolic" ] ]

[ "3b", "3c" ]

[ "Title: Virology Experts in the Boundary Zone Between Science, Policy and the Public: A Biographical Analysis\nPassage: The controversies surrounding BSE and the seal deaths show two aspects of Osterhaus' role. He was self-confident in his estimations about risks, but also acknowledged criticism from his sceptics. The tricky question was when to stick to his original position, and when to adopt the opposing view, and, consequently, the appropriate strategy. This, he says, created a tension: on the one hand he had his own gut feelings, and at the same time he tried to think through competing viewpoints. There was not only an epistemological choice to be made, but also a balancing act to carry out: considering various", "Title: Multinational, observational study of procalcitonin in ICU patients with pneumonia requiring mechanical ventilation: a multicenter observational study\nPassage: Competing interests FB received a speaker fee from BRAHMS. ER receives research support from the National Institute of Allergy and Infectious Disease and the Aggennix Corporation and has served as one-time consultant for Aggennix Corporation, Eisai Pharmaceuticals, Idaho Technologies and Astra Zeneca. RB has received research support, consulting fees, and honoraria from BRAHMS and from bioMerieux. DA has received consultant fees from BRAHMS, performed PCT assays for the PCT-7 trial, and had access to equipment and assays by BRAHMS as part of NIH-funded studies. KR has received consultant fees from BRAHMS. FMB has received consultant and speaker fees and grant/research", "Title: Do expert assessments converge? An exploratory case study of evaluating and managing a blood supply risk\nPassage: In adopting a quasi-foundational approach, there are ways to ensure rigour and the trustworthiness of interpretations. The social phenomenology of Schutz, used to derive themes and as a basis for theory development from respondent perceptions, requires meeting three postulates, namely logical consistency, subjective interpretation and adequacy. For the first, we have highlighted how the research problem and methods were derived from a real world problem on which was based the questionnaire, sampling strategy and the need to interview; for the second, by using respondents' views to develop interpretation ; and for the third, by linking second order constructs to activities", "Title: Effect of prior receipt of antibiotics on the pathogen distribution: a retrospective observational cohort study on 27,792 patients\nPassage: The proportion of bacteria in the SBA group was 96.0% , higher than that of the SAA group ; while the proportion of fungi isolated from the SAA group was 8.4%, higher than that of the SBA group . The ratio of gram-positive bacteria isolated from the SBA group was slightly more than that isolated from the SAA group , while separation rate of gram-negative bacteria was not statistically different between the two groups ." ]

[ [ "3a", "Title: Effect of prior receipt of antibiotics on the pathogen distribution: a retrospective observational cohort study on 27,792 patients" ], [ "3b", "Passage: The proportion of bacteria in the SBA group was 96.0% , higher than that of the SAA group ; while the proportion of fungi isolated from the SAA group was 8.4%, higher than that of the SBA group ." ], [ "3c", "The ratio of gram-positive bacteria isolated from the SBA group was slightly more than that isolated from the SAA group , while separation rate of gram-negative bacteria was not statistically different between the two groups ." ] ]

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

[ "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: course and died in less than 14 days. Among the 27 patients diagnosed ante-mortem, the median interval between the initial visit and starting anti-TB treatment was 12 days , and 16 of these patients had received anti-TB treatment for ≥14 days before death. The median interval from treatment initiation to death was 23 days .", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: The WHO Ebola Response Team report that the average time from symptoms to death is 5 þ 4 ¼ 9 days, while to remission the average time is 5 þ 12 ¼ 17 days.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: subsequently spreads to another . Among those with progressive illness, the median time to death is 11 to 13 days, ranging from five to 27 days . Fever and gastrointestinal symptoms may form a prodrome, after which symptoms decline, only to be followed by a more severe systemic and respiratory syndrome .", "Title: Tuberculosis mortality: patient characteristics and causes\nPassage: On the other hand, even among patients whose TB was diagnosed ante-mortem, the median time from treatment initiation to death was short. This finding was similar to that of previous reports, in which many patients died of TB within a short period of time, ranging from 1 week to 3 months after starting treatment . It was speculated that these patients were too ill on arrival and their outcomes could not be reversed even after treatment . The initial tentative diagnosis of our fatal TB patients was bacterial pneumonia in 39.5%, and sepsis or other severe infections in 20%, suggesting" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: subsequently spreads to another ." ], [ "2c", "Among those with progressive illness, the median time to death is 11 to 13 days, ranging from five to 27 days ." ], [ "2d", "Fever and gastrointestinal symptoms may form a prodrome, after which symptoms decline, only to be followed by a more severe systemic and respiratory syndrome ." ] ]

[ "2c" ]

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike protein to angiotensin converting enzyme 2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can", "Title: Role of Host Immune Response and Viral Load in the Differential Outcome of Pandemic H1N1 (2009) Influenza Virus Infection in Indian Patients\nPassage: The absence of viremia in both patient categories and relatively low viral load in the lung aspirates of the critically ill patients suggest that enhanced replication of the virus may not be an important contributor to the pathogenesis . The viral load in lung aspirates was independent of fatality. In contrast, among the Spanish patients , 93% and 57% of the mild and critical cases respectively were positive for serum viral RNA, with no significant difference in the viral load. Both studies used CDC primers for real time PCR and the critical cases were bled when already on Oseltamivir treatment,", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are" ]

[ [ "0a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: viral load respectively were similarly inconsistent across available literature." ], [ "0c", "Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability." ], [ "0d", "Monoclonal antibody treatment is progressing." ], [ "0e", "SARS-CoV enters host cells through the binding of their spike protein to angiotensin converting enzyme 2 and CD209L ." ], [ "0f", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection ." ], [ "0g", "Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively." ], [ "0h", "While such neutralizing antibodies can" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike protein to angiotensin converting enzyme 2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can", "Title: Role of Host Immune Response and Viral Load in the Differential Outcome of Pandemic H1N1 (2009) Influenza Virus Infection in Indian Patients\nPassage: The absence of viremia in both patient categories and relatively low viral load in the lung aspirates of the critically ill patients suggest that enhanced replication of the virus may not be an important contributor to the pathogenesis . The viral load in lung aspirates was independent of fatality. In contrast, among the Spanish patients , 93% and 57% of the mild and critical cases respectively were positive for serum viral RNA, with no significant difference in the viral load. Both studies used CDC primers for real time PCR and the critical cases were bled when already on Oseltamivir treatment,", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are" ]

[ [ "2a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "2b", "Passage: well-tolerated in healthy participants." ], [ "2c", "Where the biological samples are taken from also play a role in the sensitivity of these tests." ], [ "2d", "For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus." ], [ "2e", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases." ], [ "2f", "Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike protein to angiotensin converting enzyme 2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can", "Title: Role of Host Immune Response and Viral Load in the Differential Outcome of Pandemic H1N1 (2009) Influenza Virus Infection in Indian Patients\nPassage: The absence of viremia in both patient categories and relatively low viral load in the lung aspirates of the critically ill patients suggest that enhanced replication of the virus may not be an important contributor to the pathogenesis . The viral load in lung aspirates was independent of fatality. In contrast, among the Spanish patients , 93% and 57% of the mild and critical cases respectively were positive for serum viral RNA, with no significant difference in the viral load. Both studies used CDC primers for real time PCR and the critical cases were bled when already on Oseltamivir treatment,", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are" ]

[ [ "3a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "3b", "Passage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate." ], [ "3c", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens." ], [ "3d", "There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset ." ], [ "3e", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load." ], [ "3f", "Hence, serological diagnoses are likely used when nucleic amplification tests are" ] ]

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

[ "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: Text: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled receptors", "Title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features\nPassage: Nuclear receptors are ligand-activated transcription factors that regulate the activation of a variety of important target genes, which are the most important drug targets in terms of potential therapeutic application. According to our results, secondary structure and polarizability play the major role in determining the drug-NRs interactions. The conservative motif of the NR is typically described as three stacked alpha-helical sheets. The helices that make up the ''front'' and ''back'' sheets are aligned parallel to one another. The helices in the middle sheet run across the two outer sheets and only occupy the space in the upper portion of the", "Title: Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics\nPassage: Mechanisms by which expression of a single gene is regulated can be extremely complicated. Multiple phosphorylation-or ligand-dependent nuclear receptors that homo-or heterodimerize may be required to achieve activity. Each of these receptors may have different activation specificity or duration, even when acting via the same regulatory DNA sequence such as classical proximal promoter elements. These receptors may also work in combination with other transcription factors that function at sites more distal from the proximal promoter or in introns. Alternatively spliced transcripts represent another complex aspect of gene expression regulation that is influenced by extracellular and intracellular signaling but is not" ]

[ [ "0a", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking" ], [ "0b", "Passage: Text: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors." ], [ "0c", "They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology ." ], [ "0d", "The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 ." ], [ "0e", "Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled" ] ]

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

[ "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: Text: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled receptors", "Title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features\nPassage: Nuclear receptors are ligand-activated transcription factors that regulate the activation of a variety of important target genes, which are the most important drug targets in terms of potential therapeutic application. According to our results, secondary structure and polarizability play the major role in determining the drug-NRs interactions. The conservative motif of the NR is typically described as three stacked alpha-helical sheets. The helices that make up the ''front'' and ''back'' sheets are aligned parallel to one another. The helices in the middle sheet run across the two outer sheets and only occupy the space in the upper portion of the", "Title: Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics\nPassage: Mechanisms by which expression of a single gene is regulated can be extremely complicated. Multiple phosphorylation-or ligand-dependent nuclear receptors that homo-or heterodimerize may be required to achieve activity. Each of these receptors may have different activation specificity or duration, even when acting via the same regulatory DNA sequence such as classical proximal promoter elements. These receptors may also work in combination with other transcription factors that function at sites more distal from the proximal promoter or in introns. Alternatively spliced transcripts represent another complex aspect of gene expression regulation that is influenced by extracellular and intracellular signaling but is not" ]

[ [ "1a", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking" ], [ "1b", "Passage: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors." ], [ "1c", "They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology ." ], [ "1d", "The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 ." ], [ "1e", "Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled receptors" ] ]

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

[ "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: Text: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled receptors", "Title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features\nPassage: Nuclear receptors are ligand-activated transcription factors that regulate the activation of a variety of important target genes, which are the most important drug targets in terms of potential therapeutic application. According to our results, secondary structure and polarizability play the major role in determining the drug-NRs interactions. The conservative motif of the NR is typically described as three stacked alpha-helical sheets. The helices that make up the ''front'' and ''back'' sheets are aligned parallel to one another. The helices in the middle sheet run across the two outer sheets and only occupy the space in the upper portion of the", "Title: Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics\nPassage: Mechanisms by which expression of a single gene is regulated can be extremely complicated. Multiple phosphorylation-or ligand-dependent nuclear receptors that homo-or heterodimerize may be required to achieve activity. Each of these receptors may have different activation specificity or duration, even when acting via the same regulatory DNA sequence such as classical proximal promoter elements. These receptors may also work in combination with other transcription factors that function at sites more distal from the proximal promoter or in introns. Alternatively spliced transcripts represent another complex aspect of gene expression regulation that is influenced by extracellular and intracellular signaling but is not" ]

[ [ "2a", "Title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features" ], [ "2b", "Passage: Nuclear receptors are ligand-activated transcription factors that regulate the activation of a variety of important target genes, which are the most important drug targets in terms of potential therapeutic application." ], [ "2c", "According to our results, secondary structure and polarizability play the major role in determining the drug-NRs interactions." ], [ "2d", "The conservative motif of the NR is typically described as three stacked alpha-helical sheets." ], [ "2e", "The helices that make up the ''front'' and ''back'' sheets are aligned parallel to one another." ], [ "2f", "The helices in the middle sheet run across the two outer sheets and only occupy the space in the upper portion of the" ] ]

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

[ "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: Text: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled", "Title: iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking\nPassage: With the ability to directly bind to DNA and regulate the expression of adjacent genes, nuclear receptors are a class of ligand-inducible transcription factors. They regulate various biological processes, such as homeostasis, differentiation, embryonic development, and organ physiology . The NR superfamily has been classified into seven families: NR0 ; NR1 , NR2 , NR3 , NR4 , NR5 , and NR6 . Since they are involved in almost all aspects of human physiology and are implicated in many major diseases such as cancer, diabetes and osteoporosis, nuclear receptors have become major drug targets , along with G protein-coupled receptors", "Title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features\nPassage: Nuclear receptors are ligand-activated transcription factors that regulate the activation of a variety of important target genes, which are the most important drug targets in terms of potential therapeutic application. According to our results, secondary structure and polarizability play the major role in determining the drug-NRs interactions. The conservative motif of the NR is typically described as three stacked alpha-helical sheets. The helices that make up the ''front'' and ''back'' sheets are aligned parallel to one another. The helices in the middle sheet run across the two outer sheets and only occupy the space in the upper portion of the", "Title: Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics\nPassage: Mechanisms by which expression of a single gene is regulated can be extremely complicated. Multiple phosphorylation-or ligand-dependent nuclear receptors that homo-or heterodimerize may be required to achieve activity. Each of these receptors may have different activation specificity or duration, even when acting via the same regulatory DNA sequence such as classical proximal promoter elements. These receptors may also work in combination with other transcription factors that function at sites more distal from the proximal promoter or in introns. Alternatively spliced transcripts represent another complex aspect of gene expression regulation that is influenced by extracellular and intracellular signaling but is not" ]

[ [ "3a", "Title: Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics" ], [ "3b", "Passage: Mechanisms by which expression of a single gene is regulated can be extremely complicated." ], [ "3c", "Multiple phosphorylation-or ligand-dependent nuclear receptors that homo-or heterodimerize may be required to achieve activity." ], [ "3d", "Each of these receptors may have different activation specificity or duration, even when acting via the same regulatory DNA sequence such as classical proximal promoter elements." ], [ "3e", "These receptors may also work in combination with other transcription factors that function at sites more distal from the proximal promoter or in introns." ], [ "3f", "Alternatively spliced transcripts represent another complex aspect of gene expression regulation that is influenced by extracellular and intracellular signaling but is not" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations . What role maternal camel antibody might play in delaying infection of calves remains unknown . Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection. In contrast to earlier results, slaughterhouse workers who kill both younger and older", "Title: Extreme water-related weather events and waterborne disease\nPassage: may also increase the risk of flooding in many areas, increasing human exposure to waterborne pathogens . Droughts or extended dry periods are known to reduce the volume of river flow and potentially increase the concentration of effluent-derived pathogens, due to reduced dilution by stream-receiving waters .", "Title: The interconnected and cross-border nature of risks posed by infectious diseases\nPassage: been linked to the hunting or slaughtering of primates and other wild animals . The density and health of livestock, meanwhile, have been linked to disease in humans . Although inconclusive, there is some evidence to suggest that livestock production may lead to increased antibiotic resistance in human pathogens. There are certainly many pathways by which drug resistant pathogens could transmit from livestock to humans, including environmental contamination by excreted veterinary antibiotics .", "Title: Predicting wildlife reservoirs and global vulnerability to zoonotic Flaviviruses\nPassage: their ability to pose ongoing spillover risk to humans." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations ." ], [ "0c", "What role maternal camel antibody might play in delaying infection of calves remains unknown ." ], [ "0d", "Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection." ], [ "0e", "In contrast to earlier results, slaughterhouse workers who kill both younger and older" ] ]

[ "0b" ]

[ "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: Papers were clustered according to the methodology used. More precisely, for each paper we identified the list of technical keywords associated with the methods, including both general concepts and sub-analysis terms ; the full list of technical keywords is presented in the Supporting Information, S1 Table. Papers that share the same keyword are often connected. Consequently, analytical 2) What methods have been used? Ascertain the key epidemiological methods developed and used so far. Classify the methods in terms of general approaches: such as descriptive phenomenology, process based models , statistical analysis of empirical data etc.", "Title: Pandemic influenza in Papua New Guinea: a modelling study comparison with pandemic spread in a developed country\nPassage: method.", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: The statistical methods used to fit a model with the observed data were assessed with information criteria in almost 20% of cases. In a significant proportion of papers , the validation of the method was based on out-of-sample predictions, i.e. a subset of the data were used to train/calibrate the method , and then the method was applied to the rest of the data. In some cases, there was no assessment of the methods. Situations where the methods did not require comparison with real data were also present.", "Title: Operationalising resilience in longitudinal studies: a systematic review of methodological approaches\nPassage: used by the original authors." ]

[ [ "0a", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review" ], [ "0b", "Passage: Papers were clustered according to the methodology used." ], [ "0c", "More precisely, for each paper we identified the list of technical keywords associated with the methods, including both general concepts and sub-analysis terms ; the full list of technical keywords is presented in the Supporting Information, S1 Table." ], [ "0d", "Papers that share the same keyword are often connected." ], [ "0e", "Consequently, analytical 2) What methods have been used?" ], [ "0f", "Ascertain the key epidemiological methods developed and used so far." ], [ "0g", "Classify the methods in terms of general approaches: such as descriptive phenomenology, process based models , statistical analysis of empirical data etc." ] ]

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

[ "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: Papers were clustered according to the methodology used. More precisely, for each paper we identified the list of technical keywords associated with the methods, including both general concepts and sub-analysis terms ; the full list of technical keywords is presented in the Supporting Information, S1 Table. Papers that share the same keyword are often connected. Consequently, analytical 2) What methods have been used? Ascertain the key epidemiological methods developed and used so far. Classify the methods in terms of general approaches: such as descriptive phenomenology, process based models , statistical analysis of empirical data etc.", "Title: Pandemic influenza in Papua New Guinea: a modelling study comparison with pandemic spread in a developed country\nPassage: method.", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review\nPassage: The statistical methods used to fit a model with the observed data were assessed with information criteria in almost 20% of cases. In a significant proportion of papers , the validation of the method was based on out-of-sample predictions, i.e. a subset of the data were used to train/calibrate the method , and then the method was applied to the rest of the data. In some cases, there was no assessment of the methods. Situations where the methods did not require comparison with real data were also present.", "Title: Operationalising resilience in longitudinal studies: a systematic review of methodological approaches\nPassage: used by the original authors." ]

[ [ "2a", "Title: Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review" ], [ "2b", "Passage: The statistical methods used to fit a model with the observed data were assessed with information criteria in almost 20% of cases." ], [ "2c", "In a significant proportion of papers , the validation of the method was based on out-of-sample predictions, i.e. a subset of the data were used to train/calibrate the method , and then the method was applied to the rest of the data." ], [ "2d", "In some cases, there was no assessment of the methods." ], [ "2e", "Situations where the methods did not require comparison with real data were also present." ] ]

