Datasets:

param-bharat

/

ragbench-context-relevance-filtered

like 1

[ "Title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices\nPassage: Reverse transcription was carried out using PrimeScript Reverse Transcriptase with slight modifications to the manufacturer's protocol. The RT mixture contained 0.5 nmol of dNTP mix , 20,000 molecules of IAC RNA, 2 pmol of both reverse primers , 4 µl of PrimeScript reaction buffer, 5 U of reverse transcriptase, 1 U of RNase inhibitor and 5 µl of isolated RNA. The reaction was performed at 50 • C for 1 h followed by 75 • C for 15 min and a cooling step at 10 • C.", "Title: A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity\nPassage: In brief, the tailed RNA product was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 65 ∘ C for 5 min, followed by incubation on ice for 5 min. The reaction mix was then added with 20 mM Tris , 50 mM KCl, 5 mM MgCl 2 , 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III . RT reaction was performed according to the manufacturer's instructions. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 100 nt,", "Title: RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination\nPassage: Viral RNA was purified from virus stocks by using QiaAmp viral RNA purification kit and used for RT-qPCR to determine genome copies. This analysis was performed by the Genomics Core Facility of the Pennsylvania State University. DNAse-treated RNA was reverse-transcribed using the High Capacity cDNA Reverse Transcription kit following the protocol provided with the kit. Quantification by real-time qPCR was done with 2X TaqMan Universal PCR Master Mix in a volume of 20 µL, with primers 5 -ACCCCTGGTAGCAATCAATATCTTAC-3 and 5 -TTCTTTACTTCACCGGGTATGTCA-3 , and probe 5 - TGTGCGCTGCCTGAATTTGATGTGA-3 in a 7300 Real-Time qPCR System machine. A standard curve was generated using", "Title: Variation in RNA Virus Mutation Rates across Host Cells\nPassage: A 96-well plate containing 10 4 cells per well was inoculated with a limiting dilution of the viral stock such that approximately 10% of wells were infected. Plates were incubated at 37uC for 24 h, inspected under the microscope for cytopathic effects, and freezethawed to allow release of intracellular viruses. Viral RNA was purified from the supernatant of each of five positive wells and reverse-transcribed using AccuScript High Fidelity Reverse Transcripatse, and the cDNA was PCR-amplified using Phusion High Fidelity DNA polymerase and specific primers located in the P, G and L genes, as indicated. PCR products were cloned and" ]

[ [ "0a", "Title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices" ], [ "0b", "Passage: Reverse transcription was carried out using PrimeScript Reverse Transcriptase with slight modifications to the manufacturer's protocol." ], [ "0c", "The RT mixture contained 0.5 nmol of dNTP mix , 20,000 molecules of IAC RNA, 2 pmol of both reverse primers , 4 µl of PrimeScript reaction buffer, 5 U of reverse transcriptase, 1 U of RNase inhibitor and 5 µl of isolated RNA." ], [ "0d", "The reaction was performed at 50 • C for 1 h followed by 75 • C for 15 min and a cooling step at 10 • C." ] ]

[ "0c", "3d" ]

[ "Title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices\nPassage: Reverse transcription was carried out using PrimeScript Reverse Transcriptase with slight modifications to the manufacturer's protocol. The RT mixture contained 0.5 nmol of dNTP mix , 20,000 molecules of IAC RNA, 2 pmol of both reverse primers , 4 µl of PrimeScript reaction buffer, 5 U of reverse transcriptase, 1 U of RNase inhibitor and 5 µl of isolated RNA. The reaction was performed at 50 • C for 1 h followed by 75 • C for 15 min and a cooling step at 10 • C.", "Title: A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity\nPassage: In brief, the tailed RNA product was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 65 ∘ C for 5 min, followed by incubation on ice for 5 min. The reaction mix was then added with 20 mM Tris , 50 mM KCl, 5 mM MgCl 2 , 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III . RT reaction was performed according to the manufacturer's instructions. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 100 nt,", "Title: RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination\nPassage: Viral RNA was purified from virus stocks by using QiaAmp viral RNA purification kit and used for RT-qPCR to determine genome copies. This analysis was performed by the Genomics Core Facility of the Pennsylvania State University. DNAse-treated RNA was reverse-transcribed using the High Capacity cDNA Reverse Transcription kit following the protocol provided with the kit. Quantification by real-time qPCR was done with 2X TaqMan Universal PCR Master Mix in a volume of 20 µL, with primers 5 -ACCCCTGGTAGCAATCAATATCTTAC-3 and 5 -TTCTTTACTTCACCGGGTATGTCA-3 , and probe 5 - TGTGCGCTGCCTGAATTTGATGTGA-3 in a 7300 Real-Time qPCR System machine. A standard curve was generated using", "Title: Variation in RNA Virus Mutation Rates across Host Cells\nPassage: A 96-well plate containing 10 4 cells per well was inoculated with a limiting dilution of the viral stock such that approximately 10% of wells were infected. Plates were incubated at 37uC for 24 h, inspected under the microscope for cytopathic effects, and freezethawed to allow release of intracellular viruses. Viral RNA was purified from the supernatant of each of five positive wells and reverse-transcribed using AccuScript High Fidelity Reverse Transcripatse, and the cDNA was PCR-amplified using Phusion High Fidelity DNA polymerase and specific primers located in the P, G and L genes, as indicated. PCR products were cloned and" ]

[ [ "3a", "Title: Variation in RNA Virus Mutation Rates across Host Cells" ], [ "3b", "Passage: A 96-well plate containing 10 4 cells per well was inoculated with a limiting dilution of the viral stock such that approximately 10% of wells were infected." ], [ "3c", "Plates were incubated at 37uC for 24 h, inspected under the microscope for cytopathic effects, and freezethawed to allow release of intracellular viruses." ], [ "3d", "Viral RNA was purified from the supernatant of each of five positive wells and reverse-transcribed using AccuScript High Fidelity Reverse Transcripatse, and the cDNA was PCR-amplified using Phusion High Fidelity DNA polymerase and specific primers located in the P, G and L genes, as indicated." ], [ "3e", "PCR products were cloned and" ] ]

[ "0c", "3d" ]

[ "Title: Influenza B virus non-structural protein 1 counteracts ISG15 antiviral activity by sequestering ISGylated viral proteins\nPassage: that are not bound to the mutant NS1B protein, although only a small percentage of the total NP proteins in mutant virus-infected cells, act in a dominant-negative manner to terminate the oligomerization of unconjugated NP molecules, resulting in incomplete NP oligomers containing ISGylated NP. This is the first demonstration that ISGylated viral proteins can act as dominant-negative inhibitors of the oligomerization of their much more abundant unconjugated counterparts in virusinfected cells.", "Title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus\nPassage: The mechanism of dominant-negative inhibition by the C-terminal deletion mutant of hnRNP A1 To understand the underlying mechanism of the inhibition of MHV RNA transcription by the C-terminal-deletion mutant of hnRNP A1, we ®rst examined the RNA-and protein-binding properties of this mutant protein.", "Title: Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition\nPassage: In vitro DENV inhibition. Encouraged by the previous results, we investigated the in vitro inhibition of DENV through standard antiviral, plaque-forming half-maximum effective concentration assays. Briefly, the DENV viral particles were incubated with different concentrations of each inhibitor in human serum and the remaining infectivity was determined by a plaque reduction assay . The dose-dependent inhibition of DENV for the monovalent aptamer and each of the scaffold-aptamer complexes was examined . The EC 50 value of the DNA star-aptamer complex for DENV infection inhibition was 2 nM, whereas the EC 50 value for the monovalent aptamer was 15 µM .", "Title: Enterovirus Control of Translation and RNA Granule Stress Responses\nPassage: A final hypothesis is that production of G3BP1 cleavage fragments may be more important than the loss of intact G3BP1 through the production of dominant negative inhibitors. The expression of certain G3BP truncations in cells revealed some degree of dominant negative activity . The G3BP1 fragments generated by CVB3 3C pro and the C-terminal RNA binding domain are inhibitors of SGs . Further, deletion of the NTF2-like domain is sufficient produce a dominant negative factor . Taken together, this may indicate that several interaction domains along the length of G3BP are needed for SG formation. Consistent with this interpretation, G3BP1" ]

[ [ "0a", "Title: Influenza B virus non-structural protein 1 counteracts ISG15 antiviral activity by sequestering ISGylated viral proteins" ], [ "0b", "Passage: that are not bound to the mutant NS1B protein, although only a small percentage of the total NP proteins in mutant virus-infected cells, act in a dominant-negative manner to terminate the oligomerization of unconjugated NP molecules, resulting in incomplete NP oligomers containing ISGylated NP." ], [ "0c", "This is the first demonstration that ISGylated viral proteins can act as dominant-negative inhibitors of the oligomerization of their much more abundant unconjugated counterparts in virusinfected cells." ] ]

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

[ "Title: Influenza B virus non-structural protein 1 counteracts ISG15 antiviral activity by sequestering ISGylated viral proteins\nPassage: that are not bound to the mutant NS1B protein, although only a small percentage of the total NP proteins in mutant virus-infected cells, act in a dominant-negative manner to terminate the oligomerization of unconjugated NP molecules, resulting in incomplete NP oligomers containing ISGylated NP. This is the first demonstration that ISGylated viral proteins can act as dominant-negative inhibitors of the oligomerization of their much more abundant unconjugated counterparts in virusinfected cells.", "Title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus\nPassage: The mechanism of dominant-negative inhibition by the C-terminal deletion mutant of hnRNP A1 To understand the underlying mechanism of the inhibition of MHV RNA transcription by the C-terminal-deletion mutant of hnRNP A1, we ®rst examined the RNA-and protein-binding properties of this mutant protein.", "Title: Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition\nPassage: In vitro DENV inhibition. Encouraged by the previous results, we investigated the in vitro inhibition of DENV through standard antiviral, plaque-forming half-maximum effective concentration assays. Briefly, the DENV viral particles were incubated with different concentrations of each inhibitor in human serum and the remaining infectivity was determined by a plaque reduction assay . The dose-dependent inhibition of DENV for the monovalent aptamer and each of the scaffold-aptamer complexes was examined . The EC 50 value of the DNA star-aptamer complex for DENV infection inhibition was 2 nM, whereas the EC 50 value for the monovalent aptamer was 15 µM .", "Title: Enterovirus Control of Translation and RNA Granule Stress Responses\nPassage: A final hypothesis is that production of G3BP1 cleavage fragments may be more important than the loss of intact G3BP1 through the production of dominant negative inhibitors. The expression of certain G3BP truncations in cells revealed some degree of dominant negative activity . The G3BP1 fragments generated by CVB3 3C pro and the C-terminal RNA binding domain are inhibitors of SGs . Further, deletion of the NTF2-like domain is sufficient produce a dominant negative factor . Taken together, this may indicate that several interaction domains along the length of G3BP are needed for SG formation. Consistent with this interpretation, G3BP1" ]

[ [ "1a", "Title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus" ], [ "1b", "Passage: The mechanism of dominant-negative inhibition by the C-terminal deletion mutant of hnRNP A1 To understand the underlying mechanism of the inhibition of MHV RNA transcription by the C-terminal-deletion mutant of hnRNP A1, we ®rst examined the RNA-and protein-binding properties of this mutant protein." ] ]

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

[ "Title: Influenza B virus non-structural protein 1 counteracts ISG15 antiviral activity by sequestering ISGylated viral proteins\nPassage: that are not bound to the mutant NS1B protein, although only a small percentage of the total NP proteins in mutant virus-infected cells, act in a dominant-negative manner to terminate the oligomerization of unconjugated NP molecules, resulting in incomplete NP oligomers containing ISGylated NP. This is the first demonstration that ISGylated viral proteins can act as dominant-negative inhibitors of the oligomerization of their much more abundant unconjugated counterparts in virusinfected cells.", "Title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus\nPassage: The mechanism of dominant-negative inhibition by the C-terminal deletion mutant of hnRNP A1 To understand the underlying mechanism of the inhibition of MHV RNA transcription by the C-terminal-deletion mutant of hnRNP A1, we ®rst examined the RNA-and protein-binding properties of this mutant protein.", "Title: Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition\nPassage: In vitro DENV inhibition. Encouraged by the previous results, we investigated the in vitro inhibition of DENV through standard antiviral, plaque-forming half-maximum effective concentration assays. Briefly, the DENV viral particles were incubated with different concentrations of each inhibitor in human serum and the remaining infectivity was determined by a plaque reduction assay . The dose-dependent inhibition of DENV for the monovalent aptamer and each of the scaffold-aptamer complexes was examined . The EC 50 value of the DNA star-aptamer complex for DENV infection inhibition was 2 nM, whereas the EC 50 value for the monovalent aptamer was 15 µM .", "Title: Enterovirus Control of Translation and RNA Granule Stress Responses\nPassage: A final hypothesis is that production of G3BP1 cleavage fragments may be more important than the loss of intact G3BP1 through the production of dominant negative inhibitors. The expression of certain G3BP truncations in cells revealed some degree of dominant negative activity . The G3BP1 fragments generated by CVB3 3C pro and the C-terminal RNA binding domain are inhibitors of SGs . Further, deletion of the NTF2-like domain is sufficient produce a dominant negative factor . Taken together, this may indicate that several interaction domains along the length of G3BP are needed for SG formation. Consistent with this interpretation, G3BP1" ]

[ [ "3a", "Title: Enterovirus Control of Translation and RNA Granule Stress Responses" ], [ "3b", "Passage: A final hypothesis is that production of G3BP1 cleavage fragments may be more important than the loss of intact G3BP1 through the production of dominant negative inhibitors." ], [ "3c", "The expression of certain G3BP truncations in cells revealed some degree of dominant negative activity ." ], [ "3d", "The G3BP1 fragments generated by CVB3 3C pro and the C-terminal RNA binding domain are inhibitors of SGs ." ], [ "3e", "Further, deletion of the NTF2-like domain is sufficient produce a dominant negative factor ." ], [ "3f", "Taken together, this may indicate that several interaction domains along the length of G3BP are needed for SG formation." ], [ "3g", "Consistent with this interpretation, G3BP1" ] ]

