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[ "Title: Targeting the IL-22/IL-22BP axis enhances tight junctions and reduces inflammation during influenza infection\nPassage: To measure lung leak, the Evan's blue assay was used. Briefly, mice were injected intravenously with a 0.1% sterile solution of Evan's blue dye 30 min prior to sacrifice. The mouse paws and nose turning blue after injection verified dissemination of the dye visually. Evan's blue was measured in the BAL by measuring absorbance at 620 nm on a spectrophotometer.", "Title: Novel protein chip for the detection of antibodies against infectious bronchitis virus\nPassage: demonstrated that when the positive serum was diluted 1:1000, the spot still turned blue . .", "Title: Visible Light-Responsive Platinum-Containing Titania Nanoparticle-Mediated Photocatalysis Induces Nucleotide Insertion, Deletion and Substitution Mutations\nPassage: The blue-white screen was originally developed as a screening technique for rapid and convenient recombinant bacteria detection in vector-based molecular cloning experiments . The method is based on the principle of α-complementation of the β-galactosidase gene lacZ; therefore, the plasmid should contain lacZα , whereas the E. coli strain must contain mutated lacZ with a deleted sequence . Here, the plasmid was transformed into competent host E. coli XL1-blue cells , which were then plated on LB agar plates containing 100 µg/mL ampicillin, 50 g/mL X-gal and 0.1 mM isopropyl β-D-1-thiogalactopyranoside . These plates were then incubated overnight at 37", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children\nPassage: are colored red or blue , with color intensity corresponding to fold change. Modules whose expression was not significantly different are shown as points rather than squares to simplify the diagram." ]

[ [ "1a", "Title: Novel protein chip for the detection of antibodies against infectious bronchitis virus" ], [ "1b", "Passage: demonstrated that when the positive serum was diluted 1:1000, the spot still turned blue . ." ] ]

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

[ "Title: Targeting the IL-22/IL-22BP axis enhances tight junctions and reduces inflammation during influenza infection\nPassage: To measure lung leak, the Evan's blue assay was used. Briefly, mice were injected intravenously with a 0.1% sterile solution of Evan's blue dye 30 min prior to sacrifice. The mouse paws and nose turning blue after injection verified dissemination of the dye visually. Evan's blue was measured in the BAL by measuring absorbance at 620 nm on a spectrophotometer.", "Title: Novel protein chip for the detection of antibodies against infectious bronchitis virus\nPassage: demonstrated that when the positive serum was diluted 1:1000, the spot still turned blue . .", "Title: Visible Light-Responsive Platinum-Containing Titania Nanoparticle-Mediated Photocatalysis Induces Nucleotide Insertion, Deletion and Substitution Mutations\nPassage: The blue-white screen was originally developed as a screening technique for rapid and convenient recombinant bacteria detection in vector-based molecular cloning experiments . The method is based on the principle of α-complementation of the β-galactosidase gene lacZ; therefore, the plasmid should contain lacZα , whereas the E. coli strain must contain mutated lacZ with a deleted sequence . Here, the plasmid was transformed into competent host E. coli XL1-blue cells , which were then plated on LB agar plates containing 100 µg/mL ampicillin, 50 g/mL X-gal and 0.1 mM isopropyl β-D-1-thiogalactopyranoside . These plates were then incubated overnight at 37", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children\nPassage: are colored red or blue , with color intensity corresponding to fold change. Modules whose expression was not significantly different are shown as points rather than squares to simplify the diagram." ]

[ [ "2a", "Title: Visible Light-Responsive Platinum-Containing Titania Nanoparticle-Mediated Photocatalysis Induces Nucleotide Insertion, Deletion and Substitution Mutations" ], [ "2b", "Passage: The blue-white screen was originally developed as a screening technique for rapid and convenient recombinant bacteria detection in vector-based molecular cloning experiments ." ], [ "2c", "The method is based on the principle of α-complementation of the β-galactosidase gene lacZ; therefore, the plasmid should contain lacZα , whereas the E. coli strain must contain mutated lacZ with a deleted sequence ." ], [ "2d", "Here, the plasmid was transformed into competent host E. coli XL1-blue cells , which were then plated on LB agar plates containing 100 µg/mL ampicillin, 50 g/mL X-gal and 0.1 mM isopropyl β-D-1-thiogalactopyranoside ." ], [ "2e", "These plates were then incubated overnight at 37" ] ]

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

[ "Title: Targeting the IL-22/IL-22BP axis enhances tight junctions and reduces inflammation during influenza infection\nPassage: To measure lung leak, the Evan's blue assay was used. Briefly, mice were injected intravenously with a 0.1% sterile solution of Evan's blue dye 30 min prior to sacrifice. The mouse paws and nose turning blue after injection verified dissemination of the dye visually. Evan's blue was measured in the BAL by measuring absorbance at 620 nm on a spectrophotometer.", "Title: Novel protein chip for the detection of antibodies against infectious bronchitis virus\nPassage: demonstrated that when the positive serum was diluted 1:1000, the spot still turned blue . .", "Title: Visible Light-Responsive Platinum-Containing Titania Nanoparticle-Mediated Photocatalysis Induces Nucleotide Insertion, Deletion and Substitution Mutations\nPassage: The blue-white screen was originally developed as a screening technique for rapid and convenient recombinant bacteria detection in vector-based molecular cloning experiments . The method is based on the principle of α-complementation of the β-galactosidase gene lacZ; therefore, the plasmid should contain lacZα , whereas the E. coli strain must contain mutated lacZ with a deleted sequence . Here, the plasmid was transformed into competent host E. coli XL1-blue cells , which were then plated on LB agar plates containing 100 µg/mL ampicillin, 50 g/mL X-gal and 0.1 mM isopropyl β-D-1-thiogalactopyranoside . These plates were then incubated overnight at 37", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children\nPassage: are colored red or blue , with color intensity corresponding to fold change. Modules whose expression was not significantly different are shown as points rather than squares to simplify the diagram." ]

[ [ "3a", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children" ], [ "3b", "Passage: are colored red or blue , with color intensity corresponding to fold change." ], [ "3c", "Modules whose expression was not significantly different are shown as points rather than squares to simplify the diagram." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: As RV, RSV, and IFV were the most frequently studied viruses in chronic airway inflammatory diseases, most of the viruses listed are predominantly these viruses. However, the mechanisms stated here may also be applicable to other viruses but may not be listed as they were not implicated in the context of chronic airway inflammatory diseases exacerbation .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: exacerbations but to a much lesser extent . More recently, other viruses including bocavirus , human metapneumovirus , certain coronavirus strains, a specific enterovirus strain EV-D68, human cytomegalovirus and herpes simplex virus have been reported as contributing to acute exacerbations . The common feature these viruses share is that they can infect both the upper and/or lower airway, further increasing the inflammatory conditions in the diseased airway .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Despite being a major cause of exacerbation, reports linking respiratory viruses to acute exacerbations only start to emerge in the late 1950s ; with bacterial infections previously considered as the likely culprit for acute exacerbation . However, with the advent of PCR technology, more viruses were recovered during acute exacerbations events and reports implicating their role emerged in the late 1980s . Rhinovirus and respiratory syncytial virus are the predominant viruses linked to the development and exacerbation of chronic airway inflammatory diseases . Other viruses such as parainfluenza virus , influenza virus and adenovirus have also been implicated in acute", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases." ]

[ [ "0a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "0b", "Passage: As RV, RSV, and IFV were the most frequently studied viruses in chronic airway inflammatory diseases, most of the viruses listed are predominantly these viruses." ], [ "0c", "However, the mechanisms stated here may also be applicable to other viruses but may not be listed as they were not implicated in the context of chronic airway inflammatory diseases exacerbation ." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: As RV, RSV, and IFV were the most frequently studied viruses in chronic airway inflammatory diseases, most of the viruses listed are predominantly these viruses. However, the mechanisms stated here may also be applicable to other viruses but may not be listed as they were not implicated in the context of chronic airway inflammatory diseases exacerbation .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: exacerbations but to a much lesser extent . More recently, other viruses including bocavirus , human metapneumovirus , certain coronavirus strains, a specific enterovirus strain EV-D68, human cytomegalovirus and herpes simplex virus have been reported as contributing to acute exacerbations . The common feature these viruses share is that they can infect both the upper and/or lower airway, further increasing the inflammatory conditions in the diseased airway .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Despite being a major cause of exacerbation, reports linking respiratory viruses to acute exacerbations only start to emerge in the late 1950s ; with bacterial infections previously considered as the likely culprit for acute exacerbation . However, with the advent of PCR technology, more viruses were recovered during acute exacerbations events and reports implicating their role emerged in the late 1980s . Rhinovirus and respiratory syncytial virus are the predominant viruses linked to the development and exacerbation of chronic airway inflammatory diseases . Other viruses such as parainfluenza virus , influenza virus and adenovirus have also been implicated in acute", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases." ]

[ [ "1a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "1b", "Passage: exacerbations but to a much lesser extent ." ], [ "1c", "More recently, other viruses including bocavirus , human metapneumovirus , certain coronavirus strains, a specific enterovirus strain EV-D68, human cytomegalovirus and herpes simplex virus have been reported as contributing to acute exacerbations ." ], [ "1d", "The common feature these viruses share is that they can infect both the upper and/or lower airway, further increasing the inflammatory conditions in the diseased airway ." ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: As RV, RSV, and IFV were the most frequently studied viruses in chronic airway inflammatory diseases, most of the viruses listed are predominantly these viruses. However, the mechanisms stated here may also be applicable to other viruses but may not be listed as they were not implicated in the context of chronic airway inflammatory diseases exacerbation .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: exacerbations but to a much lesser extent . More recently, other viruses including bocavirus , human metapneumovirus , certain coronavirus strains, a specific enterovirus strain EV-D68, human cytomegalovirus and herpes simplex virus have been reported as contributing to acute exacerbations . The common feature these viruses share is that they can infect both the upper and/or lower airway, further increasing the inflammatory conditions in the diseased airway .", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Despite being a major cause of exacerbation, reports linking respiratory viruses to acute exacerbations only start to emerge in the late 1950s ; with bacterial infections previously considered as the likely culprit for acute exacerbation . However, with the advent of PCR technology, more viruses were recovered during acute exacerbations events and reports implicating their role emerged in the late 1980s . Rhinovirus and respiratory syncytial virus are the predominant viruses linked to the development and exacerbation of chronic airway inflammatory diseases . Other viruses such as parainfluenza virus , influenza virus and adenovirus have also been implicated in acute", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases." ]

[ [ "2a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "2b", "Passage: Despite being a major cause of exacerbation, reports linking respiratory viruses to acute exacerbations only start to emerge in the late 1950s ; with bacterial infections previously considered as the likely culprit for acute exacerbation ." ], [ "2c", "However, with the advent of PCR technology, more viruses were recovered during acute exacerbations events and reports implicating their role emerged in the late 1980s ." ], [ "2d", "Rhinovirus and respiratory syncytial virus are the predominant viruses linked to the development and exacerbation of chronic airway inflammatory diseases ." ], [ "2e", "Other viruses such as parainfluenza virus , influenza virus and adenovirus have also been implicated in acute" ] ]

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

[ "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: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia," ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: or worse, and secondary bacterial infections have been reported ." ], [ "1c", "Disease can progress to acute respiratory distress syndrome and multiorgan system failure ." ], [ "1d", "MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported ." ], [ "1e", "General supportive care is key to managing severe cases . Children under" ] ]

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

[ "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: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia," ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: but close and lengthy exposure appears to be a requirement." ], [ "2c", "The KSA is the focal point of MERS, with the majority of human cases." ], [ "2d", "In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected." ], [ "2e", "However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms." ], [ "2f", "Older males most obviously suffer severe disease and MERS patients often have comorbidities." ], [ "2g", "Compared to severe acute" ] ]

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

[ "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: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia," ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: a case definition released by the KSA Ministry of Health in June 2015 ." ], [ "3c", "The KSA has been the source of 79 % of human cases." ], [ "3d", "Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions ." ], [ "3e", "Interestingly in June 2015, an outbreak in South Korea followed a similar distribution ." ], [ "3f", "Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia ." ], [ "3g", "Patients often present to a hospital with pneumonia," ] ]

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

[ "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: Text: D espite early reports , the premise that hand-wash sink traps can act as reservoirs of bacteria that cause nosocomial infections has been frequently overlooked. There has recently been an alarming increase in sink-related outbreaks worldwide, with many reports establishing an observational link . A sink often operates as an open conduit to wastewater in a patient care area that is often in the same room as the patient.", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: from a P-trap reservoir to a vulnerable hospitalized patient. IMPORTANCE Many recent reports demonstrate that sink drain pipes become colonized with highly consequential multidrug-resistant bacteria, which then results in hospital-acquired infections. However, the mechanism of dispersal of bacteria from the sink to patients has not been fully elucidated. Through establishment of a unique sink gallery, this work found that a staged mode of transmission involving biofilm growth from the lower pipe to the sink strainer and subsequent splatter to the bowl and surrounding area occurs rather than splatter directly from the water in the lower pipe. We have also demonstrated", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: In summary, this work for the first time better models the mechanisms of spread of multidrug-resistant pathogens arising from the sink drain and infecting patients. Droplet dispersion from the P-trap does not happen directly. Rather it is a multistage process: dispersal originates from the strainer and/or the bowl after growth of the biofilm up from the microbial reservoir of the P-trap. We also demonstrate sink-to-sink transmission via a common sanitary pipe. This work could have implications for patient safety, infection control, and interventions as well as the design of future hospital plumbing systems to eliminate this mode of transmission to", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: Health care establishments often invest in desperate interventions to deal with nosocomial outbreaks. The preferred method for addressing most of the environmentrelated transmission is to employ enhanced cleaning using chemical and physical agents . Unfortunately, routine approaches are inefficient in completely eliminating drug-resistant Gammaproteobacteria in an inaccessible microbiologically active area such as a sink trap . The wet, humid, and relatively protected environment in a sink trap favors the formation of rich stable microbial communities . These communities will be exposed to liquids and waste that are discarded in a sink and may include antimicrobials, discarded beverages, soap, presumably pathogenic" ]

[ [ "1a", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs" ], [ "1b", "Passage: from a P-trap reservoir to a vulnerable hospitalized patient." ], [ "1c", "IMPORTANCE Many recent reports demonstrate that sink drain pipes become colonized with highly consequential multidrug-resistant bacteria, which then results in hospital-acquired infections." ], [ "1d", "However, the mechanism of dispersal of bacteria from the sink to patients has not been fully elucidated." ], [ "1e", "Through establishment of a unique sink gallery, this work found that a staged mode of transmission involving biofilm growth from the lower pipe to the sink strainer and subsequent splatter to the bowl and surrounding area occurs rather than splatter directly from the water in the lower pipe." ], [ "1f", "We have also demonstrated" ] ]

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

[ "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: Text: D espite early reports , the premise that hand-wash sink traps can act as reservoirs of bacteria that cause nosocomial infections has been frequently overlooked. There has recently been an alarming increase in sink-related outbreaks worldwide, with many reports establishing an observational link . A sink often operates as an open conduit to wastewater in a patient care area that is often in the same room as the patient.", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: from a P-trap reservoir to a vulnerable hospitalized patient. IMPORTANCE Many recent reports demonstrate that sink drain pipes become colonized with highly consequential multidrug-resistant bacteria, which then results in hospital-acquired infections. However, the mechanism of dispersal of bacteria from the sink to patients has not been fully elucidated. Through establishment of a unique sink gallery, this work found that a staged mode of transmission involving biofilm growth from the lower pipe to the sink strainer and subsequent splatter to the bowl and surrounding area occurs rather than splatter directly from the water in the lower pipe. We have also demonstrated", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: In summary, this work for the first time better models the mechanisms of spread of multidrug-resistant pathogens arising from the sink drain and infecting patients. Droplet dispersion from the P-trap does not happen directly. Rather it is a multistage process: dispersal originates from the strainer and/or the bowl after growth of the biofilm up from the microbial reservoir of the P-trap. We also demonstrate sink-to-sink transmission via a common sanitary pipe. This work could have implications for patient safety, infection control, and interventions as well as the design of future hospital plumbing systems to eliminate this mode of transmission to", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs\nPassage: Health care establishments often invest in desperate interventions to deal with nosocomial outbreaks. The preferred method for addressing most of the environmentrelated transmission is to employ enhanced cleaning using chemical and physical agents . Unfortunately, routine approaches are inefficient in completely eliminating drug-resistant Gammaproteobacteria in an inaccessible microbiologically active area such as a sink trap . The wet, humid, and relatively protected environment in a sink trap favors the formation of rich stable microbial communities . These communities will be exposed to liquids and waste that are discarded in a sink and may include antimicrobials, discarded beverages, soap, presumably pathogenic" ]

[ [ "2a", "Title: Spread from the Sink to the Patient: In Situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs" ], [ "2b", "Passage: In summary, this work for the first time better models the mechanisms of spread of multidrug-resistant pathogens arising from the sink drain and infecting patients." ], [ "2c", "Droplet dispersion from the P-trap does not happen directly." ], [ "2d", "Rather it is a multistage process: dispersal originates from the strainer and/or the bowl after growth of the biofilm up from the microbial reservoir of the P-trap." ], [ "2e", "We also demonstrate sink-to-sink transmission via a common sanitary pipe." ], [ "2f", "This work could have implications for patient safety, infection control, and interventions as well as the design of future hospital plumbing systems to eliminate this mode of transmission to" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Text: An email from Dr Ali Mohamed Zaki, an Egyptian virologist working at the Dr Soliman Fakeeh Hospital in Jeddah in the Kingdom of Saudi Arabia announced the first culture of a new coronavirus to the world. The email was published on the website of the professional emerging diseases network on 20 th September 2012 and described the first reported case, a 60 year old man from Bisha in the KSA. This information led to the rapid discovery of a second case of the virus, this time in an ill patient in the United Kingdom, who had been transferred from", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November." ]

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

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Text: An email from Dr Ali Mohamed Zaki, an Egyptian virologist working at the Dr Soliman Fakeeh Hospital in Jeddah in the Kingdom of Saudi Arabia announced the first culture of a new coronavirus to the world. The email was published on the website of the professional emerging diseases network on 20 th September 2012 and described the first reported case, a 60 year old man from Bisha in the KSA. This information led to the rapid discovery of a second case of the virus, this time in an ill patient in the United Kingdom, who had been transferred from", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November." ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively." ], [ "1c", "The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia ." ], [ "1d", "Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels ." ], [ "1e", "MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections." ], [ "1f", "Precisely how virus transmits to humans remains unknown" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Text: An email from Dr Ali Mohamed Zaki, an Egyptian virologist working at the Dr Soliman Fakeeh Hospital in Jeddah in the Kingdom of Saudi Arabia announced the first culture of a new coronavirus to the world. The email was published on the website of the professional emerging diseases network on 20 th September 2012 and described the first reported case, a 60 year old man from Bisha in the KSA. This information led to the rapid discovery of a second case of the virus, this time in an ill patient in the United Kingdom, who had been transferred from", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: Text: An email from Dr Ali Mohamed Zaki, an Egyptian virologist working at the Dr Soliman Fakeeh Hospital in Jeddah in the Kingdom of Saudi Arabia announced the first culture of a new coronavirus to the world." ], [ "2c", "The email was published on the website of the professional emerging diseases network on 20 th September 2012 and described the first reported case, a 60 year old man from Bisha in the KSA." ], [ "2d", "This information led to the rapid discovery of a second case of the virus, this time in an ill patient in the United Kingdom, who had been transferred from" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Text: An email from Dr Ali Mohamed Zaki, an Egyptian virologist working at the Dr Soliman Fakeeh Hospital in Jeddah in the Kingdom of Saudi Arabia announced the first culture of a new coronavirus to the world. The email was published on the website of the professional emerging diseases network on 20 th September 2012 and described the first reported case, a 60 year old man from Bisha in the KSA. This information led to the rapid discovery of a second case of the virus, this time in an ill patient in the United Kingdom, who had been transferred from", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November." ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: In 2015 two large outbreaks occurred." ], [ "3c", "South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015." ], [ "3d", "This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November." ] ]

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

[ "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: Many studies have shown that the IFITM family provides cellular resistance to viral infection in vitro, and GWAS identified IFITM3 as a resistance gene for influenza in humans . However, we show here that deletion of IFITM proteins reduces the severity of Th2 inflammation in a mouse asthma model, suggesting an evolutionary balance between conferring cellular viral resistance and susceptibility to allergic disease. This study demonstrates that the IFITM family of proteins should be viewed not only as essential proteins for cellular resistance to viral infection but also as important regulators of CD4 + Th cell differentiation and function.", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: In tissue culture experiments, IFITM proteins enable cells to resist infection by both enveloped and nonenveloped viruses, and several distinct mechanisms have been proposed to explain their ability to increase cellular resistance to different viruses .", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: To explore a possible function for the IFITM family in CD4 + T-cell activation or differentiation, we first measured expression of the Ifitm genes by RNA sequencing from CD4 + T cells for a 24 h time course following in vitro activation with anti-CD3 and anti-CD28 in Th0/Th1/Th2 skewing-conditions . This time-course analysis showed that Ifitm1 was expressed at low levels throughout the time course in all conditions. At the start of the experiment, Ifitm3 was most highly expressed of the three genes, but it was then rapidly downregulated after 4 h in response to the TCR/CD28 stimulus. In contrast,", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: responses were reduced. Thus, the IFITM family seems to provide a negative feedback loop on Th1 differentiation in CD4 + T cells, as they are IFN-inducible proteins, which function to limit Th1 differentiation." ]

[ [ "0a", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation" ], [ "0b", "Passage: Many studies have shown that the IFITM family provides cellular resistance to viral infection in vitro, and GWAS identified IFITM3 as a resistance gene for influenza in humans ." ], [ "0c", "However, we show here that deletion of IFITM proteins reduces the severity of Th2 inflammation in a mouse asthma model, suggesting an evolutionary balance between conferring cellular viral resistance and susceptibility to allergic disease." ], [ "0d", "This study demonstrates that the IFITM family of proteins should be viewed not only as essential proteins for cellular resistance to viral infection but also as important regulators of CD4 + Th cell differentiation and function." ] ]