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

[ "Title: Hepatitis C Virus Non-Structural Protein 3 Interacts with Cytosolic 5′(3′)-Deoxyribonucleotidase and Partially Inhibits Its Activity\nPassage: Hepatitis C virus is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma . Infection with HCV is also etiologically involved in the development of B-cell lymphomas . This virus belongs to the genus Hepacivirus in the family Flaviviridae. The HCV genome is a single, positive-stranded RNA with a nucleotide length of about 9.6 kb. It encodes a polyprotein precursor of approximately 3,000 amino acids. This polyprotein precursor is processed by host and viral proteases into at least 10 different proteins, which are arranged in the order of NH2-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B-COOH. C, E1, and E2 are structural proteins while NS2-NS5B", "Title: Immunization with a Recombinant Vaccinia Virus That Encodes Nonstructural Proteins of the Hepatitis C Virus Suppresses Viral Protein Levels in Mouse Liver\nPassage: in the HCV protein levels was observed in the mice treated with LC16m8, rVV-CN2, or rVV-CN5. These results indicated that HCV nonstructural proteins might be important for effects of therapeutic vaccines. In contrast, rVV-CN5 which encoded HCV structural and non-structural proteins did not show any significant effects. These results indicated that HCV structural proteins might have inhibited the therapeutic effects of the non-structural proteins. Therefore, it may be important to exclude the HCV structural proteins as antigenic proteins when developing therapeutic vaccines against chronic hepatitis C.", "Title: Hepatitis C Virus Non-Structural Protein 3 Interacts with Cytosolic 5′(3′)-Deoxyribonucleotidase and Partially Inhibits Its Activity\nPassage: For the detection of endogenous HCV NS3 and cellular cdN proteins, HCV subgenomic RNA replicon cells were used .", "Title: Hepatitis C Virus Non-Structural Protein 3 Interacts with Cytosolic 5′(3′)-Deoxyribonucleotidase and Partially Inhibits Its Activity\nPassage: HuH7 cells were cultured in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum , 100 U/ml penicillin and 100 mg/ml streptomycin . HCV sub-genomic replicon cells were cultured in DMEM with 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin and 400 mg/ml G418 . All cultured cells were maintained at 37uC with 5% CO 2 ." ]

[ [ "0a", "Title: Hepatitis C Virus Non-Structural Protein 3 Interacts with Cytosolic 5′(3′)-Deoxyribonucleotidase and Partially Inhibits Its Activity" ], [ "0b", "Passage: Hepatitis C virus is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma ." ], [ "0c", "Infection with HCV is also etiologically involved in the development of B-cell lymphomas ." ], [ "0d", "This virus belongs to the genus Hepacivirus in the family Flaviviridae." ], [ "0e", "The HCV genome is a single, positive-stranded RNA with a nucleotide length of about 9.6 kb." ], [ "0f", "It encodes a polyprotein precursor of approximately 3,000 amino acids." ], [ "0g", "This polyprotein precursor is processed by host and viral proteases into at least 10 different proteins, which are arranged in the order of NH2-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B-COOH." ], [ "0h", "C, E1, and E2 are structural proteins while NS2-NS5B" ] ]

[ "0g", "0h" ]

[ "Title: Th17 profile in COPD exacerbations\nPassage: COPD is characterized by a continuous inflammatory process of the airways, leading to obstruction or limitation of airflow, which is mainly associated with exposure to cigarette smoke. 1, 2 However, only 10%-20% of smokers will develop the disease at some day in their life. These data lead to the belief that this disease is due to multiple factors that interact with each other. Among the most prominent are genetic factors that can condition patients to have a certain susceptibility to COPD. For example, deficiency of alpha1-antitrypsin is present in at least 1% of the carriers of the disease in Europe", "Title: Th17 profile in COPD exacerbations\nPassage: two or more exacerbations per year, where the best predictor will be the history of previous treatments for exacerbations. 10 Indeed, about half of COPD patients die after 4 years of their first episode of exacerbation. 11 The symptomatology of COPD is diverse, depending on the phenotype . However, there is a range of signs and symptoms that occur more frequently, such as dyspnea of small efforts, chronic cough and increased sputum production. In addition, other clinical data that may appear are hypoxemia, hypercapnia, the so-called \"chest in barrel\" , weight loss, etc. 6, 10, 48 Molecular mechanisms in COPD", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: The symptoms of asthma and COPD are very similar, if not identical. The major differences are the degree of reversibility is often greater in asthma and the persistence of dyspnea is greater in COPD. Both are characterized by exacerbations which respond to corticosteroids and bronchodilators, infections triggering exacerbations, episodic wheezing, cough with or without mucous production, improvement with chronic inhaled corticosteroids and bronchodilators, and decreased exercise tolerance. The chronic bronchitis phenotype of COPD as opposed to the emphysematous phenotype is more likely to be confused with asthma, but the variations of phenotypes in both diseases confounds simple measures to reliably", "Title: Th17 profile in COPD exacerbations\nPassage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases. 10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication. 6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has" ]

[ [ "0a", "Title: Th17 profile in COPD exacerbations" ], [ "0b", "Passage: COPD is characterized by a continuous inflammatory process of the airways, leading to obstruction or limitation of airflow, which is mainly associated with exposure to cigarette smoke." ], [ "0c", "1, 2 However, only 10%-20% of smokers will develop the disease at some day in their life." ], [ "0d", "These data lead to the belief that this disease is due to multiple factors that interact with each other." ], [ "0e", "Among the most prominent are genetic factors that can condition patients to have a certain susceptibility to COPD." ], [ "0f", "For example, deficiency of alpha1-antitrypsin is present in at least 1% of the carriers of the disease in Europe" ] ]

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

[ "Title: Th17 profile in COPD exacerbations\nPassage: COPD is characterized by a continuous inflammatory process of the airways, leading to obstruction or limitation of airflow, which is mainly associated with exposure to cigarette smoke. 1, 2 However, only 10%-20% of smokers will develop the disease at some day in their life. These data lead to the belief that this disease is due to multiple factors that interact with each other. Among the most prominent are genetic factors that can condition patients to have a certain susceptibility to COPD. For example, deficiency of alpha1-antitrypsin is present in at least 1% of the carriers of the disease in Europe", "Title: Th17 profile in COPD exacerbations\nPassage: two or more exacerbations per year, where the best predictor will be the history of previous treatments for exacerbations. 10 Indeed, about half of COPD patients die after 4 years of their first episode of exacerbation. 11 The symptomatology of COPD is diverse, depending on the phenotype . However, there is a range of signs and symptoms that occur more frequently, such as dyspnea of small efforts, chronic cough and increased sputum production. In addition, other clinical data that may appear are hypoxemia, hypercapnia, the so-called \"chest in barrel\" , weight loss, etc. 6, 10, 48 Molecular mechanisms in COPD", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: The symptoms of asthma and COPD are very similar, if not identical. The major differences are the degree of reversibility is often greater in asthma and the persistence of dyspnea is greater in COPD. Both are characterized by exacerbations which respond to corticosteroids and bronchodilators, infections triggering exacerbations, episodic wheezing, cough with or without mucous production, improvement with chronic inhaled corticosteroids and bronchodilators, and decreased exercise tolerance. The chronic bronchitis phenotype of COPD as opposed to the emphysematous phenotype is more likely to be confused with asthma, but the variations of phenotypes in both diseases confounds simple measures to reliably", "Title: Th17 profile in COPD exacerbations\nPassage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases. 10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication. 6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has" ]

[ [ "1a", "Title: Th17 profile in COPD exacerbations" ], [ "1b", "Passage: two or more exacerbations per year, where the best predictor will be the history of previous treatments for exacerbations." ], [ "1c", "10 Indeed, about half of COPD patients die after 4 years of their first episode of exacerbation." ], [ "1d", "11 The symptomatology of COPD is diverse, depending on the phenotype ." ], [ "1e", "However, there is a range of signs and symptoms that occur more frequently, such as dyspnea of small efforts, chronic cough and increased sputum production." ], [ "1f", "In addition, other clinical data that may appear are hypoxemia, hypercapnia, the so-called \"chest in barrel\" , weight loss, etc. 6, 10, 48 Molecular mechanisms in COPD" ] ]

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

[ "Title: Th17 profile in COPD exacerbations\nPassage: COPD is characterized by a continuous inflammatory process of the airways, leading to obstruction or limitation of airflow, which is mainly associated with exposure to cigarette smoke. 1, 2 However, only 10%-20% of smokers will develop the disease at some day in their life. These data lead to the belief that this disease is due to multiple factors that interact with each other. Among the most prominent are genetic factors that can condition patients to have a certain susceptibility to COPD. For example, deficiency of alpha1-antitrypsin is present in at least 1% of the carriers of the disease in Europe", "Title: Th17 profile in COPD exacerbations\nPassage: two or more exacerbations per year, where the best predictor will be the history of previous treatments for exacerbations. 10 Indeed, about half of COPD patients die after 4 years of their first episode of exacerbation. 11 The symptomatology of COPD is diverse, depending on the phenotype . However, there is a range of signs and symptoms that occur more frequently, such as dyspnea of small efforts, chronic cough and increased sputum production. In addition, other clinical data that may appear are hypoxemia, hypercapnia, the so-called \"chest in barrel\" , weight loss, etc. 6, 10, 48 Molecular mechanisms in COPD", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: The symptoms of asthma and COPD are very similar, if not identical. The major differences are the degree of reversibility is often greater in asthma and the persistence of dyspnea is greater in COPD. Both are characterized by exacerbations which respond to corticosteroids and bronchodilators, infections triggering exacerbations, episodic wheezing, cough with or without mucous production, improvement with chronic inhaled corticosteroids and bronchodilators, and decreased exercise tolerance. The chronic bronchitis phenotype of COPD as opposed to the emphysematous phenotype is more likely to be confused with asthma, but the variations of phenotypes in both diseases confounds simple measures to reliably", "Title: Th17 profile in COPD exacerbations\nPassage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases. 10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication. 6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has" ]

[ [ "2a", "Title: Asthma in the elderly: what we know and what we have yet to know" ], [ "2b", "Passage: The symptoms of asthma and COPD are very similar, if not identical." ], [ "2c", "The major differences are the degree of reversibility is often greater in asthma and the persistence of dyspnea is greater in COPD." ], [ "2d", "Both are characterized by exacerbations which respond to corticosteroids and bronchodilators, infections triggering exacerbations, episodic wheezing, cough with or without mucous production, improvement with chronic inhaled corticosteroids and bronchodilators, and decreased exercise tolerance." ], [ "2e", "The chronic bronchitis phenotype of COPD as opposed to the emphysematous phenotype is more likely to be confused with asthma, but the variations of phenotypes in both diseases confounds simple measures to reliably" ] ]

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

[ "Title: Th17 profile in COPD exacerbations\nPassage: COPD is characterized by a continuous inflammatory process of the airways, leading to obstruction or limitation of airflow, which is mainly associated with exposure to cigarette smoke. 1, 2 However, only 10%-20% of smokers will develop the disease at some day in their life. These data lead to the belief that this disease is due to multiple factors that interact with each other. Among the most prominent are genetic factors that can condition patients to have a certain susceptibility to COPD. For example, deficiency of alpha1-antitrypsin is present in at least 1% of the carriers of the disease in Europe", "Title: Th17 profile in COPD exacerbations\nPassage: two or more exacerbations per year, where the best predictor will be the history of previous treatments for exacerbations. 10 Indeed, about half of COPD patients die after 4 years of their first episode of exacerbation. 11 The symptomatology of COPD is diverse, depending on the phenotype . However, there is a range of signs and symptoms that occur more frequently, such as dyspnea of small efforts, chronic cough and increased sputum production. In addition, other clinical data that may appear are hypoxemia, hypercapnia, the so-called \"chest in barrel\" , weight loss, etc. 6, 10, 48 Molecular mechanisms in COPD", "Title: Asthma in the elderly: what we know and what we have yet to know\nPassage: The symptoms of asthma and COPD are very similar, if not identical. The major differences are the degree of reversibility is often greater in asthma and the persistence of dyspnea is greater in COPD. Both are characterized by exacerbations which respond to corticosteroids and bronchodilators, infections triggering exacerbations, episodic wheezing, cough with or without mucous production, improvement with chronic inhaled corticosteroids and bronchodilators, and decreased exercise tolerance. The chronic bronchitis phenotype of COPD as opposed to the emphysematous phenotype is more likely to be confused with asthma, but the variations of phenotypes in both diseases confounds simple measures to reliably", "Title: Th17 profile in COPD exacerbations\nPassage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases. 10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication. 6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has" ]

[ [ "3a", "Title: Th17 profile in COPD exacerbations" ], [ "3b", "Passage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases." ], [ "3c", "10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication." ], [ "3d", "6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has" ] ]

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

[ "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Targeting viral RNAs is the most direct and effective way to curb hantaviral replication. Small interfering RNA directed against hantaviral genes could facilitate viral RNA clearance based on the RNA interfering mechanisms and has been tested as a potential antiviral strategy in vitro and in vivo. It has been demonstrated that siRNAs targeting the S, M, or L segment of ANDV could reduce viral replication in Vero E6 cells or human lung microvascular endothelial cells and that an S-targeted siRNA pool seemed to be more efficient in reducing viral transcription and replication than M-or L-targeted siRNA in Vero E6 cells.", "Title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development\nPassage: A total of 5 × 10 5 A549 cells were seeded into six-well plates, allowed to reach confluence, and then challenged with virus . Total RNA was extracted from cells using the TRIzol reagent . Following phenol-chloroform extraction and isopropanol precipitation, the RNA pellet was washed, dried, and dissolved in 20 mL of RNase-free water. The protocol of RT-PCR amplifications and Q-PCR were as described by Hsu et al 38 .", "Title: Viral RNA extraction for in-the-field analysis\nPassage: Retroviruses encode their genetic information in RNA molecules, and have a high genomic recombination rate, which allows them to mutate more rapidly and thereby pose higher risk to humans. International travel and rising population densities render infectious retroviruses such as HIV, severe acute respiratory syndrome virus, hepatitis virus and influenza virus serious health threats to the public worldwide. A clear example is the recent virulent strain of avian flu , which has the potential to transcend the species barrier and become a deadly infectious disease for humans. One important way to help combat these viral infectious diseases is early detection", "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Opening this CTI Special Feature, I outline ways these issues may be solved by creatively leveraging the so-called 'strengths' of viruses. Viral RNA polymerisation and reverse transcription enable resistance to treatment by conferring extraordinary genetic diversity. However, these exact processes ultimately restrict viral infectivity by strongly limiting virus genome sizes and their incorporation of new information. I coin this evolutionary dilemma the 'information economy paradox'. Many viruses attempt to resolve this by manipulating multifunctional or multitasking host cell proteins , thereby maximising host subversion and viral infectivity at minimal informational cost. 4 I argue this exposes an 'Achilles Heel' that" ]

[ [ "0a", "Title: Vaccines and Therapeutics Against Hantaviruses" ], [ "0b", "Passage: Targeting viral RNAs is the most direct and effective way to curb hantaviral replication." ], [ "0c", "Small interfering RNA directed against hantaviral genes could facilitate viral RNA clearance based on the RNA interfering mechanisms and has been tested as a potential antiviral strategy in vitro and in vivo." ], [ "0d", "It has been demonstrated that siRNAs targeting the S, M, or L segment of ANDV could reduce viral replication in Vero E6 cells or human lung microvascular endothelial cells and that an S-targeted siRNA pool seemed to be more efficient in reducing viral transcription and replication than M-or L-targeted siRNA in Vero E6 cells." ] ]

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

[ "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Targeting viral RNAs is the most direct and effective way to curb hantaviral replication. Small interfering RNA directed against hantaviral genes could facilitate viral RNA clearance based on the RNA interfering mechanisms and has been tested as a potential antiviral strategy in vitro and in vivo. It has been demonstrated that siRNAs targeting the S, M, or L segment of ANDV could reduce viral replication in Vero E6 cells or human lung microvascular endothelial cells and that an S-targeted siRNA pool seemed to be more efficient in reducing viral transcription and replication than M-or L-targeted siRNA in Vero E6 cells.", "Title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development\nPassage: A total of 5 × 10 5 A549 cells were seeded into six-well plates, allowed to reach confluence, and then challenged with virus . Total RNA was extracted from cells using the TRIzol reagent . Following phenol-chloroform extraction and isopropanol precipitation, the RNA pellet was washed, dried, and dissolved in 20 mL of RNase-free water. The protocol of RT-PCR amplifications and Q-PCR were as described by Hsu et al 38 .", "Title: Viral RNA extraction for in-the-field analysis\nPassage: Retroviruses encode their genetic information in RNA molecules, and have a high genomic recombination rate, which allows them to mutate more rapidly and thereby pose higher risk to humans. International travel and rising population densities render infectious retroviruses such as HIV, severe acute respiratory syndrome virus, hepatitis virus and influenza virus serious health threats to the public worldwide. A clear example is the recent virulent strain of avian flu , which has the potential to transcend the species barrier and become a deadly infectious disease for humans. One important way to help combat these viral infectious diseases is early detection", "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Opening this CTI Special Feature, I outline ways these issues may be solved by creatively leveraging the so-called 'strengths' of viruses. Viral RNA polymerisation and reverse transcription enable resistance to treatment by conferring extraordinary genetic diversity. However, these exact processes ultimately restrict viral infectivity by strongly limiting virus genome sizes and their incorporation of new information. I coin this evolutionary dilemma the 'information economy paradox'. Many viruses attempt to resolve this by manipulating multifunctional or multitasking host cell proteins , thereby maximising host subversion and viral infectivity at minimal informational cost. 4 I argue this exposes an 'Achilles Heel' that" ]