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

[ "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: The pharmacologic action of glycyrrhizin, the active component of licorice root, has been shown to produce anti-inflammatory activity, 4'5 modulation of the immune system, 6'7 inhibition of virus growth, and inactivation of viruses. 8-~° Glycyrrhizin also has been found to inhibit virus growth in mice infected with influenza viruses and to improve outcomes. ~ ~ Glycyrrhizin is most typically used to treat chronic hepatitis and allergic dermatitis as urticaria in Japan and has occasionally been used to treat URTIs without prospective, randomized, double-blind, controlled study methods. ~2", "Title: Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species\nPassage: of 3.6-13.1% in dried roots . G consists of a disaccharide of two glucuronic acid molecules bound to the pentacyclic triterpene glycyrrhetinic acid , which exists in two isomers : the trans and the cis form . G exhibits potent hydrocortisone-like anti-inflammatory, antiulcer, antiviral, and antihepatotoxic activities whereas GA is a potent antibiotic against ulcer causing Helicobacter pylori .", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: glycyrrhizin also has been used to treat human immunodeficiency virus-1. Infrequent AEs, such as increased blood pressure and hypokalemia, have been reported in some patients after several months of glycyrrhizin HCV treatment. However, in this study in which glycyrrhizin was used for a short time, no AEs were reported.", "Title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression\nPassage: Glycyrrhizin was obtained from Minophagen Pharmaceuticals Co., Ltd. ." ]

[ [ "0a", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial" ], [ "0b", "Passage: The pharmacologic action of glycyrrhizin, the active component of licorice root, has been shown to produce anti-inflammatory activity, 4'5 modulation of the immune system, 6'7 inhibition of virus growth, and inactivation of viruses." ], [ "0c", "8-~° Glycyrrhizin also has been found to inhibit virus growth in mice infected with influenza viruses and to improve outcomes." ], [ "0d", "~ ~ Glycyrrhizin is most typically used to treat chronic hepatitis and allergic dermatitis as urticaria in Japan and has occasionally been used to treat URTIs without prospective, randomized, double-blind, controlled study methods. ~2" ] ]

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

[ "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: The pharmacologic action of glycyrrhizin, the active component of licorice root, has been shown to produce anti-inflammatory activity, 4'5 modulation of the immune system, 6'7 inhibition of virus growth, and inactivation of viruses. 8-~° Glycyrrhizin also has been found to inhibit virus growth in mice infected with influenza viruses and to improve outcomes. ~ ~ Glycyrrhizin is most typically used to treat chronic hepatitis and allergic dermatitis as urticaria in Japan and has occasionally been used to treat URTIs without prospective, randomized, double-blind, controlled study methods. ~2", "Title: Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species\nPassage: of 3.6-13.1% in dried roots . G consists of a disaccharide of two glucuronic acid molecules bound to the pentacyclic triterpene glycyrrhetinic acid , which exists in two isomers : the trans and the cis form . G exhibits potent hydrocortisone-like anti-inflammatory, antiulcer, antiviral, and antihepatotoxic activities whereas GA is a potent antibiotic against ulcer causing Helicobacter pylori .", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: glycyrrhizin also has been used to treat human immunodeficiency virus-1. Infrequent AEs, such as increased blood pressure and hypokalemia, have been reported in some patients after several months of glycyrrhizin HCV treatment. However, in this study in which glycyrrhizin was used for a short time, no AEs were reported.", "Title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression\nPassage: Glycyrrhizin was obtained from Minophagen Pharmaceuticals Co., Ltd. ." ]

[ [ "1a", "Title: Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species" ], [ "1b", "Passage: of 3.6-13.1% in dried roots ." ], [ "1c", "G consists of a disaccharide of two glucuronic acid molecules bound to the pentacyclic triterpene glycyrrhetinic acid , which exists in two isomers : the trans and the cis form ." ], [ "1d", "G exhibits potent hydrocortisone-like anti-inflammatory, antiulcer, antiviral, and antihepatotoxic activities whereas GA is a potent antibiotic against ulcer causing Helicobacter pylori ." ] ]

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

[ "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: The pharmacologic action of glycyrrhizin, the active component of licorice root, has been shown to produce anti-inflammatory activity, 4'5 modulation of the immune system, 6'7 inhibition of virus growth, and inactivation of viruses. 8-~° Glycyrrhizin also has been found to inhibit virus growth in mice infected with influenza viruses and to improve outcomes. ~ ~ Glycyrrhizin is most typically used to treat chronic hepatitis and allergic dermatitis as urticaria in Japan and has occasionally been used to treat URTIs without prospective, randomized, double-blind, controlled study methods. ~2", "Title: Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species\nPassage: of 3.6-13.1% in dried roots . G consists of a disaccharide of two glucuronic acid molecules bound to the pentacyclic triterpene glycyrrhetinic acid , which exists in two isomers : the trans and the cis form . G exhibits potent hydrocortisone-like anti-inflammatory, antiulcer, antiviral, and antihepatotoxic activities whereas GA is a potent antibiotic against ulcer causing Helicobacter pylori .", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: glycyrrhizin also has been used to treat human immunodeficiency virus-1. Infrequent AEs, such as increased blood pressure and hypokalemia, have been reported in some patients after several months of glycyrrhizin HCV treatment. However, in this study in which glycyrrhizin was used for a short time, no AEs were reported.", "Title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression\nPassage: Glycyrrhizin was obtained from Minophagen Pharmaceuticals Co., Ltd. ." ]

[ [ "2a", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial" ], [ "2b", "Passage: glycyrrhizin also has been used to treat human immunodeficiency virus-1." ], [ "2c", "Infrequent AEs, such as increased blood pressure and hypokalemia, have been reported in some patients after several months of glycyrrhizin HCV treatment." ], [ "2d", "However, in this study in which glycyrrhizin was used for a short time, no AEs were reported." ] ]

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

[ "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: The pharmacologic action of glycyrrhizin, the active component of licorice root, has been shown to produce anti-inflammatory activity, 4'5 modulation of the immune system, 6'7 inhibition of virus growth, and inactivation of viruses. 8-~° Glycyrrhizin also has been found to inhibit virus growth in mice infected with influenza viruses and to improve outcomes. ~ ~ Glycyrrhizin is most typically used to treat chronic hepatitis and allergic dermatitis as urticaria in Japan and has occasionally been used to treat URTIs without prospective, randomized, double-blind, controlled study methods. ~2", "Title: Unequivocal glycyrrhizin isomer determination and comparative in vitro bioactivities of root extracts in four Glycyrrhiza species\nPassage: of 3.6-13.1% in dried roots . G consists of a disaccharide of two glucuronic acid molecules bound to the pentacyclic triterpene glycyrrhetinic acid , which exists in two isomers : the trans and the cis form . G exhibits potent hydrocortisone-like anti-inflammatory, antiulcer, antiviral, and antihepatotoxic activities whereas GA is a potent antibiotic against ulcer causing Helicobacter pylori .", "Title: Effects and cost of glycyrrhizin in the treatment of upper respiratory tract infections in members of the Japanese maritime self-defense force: Preliminary report of a prospective, randomized, double-blind, controlled, parallel-group, alternate-day treatment assignment clinical trial\nPassage: glycyrrhizin also has been used to treat human immunodeficiency virus-1. Infrequent AEs, such as increased blood pressure and hypokalemia, have been reported in some patients after several months of glycyrrhizin HCV treatment. However, in this study in which glycyrrhizin was used for a short time, no AEs were reported.", "Title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression\nPassage: Glycyrrhizin was obtained from Minophagen Pharmaceuticals Co., Ltd. ." ]

[ [ "3a", "Title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression" ], [ "3b", "Passage: Glycyrrhizin was obtained from Minophagen Pharmaceuticals Co., Ltd. ." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: Italy 9.8%", "Title: Estimating the number of infections and the impact of non-\nPassage: countries between 7 and 43 million individuals have been infected with SARS-CoV-Z up to 28th March,", "Title: Estimating the number of infections and the impact of non-\nPassage: https://www.gazzettaufficiale.it/eli/id/2020/03/08/20A01522/sg .", "Title: Estimating the number of infections and the impact of non-\nPassage: http://www.salute.gov.it/portale/nuovocoronavirus/dettaglioVideoNuovoCoronavirus.jsp?lingua=ita" ]

[ [ "0a", "Title: Estimating the number of infections and the impact of non-" ], [ "0b", "Passage: Italy 9.8%" ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: Italy 9.8%", "Title: Estimating the number of infections and the impact of non-\nPassage: countries between 7 and 43 million individuals have been infected with SARS-CoV-Z up to 28th March,", "Title: Estimating the number of infections and the impact of non-\nPassage: https://www.gazzettaufficiale.it/eli/id/2020/03/08/20A01522/sg .", "Title: Estimating the number of infections and the impact of non-\nPassage: http://www.salute.gov.it/portale/nuovocoronavirus/dettaglioVideoNuovoCoronavirus.jsp?lingua=ita" ]

[ [ "1a", "Title: Estimating the number of infections and the impact of non-" ], [ "1b", "Passage: countries between 7 and 43 million individuals have been infected with SARS-CoV-Z up to 28th March," ] ]

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

[ "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: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: All these studies on the effect of pre-existing immunity discuss the impact on humoral responses. Sevil Domenech and colleagues reported that pre-exposing animals to the homologous Salmonella vector leads to a significant reduction in CD8 + responses; however, exposure of animals to a heterologous strain leads to significantly higher CD8 + responses .", "Title: Recombinant vector vaccine evolution\nPassage: Although recombinant vector vaccines are not yet in widespread use, many are under development , and their success may rest on understanding within-host evolution. Here we explore how the combination of evolution during the process of vaccine manufacture and during its within-host dynamics following vaccination could affect the immune responses elicited by a recombinant vector vaccine and reduce its efficacy-the specific interaction between evolution and immunity. We consider viral vaccines and focus on vaccines that cause shortduration infections. The ideas we discuss also apply to live vaccines of bacteria and other pathogens." ]

[ [ "0a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "0b", "Passage: Only the study by Vijh et al. indicated that exposure to the empty vector may completely abrogate immune responses against the delivered antigens ." ], [ "0c", "However, these studies also indicate that downregulation of antigenspecific immune responses is highly dependent on dose and time." ], [ "0d", "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." ], [ "0e", "Of course, such repeated vaccination may not be practicable in real-world situations." ] ]

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

[ "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: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: All these studies on the effect of pre-existing immunity discuss the impact on humoral responses. Sevil Domenech and colleagues reported that pre-exposing animals to the homologous Salmonella vector leads to a significant reduction in CD8 + responses; however, exposure of animals to a heterologous strain leads to significantly higher CD8 + responses .", "Title: Recombinant vector vaccine evolution\nPassage: Although recombinant vector vaccines are not yet in widespread use, many are under development , and their success may rest on understanding within-host evolution. Here we explore how the combination of evolution during the process of vaccine manufacture and during its within-host dynamics following vaccination could affect the immune responses elicited by a recombinant vector vaccine and reduce its efficacy-the specific interaction between evolution and immunity. We consider viral vaccines and focus on vaccines that cause shortduration infections. The ideas we discuss also apply to live vaccines of bacteria and other pathogens." ]

[ [ "1a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "1b", "Passage: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response." ], [ "1c", "Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses." ], [ "1d", "This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes ." ], [ "1e", "As these authors conclude, it will be possible to utilize such vectors only" ] ]

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

[ "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: For viral vectors, the impact of cell-mediated immunity was more pronounced, and as depicted in Table 2 , almost always resulted in a reduction in the subsequent immune response. Presumably this is because viruses will induce neutralizing antibody on the first dose, and in subsequent doses this antibody will limit the number of transduced cells, therefore limiting the responses. This is particularly a problem with a common viral vector such as Ad, where a large proportion of the population will have immunological memory against common serotypes . As these authors conclude, it will be possible to utilize such vectors only", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: All these studies on the effect of pre-existing immunity discuss the impact on humoral responses. Sevil Domenech and colleagues reported that pre-exposing animals to the homologous Salmonella vector leads to a significant reduction in CD8 + responses; however, exposure of animals to a heterologous strain leads to significantly higher CD8 + responses .", "Title: Recombinant vector vaccine evolution\nPassage: Although recombinant vector vaccines are not yet in widespread use, many are under development , and their success may rest on understanding within-host evolution. Here we explore how the combination of evolution during the process of vaccine manufacture and during its within-host dynamics following vaccination could affect the immune responses elicited by a recombinant vector vaccine and reduce its efficacy-the specific interaction between evolution and immunity. We consider viral vaccines and focus on vaccines that cause shortduration infections. The ideas we discuss also apply to live vaccines of bacteria and other pathogens." ]

[ [ "2a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "2b", "Passage: All these studies on the effect of pre-existing immunity discuss the impact on humoral responses." ], [ "2c", "Sevil Domenech and colleagues reported that pre-exposing animals to the homologous Salmonella vector leads to a significant reduction in CD8 + responses; however, exposure of animals to a heterologous strain leads to significantly higher CD8 + responses ." ] ]

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

[ "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: Iron is a vital micronutrient that regulates enzyme activity and metabolism. This element plays a key role in basic cellular processes, such as cellular respiration, DNA replication, and electron transport and is accordingly essential for bacterial survival in host tissues . Furthermore, iron is a necessary growth factor for bacteria and is reportedly involved in the expression of bacterial virulence factors . Iron uptake factors evidently play a pivotal role in E. coli growth and pathogenesis. Bacteria employ different strategies to absorb iron from their environment, including siderophore-mediated iron uptake, which occurs on the cell surface . In addition, bacteria", "Title: Insight into the Interaction of Metal Ions with TroA from Streptococcus suis\nPassage: Almost one third of proteins in nature depend on a particular metal for their diverse functions and divalent metal cations are essential for bacteria . For instance, manganese plays a primary antioxidant role in bacteria and affects bacterial pathogenesis . Zinc is one of the most abundant metals in bacteria and is an essential co-factor of many metabolic enzymes and transcription factors . The Mn 2+ ion is characterized as hard metal and tends to prefer hard ligands, while zinc prefers soft ligands . To obtain appropriate cellular concentrations of transition metal ions, bacteria have evolved elaborate machineries to transport", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: either excessively reduce the external pH or dissolve iron oxide to meet their iron requirements by reducing ferric iron to a relatively soluble ferrous form. Another common strategy is to synthesize and secrete iron chelators, such as siderophores, as intracellular iron is rarely found in natural conditions, and Fe 2+ can be readily oxidized to Fe 3+ in the presence of oxygen and water . Siderophores then combine with the available iron to form an iron-siderophore complex, which binds to specific receptor proteins on the bacterial cell surface, consequently entering cells via the TonBdependent transport system, followed by iron release.", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: TBDRs are known to actively transport ferric-siderophore complexes in Gram-negative bacteria, and they also transport diverse antibiotics, vitamins, nickel complexes, and carbohydrates . Transporters involved in iron uptake have very strict siderophore selectivity. A strong correlation exists between the amount of iron and siderophores that bacteria can use and the number of genes encoding iron-regulated TBDRs . In simple terms, iron depletion triggers the upregulation of genes encoding TBDRs." ]