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

[ "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: Many studies have shown that the IFITM family provides cellular resistance to viral infection in vitro, and GWAS identified IFITM3 as a resistance gene for influenza in humans . However, we show here that deletion of IFITM proteins reduces the severity of Th2 inflammation in a mouse asthma model, suggesting an evolutionary balance between conferring cellular viral resistance and susceptibility to allergic disease. This study demonstrates that the IFITM family of proteins should be viewed not only as essential proteins for cellular resistance to viral infection but also as important regulators of CD4 + Th cell differentiation and function.", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: In tissue culture experiments, IFITM proteins enable cells to resist infection by both enveloped and nonenveloped viruses, and several distinct mechanisms have been proposed to explain their ability to increase cellular resistance to different viruses .", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: To explore a possible function for the IFITM family in CD4 + T-cell activation or differentiation, we first measured expression of the Ifitm genes by RNA sequencing from CD4 + T cells for a 24 h time course following in vitro activation with anti-CD3 and anti-CD28 in Th0/Th1/Th2 skewing-conditions . This time-course analysis showed that Ifitm1 was expressed at low levels throughout the time course in all conditions. At the start of the experiment, Ifitm3 was most highly expressed of the three genes, but it was then rapidly downregulated after 4 h in response to the TCR/CD28 stimulus. In contrast,", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: responses were reduced. Thus, the IFITM family seems to provide a negative feedback loop on Th1 differentiation in CD4 + T cells, as they are IFN-inducible proteins, which function to limit Th1 differentiation." ]

[ [ "1a", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation" ], [ "1b", "Passage: In tissue culture experiments, IFITM proteins enable cells to resist infection by both enveloped and nonenveloped viruses, and several distinct mechanisms have been proposed to explain their ability to increase cellular resistance to different viruses ." ] ]

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

[ "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: Many studies have shown that the IFITM family provides cellular resistance to viral infection in vitro, and GWAS identified IFITM3 as a resistance gene for influenza in humans . However, we show here that deletion of IFITM proteins reduces the severity of Th2 inflammation in a mouse asthma model, suggesting an evolutionary balance between conferring cellular viral resistance and susceptibility to allergic disease. This study demonstrates that the IFITM family of proteins should be viewed not only as essential proteins for cellular resistance to viral infection but also as important regulators of CD4 + Th cell differentiation and function.", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: In tissue culture experiments, IFITM proteins enable cells to resist infection by both enveloped and nonenveloped viruses, and several distinct mechanisms have been proposed to explain their ability to increase cellular resistance to different viruses .", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: To explore a possible function for the IFITM family in CD4 + T-cell activation or differentiation, we first measured expression of the Ifitm genes by RNA sequencing from CD4 + T cells for a 24 h time course following in vitro activation with anti-CD3 and anti-CD28 in Th0/Th1/Th2 skewing-conditions . This time-course analysis showed that Ifitm1 was expressed at low levels throughout the time course in all conditions. At the start of the experiment, Ifitm3 was most highly expressed of the three genes, but it was then rapidly downregulated after 4 h in response to the TCR/CD28 stimulus. In contrast,", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation\nPassage: responses were reduced. Thus, the IFITM family seems to provide a negative feedback loop on Th1 differentiation in CD4 + T cells, as they are IFN-inducible proteins, which function to limit Th1 differentiation." ]

[ [ "3a", "Title: IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation" ], [ "3b", "Passage: responses were reduced." ], [ "3c", "Thus, the IFITM family seems to provide a negative feedback loop on Th1 differentiation in CD4 + T cells, as they are IFN-inducible proteins, which function to limit Th1 differentiation." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: There are several approaches to avoiding pre-existing vector immunity, such as the use of vectors derived from nonhuman sources, using human viruses of rare serotypes , heterologous prime-boost approaches , homologous reimmunization and removing key neutralizing epitopes on the surface of viral capsid proteins . The inhibitory effect of pre-existing immunity can also be avoided by masking the Ad vector inside dendritic cells . In addition, mucosal vaccination or administration of higher vaccine doses can overcome pre-existing immunity problems .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: 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: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: be expected to result in a reduction in the antigenicity of the vectored antigen." ]

[ [ "0a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "0b", "Passage: There are several approaches to avoiding pre-existing vector immunity, such as the use of vectors derived from nonhuman sources, using human viruses of rare serotypes , heterologous prime-boost approaches , homologous reimmunization and removing key neutralizing epitopes on the surface of viral capsid proteins ." ], [ "0c", "The inhibitory effect of pre-existing immunity can also be avoided by masking the Ad vector inside dendritic cells ." ], [ "0d", "In addition, mucosal vaccination or administration of higher vaccine doses can overcome pre-existing immunity problems ." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: There are several approaches to avoiding pre-existing vector immunity, such as the use of vectors derived from nonhuman sources, using human viruses of rare serotypes , heterologous prime-boost approaches , homologous reimmunization and removing key neutralizing epitopes on the surface of viral capsid proteins . The inhibitory effect of pre-existing immunity can also be avoided by masking the Ad vector inside dendritic cells . In addition, mucosal vaccination or administration of higher vaccine doses can overcome pre-existing immunity problems .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: 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: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: be expected to result in a reduction in the antigenicity of the vectored antigen." ]

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

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: There are several approaches to avoiding pre-existing vector immunity, such as the use of vectors derived from nonhuman sources, using human viruses of rare serotypes , heterologous prime-boost approaches , homologous reimmunization and removing key neutralizing epitopes on the surface of viral capsid proteins . The inhibitory effect of pre-existing immunity can also be avoided by masking the Ad vector inside dendritic cells . In addition, mucosal vaccination or administration of higher vaccine doses can overcome pre-existing immunity problems .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens . However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time. Leong et al. also demonstrated that the negative impact of vector-specific immune responses can also be countered by repeated immunization with the same vaccine and dose; this in effect leads to higher priming of naive T cells against the delivered antigen. Of course, such repeated vaccination may not be practicable in real-world situations.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: 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: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: be expected to result in a reduction in the antigenicity of the vectored antigen." ]

[ [ "2a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "2b", "Passage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria." ], [ "2c", "Safety is a major concern, as even a low level of toxicity is unacceptable ." ], [ "2d", "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 ." ], [ "2e", "Similar constraints apply to veterinary vaccines, with cost often an even more important consideration." ], [ "2f", "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", "0d", "1d", "2f" ]

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: In Southeast Asia, Thailand was affected by HPAI H5N1 early, with the first official report of poultry and human outbreaks on 23 January 2004. By the end of January 2004, 32 provinces throughout the north and several in the south experienced outbreaks in many types of poultry. The disease caused 17 human cases from January 2004 to June 2005 2 . The epidemic peaked during a ''second wave'' with 1 717 outbreaks in poultry. Beginning in early 2004, Thai authorities implemented a control strategy based on the prohibition of vaccination and the use of preemptive culling. Approximately 60 million poultry", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: to extend further across the western part of the central plain of Thailand. In contrast, the extreme south of Thailand appeared to be a high-risk area for chickens, with values of relative risk significantly > 10. On the contrary, some areas were especially low-risk for both chickens and ducks despite the occurrence of outbreaks , as in northeastern Thailand and in the middle part of the peninsula. Northern Thailand had low values of relative risk only for chickens.", "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: 2004 with 990 000 volunteers conducting door-to-door surveys to check poultry in every house nationwide. From mid-2005, the number of outbreaks in poultry decreased substantially but the occurrence of poultry outbreaks in two provinces of Thailand in late 2008 indicates that the threat of HPAI in Thailand remains present." ]

[ [ "1a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "1b", "Passage: to extend further across the western part of the central plain of Thailand." ], [ "1c", "In contrast, the extreme south of Thailand appeared to be a high-risk area for chickens, with values of relative risk significantly > 10." ], [ "1d", "On the contrary, some areas were especially low-risk for both chickens and ducks despite the occurrence of outbreaks , as in northeastern Thailand and in the middle part of the peninsula." ], [ "1e", "Northern Thailand had low values of relative risk only for chickens." ] ]

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

[ "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: In Southeast Asia, Thailand was affected by HPAI H5N1 early, with the first official report of poultry and human outbreaks on 23 January 2004. By the end of January 2004, 32 provinces throughout the north and several in the south experienced outbreaks in many types of poultry. The disease caused 17 human cases from January 2004 to June 2005 2 . The epidemic peaked during a ''second wave'' with 1 717 outbreaks in poultry. Beginning in early 2004, Thai authorities implemented a control strategy based on the prohibition of vaccination and the use of preemptive culling. Approximately 60 million poultry", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model\nPassage: to extend further across the western part of the central plain of Thailand. In contrast, the extreme south of Thailand appeared to be a high-risk area for chickens, with values of relative risk significantly > 10. On the contrary, some areas were especially low-risk for both chickens and ducks despite the occurrence of outbreaks , as in northeastern Thailand and in the middle part of the peninsula. Northern Thailand had low values of relative risk only for chickens.", "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: 2004 with 990 000 volunteers conducting door-to-door surveys to check poultry in every house nationwide. From mid-2005, the number of outbreaks in poultry decreased substantially but the occurrence of poultry outbreaks in two provinces of Thailand in late 2008 indicates that the threat of HPAI in Thailand remains present." ]

[ [ "2a", "Title: Anthropogenic factors and the risk of highly pathogenic avian influenza H5N1: prospects from a spatial-based model" ], [ "2b", "Passage: control as they would enable control measures to be targeted and surveillance in ''high-risk'' areas to be strengthened." ], [ "2c", "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." ], [ "2d", "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 ." ], [ "2e", "However, the respective roles of these pathways at the global or national scale are still unclear ." ], [ "2f", "The persistence of HPAI H5N1 virus" ] ]

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

[ "Title: Phleboviruses and the Type I Interferon Response\nPassage: Expression of the transcription factor IRF7 is also enhanced by IFN signaling. While the aforementioned activation of IRF3 leads to an initial wave of type I IFN secretion, including IFN-β and IFN-α4, enhanced IRF7 expression and activation generates a second wave of type I IFN production which involves additional IFN-α subtypes .", "Title: Type 1 Interferon Induction of Natural Killer Cell Gamma Interferon Production for Defense during Lymphocytic Choriomeningitis Virus Infection\nPassage: The studies do not exclude possible roles for accessory cytokines in enhancing type 1 IFN induction of IFN-␥. Certainly, IL-12 is an activator of STAT4 and a potent inducer of IFN-␥ . The cytokine IL-18 can enhance the stimulation of IFN-␥ by either type 1 IFNs or IL-12 , and new studies deciphering pathways from different sensors have demonstrated synergism between type 1 IFNs and IL-12 for IFN-␥ induction in human cells . The results presented here, however, suggest that there may be a short burst of IFN-␥ induced by type 1 IFNs independent of IL-12, and our previous work", "Title: Phleboviruses and the Type I Interferon Response\nPassage: In addition to direct antiviral effects of ISGs and the positive feedback loop via IRF7, type I IFN signaling also induces the production of a range of cytokines and chemokines, pro-and antiapoptotic factors, and affects multiple other signaling pathways. Through modulation of the differentiation and function of dendritic cells, T cells, natural killer cells, and B cells, type I IFNs shape the antiviral immune response beyond the initial innate immune response .", "Title: Phleboviruses and the Type I Interferon Response\nPassage: Within the endosomal compartments, Toll-like receptor 3 recognizes viral dsRNA and poly, and signals via the adaptor Toll-interleukin 1 receptor domain-containing adapter-inducing IFN-β to activate IRF3, NF-κB, and AP-1, and consequently induce the production of type I IFNs as well as inflammatory cytokines . Further, recognition of single-stranded RNA by TLR7/8 and subsequent signaling via the adaptor myeloid differentiation primary response gene 88 results in the secretion of IFN-α, particularly by specialized plasmacytoid dendritic cells ." ]

[ [ "0a", "Title: Phleboviruses and the Type I Interferon Response" ], [ "0b", "Passage: Expression of the transcription factor IRF7 is also enhanced by IFN signaling." ], [ "0c", "While the aforementioned activation of IRF3 leads to an initial wave of type I IFN secretion, including IFN-β and IFN-α4, enhanced IRF7 expression and activation generates a second wave of type I IFN production which involves additional IFN-α subtypes ." ] ]

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

[ "Title: Phleboviruses and the Type I Interferon Response\nPassage: Expression of the transcription factor IRF7 is also enhanced by IFN signaling. While the aforementioned activation of IRF3 leads to an initial wave of type I IFN secretion, including IFN-β and IFN-α4, enhanced IRF7 expression and activation generates a second wave of type I IFN production which involves additional IFN-α subtypes .", "Title: Type 1 Interferon Induction of Natural Killer Cell Gamma Interferon Production for Defense during Lymphocytic Choriomeningitis Virus Infection\nPassage: The studies do not exclude possible roles for accessory cytokines in enhancing type 1 IFN induction of IFN-␥. Certainly, IL-12 is an activator of STAT4 and a potent inducer of IFN-␥ . The cytokine IL-18 can enhance the stimulation of IFN-␥ by either type 1 IFNs or IL-12 , and new studies deciphering pathways from different sensors have demonstrated synergism between type 1 IFNs and IL-12 for IFN-␥ induction in human cells . The results presented here, however, suggest that there may be a short burst of IFN-␥ induced by type 1 IFNs independent of IL-12, and our previous work", "Title: Phleboviruses and the Type I Interferon Response\nPassage: In addition to direct antiviral effects of ISGs and the positive feedback loop via IRF7, type I IFN signaling also induces the production of a range of cytokines and chemokines, pro-and antiapoptotic factors, and affects multiple other signaling pathways. Through modulation of the differentiation and function of dendritic cells, T cells, natural killer cells, and B cells, type I IFNs shape the antiviral immune response beyond the initial innate immune response .", "Title: Phleboviruses and the Type I Interferon Response\nPassage: Within the endosomal compartments, Toll-like receptor 3 recognizes viral dsRNA and poly, and signals via the adaptor Toll-interleukin 1 receptor domain-containing adapter-inducing IFN-β to activate IRF3, NF-κB, and AP-1, and consequently induce the production of type I IFNs as well as inflammatory cytokines . Further, recognition of single-stranded RNA by TLR7/8 and subsequent signaling via the adaptor myeloid differentiation primary response gene 88 results in the secretion of IFN-α, particularly by specialized plasmacytoid dendritic cells ." ]

[ [ "1a", "Title: Type 1 Interferon Induction of Natural Killer Cell Gamma Interferon Production for Defense during Lymphocytic Choriomeningitis Virus Infection" ], [ "1b", "Passage: The studies do not exclude possible roles for accessory cytokines in enhancing type 1 IFN induction of IFN-␥." ], [ "1c", "Certainly, IL-12 is an activator of STAT4 and a potent inducer of IFN-␥ ." ], [ "1d", "The cytokine IL-18 can enhance the stimulation of IFN-␥ by either type 1 IFNs or IL-12 , and new studies deciphering pathways from different sensors have demonstrated synergism between type 1 IFNs and IL-12 for IFN-␥ induction in human cells ." ], [ "1e", "The results presented here, however, suggest that there may be a short burst of IFN-␥ induced by type 1 IFNs independent of IL-12, and our previous work" ] ]

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

[ "Title: Phleboviruses and the Type I Interferon Response\nPassage: Expression of the transcription factor IRF7 is also enhanced by IFN signaling. While the aforementioned activation of IRF3 leads to an initial wave of type I IFN secretion, including IFN-β and IFN-α4, enhanced IRF7 expression and activation generates a second wave of type I IFN production which involves additional IFN-α subtypes .", "Title: Type 1 Interferon Induction of Natural Killer Cell Gamma Interferon Production for Defense during Lymphocytic Choriomeningitis Virus Infection\nPassage: The studies do not exclude possible roles for accessory cytokines in enhancing type 1 IFN induction of IFN-␥. Certainly, IL-12 is an activator of STAT4 and a potent inducer of IFN-␥ . The cytokine IL-18 can enhance the stimulation of IFN-␥ by either type 1 IFNs or IL-12 , and new studies deciphering pathways from different sensors have demonstrated synergism between type 1 IFNs and IL-12 for IFN-␥ induction in human cells . The results presented here, however, suggest that there may be a short burst of IFN-␥ induced by type 1 IFNs independent of IL-12, and our previous work", "Title: Phleboviruses and the Type I Interferon Response\nPassage: In addition to direct antiviral effects of ISGs and the positive feedback loop via IRF7, type I IFN signaling also induces the production of a range of cytokines and chemokines, pro-and antiapoptotic factors, and affects multiple other signaling pathways. Through modulation of the differentiation and function of dendritic cells, T cells, natural killer cells, and B cells, type I IFNs shape the antiviral immune response beyond the initial innate immune response .", "Title: Phleboviruses and the Type I Interferon Response\nPassage: Within the endosomal compartments, Toll-like receptor 3 recognizes viral dsRNA and poly, and signals via the adaptor Toll-interleukin 1 receptor domain-containing adapter-inducing IFN-β to activate IRF3, NF-κB, and AP-1, and consequently induce the production of type I IFNs as well as inflammatory cytokines . Further, recognition of single-stranded RNA by TLR7/8 and subsequent signaling via the adaptor myeloid differentiation primary response gene 88 results in the secretion of IFN-α, particularly by specialized plasmacytoid dendritic cells ." ]

[ [ "2a", "Title: Phleboviruses and the Type I Interferon Response" ], [ "2b", "Passage: In addition to direct antiviral effects of ISGs and the positive feedback loop via IRF7, type I IFN signaling also induces the production of a range of cytokines and chemokines, pro-and antiapoptotic factors, and affects multiple other signaling pathways." ], [ "2c", "Through modulation of the differentiation and function of dendritic cells, T cells, natural killer cells, and B cells, type I IFNs shape the antiviral immune response beyond the initial innate immune response ." ] ]

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

[ "Title: Phleboviruses and the Type I Interferon Response\nPassage: Expression of the transcription factor IRF7 is also enhanced by IFN signaling. While the aforementioned activation of IRF3 leads to an initial wave of type I IFN secretion, including IFN-β and IFN-α4, enhanced IRF7 expression and activation generates a second wave of type I IFN production which involves additional IFN-α subtypes .", "Title: Type 1 Interferon Induction of Natural Killer Cell Gamma Interferon Production for Defense during Lymphocytic Choriomeningitis Virus Infection\nPassage: The studies do not exclude possible roles for accessory cytokines in enhancing type 1 IFN induction of IFN-␥. Certainly, IL-12 is an activator of STAT4 and a potent inducer of IFN-␥ . The cytokine IL-18 can enhance the stimulation of IFN-␥ by either type 1 IFNs or IL-12 , and new studies deciphering pathways from different sensors have demonstrated synergism between type 1 IFNs and IL-12 for IFN-␥ induction in human cells . The results presented here, however, suggest that there may be a short burst of IFN-␥ induced by type 1 IFNs independent of IL-12, and our previous work", "Title: Phleboviruses and the Type I Interferon Response\nPassage: In addition to direct antiviral effects of ISGs and the positive feedback loop via IRF7, type I IFN signaling also induces the production of a range of cytokines and chemokines, pro-and antiapoptotic factors, and affects multiple other signaling pathways. Through modulation of the differentiation and function of dendritic cells, T cells, natural killer cells, and B cells, type I IFNs shape the antiviral immune response beyond the initial innate immune response .", "Title: Phleboviruses and the Type I Interferon Response\nPassage: Within the endosomal compartments, Toll-like receptor 3 recognizes viral dsRNA and poly, and signals via the adaptor Toll-interleukin 1 receptor domain-containing adapter-inducing IFN-β to activate IRF3, NF-κB, and AP-1, and consequently induce the production of type I IFNs as well as inflammatory cytokines . Further, recognition of single-stranded RNA by TLR7/8 and subsequent signaling via the adaptor myeloid differentiation primary response gene 88 results in the secretion of IFN-α, particularly by specialized plasmacytoid dendritic cells ." ]

[ [ "3a", "Title: Phleboviruses and the Type I Interferon Response" ], [ "3b", "Passage: Within the endosomal compartments, Toll-like receptor 3 recognizes viral dsRNA and poly, and signals via the adaptor Toll-interleukin 1 receptor domain-containing adapter-inducing IFN-β to activate IRF3, NF-κB, and AP-1, and consequently induce the production of type I IFNs as well as inflammatory cytokines ." ], [ "3c", "Further, recognition of single-stranded RNA by TLR7/8 and subsequent signaling via the adaptor myeloid differentiation primary response gene 88 results in the secretion of IFN-α, particularly by specialized plasmacytoid dendritic cells ." ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: current limitations of influenza vaccines.", "Title: Viral vector-based influenza vaccines\nPassage: Although currently available influenza vaccines are effective in reducing morbidity and mortality caused by seasonal influenza viruses, they have several limitations. Mainly, continuous antigenic drift of seasonal influenza viruses complicates the production of effective vaccines. The vaccine strains need to be updated almost annually in order to achieve a good antigenic match with the epidemic virus strains. If the vaccine strains do not antigenically match the circulating strains, vaccine efficacy is reduced considerably, as was the case in the 2014-2015 influenza season. Furthermore, the seasonal influenza vaccines will afford little or no protection against antigenically distinct pandemic influenza viruses, which", "Title: Improved Global Capacity for Influenza Surveillance\nPassage: Influenza viruses are constantly changing, requiring updates to the vaccine each year on the basis of which influenza viruses are infecting persons around the world, how those viruses are spreading, and how well the previous season's vaccine protects against those viruses. Therefore, the increase in the number of countries submitting specimens for seasonal vaccine strain selection is critical for selecting the most representative strains currently circulating.", "Title: Confronting Potential Influenza A (H5N1) Pandemic with Better Vaccines\nPassage: world's 6.5 billion people. Clearly, dose-sparing formulations are urgently needed." ]

[ [ "1a", "Title: Viral vector-based influenza vaccines" ], [ "1b", "Passage: Although currently available influenza vaccines are effective in reducing morbidity and mortality caused by seasonal influenza viruses, they have several limitations." ], [ "1c", "Mainly, continuous antigenic drift of seasonal influenza viruses complicates the production of effective vaccines." ], [ "1d", "The vaccine strains need to be updated almost annually in order to achieve a good antigenic match with the epidemic virus strains." ], [ "1e", "If the vaccine strains do not antigenically match the circulating strains, vaccine efficacy is reduced considerably, as was the case in the 2014-2015 influenza season." ], [ "1f", "Furthermore, the seasonal influenza vaccines will afford little or no protection against antigenically distinct pandemic influenza viruses, which" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: current limitations of influenza vaccines.", "Title: Viral vector-based influenza vaccines\nPassage: Although currently available influenza vaccines are effective in reducing morbidity and mortality caused by seasonal influenza viruses, they have several limitations. Mainly, continuous antigenic drift of seasonal influenza viruses complicates the production of effective vaccines. The vaccine strains need to be updated almost annually in order to achieve a good antigenic match with the epidemic virus strains. If the vaccine strains do not antigenically match the circulating strains, vaccine efficacy is reduced considerably, as was the case in the 2014-2015 influenza season. Furthermore, the seasonal influenza vaccines will afford little or no protection against antigenically distinct pandemic influenza viruses, which", "Title: Improved Global Capacity for Influenza Surveillance\nPassage: Influenza viruses are constantly changing, requiring updates to the vaccine each year on the basis of which influenza viruses are infecting persons around the world, how those viruses are spreading, and how well the previous season's vaccine protects against those viruses. Therefore, the increase in the number of countries submitting specimens for seasonal vaccine strain selection is critical for selecting the most representative strains currently circulating.", "Title: Confronting Potential Influenza A (H5N1) Pandemic with Better Vaccines\nPassage: world's 6.5 billion people. Clearly, dose-sparing formulations are urgently needed." ]