[ [ "3a", "Title: Frontiers in antiviral therapy and immunotherapy" ], [ "3b", "Passage: Opening this CTI Special Feature, I outline ways these issues may be solved by creatively leveraging the so-called 'strengths' of viruses." ], [ "3c", "Viral RNA polymerisation and reverse transcription enable resistance to treatment by conferring extraordinary genetic diversity." ], [ "3d", "However, these exact processes ultimately restrict viral infectivity by strongly limiting virus genome sizes and their incorporation of new information." ], [ "3e", "I coin this evolutionary dilemma the 'information economy paradox'." ], [ "3f", "Many viruses attempt to resolve this by manipulating multifunctional or multitasking host cell proteins , thereby maximising host subversion and viral infectivity at minimal informational cost." ], [ "3g", "4 I argue this exposes an 'Achilles Heel' that" ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: The E1-A226V mutation also enabled an increase in infectivity of Ae. albopictus when compared to its infectivity of Ae. aegypti , and with several factors taken together, Ae. albopictus has become the new preferred and more lethal vector for CHIKV . In fact, Tsetsarkin et al. found that a Green Fluorescent Protein tagged E1-A226V virus was 100 times more infective to Ae. albopictus than it was to Ae. aegypti . In all the Indian Ocean Islands, Ae. albopictus became the main vector for CHIKV within 1-2 y after CHIKV was introduced to the region .", "Title: Dengue Fever, Hawaii, 2001–2002\nPassage: Ae. albopictus was the vector responsible for the 2001 Hawaii outbreak. Both entomologic surveys support that Ae. albopictus is ubiquitous, often common on all the islands, whereas Ae. aegypti is restricted to a few small foci on the relatively sparsely inhabited island of Hawaii.", "Title: Dengue Fever, Hawaii, 2001–2002\nPassage: where Ae. aegypti is present. Compared with Ae aegypti, Ae. albopictus is considered to be an inefficient epidemic dengue vector because it is less anthropophilic and not as well adapted to urban domestic environments . Ae. albopictus will readily feed on humans, but usually only on a single person, and it also feeds on other animals, which decreases the probability of human contact . Lifestyle factors may also help explain why Hawaii's dengue outbreak was limited . Residences in many affected areas often had dense, uncultivated vegetation near housing and, not infrequently, an abundance of items that could serve as", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: The 2005-2006 epidemic of CHIKV in La Reunion islands in the Indian Ocean, spurred the discovery of a new vector species, Ae. albopictus . Wrecking over one-third of the island's population, this epidemic peaked its devastation between January and February 2006, when over 46,000 cases came into light every week, including 284 deaths . Ae. albopictus is common in urban areas of the United States and is already flourishing in 36 states, raising grave concerns to the immunologically naive populace of the United States ." ]

[ [ "3a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "3b", "Passage: The 2005-2006 epidemic of CHIKV in La Reunion islands in the Indian Ocean, spurred the discovery of a new vector species, Ae. albopictus ." ], [ "3c", "Wrecking over one-third of the island's population, this epidemic peaked its devastation between January and February 2006, when over 46,000 cases came into light every week, including 284 deaths . Ae." ], [ "3d", "albopictus is common in urban areas of the United States and is already flourishing in 36 states, raising grave concerns to the immunologically naive populace of the United States ." ] ]

[ "3a", "3b" ]

[ "Title: Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei\nPassage: protein. RanBP10 is a cytoplasmic guanine nucleotide exchange factor that modulates noncentrosomal microtubules involved in mitosis, while cytochrome P450 catalyses diverse reactions in fungal primary and secondary metabolism, and xenobiotic detoxification. As for PM-milR-M2, 20 potential targets were predicted, which include 13 transposon or transposable elements and seven conserved hypothetical proteins.", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In addition to RNA Polymerase I, optimal rRNA gene transcription requires a number of accessory factors that facilitate Pol I recruitment, initiation, promoter escape, elongation, termination and re-initiation . Pol I transcription begins with the formation of the preinitiation complex by the upstream binding factor and the TBP-containing complex selectively factor at the rDNA promoter. SL-1 confers promoter sequence specificity by recognizing the core promoter element and it promotes a stable interaction between UBF and the rDNA promoter . In turn, UBF binds the upstream and core promoter elements as a dimer, possibly looping the intervening DNA into a nucleosome", "Title: Translational profiling of B cells infected with the Epstein-Barr virus reveals 5′ leader ribosome recruitment through upstream open reading frames\nPassage: The out:in ratios were calculated by dividing the number of RPFs mapping within 5 leaders of a transcript by the number of RPFs mapping to the coding region of the transcript including the translation initiation codon . Read coverage was length normalized by nucleotide length of the respective feature . 5 leader:AUG ratios were calculated by dividing the number of RPFs mapping within the 5 leaders of a transcript by the number of RPFs mapping to the start codon of a transcript or non-canonical start codons. Read coverage was length normalized by nucleotide length of the respective feature.", "Title: Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells\nPassage: DBP implies that it may be an accessory factor in viral DNA replication during viral infection. Notably, in interphase cells, UBF and Nopp140 are co-localized and are known to be recruited together . RBM4 has been reported to be either predominantly nuclear or predominantly nucleolar, depending on experimental conditions . In our hands, the protein was nucleolar in Ͼ80% of cells. RBM4 has been implicated in the modulation of splice site selection, something of clear relevance to adenovirus infection, but it has also FIG. 4 . Distribution of proteins identified by SILAC as being enriched in nucleolus during viral infection." ]

[ [ "3a", "Title: Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells" ], [ "3b", "Passage: DBP implies that it may be an accessory factor in viral DNA replication during viral infection." ], [ "3c", "Notably, in interphase cells, UBF and Nopp140 are co-localized and are known to be recruited together ." ], [ "3d", "RBM4 has been reported to be either predominantly nuclear or predominantly nucleolar, depending on experimental conditions ." ], [ "3e", "In our hands, the protein was nucleolar in Ͼ80% of cells." ], [ "3f", "RBM4 has been implicated in the modulation of splice site selection, something of clear relevance to adenovirus infection, but it has also FIG. 4 ." ], [ "3g", "Distribution of proteins identified by SILAC as being enriched in nucleolus during viral infection." ] ]

[ "3c", "3d" ]

[ "Title: Results From a Hypothesis Generating Case-Control Study: Herpes Family Viruses and Schizophrenia Among Military Personnel\nPassage: A total of 180 cases and 532 controls were included in the study population. Eight cases could only be matched to 2 controls. Table 1 shows the distribution of cases and controls by demographic factors. Overall, about 83% were males, 49% were whites, 44% were blacks, over 57% were younger than 25 years, 10% were older than 35 years, about 12% were Hispanic, and over 56% were in the army. Approximately 35% of cases had greater than 3 years of military service.", "Title: CDC Summary 21 MAR 2020,\nPassage: cases in the United States by age group found that 80% of deaths were among adults 65 years and older with the highest percentage of severe outcomes occurring in people 85 years and older.", "Title: Reliability of case definitions for public health surveillance assessed by Round-Robin test methodology\nPassage: in all case definitions by 137 respondents , in the majority of case definitions by 248 , and in the minority by 11 .", "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: Results From a Hypothesis Generating Case-Control Study: Herpes Family Viruses and Schizophrenia Among Military Personnel" ], [ "0b", "Passage: A total of 180 cases and 532 controls were included in the study population." ], [ "0c", "Eight cases could only be matched to 2 controls." ], [ "0d", "Table 1 shows the distribution of cases and controls by demographic factors." ], [ "0e", "Overall, about 83% were males, 49% were whites, 44% were blacks, over 57% were younger than 25 years, 10% were older than 35 years, about 12% were Hispanic, and over 56% were in the army." ], [ "0f", "Approximately 35% of cases had greater than 3 years of military service." ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: Klosterneuburg in Austria in 2017 with 1.57 million basepairs . Pithovirus sibericum is the largest among giant viruses discovered to date with a diameter of 1.5 microns, a genome of 470,000 bp with 467 putative genes, 1.6 microns in length, and it is presumably 30,000 years old as it was recovered from permafrost in Siberia . The smaller Pandoraviruses with 1 micron in length have five times larger genomes, 2,500,000 bp .", "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: Substantial variation in genome size and complexity was also observed in many rhabdovirus genera, suggesting that the length of the genome is not heavily constrained in all members of the family. Indeed, the presence of new ORFs and/or very long stretches of non-coding sequence within or between transcriptional units was noted frequently. Previous observations have demonstrated that foreign genes of up to~6 kb can be inserted into the VSIV genome without significant disruption to viral replication in vitro . Expanded VSIV genomes were morphologically similar but proportionally longer than wild-type viruses, suggesting that the unique morphology of the rhabdovirus particle", "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: may more readily accommodate genome expansion than other virion structures. A significant body of evidence suggests that genome size in RNA viruses is likely to be constrained by low replication fidelity , and a relationship between genome size and error rate has been observed in a diverse array of organisms . However, if the genome sizes of rhabdoviruses are constrained by selective pressures other than those imposed by the background mutation rate, genome expansion may not require a concomitant reduction in polymerase error rates. As the mutation rate of rhabdoviruses has only been determined experimentally for VSIV thus far ," ]

[ [ "0a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "0b", "Passage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids." ], [ "0c", "The G + C content was 38%." ], [ "0d", "Similar to other ." ], [ "0e", "There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV ." ], [ "0f", "The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots." ] ]

[ "0b" ]

[ "Title: Herpes zoster encephalitis presenting as multiple cerebral hemorrhages – a rare presentation: a case report\nPassage: Examination of peripheral blood smear failed to demonstrate any malarial parasite. The result of a rapid malaria antigen test was negative. The cerebrospinal fluid examination revealed: lymphocytes with presence of red blood cells , protein 90mg/dL, and glucose 108mg/dL. There was no organism in Gram and Ziehl-Neelsen staining of the CSF. His hemogram showed a total leukocyte count of 12,700/μL . His platelet count, bleeding and coagulation profile were within normal limits. The results of the human immunodeficiency virus tests were negative by both enzyme-linked immunosorbent assay and rapid HIV test for HIV-1 and HIV-2 antibodies.", "Title: Clinical study of children with cryofibrinogenemia: a retrospective study from a single center\nPassage: In this study, patients with CNS involvement presented as large artery narrowing, parenchymal involvement, and hemorrhage in demyelinating lesions on the white matter and basal ganglion. The last is compatible with acute hemorrhagic encephalomyelitis , considered a hyper-acute sub-form of acute disseminated encephalomyelitis. It is frequently a fulminant inflammatory hemorrhagic demylination of the CNS white matter. Death from brain edema is common within one week of the onset of encephalopathy. The pathogenesis is known as acute vasculitis with subsequent vessel occlusion . The patient here with AHEM presented with consciousness disturbance and repeated seizures. Herpes simplex virus infection is identified", "Title: Hemorrhagic shock and encephalopathy syndrome – the markers for an early HSES diagnosis\nPassage: Although abnormal cerebral edema was seen in all the patients during their clinical courses, 5 patients appeared normal or only slightly edematous as revealed on their brain CT scans upon admission. On the initial EEG, multi-focal paroxysmal discharges were seen in 4 patients, and low-amplitude patterns were seen in 4 other patients. The CSF cell counts were within a normal range in 7 patients, while the serum level of IL-6 and soluble IL-2 receptors increased with varying ranges in all the patients .", "Title: Acute Hemorrhagic Encephalitis Responding to Combined Decompressive Craniectomy, Intravenous Immunoglobulin, and Corticosteroid Therapies: Association with Novel RANBP2 Variant\nPassage: syndrome such as high blood pressure. Macrophage activation syndrome could also lead to acute necrotic brain injury. However, it is associated to high ferritin and low triglycerides at the time of the encephalopathy, other multisystemic injuries, typical neuropathological findings, and recurrence over time, which were not noted in our patient . Parvovirus B19 has been described to cause encephalopathy in sickle cell patients. It is associated with aplastic anemia. It caused punctate areas of hemorrhages in the basal ganglia, periventricular white matter, and mainly along the posterior parietal cortex. This was attributed to parvovirus B19-induced vasculitis . In our patient," ]

[ [ "1a", "Title: Clinical study of children with cryofibrinogenemia: a retrospective study from a single center" ], [ "1b", "Passage: In this study, patients with CNS involvement presented as large artery narrowing, parenchymal involvement, and hemorrhage in demyelinating lesions on the white matter and basal ganglion." ], [ "1c", "The last is compatible with acute hemorrhagic encephalomyelitis , considered a hyper-acute sub-form of acute disseminated encephalomyelitis." ], [ "1d", "It is frequently a fulminant inflammatory hemorrhagic demylination of the CNS white matter." ], [ "1e", "Death from brain edema is common within one week of the onset of encephalopathy." ], [ "1f", "The pathogenesis is known as acute vasculitis with subsequent vessel occlusion ." ], [ "1g", "The patient here with AHEM presented with consciousness disturbance and repeated seizures." ], [ "1h", "Herpes simplex virus infection is identified" ] ]

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

[ "Title: Initial psychological responses to Influenza A, H1N1 (\"Swine flu\")\nPassage: the website http://www.swinefluques tionnaire.com. The website link was pasted onto a variety of general, non-health networking websites . Respondents were primarily from the UK and Portugal but also included 30 respondents living outside these countries and resident in Finland , Poland , Malta and France . Ten non-European based residents were then removed from the online survey before analysis.", "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", "Title: Clinical aspects and cytokine response in severe H1N1 influenza A virus infection\nPassage: Originating from Mexico and spreading initially in the United States and Canada, a novel influenza A virus infection ) of swine origin spread globally during spring 2009 to mid-February 2010. Rates of hospitalization and death have varied widely according to country . Among hospitalized patients 9 to 31% have been admitted to intensive care units where the rate of death was 14 to 46% .", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: with confi rmed swine fl u . This new strain of H1N1 swine infl uenza has a unique combination of genes from both North American and Eurasian swine lineages that has not been identifi ed previously in either swine or human populations . The virus appears to be a result of reassortment of two swine infl uenza viruses, one from North America and one from Europe with the North American virus itself the product of previous re-assortments, carrying an avian PB2 gene for at least 10 years and a human PB1 gene since 1993. The virus also has genome segments" ]

[ [ "1a", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus" ], [ "1b", "Passage: 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 ." ], [ "1c", "The WHO declared pandemic alert stage 6 on 11 June 2009, indicating an ongoing infl uenza pandemic ." ], [ "1d", "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" ] ]

[ "1b", "2b" ]

[ "Title: Initial psychological responses to Influenza A, H1N1 (\"Swine flu\")\nPassage: the website http://www.swinefluques tionnaire.com. The website link was pasted onto a variety of general, non-health networking websites . Respondents were primarily from the UK and Portugal but also included 30 respondents living outside these countries and resident in Finland , Poland , Malta and France . Ten non-European based residents were then removed from the online survey before analysis.", "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", "Title: Clinical aspects and cytokine response in severe H1N1 influenza A virus infection\nPassage: Originating from Mexico and spreading initially in the United States and Canada, a novel influenza A virus infection ) of swine origin spread globally during spring 2009 to mid-February 2010. Rates of hospitalization and death have varied widely according to country . Among hospitalized patients 9 to 31% have been admitted to intensive care units where the rate of death was 14 to 46% .", "Title: Diagnosis of influenza viruses with special reference to novel H1N1 2009 influenza virus\nPassage: with confi rmed swine fl u . This new strain of H1N1 swine infl uenza has a unique combination of genes from both North American and Eurasian swine lineages that has not been identifi ed previously in either swine or human populations . The virus appears to be a result of reassortment of two swine infl uenza viruses, one from North America and one from Europe with the North American virus itself the product of previous re-assortments, carrying an avian PB2 gene for at least 10 years and a human PB1 gene since 1993. The virus also has genome segments" ]

[ [ "2a", "Title: Clinical aspects and cytokine response in severe H1N1 influenza A virus infection" ], [ "2b", "Passage: Originating from Mexico and spreading initially in the United States and Canada, a novel influenza A virus infection ) of swine origin spread globally during spring 2009 to mid-February 2010." ], [ "2c", "Rates of hospitalization and death have varied widely according to country ." ], [ "2d", "Among hospitalized patients 9 to 31% have been admitted to intensive care units where the rate of death was 14 to 46% ." ] ]

[ "1b", "2b" ]

[ "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The second indicator of disease severity we consider is the time to peak viraemia. Several studies have shown that high viraemia levels early in infection are associated with a higher risk of developing severe disease . For primary infections, a shorter time to peak viraemia is associated with higher disease severity, while peak viraemia is rarely observed during a secondary infection, suggesting that virus peaks earlier in secondary infection relative to a primary infection . Figure 5b shows that our models recover this described negative relationship between time to peak viraemia and the peak level of endothelial activators. In secondary", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: for peak viraemia or the time to peak viraemia, because viraemia levels from patients with secondary dengue infection are generally already in decline by the time patients are admitted .", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: We first sought to determine whether the minimal model capable of reproducing the features of a primary dengue infection could reproduce the above features of a secondary dengue infection. To recover a secondary infection's shorter time to viral peak and higher level of peak viraemia, a 20% increase in the viral infectivity rate b was sufficient, resulting in a peak viraemia level of 9.8 log 10 viral copies at 7.4 days post viral inoculation. This level and timing of peak viraemia is consistent with virological data from secondary DF and DHF patients . This reparametrization can also be easily interpreted", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The first virological indicator of disease severity we consider is peak viraemia. A higher magnitude of viral load early in infection has been repeatedly associated with a higher risk of developing severe disease . When a viral peak is observed, higher values of peak viraemia are associated with a higher risk of developing severe disease . Figure 5a shows that our models reproduce the observed positive association between peak viral load and peak endothelial cell activator levels. Furthermore, figure 5a shows that during a secondary infection, both peak viral load and peak E levels are generally higher than in a" ]

[ [ "0a", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections" ], [ "0b", "Passage: The second indicator of disease severity we consider is the time to peak viraemia." ], [ "0c", "Several studies have shown that high viraemia levels early in infection are associated with a higher risk of developing severe disease ." ], [ "0d", "For primary infections, a shorter time to peak viraemia is associated with higher disease severity, while peak viraemia is rarely observed during a secondary infection, suggesting that virus peaks earlier in secondary infection relative to a primary infection ." ], [ "0e", "Figure 5b shows that our models recover this described negative relationship between time to peak viraemia and the peak level of endothelial activators. In secondary" ] ]

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

[ "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The second indicator of disease severity we consider is the time to peak viraemia. Several studies have shown that high viraemia levels early in infection are associated with a higher risk of developing severe disease . For primary infections, a shorter time to peak viraemia is associated with higher disease severity, while peak viraemia is rarely observed during a secondary infection, suggesting that virus peaks earlier in secondary infection relative to a primary infection . Figure 5b shows that our models recover this described negative relationship between time to peak viraemia and the peak level of endothelial activators. In secondary", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: for peak viraemia or the time to peak viraemia, because viraemia levels from patients with secondary dengue infection are generally already in decline by the time patients are admitted .", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: We first sought to determine whether the minimal model capable of reproducing the features of a primary dengue infection could reproduce the above features of a secondary dengue infection. To recover a secondary infection's shorter time to viral peak and higher level of peak viraemia, a 20% increase in the viral infectivity rate b was sufficient, resulting in a peak viraemia level of 9.8 log 10 viral copies at 7.4 days post viral inoculation. This level and timing of peak viraemia is consistent with virological data from secondary DF and DHF patients . This reparametrization can also be easily interpreted", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The first virological indicator of disease severity we consider is peak viraemia. A higher magnitude of viral load early in infection has been repeatedly associated with a higher risk of developing severe disease . When a viral peak is observed, higher values of peak viraemia are associated with a higher risk of developing severe disease . Figure 5a shows that our models reproduce the observed positive association between peak viral load and peak endothelial cell activator levels. Furthermore, figure 5a shows that during a secondary infection, both peak viral load and peak E levels are generally higher than in a" ]