[ [ "0a", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B" ], [ "0b", "Passage: Iron is a vital micronutrient that regulates enzyme activity and metabolism." ], [ "0c", "This element plays a key role in basic cellular processes, such as cellular respiration, DNA replication, and electron transport and is accordingly essential for bacterial survival in host tissues ." ], [ "0d", "Furthermore, iron is a necessary growth factor for bacteria and is reportedly involved in the expression of bacterial virulence factors ." ], [ "0e", "Iron uptake factors evidently play a pivotal role in E. coli growth and pathogenesis." ], [ "0f", "Bacteria employ different strategies to absorb iron from their environment, including siderophore-mediated iron uptake, which occurs on the cell surface ." ], [ "0g", "In addition, bacteria" ] ]

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

[ "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: Iron is a vital micronutrient that regulates enzyme activity and metabolism. This element plays a key role in basic cellular processes, such as cellular respiration, DNA replication, and electron transport and is accordingly essential for bacterial survival in host tissues . Furthermore, iron is a necessary growth factor for bacteria and is reportedly involved in the expression of bacterial virulence factors . Iron uptake factors evidently play a pivotal role in E. coli growth and pathogenesis. Bacteria employ different strategies to absorb iron from their environment, including siderophore-mediated iron uptake, which occurs on the cell surface . In addition, bacteria", "Title: Insight into the Interaction of Metal Ions with TroA from Streptococcus suis\nPassage: Almost one third of proteins in nature depend on a particular metal for their diverse functions and divalent metal cations are essential for bacteria . For instance, manganese plays a primary antioxidant role in bacteria and affects bacterial pathogenesis . Zinc is one of the most abundant metals in bacteria and is an essential co-factor of many metabolic enzymes and transcription factors . The Mn 2+ ion is characterized as hard metal and tends to prefer hard ligands, while zinc prefers soft ligands . To obtain appropriate cellular concentrations of transition metal ions, bacteria have evolved elaborate machineries to transport", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: either excessively reduce the external pH or dissolve iron oxide to meet their iron requirements by reducing ferric iron to a relatively soluble ferrous form. Another common strategy is to synthesize and secrete iron chelators, such as siderophores, as intracellular iron is rarely found in natural conditions, and Fe 2+ can be readily oxidized to Fe 3+ in the presence of oxygen and water . Siderophores then combine with the available iron to form an iron-siderophore complex, which binds to specific receptor proteins on the bacterial cell surface, consequently entering cells via the TonBdependent transport system, followed by iron release.", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: TBDRs are known to actively transport ferric-siderophore complexes in Gram-negative bacteria, and they also transport diverse antibiotics, vitamins, nickel complexes, and carbohydrates . Transporters involved in iron uptake have very strict siderophore selectivity. A strong correlation exists between the amount of iron and siderophores that bacteria can use and the number of genes encoding iron-regulated TBDRs . In simple terms, iron depletion triggers the upregulation of genes encoding TBDRs." ]

[ [ "2a", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B" ], [ "2b", "Passage: either excessively reduce the external pH or dissolve iron oxide to meet their iron requirements by reducing ferric iron to a relatively soluble ferrous form." ], [ "2c", "Another common strategy is to synthesize and secrete iron chelators, such as siderophores, as intracellular iron is rarely found in natural conditions, and Fe 2+ can be readily oxidized to Fe 3+ in the presence of oxygen and water ." ], [ "2d", "Siderophores then combine with the available iron to form an iron-siderophore complex, which binds to specific receptor proteins on the bacterial cell surface, consequently entering cells via the TonBdependent transport system, followed by iron release." ] ]

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

[ "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: Iron is a vital micronutrient that regulates enzyme activity and metabolism. This element plays a key role in basic cellular processes, such as cellular respiration, DNA replication, and electron transport and is accordingly essential for bacterial survival in host tissues . Furthermore, iron is a necessary growth factor for bacteria and is reportedly involved in the expression of bacterial virulence factors . Iron uptake factors evidently play a pivotal role in E. coli growth and pathogenesis. Bacteria employ different strategies to absorb iron from their environment, including siderophore-mediated iron uptake, which occurs on the cell surface . In addition, bacteria", "Title: Insight into the Interaction of Metal Ions with TroA from Streptococcus suis\nPassage: Almost one third of proteins in nature depend on a particular metal for their diverse functions and divalent metal cations are essential for bacteria . For instance, manganese plays a primary antioxidant role in bacteria and affects bacterial pathogenesis . Zinc is one of the most abundant metals in bacteria and is an essential co-factor of many metabolic enzymes and transcription factors . The Mn 2+ ion is characterized as hard metal and tends to prefer hard ligands, while zinc prefers soft ligands . To obtain appropriate cellular concentrations of transition metal ions, bacteria have evolved elaborate machineries to transport", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: either excessively reduce the external pH or dissolve iron oxide to meet their iron requirements by reducing ferric iron to a relatively soluble ferrous form. Another common strategy is to synthesize and secrete iron chelators, such as siderophores, as intracellular iron is rarely found in natural conditions, and Fe 2+ can be readily oxidized to Fe 3+ in the presence of oxygen and water . Siderophores then combine with the available iron to form an iron-siderophore complex, which binds to specific receptor proteins on the bacterial cell surface, consequently entering cells via the TonBdependent transport system, followed by iron release.", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B\nPassage: TBDRs are known to actively transport ferric-siderophore complexes in Gram-negative bacteria, and they also transport diverse antibiotics, vitamins, nickel complexes, and carbohydrates . Transporters involved in iron uptake have very strict siderophore selectivity. A strong correlation exists between the amount of iron and siderophores that bacteria can use and the number of genes encoding iron-regulated TBDRs . In simple terms, iron depletion triggers the upregulation of genes encoding TBDRs." ]

[ [ "3a", "Title: Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B" ], [ "3b", "Passage: TBDRs are known to actively transport ferric-siderophore complexes in Gram-negative bacteria, and they also transport diverse antibiotics, vitamins, nickel complexes, and carbohydrates ." ], [ "3c", "Transporters involved in iron uptake have very strict siderophore selectivity." ], [ "3d", "A strong correlation exists between the amount of iron and siderophores that bacteria can use and the number of genes encoding iron-regulated TBDRs ." ], [ "3e", "In simple terms, iron depletion triggers the upregulation of genes encoding TBDRs." ] ]

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

[ "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: To establish the phylogeographic map, HTNV tripartite genome sequences from A. agrarius captured in the endemic and military training areas near the demilitarized zone were completely acquired using RT-PCR. Compared with the genomic HTNV sequences of patients and the rodent hosts, the site where HFRS patients acquired HTNV infection was suggested by the phylogeographic analyses . ROKA13-8 and ROKA14-11 formed a cluster with HTNV strains from Cheorwon-B and TBTA-S, respectively. Patient ROKA13-8 was assigned to Hwacheon, but conducted military training in Cheorwon. ROKA13-8 was phylogenetically associated with HTNV strains in Cheorwon-B suggesting the Soldier was most likely infected with HTNV", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: during the training in Cheorwon. This result also suggested that patient ROKA14-11 conducted military activity and was the most likely infected with HTNV near TBTA-S in Paju. Phylogenetic analysis of US Army HFRS patient US8A14-2 showed a close relationship with HTNV strains from DN in Paju. This result and clinical records suggested the Soldier was the most likely infected with HTNV at DN between November 17 and 20, fell within the normal incubation period of HTNV. The US Army HFRS patient US8A15-1 conducted military training at MPRC, Pocheon. The phylogenetic association of US8A15-1 with HTNV strains in Pocheon identified the", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: For phylogeographic analyses, the whole genome sequence of 26 HTNV strains was acquired from rodents collected in endemic areas in the ROK . The HTNV strains in the phylogenetic tree consisted of 3 strains from Twin Bridge Training Area South , 3 strains from Twin Bridge Training Area North , 3 strains from Dagmar North in Paju, 2 strains from Fire Point 131 in Yeoncheon, 4 strains from Nightmare Range and Rodriguez Multi-Purpose Range Complex in Pocheon in Gyeonggi province, and 6 strains from Cheorwon-A and B , 2 strains from Hwacheon, and 3 strains from Yanggu in Gangwon province.", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: coverage of HTNV L segment from US8A14-2 was 96.1% whereas the HTNV M and S segments were completely sequenced. The genomic sequence of HTNV from US8A15-1 was acquired by 87.4%, 98.2%, and 100% for L, M, and S segments, respectively." ]

[ [ "0a", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing" ], [ "0b", "Passage: To establish the phylogeographic map, HTNV tripartite genome sequences from A. agrarius captured in the endemic and military training areas near the demilitarized zone were completely acquired using RT-PCR." ], [ "0c", "Compared with the genomic HTNV sequences of patients and the rodent hosts, the site where HFRS patients acquired HTNV infection was suggested by the phylogeographic analyses ." ], [ "0d", "ROKA13-8 and ROKA14-11 formed a cluster with HTNV strains from Cheorwon-B and TBTA-S, respectively." ], [ "0e", "Patient ROKA13-8 was assigned to Hwacheon, but conducted military training in Cheorwon." ], [ "0f", "ROKA13-8 was phylogenetically associated with HTNV strains in Cheorwon-B suggesting the Soldier was most likely infected with HTNV" ] ]

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

[ "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: To establish the phylogeographic map, HTNV tripartite genome sequences from A. agrarius captured in the endemic and military training areas near the demilitarized zone were completely acquired using RT-PCR. Compared with the genomic HTNV sequences of patients and the rodent hosts, the site where HFRS patients acquired HTNV infection was suggested by the phylogeographic analyses . ROKA13-8 and ROKA14-11 formed a cluster with HTNV strains from Cheorwon-B and TBTA-S, respectively. Patient ROKA13-8 was assigned to Hwacheon, but conducted military training in Cheorwon. ROKA13-8 was phylogenetically associated with HTNV strains in Cheorwon-B suggesting the Soldier was most likely infected with HTNV", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: during the training in Cheorwon. This result also suggested that patient ROKA14-11 conducted military activity and was the most likely infected with HTNV near TBTA-S in Paju. Phylogenetic analysis of US Army HFRS patient US8A14-2 showed a close relationship with HTNV strains from DN in Paju. This result and clinical records suggested the Soldier was the most likely infected with HTNV at DN between November 17 and 20, fell within the normal incubation period of HTNV. The US Army HFRS patient US8A15-1 conducted military training at MPRC, Pocheon. The phylogenetic association of US8A15-1 with HTNV strains in Pocheon identified the", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: For phylogeographic analyses, the whole genome sequence of 26 HTNV strains was acquired from rodents collected in endemic areas in the ROK . The HTNV strains in the phylogenetic tree consisted of 3 strains from Twin Bridge Training Area South , 3 strains from Twin Bridge Training Area North , 3 strains from Dagmar North in Paju, 2 strains from Fire Point 131 in Yeoncheon, 4 strains from Nightmare Range and Rodriguez Multi-Purpose Range Complex in Pocheon in Gyeonggi province, and 6 strains from Cheorwon-A and B , 2 strains from Hwacheon, and 3 strains from Yanggu in Gangwon province.", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: coverage of HTNV L segment from US8A14-2 was 96.1% whereas the HTNV M and S segments were completely sequenced. The genomic sequence of HTNV from US8A15-1 was acquired by 87.4%, 98.2%, and 100% for L, M, and S segments, respectively." ]

[ [ "1a", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing" ], [ "1b", "Passage: during the training in Cheorwon." ], [ "1c", "This result also suggested that patient ROKA14-11 conducted military activity and was the most likely infected with HTNV near TBTA-S in Paju." ], [ "1d", "Phylogenetic analysis of US Army HFRS patient US8A14-2 showed a close relationship with HTNV strains from DN in Paju." ], [ "1e", "This result and clinical records suggested the Soldier was the most likely infected with HTNV at DN between November 17 and 20, fell within the normal incubation period of HTNV." ], [ "1f", "The US Army HFRS patient US8A15-1 conducted military training at MPRC, Pocheon." ], [ "1g", "The phylogenetic association of US8A15-1 with HTNV strains in Pocheon identified the" ] ]

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

[ "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: To establish the phylogeographic map, HTNV tripartite genome sequences from A. agrarius captured in the endemic and military training areas near the demilitarized zone were completely acquired using RT-PCR. Compared with the genomic HTNV sequences of patients and the rodent hosts, the site where HFRS patients acquired HTNV infection was suggested by the phylogeographic analyses . ROKA13-8 and ROKA14-11 formed a cluster with HTNV strains from Cheorwon-B and TBTA-S, respectively. Patient ROKA13-8 was assigned to Hwacheon, but conducted military training in Cheorwon. ROKA13-8 was phylogenetically associated with HTNV strains in Cheorwon-B suggesting the Soldier was most likely infected with HTNV", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: during the training in Cheorwon. This result also suggested that patient ROKA14-11 conducted military activity and was the most likely infected with HTNV near TBTA-S in Paju. Phylogenetic analysis of US Army HFRS patient US8A14-2 showed a close relationship with HTNV strains from DN in Paju. This result and clinical records suggested the Soldier was the most likely infected with HTNV at DN between November 17 and 20, fell within the normal incubation period of HTNV. The US Army HFRS patient US8A15-1 conducted military training at MPRC, Pocheon. The phylogenetic association of US8A15-1 with HTNV strains in Pocheon identified the", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: For phylogeographic analyses, the whole genome sequence of 26 HTNV strains was acquired from rodents collected in endemic areas in the ROK . The HTNV strains in the phylogenetic tree consisted of 3 strains from Twin Bridge Training Area South , 3 strains from Twin Bridge Training Area North , 3 strains from Dagmar North in Paju, 2 strains from Fire Point 131 in Yeoncheon, 4 strains from Nightmare Range and Rodriguez Multi-Purpose Range Complex in Pocheon in Gyeonggi province, and 6 strains from Cheorwon-A and B , 2 strains from Hwacheon, and 3 strains from Yanggu in Gangwon province.", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing\nPassage: coverage of HTNV L segment from US8A14-2 was 96.1% whereas the HTNV M and S segments were completely sequenced. The genomic sequence of HTNV from US8A15-1 was acquired by 87.4%, 98.2%, and 100% for L, M, and S segments, respectively." ]