[ [ "2a", "Title: Improved Global Capacity for Influenza Surveillance" ], [ "2b", "Passage: Influenza viruses are constantly changing, requiring updates to the vaccine each year on the basis of which influenza viruses are infecting persons around the world, how those viruses are spreading, and how well the previous season's vaccine protects against those viruses." ], [ "2c", "Therefore, the increase in the number of countries submitting specimens for seasonal vaccine strain selection is critical for selecting the most representative strains currently circulating." ] ]

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

[ "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: was m = 63.1 million per year in 2017 , of which 100q = 2.1% were from Wuhan , a home of n = 19.0 million people as the catchment population of Wuhan airport. Two other locations with confirmed cases, i.e., Macau and Hong Kong, were excluded from the analysis, because it is commutable by land transporation and the first case in Hong Kong was indeed not via airtravel. As we already know from elsewhere , given the observed cumulative count of c exported cases, we have a balance equation of the cumulative risk of infection:", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: Our latest estimate is comparable to a preliminary report posted by a research group at Imperial College London on their own homepage on 22 January 2020 that estimated the incidence based on three importation events at 4000 cases . Possible reasons for the slight difference include the number of travelers in the previous study was derived from airline passenger data and the assumed length of T was different. Two other estimates have also been published: a preliminary study by a Northeastern University group estimated 1250 cases as of 17 January 2020 and a University of Hong Kong group estimated 1343", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: Wuhan was about 11 million at the end of 2018 , the rate of people traveling out from Wuhan City would be 0.018 per day. However, we assumed that the normal population mobility before January 1 was 0.1 times as that after January 10. Therefore, we set the rate of people moving into and moving out from Wuhan City as 0.0018 per day .", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

[ [ "0a", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020" ], [ "0b", "Passage: was m = 63.1 million per year in 2017 , of which 100q = 2.1% were from Wuhan , a home of n = 19.0 million people as the catchment population of Wuhan airport." ], [ "0c", "Two other locations with confirmed cases, i.e., Macau and Hong Kong, were excluded from the analysis, because it is commutable by land transporation and the first case in Hong Kong was indeed not via airtravel." ], [ "0d", "As we already know from elsewhere , given the observed cumulative count of c exported cases, we have a balance equation of the cumulative risk of infection:" ] ]

[ "0b" ]

[ "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide . In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality . This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 . However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: . For instance, estimates of pandemic excess respiratory death rates have ranged from 6.1 per 10,000 for the Canary Islands to 169.7 per 10,000 for Burgos . Moreover, approximately 40% of between-province variation in cumulative excess death rates in Spain during 1918-1919 are explained by spatial factors, such as latitude, population density, and the proportion of children, have explained . However, in few of these analyses did researchers take into account a recrudescent wave in Spain, which peaked in Madrid in late December 1919 and in later months in the rest of Spain .", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: We retrieved all death certificates from the Madrid Civil Registry to construct time series of deaths during the 1918-1920 influenza pandemic . Each record provides specific details of the deceased, including the date of death, age, and causes of death. For years 1917-1920, the registry holds a total of 70,061 death records . Cause-of-death information for each death record allowed us to extract data on deaths attributed to influenza and respiratory causes.", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Spain experienced one of the highest excess mortality rates during the 1918 influenza pandemic in Europe , although this country did not take part in World War I. Perhaps this pandemic outcome is associated with the fact that Spain was going through a demographic transition and experiencing elevated death rates that were only comparable to those of eastern Europe. Of note, the life expectancy in Spain was 41 years in 1910 and 40 years in 1920 ." ]

[ [ "0a", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain" ], [ "0b", "Passage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide ." ], [ "0c", "In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality ." ], [ "0d", "This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 ." ], [ "0e", "However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the" ] ]

[ "0b", "3b" ]

[ "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: The 1918-1920 influenza pandemic, or the so-called Spanish flu, was responsible for more than 50 million deaths worldwide . In Europe, the excess mortality rate associated with the 1918-1919 influenza pandemic has been estimated at 1.1%, or approximately an 86% increase in all-cause mortality . This pandemic rapidly spread in a series of pandemic waves that gripped the world beginning in early 1918 . However, according to results of various phylogenetic and molecularclock analyses, the initial circulation of the virus from avian or swine and other mammal species to humans may have occurred a few years earlier . Moreover, the", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: . For instance, estimates of pandemic excess respiratory death rates have ranged from 6.1 per 10,000 for the Canary Islands to 169.7 per 10,000 for Burgos . Moreover, approximately 40% of between-province variation in cumulative excess death rates in Spain during 1918-1919 are explained by spatial factors, such as latitude, population density, and the proportion of children, have explained . However, in few of these analyses did researchers take into account a recrudescent wave in Spain, which peaked in Madrid in late December 1919 and in later months in the rest of Spain .", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: We retrieved all death certificates from the Madrid Civil Registry to construct time series of deaths during the 1918-1920 influenza pandemic . Each record provides specific details of the deceased, including the date of death, age, and causes of death. For years 1917-1920, the registry holds a total of 70,061 death records . Cause-of-death information for each death record allowed us to extract data on deaths attributed to influenza and respiratory causes.", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Spain experienced one of the highest excess mortality rates during the 1918 influenza pandemic in Europe , although this country did not take part in World War I. Perhaps this pandemic outcome is associated with the fact that Spain was going through a demographic transition and experiencing elevated death rates that were only comparable to those of eastern Europe. Of note, the life expectancy in Spain was 41 years in 1910 and 40 years in 1920 ." ]

[ [ "3a", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain" ], [ "3b", "Passage: Spain experienced one of the highest excess mortality rates during the 1918 influenza pandemic in Europe , although this country did not take part in World War I." ], [ "3c", "Perhaps this pandemic outcome is associated with the fact that Spain was going through a demographic transition and experiencing elevated death rates that were only comparable to those of eastern Europe." ], [ "3d", "Of note, the life expectancy in Spain was 41 years in 1910 and 40 years in 1920 ." ] ]

[ "0b", "3b" ]

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: our ability to identify truly high-risk prepandemic threats: notably, preparation of seed vaccine stocks for candidate pandemic strains, stockpiling of subtype-specific vaccines, and culling of poultry infected with such strains. Other types of countermeasures, ranging from strengthening local public health departments to stockpiling antivirals or ventilators to developing faster processes for vaccine manufacture to universal vaccines that should be effective against any influenza A strain, should provide benefits whether or not we have advance notice of the strain causing the next pandemic. A comprehensive assessment of priorities to prevent or mitigate the next influenza pandemic should consider the balance between", "Title: Viral factors in influenza pandemic risk assessment\nPassage: Even with all of the foregoing suggestions in place, it may be improbable that we can reliably identify the 'needle in the haystack' that is the next pandemic influenza strain. Ultimately, the goal is not risk assessment for its own sake, but preparedness and early response to pandemic threats. In other areas where security is at stake, it has been argued that making and improving predictions should be accompanied by a systematic effort to design responses that will not fail even if the predictions are wrong . In the influenza context, the value of some countermeasures is strongly reliant on", "Title: Viral factors in influenza pandemic risk assessment\nPassage: We conclude with some recommendations for future research and for the practice of pandemic risk assessment.", "Title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States\nPassage: This study highlights several key components to pandemic influenza preparedness, especially for a severe pandemic, including the importance of ensuring readiness to initiate large-scale vaccination programs as early as possible and ideally before the introduction of a novel influenza virus into the United States . Factors that may impact vaccine dose availability include how soon we develop an appropriate vaccine virus candidate, growth characteristics of vaccine virus candidates, influenza vaccine production capacity, efficiency of vaccine allocation and distribution, and vaccine administration capacity. Increased investment and research in vaccine production technologies, including the use of cell-derived recombinant proteins , virus-like particles" ]

[ [ "0a", "Title: Viral factors in influenza pandemic risk assessment" ], [ "0b", "Passage: our ability to identify truly high-risk prepandemic threats: notably, preparation of seed vaccine stocks for candidate pandemic strains, stockpiling of subtype-specific vaccines, and culling of poultry infected with such strains." ], [ "0c", "Other types of countermeasures, ranging from strengthening local public health departments to stockpiling antivirals or ventilators to developing faster processes for vaccine manufacture to universal vaccines that should be effective against any influenza A strain, should provide benefits whether or not we have advance notice of the strain causing the next pandemic." ], [ "0d", "A comprehensive assessment of priorities to prevent or mitigate the next influenza pandemic should consider the balance between" ] ]

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

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: our ability to identify truly high-risk prepandemic threats: notably, preparation of seed vaccine stocks for candidate pandemic strains, stockpiling of subtype-specific vaccines, and culling of poultry infected with such strains. Other types of countermeasures, ranging from strengthening local public health departments to stockpiling antivirals or ventilators to developing faster processes for vaccine manufacture to universal vaccines that should be effective against any influenza A strain, should provide benefits whether or not we have advance notice of the strain causing the next pandemic. A comprehensive assessment of priorities to prevent or mitigate the next influenza pandemic should consider the balance between", "Title: Viral factors in influenza pandemic risk assessment\nPassage: Even with all of the foregoing suggestions in place, it may be improbable that we can reliably identify the 'needle in the haystack' that is the next pandemic influenza strain. Ultimately, the goal is not risk assessment for its own sake, but preparedness and early response to pandemic threats. In other areas where security is at stake, it has been argued that making and improving predictions should be accompanied by a systematic effort to design responses that will not fail even if the predictions are wrong . In the influenza context, the value of some countermeasures is strongly reliant on", "Title: Viral factors in influenza pandemic risk assessment\nPassage: We conclude with some recommendations for future research and for the practice of pandemic risk assessment.", "Title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States\nPassage: This study highlights several key components to pandemic influenza preparedness, especially for a severe pandemic, including the importance of ensuring readiness to initiate large-scale vaccination programs as early as possible and ideally before the introduction of a novel influenza virus into the United States . Factors that may impact vaccine dose availability include how soon we develop an appropriate vaccine virus candidate, growth characteristics of vaccine virus candidates, influenza vaccine production capacity, efficiency of vaccine allocation and distribution, and vaccine administration capacity. Increased investment and research in vaccine production technologies, including the use of cell-derived recombinant proteins , virus-like particles" ]

[ [ "1a", "Title: Viral factors in influenza pandemic risk assessment" ], [ "1b", "Passage: Even with all of the foregoing suggestions in place, it may be improbable that we can reliably identify the 'needle in the haystack' that is the next pandemic influenza strain." ], [ "1c", "Ultimately, the goal is not risk assessment for its own sake, but preparedness and early response to pandemic threats." ], [ "1d", "In other areas where security is at stake, it has been argued that making and improving predictions should be accompanied by a systematic effort to design responses that will not fail even if the predictions are wrong ." ], [ "1e", "In the influenza context, the value of some countermeasures is strongly reliant on" ] ]

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

[ "Title: Viral factors in influenza pandemic risk assessment\nPassage: our ability to identify truly high-risk prepandemic threats: notably, preparation of seed vaccine stocks for candidate pandemic strains, stockpiling of subtype-specific vaccines, and culling of poultry infected with such strains. Other types of countermeasures, ranging from strengthening local public health departments to stockpiling antivirals or ventilators to developing faster processes for vaccine manufacture to universal vaccines that should be effective against any influenza A strain, should provide benefits whether or not we have advance notice of the strain causing the next pandemic. A comprehensive assessment of priorities to prevent or mitigate the next influenza pandemic should consider the balance between", "Title: Viral factors in influenza pandemic risk assessment\nPassage: Even with all of the foregoing suggestions in place, it may be improbable that we can reliably identify the 'needle in the haystack' that is the next pandemic influenza strain. Ultimately, the goal is not risk assessment for its own sake, but preparedness and early response to pandemic threats. In other areas where security is at stake, it has been argued that making and improving predictions should be accompanied by a systematic effort to design responses that will not fail even if the predictions are wrong . In the influenza context, the value of some countermeasures is strongly reliant on", "Title: Viral factors in influenza pandemic risk assessment\nPassage: We conclude with some recommendations for future research and for the practice of pandemic risk assessment.", "Title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States\nPassage: This study highlights several key components to pandemic influenza preparedness, especially for a severe pandemic, including the importance of ensuring readiness to initiate large-scale vaccination programs as early as possible and ideally before the introduction of a novel influenza virus into the United States . Factors that may impact vaccine dose availability include how soon we develop an appropriate vaccine virus candidate, growth characteristics of vaccine virus candidates, influenza vaccine production capacity, efficiency of vaccine allocation and distribution, and vaccine administration capacity. Increased investment and research in vaccine production technologies, including the use of cell-derived recombinant proteins , virus-like particles" ]

[ [ "3a", "Title: Estimating the Potential Effects of a Vaccine Program Against an Emerging Influenza Pandemic—United States" ], [ "3b", "Passage: This study highlights several key components to pandemic influenza preparedness, especially for a severe pandemic, including the importance of ensuring readiness to initiate large-scale vaccination programs as early as possible and ideally before the introduction of a novel influenza virus into the United States ." ], [ "3c", "Factors that may impact vaccine dose availability include how soon we develop an appropriate vaccine virus candidate, growth characteristics of vaccine virus candidates, influenza vaccine production capacity, efficiency of vaccine allocation and distribution, and vaccine administration capacity." ], [ "3d", "Increased investment and research in vaccine production technologies, including the use of cell-derived recombinant proteins , virus-like particles" ] ]

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

[ "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: Using GPS Technology to Quantify Human Mobility, Dynamic Contacts and Infectious Disease Dynamics in a Resource-Poor Urban Environment\nPassage: Despite living in different houses and neighborhoods, the tracked individuals showed a high degree of connectivity, with the largest network component accounting for 96.2% of all individuals and 97.8% of all edges . N ij was projected into its constituent affiliation networks: N L and N P . The degree distributions of N L and N P were best fitted by a truncated power-law distribution of the Table 1 . Glossary of network topology terms used in the manuscript.", "Title: A multidimensional classification of public health activity in Australia\nPassage: other investors; the links to employment and education; and public health investment by, and outcomes in, other sectors such as transport and housing.", "Title: Recent Progress in Studies of Arterivirus- and Coronavirus-Host Interactions\nPassage: It has also been observed that the N protein of several coronaviruses can localize in the nucleolus where it may perturb cell cycle activities of the host cell for the benefit of viral mRNA synthesis . IBV N, for example, appears to target CDK2, cyclins A and D1 for proteasomemediated degradation and cause the accumulation of hypophosphorylated retinoblastoma , resulting in the downregulation of CDK1, cyclins E and B1 ." ]

[ [ "0a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "0b", "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." ], [ "0c", "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 ." ], [ "0d", "N is also reported to interact with actin microfilaments, and the SUMO-1 protein ." ], [ "0e", "Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in" ] ]

[ "0b", "0c" ]

[ "Title: Inhibiting the Ins and Outs of HIV Replication: Cell-Intrinsic Antiretroviral Restrictions at the Plasma Membrane\nPassage: The use of CCR5 appears to be essential for sexual transmission of HIV-1. Viruses that use CCR5 alone , or more rarely CCR5 and CXCR4 ], predominate in early infection . Individuals homozygous for a 32 base pair deletion in CCR5 that disrupts its expression are largely HIV-1 resistant . X4-using viruses tend to arise later in infection in some, but not all, individuals, and are associated with more rapid progression to AIDS. Whilst they can be transmitted by intravenous drug-use/transfusion, it is not clear why X4 viruses are almost never transmitted sexually given that target CD4+ T cells in", "Title: Selective use of primate CD4 receptors by HIV-1\nPassage: Next, we wanted to understand more about why blood-derived HIV-1 Env isolates demonstrate this selective use of only some primate CD4 receptors. Thus far, all of the Envs that we have tested are from CCR5-tropic viruses isolated from the blood. There are three types of HIV-1 in the body of an infected person: CCR5 T cell-tropic , CXCR4 T cell-tropic ), and CCR5 macrophage-tropic . Only the first of these transmits to new individuals, whereas the latter two types arise in special evolutionary niches within the human body during the course of chronic infection and rarely transmit . In this", "Title: Selective use of primate CD4 receptors by HIV-1\nPassage: data file . CCR5, C-C motif chemokine receptor 5; GFP, green fluorescent protein. receptors with early HIV-1 isolates representing each of the four major group M HIV-1 subtypes. These four Envs, isolated from patient blood shortly after initial infection , were pseudotyped onto the Q23ΔEnv-GFP virus, as described before. While human CD4 supported entry of all of these viruses, primate CD4 orthologs supported levels of HIV-1 entry that ranged from 2-to 58-fold lower . Collectively, our study has explored a breadth of HIV-1 isolates taken from patient blood, representing all of the major subtypes found globally, and has found that", "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1\nPassage: Beside DC-SIGNR, other HIV-1 receptors are known to influence MTCT of HIV-1 ). Genetic variants in CCR5 have been shown to influence vertical transmission of HIV-1. CCR5 promoter variants resulting in higher expression of the receptor were associated with increased risk of MTCT of HIV-1 among sub-Saharan Africans . The 32-pb deletion polymorphism in CCR5 has be shown to protect from vertical transmission of HIV-1 , but this variant is virtually absent among African populations . High copy numbers of CCL3L1, a potent HIV-1 suppressive ligand for CCR5, are associated with higher chemokine production and lower risk of MTCT of" ]

[ [ "0a", "Title: Inhibiting the Ins and Outs of HIV Replication: Cell-Intrinsic Antiretroviral Restrictions at the Plasma Membrane" ], [ "0b", "Passage: The use of CCR5 appears to be essential for sexual transmission of HIV-1." ], [ "0c", "Viruses that use CCR5 alone , or more rarely CCR5 and CXCR4 ], predominate in early infection ." ], [ "0d", "Individuals homozygous for a 32 base pair deletion in CCR5 that disrupts its expression are largely HIV-1 resistant ." ], [ "0e", "X4-using viruses tend to arise later in infection in some, but not all, individuals, and are associated with more rapid progression to AIDS." ], [ "0f", "Whilst they can be transmitted by intravenous drug-use/transfusion, it is not clear why X4 viruses are almost never transmitted sexually given that target CD4+ T cells in" ] ]

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

[ "Title: Inhibiting the Ins and Outs of HIV Replication: Cell-Intrinsic Antiretroviral Restrictions at the Plasma Membrane\nPassage: The use of CCR5 appears to be essential for sexual transmission of HIV-1. Viruses that use CCR5 alone , or more rarely CCR5 and CXCR4 ], predominate in early infection . Individuals homozygous for a 32 base pair deletion in CCR5 that disrupts its expression are largely HIV-1 resistant . X4-using viruses tend to arise later in infection in some, but not all, individuals, and are associated with more rapid progression to AIDS. Whilst they can be transmitted by intravenous drug-use/transfusion, it is not clear why X4 viruses are almost never transmitted sexually given that target CD4+ T cells in", "Title: Selective use of primate CD4 receptors by HIV-1\nPassage: Next, we wanted to understand more about why blood-derived HIV-1 Env isolates demonstrate this selective use of only some primate CD4 receptors. Thus far, all of the Envs that we have tested are from CCR5-tropic viruses isolated from the blood. There are three types of HIV-1 in the body of an infected person: CCR5 T cell-tropic , CXCR4 T cell-tropic ), and CCR5 macrophage-tropic . Only the first of these transmits to new individuals, whereas the latter two types arise in special evolutionary niches within the human body during the course of chronic infection and rarely transmit . In this", "Title: Selective use of primate CD4 receptors by HIV-1\nPassage: data file . CCR5, C-C motif chemokine receptor 5; GFP, green fluorescent protein. receptors with early HIV-1 isolates representing each of the four major group M HIV-1 subtypes. These four Envs, isolated from patient blood shortly after initial infection , were pseudotyped onto the Q23ΔEnv-GFP virus, as described before. While human CD4 supported entry of all of these viruses, primate CD4 orthologs supported levels of HIV-1 entry that ranged from 2-to 58-fold lower . Collectively, our study has explored a breadth of HIV-1 isolates taken from patient blood, representing all of the major subtypes found globally, and has found that", "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1\nPassage: Beside DC-SIGNR, other HIV-1 receptors are known to influence MTCT of HIV-1 ). Genetic variants in CCR5 have been shown to influence vertical transmission of HIV-1. CCR5 promoter variants resulting in higher expression of the receptor were associated with increased risk of MTCT of HIV-1 among sub-Saharan Africans . The 32-pb deletion polymorphism in CCR5 has be shown to protect from vertical transmission of HIV-1 , but this variant is virtually absent among African populations . High copy numbers of CCL3L1, a potent HIV-1 suppressive ligand for CCR5, are associated with higher chemokine production and lower risk of MTCT of" ]

[ [ "3a", "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1" ], [ "3b", "Passage: Beside DC-SIGNR, other HIV-1 receptors are known to influence MTCT of HIV-1 )." ], [ "3c", "Genetic variants in CCR5 have been shown to influence vertical transmission of HIV-1." ], [ "3d", "CCR5 promoter variants resulting in higher expression of the receptor were associated with increased risk of MTCT of HIV-1 among sub-Saharan Africans ." ], [ "3e", "The 32-pb deletion polymorphism in CCR5 has be shown to protect from vertical transmission of HIV-1 , but this variant is virtually absent among African populations ." ], [ "3f", "High copy numbers of CCL3L1, a potent HIV-1 suppressive ligand for CCR5, are associated with higher chemokine production and lower risk of MTCT of" ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: distance from others.", "Title: Estimating the number of infections and the impact of non-\nPassage: 15. Nouvellet, P. et al. A simple approach to measure transmissibility and forecast incidence.", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic\nPassage: Many kinds of data such as sentinel surveillance of influenza-like-illness , serological survey, and syndromic data are able to infer the transmissibility of infectious diseases. Common surveillance data can be fitted into an exponential growth model or Kermack-McKendricktype models to estimate R 0 . Likelihood-based methods are an alternative . Chowell et al. showed that these types of methods are not sensitive on R 0 estimation given an acceptable goodness of fit. Nevertheless, one of the caveats of using ILI surveillance data is the underreporting although several approaches were developed to adjust this problem .", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic\nPassage: Serological data is another source for inferring transmissibility of an influenza virus . This kind of data helps detecting subclinical infections and the sampling is not affected by the reporting practices. However, it is comparatively costly and requires laboratory resources. A longer time will be taken to ascertain a disease and thus it cannot provide initial estimate for a pandemic outbreak . Seroprevalence surveys are usually suggested to monitor the level of disease spread after a local outbreak in community ." ]