[ [ "1a", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections" ], [ "1b", "Passage: for peak viraemia or the time to peak viraemia, because viraemia levels from patients with secondary dengue infection are generally already in decline by the time patients are admitted ." ] ]

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

[ "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The second indicator of disease severity we consider is the time to peak viraemia. Several studies have shown that high viraemia levels early in infection are associated with a higher risk of developing severe disease . For primary infections, a shorter time to peak viraemia is associated with higher disease severity, while peak viraemia is rarely observed during a secondary infection, suggesting that virus peaks earlier in secondary infection relative to a primary infection . Figure 5b shows that our models recover this described negative relationship between time to peak viraemia and the peak level of endothelial activators. In secondary", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: for peak viraemia or the time to peak viraemia, because viraemia levels from patients with secondary dengue infection are generally already in decline by the time patients are admitted .", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: We first sought to determine whether the minimal model capable of reproducing the features of a primary dengue infection could reproduce the above features of a secondary dengue infection. To recover a secondary infection's shorter time to viral peak and higher level of peak viraemia, a 20% increase in the viral infectivity rate b was sufficient, resulting in a peak viraemia level of 9.8 log 10 viral copies at 7.4 days post viral inoculation. This level and timing of peak viraemia is consistent with virological data from secondary DF and DHF patients . This reparametrization can also be easily interpreted", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The first virological indicator of disease severity we consider is peak viraemia. A higher magnitude of viral load early in infection has been repeatedly associated with a higher risk of developing severe disease . When a viral peak is observed, higher values of peak viraemia are associated with a higher risk of developing severe disease . Figure 5a shows that our models reproduce the observed positive association between peak viral load and peak endothelial cell activator levels. Furthermore, figure 5a shows that during a secondary infection, both peak viral load and peak E levels are generally higher than in a" ]

[ [ "2a", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections" ], [ "2b", "Passage: We first sought to determine whether the minimal model capable of reproducing the features of a primary dengue infection could reproduce the above features of a secondary dengue infection." ], [ "2c", "To recover a secondary infection's shorter time to viral peak and higher level of peak viraemia, a 20% increase in the viral infectivity rate b was sufficient, resulting in a peak viraemia level of 9.8 log 10 viral copies at 7.4 days post viral inoculation." ], [ "2d", "This level and timing of peak viraemia is consistent with virological data from secondary DF and DHF patients ." ], [ "2e", "This reparametrization can also be easily interpreted" ] ]

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

[ "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The second indicator of disease severity we consider is the time to peak viraemia. Several studies have shown that high viraemia levels early in infection are associated with a higher risk of developing severe disease . For primary infections, a shorter time to peak viraemia is associated with higher disease severity, while peak viraemia is rarely observed during a secondary infection, suggesting that virus peaks earlier in secondary infection relative to a primary infection . Figure 5b shows that our models recover this described negative relationship between time to peak viraemia and the peak level of endothelial activators. In secondary", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: for peak viraemia or the time to peak viraemia, because viraemia levels from patients with secondary dengue infection are generally already in decline by the time patients are admitted .", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: We first sought to determine whether the minimal model capable of reproducing the features of a primary dengue infection could reproduce the above features of a secondary dengue infection. To recover a secondary infection's shorter time to viral peak and higher level of peak viraemia, a 20% increase in the viral infectivity rate b was sufficient, resulting in a peak viraemia level of 9.8 log 10 viral copies at 7.4 days post viral inoculation. This level and timing of peak viraemia is consistent with virological data from secondary DF and DHF patients . This reparametrization can also be easily interpreted", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections\nPassage: The first virological indicator of disease severity we consider is peak viraemia. A higher magnitude of viral load early in infection has been repeatedly associated with a higher risk of developing severe disease . When a viral peak is observed, higher values of peak viraemia are associated with a higher risk of developing severe disease . Figure 5a shows that our models reproduce the observed positive association between peak viral load and peak endothelial cell activator levels. Furthermore, figure 5a shows that during a secondary infection, both peak viral load and peak E levels are generally higher than in a" ]

[ [ "3a", "Title: Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections" ], [ "3b", "Passage: The first virological indicator of disease severity we consider is peak viraemia." ], [ "3c", "A higher magnitude of viral load early in infection has been repeatedly associated with a higher risk of developing severe disease ." ], [ "3d", "When a viral peak is observed, higher values of peak viraemia are associated with a higher risk of developing severe disease ." ], [ "3e", "Figure 5a shows that our models reproduce the observed positive association between peak viral load and peak endothelial cell activator levels." ], [ "3f", "Furthermore, figure 5a shows that during a secondary infection, both peak viral load and peak E levels are generally higher than in a" ] ]

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

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

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

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

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

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

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

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

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

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

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

[ [ "3a", "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells" ], [ "3b", "Passage: Hepcidin is effective on iron transfer from macrophages." ], [ "3c", "In the presence of hepcidin, ferritin is transmitted into the macrophage and is destroyed by lysosomes, resulting in storage of iron inside the cell." ], [ "3d", "In low concentrations of hepcidin, ferritin is present in the cell membrane, allowing the release of iron." ], [ "3e", "After leaving the cell, iron oxide is rapidly oxidized by ceruloplasmin, a copper-rich ferroxidase and converted into ferric iron and then bound to transferrin ." ] ]

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

[ "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: are used and recommended for IRS .", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: sample material.", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: Our compendium provides a perspective that can help draw a roadmap for a scientific research program when the project outputs and metrics are incorporated. In addition, aligning program objectives and exacting expectations across participants and stakeholders contribute to the roadmap that ultimately builds that partner country's capability and capacity necessary for sustainability. Tracking the evolution of program projects and studies, especially collaborations and networks, is emphasized to capture important activities that are often omitted when large programs evolve and institutional memory is lost through turnover of human resources. To advance science through increased transparency and mature capabilities, a multi-sectoral approach,", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: extracted the information as is from Scopus. However, due to different spelling of authors or institutions, it is possible that some authors have multiple affiliations that the authors were not aware of and thus the ranking might not be 100% accurate. Finally, in VOSviewer, we always used a minimum number or threshold to draw the maps, thus not all the items are shown. Not being shown in the map does not mean that the item is not important or that the authors were biased toward any particular item. The authors were aware of all these limitations and did their best" ]

[ [ "0a", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)" ], [ "0b", "Passage: are used and recommended for IRS ." ] ]

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

[ "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: are used and recommended for IRS .", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: sample material.", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: Our compendium provides a perspective that can help draw a roadmap for a scientific research program when the project outputs and metrics are incorporated. In addition, aligning program objectives and exacting expectations across participants and stakeholders contribute to the roadmap that ultimately builds that partner country's capability and capacity necessary for sustainability. Tracking the evolution of program projects and studies, especially collaborations and networks, is emphasized to capture important activities that are often omitted when large programs evolve and institutional memory is lost through turnover of human resources. To advance science through increased transparency and mature capabilities, a multi-sectoral approach,", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: extracted the information as is from Scopus. However, due to different spelling of authors or institutions, it is possible that some authors have multiple affiliations that the authors were not aware of and thus the ranking might not be 100% accurate. Finally, in VOSviewer, we always used a minimum number or threshold to draw the maps, thus not all the items are shown. Not being shown in the map does not mean that the item is not important or that the authors were biased toward any particular item. The authors were aware of all these limitations and did their best" ]

[ [ "1a", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan" ], [ "1b", "Passage: sample material." ] ]

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

[ "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: are used and recommended for IRS .", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: sample material.", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: Our compendium provides a perspective that can help draw a roadmap for a scientific research program when the project outputs and metrics are incorporated. In addition, aligning program objectives and exacting expectations across participants and stakeholders contribute to the roadmap that ultimately builds that partner country's capability and capacity necessary for sustainability. Tracking the evolution of program projects and studies, especially collaborations and networks, is emphasized to capture important activities that are often omitted when large programs evolve and institutional memory is lost through turnover of human resources. To advance science through increased transparency and mature capabilities, a multi-sectoral approach,", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: extracted the information as is from Scopus. However, due to different spelling of authors or institutions, it is possible that some authors have multiple affiliations that the authors were not aware of and thus the ranking might not be 100% accurate. Finally, in VOSviewer, we always used a minimum number or threshold to draw the maps, thus not all the items are shown. Not being shown in the map does not mean that the item is not important or that the authors were biased toward any particular item. The authors were aware of all these limitations and did their best" ]

[ [ "2a", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan" ], [ "2b", "Passage: Our compendium provides a perspective that can help draw a roadmap for a scientific research program when the project outputs and metrics are incorporated." ], [ "2c", "In addition, aligning program objectives and exacting expectations across participants and stakeholders contribute to the roadmap that ultimately builds that partner country's capability and capacity necessary for sustainability." ], [ "2d", "Tracking the evolution of program projects and studies, especially collaborations and networks, is emphasized to capture important activities that are often omitted when large programs evolve and institutional memory is lost through turnover of human resources." ], [ "2e", "To advance science through increased transparency and mature capabilities, a multi-sectoral approach," ] ]

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

[ "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: are used and recommended for IRS .", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: sample material.", "Title: A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan\nPassage: Our compendium provides a perspective that can help draw a roadmap for a scientific research program when the project outputs and metrics are incorporated. In addition, aligning program objectives and exacting expectations across participants and stakeholders contribute to the roadmap that ultimately builds that partner country's capability and capacity necessary for sustainability. Tracking the evolution of program projects and studies, especially collaborations and networks, is emphasized to capture important activities that are often omitted when large programs evolve and institutional memory is lost through turnover of human resources. To advance science through increased transparency and mature capabilities, a multi-sectoral approach,", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)\nPassage: extracted the information as is from Scopus. However, due to different spelling of authors or institutions, it is possible that some authors have multiple affiliations that the authors were not aware of and thus the ranking might not be 100% accurate. Finally, in VOSviewer, we always used a minimum number or threshold to draw the maps, thus not all the items are shown. Not being shown in the map does not mean that the item is not important or that the authors were biased toward any particular item. The authors were aware of all these limitations and did their best" ]

[ [ "3a", "Title: A bibliometric analysis of literature on malaria vector resistance: (1996 – 2015)" ], [ "3b", "Passage: extracted the information as is from Scopus." ], [ "3c", "However, due to different spelling of authors or institutions, it is possible that some authors have multiple affiliations that the authors were not aware of and thus the ranking might not be 100% accurate." ], [ "3d", "Finally, in VOSviewer, we always used a minimum number or threshold to draw the maps, thus not all the items are shown." ], [ "3e", "Not being shown in the map does not mean that the item is not important or that the authors were biased toward any particular item." ], [ "3f", "The authors were aware of all these limitations and did their best" ] ]

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

[ "Title: A Global Champion for Health—WHO’s Next?\nPassage: Chan will step down from WHO on June 30, 2017 after more than a decade in the post. The process for choosing WHO's next leader has begun, promising to be protracted and rigorous as befits the importance of the role. Factoring in the many influential stakeholders in the process of appointing Chan's successor, however, transparency of the selection process may be one area unlikely to attract plaudits. Although too soon to speculate about the identity of WHO's next Director-General, it is worth reflecting on what qualities an incoming leader should bring to WHO and how that person might need to", "Title: A Global Champion for Health—WHO’s Next?\nPassage: Instead of electing a new Director-General, Lorenz Von Seidlein of Mahidol University, Thailand, argued that \"the problems. . .are now so deeply ingrained that replacing the WHO with new, more appropriate organizations is the logical solution. . .at a fraction of current cost, free of cumbersome, archaic obligations and entitlements and an ability to respond to new problems.\" This viewpoint is indicative of the strength of feeling that WHO's deficiencies have come to evoke in some of those committed to the cause of improving the health of people in low-income and middle-income countries. But this perception acknowledges that an accountable", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: during March 17-28, the WHO Director-General declared on March 29, 2016 the end of the Public Health Emergency of International Concern regarding the EVD outbreak in West Africa .", "Title: A Global Champion for Health—WHO’s Next?\nPassage: WHO's next Director-General should be a proven leader and advocate, perhaps from a lowincome or middle-income country. The new recruit will be greeted by a full in-tray, and featuring prominently are likely to be the constraints imposed by WHO's current funding mechanisms. A substantial proportion of WHO's existing budget is earmarked for specific projects, leaving the organization with little financial flexibility to respond to unanticipated demands. However, any improved funding mechanism is likely to follow, and be dependent on, organizational reform. According to Kruk, \"WHO is both essential and hamstrung. . .the election of the Director-General should be a moment" ]

[ [ "0a", "Title: A Global Champion for Health—WHO’s Next?" ], [ "0b", "Passage: Chan will step down from WHO on June 30, 2017 after more than a decade in the post." ], [ "0c", "The process for choosing WHO's next leader has begun, promising to be protracted and rigorous as befits the importance of the role." ], [ "0d", "Factoring in the many influential stakeholders in the process of appointing Chan's successor, however, transparency of the selection process may be one area unlikely to attract plaudits." ], [ "0e", "Although too soon to speculate about the identity of WHO's next Director-General, it is worth reflecting on what qualities an incoming leader should bring to WHO and how that person might need to" ] ]

[ "0b" ]

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: The shorter nucleocapsid or N protein is a structural component of the viral nucleocapsid, along with the genomic viral RNA segments. As an RNA-binding protein that engages the hairpin termini of the genomic segments with high affinity , it limits the access of the RNA to host nucleases and helps to render viral replication a closed process within the cytoplasm. It also acts as a peripheral membrane protein, as does the L protein , an activity that could play a role in its presumed, but not yet demonstrated function as matrix . Until recently, it had not been appreciated that", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell. Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences . N is also reported to interact with actin microfilaments, and the SUMO-1 protein . Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: encoded protein in comparison to native mRNAs . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement", "Title: The Long Noncoding RNA NEAT1 Exerts Antihantaviral Effects by Acting as Positive Feedback for RIG-I Signaling\nPassage: Text: glycoprotein , and viral RNA-dependent polymerase protein , respectively. Humans become infected by inhaling contaminated aerosols or by coming into contact with rodent excreta, and they develop two severe acute diseases, namely, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome . Hantavirus infection affects up to 100,000 to 200,000 humans annually, with fulminant HFRS cases most represented in China . Chinese HFRS cases, mainly caused by Hantaan virus infection, account for approximately 90% of all global cases, with a mortality rate ranging from 0.1 to 15% . Since there is neither an effective therapeutic nor FDA-licensed vaccine, further" ]

[ [ "0a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "0b", "Passage: The shorter nucleocapsid or N protein is a structural component of the viral nucleocapsid, along with the genomic viral RNA segments." ], [ "0c", "As an RNA-binding protein that engages the hairpin termini of the genomic segments with high affinity , it limits the access of the RNA to host nucleases and helps to render viral replication a closed process within the cytoplasm." ], [ "0d", "It also acts as a peripheral membrane protein, as does the L protein , an activity that could play a role in its presumed, but not yet demonstrated function as matrix ." ], [ "0e", "Until recently, it had not been appreciated that" ] ]

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

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: The shorter nucleocapsid or N protein is a structural component of the viral nucleocapsid, along with the genomic viral RNA segments. As an RNA-binding protein that engages the hairpin termini of the genomic segments with high affinity , it limits the access of the RNA to host nucleases and helps to render viral replication a closed process within the cytoplasm. It also acts as a peripheral membrane protein, as does the L protein , an activity that could play a role in its presumed, but not yet demonstrated function as matrix . Until recently, it had not been appreciated that", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell. Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences . N is also reported to interact with actin microfilaments, and the SUMO-1 protein . Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: encoded protein in comparison to native mRNAs . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement", "Title: The Long Noncoding RNA NEAT1 Exerts Antihantaviral Effects by Acting as Positive Feedback for RIG-I Signaling\nPassage: Text: glycoprotein , and viral RNA-dependent polymerase protein , respectively. Humans become infected by inhaling contaminated aerosols or by coming into contact with rodent excreta, and they develop two severe acute diseases, namely, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome . Hantavirus infection affects up to 100,000 to 200,000 humans annually, with fulminant HFRS cases most represented in China . Chinese HFRS cases, mainly caused by Hantaan virus infection, account for approximately 90% of all global cases, with a mortality rate ranging from 0.1 to 15% . Since there is neither an effective therapeutic nor FDA-licensed vaccine, further" ]

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

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

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: The shorter nucleocapsid or N protein is a structural component of the viral nucleocapsid, along with the genomic viral RNA segments. As an RNA-binding protein that engages the hairpin termini of the genomic segments with high affinity , it limits the access of the RNA to host nucleases and helps to render viral replication a closed process within the cytoplasm. It also acts as a peripheral membrane protein, as does the L protein , an activity that could play a role in its presumed, but not yet demonstrated function as matrix . Until recently, it had not been appreciated that", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell. Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences . N is also reported to interact with actin microfilaments, and the SUMO-1 protein . Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: encoded protein in comparison to native mRNAs . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement", "Title: The Long Noncoding RNA NEAT1 Exerts Antihantaviral Effects by Acting as Positive Feedback for RIG-I Signaling\nPassage: Text: glycoprotein , and viral RNA-dependent polymerase protein , respectively. Humans become infected by inhaling contaminated aerosols or by coming into contact with rodent excreta, and they develop two severe acute diseases, namely, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome . Hantavirus infection affects up to 100,000 to 200,000 humans annually, with fulminant HFRS cases most represented in China . Chinese HFRS cases, mainly caused by Hantaan virus infection, account for approximately 90% of all global cases, with a mortality rate ranging from 0.1 to 15% . Since there is neither an effective therapeutic nor FDA-licensed vaccine, further" ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: encoded protein in comparison to native mRNAs ." ], [ "2c", "N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways." ], [ "2d", "It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures ." ], [ "2e", "Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature." ], [ "2f", "It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement" ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Identification of Three Antiviral Inhibitors against Japanese Encephalitis Virus from Library of Pharmacologically Active Compounds 1280\nPassage: Japanese encephalitis virus , a member of the genus Flavivirus in the family Flaviviridae, is a mosquito-transmitted and zoonotic pathogen that causes 50,000 cases and 10,000 deaths per year . There are .70 arboviruses in the genus Flavivirus including JEV, dengue virus , West Nile virus , and yellow fever virus . JEV can cause severe central nervous disorders such as poliomyelitis-like paralysis, aseptic meningitis, and encephalitis in humans. The fatality rate caused by JEV is 10-50% and half of the survivors have severe neurological sequelae, including persistent motor defects and severe cognitive and language impairments . The geographic range", "Title: Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks\nPassage: Tick-borne encephalitis virus causes up to 14,000 human cases of tick-borne encephalitis across Eurasia annually . TBE outbreaks are now registered in about 30 European countries with a recorded morbidity increase of about 400% during the past 30 years . TBEV is a member of the tick-borne flavivirus group that, together with mosquito-borne and no-known vector virus groups comprise the genus Flavivirus within the family Flaviviridae. Human pathogens within the genus Flavivirus include Japanese encephalitis virus, Dengue virus and Yellow fever virus that cause annual epidemics of fever, encephalitis and hemorrhagic fever in the tropics and some sub-tropical regions ." ]