[ [ "2a", "Title: Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing" ], [ "2b", "Passage: For phylogeographic analyses, the whole genome sequence of 26 HTNV strains was acquired from rodents collected in endemic areas in the ROK ." ], [ "2c", "The HTNV strains in the phylogenetic tree consisted of 3 strains from Twin Bridge Training Area South , 3 strains from Twin Bridge Training Area North , 3 strains from Dagmar North in Paju, 2 strains from Fire Point 131 in Yeoncheon, 4 strains from Nightmare Range and Rodriguez Multi-Purpose Range Complex in Pocheon in Gyeonggi province, and 6 strains from Cheorwon-A and B , 2 strains from Hwacheon, and 3 strains from Yanggu in Gangwon province." ] ]

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

[ "Title: Primary biliary cirrhosis\nPassage: . Stage 1 disease is characterized by portal inflammation with granulomatous destruction of the bile ducts, although granulomas are often not seen. Stage 2 is characterized by periportal hepatitis and bile duct proliferation. Presence of fibrous septa or bridging necrosis is defined as stage 3 and cirrhosis as stage 4 . Findings of fibrotic or cirrhotic changes are accompanied by a worse prognosis . Florid duct lesions as defined by focal duct obliteration and granuloma formation are regarded as typical for PBC. The liver is not uniformly involved, and features of all four stages of PBC can be found in", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: episodes .", "Title: Th17 profile in COPD exacerbations\nPassage: The Global Initiative for Chronic Obstructive Lung Disease defines COPD as a common and treatable disease characterized by the persistent limitation of airflow, which is usually progressive and associated with an increase in the inflammatory response in the airways and in the lungs by harmful particles and gases. 10 Also, this guide defines exacerbations as an acute event characterized by worsening of patient's respiratory symptoms that go beyond daily variations and leads to a change in medication. 6, 10, 48 In addition, the guide also points out that a patient with frequent exacerbating COPD will be considered when he has", "Title: Markers of exacerbation severity in chronic obstructive pulmonary disease\nPassage: Chronic obstructive pulmonary disease is a respiratory disease characterized by an airflow limitation and inflammation of the lower airways . As the disease worsens, some patients experience 'exacerbations' of their principal symptoms of dyspnoea, cough and sputum. These exacerbations frequently result in a visit to a general practitioner's office or to a local hospital for treatment. Exacerbations occur in COPD patients at a median of three times a year with half of them being unreported . The heterogeneity of COPD exacerbations make them difficult to define, classify and manage due to their range of symptoms, varied treatment requirements, seasonal occurrence," ]

[ [ "0a", "Title: Primary biliary cirrhosis Passage: ." ], [ "0b", "Stage 1 disease is characterized by portal inflammation with granulomatous destruction of the bile ducts, although granulomas are often not seen." ], [ "0c", "Stage 2 is characterized by periportal hepatitis and bile duct proliferation." ], [ "0d", "Presence of fibrous septa or bridging necrosis is defined as stage 3 and cirrhosis as stage 4 ." ], [ "0e", "Findings of fibrotic or cirrhotic changes are accompanied by a worse prognosis ." ], [ "0f", "Florid duct lesions as defined by focal duct obliteration and granuloma formation are regarded as typical for PBC." ], [ "0g", "The liver is not uniformly involved, and features of all four stages of PBC can be found in" ] ]

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

[ "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: Cancer Biomarker Discovery: The Entropic Hallmark\nPassage: however, that the 29 samples seem to be separating in three different clusters. Whether we can argue about the existence or not of these gaps in Normalized Shannon Entropy, it is clear that there seems to be a progression as we have seen with Lapointe et al's dataset. There is a group of three samples with Gleason pattern 3 that seem to have the the largest Normalized Shannon Entropy values. There is also a cluster that only contains samples of either Gleason pattern 4 and 5, all with Normalized Shannon Entropy values smaller than 0.985.", "Title: Cancer Biomarker Discovery: The Entropic Hallmark\nPassage: This raised a suspicion about the true nature of this phenomenon. If the labelling is correct, this may indicate a subsampled group of prostate cancer that has Gleason 3 pattern characteristics but very low entropy. Alternatively, it may indicate an experimental bias for reasons we can not explain with the available clinical information. In order to clarify the situation, and see if we can declare these two samples as outliers of the other group, we performed another experiment. We have now computed two modified complexities, which we will call M- Gleason 3 and M-Gleason 5 . The names are probably" ]

[ [ "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" ] ]

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

[ "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: Cancer Biomarker Discovery: The Entropic Hallmark\nPassage: however, that the 29 samples seem to be separating in three different clusters. Whether we can argue about the existence or not of these gaps in Normalized Shannon Entropy, it is clear that there seems to be a progression as we have seen with Lapointe et al's dataset. There is a group of three samples with Gleason pattern 3 that seem to have the the largest Normalized Shannon Entropy values. There is also a cluster that only contains samples of either Gleason pattern 4 and 5, all with Normalized Shannon Entropy values smaller than 0.985.", "Title: Cancer Biomarker Discovery: The Entropic Hallmark\nPassage: This raised a suspicion about the true nature of this phenomenon. If the labelling is correct, this may indicate a subsampled group of prostate cancer that has Gleason 3 pattern characteristics but very low entropy. Alternatively, it may indicate an experimental bias for reasons we can not explain with the available clinical information. In order to clarify the situation, and see if we can declare these two samples as outliers of the other group, we performed another experiment. We have now computed two modified complexities, which we will call M- Gleason 3 and M-Gleason 5 . The names are probably" ]

[ [ "1a", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond" ], [ "1b", "Passage: 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 ." ] ]

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

[ "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: Overall, few cases of H7 virus transmission to mammals have ever been reported in Asia and N9 virus infections in human have never been documented anywhere in the world except H7N9 . The H7N9 variants currently in circulation most likely evolved through a combination of genes from viruses in Beijing bramblings, Zhejiang ducks, and Korean wild birds according to report by Chinese scientists. Human infections with highly pathogenic H7 viruses generally resulted in conjunctivitis or uncomplicated influenza", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China\nPassage: From our study we found that most H7N9 cases had LPMs exposure history, and in Zhejiang Province and Guangdong Province, routine environmental surveillance showed that LPMs were the most contaminated place by H7N9 virus, and the detection of H7N9 virus spiked in cold months , which was in accordance with the epidemic trends of the H7N9 in mainland China. And several other subtypes of human infections of avian influenza have also been detected in China, including H5N1, H5N6, H10N8, and H9N2 et al. Most of the infections also resulted from the live poultry exposure or poultry related environment exposure, especially", "Title: Epidemiological, clinical, and virologic features of two family clusters of avian influenza A (H7N9) virus infections in Southeast China\nPassage: In early 2013, an outbreak of H7N9 virus infections occurred in Eastern China, which generated global concern 1 . To date, the virus has caused four outbreaks in humans, and most cases occurred during winter and spring 25 . The H7N9 virus is a low pathogenic avian influenza A virus, and it does not cause identifiable illness or death in poultry, whereas humans act as sentinels for the presence of these viruses in avian infections 17 . Currently, humans get infected with the H7N9 virus predominantly through contact with asymptomatic poultry, and sporadically via direct contact or exposure to environments", "Title: A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China\nPassage: Following written informed consent, a structured questionnaire was used to gather demographic information and data on use of personal protective equipment, antiviral chemoprophylaxis, symptoms, and potential risk factors for H7N9 infection during the two weeks starting from their last exposure to H7N9-infected cases." ]

[ [ "1a", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China" ], [ "1b", "Passage: From our study we found that most H7N9 cases had LPMs exposure history, and in Zhejiang Province and Guangdong Province, routine environmental surveillance showed that LPMs were the most contaminated place by H7N9 virus, and the detection of H7N9 virus spiked in cold months , which was in accordance with the epidemic trends of the H7N9 in mainland China." ], [ "1c", "And several other subtypes of human infections of avian influenza have also been detected in China, including H5N1, H5N6, H10N8, and H9N2 et al. Most of the infections also resulted from the live poultry exposure or poultry related environment exposure, especially" ] ]

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

[ "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: Overall, few cases of H7 virus transmission to mammals have ever been reported in Asia and N9 virus infections in human have never been documented anywhere in the world except H7N9 . The H7N9 variants currently in circulation most likely evolved through a combination of genes from viruses in Beijing bramblings, Zhejiang ducks, and Korean wild birds according to report by Chinese scientists. Human infections with highly pathogenic H7 viruses generally resulted in conjunctivitis or uncomplicated influenza", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China\nPassage: From our study we found that most H7N9 cases had LPMs exposure history, and in Zhejiang Province and Guangdong Province, routine environmental surveillance showed that LPMs were the most contaminated place by H7N9 virus, and the detection of H7N9 virus spiked in cold months , which was in accordance with the epidemic trends of the H7N9 in mainland China. And several other subtypes of human infections of avian influenza have also been detected in China, including H5N1, H5N6, H10N8, and H9N2 et al. Most of the infections also resulted from the live poultry exposure or poultry related environment exposure, especially", "Title: Epidemiological, clinical, and virologic features of two family clusters of avian influenza A (H7N9) virus infections in Southeast China\nPassage: In early 2013, an outbreak of H7N9 virus infections occurred in Eastern China, which generated global concern 1 . To date, the virus has caused four outbreaks in humans, and most cases occurred during winter and spring 25 . The H7N9 virus is a low pathogenic avian influenza A virus, and it does not cause identifiable illness or death in poultry, whereas humans act as sentinels for the presence of these viruses in avian infections 17 . Currently, humans get infected with the H7N9 virus predominantly through contact with asymptomatic poultry, and sporadically via direct contact or exposure to environments", "Title: A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China\nPassage: Following written informed consent, a structured questionnaire was used to gather demographic information and data on use of personal protective equipment, antiviral chemoprophylaxis, symptoms, and potential risk factors for H7N9 infection during the two weeks starting from their last exposure to H7N9-infected cases." ]

[ [ "2a", "Title: Epidemiological, clinical, and virologic features of two family clusters of avian influenza A (H7N9) virus infections in Southeast China" ], [ "2b", "Passage: In early 2013, an outbreak of H7N9 virus infections occurred in Eastern China, which generated global concern 1 ." ], [ "2c", "To date, the virus has caused four outbreaks in humans, and most cases occurred during winter and spring 25 ." ], [ "2d", "The H7N9 virus is a low pathogenic avian influenza A virus, and it does not cause identifiable illness or death in poultry, whereas humans act as sentinels for the presence of these viruses in avian infections 17 ." ], [ "2e", "Currently, humans get infected with the H7N9 virus predominantly through contact with asymptomatic poultry, and sporadically via direct contact or exposure to environments" ] ]

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

[ "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: Overall, few cases of H7 virus transmission to mammals have ever been reported in Asia and N9 virus infections in human have never been documented anywhere in the world except H7N9 . The H7N9 variants currently in circulation most likely evolved through a combination of genes from viruses in Beijing bramblings, Zhejiang ducks, and Korean wild birds according to report by Chinese scientists. Human infections with highly pathogenic H7 viruses generally resulted in conjunctivitis or uncomplicated influenza", "Title: Comparison of the first three waves of avian influenza A(H7N9) virus circulation in the mainland of the People’s Republic of China\nPassage: From our study we found that most H7N9 cases had LPMs exposure history, and in Zhejiang Province and Guangdong Province, routine environmental surveillance showed that LPMs were the most contaminated place by H7N9 virus, and the detection of H7N9 virus spiked in cold months , which was in accordance with the epidemic trends of the H7N9 in mainland China. And several other subtypes of human infections of avian influenza have also been detected in China, including H5N1, H5N6, H10N8, and H9N2 et al. Most of the infections also resulted from the live poultry exposure or poultry related environment exposure, especially", "Title: Epidemiological, clinical, and virologic features of two family clusters of avian influenza A (H7N9) virus infections in Southeast China\nPassage: In early 2013, an outbreak of H7N9 virus infections occurred in Eastern China, which generated global concern 1 . To date, the virus has caused four outbreaks in humans, and most cases occurred during winter and spring 25 . The H7N9 virus is a low pathogenic avian influenza A virus, and it does not cause identifiable illness or death in poultry, whereas humans act as sentinels for the presence of these viruses in avian infections 17 . Currently, humans get infected with the H7N9 virus predominantly through contact with asymptomatic poultry, and sporadically via direct contact or exposure to environments", "Title: A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China\nPassage: Following written informed consent, a structured questionnaire was used to gather demographic information and data on use of personal protective equipment, antiviral chemoprophylaxis, symptoms, and potential risk factors for H7N9 infection during the two weeks starting from their last exposure to H7N9-infected cases." ]

[ [ "3a", "Title: A family cluster of three confirmed cases infected with avian influenza A (H7N9) virus in Zhejiang Province of China" ], [ "3b", "Passage: Following written informed consent, a structured questionnaire was used to gather demographic information and data on use of personal protective equipment, antiviral chemoprophylaxis, symptoms, and potential risk factors for H7N9 infection during the two weeks starting from their last exposure to H7N9-infected cases." ] ]

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

[ "Title: Automatic Detection and Quantification of Tree-in-Bud (TIB) Opacities from CT Scans\nPassage: The SI is a statistical measurement and used to define intrinsic shape of the localized structure within the image , . SI values are encoded as a continuous range of values between −1 and 1, with zero SI indicates saddle-like local structures, +1 and −1 SI values indicate umbilical minima and maxima , and midpoints of the two half-intervals indicate concave and convex parabolic or line-like structures . SI can simply be computed through principal curvatures as follows:", "Title: The social benefits of private infectious disease-risk mitigation\nPassage: As is standard with such a model, we let c be the nominal contact volume of all individuals. P SI is the conditional probability that a contact made by a susceptible individual, S, is with an infectious individual, I, and γ is the rate at which an individual recovers and becomes immune, R.", "Title: Validation of the Munich ChronoType Questionnaire in Korean Older Adults(*)\nPassage: The ISI is a 7-item index developed by Bastien et al. 38 and assesses the severity of insomnia, satisfaction with current sleep, and worries about sleep problems during the last two weeks. The ISI total score ranges from 0 to 28, with higher scores reflecting higher severity of insomnia symptoms. A Korean version of the ISI has been validated in Korean samples. 39 The internal consistency was 0.83 in this sample.", "Title: Social clustering in epidemic spread on coevolving networks\nPassage: Moreover, inspired by Ref. , in Fig. 21 we include the evolution of the fraction of SI links S I , the effective branching factor κ S IS ≡ S SI /S I , and the average number of connections that susceptible nodes share with other susceptibles C SS ≡ S S / as well as the AME approximation for these quantities. In an SIS model, S I measures the level of links that could potentially pass the disease, κ S IS measures the average number of susceptible neighbors that the infected end of a SI link has, and C" ]