[ [ "2a", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic" ], [ "2b", "Passage: Many kinds of data such as sentinel surveillance of influenza-like-illness , serological survey, and syndromic data are able to infer the transmissibility of infectious diseases." ], [ "2c", "Common surveillance data can be fitted into an exponential growth model or Kermack-McKendricktype models to estimate R 0 ." ], [ "2d", "Likelihood-based methods are an alternative ." ], [ "2e", "Chowell et al. showed that these types of methods are not sensitive on R 0 estimation given an acceptable goodness of fit." ], [ "2f", "Nevertheless, one of the caveats of using ILI surveillance data is the underreporting although several approaches were developed to adjust this problem ." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: distance from others.", "Title: Estimating the number of infections and the impact of non-\nPassage: 15. Nouvellet, P. et al. A simple approach to measure transmissibility and forecast incidence.", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic\nPassage: Many kinds of data such as sentinel surveillance of influenza-like-illness , serological survey, and syndromic data are able to infer the transmissibility of infectious diseases. Common surveillance data can be fitted into an exponential growth model or Kermack-McKendricktype models to estimate R 0 . Likelihood-based methods are an alternative . Chowell et al. showed that these types of methods are not sensitive on R 0 estimation given an acceptable goodness of fit. Nevertheless, one of the caveats of using ILI surveillance data is the underreporting although several approaches were developed to adjust this problem .", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic\nPassage: Serological data is another source for inferring transmissibility of an influenza virus . This kind of data helps detecting subclinical infections and the sampling is not affected by the reporting practices. However, it is comparatively costly and requires laboratory resources. A longer time will be taken to ascertain a disease and thus it cannot provide initial estimate for a pandemic outbreak . Seroprevalence surveys are usually suggested to monitor the level of disease spread after a local outbreak in community ." ]

[ [ "3a", "Title: A statistical method utilizing information of imported cases to estimate the transmissibility for an influenza pandemic" ], [ "3b", "Passage: Serological data is another source for inferring transmissibility of an influenza virus ." ], [ "3c", "This kind of data helps detecting subclinical infections and the sampling is not affected by the reporting practices." ], [ "3d", "However, it is comparatively costly and requires laboratory resources." ], [ "3e", "A longer time will be taken to ascertain a disease and thus it cannot provide initial estimate for a pandemic outbreak ." ], [ "3f", "Seroprevalence surveys are usually suggested to monitor the level of disease spread after a local outbreak in community ." ] ]

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

[ "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: compounds 8012-0652, C481-1256, and G319-0078 were screened out with potency in the nanomolar range against infection of a panel of hantaviruses, including SNV, ANDV, and HTNV . Further studies should be performed to evaluate the safety and efficacy of these small molecules in vivo.", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: to impaired barrier structure of adherent junctions, which could lead to incremental cellular permeability . It has been demonstrated HTNV or ANDV infection could disrupt the interaction of β3 integrin with VEGFR2 and induce VEGFR2 hyper phosphorylation, which may enhance the permeability of infected endothelial cells by sensitizing them to VEGF . As increased VEGF content has been noted in the plasma of HFRS and HCPS patients and is closely related to disease severity in the acute phase , it is feasible to repurpose those FDA-approved drugs targeting vasoactive mediators for use as hantaviral infection therapy. In line with this", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: are suspected or presumed to have a potent interferon-pathway antagonism mechanism relative to other viruses, a mechanism that acts positively to prevent an effective innate response from forming, at least early in infection . Yet some instances are reported wherein highly pathogenic hantaviruses, such as SNV, are also able to induce expression of interferon-stimulated gene mRNAs, even very early in infection, with ISG proteins, as expected, taking longer to appear in the cell . Anti-interferon activities have also been attributed to the NSs protein that may be elaborated in cells infected by serotypes that encode this protein . Other investigators", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: have examined the activities of hantavirus glycoproteins and other proteins that might themselves directly affect some aspects of the pathogenic progression associated with hantavirus infection of humans, such as vascular permeability changes. While early attempts to directly cause increases in permeability of endothelial monolayers with viral particles or viral infection were largely disappointing, hantaviruses have been identified as adversely affecting endothelial migration over substrata and in potentiating VEG-F-induced endothelial permeability ." ]

[ [ "3a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "3b", "Passage: have examined the activities of hantavirus glycoproteins and other proteins that might themselves directly affect some aspects of the pathogenic progression associated with hantavirus infection of humans, such as vascular permeability changes." ], [ "3c", "While early attempts to directly cause increases in permeability of endothelial monolayers with viral particles or viral infection were largely disappointing, hantaviruses have been identified as adversely affecting endothelial migration over substrata and in potentiating VEG-F-induced endothelial permeability ." ] ]

[ "3c" ]

[ "Title: The protective and pathogenic roles of IL-17 in viral infections: friend or foe?\nPassage: Viral infections are common causes of both chronic and acute tissue pathology that create a significant health burden worldwide. For example, human papillomaviruses are the causative agents of epithelial hyperplasia of the skin and genital tract . Persistent infection of HPV can result in malignant lesions, the most common being cervical cancer, which had caused an estimated 0.6 million new cases in 2018 and contributed to more than 0.3 billion deaths . Hepatitis B virus and hepatitis C virus are the major causes of hepatitis and can progress to liver fibrosis, cirrhosis and eventually liver cancer . Human immunodeficiency virus", "Title: Anxiety and Depression: Linkages with Viral Diseases\nPassage: the specific mechanisms can vary by viral illness. Mental conditions such as major depression can delay help-seeking or reduce the likelihood of detection of other health conditions including communicable diseases. 1 Depression and psychological stress have been shown to have a number of biological effects including reduced cell-mediated immunity and increased inflammatory processes. 3 A further issue is that some viral diseases can directly affect the brain and result in mood disorders or cognitive impairment. 1", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: Symptoms are common to each infection and manifest on a gradient. Generally, but far from always, influenza infection is more likely to result in a patient feeling so unwell as to take to their bed and have a fever, than RSV, an HRV, CoV or other common cold virus infection, during which daily life is usually less impacted." ]

[ [ "0a", "Title: The protective and pathogenic roles of IL-17 in viral infections: friend or foe?" ], [ "0b", "Passage: Viral infections are common causes of both chronic and acute tissue pathology that create a significant health burden worldwide." ], [ "0c", "For example, human papillomaviruses are the causative agents of epithelial hyperplasia of the skin and genital tract ." ], [ "0d", "Persistent infection of HPV can result in malignant lesions, the most common being cervical cancer, which had caused an estimated 0.6 million new cases in 2018 and contributed to more than 0.3 billion deaths ." ], [ "0e", "Hepatitis B virus and hepatitis C virus are the major causes of hepatitis and can progress to liver fibrosis, cirrhosis and eventually liver cancer ." ], [ "0f", "Human immunodeficiency virus" ] ]

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

[ "Title: The protective and pathogenic roles of IL-17 in viral infections: friend or foe?\nPassage: Viral infections are common causes of both chronic and acute tissue pathology that create a significant health burden worldwide. For example, human papillomaviruses are the causative agents of epithelial hyperplasia of the skin and genital tract . Persistent infection of HPV can result in malignant lesions, the most common being cervical cancer, which had caused an estimated 0.6 million new cases in 2018 and contributed to more than 0.3 billion deaths . Hepatitis B virus and hepatitis C virus are the major causes of hepatitis and can progress to liver fibrosis, cirrhosis and eventually liver cancer . Human immunodeficiency virus", "Title: Anxiety and Depression: Linkages with Viral Diseases\nPassage: the specific mechanisms can vary by viral illness. Mental conditions such as major depression can delay help-seeking or reduce the likelihood of detection of other health conditions including communicable diseases. 1 Depression and psychological stress have been shown to have a number of biological effects including reduced cell-mediated immunity and increased inflammatory processes. 3 A further issue is that some viral diseases can directly affect the brain and result in mood disorders or cognitive impairment. 1", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: Symptoms are common to each infection and manifest on a gradient. Generally, but far from always, influenza infection is more likely to result in a patient feeling so unwell as to take to their bed and have a fever, than RSV, an HRV, CoV or other common cold virus infection, during which daily life is usually less impacted." ]

[ [ "1a", "Title: Anxiety and Depression: Linkages with Viral Diseases" ], [ "1b", "Passage: the specific mechanisms can vary by viral illness." ], [ "1c", "Mental conditions such as major depression can delay help-seeking or reduce the likelihood of detection of other health conditions including communicable diseases." ], [ "1d", "1 Depression and psychological stress have been shown to have a number of biological effects including reduced cell-mediated immunity and increased inflammatory processes." ], [ "1e", "3 A further issue is that some viral diseases can directly affect the brain and result in mood disorders or cognitive impairment. 1" ] ]

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

[ "Title: The protective and pathogenic roles of IL-17 in viral infections: friend or foe?\nPassage: Viral infections are common causes of both chronic and acute tissue pathology that create a significant health burden worldwide. For example, human papillomaviruses are the causative agents of epithelial hyperplasia of the skin and genital tract . Persistent infection of HPV can result in malignant lesions, the most common being cervical cancer, which had caused an estimated 0.6 million new cases in 2018 and contributed to more than 0.3 billion deaths . Hepatitis B virus and hepatitis C virus are the major causes of hepatitis and can progress to liver fibrosis, cirrhosis and eventually liver cancer . Human immunodeficiency virus", "Title: Anxiety and Depression: Linkages with Viral Diseases\nPassage: the specific mechanisms can vary by viral illness. Mental conditions such as major depression can delay help-seeking or reduce the likelihood of detection of other health conditions including communicable diseases. 1 Depression and psychological stress have been shown to have a number of biological effects including reduced cell-mediated immunity and increased inflammatory processes. 3 A further issue is that some viral diseases can directly affect the brain and result in mood disorders or cognitive impairment. 1", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration. Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration. This also increases the chances of allergens coming into contact with airway immune cells. For example, IFV infection was found to induce oncostatin M which causes tight junction opening . Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: Symptoms are common to each infection and manifest on a gradient. Generally, but far from always, influenza infection is more likely to result in a patient feeling so unwell as to take to their bed and have a fever, than RSV, an HRV, CoV or other common cold virus infection, during which daily life is usually less impacted." ]

[ [ "2a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "2b", "Passage: Another mechanism that viral infections may use to drive acute exacerbations is the induction of vasodilation or tight junction opening factors which may increase the rate of infiltration." ], [ "2c", "Infection with a multitude of respiratory viruses causes disruption of tight junctions with the resulting increased rate of viral infiltration." ], [ "2d", "This also increases the chances of allergens coming into contact with airway immune cells." ], [ "2e", "For example, IFV infection was found to induce oncostatin M which causes tight junction opening ." ], [ "2f", "Similarly, RV and RSV infections usually cause tight junction opening which may also increase the infiltration rate of eosinophils and thus worsening" ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: also been identified in bat with potential severe outcomes. Lyssaviruses in the Rhabdoviridae family have been linked with severe fatal human cases, even in the developed countries, including Australia, with the bites of bats in the city . The potential roles of these viruses in bats for interspecies transmission are yet to be elucidated.", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Text: Bats have received much attention in recent years for their role as reservoir hosts for emerging viral zoonoses, including rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS coronavirus . In most non-Chiropteran mammals, henipaviruses, filoviruses, and coronaviruses induce substantial morbidity and mortality, display short durations of infection, and elicit robust, long-term immunity in hosts surviving infection . Bats, by contrast, demonstrate no obvious disease symptoms upon infection with pathogens that are highly virulent in non-volant mammals but may, instead, support viruses as longterm persistent infections, rather than transient, immunizing pathologies .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats. up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including", "Title: Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses\nPassage: The identification of high neutralizing antibody titers indicates that bats experience infections followed by seroconversion, which in case of humans is correlated with clearance of the virus and survival of infection 48 . CCHFV might thus exemplify another highly pathogenic agent that is effectively controlled in bats." ]

[ [ "0a", "Title: Haunted with and hunting for viruses" ], [ "0b", "Passage: also been identified in bat with potential severe outcomes." ], [ "0c", "Lyssaviruses in the Rhabdoviridae family have been linked with severe fatal human cases, even in the developed countries, including Australia, with the bites of bats in the city ." ], [ "0d", "The potential roles of these viruses in bats for interspecies transmission are yet to be elucidated." ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: also been identified in bat with potential severe outcomes. Lyssaviruses in the Rhabdoviridae family have been linked with severe fatal human cases, even in the developed countries, including Australia, with the bites of bats in the city . The potential roles of these viruses in bats for interspecies transmission are yet to be elucidated.", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Text: Bats have received much attention in recent years for their role as reservoir hosts for emerging viral zoonoses, including rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS coronavirus . In most non-Chiropteran mammals, henipaviruses, filoviruses, and coronaviruses induce substantial morbidity and mortality, display short durations of infection, and elicit robust, long-term immunity in hosts surviving infection . Bats, by contrast, demonstrate no obvious disease symptoms upon infection with pathogens that are highly virulent in non-volant mammals but may, instead, support viruses as longterm persistent infections, rather than transient, immunizing pathologies .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats. up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including", "Title: Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses\nPassage: The identification of high neutralizing antibody titers indicates that bats experience infections followed by seroconversion, which in case of humans is correlated with clearance of the virus and survival of infection 48 . CCHFV might thus exemplify another highly pathogenic agent that is effectively controlled in bats." ]

[ [ "1a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "1b", "Passage: Text: Bats have received much attention in recent years for their role as reservoir hosts for emerging viral zoonoses, including rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS coronavirus ." ], [ "1c", "In most non-Chiropteran mammals, henipaviruses, filoviruses, and coronaviruses induce substantial morbidity and mortality, display short durations of infection, and elicit robust, long-term immunity in hosts surviving infection ." ], [ "1d", "Bats, by contrast, demonstrate no obvious disease symptoms upon infection with pathogens that are highly virulent in non-volant mammals but may, instead, support viruses as longterm persistent infections, rather than transient, immunizing pathologies ." ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: also been identified in bat with potential severe outcomes. Lyssaviruses in the Rhabdoviridae family have been linked with severe fatal human cases, even in the developed countries, including Australia, with the bites of bats in the city . The potential roles of these viruses in bats for interspecies transmission are yet to be elucidated.", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Text: Bats have received much attention in recent years for their role as reservoir hosts for emerging viral zoonoses, including rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS coronavirus . In most non-Chiropteran mammals, henipaviruses, filoviruses, and coronaviruses induce substantial morbidity and mortality, display short durations of infection, and elicit robust, long-term immunity in hosts surviving infection . Bats, by contrast, demonstrate no obvious disease symptoms upon infection with pathogens that are highly virulent in non-volant mammals but may, instead, support viruses as longterm persistent infections, rather than transient, immunizing pathologies .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats. up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including", "Title: Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses\nPassage: The identification of high neutralizing antibody titers indicates that bats experience infections followed by seroconversion, which in case of humans is correlated with clearance of the virus and survival of infection 48 . CCHFV might thus exemplify another highly pathogenic agent that is effectively controlled in bats." ]

[ [ "2a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "2b", "Passage: The findings may help to explain why bats are often the source for viruses that are deadly in humans." ], [ "2c", "Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans." ], [ "2d", "More studies are needed in bats to help these efforts." ], [ "2e", "In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats." ], [ "2f", "up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including" ] ]

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

[ "Title: Haunted with and hunting for viruses\nPassage: also been identified in bat with potential severe outcomes. Lyssaviruses in the Rhabdoviridae family have been linked with severe fatal human cases, even in the developed countries, including Australia, with the bites of bats in the city . The potential roles of these viruses in bats for interspecies transmission are yet to be elucidated.", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Text: Bats have received much attention in recent years for their role as reservoir hosts for emerging viral zoonoses, including rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and SARS coronavirus . In most non-Chiropteran mammals, henipaviruses, filoviruses, and coronaviruses induce substantial morbidity and mortality, display short durations of infection, and elicit robust, long-term immunity in hosts surviving infection . Bats, by contrast, demonstrate no obvious disease symptoms upon infection with pathogens that are highly virulent in non-volant mammals but may, instead, support viruses as longterm persistent infections, rather than transient, immunizing pathologies .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: The findings may help to explain why bats are often the source for viruses that are deadly in humans. Learning more about bats' antiviral defenses and how they drive virus evolution may help scientists develop better ways to predict, prevent or limit the spread of viruses from bats to humans. More studies are needed in bats to help these efforts. In the meantime, the experiments highlight the importance of warning people to avoid direct contact with wild bats. up resource supply of infection-susceptible host cells, were first developed for HIV but have since been applied to other chronic infections, including", "Title: Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses\nPassage: The identification of high neutralizing antibody titers indicates that bats experience infections followed by seroconversion, which in case of humans is correlated with clearance of the virus and survival of infection 48 . CCHFV might thus exemplify another highly pathogenic agent that is effectively controlled in bats." ]

[ [ "3a", "Title: Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses" ], [ "3b", "Passage: The identification of high neutralizing antibody titers indicates that bats experience infections followed by seroconversion, which in case of humans is correlated with clearance of the virus and survival of infection 48 ." ], [ "3c", "CCHFV might thus exemplify another highly pathogenic agent that is effectively controlled in bats." ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: viruses in the clinical sample and their prevalence in the community. Finally, some of the viruses detected in this study have not been detected and implicated with ARIs in Nigeria. There is no report, to the best of our knowledge, implicating coronavirus in ARIs in Nigeria, and it was detected in 12 subjects in this study. Although cases of double and triple infections were observed in a study in Nigeria in 2011 , as far as we are aware, reports of quadruple infections are rare and have not been reported in Nigeria previously.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ]

[ [ "0a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "0b", "Passage: and 5 of quadruple." ], [ "0c", "Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects ." ], [ "0d", "Coronavirus OC43 was the most common virus detected in community members ." ], [ "0e", "A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community." ], [ "0f", "This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ] ]

[ "0d", "1f" ]

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: viruses in the clinical sample and their prevalence in the community. Finally, some of the viruses detected in this study have not been detected and implicated with ARIs in Nigeria. There is no report, to the best of our knowledge, implicating coronavirus in ARIs in Nigeria, and it was detected in 12 subjects in this study. Although cases of double and triple infections were observed in a study in Nigeria in 2011 , as far as we are aware, reports of quadruple infections are rare and have not been reported in Nigeria previously.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ]

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

[ "0d", "1f" ]

[ "Title: Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review\nPassage: One reviewer screened and evaluated the titles and abstracts. Articles were widely included in a first stage. The full-text review and the final selection of the articles were made by two reviewers.", "Title: Cochrane Systematic Reviews of Chinese Herbal Medicines: An Overview\nPassage: based on how well the review scored on the first 9 questions.", "Title: Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude\nPassage: We appreciate the positive comments from the reviewers, who described our results as \"interesting and novel,\" \"engaging,\" \"well written,\" \"clear,\" \"quite intriguing,\" and \"very powerful.\" Further a reviewer noted that the manuscript does a \"good job of convincing me that this approach can be translatable.\" We also thank the Reviewers for their constructive feedback, which we are confident has strengthened the manuscript. We have addressed the comments by collecting additional data, performing additional analyses, and clarifying our conclusions. Below is a point-by-point response to the reviewers comments.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed ." ]

[ [ "0a", "Title: Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review" ], [ "0b", "Passage: One reviewer screened and evaluated the titles and abstracts." ], [ "0c", "Articles were widely included in a first stage." ], [ "0d", "The full-text review and the final selection of the articles were made by two reviewers." ] ]

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

[ "Title: Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review\nPassage: One reviewer screened and evaluated the titles and abstracts. Articles were widely included in a first stage. The full-text review and the final selection of the articles were made by two reviewers.", "Title: Cochrane Systematic Reviews of Chinese Herbal Medicines: An Overview\nPassage: based on how well the review scored on the first 9 questions.", "Title: Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude\nPassage: We appreciate the positive comments from the reviewers, who described our results as \"interesting and novel,\" \"engaging,\" \"well written,\" \"clear,\" \"quite intriguing,\" and \"very powerful.\" Further a reviewer noted that the manuscript does a \"good job of convincing me that this approach can be translatable.\" We also thank the Reviewers for their constructive feedback, which we are confident has strengthened the manuscript. We have addressed the comments by collecting additional data, performing additional analyses, and clarifying our conclusions. Below is a point-by-point response to the reviewers comments.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed ." ]

[ [ "1a", "Title: Cochrane Systematic Reviews of Chinese Herbal Medicines: An Overview" ], [ "1b", "Passage: based on how well the review scored on the first 9 questions." ] ]

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

[ "Title: Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review\nPassage: One reviewer screened and evaluated the titles and abstracts. Articles were widely included in a first stage. The full-text review and the final selection of the articles were made by two reviewers.", "Title: Cochrane Systematic Reviews of Chinese Herbal Medicines: An Overview\nPassage: based on how well the review scored on the first 9 questions.", "Title: Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude\nPassage: We appreciate the positive comments from the reviewers, who described our results as \"interesting and novel,\" \"engaging,\" \"well written,\" \"clear,\" \"quite intriguing,\" and \"very powerful.\" Further a reviewer noted that the manuscript does a \"good job of convincing me that this approach can be translatable.\" We also thank the Reviewers for their constructive feedback, which we are confident has strengthened the manuscript. We have addressed the comments by collecting additional data, performing additional analyses, and clarifying our conclusions. Below is a point-by-point response to the reviewers comments.", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: The health-evidence.ca registry was used to identify gaps and areas of wealth in the public health review literature. Each of the 21 Focus of Review topic areas were searched, and the quantity and proportion of reviews rated methodologically strong, moderate, and weak were identified. Three categories were used to define availability of reviews within each topic area: few, representing 1-150 reviews; moderate, representing 151-300 reviews; and, many, representing topic areas possessing greater than 301 reviews. Reviews that addressed multiple topics were accounted for within each topic area that they addressed ." ]

[ [ "2a", "Title: Red blood cell-hitchhiking boosts delivery of nanocarriers to chosen organs by orders of magnitude" ], [ "2b", "Passage: We appreciate the positive comments from the reviewers, who described our results as \"interesting and novel,\" \"engaging,\" \"well written,\" \"clear,\" \"quite intriguing,\" and \"very powerful.\"" ], [ "2c", "Further a reviewer noted that the manuscript does a \"good job of convincing me that this approach can be translatable.\"" ], [ "2d", "We also thank the Reviewers for their constructive feedback, which we are confident has strengthened the manuscript." ], [ "2e", "We have addressed the comments by collecting additional data, performing additional analyses, and clarifying our conclusions." ], [ "2f", "Below is a point-by-point response to the reviewers comments." ] ]

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: According to World Health Organization statistics, influenza occurs globally with an estimated annual attack rate of 5%-10% in adults and 20%-30% in children . These annual epidemics are estimated to result in approximately 3 to 5 million cases of severe illness worldwide and around 250 000 to 500 000 deaths, which is a major cause of losses in human lives and a grave global public health issue." ]