[ [ "0a", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection" ], [ "0b", "Passage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus ." ], [ "0c", "Most flaviviruses are arthropod borne and cause public health problems worldwide ." ], [ "0d", "The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available." ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Identification of Three Antiviral Inhibitors against Japanese Encephalitis Virus from Library of Pharmacologically Active Compounds 1280\nPassage: Japanese encephalitis virus , a member of the genus Flavivirus in the family Flaviviridae, is a mosquito-transmitted and zoonotic pathogen that causes 50,000 cases and 10,000 deaths per year . There are .70 arboviruses in the genus Flavivirus including JEV, dengue virus , West Nile virus , and yellow fever virus . JEV can cause severe central nervous disorders such as poliomyelitis-like paralysis, aseptic meningitis, and encephalitis in humans. The fatality rate caused by JEV is 10-50% and half of the survivors have severe neurological sequelae, including persistent motor defects and severe cognitive and language impairments . The geographic range", "Title: Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks\nPassage: Tick-borne encephalitis virus causes up to 14,000 human cases of tick-borne encephalitis across Eurasia annually . TBE outbreaks are now registered in about 30 European countries with a recorded morbidity increase of about 400% during the past 30 years . TBEV is a member of the tick-borne flavivirus group that, together with mosquito-borne and no-known vector virus groups comprise the genus Flavivirus within the family Flaviviridae. Human pathogens within the genus Flavivirus include Japanese encephalitis virus, Dengue virus and Yellow fever virus that cause annual epidemics of fever, encephalitis and hemorrhagic fever in the tropics and some sub-tropical regions ." ]

[ [ "1a", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection" ], [ "1b", "Passage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus ." ], [ "1c", "Most flaviviruses are arthropod borne and cause public health problems worldwide ." ], [ "1d", "The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available." ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Identification of Three Antiviral Inhibitors against Japanese Encephalitis Virus from Library of Pharmacologically Active Compounds 1280\nPassage: Japanese encephalitis virus , a member of the genus Flavivirus in the family Flaviviridae, is a mosquito-transmitted and zoonotic pathogen that causes 50,000 cases and 10,000 deaths per year . There are .70 arboviruses in the genus Flavivirus including JEV, dengue virus , West Nile virus , and yellow fever virus . JEV can cause severe central nervous disorders such as poliomyelitis-like paralysis, aseptic meningitis, and encephalitis in humans. The fatality rate caused by JEV is 10-50% and half of the survivors have severe neurological sequelae, including persistent motor defects and severe cognitive and language impairments . The geographic range", "Title: Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks\nPassage: Tick-borne encephalitis virus causes up to 14,000 human cases of tick-borne encephalitis across Eurasia annually . TBE outbreaks are now registered in about 30 European countries with a recorded morbidity increase of about 400% during the past 30 years . TBEV is a member of the tick-borne flavivirus group that, together with mosquito-borne and no-known vector virus groups comprise the genus Flavivirus within the family Flaviviridae. Human pathogens within the genus Flavivirus include Japanese encephalitis virus, Dengue virus and Yellow fever virus that cause annual epidemics of fever, encephalitis and hemorrhagic fever in the tropics and some sub-tropical regions ." ]

[ [ "2a", "Title: Identification of Three Antiviral Inhibitors against Japanese Encephalitis Virus from Library of Pharmacologically Active Compounds 1280" ], [ "2b", "Passage: Japanese encephalitis virus , a member of the genus Flavivirus in the family Flaviviridae, is a mosquito-transmitted and zoonotic pathogen that causes 50,000 cases and 10,000 deaths per year ." ], [ "2c", "There are .70 arboviruses in the genus Flavivirus including JEV, dengue virus , West Nile virus , and yellow fever virus ." ], [ "2d", "JEV can cause severe central nervous disorders such as poliomyelitis-like paralysis, aseptic meningitis, and encephalitis in humans." ], [ "2e", "The fatality rate caused by JEV is 10-50% and half of the survivors have severe neurological sequelae, including persistent motor defects and severe cognitive and language impairments ." ], [ "2f", "The geographic range" ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: These viruses comprise over 70 different pathogens, such as Japanese encephalitis virus , Zika virus , dengue virus , West Nile virus , and yellow fever virus . Most flaviviruses are arthropod borne and cause public health problems worldwide . The development and usage of vaccines against some flaviviruses, such as JEV, YFV, and tick-borne encephalitis virus , have decreased the rates of morbidity and mortality from infections caused by these viruses ; however, flavivirus-induced diseases are still pandemic, and few therapies beyond intensive supportive care are currently available.", "Title: Identification of Three Antiviral Inhibitors against Japanese Encephalitis Virus from Library of Pharmacologically Active Compounds 1280\nPassage: Japanese encephalitis virus , a member of the genus Flavivirus in the family Flaviviridae, is a mosquito-transmitted and zoonotic pathogen that causes 50,000 cases and 10,000 deaths per year . There are .70 arboviruses in the genus Flavivirus including JEV, dengue virus , West Nile virus , and yellow fever virus . JEV can cause severe central nervous disorders such as poliomyelitis-like paralysis, aseptic meningitis, and encephalitis in humans. The fatality rate caused by JEV is 10-50% and half of the survivors have severe neurological sequelae, including persistent motor defects and severe cognitive and language impairments . The geographic range", "Title: Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks\nPassage: Tick-borne encephalitis virus causes up to 14,000 human cases of tick-borne encephalitis across Eurasia annually . TBE outbreaks are now registered in about 30 European countries with a recorded morbidity increase of about 400% during the past 30 years . TBEV is a member of the tick-borne flavivirus group that, together with mosquito-borne and no-known vector virus groups comprise the genus Flavivirus within the family Flaviviridae. Human pathogens within the genus Flavivirus include Japanese encephalitis virus, Dengue virus and Yellow fever virus that cause annual epidemics of fever, encephalitis and hemorrhagic fever in the tropics and some sub-tropical regions ." ]

[ [ "3a", "Title: Non-Hemagglutinating Flaviviruses: Molecular Mechanisms for the Emergence of New Strains via Adaptation to European Ticks" ], [ "3b", "Passage: Tick-borne encephalitis virus causes up to 14,000 human cases of tick-borne encephalitis across Eurasia annually ." ], [ "3c", "TBE outbreaks are now registered in about 30 European countries with a recorded morbidity increase of about 400% during the past 30 years ." ], [ "3d", "TBEV is a member of the tick-borne flavivirus group that, together with mosquito-borne and no-known vector virus groups comprise the genus Flavivirus within the family Flaviviridae." ], [ "3e", "Human pathogens within the genus Flavivirus include Japanese encephalitis virus, Dengue virus and Yellow fever virus that cause annual epidemics of fever, encephalitis and hemorrhagic fever in the tropics and some sub-tropical regions ." ] ]

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

[ "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Of the more than four thousand known mammalian species, 50% are rodents and 25% are bats. This rich species diversity, plus other ecological traits , suggests that surveillance efforts focused on rodents and bats could offer high value. Rodents are typically small and can be trapped in large numbers for surveillance, and they are easier to handle and less expensive to keep in laboratory settings than large animals. The ability to study viral infections in animal hosts under controlled laboratory conditions is central to understanding virus-host ecology at molecular and organismal levels, including the duration and severity of infection, immune", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: Of the more than four thousand known mammalian species, ~50% are rodents and ~25% are bats. This rich species diversity, plus other ecological traits , suggests that surveillance efforts focused on rodents and bats could offer high value. Rodents are typically small and can be trapped in large numbers for surveillance, and they are easier to handle and less expensive to keep in laboratory settings than large animals. The ability to study viral infections in animal hosts under controlled laboratory conditions is central to understanding virus-host ecology at molecular and organismal levels, including the duration and severity of infection, immune", "Title: High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress\nPassage: Bats are the only mammal that have mastered true flight, and consequently, they must endure elevated body temperatures throughout flight. Additionally, most have longer lifespans than terrestrial mammals of similar body sizes, despite their high metabolic rate and its predicted consequences on oxidative metabolism. As such, they have one of the greatest disparities between body mass and longevity . Their longevity has been attributed, at least in part, to enhanced oxidative stress resistance and protein homeostasis Yin et al. 2016) . The body temperature of bats raises drastically during flight , and there is an excessive increase in metabolic rate", "Title: Temporal Anomalies in Immunological Gene Expression in a Time Series of Wild Mice: Signature of an Epidemic?\nPassage: could occur because animals in better starting condition might be more likely to survive infection, thus raising their representation in infected classes by differential mortality. The immunoregulatory influence of macroparasites might also be important in this context: dampening potentially lethal immunopathogenic inflammatory responses. A further possibility is that individual mice respond to infection by adjusting life history traits in a way that produces an overcompensatory response in body condition. For example, A. sylvaticus infected with cowpox virus in summer may show positive effects on survival due to a diversion of resources from reproduction ." ]

[ [ "3a", "Title: Temporal Anomalies in Immunological Gene Expression in a Time Series of Wild Mice: Signature of an Epidemic?" ], [ "3b", "Passage: could occur because animals in better starting condition might be more likely to survive infection, thus raising their representation in infected classes by differential mortality." ], [ "3c", "The immunoregulatory influence of macroparasites might also be important in this context: dampening potentially lethal immunopathogenic inflammatory responses." ], [ "3d", "A further possibility is that individual mice respond to infection by adjusting life history traits in a way that produces an overcompensatory response in body condition." ], [ "3e", "For example, A. sylvaticus infected with cowpox virus in summer may show positive effects on survival due to a diversion of resources from reproduction ." ] ]

[ "3d", "3e" ]

[ "Title: CDC Summary 21 MAR 2020,\nPassage: If you have been in China or another affected area or have been exposed to someone sick with COVID-19 in the last 14 days, you will face some limitations on your movement and activity. Please follow instructions during this time. Your cooperation is integral to the ongoing public health response to try to slow spread of this virus.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: have been mild .", "Title: Estimating the number of infections and the impact of non-\nPassage: In China, strict movement restrictions and other measures including case isolation and quarantine", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We define period A as beginning from the time when the first cases were identified . During this period, extensive infection control measures were imposed, including: closing theatres and public places of entertainment; compulsory wearing of masks on all public transport and in public places; closure of schools; prohibition of race meetings and church services; and removal of patients to hospital and strict quarantine of contact for a complete list). As the incidence remained low in comparison with severe epidemics reported from elsewhere around the world, authorities deemed that the threat had passed and most measures were lifted on 1" ]

[ [ "0a", "Title: CDC Summary 21 MAR 2020," ], [ "0b", "Passage: If you have been in China or another affected area or have been exposed to someone sick with COVID-19 in the last 14 days, you will face some limitations on your movement and activity." ], [ "0c", "Please follow instructions during this time." ], [ "0d", "Your cooperation is integral to the ongoing public health response to try to slow spread of this virus." ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: If you have been in China or another affected area or have been exposed to someone sick with COVID-19 in the last 14 days, you will face some limitations on your movement and activity. Please follow instructions during this time. Your cooperation is integral to the ongoing public health response to try to slow spread of this virus.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: have been mild .", "Title: Estimating the number of infections and the impact of non-\nPassage: In China, strict movement restrictions and other measures including case isolation and quarantine", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We define period A as beginning from the time when the first cases were identified . During this period, extensive infection control measures were imposed, including: closing theatres and public places of entertainment; compulsory wearing of masks on all public transport and in public places; closure of schools; prohibition of race meetings and church services; and removal of patients to hospital and strict quarantine of contact for a complete list). As the incidence remained low in comparison with severe epidemics reported from elsewhere around the world, authorities deemed that the threat had passed and most measures were lifted on 1" ]

[ [ "2a", "Title: Estimating the number of infections and the impact of non-" ], [ "2b", "Passage: In China, strict movement restrictions and other measures including case isolation and quarantine" ] ]

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

[ "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: mice have two other IFITM genes: IFITM6 and IFITM7. . These proteins inhibit viral membrane fusion, thus resulting in cellular protection from a diverse range of infections. An early observation of IFITM proteins controlling viral infection was reported in 1996 , where overexpression of IFITM1 was shown to inhibit VSV replication, although less potently than the IFN-induced protein MxA . This study is the first description of the antiviral activity of an IFITM protein.", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: All IFITM proteins have been shown to restrict cell entry of many viruses . However, IFITM3 is the most potent IFITM family member in restricting viral replication in cell culture . IFITM3 inhibits a VSV entry step following endocytosis, but at or before the point of primary transcription of incoming viral genomes . Both the N-terminal 21 amino acid residues and C-terminal transmembrane region of IFITM3 are required for its antiviral function. In addition, IFITM3 has been shown to inhibit an early stage of the RABV replication cycle by targeting entry mediated by the viral glycoprotein .", "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: Interferon-induced transmembrane protein 3 is a1 33 amino acid membrane-associated protein that inhibits the replication of pathogenic viruses.This protein was first named fragilis and reported by Saitou and co-workers in 2002, but interest surged when its antiviral properties came to light during the 2009 H1N1 influenza pandemic. Everitt and co-workers reported that patients lacking full IFITM3 were more quickly and severely infected, leading to adramatic increase in mortality.S ubsequent studies have shown that IFITM3 exhibits antiviral activity against al arge number of viruses, including West Nile virus, Dengue virus, Filoviruses , SARS Coronavirus, Rift Va lley fever virus, HIV-1 and,", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: The IFN-inducible transmembrane genes are enhanced by cell treatment with IFNs since they contain the ISREs in their promoter. IFITM proteins belong to the CD225 protein superfamily, which can be found in nearly every domain of life, ranging from bacteria to invertebrates to primates. In humans, there are at least four functional members of IFITM proteins: IFITM1, IFITM2 and IFITM3, previously named 9-27, 1-8D and 1-8U, respectively, are expressed in a variety of tissues; IFITM5 is limited to the bone. IFIM4P is a pseudogene ). Mouse IFITM1, IFITM2, IFITM3 and IFITM5 genes are orthologues to their human counterparts. In addition," ]

[ [ "0a", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses" ], [ "0b", "Passage: mice have two other IFITM genes: IFITM6 and IFITM7. ." ], [ "0c", "These proteins inhibit viral membrane fusion, thus resulting in cellular protection from a diverse range of infections." ], [ "0d", "An early observation of IFITM proteins controlling viral infection was reported in 1996 , where overexpression of IFITM1 was shown to inhibit VSV replication, although less potently than the IFN-induced protein MxA ." ], [ "0e", "This study is the first description of the antiviral activity of an IFITM protein." ] ]

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

[ "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: mice have two other IFITM genes: IFITM6 and IFITM7. . These proteins inhibit viral membrane fusion, thus resulting in cellular protection from a diverse range of infections. An early observation of IFITM proteins controlling viral infection was reported in 1996 , where overexpression of IFITM1 was shown to inhibit VSV replication, although less potently than the IFN-induced protein MxA . This study is the first description of the antiviral activity of an IFITM protein.", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: All IFITM proteins have been shown to restrict cell entry of many viruses . However, IFITM3 is the most potent IFITM family member in restricting viral replication in cell culture . IFITM3 inhibits a VSV entry step following endocytosis, but at or before the point of primary transcription of incoming viral genomes . Both the N-terminal 21 amino acid residues and C-terminal transmembrane region of IFITM3 are required for its antiviral function. In addition, IFITM3 has been shown to inhibit an early stage of the RABV replication cycle by targeting entry mediated by the viral glycoprotein .", "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: Interferon-induced transmembrane protein 3 is a1 33 amino acid membrane-associated protein that inhibits the replication of pathogenic viruses.This protein was first named fragilis and reported by Saitou and co-workers in 2002, but interest surged when its antiviral properties came to light during the 2009 H1N1 influenza pandemic. Everitt and co-workers reported that patients lacking full IFITM3 were more quickly and severely infected, leading to adramatic increase in mortality.S ubsequent studies have shown that IFITM3 exhibits antiviral activity against al arge number of viruses, including West Nile virus, Dengue virus, Filoviruses , SARS Coronavirus, Rift Va lley fever virus, HIV-1 and,", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: The IFN-inducible transmembrane genes are enhanced by cell treatment with IFNs since they contain the ISREs in their promoter. IFITM proteins belong to the CD225 protein superfamily, which can be found in nearly every domain of life, ranging from bacteria to invertebrates to primates. In humans, there are at least four functional members of IFITM proteins: IFITM1, IFITM2 and IFITM3, previously named 9-27, 1-8D and 1-8U, respectively, are expressed in a variety of tissues; IFITM5 is limited to the bone. IFIM4P is a pseudogene ). Mouse IFITM1, IFITM2, IFITM3 and IFITM5 genes are orthologues to their human counterparts. In addition," ]

[ [ "1a", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses" ], [ "1b", "Passage: All IFITM proteins have been shown to restrict cell entry of many viruses ." ], [ "1c", "However, IFITM3 is the most potent IFITM family member in restricting viral replication in cell culture ." ], [ "1d", "IFITM3 inhibits a VSV entry step following endocytosis, but at or before the point of primary transcription of incoming viral genomes ." ], [ "1e", "Both the N-terminal 21 amino acid residues and C-terminal transmembrane region of IFITM3 are required for its antiviral function." ], [ "1f", "In addition, IFITM3 has been shown to inhibit an early stage of the RABV replication cycle by targeting entry mediated by the viral glycoprotein ." ] ]