[ [ "0a", "Title: Automatic Detection and Quantification of Tree-in-Bud (TIB) Opacities from CT Scans" ], [ "0b", "Passage: The SI is a statistical measurement and used to define intrinsic shape of the localized structure within the image , ." ], [ "0c", "SI values are encoded as a continuous range of values between −1 and 1, with zero SI indicates saddle-like local structures, +1 and −1 SI values indicate umbilical minima and maxima , and midpoints of the two half-intervals indicate concave and convex parabolic or line-like structures ." ], [ "0d", "SI can simply be computed through principal curvatures as follows:" ] ]

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

[ "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection\nPassage: Indeed, studies based on historical registries indicated that genetic factors affect the risk of death due to influenza virus infection . Likewise, the familial aggregation of influenza A/H5N1 cases, the paucity of cases among highly exposed groups, and the occurrence of related cases separated in time and space led Horby and coworkers to indicate that host genetic factors play an important role in the susceptibility to this infection .", "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection\nPassage: Clearly, the identification of host genetic factors that modulate the susceptibility to and the severity of influenza virus infection is of paramount importance to develop preventive strategies and therapeutic interventions.", "Title: Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness\nPassage: virus to accommodate or even select for the H275Y mutation.", "Title: Multiple gene mutations identified in patients infected with influenza A (H7N9) virus\nPassage: susceptibility to viral infection, and that in the future, these mutations could provide information regarding risk of infection, especially poultry workers or family members of infected patients. Using a variety of computational genetic techniques, we identified 21 genes that showed a high rate of mutation in patients infected with H7N9 when compared to the general population. Among these genes, some have been identified in prior studies of H7N9 susceptibility genes 14 . For example, Wang et al. reported that IFITM3 dysfunction is associated with increased cytokine production during H7N9 infection and is correlated with mortality 14 . IFITM3 was reported" ]

[ [ "0a", "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection" ], [ "0b", "Passage: Indeed, studies based on historical registries indicated that genetic factors affect the risk of death due to influenza virus infection ." ], [ "0c", "Likewise, the familial aggregation of influenza A/H5N1 cases, the paucity of cases among highly exposed groups, and the occurrence of related cases separated in time and space led Horby and coworkers to indicate that host genetic factors play an important role in the susceptibility to this infection ." ] ]

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

[ "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection\nPassage: Indeed, studies based on historical registries indicated that genetic factors affect the risk of death due to influenza virus infection . Likewise, the familial aggregation of influenza A/H5N1 cases, the paucity of cases among highly exposed groups, and the occurrence of related cases separated in time and space led Horby and coworkers to indicate that host genetic factors play an important role in the susceptibility to this infection .", "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection\nPassage: Clearly, the identification of host genetic factors that modulate the susceptibility to and the severity of influenza virus infection is of paramount importance to develop preventive strategies and therapeutic interventions.", "Title: Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness\nPassage: virus to accommodate or even select for the H275Y mutation.", "Title: Multiple gene mutations identified in patients infected with influenza A (H7N9) virus\nPassage: susceptibility to viral infection, and that in the future, these mutations could provide information regarding risk of infection, especially poultry workers or family members of infected patients. Using a variety of computational genetic techniques, we identified 21 genes that showed a high rate of mutation in patients infected with H7N9 when compared to the general population. Among these genes, some have been identified in prior studies of H7N9 susceptibility genes 14 . For example, Wang et al. reported that IFITM3 dysfunction is associated with increased cytokine production during H7N9 infection and is correlated with mortality 14 . IFITM3 was reported" ]

[ [ "1a", "Title: The CCR5Δ32 allele is not a major predisposing factor for severe H1N1pdm09 infection" ], [ "1b", "Passage: Clearly, the identification of host genetic factors that modulate the susceptibility to and the severity of influenza virus infection is of paramount importance to develop preventive strategies and therapeutic interventions." ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: stem loop. Bat SARS-related CoV ZC45 did not have the SARS-COV SL6-like stem loop. Instead, it possessed two other stem loops in this region. All three strains had similar SL7 and SL8. The bat SARS-like CoV ZC45 also had an additional stem loop between SL7 and SL8. Overall, the 5 ′ -UTR of 2019-nCoV was more similar to that of SARS-CoV than the bat SARS-related CoV ZC 45. The biological relevance and effects of virulence of the 5 ′ -UTR structures should be investigated further. The 2019-nCoV had various 3 ′ -UTR structures, including BSL, S1, S2, S3, S4, L1,", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins\nPassage: Genomes were assembled using Sequencher 4.1.4 . Putative ORFs >100 amino acids were identified and annotated using SeqBuilder version 11.2.1 . Partial genes or genes that seemed interrupted were analyzed for potential introns using GENSCAN . The potential origin of replication for each genome was identified by locating a canonical nonanucleotide motif and confirming predicted stem-loop structures using Mfold with constraints applied to prevent hairpin formation within the nonanucleotide motif and a folding temperature set at 17 • C . Final annotated genomes have been deposited to GenBank with accession numbers KR528543-KR528569." ]

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

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: stem loop. Bat SARS-related CoV ZC45 did not have the SARS-COV SL6-like stem loop. Instead, it possessed two other stem loops in this region. All three strains had similar SL7 and SL8. The bat SARS-like CoV ZC45 also had an additional stem loop between SL7 and SL8. Overall, the 5 ′ -UTR of 2019-nCoV was more similar to that of SARS-CoV than the bat SARS-related CoV ZC 45. The biological relevance and effects of virulence of the 5 ′ -UTR structures should be investigated further. The 2019-nCoV had various 3 ′ -UTR structures, including BSL, S1, S2, S3, S4, L1,", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins\nPassage: Genomes were assembled using Sequencher 4.1.4 . Putative ORFs >100 amino acids were identified and annotated using SeqBuilder version 11.2.1 . Partial genes or genes that seemed interrupted were analyzed for potential introns using GENSCAN . The potential origin of replication for each genome was identified by locating a canonical nonanucleotide motif and confirming predicted stem-loop structures using Mfold with constraints applied to prevent hairpin formation within the nonanucleotide motif and a folding temperature set at 17 • C . Final annotated genomes have been deposited to GenBank with accession numbers KR528543-KR528569." ]

[ [ "1a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "1b", "Passage: stem loop." ], [ "1c", "Bat SARS-related CoV ZC45 did not have the SARS-COV SL6-like stem loop." ], [ "1d", "Instead, it possessed two other stem loops in this region." ], [ "1e", "All three strains had similar SL7 and SL8." ], [ "1f", "The bat SARS-like CoV ZC45 also had an additional stem loop between SL7 and SL8." ], [ "1g", "Overall, the 5 ′ -UTR of 2019-nCoV was more similar to that of SARS-CoV than the bat SARS-related CoV ZC 45." ], [ "1h", "The biological relevance and effects of virulence of the 5 ′ -UTR structures should be investigated further." ], [ "1i", "The 2019-nCoV had various 3 ′ -UTR structures, including BSL, S1, S2, S3, S4, L1," ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots.", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: stem loop. Bat SARS-related CoV ZC45 did not have the SARS-COV SL6-like stem loop. Instead, it possessed two other stem loops in this region. All three strains had similar SL7 and SL8. The bat SARS-like CoV ZC45 also had an additional stem loop between SL7 and SL8. Overall, the 5 ′ -UTR of 2019-nCoV was more similar to that of SARS-CoV than the bat SARS-related CoV ZC 45. The biological relevance and effects of virulence of the 5 ′ -UTR structures should be investigated further. The 2019-nCoV had various 3 ′ -UTR structures, including BSL, S1, S2, S3, S4, L1,", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins\nPassage: Genomes were assembled using Sequencher 4.1.4 . Putative ORFs >100 amino acids were identified and annotated using SeqBuilder version 11.2.1 . Partial genes or genes that seemed interrupted were analyzed for potential introns using GENSCAN . The potential origin of replication for each genome was identified by locating a canonical nonanucleotide motif and confirming predicted stem-loop structures using Mfold with constraints applied to prevent hairpin formation within the nonanucleotide motif and a folding temperature set at 17 • C . Final annotated genomes have been deposited to GenBank with accession numbers KR528543-KR528569." ]

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

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

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Hantavirus diseases of man have long been suspected of having an immunopathogenic basis in part because of their relatively long incubation period of 2-3 weeks and the observed temporal association between immunologic derangements and the first appearance of signs and symptoms of hantavirus illness. HFRS and HCPS share many clinical features, leading many investigators to consider them to be, in essence, different manifestations of a similar pathogenic process, differing mainly in the primary target organs of disease expression . The pathogenesis of hantavirus infections is the topic of a continuously-updated review in the series UpToDate .", "Title: Interval Between Infections and Viral Hierarchy Are Determinants of Viral Interference Following Influenza Virus Infection in a Ferret Model\nPassage: Because prevention of challenge virus infection occurred only for intervals of ≤7 days and primary virus was detected for 5-7 days , a temporary state of immunity that affects challenge outcome may require the presence of primary virus. Animals shedding secondary virus after challenge were grouped according to whether the primary infection virus could be detected in URT samples after challenge, as a proxy for the presence of virus on the day of challenge. The kinetics of challenge virus shedding were compared between the groups .", "Title: Interval Between Infections and Viral Hierarchy Are Determinants of Viral Interference Following Influenza Virus Infection in a Ferret Model\nPassage: To investigate viral interference following infection with influenza virus, we systematically assessed the influence of a primary virus infection on the kinetics of a secondary virus challenge in the ferret model . Two intervals represented the start and peak of virus shedding, respectively, in the upper respiratory tract ; one interval corresponded to decreased virus shedding; and one interval reflected the end of virus shedding. Seroconversion typically occurs 7-12 days following infection ; thus, the 7-day interval and 2 later intervals represented the adaptive immune response .", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: adults in multicenter phase III clinical trials, three dose schedules at 0, 1, and 13 months were used. The seroconversion rate was 90.14% by IFA but only 23.24% by PRNT50 after two primary doses. One month after vaccination, the positive rate of serum was 87.32 and 45.07% according to IFA and PRNT50, respectively. The neutralizing antibody response of the two initial doses of Hantavax TM was very poor. Therefore, it is necessary to carry out enhanced immunization within 2-6 months to provide timely protection for high-risk groups ." ]

[ [ "0a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "0b", "Passage: Hantavirus diseases of man have long been suspected of having an immunopathogenic basis in part because of their relatively long incubation period of 2-3 weeks and the observed temporal association between immunologic derangements and the first appearance of signs and symptoms of hantavirus illness." ], [ "0c", "HFRS and HCPS share many clinical features, leading many investigators to consider them to be, in essence, different manifestations of a similar pathogenic process, differing mainly in the primary target organs of disease expression ." ], [ "0d", "The pathogenesis of hantavirus infections is the topic of a continuously-updated review in the series UpToDate ." ] ]

[ "0b", "0c" ]

[ "Title: Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors\nPassage: To mimic infectious stressors, we chose Lipopolysaccharide , present in the external wall of Gram-negative bacteria and largely responsible for their toxicity. LPS is recognized by TLR4-coreceptors MD2 and CD14, which recognize the lipid A core of LPS. TLR4 transduces the signal via MyD88 and TRIF adapters to activate NF-jB-and/or IRF3mediated transcription of genes encoding pivotal molecules of the immune system, including cytokines and chemokines, which mimics major inflammatory response models . Moreover, LPS is of concern since it is a common contaminant of cell cultures. It is an amphipathic molecule which adheres to hydrophobic materials like plastics and glassware.", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is composed of three distinct domains, lipid A, a short core of oligosaccharide and the O-antigen polysaccharide . The lipid A domain is the bioactive component and is recognized during human infection. The composition of the O-antigen varies between different Gram-negative bacterial strains. The presence or absence of O chains determines whether LPS is considered rough or smooth . Full length O chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough .", "Title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide\nPassage: Acute and chronic infection, especially that induced by Gramnegative bacteria is associated with increased risk of thrombosis and atherosclerotic disease . Little is known about the underlying cellular mechanisms responsible for these risks. Lipopolysaccharide , a component of the cell wall of Gram-negative bacteria, is an antigen which initiates inflammation and innate immune responses by interacting with Toll-like receptor 4 . TLR4 is expressed on the surface of cells, including leukocytes and platelets . Under physiological conditions, platelets and leukocytes circulate in quiescent state and do not interact with each other. However, once activated under pathophysiological conditions such as those", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is a potential drug target since its presence is critical in membrane stability and also it plays a prominent role in raising an immune response . LPS triggers the release of many inflammatory cytokines, in particular TNFα, interleukin-1β and IL-6, and it has been implicated as the etiological agent of a variety of pathologies ranging from mild to lethal . Thus the structure, function and biosynthesis of LPS have been areas of intense research in the last decade ." ]

[ [ "0a", "Title: Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors" ], [ "0b", "Passage: To mimic infectious stressors, we chose Lipopolysaccharide , present in the external wall of Gram-negative bacteria and largely responsible for their toxicity." ], [ "0c", "LPS is recognized by TLR4-coreceptors MD2 and CD14, which recognize the lipid A core of LPS." ], [ "0d", "TLR4 transduces the signal via MyD88 and TRIF adapters to activate NF-jB-and/or IRF3mediated transcription of genes encoding pivotal molecules of the immune system, including cytokines and chemokines, which mimics major inflammatory response models ." ], [ "0e", "Moreover, LPS is of concern since it is a common contaminant of cell cultures." ], [ "0f", "It is an amphipathic molecule which adheres to hydrophobic materials like plastics and glassware." ] ]

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

[ "Title: Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors\nPassage: To mimic infectious stressors, we chose Lipopolysaccharide , present in the external wall of Gram-negative bacteria and largely responsible for their toxicity. LPS is recognized by TLR4-coreceptors MD2 and CD14, which recognize the lipid A core of LPS. TLR4 transduces the signal via MyD88 and TRIF adapters to activate NF-jB-and/or IRF3mediated transcription of genes encoding pivotal molecules of the immune system, including cytokines and chemokines, which mimics major inflammatory response models . Moreover, LPS is of concern since it is a common contaminant of cell cultures. It is an amphipathic molecule which adheres to hydrophobic materials like plastics and glassware.", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is composed of three distinct domains, lipid A, a short core of oligosaccharide and the O-antigen polysaccharide . The lipid A domain is the bioactive component and is recognized during human infection. The composition of the O-antigen varies between different Gram-negative bacterial strains. The presence or absence of O chains determines whether LPS is considered rough or smooth . Full length O chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough .", "Title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide\nPassage: Acute and chronic infection, especially that induced by Gramnegative bacteria is associated with increased risk of thrombosis and atherosclerotic disease . Little is known about the underlying cellular mechanisms responsible for these risks. Lipopolysaccharide , a component of the cell wall of Gram-negative bacteria, is an antigen which initiates inflammation and innate immune responses by interacting with Toll-like receptor 4 . TLR4 is expressed on the surface of cells, including leukocytes and platelets . Under physiological conditions, platelets and leukocytes circulate in quiescent state and do not interact with each other. However, once activated under pathophysiological conditions such as those", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is a potential drug target since its presence is critical in membrane stability and also it plays a prominent role in raising an immune response . LPS triggers the release of many inflammatory cytokines, in particular TNFα, interleukin-1β and IL-6, and it has been implicated as the etiological agent of a variety of pathologies ranging from mild to lethal . Thus the structure, function and biosynthesis of LPS have been areas of intense research in the last decade ." ]