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

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: According to World Health Organization statistics, influenza occurs globally with an estimated annual attack rate of 5%-10% in adults and 20%-30% in children . These annual epidemics are estimated to result in approximately 3 to 5 million cases of severe illness worldwide and around 250 000 to 500 000 deaths, which is a major cause of losses in human lives and a grave global public health issue." ]

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

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: According to World Health Organization statistics, influenza occurs globally with an estimated annual attack rate of 5%-10% in adults and 20%-30% in children . These annual epidemics are estimated to result in approximately 3 to 5 million cases of severe illness worldwide and around 250 000 to 500 000 deaths, which is a major cause of losses in human lives and a grave global public health issue." ]

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

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

[ "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: Influenza is an infectious disease affecting mainly upper respiratory tract worldwide. Influenza virus causes between three and five million severe cases and an estimated 250,000-350,000 deaths annually. In the European Union, there are between 40,000 and 220,000 annual deaths attributable to influenza. However, mortality is only the tip of the iceberg in terms of the disease burden, since influenza also causes a decrease in functional status and increased dependency in the elderly . Estimating the burden of disease caused by influenza is difficult because many cases do not require medical care, or no confirmatory laboratory tests are widely performed to", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Seasonal influenza remains an important infectious cause of morbidity and mortality . In the USA alone, estimates of annual incidence range from 9.2 million to 35.6 million cases, resulting in 140 000 to 710 000 hospitalizations and 12 000 to 56 000 deaths .", "Title: Forecasting the 2013–2014 Influenza Season Using Wikipedia\nPassage: hospitalized from seasonal influenza complications, and 3,000-49,000 people die each year . The result is a significant public health and economic burden for the U.S. population .", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: According to World Health Organization statistics, influenza occurs globally with an estimated annual attack rate of 5%-10% in adults and 20%-30% in children . These annual epidemics are estimated to result in approximately 3 to 5 million cases of severe illness worldwide and around 250 000 to 500 000 deaths, which is a major cause of losses in human lives and a grave global public health issue." ]

[ [ "3a", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic" ], [ "3b", "Passage: According to World Health Organization statistics, influenza occurs globally with an estimated annual attack rate of 5%-10% in adults and 20%-30% in children ." ], [ "3c", "These annual epidemics are estimated to result in approximately 3 to 5 million cases of severe illness worldwide and around 250 000 to 500 000 deaths, which is a major cause of losses in human lives and a grave global public health issue." ] ]

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

[ "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: Clinical investigation found that high concentration of cytokines were detected in the plasma of critically ill patients infected with SARS-CoV-2, suggesting that cytokine storm was associated with disease severity 12 . Other than its direct antiviral activity, HCQ is a safe and successful anti-inflammatory agent that has been used extensively in autoimmune diseases and can significantly decrease the production of cytokines and, in particular, pro-inflammatory factors. Therefore, in COVID-19 patients, HCQ may also contribute to attenuating the inflammatory response. In conclusion, our results show that HCQ can efficiently inhibit SARS-CoV-2 infection in vitro. In combination with its anti-inflammatory function, we", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: different expression levels of virus nucleoprotein at the indicated drug concentrations at 48 h p.i. . Taken together, the data suggest that the anti-SARS-CoV-2 activity of HCQ seems to be less potent compared to CQ, at least at certain MOIs.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: well as over 10,566 confirmed cases in 72 other countries. Such huge numbers of infected and dead people call for an urgent demand of effective, available, and affordable drugs to control and diminish the epidemic.", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro\nPassage: To this end, we evaluated the antiviral effect of HCQ against SARS-CoV-2 infection in comparison to CQ in vitro. First, the cytotoxicity of HCQ and CQ in African green monkey kidney VeroE6 cells was measured by standard CCK8 assay, and the result showed © The Author 2020" ]

[ [ "0a", "Title: Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro" ], [ "0b", "Passage: Clinical investigation found that high concentration of cytokines were detected in the plasma of critically ill patients infected with SARS-CoV-2, suggesting that cytokine storm was associated with disease severity 12 ." ], [ "0c", "Other than its direct antiviral activity, HCQ is a safe and successful anti-inflammatory agent that has been used extensively in autoimmune diseases and can significantly decrease the production of cytokines and, in particular, pro-inflammatory factors." ], [ "0d", "Therefore, in COVID-19 patients, HCQ may also contribute to attenuating the inflammatory response." ], [ "0e", "In conclusion, our results show that HCQ can efficiently inhibit SARS-CoV-2 infection in vitro." ], [ "0f", "In combination with its anti-inflammatory function, we" ] ]

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

[ "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Finally, rVSV-G and rVSV-EBOV trials on PaKiT01 cells were best fit by models assuming constitutive immunity, while rVSV-MARV infections on PaKiT01 were matched equivalently by models assuming either induced or constitutive immunity-with induced models favored over constitutive in AIC comparisons because one fewer parameter was estimated . For all virus infections, PaKiT01 cell lines yielded b estimates a full order of magnitude higher than Vero or RoNi/7.1 cells, with each b balanced by an immune response also an order of magnitude higher than that recovered for the other cell lines . As in RoNi/7.1 cells, PaKiT01 parameter fits localized in", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Because and \" both contribute to this initial antiviral rate, induced and constitutive immune assumptions are capable of yielding equally rapid rates, depending on parameter fits. Indeed, under fully induced immune assumptions, the induced antiviral acquisition rate estimated for rVSV-MARV infection on PaKiT01 cells was so high that the initial antiviral rate exceeded even that estimated under constitutive assumptions for this cell-virus combination . In reality, we know that NPC1 receptor incompatibilities make PaKiT01 cell lines constitutively refractory to rVSV-MARV infection and that PaKiT01 cells also constitutively express the antiviral cytokine, IFN-a. Model fitting results suggest that this constitutive expression", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: of these viruses, rVSV-EBOV and rVSV-MARV, are recombinants for which cell entry is mediated by the glycoprotein of the bat-evolved filoviruses, Ebola and Marburg , thus allowing us to modulate the extent of structural, as well as immunological, antiviral defense at play in each infection. Previous work in this lab has demonstrated incompatibilities in the NPC1 filovirus receptor which render PaKiT01 cells refractory to infection with rVSV-MARV , making them structurally antiviral, over and above their constitutive expression of IFN-a. All three cell lines were challenged with all three viruses at two multiplicities of infection : 0.001 and 0.0001. Between", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Total monolayer destruction occurred in all cell-virus combinations excepting rVSV-EBOV infections on RoNi/7.1 cells and rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells. Monolayer destruction corresponded to susceptible cell depletion and epidemic turnover where R-effective was reduced below one . For rVSV-EBOV infections on RoNi/7.1, induced antiviral cells safeguarded remnant live cells, which birthed new susceptible cells late in the time series. In rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells, this antiviral protection halted the epidemic before susceptibles fully declined. In the case of rVSV-EBOV on PaKiT01, the birth of new susceptibles from remnant live cells protected by antiviral status maintained" ]

[ [ "1a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "1b", "Passage: Because and \" both contribute to this initial antiviral rate, induced and constitutive immune assumptions are capable of yielding equally rapid rates, depending on parameter fits." ], [ "1c", "Indeed, under fully induced immune assumptions, the induced antiviral acquisition rate estimated for rVSV-MARV infection on PaKiT01 cells was so high that the initial antiviral rate exceeded even that estimated under constitutive assumptions for this cell-virus combination ." ], [ "1d", "In reality, we know that NPC1 receptor incompatibilities make PaKiT01 cell lines constitutively refractory to rVSV-MARV infection and that PaKiT01 cells also constitutively express the antiviral cytokine, IFN-a." ], [ "1e", "Model fitting results suggest that this constitutive expression" ] ]

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

[ "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Finally, rVSV-G and rVSV-EBOV trials on PaKiT01 cells were best fit by models assuming constitutive immunity, while rVSV-MARV infections on PaKiT01 were matched equivalently by models assuming either induced or constitutive immunity-with induced models favored over constitutive in AIC comparisons because one fewer parameter was estimated . For all virus infections, PaKiT01 cell lines yielded b estimates a full order of magnitude higher than Vero or RoNi/7.1 cells, with each b balanced by an immune response also an order of magnitude higher than that recovered for the other cell lines . As in RoNi/7.1 cells, PaKiT01 parameter fits localized in", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Because and \" both contribute to this initial antiviral rate, induced and constitutive immune assumptions are capable of yielding equally rapid rates, depending on parameter fits. Indeed, under fully induced immune assumptions, the induced antiviral acquisition rate estimated for rVSV-MARV infection on PaKiT01 cells was so high that the initial antiviral rate exceeded even that estimated under constitutive assumptions for this cell-virus combination . In reality, we know that NPC1 receptor incompatibilities make PaKiT01 cell lines constitutively refractory to rVSV-MARV infection and that PaKiT01 cells also constitutively express the antiviral cytokine, IFN-a. Model fitting results suggest that this constitutive expression", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: of these viruses, rVSV-EBOV and rVSV-MARV, are recombinants for which cell entry is mediated by the glycoprotein of the bat-evolved filoviruses, Ebola and Marburg , thus allowing us to modulate the extent of structural, as well as immunological, antiviral defense at play in each infection. Previous work in this lab has demonstrated incompatibilities in the NPC1 filovirus receptor which render PaKiT01 cells refractory to infection with rVSV-MARV , making them structurally antiviral, over and above their constitutive expression of IFN-a. All three cell lines were challenged with all three viruses at two multiplicities of infection : 0.001 and 0.0001. Between", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Total monolayer destruction occurred in all cell-virus combinations excepting rVSV-EBOV infections on RoNi/7.1 cells and rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells. Monolayer destruction corresponded to susceptible cell depletion and epidemic turnover where R-effective was reduced below one . For rVSV-EBOV infections on RoNi/7.1, induced antiviral cells safeguarded remnant live cells, which birthed new susceptible cells late in the time series. In rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells, this antiviral protection halted the epidemic before susceptibles fully declined. In the case of rVSV-EBOV on PaKiT01, the birth of new susceptibles from remnant live cells protected by antiviral status maintained" ]

[ [ "2a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "2b", "Passage: of these viruses, rVSV-EBOV and rVSV-MARV, are recombinants for which cell entry is mediated by the glycoprotein of the bat-evolved filoviruses, Ebola and Marburg , thus allowing us to modulate the extent of structural, as well as immunological, antiviral defense at play in each infection." ], [ "2c", "Previous work in this lab has demonstrated incompatibilities in the NPC1 filovirus receptor which render PaKiT01 cells refractory to infection with rVSV-MARV , making them structurally antiviral, over and above their constitutive expression of IFN-a." ], [ "2d", "All three cell lines were challenged with all three viruses at two multiplicities of infection : 0.001 and 0.0001. Between" ] ]

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

[ "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Finally, rVSV-G and rVSV-EBOV trials on PaKiT01 cells were best fit by models assuming constitutive immunity, while rVSV-MARV infections on PaKiT01 were matched equivalently by models assuming either induced or constitutive immunity-with induced models favored over constitutive in AIC comparisons because one fewer parameter was estimated . For all virus infections, PaKiT01 cell lines yielded b estimates a full order of magnitude higher than Vero or RoNi/7.1 cells, with each b balanced by an immune response also an order of magnitude higher than that recovered for the other cell lines . As in RoNi/7.1 cells, PaKiT01 parameter fits localized in", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Because and \" both contribute to this initial antiviral rate, induced and constitutive immune assumptions are capable of yielding equally rapid rates, depending on parameter fits. Indeed, under fully induced immune assumptions, the induced antiviral acquisition rate estimated for rVSV-MARV infection on PaKiT01 cells was so high that the initial antiviral rate exceeded even that estimated under constitutive assumptions for this cell-virus combination . In reality, we know that NPC1 receptor incompatibilities make PaKiT01 cell lines constitutively refractory to rVSV-MARV infection and that PaKiT01 cells also constitutively express the antiviral cytokine, IFN-a. Model fitting results suggest that this constitutive expression", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: of these viruses, rVSV-EBOV and rVSV-MARV, are recombinants for which cell entry is mediated by the glycoprotein of the bat-evolved filoviruses, Ebola and Marburg , thus allowing us to modulate the extent of structural, as well as immunological, antiviral defense at play in each infection. Previous work in this lab has demonstrated incompatibilities in the NPC1 filovirus receptor which render PaKiT01 cells refractory to infection with rVSV-MARV , making them structurally antiviral, over and above their constitutive expression of IFN-a. All three cell lines were challenged with all three viruses at two multiplicities of infection : 0.001 and 0.0001. Between", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Total monolayer destruction occurred in all cell-virus combinations excepting rVSV-EBOV infections on RoNi/7.1 cells and rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells. Monolayer destruction corresponded to susceptible cell depletion and epidemic turnover where R-effective was reduced below one . For rVSV-EBOV infections on RoNi/7.1, induced antiviral cells safeguarded remnant live cells, which birthed new susceptible cells late in the time series. In rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells, this antiviral protection halted the epidemic before susceptibles fully declined. In the case of rVSV-EBOV on PaKiT01, the birth of new susceptibles from remnant live cells protected by antiviral status maintained" ]

[ [ "3a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "3b", "Passage: Total monolayer destruction occurred in all cell-virus combinations excepting rVSV-EBOV infections on RoNi/7.1 cells and rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells." ], [ "3c", "Monolayer destruction corresponded to susceptible cell depletion and epidemic turnover where R-effective was reduced below one ." ], [ "3d", "For rVSV-EBOV infections on RoNi/7.1, induced antiviral cells safeguarded remnant live cells, which birthed new susceptible cells late in the time series." ], [ "3e", "In rVSV-EBOV and rVSV-MARV infections on PaKiT01 cells, this antiviral protection halted the epidemic before susceptibles fully declined." ], [ "3f", "In the case of rVSV-EBOV on PaKiT01, the birth of new susceptibles from remnant live cells protected by antiviral status maintained" ] ]

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

[ "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Multiple, patchy, sub-segmental or segmental groundglass density shadows in both lungs. They were classified as \"paving stone-like\" changes by fine-grid or small honeycomb-like thickening of interlobular septa. The thinner the CT scan layers, the clearer the ground-glass opacity and thickening of interlobular septa were displayed. A slightly high-density and ground-glass change with fuzzy edge in the fine-grid or small honeycomb-like thickening of interlobular septa were presented by the high-resolution computed tomography , . The resolution of X-ray was worse lower than that of CT in the resolution, which was basically manifested as ground-glass When coughing or sneezing, it is", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Atypical CT/X-ray imaging manifestation, including Single, or multiple, or extensive subpleural grid-like or honeycomb-like thickening of interlobular septum, thickening of the bronchial wall, and tortuous and thick strand-like opacity. Several patchy consolidations, occasionally with a small amount pleural effusion or enlargement of mediastinal lymph nodes, can be seen . This is mostly seen in the elderly.", "Title: Tidal changes on CT and progression of ARDS\nPassage: Images were reconstructed to voxel size of 0.98*0.98*1 mm with standard Filtered Back Projection FBP. The dosage for each scan was 9 1.4 mSv. For the current study, inspiratory and expiratory images were registered, manually segmented by trained operators, and replotted in PRM using the same methodology used for the animal scans. High risk and severely injured voxels were identified and measured using the inspiratory-expiratory density ranges derived from the animal experiments. In addition to PRM analysis, CT density analysis was performed, using methods described in the original publication. Briefly, three dimensional regions of interest were segmented on the original", "Title: Radiological and Clinical Characteristics of a Military Outbreak of Pandemic H1N1 2009 Influenza Virus Infection\nPassage: All radiographic examinations were performed using digital radiographic equipment and a standardized technique . Thin-section CTs of the thorax were performed using a 16 channel CT scanner , with the following parameters: 1.25 mm slice thickness with a 2.5 mm gap, supine position, scanning during inspiration, 6 seconds scan time, 120kV, auto mA." ]

[ [ "0a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "0b", "Passage: Multiple, patchy, sub-segmental or segmental groundglass density shadows in both lungs." ], [ "0c", "They were classified as \"paving stone-like\" changes by fine-grid or small honeycomb-like thickening of interlobular septa." ], [ "0d", "The thinner the CT scan layers, the clearer the ground-glass opacity and thickening of interlobular septa were displayed." ], [ "0e", "A slightly high-density and ground-glass change with fuzzy edge in the fine-grid or small honeycomb-like thickening of interlobular septa were presented by the high-resolution computed tomography , ." ], [ "0f", "The resolution of X-ray was worse lower than that of CT in the resolution, which was basically manifested as ground-glass When coughing or sneezing, it is" ] ]

[ "0d", "3c" ]

[ "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Multiple, patchy, sub-segmental or segmental groundglass density shadows in both lungs. They were classified as \"paving stone-like\" changes by fine-grid or small honeycomb-like thickening of interlobular septa. The thinner the CT scan layers, the clearer the ground-glass opacity and thickening of interlobular septa were displayed. A slightly high-density and ground-glass change with fuzzy edge in the fine-grid or small honeycomb-like thickening of interlobular septa were presented by the high-resolution computed tomography , . The resolution of X-ray was worse lower than that of CT in the resolution, which was basically manifested as ground-glass When coughing or sneezing, it is", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Atypical CT/X-ray imaging manifestation, including Single, or multiple, or extensive subpleural grid-like or honeycomb-like thickening of interlobular septum, thickening of the bronchial wall, and tortuous and thick strand-like opacity. Several patchy consolidations, occasionally with a small amount pleural effusion or enlargement of mediastinal lymph nodes, can be seen . This is mostly seen in the elderly.", "Title: Tidal changes on CT and progression of ARDS\nPassage: Images were reconstructed to voxel size of 0.98*0.98*1 mm with standard Filtered Back Projection FBP. The dosage for each scan was 9 1.4 mSv. For the current study, inspiratory and expiratory images were registered, manually segmented by trained operators, and replotted in PRM using the same methodology used for the animal scans. High risk and severely injured voxels were identified and measured using the inspiratory-expiratory density ranges derived from the animal experiments. In addition to PRM analysis, CT density analysis was performed, using methods described in the original publication. Briefly, three dimensional regions of interest were segmented on the original", "Title: Radiological and Clinical Characteristics of a Military Outbreak of Pandemic H1N1 2009 Influenza Virus Infection\nPassage: All radiographic examinations were performed using digital radiographic equipment and a standardized technique . Thin-section CTs of the thorax were performed using a 16 channel CT scanner , with the following parameters: 1.25 mm slice thickness with a 2.5 mm gap, supine position, scanning during inspiration, 6 seconds scan time, 120kV, auto mA." ]

[ [ "3a", "Title: Radiological and Clinical Characteristics of a Military Outbreak of Pandemic H1N1 2009 Influenza Virus Infection" ], [ "3b", "Passage: All radiographic examinations were performed using digital radiographic equipment and a standardized technique ." ], [ "3c", "Thin-section CTs of the thorax were performed using a 16 channel CT scanner , with the following parameters: 1.25 mm slice thickness with a 2.5 mm gap, supine position, scanning during inspiration, 6 seconds scan time, 120kV, auto mA." ] ]

[ "0d", "3c" ]

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection\nPassage: Antibodies were tested at 10 µg/ml and threefold serial dilutions until a nonbinding concentration was determined. Each antibody was tested in at least two replicates for specificity and affinity estimations. Note that only 14 of 15 HA-binding antibodies have curves in G because one of the HA-reactive antibodies only binds HA on whole virions, not on the recombinant protein.", "Title: Generation and comparative genomics of synthetic dengue viruses\nPassage: titers from serum taken 14 dpi . Note that there were not sufficient quantities of serum for 5 samples: 2 from group 1, 1 from group 2 and 2 from control group for quantification of neutralizing Ab detection . Despite the lower rate of detection of viral RNA in these samples, the mean viral RNA level in this group was significantly elevated as compared with controls. No viral RNA was detected in the serum of sham-infected mice." ]

[ [ "0a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: doses, respectively, and was maintained in 79% participants up to study end at week 60." ], [ "0c", "Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study." ], [ "0d", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively." ], [ "0e", "There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection\nPassage: Antibodies were tested at 10 µg/ml and threefold serial dilutions until a nonbinding concentration was determined. Each antibody was tested in at least two replicates for specificity and affinity estimations. Note that only 14 of 15 HA-binding antibodies have curves in G because one of the HA-reactive antibodies only binds HA on whole virions, not on the recombinant protein.", "Title: Generation and comparative genomics of synthetic dengue viruses\nPassage: titers from serum taken 14 dpi . Note that there were not sufficient quantities of serum for 5 samples: 2 from group 1, 1 from group 2 and 2 from control group for quantification of neutralizing Ab detection . Despite the lower rate of detection of viral RNA in these samples, the mean viral RNA level in this group was significantly elevated as compared with controls. No viral RNA was detected in the serum of sham-infected mice." ]

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

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60.", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests are", "Title: Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection\nPassage: Antibodies were tested at 10 µg/ml and threefold serial dilutions until a nonbinding concentration was determined. Each antibody was tested in at least two replicates for specificity and affinity estimations. Note that only 14 of 15 HA-binding antibodies have curves in G because one of the HA-reactive antibodies only binds HA on whole virions, not on the recombinant protein.", "Title: Generation and comparative genomics of synthetic dengue viruses\nPassage: titers from serum taken 14 dpi . Note that there were not sufficient quantities of serum for 5 samples: 2 from group 1, 1 from group 2 and 2 from control group for quantification of neutralizing Ab detection . Despite the lower rate of detection of viral RNA in these samples, the mean viral RNA level in this group was significantly elevated as compared with controls. No viral RNA was detected in the serum of sham-infected mice." ]

[ [ "3a", "Title: Generation and comparative genomics of synthetic dengue viruses" ], [ "3b", "Passage: titers from serum taken 14 dpi ." ], [ "3c", "Note that there were not sufficient quantities of serum for 5 samples: 2 from group 1, 1 from group 2 and 2 from control group for quantification of neutralizing Ab detection ." ], [ "3d", "Despite the lower rate of detection of viral RNA in these samples, the mean viral RNA level in this group was significantly elevated as compared with controls." ], [ "3e", "No viral RNA was detected in the serum of sham-infected mice." ] ]