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

[ "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: mice have two other IFITM genes: IFITM6 and IFITM7. . These proteins inhibit viral membrane fusion, thus resulting in cellular protection from a diverse range of infections. An early observation of IFITM proteins controlling viral infection was reported in 1996 , where overexpression of IFITM1 was shown to inhibit VSV replication, although less potently than the IFN-induced protein MxA . This study is the first description of the antiviral activity of an IFITM protein.", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: All IFITM proteins have been shown to restrict cell entry of many viruses . However, IFITM3 is the most potent IFITM family member in restricting viral replication in cell culture . IFITM3 inhibits a VSV entry step following endocytosis, but at or before the point of primary transcription of incoming viral genomes . Both the N-terminal 21 amino acid residues and C-terminal transmembrane region of IFITM3 are required for its antiviral function. In addition, IFITM3 has been shown to inhibit an early stage of the RABV replication cycle by targeting entry mediated by the viral glycoprotein .", "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: Interferon-induced transmembrane protein 3 is a1 33 amino acid membrane-associated protein that inhibits the replication of pathogenic viruses.This protein was first named fragilis and reported by Saitou and co-workers in 2002, but interest surged when its antiviral properties came to light during the 2009 H1N1 influenza pandemic. Everitt and co-workers reported that patients lacking full IFITM3 were more quickly and severely infected, leading to adramatic increase in mortality.S ubsequent studies have shown that IFITM3 exhibits antiviral activity against al arge number of viruses, including West Nile virus, Dengue virus, Filoviruses , SARS Coronavirus, Rift Va lley fever virus, HIV-1 and,", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: The IFN-inducible transmembrane genes are enhanced by cell treatment with IFNs since they contain the ISREs in their promoter. IFITM proteins belong to the CD225 protein superfamily, which can be found in nearly every domain of life, ranging from bacteria to invertebrates to primates. In humans, there are at least four functional members of IFITM proteins: IFITM1, IFITM2 and IFITM3, previously named 9-27, 1-8D and 1-8U, respectively, are expressed in a variety of tissues; IFITM5 is limited to the bone. IFIM4P is a pseudogene ). Mouse IFITM1, IFITM2, IFITM3 and IFITM5 genes are orthologues to their human counterparts. In addition," ]

[ [ "2a", "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants" ], [ "2b", "Passage: Interferon-induced transmembrane protein 3 is a1 33 amino acid membrane-associated protein that inhibits the replication of pathogenic viruses.This protein was first named fragilis and reported by Saitou and co-workers in 2002, but interest surged when its antiviral properties came to light during the 2009 H1N1 influenza pandemic." ], [ "2c", "Everitt and co-workers reported that patients lacking full IFITM3 were more quickly and severely infected, leading to adramatic increase in mortality.S ubsequent studies have shown that IFITM3 exhibits antiviral activity against al arge number of viruses, including West Nile virus, Dengue virus, Filoviruses , SARS Coronavirus, Rift Va lley fever virus, HIV-1 and," ] ]

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

[ "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: mice have two other IFITM genes: IFITM6 and IFITM7. . These proteins inhibit viral membrane fusion, thus resulting in cellular protection from a diverse range of infections. An early observation of IFITM proteins controlling viral infection was reported in 1996 , where overexpression of IFITM1 was shown to inhibit VSV replication, although less potently than the IFN-induced protein MxA . This study is the first description of the antiviral activity of an IFITM protein.", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: All IFITM proteins have been shown to restrict cell entry of many viruses . However, IFITM3 is the most potent IFITM family member in restricting viral replication in cell culture . IFITM3 inhibits a VSV entry step following endocytosis, but at or before the point of primary transcription of incoming viral genomes . Both the N-terminal 21 amino acid residues and C-terminal transmembrane region of IFITM3 are required for its antiviral function. In addition, IFITM3 has been shown to inhibit an early stage of the RABV replication cycle by targeting entry mediated by the viral glycoprotein .", "Title: Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane‐Associated Protein IFITM3 and Modified Variants\nPassage: Interferon-induced transmembrane protein 3 is a1 33 amino acid membrane-associated protein that inhibits the replication of pathogenic viruses.This protein was first named fragilis and reported by Saitou and co-workers in 2002, but interest surged when its antiviral properties came to light during the 2009 H1N1 influenza pandemic. Everitt and co-workers reported that patients lacking full IFITM3 were more quickly and severely infected, leading to adramatic increase in mortality.S ubsequent studies have shown that IFITM3 exhibits antiviral activity against al arge number of viruses, including West Nile virus, Dengue virus, Filoviruses , SARS Coronavirus, Rift Va lley fever virus, HIV-1 and,", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses\nPassage: The IFN-inducible transmembrane genes are enhanced by cell treatment with IFNs since they contain the ISREs in their promoter. IFITM proteins belong to the CD225 protein superfamily, which can be found in nearly every domain of life, ranging from bacteria to invertebrates to primates. In humans, there are at least four functional members of IFITM proteins: IFITM1, IFITM2 and IFITM3, previously named 9-27, 1-8D and 1-8U, respectively, are expressed in a variety of tissues; IFITM5 is limited to the bone. IFIM4P is a pseudogene ). Mouse IFITM1, IFITM2, IFITM3 and IFITM5 genes are orthologues to their human counterparts. In addition," ]

[ [ "3a", "Title: Resistance to Rhabdoviridae Infection and Subversion of Antiviral Responses" ], [ "3b", "Passage: The IFN-inducible transmembrane genes are enhanced by cell treatment with IFNs since they contain the ISREs in their promoter." ], [ "3c", "IFITM proteins belong to the CD225 protein superfamily, which can be found in nearly every domain of life, ranging from bacteria to invertebrates to primates." ], [ "3d", "In humans, there are at least four functional members of IFITM proteins: IFITM1, IFITM2 and IFITM3, previously named 9-27, 1-8D and 1-8U, respectively, are expressed in a variety of tissues; IFITM5 is limited to the bone." ], [ "3e", "IFIM4P is a pseudogene )." ], [ "3f", "Mouse IFITM1, IFITM2, IFITM3 and IFITM5 genes are orthologues to their human counterparts. In addition," ] ]

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

[ "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients\nPassage: binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms . However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions .", "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients\nPassage: the binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms . However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions .", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: The primary mechanism to explain the antiviral effect of nucleoside analogs is based on their direct action on viral polymerization. Nucleoside analogs are transported into the cells and phosphorylated by the consecutive action of viral or cellular kinases, eventually generating nucleotide triphosphates. Mature nucleotide analogs, which are similar to physiological nucleotides, can directly incorporate into the growing viral genome during polymerization, resulting in the termination of chain reaction or the accumulation of mutations . Alternatively, nucleotide analogs can bind to the nucleotide-binding region on viral polymerases and block the entry of incoming natural nucleotides. The other mechanism is based on", "Title: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases\nPassage: efforts support the hypothesis that the mechanism of action of this compound class establishes a strong barrier against rapid viral escape from inhibition." ]

[ [ "0a", "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients" ], [ "0b", "Passage: binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms ." ], [ "0c", "However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions ." ] ]

[ "0b", "1b" ]

[ "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients\nPassage: binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms . However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions .", "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients\nPassage: the binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms . However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions .", "Title: Gemcitabine and Nucleos(t)ide Synthesis Inhibitors Are Broad-Spectrum Antiviral Drugs that Activate Innate Immunity\nPassage: The primary mechanism to explain the antiviral effect of nucleoside analogs is based on their direct action on viral polymerization. Nucleoside analogs are transported into the cells and phosphorylated by the consecutive action of viral or cellular kinases, eventually generating nucleotide triphosphates. Mature nucleotide analogs, which are similar to physiological nucleotides, can directly incorporate into the growing viral genome during polymerization, resulting in the termination of chain reaction or the accumulation of mutations . Alternatively, nucleotide analogs can bind to the nucleotide-binding region on viral polymerases and block the entry of incoming natural nucleotides. The other mechanism is based on", "Title: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases\nPassage: efforts support the hypothesis that the mechanism of action of this compound class establishes a strong barrier against rapid viral escape from inhibition." ]

[ [ "1a", "Title: Pretreatment Hepatitis C Virus NS5A/NS5B Resistance-Associated Substitutions in Genotype 1 Uruguayan Infected Patients" ], [ "1b", "Passage: the binding of the incoming nucleotide; nonnucleoside NS5B polymerase inhibitors interact with either the thumb 1, thumb 2, palm 1, or palm 2 domain of NS5B and inhibit polymerase activity by allosteric mechanisms ." ], [ "1c", "However, the extreme mutation and high replication rates of HCV, together with the immune system pressure, lead to a remarkable genetic variability that can compromise the high response rates to DAAs due to the preexistence of resistanceassociated substitutions ." ] ]

[ "0b", "1b" ]

[ "Title: Assessment of Temporary Community-Based Health Care Facilities During Arbaeenia Mass Gathering at Karbala, Iraq: Cross-Sectional Survey Study\nPassage: Any new systems should be in place for a sufficient length of time prior to the MG to allow baselines to be determined, to assess the effectiveness of collection, analysis and interpretation of the data, and to allow the persons involved to become comfortable with the system. Key questions that must be asked by host countries in establishing pre-MG surveillance are as follows:", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Data are produced in response to some perceived need, which must be articulated in questions that determine what data are collected, and in analyses determining how they will be understood. Those choosing the questions may or may not be the end users of the data; but their interests and aims will certainly influence the utility of the data to all potential users.", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: a. What information ought to be provided? This will usually include the following elements: the reasons for doing research, details about who is doing the research, why the potential participant is being asked to be involved, details about what any intervention might involve and any on-going commitments of participation, details about anticipated risks and benefits, the fact that participants are free to refuse or withdraw, that any findings will be communicated back to the participants etc. The information given should be proportionate to any risks, but this does not mean that the higher the risk, the more information ought to", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: In middle-and higher-income countries, subnational data collection is part of the routine function of health systems funded out of routine government spending. In low-income countries they may be externally funded through international survey programmes such as the Demographic and Health Surveys or the Multi-Indicator Cluster Surveys. These surveys, like routine data collection, are generally carried out by government staff. This creates an institutional imperative to use the data: they are locally owned, produced by colleagues who may be directly involved in communicating results and who can help explain anomalies in the data and their meaning in the specific local situation" ]

[ [ "0a", "Title: Assessment of Temporary Community-Based Health Care Facilities During Arbaeenia Mass Gathering at Karbala, Iraq: Cross-Sectional Survey Study" ], [ "0b", "Passage: Any new systems should be in place for a sufficient length of time prior to the MG to allow baselines to be determined, to assess the effectiveness of collection, analysis and interpretation of the data, and to allow the persons involved to become comfortable with the system." ], [ "0c", "Key questions that must be asked by host countries in establishing pre-MG surveillance are as follows:" ] ]

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

[ "Title: Assessment of Temporary Community-Based Health Care Facilities During Arbaeenia Mass Gathering at Karbala, Iraq: Cross-Sectional Survey Study\nPassage: Any new systems should be in place for a sufficient length of time prior to the MG to allow baselines to be determined, to assess the effectiveness of collection, analysis and interpretation of the data, and to allow the persons involved to become comfortable with the system. Key questions that must be asked by host countries in establishing pre-MG surveillance are as follows:", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Data are produced in response to some perceived need, which must be articulated in questions that determine what data are collected, and in analyses determining how they will be understood. Those choosing the questions may or may not be the end users of the data; but their interests and aims will certainly influence the utility of the data to all potential users.", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: a. What information ought to be provided? This will usually include the following elements: the reasons for doing research, details about who is doing the research, why the potential participant is being asked to be involved, details about what any intervention might involve and any on-going commitments of participation, details about anticipated risks and benefits, the fact that participants are free to refuse or withdraw, that any findings will be communicated back to the participants etc. The information given should be proportionate to any risks, but this does not mean that the higher the risk, the more information ought to", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: In middle-and higher-income countries, subnational data collection is part of the routine function of health systems funded out of routine government spending. In low-income countries they may be externally funded through international survey programmes such as the Demographic and Health Surveys or the Multi-Indicator Cluster Surveys. These surveys, like routine data collection, are generally carried out by government staff. This creates an institutional imperative to use the data: they are locally owned, produced by colleagues who may be directly involved in communicating results and who can help explain anomalies in the data and their meaning in the specific local situation" ]

[ [ "1a", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust" ], [ "1b", "Passage: Data are produced in response to some perceived need, which must be articulated in questions that determine what data are collected, and in analyses determining how they will be understood." ], [ "1c", "Those choosing the questions may or may not be the end users of the data; but their interests and aims will certainly influence the utility of the data to all potential users." ] ]

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

[ "Title: Assessment of Temporary Community-Based Health Care Facilities During Arbaeenia Mass Gathering at Karbala, Iraq: Cross-Sectional Survey Study\nPassage: Any new systems should be in place for a sufficient length of time prior to the MG to allow baselines to be determined, to assess the effectiveness of collection, analysis and interpretation of the data, and to allow the persons involved to become comfortable with the system. Key questions that must be asked by host countries in establishing pre-MG surveillance are as follows:", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Data are produced in response to some perceived need, which must be articulated in questions that determine what data are collected, and in analyses determining how they will be understood. Those choosing the questions may or may not be the end users of the data; but their interests and aims will certainly influence the utility of the data to all potential users.", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: a. What information ought to be provided? This will usually include the following elements: the reasons for doing research, details about who is doing the research, why the potential participant is being asked to be involved, details about what any intervention might involve and any on-going commitments of participation, details about anticipated risks and benefits, the fact that participants are free to refuse or withdraw, that any findings will be communicated back to the participants etc. The information given should be proportionate to any risks, but this does not mean that the higher the risk, the more information ought to", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: In middle-and higher-income countries, subnational data collection is part of the routine function of health systems funded out of routine government spending. In low-income countries they may be externally funded through international survey programmes such as the Demographic and Health Surveys or the Multi-Indicator Cluster Surveys. These surveys, like routine data collection, are generally carried out by government staff. This creates an institutional imperative to use the data: they are locally owned, produced by colleagues who may be directly involved in communicating results and who can help explain anomalies in the data and their meaning in the specific local situation" ]

[ [ "2a", "Title: Innovations in research ethics governance in humanitarian settings Passage: a." ], [ "2b", "What information ought to be provided?" ], [ "2c", "This will usually include the following elements: the reasons for doing research, details about who is doing the research, why the potential participant is being asked to be involved, details about what any intervention might involve and any on-going commitments of participation, details about anticipated risks and benefits, the fact that participants are free to refuse or withdraw, that any findings will be communicated back to the participants etc. The information given should be proportionate to any risks, but this does not mean that the higher the risk, the more information ought to" ] ]

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

[ "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In human cells 300 copies of the rRNA genes are arranged in repeated arrays located in nucleolar organizer regions on the short arms of the acrocentric chromosomes . Pol I transcribes rDNA to produce the 47S rRNA, which is the precursor of the mature 28S, 5.8S, and 18S rRNAs. Together with the 5S rRNA transcribed by Pol III in the nucleoplasm, these rRNAs form the nucleic acid backbone of the ribosome. The other major components of the ribosome are the~78 ribosomal proteins , whose genes are transcribed by Pol II, and are assembled with the rRNAs to form functional ribosomes", "Title: Nucleolus: the fascinating nuclear body\nPassage: The nucleolus is the ribosome factory of the cell. In the nucleolus rDNAs are transcribed, the 47S precursor ribosomal RNAs are cleaved, processed and assembled with the 80 ribosomal proteins and the 5S RNA to form the 40S and 60S ribosomal subunits . This complex series of maturation and processing events, presently better characterized in yeast than in higher eukaryotes is under the control of about 150 small nucleolar RNAs and 2 large RNP complexes: the small subunit processome containing the U3 snoR-NAs and 40 proteins or Utps required for the 40S ribosomal subunit, and the large subunit processome required", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: The nucleolus is the subnuclear site of ribosome biogenesis and its formation around active NORs requires ongoing rDNA transcription. The structure of nucleoli is highly dynamic and is tightly coordinated with cell cycle progression. Nucleoli disassemble at the onset of mitosis coinciding with inactivation of Pol I transcription and reassemble during telophase as rDNA transcription is reinitiated. The rate of rRNA gene transcription reaches a maximum in S-and G2 phases, is halted at the onset of mitosis and slowly reactivated as cell enter G1 . Cell cycle mediated regulation of rDNA transcription is facilitated by post-translational modifications of components of", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: nucleolar ribonucleoproteins necessary for the first steps of rRNA processing, whereas the late steps of rRNA processing and assembly of the small and large ribosome subunits take place in the GCs ." ]

[ [ "0a", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease" ], [ "0b", "Passage: In human cells 300 copies of the rRNA genes are arranged in repeated arrays located in nucleolar organizer regions on the short arms of the acrocentric chromosomes ." ], [ "0c", "Pol I transcribes rDNA to produce the 47S rRNA, which is the precursor of the mature 28S, 5.8S, and 18S rRNAs." ], [ "0d", "Together with the 5S rRNA transcribed by Pol III in the nucleoplasm, these rRNAs form the nucleic acid backbone of the ribosome." ], [ "0e", "The other major components of the ribosome are the~78 ribosomal proteins , whose genes are transcribed by Pol II, and are assembled with the rRNAs to form functional ribosomes" ] ]

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

[ "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In human cells 300 copies of the rRNA genes are arranged in repeated arrays located in nucleolar organizer regions on the short arms of the acrocentric chromosomes . Pol I transcribes rDNA to produce the 47S rRNA, which is the precursor of the mature 28S, 5.8S, and 18S rRNAs. Together with the 5S rRNA transcribed by Pol III in the nucleoplasm, these rRNAs form the nucleic acid backbone of the ribosome. The other major components of the ribosome are the~78 ribosomal proteins , whose genes are transcribed by Pol II, and are assembled with the rRNAs to form functional ribosomes", "Title: Nucleolus: the fascinating nuclear body\nPassage: The nucleolus is the ribosome factory of the cell. In the nucleolus rDNAs are transcribed, the 47S precursor ribosomal RNAs are cleaved, processed and assembled with the 80 ribosomal proteins and the 5S RNA to form the 40S and 60S ribosomal subunits . This complex series of maturation and processing events, presently better characterized in yeast than in higher eukaryotes is under the control of about 150 small nucleolar RNAs and 2 large RNP complexes: the small subunit processome containing the U3 snoR-NAs and 40 proteins or Utps required for the 40S ribosomal subunit, and the large subunit processome required", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: The nucleolus is the subnuclear site of ribosome biogenesis and its formation around active NORs requires ongoing rDNA transcription. The structure of nucleoli is highly dynamic and is tightly coordinated with cell cycle progression. Nucleoli disassemble at the onset of mitosis coinciding with inactivation of Pol I transcription and reassemble during telophase as rDNA transcription is reinitiated. The rate of rRNA gene transcription reaches a maximum in S-and G2 phases, is halted at the onset of mitosis and slowly reactivated as cell enter G1 . Cell cycle mediated regulation of rDNA transcription is facilitated by post-translational modifications of components of", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: nucleolar ribonucleoproteins necessary for the first steps of rRNA processing, whereas the late steps of rRNA processing and assembly of the small and large ribosome subunits take place in the GCs ." ]