[ [ "1a", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases" ], [ "1b", "Passage: Lipopolysaccharide is composed of three distinct domains, lipid A, a short core of oligosaccharide and the O-antigen polysaccharide ." ], [ "1c", "The lipid A domain is the bioactive component and is recognized during human infection." ], [ "1d", "The composition of the O-antigen varies between different Gram-negative bacterial strains." ], [ "1e", "The presence or absence of O chains determines whether LPS is considered rough or smooth ." ], [ "1f", "Full length O chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough ." ] ]

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

[ "Title: Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors\nPassage: To mimic infectious stressors, we chose Lipopolysaccharide , present in the external wall of Gram-negative bacteria and largely responsible for their toxicity. LPS is recognized by TLR4-coreceptors MD2 and CD14, which recognize the lipid A core of LPS. TLR4 transduces the signal via MyD88 and TRIF adapters to activate NF-jB-and/or IRF3mediated transcription of genes encoding pivotal molecules of the immune system, including cytokines and chemokines, which mimics major inflammatory response models . Moreover, LPS is of concern since it is a common contaminant of cell cultures. It is an amphipathic molecule which adheres to hydrophobic materials like plastics and glassware.", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is composed of three distinct domains, lipid A, a short core of oligosaccharide and the O-antigen polysaccharide . The lipid A domain is the bioactive component and is recognized during human infection. The composition of the O-antigen varies between different Gram-negative bacterial strains. The presence or absence of O chains determines whether LPS is considered rough or smooth . Full length O chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough .", "Title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide\nPassage: Acute and chronic infection, especially that induced by Gramnegative bacteria is associated with increased risk of thrombosis and atherosclerotic disease . Little is known about the underlying cellular mechanisms responsible for these risks. Lipopolysaccharide , a component of the cell wall of Gram-negative bacteria, is an antigen which initiates inflammation and innate immune responses by interacting with Toll-like receptor 4 . TLR4 is expressed on the surface of cells, including leukocytes and platelets . Under physiological conditions, platelets and leukocytes circulate in quiescent state and do not interact with each other. However, once activated under pathophysiological conditions such as those", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is a potential drug target since its presence is critical in membrane stability and also it plays a prominent role in raising an immune response . LPS triggers the release of many inflammatory cytokines, in particular TNFα, interleukin-1β and IL-6, and it has been implicated as the etiological agent of a variety of pathologies ranging from mild to lethal . Thus the structure, function and biosynthesis of LPS have been areas of intense research in the last decade ." ]

[ [ "2a", "Title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide" ], [ "2b", "Passage: Acute and chronic infection, especially that induced by Gramnegative bacteria is associated with increased risk of thrombosis and atherosclerotic disease ." ], [ "2c", "Little is known about the underlying cellular mechanisms responsible for these risks." ], [ "2d", "Lipopolysaccharide , a component of the cell wall of Gram-negative bacteria, is an antigen which initiates inflammation and innate immune responses by interacting with Toll-like receptor 4 ." ], [ "2e", "TLR4 is expressed on the surface of cells, including leukocytes and platelets ." ], [ "2f", "Under physiological conditions, platelets and leukocytes circulate in quiescent state and do not interact with each other." ], [ "2g", "However, once activated under pathophysiological conditions such as those" ] ]

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

[ "Title: Characterization of MDCK cells and evaluation of their ability to respond to infectious and non-infectious stressors\nPassage: To mimic infectious stressors, we chose Lipopolysaccharide , present in the external wall of Gram-negative bacteria and largely responsible for their toxicity. LPS is recognized by TLR4-coreceptors MD2 and CD14, which recognize the lipid A core of LPS. TLR4 transduces the signal via MyD88 and TRIF adapters to activate NF-jB-and/or IRF3mediated transcription of genes encoding pivotal molecules of the immune system, including cytokines and chemokines, which mimics major inflammatory response models . Moreover, LPS is of concern since it is a common contaminant of cell cultures. It is an amphipathic molecule which adheres to hydrophobic materials like plastics and glassware.", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is composed of three distinct domains, lipid A, a short core of oligosaccharide and the O-antigen polysaccharide . The lipid A domain is the bioactive component and is recognized during human infection. The composition of the O-antigen varies between different Gram-negative bacterial strains. The presence or absence of O chains determines whether LPS is considered rough or smooth . Full length O chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough .", "Title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide\nPassage: Acute and chronic infection, especially that induced by Gramnegative bacteria is associated with increased risk of thrombosis and atherosclerotic disease . Little is known about the underlying cellular mechanisms responsible for these risks. Lipopolysaccharide , a component of the cell wall of Gram-negative bacteria, is an antigen which initiates inflammation and innate immune responses by interacting with Toll-like receptor 4 . TLR4 is expressed on the surface of cells, including leukocytes and platelets . Under physiological conditions, platelets and leukocytes circulate in quiescent state and do not interact with each other. However, once activated under pathophysiological conditions such as those", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases\nPassage: Lipopolysaccharide is a potential drug target since its presence is critical in membrane stability and also it plays a prominent role in raising an immune response . LPS triggers the release of many inflammatory cytokines, in particular TNFα, interleukin-1β and IL-6, and it has been implicated as the etiological agent of a variety of pathologies ranging from mild to lethal . Thus the structure, function and biosynthesis of LPS have been areas of intense research in the last decade ." ]

[ [ "3a", "Title: Discovery and Development of Toll-Like Receptor 4 (TLR4) Antagonists: A New Paradigm for Treating Sepsis and Other Diseases" ], [ "3b", "Passage: Lipopolysaccharide is a potential drug target since its presence is critical in membrane stability and also it plays a prominent role in raising an immune response ." ], [ "3c", "LPS triggers the release of many inflammatory cytokines, in particular TNFα, interleukin-1β and IL-6, and it has been implicated as the etiological agent of a variety of pathologies ranging from mild to lethal ." ], [ "3d", "Thus the structure, function and biosynthesis of LPS have been areas of intense research in the last decade ." ] ]

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

[ "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: are responsible for the cytopathic response mediated by this receptor variant.", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection\nPassage: CIITA . In addition, DNA-dependent activator of interferon regulatory factors has been identified as a DNA sensor . Various microbial components are recognized as their vague and common molecular shapes by PRRs. Early responses against virus infection are initiated on recognition of pathogen-associated molecular patterns by pattern recognition molecules, triggering two responses. One is the production of interferons resulting in an antiviral state as part of the innate immune response, and the second is maturation of dendritic cells to establish acquired immunity. In order to establish an infection within a host, viruses must escape from and/or suppress the immune system", "Title: Host Modulators of H1N1 Cytopathogenicity\nPassage: the participation of endosomes as a viral entry mechanism , it is tempting to speculate that RRAGD is a limiting host factor for viral corruption of mTOR regulation. Additional factors in this group are involved with the host defense response, p53-mediated cell death and vesicle maturation and trafficking. To test for false positives arising from off-target effects of siRNA treatment, we retested 88 siRNA pools as four individual oligos. Approximately 60% of siRNAs retested with two or more oligos reproducing the original phenotype .", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: The fact that these two viruses are only cytopathic in M. dunni cells suggests involvement of the receptor-virus interaction for two reasons. First, the amino acid residue that is modified in both viruses has been identified as one of the critical amino acids forming the receptor binding site . Second, M. dunni cells differ from other mouse cells in their resistance to MoMLV , and these cells are known to carry a modified CAT-1 receptor . The dCAT-1 gene of M. dunni cells differs from the prototypical CAT-1 gene of the laboratory mouse in that the third extracellular loop that" ]

[ [ "0a", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses" ], [ "0b", "Passage: are responsible for the cytopathic response mediated by this receptor variant." ] ]

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

[ "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: are responsible for the cytopathic response mediated by this receptor variant.", "Title: The Battle between Virus and Host: Modulation of Toll-Like Receptor Signaling Pathways by Virus Infection\nPassage: CIITA . In addition, DNA-dependent activator of interferon regulatory factors has been identified as a DNA sensor . Various microbial components are recognized as their vague and common molecular shapes by PRRs. Early responses against virus infection are initiated on recognition of pathogen-associated molecular patterns by pattern recognition molecules, triggering two responses. One is the production of interferons resulting in an antiviral state as part of the innate immune response, and the second is maturation of dendritic cells to establish acquired immunity. In order to establish an infection within a host, viruses must escape from and/or suppress the immune system", "Title: Host Modulators of H1N1 Cytopathogenicity\nPassage: the participation of endosomes as a viral entry mechanism , it is tempting to speculate that RRAGD is a limiting host factor for viral corruption of mTOR regulation. Additional factors in this group are involved with the host defense response, p53-mediated cell death and vesicle maturation and trafficking. To test for false positives arising from off-target effects of siRNA treatment, we retested 88 siRNA pools as four individual oligos. Approximately 60% of siRNAs retested with two or more oligos reproducing the original phenotype .", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: The fact that these two viruses are only cytopathic in M. dunni cells suggests involvement of the receptor-virus interaction for two reasons. First, the amino acid residue that is modified in both viruses has been identified as one of the critical amino acids forming the receptor binding site . Second, M. dunni cells differ from other mouse cells in their resistance to MoMLV , and these cells are known to carry a modified CAT-1 receptor . The dCAT-1 gene of M. dunni cells differs from the prototypical CAT-1 gene of the laboratory mouse in that the third extracellular loop that" ]

[ [ "3a", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses" ], [ "3b", "Passage: The fact that these two viruses are only cytopathic in M. dunni cells suggests involvement of the receptor-virus interaction for two reasons." ], [ "3c", "First, the amino acid residue that is modified in both viruses has been identified as one of the critical amino acids forming the receptor binding site ." ], [ "3d", "Second, M. dunni cells differ from other mouse cells in their resistance to MoMLV , and these cells are known to carry a modified CAT-1 receptor ." ], [ "3e", "The dCAT-1 gene of M. dunni cells differs from the prototypical CAT-1 gene of the laboratory mouse in that the third extracellular loop that" ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Moreover, to link the intracellular iron content to the function of alveolar macrophages, we assessed the phagocytosis of alveolar macrophages, and found that the alveolar macrophages from Ad-shHepc1-treated mice showed less phagocytic ability than those from the control animals .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin regulates iron metabolism by binding to ferroportin and causing its internalization and degradation. We therefore investigated the ferroportin levels in both whole lung tissue and alveolar macrophages. As expected, the ferroportin in the control mice was almost totally degraded, whereas a higher ferroportin level was observed in the hepcidin knockdown mice .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: We further asked whether hepcidin gene modification in AECs had an impact on local and systemic iron metabolism. Of note, the knockdown of hepcidin in AECs resulted in less iron retention in the alveolar macrophages , whereas the iron contents in the spleen macrophages and serum iron concentration between the two groups showed no significant differences .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: from Ad-shHepc1-treated mice showed less phagocytosis ability than those from the control animals. Since liver is the major source of systemic hepcidin, in the current study liver hepcidin levels were not affected and circulating iron concentrations were comparable between the Ad-shNeg-and Ad-shHepc1-treated mice. Therefore, the function of circulating leukocytes should not be influenced. Although the inciting injury is remote, when the bacteria circulating in the blood stream invaded the lung after CLP, the decreased phagocytosis function of the alveolar macrophages from the Ad-shHepc1-treated mice could result in bacterial accumulation in the lung. In addition, as hepcidin exhibits broad spectrum antimicrobial" ]

[ [ "0a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "0b", "Passage: Moreover, to link the intracellular iron content to the function of alveolar macrophages, we assessed the phagocytosis of alveolar macrophages, and found that the alveolar macrophages from Ad-shHepc1-treated mice showed less phagocytic ability than those from the control animals ." ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Moreover, to link the intracellular iron content to the function of alveolar macrophages, we assessed the phagocytosis of alveolar macrophages, and found that the alveolar macrophages from Ad-shHepc1-treated mice showed less phagocytic ability than those from the control animals .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin regulates iron metabolism by binding to ferroportin and causing its internalization and degradation. We therefore investigated the ferroportin levels in both whole lung tissue and alveolar macrophages. As expected, the ferroportin in the control mice was almost totally degraded, whereas a higher ferroportin level was observed in the hepcidin knockdown mice .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: We further asked whether hepcidin gene modification in AECs had an impact on local and systemic iron metabolism. Of note, the knockdown of hepcidin in AECs resulted in less iron retention in the alveolar macrophages , whereas the iron contents in the spleen macrophages and serum iron concentration between the two groups showed no significant differences .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: from Ad-shHepc1-treated mice showed less phagocytosis ability than those from the control animals. Since liver is the major source of systemic hepcidin, in the current study liver hepcidin levels were not affected and circulating iron concentrations were comparable between the Ad-shNeg-and Ad-shHepc1-treated mice. Therefore, the function of circulating leukocytes should not be influenced. Although the inciting injury is remote, when the bacteria circulating in the blood stream invaded the lung after CLP, the decreased phagocytosis function of the alveolar macrophages from the Ad-shHepc1-treated mice could result in bacterial accumulation in the lung. In addition, as hepcidin exhibits broad spectrum antimicrobial" ]