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

[ "Title: HBV Immune-Therapy: From Molecular Mechanisms to Clinical Applications\nPassage: First reported in chronic Lymphocytic Choriomeningitis Virus infection, the up-regulation of co-inhibitory receptors, or immune checkpoints, has then been widely described as a common hallmark of exhausted CD8 T cells in different chronic infection and tumor models. Indeed, gene expression profiling and functional T cell analysis of virus-specific CD8 T cells from chronically LCMV-infected mice led to the characterization of the role played by PD-1 and other highly co-expressed inhibitory molecules, such as 2B4, CTLA-4, Tim-3, Lag-3, TIGIT, BTLA, CD160, PSGL1, in promoting a dysfunctional phenotype in exhausted antigen-specific CD8 T cells . Later on, the evidence that an efficient", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection\nPassage: Furthermore, Nef inhibits T cell receptor induced lymphocyte activation . These strategies contribute to the suppression of HIV proliferation in the lymph nodes, and also inhibit the propagation of infection. Other immunosuppressive mechanisms used by HIV have also been reported. Cosuppressive molecules, such as B7-H1 on DCs and PD1 on T lymphocytes, are upregulated in patients with HIV, and induce apoptosis through their interaction with DCs and T lymphocytes. In addition, HIV is thought to induce regulatory T cells .", "Title: Confounding roles for type I interferons during bacterial and viral pathogenesis\nPassage: Several hallmarks of the negative effects of chronic viral infection have been discovered using this system. Mice become chronically infected with LCMV because of T-cell 'exhaustion' that prevents normal clearance . Several factors have been implicated in the suppression of T-cellmediated clearance of chronic LCMV; most salient among them are IL-10 and PD-1 . IL-10 is known to antagonize inflammatory activation on multiple immune cell types and its neutralization prevents chronic infection with LCMV . PD-1, a member of the CD28/CTLA4 family of T-cell regulators, is upregulated on exhausted T cells found in chronically infected mice. Its ligands, PD-1L and", "Title: Tumor Restrictions to Oncolytic Virus\nPassage: On a cellular level, virus replication is controlled by antiviral defense molecules , which in turn are primarily controlled by type I IFN signaling. In addition to classical type I IFN-or cytokine-induced antiviral signaling, tumors may employ other antiviral defense mechanisms. For example, stromal cells may secrete peptides with antiviral properties called defensins . The defensins are amphiphatic and typically 29-42 amino acids in length and interfere with viruses by physically binding to and disrupting virus particles and/or by inducing antiviral responses in target cells via pattern recognition receptors. At least oral squamous cell carcinomas were found to overexpress defensins" ]

[ [ "0a", "Title: HBV Immune-Therapy: From Molecular Mechanisms to Clinical Applications" ], [ "0b", "Passage: First reported in chronic Lymphocytic Choriomeningitis Virus infection, the up-regulation of co-inhibitory receptors, or immune checkpoints, has then been widely described as a common hallmark of exhausted CD8 T cells in different chronic infection and tumor models." ], [ "0c", "Indeed, gene expression profiling and functional T cell analysis of virus-specific CD8 T cells from chronically LCMV-infected mice led to the characterization of the role played by PD-1 and other highly co-expressed inhibitory molecules, such as 2B4, CTLA-4, Tim-3, Lag-3, TIGIT, BTLA, CD160, PSGL1, in promoting a dysfunctional phenotype in exhausted antigen-specific CD8 T cells ." ], [ "0d", "Later on, the evidence that an efficient" ] ]

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

[ "Title: HBV Immune-Therapy: From Molecular Mechanisms to Clinical Applications\nPassage: First reported in chronic Lymphocytic Choriomeningitis Virus infection, the up-regulation of co-inhibitory receptors, or immune checkpoints, has then been widely described as a common hallmark of exhausted CD8 T cells in different chronic infection and tumor models. Indeed, gene expression profiling and functional T cell analysis of virus-specific CD8 T cells from chronically LCMV-infected mice led to the characterization of the role played by PD-1 and other highly co-expressed inhibitory molecules, such as 2B4, CTLA-4, Tim-3, Lag-3, TIGIT, BTLA, CD160, PSGL1, in promoting a dysfunctional phenotype in exhausted antigen-specific CD8 T cells . Later on, the evidence that an efficient", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection\nPassage: Furthermore, Nef inhibits T cell receptor induced lymphocyte activation . These strategies contribute to the suppression of HIV proliferation in the lymph nodes, and also inhibit the propagation of infection. Other immunosuppressive mechanisms used by HIV have also been reported. Cosuppressive molecules, such as B7-H1 on DCs and PD1 on T lymphocytes, are upregulated in patients with HIV, and induce apoptosis through their interaction with DCs and T lymphocytes. In addition, HIV is thought to induce regulatory T cells .", "Title: Confounding roles for type I interferons during bacterial and viral pathogenesis\nPassage: Several hallmarks of the negative effects of chronic viral infection have been discovered using this system. Mice become chronically infected with LCMV because of T-cell 'exhaustion' that prevents normal clearance . Several factors have been implicated in the suppression of T-cellmediated clearance of chronic LCMV; most salient among them are IL-10 and PD-1 . IL-10 is known to antagonize inflammatory activation on multiple immune cell types and its neutralization prevents chronic infection with LCMV . PD-1, a member of the CD28/CTLA4 family of T-cell regulators, is upregulated on exhausted T cells found in chronically infected mice. Its ligands, PD-1L and", "Title: Tumor Restrictions to Oncolytic Virus\nPassage: On a cellular level, virus replication is controlled by antiviral defense molecules , which in turn are primarily controlled by type I IFN signaling. In addition to classical type I IFN-or cytokine-induced antiviral signaling, tumors may employ other antiviral defense mechanisms. For example, stromal cells may secrete peptides with antiviral properties called defensins . The defensins are amphiphatic and typically 29-42 amino acids in length and interfere with viruses by physically binding to and disrupting virus particles and/or by inducing antiviral responses in target cells via pattern recognition receptors. At least oral squamous cell carcinomas were found to overexpress defensins" ]

[ [ "1a", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection" ], [ "1b", "Passage: Furthermore, Nef inhibits T cell receptor induced lymphocyte activation ." ], [ "1c", "These strategies contribute to the suppression of HIV proliferation in the lymph nodes, and also inhibit the propagation of infection." ], [ "1d", "Other immunosuppressive mechanisms used by HIV have also been reported." ], [ "1e", "Cosuppressive molecules, such as B7-H1 on DCs and PD1 on T lymphocytes, are upregulated in patients with HIV, and induce apoptosis through their interaction with DCs and T lymphocytes." ], [ "1f", "In addition, HIV is thought to induce regulatory T cells ." ] ]

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

[ "Title: HBV Immune-Therapy: From Molecular Mechanisms to Clinical Applications\nPassage: First reported in chronic Lymphocytic Choriomeningitis Virus infection, the up-regulation of co-inhibitory receptors, or immune checkpoints, has then been widely described as a common hallmark of exhausted CD8 T cells in different chronic infection and tumor models. Indeed, gene expression profiling and functional T cell analysis of virus-specific CD8 T cells from chronically LCMV-infected mice led to the characterization of the role played by PD-1 and other highly co-expressed inhibitory molecules, such as 2B4, CTLA-4, Tim-3, Lag-3, TIGIT, BTLA, CD160, PSGL1, in promoting a dysfunctional phenotype in exhausted antigen-specific CD8 T cells . Later on, the evidence that an efficient", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection\nPassage: Furthermore, Nef inhibits T cell receptor induced lymphocyte activation . These strategies contribute to the suppression of HIV proliferation in the lymph nodes, and also inhibit the propagation of infection. Other immunosuppressive mechanisms used by HIV have also been reported. Cosuppressive molecules, such as B7-H1 on DCs and PD1 on T lymphocytes, are upregulated in patients with HIV, and induce apoptosis through their interaction with DCs and T lymphocytes. In addition, HIV is thought to induce regulatory T cells .", "Title: Confounding roles for type I interferons during bacterial and viral pathogenesis\nPassage: Several hallmarks of the negative effects of chronic viral infection have been discovered using this system. Mice become chronically infected with LCMV because of T-cell 'exhaustion' that prevents normal clearance . Several factors have been implicated in the suppression of T-cellmediated clearance of chronic LCMV; most salient among them are IL-10 and PD-1 . IL-10 is known to antagonize inflammatory activation on multiple immune cell types and its neutralization prevents chronic infection with LCMV . PD-1, a member of the CD28/CTLA4 family of T-cell regulators, is upregulated on exhausted T cells found in chronically infected mice. Its ligands, PD-1L and", "Title: Tumor Restrictions to Oncolytic Virus\nPassage: On a cellular level, virus replication is controlled by antiviral defense molecules , which in turn are primarily controlled by type I IFN signaling. In addition to classical type I IFN-or cytokine-induced antiviral signaling, tumors may employ other antiviral defense mechanisms. For example, stromal cells may secrete peptides with antiviral properties called defensins . The defensins are amphiphatic and typically 29-42 amino acids in length and interfere with viruses by physically binding to and disrupting virus particles and/or by inducing antiviral responses in target cells via pattern recognition receptors. At least oral squamous cell carcinomas were found to overexpress defensins" ]

[ [ "2a", "Title: Confounding roles for type I interferons during bacterial and viral pathogenesis" ], [ "2b", "Passage: Several hallmarks of the negative effects of chronic viral infection have been discovered using this system." ], [ "2c", "Mice become chronically infected with LCMV because of T-cell 'exhaustion' that prevents normal clearance ." ], [ "2d", "Several factors have been implicated in the suppression of T-cellmediated clearance of chronic LCMV; most salient among them are IL-10 and PD-1 ." ], [ "2e", "IL-10 is known to antagonize inflammatory activation on multiple immune cell types and its neutralization prevents chronic infection with LCMV ." ], [ "2f", "PD-1, a member of the CD28/CTLA4 family of T-cell regulators, is upregulated on exhausted T cells found in chronically infected mice." ], [ "2g", "Its ligands, PD-1L and" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: IFITM family members contain a conservative CD225 domain and two terminal hypervariable regions . The CD225 domain accounts for more than half of the protein in length, containing one intact transmembrane domain , two S-palmitoylation sites regions and partial TMD in the C-terminus of the protein. The S-palmitoylation sites have been demonstrated to play important roles in post-translational processing and stability of IFITM proteins . The N-terminal hypervariable region generally contains 21 amino acid residues and the C-terminal one includes a TMD .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop . All of these cysteines are highly conserved among the mammalian IFITM family proteins . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the" ]

[ [ "0a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "0b", "Passage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice." ], [ "0c", "The conserved residues are highlighted in black." ], [ "0d", "The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 ." ], [ "0e", "The residues unique in IFITM5 are highlighted in gray." ], [ "0f", "The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively." ], [ "0g", "The TM domains were predicted by SOSUI." ], [ "0h", "The aspartates at the C-terminal region in IFITM5 are shown in blue." ], [ "0i", "B) The schematic illustration" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: IFITM family members contain a conservative CD225 domain and two terminal hypervariable regions . The CD225 domain accounts for more than half of the protein in length, containing one intact transmembrane domain , two S-palmitoylation sites regions and partial TMD in the C-terminus of the protein. The S-palmitoylation sites have been demonstrated to play important roles in post-translational processing and stability of IFITM proteins . The N-terminal hypervariable region generally contains 21 amino acid residues and the C-terminal one includes a TMD .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop . All of these cysteines are highly conserved among the mammalian IFITM family proteins . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the" ]

[ [ "1a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "1b", "Passage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice." ], [ "1c", "The conserved residues are highlighted in black." ], [ "1d", "The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 ." ], [ "1e", "The residues unique in IFITM5 are highlighted in gray." ], [ "1f", "The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively." ], [ "1g", "The TM domains were predicted by SOSUI." ], [ "1h", "The aspartates at the C-terminal region in IFITM5 are shown in blue." ], [ "1i", "B) The schematic illustration" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: IFITM family members contain a conservative CD225 domain and two terminal hypervariable regions . The CD225 domain accounts for more than half of the protein in length, containing one intact transmembrane domain , two S-palmitoylation sites regions and partial TMD in the C-terminus of the protein. The S-palmitoylation sites have been demonstrated to play important roles in post-translational processing and stability of IFITM proteins . The N-terminal hypervariable region generally contains 21 amino acid residues and the C-terminal one includes a TMD .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop . All of these cysteines are highly conserved among the mammalian IFITM family proteins . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the" ]

[ [ "2a", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates" ], [ "2b", "Passage: IFITM family members contain a conservative CD225 domain and two terminal hypervariable regions ." ], [ "2c", "The CD225 domain accounts for more than half of the protein in length, containing one intact transmembrane domain , two S-palmitoylation sites regions and partial TMD in the C-terminus of the protein." ], [ "2d", "The S-palmitoylation sites have been demonstrated to play important roles in post-translational processing and stability of IFITM proteins ." ], [ "2e", "The N-terminal hypervariable region generally contains 21 amino acid residues and the C-terminal one includes a TMD ." ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Evolutionary Dynamics of the Interferon-Induced Transmembrane Gene Family in Vertebrates\nPassage: IFITM family members contain a conservative CD225 domain and two terminal hypervariable regions . The CD225 domain accounts for more than half of the protein in length, containing one intact transmembrane domain , two S-palmitoylation sites regions and partial TMD in the C-terminus of the protein. The S-palmitoylation sites have been demonstrated to play important roles in post-translational processing and stability of IFITM proteins . The N-terminal hypervariable region generally contains 21 amino acid residues and the C-terminal one includes a TMD .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop . All of these cysteines are highly conserved among the mammalian IFITM family proteins . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the" ]

[ [ "3a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "3b", "Passage: As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation." ], [ "3c", "IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop ." ], [ "3d", "All of these cysteines are highly conserved among the mammalian IFITM family proteins ." ], [ "3e", "To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A ." ], [ "3f", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted." ], [ "3g", "Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the" ] ]

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

[ "Title: Targeting cancer stem cell pathways for cancer therapy\nPassage: Additionally, there are other ways to separate CSCs from tumors. In 1996, Dr. Goodell observed that after adding Hoechst 33342 to a culture of bone marrow cells, a few cells did not accumulate dyes, and he claimed that these few cells were side population cells. Therefore, SP cells can be separated by fluorescence screening after the outflow of Hoechst 33342. Recently, SP cells have been identified in various normal tissues and tumor cells. SP cells have high homology, self-renewal and multidirectional differentiation potential. 47,48 Some reports have shown that ABCG2 is highly expressed in SP cells. 47,49 ABCG2 is highly", "Title: Oct-4 Expression Maintained Cancer Stem-Like Properties in Lung Cancer-Derived CD133-Positive Cells\nPassage: and are responsible for tumor maintenance and metastasis . Stem cells have been isolated by their ability to efflux Hoechst 33342 dye and are referred to as the ''side population '' . Ho and colleagues isolated and characterized SP cells from six human lung cancer cell lines and showed that an elevated expression of ABCG2 as well as other ATP-binding cassette transporters were positively correlated with resistance to multiple chemotherapeutic drugs . In addition, Gutova and colleagues have purified uPAR-positive CSCs from three lung cancer cell lines. These uPAR-positive cells co-expressed with CD44 and MDR1, and had the ability to", "Title: Oct-4 Expression Maintained Cancer Stem-Like Properties in Lung Cancer-Derived CD133-Positive Cells\nPassage: For cell surface marker identification, a single cell suspension of sixth-to eighth-passage cells from trypsinized spheres was stained with anti-CD133, CD117 , or ABCG2 and secondary fluorescein -or phycoerythrin -coupled antibodies . Cells were fixed with 2% paraformaldehyde and were analyzed with a BD FACSCalibur apparatus .", "Title: Building Cell Selectivity into CPP-Mediated Strategies\nPassage: . Identification of a peptide that selectively enters colon cancer cells is very promising for developing new colon cancer diagnostic tools and therapeutic agents, such as RPMrel-D 2 . Colorectal cancer causes 655,000 deaths worldwide per year, and it is the third most common form of cancer and the third leading cause of cancer-related death in the western world. RPMrel could lead to the development of new direct targeting agents to fight against this disease." ]

[ [ "3a", "Title: Building Cell Selectivity into CPP-Mediated Strategies Passage: ." ], [ "3b", "Identification of a peptide that selectively enters colon cancer cells is very promising for developing new colon cancer diagnostic tools and therapeutic agents, such as RPMrel-D 2 ." ], [ "3c", "Colorectal cancer causes 655,000 deaths worldwide per year, and it is the third most common form of cancer and the third leading cause of cancer-related death in the western world." ], [ "3d", "RPMrel could lead to the development of new direct targeting agents to fight against this disease." ] ]

[ "3a", "3b" ]

[ "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We do not observe i and must infer it from the daily death and/or hospitalization data. In the case of deaths ), we must account for the time delay between infection and death. The time from symptom onset to death was remarkably similar across all age groups with a mode of 7 days . We add 1.5 days for the incubation period and round to the nearest integer, so that tZ9.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: One of the critical issues in infectious disease epidemiology is that the time of infection event is seldom directly observable. For this reason, the time of infection needs to be statistically estimated, employing a backcalculation method . Using a sophisticated statistical model with doubly intervalcensored likelihood and right truncation with an exponential growth of cases, the mean incubation period has been estimated to be about 5.0 days . To understand the time-dependent risk of infection throughout the course of outbreak and estimate the effectiveness of the quarantine measure from 5 to 19 February 2020, I aimed to estimate the incidence" ]

[ [ "0a", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus" ], [ "0b", "Passage: hospitalization, and ultimately die." ], [ "0c", "22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses." ], [ "0d", "The 14-day criterion for epidemiological risk assumes the longest estimated incubation time." ], [ "0e", "23 In addition, the World Health Organization has created its own interim case definition. 24" ] ]

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

[ "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We do not observe i and must infer it from the daily death and/or hospitalization data. In the case of deaths ), we must account for the time delay between infection and death. The time from symptom onset to death was remarkably similar across all age groups with a mode of 7 days . We add 1.5 days for the incubation period and round to the nearest integer, so that tZ9.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: One of the critical issues in infectious disease epidemiology is that the time of infection event is seldom directly observable. For this reason, the time of infection needs to be statistically estimated, employing a backcalculation method . Using a sophisticated statistical model with doubly intervalcensored likelihood and right truncation with an exponential growth of cases, the mean incubation period has been estimated to be about 5.0 days . To understand the time-dependent risk of infection throughout the course of outbreak and estimate the effectiveness of the quarantine measure from 5 to 19 February 2020, I aimed to estimate the incidence" ]

[ [ "2a", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus" ], [ "2b", "Passage: a) The mean incubation period was 5.2 days : 4.1-7.0) ." ], [ "2c", "We set the same value of the incubation period and the latent period in this study." ], [ "2d", "Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case ." ], [ "2e", "The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days ." ], [ "2f", "In our model, we set the infectious period of the cases as 5.8 days." ], [ "2g", "Therefore, γ P = 0.1724. c)" ] ]

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

[ "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: We do not observe i and must infer it from the daily death and/or hospitalization data. In the case of deaths ), we must account for the time delay between infection and death. The time from symptom onset to death was remarkably similar across all age groups with a mode of 7 days . We add 1.5 days for the incubation period and round to the nearest integer, so that tZ9.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess\nPassage: One of the critical issues in infectious disease epidemiology is that the time of infection event is seldom directly observable. For this reason, the time of infection needs to be statistically estimated, employing a backcalculation method . Using a sophisticated statistical model with doubly intervalcensored likelihood and right truncation with an exponential growth of cases, the mean incubation period has been estimated to be about 5.0 days . To understand the time-dependent risk of infection throughout the course of outbreak and estimate the effectiveness of the quarantine measure from 5 to 19 February 2020, I aimed to estimate the incidence" ]

[ [ "3a", "Title: Backcalculating the Incidence of Infection with COVID-19 on the Diamond Princess" ], [ "3b", "Passage: One of the critical issues in infectious disease epidemiology is that the time of infection event is seldom directly observable." ], [ "3c", "For this reason, the time of infection needs to be statistically estimated, employing a backcalculation method ." ], [ "3d", "Using a sophisticated statistical model with doubly intervalcensored likelihood and right truncation with an exponential growth of cases, the mean incubation period has been estimated to be about 5.0 days ." ], [ "3e", "To understand the time-dependent risk of infection throughout the course of outbreak and estimate the effectiveness of the quarantine measure from 5 to 19 February 2020, I aimed to estimate the incidence" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine . There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines. In split virus vaccines, the virus is disrupted by a detergent. In subunit vaccines, HA and NA have been further purified by removal of other viral components. TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains. TIV efficacy is measured by", "Title: Current and Novel Approaches in Influenza Management\nPassage: Three types of vaccines against influenza are currently used worldwide including inactivated influenza vaccine , live-attenuated influenza vaccine and influenza virus subunit vaccine: each of which has its own advantages and drawbacks. IIV is formulated with replication-incompetent virus, due to whole pathogen inactivation usually achieved by formaldehyde treatment or split virion vaccines generated by disruption of the viral membrane . Intramuscular administration of the IIV has been shown to induce both local and systemic immunity . However, to maintain the antibody titers, booster vaccinations are required. Additional considerations on the vaccine efficacy were raised following metadata analysis suggesting only 40%", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: serotypes such as adenovirus types 3, 7, 11, and 35 can evade anti-Ad5 immune responses while maintaining effective antigen delivery and immunogenicity . Prime-boost strategies, using DNA or protein immunization in conjunction with an adenovirus vaccine booster immunization have also been explored as a means to avoided preexisting immunity .", "Title: Viral vector-based influenza vaccines\nPassage: Several different vaccine formulations are available: trivalent or quadrivalent inactivated virus vaccines or live attenuated influenza virus vaccines . Most vaccines are produced in embryonated chicken eggs, but vaccines produced in mammalian or insect cells are also available. Inactivated vaccines are administered intramuscularly or sometimes intradermally and predominantly aim at the induction of serum antibody responses against the viral hemagglutinin and neuraminidase to a lesser extent. Protection from disease is mainly mediated by virus neutralizing antibodies against HA, but NA-specific antibodies also contribute to protective immunity. 1 Currently licensed LAIV are administered locally via nasal spray. Viruses are attenuated by" ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine ." ], [ "0c", "There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines." ], [ "0d", "In split virus vaccines, the virus is disrupted by a detergent." ], [ "0e", "In subunit vaccines, HA and NA have been further purified by removal of other viral components." ], [ "0f", "TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains." ], [ "0g", "TIV efficacy is measured by" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine . There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines. In split virus vaccines, the virus is disrupted by a detergent. In subunit vaccines, HA and NA have been further purified by removal of other viral components. TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains. TIV efficacy is measured by", "Title: Current and Novel Approaches in Influenza Management\nPassage: Three types of vaccines against influenza are currently used worldwide including inactivated influenza vaccine , live-attenuated influenza vaccine and influenza virus subunit vaccine: each of which has its own advantages and drawbacks. IIV is formulated with replication-incompetent virus, due to whole pathogen inactivation usually achieved by formaldehyde treatment or split virion vaccines generated by disruption of the viral membrane . Intramuscular administration of the IIV has been shown to induce both local and systemic immunity . However, to maintain the antibody titers, booster vaccinations are required. Additional considerations on the vaccine efficacy were raised following metadata analysis suggesting only 40%", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: serotypes such as adenovirus types 3, 7, 11, and 35 can evade anti-Ad5 immune responses while maintaining effective antigen delivery and immunogenicity . Prime-boost strategies, using DNA or protein immunization in conjunction with an adenovirus vaccine booster immunization have also been explored as a means to avoided preexisting immunity .", "Title: Viral vector-based influenza vaccines\nPassage: Several different vaccine formulations are available: trivalent or quadrivalent inactivated virus vaccines or live attenuated influenza virus vaccines . Most vaccines are produced in embryonated chicken eggs, but vaccines produced in mammalian or insect cells are also available. Inactivated vaccines are administered intramuscularly or sometimes intradermally and predominantly aim at the induction of serum antibody responses against the viral hemagglutinin and neuraminidase to a lesser extent. Protection from disease is mainly mediated by virus neutralizing antibodies against HA, but NA-specific antibodies also contribute to protective immunity. 1 Currently licensed LAIV are administered locally via nasal spray. Viruses are attenuated by" ]