[ [ "1a", "Title: Nucleolus: the fascinating nuclear body" ], [ "1b", "Passage: The nucleolus is the ribosome factory of the cell." ], [ "1c", "In the nucleolus rDNAs are transcribed, the 47S precursor ribosomal RNAs are cleaved, processed and assembled with the 80 ribosomal proteins and the 5S RNA to form the 40S and 60S ribosomal subunits ." ], [ "1d", "This complex series of maturation and processing events, presently better characterized in yeast than in higher eukaryotes is under the control of about 150 small nucleolar RNAs and 2 large RNP complexes: the small subunit processome containing the U3 snoR-NAs and 40 proteins or Utps required for the 40S ribosomal subunit, and the large subunit processome required" ] ]

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

[ "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In human cells 300 copies of the rRNA genes are arranged in repeated arrays located in nucleolar organizer regions on the short arms of the acrocentric chromosomes . Pol I transcribes rDNA to produce the 47S rRNA, which is the precursor of the mature 28S, 5.8S, and 18S rRNAs. Together with the 5S rRNA transcribed by Pol III in the nucleoplasm, these rRNAs form the nucleic acid backbone of the ribosome. The other major components of the ribosome are the~78 ribosomal proteins , whose genes are transcribed by Pol II, and are assembled with the rRNAs to form functional ribosomes", "Title: Nucleolus: the fascinating nuclear body\nPassage: The nucleolus is the ribosome factory of the cell. In the nucleolus rDNAs are transcribed, the 47S precursor ribosomal RNAs are cleaved, processed and assembled with the 80 ribosomal proteins and the 5S RNA to form the 40S and 60S ribosomal subunits . This complex series of maturation and processing events, presently better characterized in yeast than in higher eukaryotes is under the control of about 150 small nucleolar RNAs and 2 large RNP complexes: the small subunit processome containing the U3 snoR-NAs and 40 proteins or Utps required for the 40S ribosomal subunit, and the large subunit processome required", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: The nucleolus is the subnuclear site of ribosome biogenesis and its formation around active NORs requires ongoing rDNA transcription. The structure of nucleoli is highly dynamic and is tightly coordinated with cell cycle progression. Nucleoli disassemble at the onset of mitosis coinciding with inactivation of Pol I transcription and reassemble during telophase as rDNA transcription is reinitiated. The rate of rRNA gene transcription reaches a maximum in S-and G2 phases, is halted at the onset of mitosis and slowly reactivated as cell enter G1 . Cell cycle mediated regulation of rDNA transcription is facilitated by post-translational modifications of components of", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: nucleolar ribonucleoproteins necessary for the first steps of rRNA processing, whereas the late steps of rRNA processing and assembly of the small and large ribosome subunits take place in the GCs ." ]

[ [ "2a", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease" ], [ "2b", "Passage: The nucleolus is the subnuclear site of ribosome biogenesis and its formation around active NORs requires ongoing rDNA transcription." ], [ "2c", "The structure of nucleoli is highly dynamic and is tightly coordinated with cell cycle progression." ], [ "2d", "Nucleoli disassemble at the onset of mitosis coinciding with inactivation of Pol I transcription and reassemble during telophase as rDNA transcription is reinitiated." ], [ "2e", "The rate of rRNA gene transcription reaches a maximum in S-and G2 phases, is halted at the onset of mitosis and slowly reactivated as cell enter G1 ." ], [ "2f", "Cell cycle mediated regulation of rDNA transcription is facilitated by post-translational modifications of components of" ] ]

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

[ "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In human cells 300 copies of the rRNA genes are arranged in repeated arrays located in nucleolar organizer regions on the short arms of the acrocentric chromosomes . Pol I transcribes rDNA to produce the 47S rRNA, which is the precursor of the mature 28S, 5.8S, and 18S rRNAs. Together with the 5S rRNA transcribed by Pol III in the nucleoplasm, these rRNAs form the nucleic acid backbone of the ribosome. The other major components of the ribosome are the~78 ribosomal proteins , whose genes are transcribed by Pol II, and are assembled with the rRNAs to form functional ribosomes", "Title: Nucleolus: the fascinating nuclear body\nPassage: The nucleolus is the ribosome factory of the cell. In the nucleolus rDNAs are transcribed, the 47S precursor ribosomal RNAs are cleaved, processed and assembled with the 80 ribosomal proteins and the 5S RNA to form the 40S and 60S ribosomal subunits . This complex series of maturation and processing events, presently better characterized in yeast than in higher eukaryotes is under the control of about 150 small nucleolar RNAs and 2 large RNP complexes: the small subunit processome containing the U3 snoR-NAs and 40 proteins or Utps required for the 40S ribosomal subunit, and the large subunit processome required", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: The nucleolus is the subnuclear site of ribosome biogenesis and its formation around active NORs requires ongoing rDNA transcription. The structure of nucleoli is highly dynamic and is tightly coordinated with cell cycle progression. Nucleoli disassemble at the onset of mitosis coinciding with inactivation of Pol I transcription and reassemble during telophase as rDNA transcription is reinitiated. The rate of rRNA gene transcription reaches a maximum in S-and G2 phases, is halted at the onset of mitosis and slowly reactivated as cell enter G1 . Cell cycle mediated regulation of rDNA transcription is facilitated by post-translational modifications of components of", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: nucleolar ribonucleoproteins necessary for the first steps of rRNA processing, whereas the late steps of rRNA processing and assembly of the small and large ribosome subunits take place in the GCs ." ]

[ [ "3a", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease" ], [ "3b", "Passage: nucleolar ribonucleoproteins necessary for the first steps of rRNA processing, whereas the late steps of rRNA processing and assembly of the small and large ribosome subunits take place in the GCs ." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: after-italian-lockdown .", "Title: Estimating the number of infections and the impact of non-\nPassage: https://edition.cnn.com/2020/03/08/europe/italy-coronavirus-lockdown-europe-intl/index.html", "Title: Estimating the number of infections and the impact of non-\nPassage: 39. CNN. Italy prohibits travel and cancels all public events in its northern region. CNN", "Title: Estimating the number of infections and the impact of non-\nPassage: Italy measures and quarantine if tested positive.41 9/3/2020" ]

[ [ "2a", "Title: Estimating the number of infections and the impact of non- Passage: 39. CNN." ], [ "2b", "Italy prohibits travel and cancels all public events in its northern region. CNN" ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: after-italian-lockdown .", "Title: Estimating the number of infections and the impact of non-\nPassage: https://edition.cnn.com/2020/03/08/europe/italy-coronavirus-lockdown-europe-intl/index.html", "Title: Estimating the number of infections and the impact of non-\nPassage: 39. CNN. Italy prohibits travel and cancels all public events in its northern region. CNN", "Title: Estimating the number of infections and the impact of non-\nPassage: Italy measures and quarantine if tested positive.41 9/3/2020" ]

[ [ "3a", "Title: Estimating the number of infections and the impact of non-" ], [ "3b", "Passage: Italy measures and quarantine if tested positive.41 9/3/2020" ] ]

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

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: After emerging in southern China in the mid-1990s, the highly pathogenic avian influenza H5N1 virus spread across east and Southeast Asia, causing unprecedented epidemics in 2003-2004 . As of 24 September 2009, the virus has caused 442 human cases, with 262 deaths worldwide 1 . Controlling the spread of H5N1 disease in poultry may contribute to the reduction of risk for humans by preventing the emergence of a viral form with efficient human-to-human transmission capable of triggering a global pandemic . Determining the factors involved in the spread of H5N1 in poultry and producing risk maps are critical to disease", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened. The HPAI H5N1 virus is now well established in the poultry population in Asia, where the virus has been able to maintain itself and spread as well as periodically re-emerge. The main pathways that have been identified for the spread of H5N1 are the migration and trade of wild birds and the transport of poultry and poultry products . However, the respective roles of these pathways at the global or national scale are still unclear . The persistence of HPAI H5N1 virus", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: The H5N1 virus may now be well established in different Southeast Asian countries. Despite the implementation of control measures, it is probable that these countries will continue to face new outbreaks in poultry. The conditions under which the virus maintains itself in the environment are not well known. It is difficult to prevent virus re-emergence in possible local persistence spots, or the periodic reintroduction of the virus . Controlling the disease within the poultry population is a critical issue for both the public health and agricultural economic systems. The restructuring of poultry production from open-housed to closed systems has started", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: in Thailand but the process will take time and considerable cooperative effort. Therefore, to limit the number and size of future outbreaks in the poultry population, the focus of efforts should be on controlling the movement of both live poultry and avian products." ]

[ [ "0a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "0b", "Passage: After emerging in southern China in the mid-1990s, the highly pathogenic avian influenza H5N1 virus spread across east and Southeast Asia, causing unprecedented epidemics in 2003-2004 ." ], [ "0c", "As of 24 September 2009, the virus has caused 442 human cases, with 262 deaths worldwide 1 ." ], [ "0d", "Controlling the spread of H5N1 disease in poultry may contribute to the reduction of risk for humans by preventing the emergence of a viral form with efficient human-to-human transmission capable of triggering a global pandemic ." ], [ "0e", "Determining the factors involved in the spread of H5N1 in poultry and producing risk maps are critical to disease" ] ]

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

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: After emerging in southern China in the mid-1990s, the highly pathogenic avian influenza H5N1 virus spread across east and Southeast Asia, causing unprecedented epidemics in 2003-2004 . As of 24 September 2009, the virus has caused 442 human cases, with 262 deaths worldwide 1 . Controlling the spread of H5N1 disease in poultry may contribute to the reduction of risk for humans by preventing the emergence of a viral form with efficient human-to-human transmission capable of triggering a global pandemic . Determining the factors involved in the spread of H5N1 in poultry and producing risk maps are critical to disease", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened. The HPAI H5N1 virus is now well established in the poultry population in Asia, where the virus has been able to maintain itself and spread as well as periodically re-emerge. The main pathways that have been identified for the spread of H5N1 are the migration and trade of wild birds and the transport of poultry and poultry products . However, the respective roles of these pathways at the global or national scale are still unclear . The persistence of HPAI H5N1 virus", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: The H5N1 virus may now be well established in different Southeast Asian countries. Despite the implementation of control measures, it is probable that these countries will continue to face new outbreaks in poultry. The conditions under which the virus maintains itself in the environment are not well known. It is difficult to prevent virus re-emergence in possible local persistence spots, or the periodic reintroduction of the virus . Controlling the disease within the poultry population is a critical issue for both the public health and agricultural economic systems. The restructuring of poultry production from open-housed to closed systems has started", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: in Thailand but the process will take time and considerable cooperative effort. Therefore, to limit the number and size of future outbreaks in the poultry population, the focus of efforts should be on controlling the movement of both live poultry and avian products." ]

[ [ "1a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "1b", "Passage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened." ], [ "1c", "The HPAI H5N1 virus is now well established in the poultry population in Asia, where the virus has been able to maintain itself and spread as well as periodically re-emerge." ], [ "1d", "The main pathways that have been identified for the spread of H5N1 are the migration and trade of wild birds and the transport of poultry and poultry products ." ], [ "1e", "However, the respective roles of these pathways at the global or national scale are still unclear ." ], [ "1f", "The persistence of HPAI H5N1 virus" ] ]

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

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: After emerging in southern China in the mid-1990s, the highly pathogenic avian influenza H5N1 virus spread across east and Southeast Asia, causing unprecedented epidemics in 2003-2004 . As of 24 September 2009, the virus has caused 442 human cases, with 262 deaths worldwide 1 . Controlling the spread of H5N1 disease in poultry may contribute to the reduction of risk for humans by preventing the emergence of a viral form with efficient human-to-human transmission capable of triggering a global pandemic . Determining the factors involved in the spread of H5N1 in poultry and producing risk maps are critical to disease", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened. The HPAI H5N1 virus is now well established in the poultry population in Asia, where the virus has been able to maintain itself and spread as well as periodically re-emerge. The main pathways that have been identified for the spread of H5N1 are the migration and trade of wild birds and the transport of poultry and poultry products . However, the respective roles of these pathways at the global or national scale are still unclear . The persistence of HPAI H5N1 virus", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: The H5N1 virus may now be well established in different Southeast Asian countries. Despite the implementation of control measures, it is probable that these countries will continue to face new outbreaks in poultry. The conditions under which the virus maintains itself in the environment are not well known. It is difficult to prevent virus re-emergence in possible local persistence spots, or the periodic reintroduction of the virus . Controlling the disease within the poultry population is a critical issue for both the public health and agricultural economic systems. The restructuring of poultry production from open-housed to closed systems has started", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: in Thailand but the process will take time and considerable cooperative effort. Therefore, to limit the number and size of future outbreaks in the poultry population, the focus of efforts should be on controlling the movement of both live poultry and avian products." ]

[ [ "2a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "2b", "Passage: The H5N1 virus may now be well established in different Southeast Asian countries." ], [ "2c", "Despite the implementation of control measures, it is probable that these countries will continue to face new outbreaks in poultry." ], [ "2d", "The conditions under which the virus maintains itself in the environment are not well known." ], [ "2e", "It is difficult to prevent virus re-emergence in possible local persistence spots, or the periodic reintroduction of the virus ." ], [ "2f", "Controlling the disease within the poultry population is a critical issue for both the public health and agricultural economic systems." ], [ "2g", "The restructuring of poultry production from open-housed to closed systems has started" ] ]

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

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: After emerging in southern China in the mid-1990s, the highly pathogenic avian influenza H5N1 virus spread across east and Southeast Asia, causing unprecedented epidemics in 2003-2004 . As of 24 September 2009, the virus has caused 442 human cases, with 262 deaths worldwide 1 . Controlling the spread of H5N1 disease in poultry may contribute to the reduction of risk for humans by preventing the emergence of a viral form with efficient human-to-human transmission capable of triggering a global pandemic . Determining the factors involved in the spread of H5N1 in poultry and producing risk maps are critical to disease", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened. The HPAI H5N1 virus is now well established in the poultry population in Asia, where the virus has been able to maintain itself and spread as well as periodically re-emerge. The main pathways that have been identified for the spread of H5N1 are the migration and trade of wild birds and the transport of poultry and poultry products . However, the respective roles of these pathways at the global or national scale are still unclear . The persistence of HPAI H5N1 virus", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: The H5N1 virus may now be well established in different Southeast Asian countries. Despite the implementation of control measures, it is probable that these countries will continue to face new outbreaks in poultry. The conditions under which the virus maintains itself in the environment are not well known. It is difficult to prevent virus re-emergence in possible local persistence spots, or the periodic reintroduction of the virus . Controlling the disease within the poultry population is a critical issue for both the public health and agricultural economic systems. The restructuring of poultry production from open-housed to closed systems has started", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: in Thailand but the process will take time and considerable cooperative effort. Therefore, to limit the number and size of future outbreaks in the poultry population, the focus of efforts should be on controlling the movement of both live poultry and avian products." ]

[ [ "3a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "3b", "Passage: in Thailand but the process will take time and considerable cooperative effort." ], [ "3c", "Therefore, to limit the number and size of future outbreaks in the poultry population, the focus of efforts should be on controlling the movement of both live poultry and avian products." ] ]

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

[ "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Text: Feline Infectious Peritonitis Virus is an enveloped virus with a nonsegmented, positive sense, single-stranded RNA genome. FIPV is grouped as feline coronavirus , under the family Coronaviridae. FCoV is divided into two biotypes, namely, Feline Enteric Coronavirus , a ubiquitous enteric biotype of FCoV, and FIPV, a virulent biotype of FCoV . The relationship between these two biotypes still remains unclear. Two hypotheses have been proposed, internal mutation theory and circulating high virulent-low virulent theory. Internal mutation theory stated that the development of FIP is due to the exposure of cat to variants of FCoV which have been mutated", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces . About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease . The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV.", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950953/", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: ORF1a/1b and 14048-14061" ]

[ [ "0a", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication" ], [ "0b", "Passage: Text: Feline Infectious Peritonitis Virus is an enveloped virus with a nonsegmented, positive sense, single-stranded RNA genome." ], [ "0c", "FIPV is grouped as feline coronavirus , under the family Coronaviridae." ], [ "0d", "FCoV is divided into two biotypes, namely, Feline Enteric Coronavirus , a ubiquitous enteric biotype of FCoV, and FIPV, a virulent biotype of FCoV ." ], [ "0e", "The relationship between these two biotypes still remains unclear." ], [ "0f", "Two hypotheses have been proposed, internal mutation theory and circulating high virulent-low virulent theory." ], [ "0g", "Internal mutation theory stated that the development of FIP is due to the exposure of cat to variants of FCoV which have been mutated" ] ]

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

[ "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Text: Feline Infectious Peritonitis Virus is an enveloped virus with a nonsegmented, positive sense, single-stranded RNA genome. FIPV is grouped as feline coronavirus , under the family Coronaviridae. FCoV is divided into two biotypes, namely, Feline Enteric Coronavirus , a ubiquitous enteric biotype of FCoV, and FIPV, a virulent biotype of FCoV . The relationship between these two biotypes still remains unclear. Two hypotheses have been proposed, internal mutation theory and circulating high virulent-low virulent theory. Internal mutation theory stated that the development of FIP is due to the exposure of cat to variants of FCoV which have been mutated", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces . About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease . The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV.", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950953/", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: ORF1a/1b and 14048-14061" ]

[ [ "1a", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication" ], [ "1b", "Passage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces ." ], [ "1c", "About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease ." ], [ "1d", "The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV." ] ]