[ [ "1a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "1b", "Passage: Hepcidin regulates iron metabolism by binding to ferroportin and causing its internalization and degradation." ], [ "1c", "We therefore investigated the ferroportin levels in both whole lung tissue and alveolar macrophages." ], [ "1d", "As expected, the ferroportin in the control mice was almost totally degraded, whereas a higher ferroportin level was observed in the hepcidin knockdown mice ." ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Moreover, to link the intracellular iron content to the function of alveolar macrophages, we assessed the phagocytosis of alveolar macrophages, and found that the alveolar macrophages from Ad-shHepc1-treated mice showed less phagocytic ability than those from the control animals .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin regulates iron metabolism by binding to ferroportin and causing its internalization and degradation. We therefore investigated the ferroportin levels in both whole lung tissue and alveolar macrophages. As expected, the ferroportin in the control mice was almost totally degraded, whereas a higher ferroportin level was observed in the hepcidin knockdown mice .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: We further asked whether hepcidin gene modification in AECs had an impact on local and systemic iron metabolism. Of note, the knockdown of hepcidin in AECs resulted in less iron retention in the alveolar macrophages , whereas the iron contents in the spleen macrophages and serum iron concentration between the two groups showed no significant differences .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: from Ad-shHepc1-treated mice showed less phagocytosis ability than those from the control animals. Since liver is the major source of systemic hepcidin, in the current study liver hepcidin levels were not affected and circulating iron concentrations were comparable between the Ad-shNeg-and Ad-shHepc1-treated mice. Therefore, the function of circulating leukocytes should not be influenced. Although the inciting injury is remote, when the bacteria circulating in the blood stream invaded the lung after CLP, the decreased phagocytosis function of the alveolar macrophages from the Ad-shHepc1-treated mice could result in bacterial accumulation in the lung. In addition, as hepcidin exhibits broad spectrum antimicrobial" ]

[ [ "2a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "2b", "Passage: We further asked whether hepcidin gene modification in AECs had an impact on local and systemic iron metabolism." ], [ "2c", "Of note, the knockdown of hepcidin in AECs resulted in less iron retention in the alveolar macrophages , whereas the iron contents in the spleen macrophages and serum iron concentration between the two groups showed no significant differences ." ] ]

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

[ "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Moreover, to link the intracellular iron content to the function of alveolar macrophages, we assessed the phagocytosis of alveolar macrophages, and found that the alveolar macrophages from Ad-shHepc1-treated mice showed less phagocytic ability than those from the control animals .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin regulates iron metabolism by binding to ferroportin and causing its internalization and degradation. We therefore investigated the ferroportin levels in both whole lung tissue and alveolar macrophages. As expected, the ferroportin in the control mice was almost totally degraded, whereas a higher ferroportin level was observed in the hepcidin knockdown mice .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: We further asked whether hepcidin gene modification in AECs had an impact on local and systemic iron metabolism. Of note, the knockdown of hepcidin in AECs resulted in less iron retention in the alveolar macrophages , whereas the iron contents in the spleen macrophages and serum iron concentration between the two groups showed no significant differences .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: from Ad-shHepc1-treated mice showed less phagocytosis ability than those from the control animals. Since liver is the major source of systemic hepcidin, in the current study liver hepcidin levels were not affected and circulating iron concentrations were comparable between the Ad-shNeg-and Ad-shHepc1-treated mice. Therefore, the function of circulating leukocytes should not be influenced. Although the inciting injury is remote, when the bacteria circulating in the blood stream invaded the lung after CLP, the decreased phagocytosis function of the alveolar macrophages from the Ad-shHepc1-treated mice could result in bacterial accumulation in the lung. In addition, as hepcidin exhibits broad spectrum antimicrobial" ]

[ [ "3a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "3b", "Passage: from Ad-shHepc1-treated mice showed less phagocytosis ability than those from the control animals." ], [ "3c", "Since liver is the major source of systemic hepcidin, in the current study liver hepcidin levels were not affected and circulating iron concentrations were comparable between the Ad-shNeg-and Ad-shHepc1-treated mice." ], [ "3d", "Therefore, the function of circulating leukocytes should not be influenced." ], [ "3e", "Although the inciting injury is remote, when the bacteria circulating in the blood stream invaded the lung after CLP, the decreased phagocytosis function of the alveolar macrophages from the Ad-shHepc1-treated mice could result in bacterial accumulation in the lung." ], [ "3f", "In addition, as hepcidin exhibits broad spectrum antimicrobial" ] ]

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

[ "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: An SSI can increase hospital stay by about six days and can add 10-20 % to hospital costs, even leading to death; therefore, prevention and control should be an . SSIs may occur following any surgical incision, even after the use of minimally invasive techniques, so SSIs need to be reported through systematic monitoring programmes for nosocomial infection . We showed that patients suffering from SSI in our cohort had longer ICU stays. However, we do not think this was simply a surrogate of higher illness severity in the SSI group because of the comparable severity scores between groups.", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: The increasing trend to reduce hospital stays by implementing innovative surgical techniques makes it necessary to ensure that accurate measurement and monitoring of adverse events can take place after discharge. Without doing so, we cannot establish the real impact of SSI on morbidity and mortality . Control measures with an emphasis on the education of healthcare professionals, such as frequent hand washing and the need to isolate patients with multi-resistant bacteria in cluster units, are necessary to reduce SSI rates . Although the total elimination of SSI is not possible, a reduction in the rate of infection to a minimum", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: or drainage . Consequently, the treatment of SSI leads to increased costs, especially when we consider the high number of surgical procedures and their complexity in a typical referral hospital .", "Title: Low usage of government healthcare facilities for acute respiratory infections in guatemala: implications for influenza surveillance\nPassage: respiratory infections and SARI-related mortality and another for influenza-like illness based in ambulatory clinics. Sentinel surveillance for influenza can provide information on trends in viral circulation patterns and seasonality, along with virus characteristics to help guide decisions on vaccine composition. However, healthcare seeking behaviors can affect who accesses care at the sentinel site, limiting the ability to gather information to guide public health policies. Without understanding patterns of healthcare seeking behavior, it is not possible to calculate the burden of disease, generalize findings to a larger population or identify risk groups." ]

[ [ "0a", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes" ], [ "0b", "Passage: An SSI can increase hospital stay by about six days and can add 10-20 % to hospital costs, even leading to death; therefore, prevention and control should be an ." ], [ "0c", "SSIs may occur following any surgical incision, even after the use of minimally invasive techniques, so SSIs need to be reported through systematic monitoring programmes for nosocomial infection ." ], [ "0d", "We showed that patients suffering from SSI in our cohort had longer ICU stays." ], [ "0e", "However, we do not think this was simply a surrogate of higher illness severity in the SSI group because of the comparable severity scores between groups." ] ]

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

[ "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: An SSI can increase hospital stay by about six days and can add 10-20 % to hospital costs, even leading to death; therefore, prevention and control should be an . SSIs may occur following any surgical incision, even after the use of minimally invasive techniques, so SSIs need to be reported through systematic monitoring programmes for nosocomial infection . We showed that patients suffering from SSI in our cohort had longer ICU stays. However, we do not think this was simply a surrogate of higher illness severity in the SSI group because of the comparable severity scores between groups.", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: The increasing trend to reduce hospital stays by implementing innovative surgical techniques makes it necessary to ensure that accurate measurement and monitoring of adverse events can take place after discharge. Without doing so, we cannot establish the real impact of SSI on morbidity and mortality . Control measures with an emphasis on the education of healthcare professionals, such as frequent hand washing and the need to isolate patients with multi-resistant bacteria in cluster units, are necessary to reduce SSI rates . Although the total elimination of SSI is not possible, a reduction in the rate of infection to a minimum", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: or drainage . Consequently, the treatment of SSI leads to increased costs, especially when we consider the high number of surgical procedures and their complexity in a typical referral hospital .", "Title: Low usage of government healthcare facilities for acute respiratory infections in guatemala: implications for influenza surveillance\nPassage: respiratory infections and SARI-related mortality and another for influenza-like illness based in ambulatory clinics. Sentinel surveillance for influenza can provide information on trends in viral circulation patterns and seasonality, along with virus characteristics to help guide decisions on vaccine composition. However, healthcare seeking behaviors can affect who accesses care at the sentinel site, limiting the ability to gather information to guide public health policies. Without understanding patterns of healthcare seeking behavior, it is not possible to calculate the burden of disease, generalize findings to a larger population or identify risk groups." ]

[ [ "1a", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes" ], [ "1b", "Passage: The increasing trend to reduce hospital stays by implementing innovative surgical techniques makes it necessary to ensure that accurate measurement and monitoring of adverse events can take place after discharge." ], [ "1c", "Without doing so, we cannot establish the real impact of SSI on morbidity and mortality ." ], [ "1d", "Control measures with an emphasis on the education of healthcare professionals, such as frequent hand washing and the need to isolate patients with multi-resistant bacteria in cluster units, are necessary to reduce SSI rates ." ], [ "1e", "Although the total elimination of SSI is not possible, a reduction in the rate of infection to a minimum" ] ]

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

[ "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: An SSI can increase hospital stay by about six days and can add 10-20 % to hospital costs, even leading to death; therefore, prevention and control should be an . SSIs may occur following any surgical incision, even after the use of minimally invasive techniques, so SSIs need to be reported through systematic monitoring programmes for nosocomial infection . We showed that patients suffering from SSI in our cohort had longer ICU stays. However, we do not think this was simply a surrogate of higher illness severity in the SSI group because of the comparable severity scores between groups.", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: The increasing trend to reduce hospital stays by implementing innovative surgical techniques makes it necessary to ensure that accurate measurement and monitoring of adverse events can take place after discharge. Without doing so, we cannot establish the real impact of SSI on morbidity and mortality . Control measures with an emphasis on the education of healthcare professionals, such as frequent hand washing and the need to isolate patients with multi-resistant bacteria in cluster units, are necessary to reduce SSI rates . Although the total elimination of SSI is not possible, a reduction in the rate of infection to a minimum", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes\nPassage: or drainage . Consequently, the treatment of SSI leads to increased costs, especially when we consider the high number of surgical procedures and their complexity in a typical referral hospital .", "Title: Low usage of government healthcare facilities for acute respiratory infections in guatemala: implications for influenza surveillance\nPassage: respiratory infections and SARI-related mortality and another for influenza-like illness based in ambulatory clinics. Sentinel surveillance for influenza can provide information on trends in viral circulation patterns and seasonality, along with virus characteristics to help guide decisions on vaccine composition. However, healthcare seeking behaviors can affect who accesses care at the sentinel site, limiting the ability to gather information to guide public health policies. Without understanding patterns of healthcare seeking behavior, it is not possible to calculate the burden of disease, generalize findings to a larger population or identify risk groups." ]

[ [ "2a", "Title: Surgical site infection in critically ill patients with secondary and tertiary peritonitis: epidemiology, microbiology and influence in outcomes" ], [ "2b", "Passage: or drainage ." ], [ "2c", "Consequently, the treatment of SSI leads to increased costs, especially when we consider the high number of surgical procedures and their complexity in a typical referral hospital ." ] ]

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

[ "Title: Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection\nPassage: as 3 days postfertilization, coinciding with the attachment of the blastocyst to the uterine wall, and were believed to be critical for protecting the semiallotypic fetus from the maternal immune system during pregnancy in, at least, primates .", "Title: Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein\nPassage: The first signs of disruption of Golgi morphology largely began during or even preceding the accumulation of visible 3A signal , suggesting that local changes to morphology occur rapidly and may be triggered by 3A accumulation in regions of the Golgi apparatus outside the imaging plane. To facilitate the detection of the whole Golgi complex and to monitor large-scale changes in Golgi morphology, imaging was carried out using a wider confocal pinhole . Global Golgi fragmentation typically began 10 to 30 min after 3A started to accumulate in large amounts , which presumably reflects the time taken for the cumulative", "Title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast\nPassage: W235 situated downstream of the expected cleavage sites . Similarly, major cleavage sites were analysed in 16-day old chronologically aged cells using the same primers and mapped at positions +601-602 and +478-501. According to the secondary structure of the 25S rRNA taken from , the regions where mapped cleavages occur are located at unpaired nucleotides in loops or bulges. This points to the action of single-stranded RNA nucleases.", "Title: Dynamics of the Developing Chick Chorioallantoic Membrane Assessed by Stereology, Allometry, Immunohistochemistry and Molecular Analysis\nPassage: It has previously been reported that the rapid phase of angiogenesis is E10 and after initiation of endothelial cytodifferentiation at E14 . Elsewhere, Baum and co-workers found expression of VEGF-A to have peaks at E8-E9 and also at E11-E12 while recently, a peak at E7 and E18 was reported ." ]

[ [ "0a", "Title: Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection" ], [ "0b", "Passage: as 3 days postfertilization, coinciding with the attachment of the blastocyst to the uterine wall, and were believed to be critical for protecting the semiallotypic fetus from the maternal immune system during pregnancy in, at least, primates ." ] ]

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

[ "Title: Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection\nPassage: as 3 days postfertilization, coinciding with the attachment of the blastocyst to the uterine wall, and were believed to be critical for protecting the semiallotypic fetus from the maternal immune system during pregnancy in, at least, primates .", "Title: Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein\nPassage: The first signs of disruption of Golgi morphology largely began during or even preceding the accumulation of visible 3A signal , suggesting that local changes to morphology occur rapidly and may be triggered by 3A accumulation in regions of the Golgi apparatus outside the imaging plane. To facilitate the detection of the whole Golgi complex and to monitor large-scale changes in Golgi morphology, imaging was carried out using a wider confocal pinhole . Global Golgi fragmentation typically began 10 to 30 min after 3A started to accumulate in large amounts , which presumably reflects the time taken for the cumulative", "Title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast\nPassage: W235 situated downstream of the expected cleavage sites . Similarly, major cleavage sites were analysed in 16-day old chronologically aged cells using the same primers and mapped at positions +601-602 and +478-501. According to the secondary structure of the 25S rRNA taken from , the regions where mapped cleavages occur are located at unpaired nucleotides in loops or bulges. This points to the action of single-stranded RNA nucleases.", "Title: Dynamics of the Developing Chick Chorioallantoic Membrane Assessed by Stereology, Allometry, Immunohistochemistry and Molecular Analysis\nPassage: It has previously been reported that the rapid phase of angiogenesis is E10 and after initiation of endothelial cytodifferentiation at E14 . Elsewhere, Baum and co-workers found expression of VEGF-A to have peaks at E8-E9 and also at E11-E12 while recently, a peak at E7 and E18 was reported ." ]

[ [ "1a", "Title: Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein" ], [ "1b", "Passage: The first signs of disruption of Golgi morphology largely began during or even preceding the accumulation of visible 3A signal , suggesting that local changes to morphology occur rapidly and may be triggered by 3A accumulation in regions of the Golgi apparatus outside the imaging plane." ], [ "1c", "To facilitate the detection of the whole Golgi complex and to monitor large-scale changes in Golgi morphology, imaging was carried out using a wider confocal pinhole ." ], [ "1d", "Global Golgi fragmentation typically began 10 to 30 min after 3A started to accumulate in large amounts , which presumably reflects the time taken for the cumulative" ] ]