[ [ "1a", "Title: Current and Novel Approaches in Influenza Management" ], [ "1b", "Passage: Three types of vaccines against influenza are currently used worldwide including inactivated influenza vaccine , live-attenuated influenza vaccine and influenza virus subunit vaccine: each of which has its own advantages and drawbacks." ], [ "1c", "IIV is formulated with replication-incompetent virus, due to whole pathogen inactivation usually achieved by formaldehyde treatment or split virion vaccines generated by disruption of the viral membrane ." ], [ "1d", "Intramuscular administration of the IIV has been shown to induce both local and systemic immunity ." ], [ "1e", "However, to maintain the antibody titers, booster vaccinations are required." ], [ "1f", "Additional considerations on the vaccine efficacy were raised following metadata analysis suggesting only 40%" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine . There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines. In split virus vaccines, the virus is disrupted by a detergent. In subunit vaccines, HA and NA have been further purified by removal of other viral components. TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains. TIV efficacy is measured by", "Title: Current and Novel Approaches in Influenza Management\nPassage: Three types of vaccines against influenza are currently used worldwide including inactivated influenza vaccine , live-attenuated influenza vaccine and influenza virus subunit vaccine: each of which has its own advantages and drawbacks. IIV is formulated with replication-incompetent virus, due to whole pathogen inactivation usually achieved by formaldehyde treatment or split virion vaccines generated by disruption of the viral membrane . Intramuscular administration of the IIV has been shown to induce both local and systemic immunity . However, to maintain the antibody titers, booster vaccinations are required. Additional considerations on the vaccine efficacy were raised following metadata analysis suggesting only 40%", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: serotypes such as adenovirus types 3, 7, 11, and 35 can evade anti-Ad5 immune responses while maintaining effective antigen delivery and immunogenicity . Prime-boost strategies, using DNA or protein immunization in conjunction with an adenovirus vaccine booster immunization have also been explored as a means to avoided preexisting immunity .", "Title: Viral vector-based influenza vaccines\nPassage: Several different vaccine formulations are available: trivalent or quadrivalent inactivated virus vaccines or live attenuated influenza virus vaccines . Most vaccines are produced in embryonated chicken eggs, but vaccines produced in mammalian or insect cells are also available. Inactivated vaccines are administered intramuscularly or sometimes intradermally and predominantly aim at the induction of serum antibody responses against the viral hemagglutinin and neuraminidase to a lesser extent. Protection from disease is mainly mediated by virus neutralizing antibodies against HA, but NA-specific antibodies also contribute to protective immunity. 1 Currently licensed LAIV are administered locally via nasal spray. Viruses are attenuated by" ]

[ [ "3a", "Title: Viral vector-based influenza vaccines" ], [ "3b", "Passage: Several different vaccine formulations are available: trivalent or quadrivalent inactivated virus vaccines or live attenuated influenza virus vaccines ." ], [ "3c", "Most vaccines are produced in embryonated chicken eggs, but vaccines produced in mammalian or insect cells are also available." ], [ "3d", "Inactivated vaccines are administered intramuscularly or sometimes intradermally and predominantly aim at the induction of serum antibody responses against the viral hemagglutinin and neuraminidase to a lesser extent." ], [ "3e", "Protection from disease is mainly mediated by virus neutralizing antibodies against HA, but NA-specific antibodies also contribute to protective immunity." ], [ "3f", "1 Currently licensed LAIV are administered locally via nasal spray." ], [ "3g", "Viruses are attenuated by" ] ]

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

[ "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: Koch recognized as early as 1891 that associating the presence of a certain agent with a certain disease is complex, and he therefore postulated guidelines that should be followed before an agent can be classified as a pathogen . His postulates can be summarized in three points: The microbe occurs in every case of the disease in question and under circumstances which can account for the pathological changes and clinical course of the disease; the microbe occurs in no other disease as a fortuitous and nonpathogenic parasite; and , after being fully isolated from the body and repeatedly grown in", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: been made to adjust the Koch's postulates specifically for viruses and the current methodologies deployed , fulfilling these postulates is still not feasible on most occasions due to the lack of an efficient cell culture system, difficulties in antigen synthesis and high levels of viral genetic diversity within viral groups, reviewed in the literature .", "Title: Mechanisms of Adaptive Immunity to Porcine Reproductive and Respiratory Syndrome Virus\nPassage: for the new disease syndrome were unsuccessful, leading to the disease being temporarily designated mystery swine disease in North America. Koch's postulates for MSD were fulfilled in 1991 with a previously unidentified RNA virus discovered in Europe, named Lelystad virus . The discovery was quickly followed by isolation of the virus, initially referred to as swine infertility and respiratory syndrome virus or SIRS virus, in North America .", "Title: The social benefits of private infectious disease-risk mitigation\nPassage: The first two axioms imply that P is a matrix of conditional probabilities, and the third implies that it is symmetric." ]

[ [ "0a", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond" ], [ "0b", "Passage: Koch recognized as early as 1891 that associating the presence of a certain agent with a certain disease is complex, and he therefore postulated guidelines that should be followed before an agent can be classified as a pathogen ." ], [ "0c", "His postulates can be summarized in three points: The microbe occurs in every case of the disease in question and under circumstances which can account for the pathological changes and clinical course of the disease; the microbe occurs in no other disease as a fortuitous and nonpathogenic parasite; and , after being fully isolated from the body and repeatedly grown in" ] ]

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

[ "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: infections for both of these two strains during some parts of that half year and 1 ). Although we note that a much larger study period than our data allows would likely offer more insights. 5 . It has been proposed that, due to school/business closure due to traditional lunar New Year holidays in Taiwan that falls typically between week 4 to week 8 of each year, more frequent contacts in the households among family members who spent more time at home during the holidays tends to result in increased transmission . It is interesting to note that during 2008-2014,", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: shown that excess influenza deaths during these months similar to those in the temperate zones can also observed in Taiwan . It has also been proposed previously that Taiwan is an evolutionarily leading region for global circulation of influenza virus A . Moreover, past studies on sequence comparison of seasonal influenza strains A in Taiwan versus vaccine strains have showed that many vaccine-like Taiwanese strains in 1995-2003 were circulating at least 2 years before the vaccine strains were introduced . Hence investigating circulation patterns of seasonal influenza virus strains might shed lights on possible global circulation patterns in the following", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: When there is more than one wave of infections, as in our current study, a variation of the Richards model can be utilized, which makes the distinction between two types of turning points ; one type which occurs at the peak incidence, and a second type which occurs in a multi-wave epidemic when the growth rate of the cumulative case number begins to increase again, indicating the beginning of the next wave.", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: This data issue is even more glaring during summers, when there are typically less clinical cases and hence less number of samples being collected for laboratory testing. During the second half of 2012, no significant wave can be detected via the Richards model. However, we note that most of the samples tested during that time was determined to be H3N2 , although the typically low weekly number of samples being tested during summer, due to more mild and subclinical cases in summers, became an obstacle for good model fitting. Nevertheless, the study, designed to qualitatively compare the temporal patterns and" ]

[ [ "0a", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic" ], [ "0b", "Passage: infections for both of these two strains during some parts of that half year and 1 )." ], [ "0c", "Although we note that a much larger study period than our data allows would likely offer more insights. 5 ." ], [ "0d", "It has been proposed that, due to school/business closure due to traditional lunar New Year holidays in Taiwan that falls typically between week 4 to week 8 of each year, more frequent contacts in the households among family members who spent more time at home during the holidays tends to result in increased transmission ." ], [ "0e", "It is interesting to note that during 2008-2014," ] ]

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

[ "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: infections for both of these two strains during some parts of that half year and 1 ). Although we note that a much larger study period than our data allows would likely offer more insights. 5 . It has been proposed that, due to school/business closure due to traditional lunar New Year holidays in Taiwan that falls typically between week 4 to week 8 of each year, more frequent contacts in the households among family members who spent more time at home during the holidays tends to result in increased transmission . It is interesting to note that during 2008-2014,", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: shown that excess influenza deaths during these months similar to those in the temperate zones can also observed in Taiwan . It has also been proposed previously that Taiwan is an evolutionarily leading region for global circulation of influenza virus A . Moreover, past studies on sequence comparison of seasonal influenza strains A in Taiwan versus vaccine strains have showed that many vaccine-like Taiwanese strains in 1995-2003 were circulating at least 2 years before the vaccine strains were introduced . Hence investigating circulation patterns of seasonal influenza virus strains might shed lights on possible global circulation patterns in the following", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: When there is more than one wave of infections, as in our current study, a variation of the Richards model can be utilized, which makes the distinction between two types of turning points ; one type which occurs at the peak incidence, and a second type which occurs in a multi-wave epidemic when the growth rate of the cumulative case number begins to increase again, indicating the beginning of the next wave.", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: This data issue is even more glaring during summers, when there are typically less clinical cases and hence less number of samples being collected for laboratory testing. During the second half of 2012, no significant wave can be detected via the Richards model. However, we note that most of the samples tested during that time was determined to be H3N2 , although the typically low weekly number of samples being tested during summer, due to more mild and subclinical cases in summers, became an obstacle for good model fitting. Nevertheless, the study, designed to qualitatively compare the temporal patterns and" ]

[ [ "1a", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic" ], [ "1b", "Passage: shown that excess influenza deaths during these months similar to those in the temperate zones can also observed in Taiwan ." ], [ "1c", "It has also been proposed previously that Taiwan is an evolutionarily leading region for global circulation of influenza virus A ." ], [ "1d", "Moreover, past studies on sequence comparison of seasonal influenza strains A in Taiwan versus vaccine strains have showed that many vaccine-like Taiwanese strains in 1995-2003 were circulating at least 2 years before the vaccine strains were introduced ." ], [ "1e", "Hence investigating circulation patterns of seasonal influenza virus strains might shed lights on possible global circulation patterns in the following" ] ]

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

[ "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: infections for both of these two strains during some parts of that half year and 1 ). Although we note that a much larger study period than our data allows would likely offer more insights. 5 . It has been proposed that, due to school/business closure due to traditional lunar New Year holidays in Taiwan that falls typically between week 4 to week 8 of each year, more frequent contacts in the households among family members who spent more time at home during the holidays tends to result in increased transmission . It is interesting to note that during 2008-2014,", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: shown that excess influenza deaths during these months similar to those in the temperate zones can also observed in Taiwan . It has also been proposed previously that Taiwan is an evolutionarily leading region for global circulation of influenza virus A . Moreover, past studies on sequence comparison of seasonal influenza strains A in Taiwan versus vaccine strains have showed that many vaccine-like Taiwanese strains in 1995-2003 were circulating at least 2 years before the vaccine strains were introduced . Hence investigating circulation patterns of seasonal influenza virus strains might shed lights on possible global circulation patterns in the following", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: When there is more than one wave of infections, as in our current study, a variation of the Richards model can be utilized, which makes the distinction between two types of turning points ; one type which occurs at the peak incidence, and a second type which occurs in a multi-wave epidemic when the growth rate of the cumulative case number begins to increase again, indicating the beginning of the next wave.", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic\nPassage: This data issue is even more glaring during summers, when there are typically less clinical cases and hence less number of samples being collected for laboratory testing. During the second half of 2012, no significant wave can be detected via the Richards model. However, we note that most of the samples tested during that time was determined to be H3N2 , although the typically low weekly number of samples being tested during summer, due to more mild and subclinical cases in summers, became an obstacle for good model fitting. Nevertheless, the study, designed to qualitatively compare the temporal patterns and" ]

[ [ "3a", "Title: On Temporal Patterns and Circulation of Influenza Virus Strains in Taiwan, 2008-2014: Implications of 2009 pH1N1 Pandemic" ], [ "3b", "Passage: This data issue is even more glaring during summers, when there are typically less clinical cases and hence less number of samples being collected for laboratory testing." ], [ "3c", "During the second half of 2012, no significant wave can be detected via the Richards model." ], [ "3d", "However, we note that most of the samples tested during that time was determined to be H3N2 , although the typically low weekly number of samples being tested during summer, due to more mild and subclinical cases in summers, became an obstacle for good model fitting." ], [ "3e", "Nevertheless, the study, designed to qualitatively compare the temporal patterns and" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The VEE replicon systems are particularly appealing as the VEE targets antigen-presenting cells in the lymphatic tissues, priming rapid and robust immune responses . VEE replicon systems can induce robust mucosal immune responses through intranasal or subcutaneous immunization , and subcutaneous immunization with virus-like replicon particles expressing HA-induced antigen-specific systemic IgG and fecal IgA antibodies . VRPs derived from VEE virus have been developed as candidate vaccines for cytomegalovirus . A phase I clinical trial with the CMV VRP showed the vaccine was immunogenic, inducing CMV-neutralizing antibody responses and potent T cell responses. Moreover, the vaccine was well tolerated and", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: Venezuelan equine encephalitis virus replicon , lacks its structural protein genes and expresses green fluorescent protein under its subgenomic promoter. Transformed Escherichia coli containing the WNV and VEE replicon plasmids were grown at 37˚C. E. coli stocks containing the packaging vector were grown at 25˚C. WNV, VEE, and Semliki Forest virus replicon plasmids were linearized with Xba1, Not1, or Spe1 , respectively. RNA was in vitro transcribed using mMESSAGE mMACHINE mRNA kit according to the manufacturer's instructions.", "Title: Viral vector-based influenza vaccines\nPassage: VEE is an appealing vaccine vector, as it was previously shown that VEE mainly targets antigen-presenting cells in the lymphoid tissues and therefore primes rapid and robust immune responses. 103 SIN, SFV and VEE have all been tested as influenza vaccine vectors . An SFV vaccine expressing the HA and NP genes could protect mice from infection with A virus; 99 the same held true for a SIN replicon expressing either the HA gene or an immunodominant CD8 C T-cell NP epitope. 104, 105 VEE was more extensively evaluated as an influenza vaccine vector, VEE-H1 vaccination protected mice from infection", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: experimental procedure, allowing for more efficient optimization of other parameters, we used FlyFectin in subsequent experiments at an RNA to reagent ratio of 1 μg RNA to 4 μL FlyFectin. Transfection efficiency for these parameters was quantified using a VEE replicon RNA that expresses high levels of GFP under the subgenomic promoter. Both VEE and WNV efficiently replicate in C6/36 cells . The VEE system was used because it is more specific and sensitive than using an antibody to detect cells transfected with WNV replicon in C6/36 cells, which are highly autofluorescent. The percentage of GFP-positive cells was determined by" ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: The VEE replicon systems are particularly appealing as the VEE targets antigen-presenting cells in the lymphatic tissues, priming rapid and robust immune responses ." ], [ "0c", "VEE replicon systems can induce robust mucosal immune responses through intranasal or subcutaneous immunization , and subcutaneous immunization with virus-like replicon particles expressing HA-induced antigen-specific systemic IgG and fecal IgA antibodies ." ], [ "0d", "VRPs derived from VEE virus have been developed as candidate vaccines for cytomegalovirus ." ], [ "0e", "A phase I clinical trial with the CMV VRP showed the vaccine was immunogenic, inducing CMV-neutralizing antibody responses and potent T cell responses." ], [ "0f", "Moreover, the vaccine was well tolerated and" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The VEE replicon systems are particularly appealing as the VEE targets antigen-presenting cells in the lymphatic tissues, priming rapid and robust immune responses . VEE replicon systems can induce robust mucosal immune responses through intranasal or subcutaneous immunization , and subcutaneous immunization with virus-like replicon particles expressing HA-induced antigen-specific systemic IgG and fecal IgA antibodies . VRPs derived from VEE virus have been developed as candidate vaccines for cytomegalovirus . A phase I clinical trial with the CMV VRP showed the vaccine was immunogenic, inducing CMV-neutralizing antibody responses and potent T cell responses. Moreover, the vaccine was well tolerated and", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: Venezuelan equine encephalitis virus replicon , lacks its structural protein genes and expresses green fluorescent protein under its subgenomic promoter. Transformed Escherichia coli containing the WNV and VEE replicon plasmids were grown at 37˚C. E. coli stocks containing the packaging vector were grown at 25˚C. WNV, VEE, and Semliki Forest virus replicon plasmids were linearized with Xba1, Not1, or Spe1 , respectively. RNA was in vitro transcribed using mMESSAGE mMACHINE mRNA kit according to the manufacturer's instructions.", "Title: Viral vector-based influenza vaccines\nPassage: VEE is an appealing vaccine vector, as it was previously shown that VEE mainly targets antigen-presenting cells in the lymphoid tissues and therefore primes rapid and robust immune responses. 103 SIN, SFV and VEE have all been tested as influenza vaccine vectors . An SFV vaccine expressing the HA and NP genes could protect mice from infection with A virus; 99 the same held true for a SIN replicon expressing either the HA gene or an immunodominant CD8 C T-cell NP epitope. 104, 105 VEE was more extensively evaluated as an influenza vaccine vector, VEE-H1 vaccination protected mice from infection", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: experimental procedure, allowing for more efficient optimization of other parameters, we used FlyFectin in subsequent experiments at an RNA to reagent ratio of 1 μg RNA to 4 μL FlyFectin. Transfection efficiency for these parameters was quantified using a VEE replicon RNA that expresses high levels of GFP under the subgenomic promoter. Both VEE and WNV efficiently replicate in C6/36 cells . The VEE system was used because it is more specific and sensitive than using an antibody to detect cells transfected with WNV replicon in C6/36 cells, which are highly autofluorescent. The percentage of GFP-positive cells was determined by" ]

[ [ "1a", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice" ], [ "1b", "Passage: Venezuelan equine encephalitis virus replicon , lacks its structural protein genes and expresses green fluorescent protein under its subgenomic promoter." ], [ "1c", "Transformed Escherichia coli containing the WNV and VEE replicon plasmids were grown at 37˚C." ], [ "1d", "E. coli stocks containing the packaging vector were grown at 25˚C." ], [ "1e", "WNV, VEE, and Semliki Forest virus replicon plasmids were linearized with Xba1, Not1, or Spe1 , respectively." ], [ "1f", "RNA was in vitro transcribed using mMESSAGE mMACHINE mRNA kit according to the manufacturer's instructions." ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The VEE replicon systems are particularly appealing as the VEE targets antigen-presenting cells in the lymphatic tissues, priming rapid and robust immune responses . VEE replicon systems can induce robust mucosal immune responses through intranasal or subcutaneous immunization , and subcutaneous immunization with virus-like replicon particles expressing HA-induced antigen-specific systemic IgG and fecal IgA antibodies . VRPs derived from VEE virus have been developed as candidate vaccines for cytomegalovirus . A phase I clinical trial with the CMV VRP showed the vaccine was immunogenic, inducing CMV-neutralizing antibody responses and potent T cell responses. Moreover, the vaccine was well tolerated and", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: Venezuelan equine encephalitis virus replicon , lacks its structural protein genes and expresses green fluorescent protein under its subgenomic promoter. Transformed Escherichia coli containing the WNV and VEE replicon plasmids were grown at 37˚C. E. coli stocks containing the packaging vector were grown at 25˚C. WNV, VEE, and Semliki Forest virus replicon plasmids were linearized with Xba1, Not1, or Spe1 , respectively. RNA was in vitro transcribed using mMESSAGE mMACHINE mRNA kit according to the manufacturer's instructions.", "Title: Viral vector-based influenza vaccines\nPassage: VEE is an appealing vaccine vector, as it was previously shown that VEE mainly targets antigen-presenting cells in the lymphoid tissues and therefore primes rapid and robust immune responses. 103 SIN, SFV and VEE have all been tested as influenza vaccine vectors . An SFV vaccine expressing the HA and NP genes could protect mice from infection with A virus; 99 the same held true for a SIN replicon expressing either the HA gene or an immunodominant CD8 C T-cell NP epitope. 104, 105 VEE was more extensively evaluated as an influenza vaccine vector, VEE-H1 vaccination protected mice from infection", "Title: Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice\nPassage: experimental procedure, allowing for more efficient optimization of other parameters, we used FlyFectin in subsequent experiments at an RNA to reagent ratio of 1 μg RNA to 4 μL FlyFectin. Transfection efficiency for these parameters was quantified using a VEE replicon RNA that expresses high levels of GFP under the subgenomic promoter. Both VEE and WNV efficiently replicate in C6/36 cells . The VEE system was used because it is more specific and sensitive than using an antibody to detect cells transfected with WNV replicon in C6/36 cells, which are highly autofluorescent. The percentage of GFP-positive cells was determined by" ]

[ [ "2a", "Title: Viral vector-based influenza vaccines" ], [ "2b", "Passage: VEE is an appealing vaccine vector, as it was previously shown that VEE mainly targets antigen-presenting cells in the lymphoid tissues and therefore primes rapid and robust immune responses." ], [ "2c", "103 SIN, SFV and VEE have all been tested as influenza vaccine vectors ." ], [ "2d", "An SFV vaccine expressing the HA and NP genes could protect mice from infection with A virus; 99 the same held true for a SIN replicon expressing either the HA gene or an immunodominant CD8 C T-cell NP epitope." ], [ "2e", "104, 105 VEE was more extensively evaluated as an influenza vaccine vector, VEE-H1 vaccination protected mice from infection" ] ]

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

[ "Title: The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis\nPassage: Viral fulminant hepatitis is a clinical syndrome characterized by massive necrosis of hepatocytes along with hepatic encephalopathy during the infections . Despite advances in the development of antiviral drugs, a poor understanding of the immune mechanisms underlying viral FH has largely stalled the identification of effective clinical interventions. Fortunately, the recent development of an animal model of FH using murine hepatitis virus strain-3 infection has provided insights in understanding the pathogenesis and developing novel therapeutics for the disease .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Hepatitis A virus , hepatitis B virus , hepatitis C virus , and hepatitis E virus are the most common liver-tropic viruses in humans. HAV and HEV typically cause an acute form of hepatitis, whereas HBV and HCV frequently cause chronic hepatitis, increasing the risk of cirrhosis and hepatocellular carcinoma . HEV may also cause chronic infection . In rare cases, primary infections with these viruses, particularly for HAV, HBV, and HEV, can lead to fulminant viral hepatitis . FVH is defined as severe liver destruction in the absence of preexisting liver disease, leading to encephalopathy within 8 wk of", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: in the absence of liver transplantation. However, survival rates may reach 80% after liver transplantation . FVH is typically sporadic, as opposed to epidemic, suggesting that it is not caused by a new more virulent viral strain .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Factor V, 100% . On day 8 of infection, the patient was hospitalized for incoherent speech, jaundice, appetite loss, gingival bleeding, and petechiae. During physical examination at the emergency unit, the patient was unconscious, with icterus, hepatomegaly, and a fever . The patient was diagnosed with FVH due to HAV infection. On day 9, liver function tests revealed high levels of cytolysis, with a PT of 14%, factor V levels at 30%, and a Glasgow coma scale score of 8 . The patient underwent liver transplantation but died a day later of multiple organ failure . Histological examinations of the" ]