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

[ "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Text: Feline Infectious Peritonitis Virus is an enveloped virus with a nonsegmented, positive sense, single-stranded RNA genome. FIPV is grouped as feline coronavirus , under the family Coronaviridae. FCoV is divided into two biotypes, namely, Feline Enteric Coronavirus , a ubiquitous enteric biotype of FCoV, and FIPV, a virulent biotype of FCoV . The relationship between these two biotypes still remains unclear. Two hypotheses have been proposed, internal mutation theory and circulating high virulent-low virulent theory. Internal mutation theory stated that the development of FIP is due to the exposure of cat to variants of FCoV which have been mutated", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces . About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease . The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV.", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950953/", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: ORF1a/1b and 14048-14061" ]

[ [ "3a", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication" ], [ "3b", "Passage: ORF1a/1b and 14048-14061" ] ]

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

[ "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" ] ]

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

[ "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" ]

[ [ "1a", "Title: Introducing the Outbreak Threshold in Epidemiology" ], [ "1b", "Passage: as the fact that the incubation period is around 5 days, by which point it had easily caused more secondary cases." ], [ "1c", "However, in subsequent outbreaks super-spreaders might not be infected early on, allowing more time to contain the spread." ] ]

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

[ "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" ] ]

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

[ "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" ]

[ [ "3a", "Title: Incubation periods of viral gastroenteritis: a systematic review" ], [ "3b", "Passage: Despite its importance, the incubation periods of enteric viruses are not well characterized in the medical literature." ], [ "3c", "Statements of the incubation period tend to be a single number ) or a poorly defined range )." ], [ "3d", "It is difficult to translate these statements of incubation period into the realities of prevention and control." ], [ "3e", "The single number estimate could represent the mean, median, upper limit, or some other measure of the incubation period." ], [ "3f", "The range could represent an exhaustive range of all observations, or some unspecified quantile ." ], [ "3g", "Furthermore, the strength of the evidence behind these estimates is often unclear. Statements of" ] ]

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

[ "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Another important consideration for future clinical trials is the assessment of treatment effect based on predictions of exacerbation frequency and intensity. In other words, the collection of data such as the rate of onset and resolution of an exacerbation from longitudinal studies could be used to determine probabilities of second, third, fourth, etc., exacerbation events in individual patients . The alteration of such probabilities with an experimental treatment could be a more sensitive and reliable approach for assessing treatment effect in clinical trials than recording daily changes in symptoms or medical management.", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children\nPassage: 1b. Visits were defined as an exacerbation event if the participant was treated by a physician with systemic corticosteroids in the 10 d following onset of cold symptoms; otherwise, they were defined as a cold without exacerbation . Criteria for the initiation of systemic corticosteroids were as previously specified in Inner-City Asthma Consortium trials 4 . Participants were treated with systemic corticosteroids if albuterol was needed by inhaler or nebulization for more than six individual treatments over 24 h; moderate-to-severe wheeze, cough, shortness of breath, and/or chest tightness or pain occurred for at least 5 of the preceding 7 d;", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Finally, the compatibility between the studies of COPD exacerbation that we analysed may have been limited by substantial variations in the time and location of studies. Exacerbations are more likely in summer but many studies failed to report the time of year or the time period for study implementation. Thus, seasonal effects, combined with the low incidence of exacerbations per patient, could represent an inherent bias. In addition, different institutions probably had different standards with respect to diagnosis and management of COPD exacerbations when these studies were performed. Such variations may also explain any observed inconsistencies in our findings. However,", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: well as suggested markers of the severity of the exacerbation at baseline conditions, i.e., immediately prior to, or during the exacerbation event but before the time in which the intervention of interest was investigated . Whenever such variables were measured in stable conditions, we also abstracted this information. For each study, we noted the type of definition used to define an exacerbation such as symptom-or event-based as well as the research question asked, the experimental design used, any sponsorship, and the presence or absence of data from individual study patients. Data was then further organized according to sample size and" ]

[ [ "1a", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children Passage: 1b." ], [ "1b", "Visits were defined as an exacerbation event if the participant was treated by a physician with systemic corticosteroids in the 10 d following onset of cold symptoms; otherwise, they were defined as a cold without exacerbation ." ], [ "1c", "Criteria for the initiation of systemic corticosteroids were as previously specified in Inner-City Asthma Consortium trials 4 ." ], [ "1d", "Participants were treated with systemic corticosteroids if albuterol was needed by inhaler or nebulization for more than six individual treatments over 24 h; moderate-to-severe wheeze, cough, shortness of breath, and/or chest tightness or pain occurred for at least 5 of the preceding 7 d;" ] ]

[ "1b", "1d" ]

[ "Title: Assay Challenges for Emerging Infectious Diseases: The Zika Experience\nPassage: If assay performance consistency and quality is not demonstrated, the validity of clinical study results may be questioned.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: per experiment, two plates for detecting inhibition of EBOV, and one mock plate for determining drug cytotoxicity. After 1 h of predilution and transport to the BSL4 laboratory, 50 μl of virus at the desired MOI was added to cells. At 48, 72 or 96 hpi, assay plates were fixed at final concentration of 10% NBF for 24 h before transferring to a BSL-2 lab for staining. Infected cells were detected as described above. To further confirm the accuracy of assays with high background, chemiluminescence assay was performed afterwards.", "Title: Cas12a-Based On-Site and Rapid Nucleic Acid Detection of African Swine Fever\nPassage: The gray values of the test bands in the CORDS assays were measured and recorded. A positive result was recorded when the concentration of the dsDNA target was 1 × 10 −15 M, which further confirmed the assay's sensitivity . The 13 NA samples from typical porcine viruses were tested with this assay, all of which were negative. Thus, no cross-reactions were observed .", "Title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis\nPassage: For further analysis of the 40 specimens that yielded discrepant results with the developed STI-MS assay and the confirmatory tests, ultrasensitive digital PCR was performed. Among these 40 STI-MS-positive and confirmatory test-negative samples, 31 were confirmed as positive by a digital PCR assay, whereas 9 remained unverified after the resolution of the discordant results, including 4 single organism samples and 5 multiple agent combination samples . The results of the confirmatory tests and arbitration testing revealed that all retested specimens that were verified as positive by either of the tests were indeed accurate positive, irrespective of their classification as negative" ]

[ [ "1a", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs" ], [ "1b", "Passage: per experiment, two plates for detecting inhibition of EBOV, and one mock plate for determining drug cytotoxicity." ], [ "1c", "After 1 h of predilution and transport to the BSL4 laboratory, 50 μl of virus at the desired MOI was added to cells." ], [ "1d", "At 48, 72 or 96 hpi, assay plates were fixed at final concentration of 10% NBF for 24 h before transferring to a BSL-2 lab for staining." ], [ "1e", "Infected cells were detected as described above." ], [ "1f", "To further confirm the accuracy of assays with high background, chemiluminescence assay was performed afterwards." ] ]

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

[ "Title: Assay Challenges for Emerging Infectious Diseases: The Zika Experience\nPassage: If assay performance consistency and quality is not demonstrated, the validity of clinical study results may be questioned.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: per experiment, two plates for detecting inhibition of EBOV, and one mock plate for determining drug cytotoxicity. After 1 h of predilution and transport to the BSL4 laboratory, 50 μl of virus at the desired MOI was added to cells. At 48, 72 or 96 hpi, assay plates were fixed at final concentration of 10% NBF for 24 h before transferring to a BSL-2 lab for staining. Infected cells were detected as described above. To further confirm the accuracy of assays with high background, chemiluminescence assay was performed afterwards.", "Title: Cas12a-Based On-Site and Rapid Nucleic Acid Detection of African Swine Fever\nPassage: The gray values of the test bands in the CORDS assays were measured and recorded. A positive result was recorded when the concentration of the dsDNA target was 1 × 10 −15 M, which further confirmed the assay's sensitivity . The 13 NA samples from typical porcine viruses were tested with this assay, all of which were negative. Thus, no cross-reactions were observed .", "Title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis\nPassage: For further analysis of the 40 specimens that yielded discrepant results with the developed STI-MS assay and the confirmatory tests, ultrasensitive digital PCR was performed. Among these 40 STI-MS-positive and confirmatory test-negative samples, 31 were confirmed as positive by a digital PCR assay, whereas 9 remained unverified after the resolution of the discordant results, including 4 single organism samples and 5 multiple agent combination samples . The results of the confirmatory tests and arbitration testing revealed that all retested specimens that were verified as positive by either of the tests were indeed accurate positive, irrespective of their classification as negative" ]

[ [ "2a", "Title: Cas12a-Based On-Site and Rapid Nucleic Acid Detection of African Swine Fever" ], [ "2b", "Passage: The gray values of the test bands in the CORDS assays were measured and recorded." ], [ "2c", "A positive result was recorded when the concentration of the dsDNA target was 1 × 10 −15 M, which further confirmed the assay's sensitivity ." ], [ "2d", "The 13 NA samples from typical porcine viruses were tested with this assay, all of which were negative." ], [ "2e", "Thus, no cross-reactions were observed ." ] ]

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

[ "Title: Assay Challenges for Emerging Infectious Diseases: The Zika Experience\nPassage: If assay performance consistency and quality is not demonstrated, the validity of clinical study results may be questioned.", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: per experiment, two plates for detecting inhibition of EBOV, and one mock plate for determining drug cytotoxicity. After 1 h of predilution and transport to the BSL4 laboratory, 50 μl of virus at the desired MOI was added to cells. At 48, 72 or 96 hpi, assay plates were fixed at final concentration of 10% NBF for 24 h before transferring to a BSL-2 lab for staining. Infected cells were detected as described above. To further confirm the accuracy of assays with high background, chemiluminescence assay was performed afterwards.", "Title: Cas12a-Based On-Site and Rapid Nucleic Acid Detection of African Swine Fever\nPassage: The gray values of the test bands in the CORDS assays were measured and recorded. A positive result was recorded when the concentration of the dsDNA target was 1 × 10 −15 M, which further confirmed the assay's sensitivity . The 13 NA samples from typical porcine viruses were tested with this assay, all of which were negative. Thus, no cross-reactions were observed .", "Title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis\nPassage: For further analysis of the 40 specimens that yielded discrepant results with the developed STI-MS assay and the confirmatory tests, ultrasensitive digital PCR was performed. Among these 40 STI-MS-positive and confirmatory test-negative samples, 31 were confirmed as positive by a digital PCR assay, whereas 9 remained unverified after the resolution of the discordant results, including 4 single organism samples and 5 multiple agent combination samples . The results of the confirmatory tests and arbitration testing revealed that all retested specimens that were verified as positive by either of the tests were indeed accurate positive, irrespective of their classification as negative" ]

[ [ "3a", "Title: Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis" ], [ "3b", "Passage: For further analysis of the 40 specimens that yielded discrepant results with the developed STI-MS assay and the confirmatory tests, ultrasensitive digital PCR was performed." ], [ "3c", "Among these 40 STI-MS-positive and confirmatory test-negative samples, 31 were confirmed as positive by a digital PCR assay, whereas 9 remained unverified after the resolution of the discordant results, including 4 single organism samples and 5 multiple agent combination samples ." ], [ "3d", "The results of the confirmatory tests and arbitration testing revealed that all retested specimens that were verified as positive by either of the tests were indeed accurate positive, irrespective of their classification as negative" ] ]

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

[ "Title: Chinese journals: a guide for epidemiologists\nPassage: results. However, subsequent studies found little evidence supporting this assertion. Pham et al. found that language bias led to an under-estimation of the protective effect of intervention in RCTs in complementary and alternative medicine systematic reviews but not in that of conventional medicine .", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: We observed generally low adherence to interventions. More than one in four household contacts in the face mask group did not wear a surgical mask at all during the follow-up period. Adherence to the face mask intervention was higher in the index subjects, likely due to their intention to reduce the probability of infecting other household members and possibly because of the recent memory of SARS in 2003, during which the majority of the general public reported that they wore face masks in public, and most engaged in numerous protective practices . However more than one in four index cases", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: In terms of adherence, 45% of index subjects in the face mask arm reported wearing a mask often or always during the follow-up period, compared to 30% and 28% in the control and hand hygiene arms, respectively. The higher reported compliance in index subjects in the face mask group compared to household contacts was validated when at the final home visits the index subjects had used a median of 12 masks whereas household contacts had only used a median of 6 ; these include the mask worn and then disposed of by each individual as part of the demonstration and", "Title: The Trojan Chicken Study, Minnesota\nPassage: Some of our study findings were unanticipated. We expected contamination proportions to vary by age, gender, and role because we expected these factors to affect the amount of contact with birds and handwashing behavior. However the rates did not vary by these variables. This finding could be due to the study's limited power to detect such differences. If the differences between those exposed and those unexposed were statistically significant , they might be consistent with studies that suggest that animal handlers practice better hygiene compared to nonhandlers in the same environment. Alternatively, animal handlers may engage in other behavior that" ]

[ [ "3a", "Title: The Trojan Chicken Study, Minnesota" ], [ "3b", "Passage: Some of our study findings were unanticipated." ], [ "3c", "We expected contamination proportions to vary by age, gender, and role because we expected these factors to affect the amount of contact with birds and handwashing behavior." ], [ "3d", "However the rates did not vary by these variables." ], [ "3e", "This finding could be due to the study's limited power to detect such differences." ], [ "3f", "If the differences between those exposed and those unexposed were statistically significant , they might be consistent with studies that suggest that animal handlers practice better hygiene compared to nonhandlers in the same environment." ], [ "3g", "Alternatively, animal handlers may engage in other behavior that" ] ]

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

[ "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Filamentous bacteriophages used in phage display techniques are viruses that belong to the Inoviridae family. There are fewer of these filamentous phages in this genus compared with tailed phages. Inovirus virions are 7 mm in diameter, contain circular DNA enclosed in a protein capsid, and infect both Gram negative and positive bacteria. They do not lyse host cells, instead, they are packed and extrude at the surface .", "Title: Architectural Insight into Inovirus-Associated Vectors (IAVs) and Development of IAV-Based Vaccines Inducing Humoral and Cellular Responses: Implications in HIV-1 Vaccines\nPassage: Text: Filamentous bacterial viruses are a group of thread-like viruses containing single-stranded DNA genomes. Collectively, they constitute the genus Inovirus in the family Inoviridae, the terms deriving from the Greek word Ίνα for filament , and they are commonly called filamentous bacteriophages. There are over 50 different known individual species of filamentous viruses; the majority of them capable of infecting Gram-negative bacteria. The complex interaction between filamentous phages and their bacterial hosts is specified by receptor organelles that are usually encoded by transmissible plasmids . One of the most intriguing features of inoviruses is that they are assembled at the", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Long before the identification of filamentous phage, other types of bacteriophage were already being used for antibacterial therapy in the former Soviet Union and Eastern Europe . The filamentous phage, with its nonlytic life cycle, has less obvious clinical uses, despite the fact that the host specificity of Inovirus and Plectrovirus includes many pathogens of medical importance, including Salmonella, E. coli, Shigella, Pseudomonas, Clostridium, and Mycoplasma species.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Long before the identification of filamentous phage, other types of bacteriophage were already being used for antibacterial therapy in the former Soviet Union and Eastern Europe . The filamentous phage, with its nonlytic life cycle, has less obvious clinical uses, despite the fact that the host specificity of Inovirus and Plectrovirus includes many pathogens of medical importance, including Salmonella, E. coli, Shigella, Pseudomonas, Clostridium, and Mycoplasma species." ]

[ [ "0a", "Title: Antibody Engineering for Pursuing a Healthier Future" ], [ "0b", "Passage: Filamentous bacteriophages used in phage display techniques are viruses that belong to the Inoviridae family." ], [ "0c", "There are fewer of these filamentous phages in this genus compared with tailed phages." ], [ "0d", "Inovirus virions are 7 mm in diameter, contain circular DNA enclosed in a protein capsid, and infect both Gram negative and positive bacteria." ], [ "0e", "They do not lyse host cells, instead, they are packed and extrude at the surface ." ] ]

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

[ "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Filamentous bacteriophages used in phage display techniques are viruses that belong to the Inoviridae family. There are fewer of these filamentous phages in this genus compared with tailed phages. Inovirus virions are 7 mm in diameter, contain circular DNA enclosed in a protein capsid, and infect both Gram negative and positive bacteria. They do not lyse host cells, instead, they are packed and extrude at the surface .", "Title: Architectural Insight into Inovirus-Associated Vectors (IAVs) and Development of IAV-Based Vaccines Inducing Humoral and Cellular Responses: Implications in HIV-1 Vaccines\nPassage: Text: Filamentous bacterial viruses are a group of thread-like viruses containing single-stranded DNA genomes. Collectively, they constitute the genus Inovirus in the family Inoviridae, the terms deriving from the Greek word Ίνα for filament , and they are commonly called filamentous bacteriophages. There are over 50 different known individual species of filamentous viruses; the majority of them capable of infecting Gram-negative bacteria. The complex interaction between filamentous phages and their bacterial hosts is specified by receptor organelles that are usually encoded by transmissible plasmids . One of the most intriguing features of inoviruses is that they are assembled at the", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Long before the identification of filamentous phage, other types of bacteriophage were already being used for antibacterial therapy in the former Soviet Union and Eastern Europe . The filamentous phage, with its nonlytic life cycle, has less obvious clinical uses, despite the fact that the host specificity of Inovirus and Plectrovirus includes many pathogens of medical importance, including Salmonella, E. coli, Shigella, Pseudomonas, Clostridium, and Mycoplasma species.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Long before the identification of filamentous phage, other types of bacteriophage were already being used for antibacterial therapy in the former Soviet Union and Eastern Europe . The filamentous phage, with its nonlytic life cycle, has less obvious clinical uses, despite the fact that the host specificity of Inovirus and Plectrovirus includes many pathogens of medical importance, including Salmonella, E. coli, Shigella, Pseudomonas, Clostridium, and Mycoplasma species." ]

[ [ "1a", "Title: Architectural Insight into Inovirus-Associated Vectors (IAVs) and Development of IAV-Based Vaccines Inducing Humoral and Cellular Responses: Implications in HIV-1 Vaccines" ], [ "1b", "Passage: Text: Filamentous bacterial viruses are a group of thread-like viruses containing single-stranded DNA genomes." ], [ "1c", "Collectively, they constitute the genus Inovirus in the family Inoviridae, the terms deriving from the Greek word Ίνα for filament , and they are commonly called filamentous bacteriophages." ], [ "1d", "There are over 50 different known individual species of filamentous viruses; the majority of them capable of infecting Gram-negative bacteria." ], [ "1e", "The complex interaction between filamentous phages and their bacterial hosts is specified by receptor organelles that are usually encoded by transmissible plasmids ." ], [ "1f", "One of the most intriguing features of inoviruses is that they are assembled at the" ] ]

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