[ [ "0a", "Title: The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis" ], [ "0b", "Passage: Viral fulminant hepatitis is a clinical syndrome characterized by massive necrosis of hepatocytes along with hepatic encephalopathy during the infections ." ], [ "0c", "Despite advances in the development of antiviral drugs, a poor understanding of the immune mechanisms underlying viral FH has largely stalled the identification of effective clinical interventions." ], [ "0d", "Fortunately, the recent development of an animal model of FH using murine hepatitis virus strain-3 infection has provided insights in understanding the pathogenesis and developing novel therapeutics for the disease ." ] ]

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

[ "Title: The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis\nPassage: Viral fulminant hepatitis is a clinical syndrome characterized by massive necrosis of hepatocytes along with hepatic encephalopathy during the infections . Despite advances in the development of antiviral drugs, a poor understanding of the immune mechanisms underlying viral FH has largely stalled the identification of effective clinical interventions. Fortunately, the recent development of an animal model of FH using murine hepatitis virus strain-3 infection has provided insights in understanding the pathogenesis and developing novel therapeutics for the disease .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Hepatitis A virus , hepatitis B virus , hepatitis C virus , and hepatitis E virus are the most common liver-tropic viruses in humans. HAV and HEV typically cause an acute form of hepatitis, whereas HBV and HCV frequently cause chronic hepatitis, increasing the risk of cirrhosis and hepatocellular carcinoma . HEV may also cause chronic infection . In rare cases, primary infections with these viruses, particularly for HAV, HBV, and HEV, can lead to fulminant viral hepatitis . FVH is defined as severe liver destruction in the absence of preexisting liver disease, leading to encephalopathy within 8 wk of", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: in the absence of liver transplantation. However, survival rates may reach 80% after liver transplantation . FVH is typically sporadic, as opposed to epidemic, suggesting that it is not caused by a new more virulent viral strain .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Factor V, 100% . On day 8 of infection, the patient was hospitalized for incoherent speech, jaundice, appetite loss, gingival bleeding, and petechiae. During physical examination at the emergency unit, the patient was unconscious, with icterus, hepatomegaly, and a fever . The patient was diagnosed with FVH due to HAV infection. On day 9, liver function tests revealed high levels of cytolysis, with a PT of 14%, factor V levels at 30%, and a Glasgow coma scale score of 8 . The patient underwent liver transplantation but died a day later of multiple organ failure . Histological examinations of the" ]

[ [ "1a", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis" ], [ "1b", "Passage: Hepatitis A virus , hepatitis B virus , hepatitis C virus , and hepatitis E virus are the most common liver-tropic viruses in humans." ], [ "1c", "HAV and HEV typically cause an acute form of hepatitis, whereas HBV and HCV frequently cause chronic hepatitis, increasing the risk of cirrhosis and hepatocellular carcinoma ." ], [ "1d", "HEV may also cause chronic infection ." ], [ "1e", "In rare cases, primary infections with these viruses, particularly for HAV, HBV, and HEV, can lead to fulminant viral hepatitis ." ], [ "1f", "FVH is defined as severe liver destruction in the absence of preexisting liver disease, leading to encephalopathy within 8 wk of" ] ]

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

[ "Title: The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis\nPassage: Viral fulminant hepatitis is a clinical syndrome characterized by massive necrosis of hepatocytes along with hepatic encephalopathy during the infections . Despite advances in the development of antiviral drugs, a poor understanding of the immune mechanisms underlying viral FH has largely stalled the identification of effective clinical interventions. Fortunately, the recent development of an animal model of FH using murine hepatitis virus strain-3 infection has provided insights in understanding the pathogenesis and developing novel therapeutics for the disease .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Hepatitis A virus , hepatitis B virus , hepatitis C virus , and hepatitis E virus are the most common liver-tropic viruses in humans. HAV and HEV typically cause an acute form of hepatitis, whereas HBV and HCV frequently cause chronic hepatitis, increasing the risk of cirrhosis and hepatocellular carcinoma . HEV may also cause chronic infection . In rare cases, primary infections with these viruses, particularly for HAV, HBV, and HEV, can lead to fulminant viral hepatitis . FVH is defined as severe liver destruction in the absence of preexisting liver disease, leading to encephalopathy within 8 wk of", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: in the absence of liver transplantation. However, survival rates may reach 80% after liver transplantation . FVH is typically sporadic, as opposed to epidemic, suggesting that it is not caused by a new more virulent viral strain .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Factor V, 100% . On day 8 of infection, the patient was hospitalized for incoherent speech, jaundice, appetite loss, gingival bleeding, and petechiae. During physical examination at the emergency unit, the patient was unconscious, with icterus, hepatomegaly, and a fever . The patient was diagnosed with FVH due to HAV infection. On day 9, liver function tests revealed high levels of cytolysis, with a PT of 14%, factor V levels at 30%, and a Glasgow coma scale score of 8 . The patient underwent liver transplantation but died a day later of multiple organ failure . Histological examinations of the" ]

[ [ "2a", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis" ], [ "2b", "Passage: in the absence of liver transplantation." ], [ "2c", "However, survival rates may reach 80% after liver transplantation ." ], [ "2d", "FVH is typically sporadic, as opposed to epidemic, suggesting that it is not caused by a new more virulent viral strain ." ] ]

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

[ "Title: The NLRP3 Inflammasome and IL-1β Accelerate Immunologically Mediated Pathology in Experimental Viral Fulminant Hepatitis\nPassage: Viral fulminant hepatitis is a clinical syndrome characterized by massive necrosis of hepatocytes along with hepatic encephalopathy during the infections . Despite advances in the development of antiviral drugs, a poor understanding of the immune mechanisms underlying viral FH has largely stalled the identification of effective clinical interventions. Fortunately, the recent development of an animal model of FH using murine hepatitis virus strain-3 infection has provided insights in understanding the pathogenesis and developing novel therapeutics for the disease .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Hepatitis A virus , hepatitis B virus , hepatitis C virus , and hepatitis E virus are the most common liver-tropic viruses in humans. HAV and HEV typically cause an acute form of hepatitis, whereas HBV and HCV frequently cause chronic hepatitis, increasing the risk of cirrhosis and hepatocellular carcinoma . HEV may also cause chronic infection . In rare cases, primary infections with these viruses, particularly for HAV, HBV, and HEV, can lead to fulminant viral hepatitis . FVH is defined as severe liver destruction in the absence of preexisting liver disease, leading to encephalopathy within 8 wk of", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: in the absence of liver transplantation. However, survival rates may reach 80% after liver transplantation . FVH is typically sporadic, as opposed to epidemic, suggesting that it is not caused by a new more virulent viral strain .", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis\nPassage: Factor V, 100% . On day 8 of infection, the patient was hospitalized for incoherent speech, jaundice, appetite loss, gingival bleeding, and petechiae. During physical examination at the emergency unit, the patient was unconscious, with icterus, hepatomegaly, and a fever . The patient was diagnosed with FVH due to HAV infection. On day 9, liver function tests revealed high levels of cytolysis, with a PT of 14%, factor V levels at 30%, and a Glasgow coma scale score of 8 . The patient underwent liver transplantation but died a day later of multiple organ failure . Histological examinations of the" ]

[ [ "3a", "Title: Inherited IL-18BP deficiency in human fulminant viral hepatitis" ], [ "3b", "Passage: Factor V, 100% ." ], [ "3c", "On day 8 of infection, the patient was hospitalized for incoherent speech, jaundice, appetite loss, gingival bleeding, and petechiae." ], [ "3d", "During physical examination at the emergency unit, the patient was unconscious, with icterus, hepatomegaly, and a fever ." ], [ "3e", "The patient was diagnosed with FVH due to HAV infection." ], [ "3f", "On day 9, liver function tests revealed high levels of cytolysis, with a PT of 14%, factor V levels at 30%, and a Glasgow coma scale score of 8 ." ], [ "3g", "The patient underwent liver transplantation but died a day later of multiple organ failure ." ], [ "3h", "Histological examinations of the" ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: The true number of infected individuals, C, is modelled using a discrete renewal process. This approach", "Title: Estimating the number of infections and the impact of non-\nPassage: people infected.", "Title: Estimating the number of infections and the impact of non-\nPassage: gain intuition that this is data driven and not simply a consequence of highly constrained model", "Title: Estimating the number of infections and the impact of non-\nPassage: appropriate and plausible." ]

[ [ "0a", "Title: Estimating the number of infections and the impact of non-" ], [ "0b", "Passage: The true number of infected individuals, C, is modelled using a discrete renewal process. This approach" ] ]

[ "0a", "0b" ]

[ "Title: Virus contaminations of cell cultures – A biotechnological view\nPassage: Only few harvests need to be tested . c Old cells may be from production runs or from a separate culture kept in continuous culture for a long period and prepared for this analysis of 'limit of cell age' only . Extensive testing performed as part of the qualification of the MCB regarding absence of latent virus, inducible by cultivation on production conditions. d A very large sample volume for testing would be required for statistics of a sufficiently sensitive detection of low virus titers.", "Title: Production of high titre disabled infectious single cycle (DISC) HSV from a microcarrier culture\nPassage: CPE 60-72 h after infection, the cultures were harvested. Infectious DISC-HSV released from the CR2 cells was quantified using a TCID 50 assay and was again compared to the titre achieved from the equivalent roller bottle culture harvests. The results are shown in Table 1 . Typically 4-7.0 × 10 11 total pfu from a 15 l culture was achieved, with a period of approximately 9 h during which this high titre was sustained. From an equivalent number of 388 roller bottles we would expect to achieve approximately 3.88 × 10 11 total pfu. Our results, therefore, compare very favourably", "Title: Tips and Tricks for Validation of Quality Control Analytical Methods in Good Manufacturing Practice Mesenchymal Stromal Cell Production\nPassage: measuring the quantity as absorbance , the cell suspensions were diluted to obtain two concentrations, one of 10-100 CFU/mL and one of 100-1000 CFU/mL. Each batch of culture medium was tested for sterility and fertility before use according to Ph considering the quantity results shown on the report of the external quality program.", "Title: Tips and Tricks for Validation of Quality Control Analytical Methods in Good Manufacturing Practice Mesenchymal Stromal Cell Production\nPassage: removed by washing with phosphate-buffered saline with complete medium change. The cultures were daily monitored for colony appearance, and the culture medium was changed every three days. At 80% confluence, the cells were detached using 25 mL/layer of TrypLE-Select , at the version in use at the moment of validation. The lyophilized bacterial strains, yeast, and fungus were appropriately prepared and isolated in Casein Soybean Digest Agar and Sabouraud, right-agar plates . After incubation at the optimum growth conditions, the strains were stored at 4°C ± 2. For use, they were recultivated in agar plates in specific conditions and after" ]

[ [ "1a", "Title: Production of high titre disabled infectious single cycle (DISC) HSV from a microcarrier culture" ], [ "1b", "Passage: CPE 60-72 h after infection, the cultures were harvested." ], [ "1c", "Infectious DISC-HSV released from the CR2 cells was quantified using a TCID 50 assay and was again compared to the titre achieved from the equivalent roller bottle culture harvests." ], [ "1d", "The results are shown in Table 1 ." ], [ "1e", "Typically 4-7.0 × 10 11 total pfu from a 15 l culture was achieved, with a period of approximately 9 h during which this high titre was sustained." ], [ "1f", "From an equivalent number of 388 roller bottles we would expect to achieve approximately 3.88 × 10 11 total pfu." ], [ "1g", "Our results, therefore, compare very favourably" ] ]

[ "1e", "1f" ]

[ "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: We shall analyze the daily data for the number of confirmed cases in mainland China, which origins from the National Health Commission of the People's Republic of China . A part of the official diagram is shown in Fig. 1 . For calculations, we have used the data for the period of time from January 16 to February 9, 2020. The numbers shown after February 9 were used for verification of predictions.", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: 9 1975 10 25 42638 Unknown 26 10 2744 11 26 44653 Unknown 27 11 4515 12 27 46472 58761 28 12 5974 13 28 48467 63851 29 13 7711 14 29 49970 66492 30 14 9692 ----31 15 11791 ----", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: On February 12, 2020, the National Health Commission of the People's Republic of China has added 12289 new cases as \"clinically diagnosed cases\". The cases, reported by this official organization before, have the name of \"tested confirmed cases\" . To avoid confusiong, we will denote \"tested confirmed cases\" as Wj; j corresponds to the different time moments tj . Let us denote the \"clinically diagnosed cases\" as Qj. The sum of Wj and Qj is shown in the last column in Fig. 1 and in the Table. The Table shows that the precise time of the epidemic beginning t0 is", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

[ [ "0a", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China" ], [ "0b", "Passage: We shall analyze the daily data for the number of confirmed cases in mainland China, which origins from the National Health Commission of the People's Republic of China ." ], [ "0c", "A part of the official diagram is shown in Fig. 1 ." ], [ "0d", "For calculations, we have used the data for the period of time from January 16 to February 9, 2020." ], [ "0e", "The numbers shown after February 9 were used for verification of predictions." ] ]

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

[ "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: We shall analyze the daily data for the number of confirmed cases in mainland China, which origins from the National Health Commission of the People's Republic of China . A part of the official diagram is shown in Fig. 1 . For calculations, we have used the data for the period of time from January 16 to February 9, 2020. The numbers shown after February 9 were used for verification of predictions.", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: 9 1975 10 25 42638 Unknown 26 10 2744 11 26 44653 Unknown 27 11 4515 12 27 46472 58761 28 12 5974 13 28 48467 63851 29 13 7711 14 29 49970 66492 30 14 9692 ----31 15 11791 ----", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: On February 12, 2020, the National Health Commission of the People's Republic of China has added 12289 new cases as \"clinically diagnosed cases\". The cases, reported by this official organization before, have the name of \"tested confirmed cases\" . To avoid confusiong, we will denote \"tested confirmed cases\" as Wj; j corresponds to the different time moments tj . Let us denote the \"clinically diagnosed cases\" as Qj. The sum of Wj and Qj is shown in the last column in Fig. 1 and in the Table. The Table shows that the precise time of the epidemic beginning t0 is", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

[ [ "1a", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China" ], [ "1b", "Passage: 9 1975 10 25 42638 Unknown 26 10 2744 11 26 44653 Unknown 27 11 4515 12 27 46472 58761 28 12 5974 13 28 48467 63851 29 13 7711 14 29 49970 66492 30 14 9692 ----31 15 11791 ----" ] ]

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

[ "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: We shall analyze the daily data for the number of confirmed cases in mainland China, which origins from the National Health Commission of the People's Republic of China . A part of the official diagram is shown in Fig. 1 . For calculations, we have used the data for the period of time from January 16 to February 9, 2020. The numbers shown after February 9 were used for verification of predictions.", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: 9 1975 10 25 42638 Unknown 26 10 2744 11 26 44653 Unknown 27 11 4515 12 27 46472 58761 28 12 5974 13 28 48467 63851 29 13 7711 14 29 49970 66492 30 14 9692 ----31 15 11791 ----", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: On February 12, 2020, the National Health Commission of the People's Republic of China has added 12289 new cases as \"clinically diagnosed cases\". The cases, reported by this official organization before, have the name of \"tested confirmed cases\" . To avoid confusiong, we will denote \"tested confirmed cases\" as Wj; j corresponds to the different time moments tj . Let us denote the \"clinically diagnosed cases\" as Qj. The sum of Wj and Qj is shown in the last column in Fig. 1 and in the Table. The Table shows that the precise time of the epidemic beginning t0 is", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

[ [ "2a", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China" ], [ "2b", "Passage: On February 12, 2020, the National Health Commission of the People's Republic of China has added 12289 new cases as \"clinically diagnosed cases\"." ], [ "2c", "The cases, reported by this official organization before, have the name of \"tested confirmed cases\" ." ], [ "2d", "To avoid confusiong, we will denote \"tested confirmed cases\" as Wj; j corresponds to the different time moments tj ." ], [ "2e", "Let us denote the \"clinically diagnosed cases\" as Qj." ], [ "2f", "The sum of Wj and Qj is shown in the last column in Fig." ], [ "2g", "1 and in the Table." ], [ "2h", "The Table shows that the precise time of the epidemic beginning t0 is" ] ]

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

[ "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: We shall analyze the daily data for the number of confirmed cases in mainland China, which origins from the National Health Commission of the People's Republic of China . A part of the official diagram is shown in Fig. 1 . For calculations, we have used the data for the period of time from January 16 to February 9, 2020. The numbers shown after February 9 were used for verification of predictions.", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: 9 1975 10 25 42638 Unknown 26 10 2744 11 26 44653 Unknown 27 11 4515 12 27 46472 58761 28 12 5974 13 28 48467 63851 29 13 7711 14 29 49970 66492 30 14 9692 ----31 15 11791 ----", "Title: Statistics-Based Predictions of Coronavirus Epidemic Spreading in Mainland China\nPassage: On February 12, 2020, the National Health Commission of the People's Republic of China has added 12289 new cases as \"clinically diagnosed cases\". The cases, reported by this official organization before, have the name of \"tested confirmed cases\" . To avoid confusiong, we will denote \"tested confirmed cases\" as Wj; j corresponds to the different time moments tj . Let us denote the \"clinically diagnosed cases\" as Qj. The sum of Wj and Qj is shown in the last column in Fig. 1 and in the Table. The Table shows that the precise time of the epidemic beginning t0 is", "Title: The Extent of Transmission of Novel Coronavirus in Wuhan, China, 2020\nPassage: As of 24 January 2020, the cumulative incidence in China is 830 cases, of which 549 cases were diagnosed in Hubei, 26 in Beijing, 20 in Shanghai, and 53 in Guangdong. Additionally, twenty-six deaths have been linked to the outbreak , and thirteen cases were exported to Japan, Singapore, South Korea, Taiwan, Thailand, Vietnam and the United States as of 22 January 2020. Considering that enhanced surveillance has been underway in these importing countries, case ascertainment has been perhaps better in exported case data." ]

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

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

[ "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: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: families and healthcare settings . Clinical pictures of this infection varied from asymptomatic to mild respiratory symptoms to severe respiratory distress and death . Severe ailment can often cause respiratory catastrophes that need mechanical ventilation and support in ICUs across different healthcare settings . Studies have suggested an incubation period of 16 days with a mean of 5-6 days , while the median time until death is 11-13 days among severely ill patients . e gold standard test for the detection of this virus is real-time reverse-transcription polymerase chain reaction assays .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Although DCs appear to suffer the equivalent of a 'common cold' from MERS-CoV infection, in humans, the virus can be a more serious and opportunistic pathogen associated with the death of up to 40 % of reported cases. It has yet to be established whether infections thought to have been acquired from an animal source produce a more severe outcome than those spread between humans . Studies have established that the mean incubation period for MERS is five to six days, ranging from two to 16 days, with 13 to 14 days between when illness begins in one person and", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: 7 days, and the test is subsequently repeated after every 3 days until a negative result is obtained ." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: subsequently spreads to another ." ], [ "0c", "Among those with progressive illness, the median time to death is 11 to 13 days, ranging from five to 27 days ." ], [ "0d", "Fever and gastrointestinal symptoms may form a prodrome, after which symptoms decline, only to be followed by a more severe systemic and respiratory syndrome ." ] ]

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

[ "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: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: families and healthcare settings . Clinical pictures of this infection varied from asymptomatic to mild respiratory symptoms to severe respiratory distress and death . Severe ailment can often cause respiratory catastrophes that need mechanical ventilation and support in ICUs across different healthcare settings . Studies have suggested an incubation period of 16 days with a mean of 5-6 days , while the median time until death is 11-13 days among severely ill patients . e gold standard test for the detection of this virus is real-time reverse-transcription polymerase chain reaction assays .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Although DCs appear to suffer the equivalent of a 'common cold' from MERS-CoV infection, in humans, the virus can be a more serious and opportunistic pathogen associated with the death of up to 40 % of reported cases. It has yet to be established whether infections thought to have been acquired from an animal source produce a more severe outcome than those spread between humans . Studies have established that the mean incubation period for MERS is five to six days, ranging from two to 16 days, with 13 to 14 days between when illness begins in one person and", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: 7 days, and the test is subsequently repeated after every 3 days until a negative result is obtained ." ]

[ [ "1a", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory" ], [ "1b", "Passage: families and healthcare settings ." ], [ "1c", "Clinical pictures of this infection varied from asymptomatic to mild respiratory symptoms to severe respiratory distress and death ." ], [ "1d", "Severe ailment can often cause respiratory catastrophes that need mechanical ventilation and support in ICUs across different healthcare settings ." ], [ "1e", "Studies have suggested an incubation period of 16 days with a mean of 5-6 days , while the median time until death is 11-13 days among severely ill patients ." ], [ "1f", "e gold standard test for the detection of this virus is real-time reverse-transcription polymerase chain reaction assays ." ] ]

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

[ "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: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: families and healthcare settings . Clinical pictures of this infection varied from asymptomatic to mild respiratory symptoms to severe respiratory distress and death . Severe ailment can often cause respiratory catastrophes that need mechanical ventilation and support in ICUs across different healthcare settings . Studies have suggested an incubation period of 16 days with a mean of 5-6 days , while the median time until death is 11-13 days among severely ill patients . e gold standard test for the detection of this virus is real-time reverse-transcription polymerase chain reaction assays .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Although DCs appear to suffer the equivalent of a 'common cold' from MERS-CoV infection, in humans, the virus can be a more serious and opportunistic pathogen associated with the death of up to 40 % of reported cases. It has yet to be established whether infections thought to have been acquired from an animal source produce a more severe outcome than those spread between humans . Studies have established that the mean incubation period for MERS is five to six days, ranging from two to 16 days, with 13 to 14 days between when illness begins in one person and", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: 7 days, and the test is subsequently repeated after every 3 days until a negative result is obtained ." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: Although DCs appear to suffer the equivalent of a 'common cold' from MERS-CoV infection, in humans, the virus can be a more serious and opportunistic pathogen associated with the death of up to 40 % of reported cases." ], [ "2c", "It has yet to be established whether infections thought to have been acquired from an animal source produce a more severe outcome than those spread between humans ." ], [ "2d", "Studies have established that the mean incubation period for MERS is five to six days, ranging from two to 16 days, with 13 to 14 days between when illness begins in one person and" ] ]

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