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

[ "Title: Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection\nPassage: as 3 days postfertilization, coinciding with the attachment of the blastocyst to the uterine wall, and were believed to be critical for protecting the semiallotypic fetus from the maternal immune system during pregnancy in, at least, primates .", "Title: Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein\nPassage: The first signs of disruption of Golgi morphology largely began during or even preceding the accumulation of visible 3A signal , suggesting that local changes to morphology occur rapidly and may be triggered by 3A accumulation in regions of the Golgi apparatus outside the imaging plane. To facilitate the detection of the whole Golgi complex and to monitor large-scale changes in Golgi morphology, imaging was carried out using a wider confocal pinhole . Global Golgi fragmentation typically began 10 to 30 min after 3A started to accumulate in large amounts , which presumably reflects the time taken for the cumulative", "Title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast\nPassage: W235 situated downstream of the expected cleavage sites . Similarly, major cleavage sites were analysed in 16-day old chronologically aged cells using the same primers and mapped at positions +601-602 and +478-501. According to the secondary structure of the 25S rRNA taken from , the regions where mapped cleavages occur are located at unpaired nucleotides in loops or bulges. This points to the action of single-stranded RNA nucleases.", "Title: Dynamics of the Developing Chick Chorioallantoic Membrane Assessed by Stereology, Allometry, Immunohistochemistry and Molecular Analysis\nPassage: It has previously been reported that the rapid phase of angiogenesis is E10 and after initiation of endothelial cytodifferentiation at E14 . Elsewhere, Baum and co-workers found expression of VEGF-A to have peaks at E8-E9 and also at E11-E12 while recently, a peak at E7 and E18 was reported ." ]

[ [ "2a", "Title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast" ], [ "2b", "Passage: W235 situated downstream of the expected cleavage sites ." ], [ "2c", "Similarly, major cleavage sites were analysed in 16-day old chronologically aged cells using the same primers and mapped at positions +601-602 and +478-501." ], [ "2d", "According to the secondary structure of the 25S rRNA taken from , the regions where mapped cleavages occur are located at unpaired nucleotides in loops or bulges." ], [ "2e", "This points to the action of single-stranded RNA nucleases." ] ]

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

[ "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ]

[ [ "0a", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else? Passage: hosts." ], [ "0b", "However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event ." ], [ "0c", "The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results )." ], [ "0d", "A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions ." ] ]

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

[ "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ]

[ [ "1a", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else? Passage: hosts." ], [ "1b", "However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event ." ], [ "1c", "The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results )." ], [ "1d", "A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions ." ] ]

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

[ "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ]

[ [ "2a", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?" ], [ "2b", "Passage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge." ], [ "2c", "Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts." ], [ "2d", "Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host." ], [ "2e", "Main maintenance hypothesis: there is one bat Figure 1 ." ], [ "2f", "Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge." ], [ "2g", "Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts." ], [ "2h", "Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ] ]

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

[ "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: hosts. However, these data indicate their possible involvement in the transmission function of EBOV, bridging the maintenance host with human populations during a spillover event . The EBOV susceptibility and exposure of many other potential forest hosts, including invertebrates, birds, bats, monkeys, rodents, and other small mammals, have been tested in the field or experimentally with an interestingly large amount of negative results ). A few monkey and bat individuals serologically positive to EBV antigen represent the only exceptions .", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?\nPassage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host. Main maintenance hypothesis: there is one bat Figure 1 . Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge. Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts. Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ]

[ [ "3a", "Title: Ebola Virus Maintenance: If Not (Only) Bats, What Else?" ], [ "3b", "Passage: Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge." ], [ "3c", "Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts." ], [ "3d", "Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally to ebolavirus directly or indirectly through the main maintenance host." ], [ "3e", "Main maintenance hypothesis: there is one bat Figure 1 ." ], [ "3f", "Potential maintenance mechanisms of ebolaviruses in wildlife, according to current knowledge." ], [ "3g", "Circles indicate a maintenance function play by the host; arrows represent infectious transmission pathways between hosts." ], [ "3h", "Humans, non-human primates, and duikers are examples of known non-maintenance hosts, exposed occasionally" ] ]

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

[ "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa\nPassage: can reveal structural changes in transmission due to control or behavioural changes, and it can capture fluctuating incidence data, e.g. in Conakry, Guinea. Also, the migration fractions are independent of the extent of the spatial dispersal. This allows for the situation where few people migrate, but when they do, they do so over large distances, as has, for instance, been estimated for Liberia. The method by Yang et al. does not make this distinction, but includes the home district in the migration matrix. This may explain why they find a lower proportion of local transmissions than we do . By", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: This is an interesting point, though we feel the increased sample size gained by inclusion of the SPARTAC cohort outweighs any issues with sampling design." ]

[ [ "0a", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets" ], [ "0b", "Passage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal ." ] ]

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

[ "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa\nPassage: can reveal structural changes in transmission due to control or behavioural changes, and it can capture fluctuating incidence data, e.g. in Conakry, Guinea. Also, the migration fractions are independent of the extent of the spatial dispersal. This allows for the situation where few people migrate, but when they do, they do so over large distances, as has, for instance, been estimated for Liberia. The method by Yang et al. does not make this distinction, but includes the home district in the migration matrix. This may explain why they find a lower proportion of local transmissions than we do . By", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: This is an interesting point, though we feel the increased sample size gained by inclusion of the SPARTAC cohort outweighs any issues with sampling design." ]

[ [ "1a", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets" ], [ "1b", "Passage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal ." ] ]

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

[ "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: f. It might be noted that including the early infection SPARTAC cohort may be reducing their power, as these individuals may not have been infected long enough for escape to have occurred, thereby diluting the escape signal .", "Title: Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa\nPassage: can reveal structural changes in transmission due to control or behavioural changes, and it can capture fluctuating incidence data, e.g. in Conakry, Guinea. Also, the migration fractions are independent of the extent of the spatial dispersal. This allows for the situation where few people migrate, but when they do, they do so over large distances, as has, for instance, been estimated for Liberia. The method by Yang et al. does not make this distinction, but includes the home district in the migration matrix. This may explain why they find a lower proportion of local transmissions than we do . By", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets\nPassage: This is an interesting point, though we feel the increased sample size gained by inclusion of the SPARTAC cohort outweighs any issues with sampling design." ]

[ [ "3a", "Title: Mapping the drivers of within-host pathogen evolution using massive data sets" ], [ "3b", "Passage: This is an interesting point, though we feel the increased sample size gained by inclusion of the SPARTAC cohort outweighs any issues with sampling design." ] ]

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

[ "Title: Inferring viral quasispecies spectra from 454 pyrosequencing reads\nPassage: of the reads that varies from 20K up to 100K and the average read length that varies from 200bp up to 600bp.", "Title: Inferring viral quasispecies spectra from 454 pyrosequencing reads\nPassage: The data set Data1 has been received from HCV Research Group in Institute of Biomedical Research, at University of Birmingham. Data1 contains 30,927 reads obtained from the 5.2kb-long fragment of HCV-1a genome . The average read length average is 292bp but it significantly varies as well as the depth of position coverage . The depth of reads coverage variability is due to a strong bias in the sequence start points, reflecting the secondary structure of the template DNA or RNA used to generate the initial PCR products. As a result, shorter reads are produced by GC-rich sequences. Data1 is available", "Title: Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands\nPassage: further study . Median length of predicted proteins on these reads was 75 amino acids showing error correction had not been sufficient to correct for the enriched presence of stop codons resulting from indel errors. Therefore, an alternative approach to gene calling was developed. VirION reads spanning genomic islands were trimmed at the 5' and 3' end to leave only the read fragment mapping within the genomic island, and these fragments were used as a query in a BLASTx search against the NR database using diamond , with the following settings:", "Title: Deep Sequencing to Identify the Causes of Viral Encephalitis\nPassage: Assembly of reads that aligned to the taxon-specific follow up databases resulted in apparently viral contigs ranging from 66 to 4019 bp long in 5 of the 7 encephalitis samples . These contigs were re-aligned to the taxon-specific database as well as the human genome with MegaBLAST." ]

[ [ "1a", "Title: Inferring viral quasispecies spectra from 454 pyrosequencing reads" ], [ "1b", "Passage: The data set Data1 has been received from HCV Research Group in Institute of Biomedical Research, at University of Birmingham." ], [ "1c", "Data1 contains 30,927 reads obtained from the 5.2kb-long fragment of HCV-1a genome ." ], [ "1d", "The average read length average is 292bp but it significantly varies as well as the depth of position coverage ." ], [ "1e", "The depth of reads coverage variability is due to a strong bias in the sequence start points, reflecting the secondary structure of the template DNA or RNA used to generate the initial PCR products." ], [ "1f", "As a result, shorter reads are produced by GC-rich sequences." ], [ "1g", "Data1 is available" ] ]

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

[ "Title: Inferring viral quasispecies spectra from 454 pyrosequencing reads\nPassage: of the reads that varies from 20K up to 100K and the average read length that varies from 200bp up to 600bp.", "Title: Inferring viral quasispecies spectra from 454 pyrosequencing reads\nPassage: The data set Data1 has been received from HCV Research Group in Institute of Biomedical Research, at University of Birmingham. Data1 contains 30,927 reads obtained from the 5.2kb-long fragment of HCV-1a genome . The average read length average is 292bp but it significantly varies as well as the depth of position coverage . The depth of reads coverage variability is due to a strong bias in the sequence start points, reflecting the secondary structure of the template DNA or RNA used to generate the initial PCR products. As a result, shorter reads are produced by GC-rich sequences. Data1 is available", "Title: Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands\nPassage: further study . Median length of predicted proteins on these reads was 75 amino acids showing error correction had not been sufficient to correct for the enriched presence of stop codons resulting from indel errors. Therefore, an alternative approach to gene calling was developed. VirION reads spanning genomic islands were trimmed at the 5' and 3' end to leave only the read fragment mapping within the genomic island, and these fragments were used as a query in a BLASTx search against the NR database using diamond , with the following settings:", "Title: Deep Sequencing to Identify the Causes of Viral Encephalitis\nPassage: Assembly of reads that aligned to the taxon-specific follow up databases resulted in apparently viral contigs ranging from 66 to 4019 bp long in 5 of the 7 encephalitis samples . These contigs were re-aligned to the taxon-specific database as well as the human genome with MegaBLAST." ]

[ [ "2a", "Title: Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands" ], [ "2b", "Passage: further study ." ], [ "2c", "Median length of predicted proteins on these reads was 75 amino acids showing error correction had not been sufficient to correct for the enriched presence of stop codons resulting from indel errors." ], [ "2d", "Therefore, an alternative approach to gene calling was developed." ], [ "2e", "VirION reads spanning genomic islands were trimmed at the 5' and 3' end to leave only the read fragment mapping within the genomic island, and these fragments were used as a query in a BLASTx search against the NR database using diamond , with the following settings:" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: effective management of chronic inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Text: The prevalence of chronic airway inflammatory disease is increasing worldwide especially in developed nations . This disease is characterized by airway inflammation leading to complications such as coughing, wheezing and shortness of breath. The disease can manifest in both the upper airway and lower airway which greatly affect the patients' quality of life . Treatment and management vary greatly in efficacy due to the complexity and heterogeneity of the disease. This is further complicated by the effect of episodic exacerbations of the disease, defined as worsening of disease symptoms including wheeze, cough, breathlessness and chest tightness . Such exacerbations", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: specific mediators to facilitate viral targeting and clearance, including type II interferon , IL-2, IL-4, IL-5, IL-9, and IL-12 . These factors heighten local inflammation and the infiltration of granulocytes, T-cells and B-cells . The increased inflammation, in turn, worsens the symptoms of airway diseases." ]

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

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: effective management of chronic inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Text: The prevalence of chronic airway inflammatory disease is increasing worldwide especially in developed nations . This disease is characterized by airway inflammation leading to complications such as coughing, wheezing and shortness of breath. The disease can manifest in both the upper airway and lower airway which greatly affect the patients' quality of life . Treatment and management vary greatly in efficacy due to the complexity and heterogeneity of the disease. This is further complicated by the effect of episodic exacerbations of the disease, defined as worsening of disease symptoms including wheeze, cough, breathlessness and chest tightness . Such exacerbations", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: specific mediators to facilitate viral targeting and clearance, including type II interferon , IL-2, IL-4, IL-5, IL-9, and IL-12 . These factors heighten local inflammation and the infiltration of granulocytes, T-cells and B-cells . The increased inflammation, in turn, worsens the symptoms of airway diseases." ]

[ [ "3a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "3b", "Passage: specific mediators to facilitate viral targeting and clearance, including type II interferon , IL-2, IL-4, IL-5, IL-9, and IL-12 ." ], [ "3c", "These factors heighten local inflammation and the infiltration of granulocytes, T-cells and B-cells ." ], [ "3d", "The increased inflammation, in turn, worsens the symptoms of airway diseases." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: countries between 7 and 43 million individuals have been infected with SARS-CoV-Z up to 28th March,", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: According to the situation report published by the WHO on 28 January 2020 , a total of 2798 confirmed 2019-nCoV cases have been reported globally; of these, 2761 cases were from China, including Hong Kong , Macau and Taipei . Thirty-seven confirmed cases have been reported outside of China in eleven countries in Europe, North America, Australia and Asia; of these 37 exported cases, 36 had a travel history from China or an epidemiological link to a case from China. Of the confirmed cases in China, 461 have been reported as severely ill, with 80 deaths to date.", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: SARS-CoV and MERS-CoV cause severe disease, but despite the initial R0 estimations of greater than 2.0 for SARS-CoV , and some large outbreaks, neither were as transmissible as initial concerns suggested. SARS-CoV caused 8098 reported cases and 774 deaths in 37 countries before the epidemic was controlled. Control was thought to have been possible because a high proportion of cases were severe, making it easier to rapidly identify and isolate infected individuals. In addition, the virus was present at lower levels in upper airway secretions. There was no secondary transmission in the United States from the 8 imported cases, although", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: Text: The emergence and outbreak of a newly discovered acute respiratory disease in Wuhan, China, has affected greater than 40,000 people, and killed more than 1,000 as of Feb. 10, 2020. A new human coronavirus, SARS-CoV-2, was quickly identified, and the associated disease is now referred to as coronavirus disease discovered in 2019 ." ]

[ [ "2a", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus" ], [ "2b", "Passage: SARS-CoV and MERS-CoV cause severe disease, but despite the initial R0 estimations of greater than 2.0 for SARS-CoV , and some large outbreaks, neither were as transmissible as initial concerns suggested." ], [ "2c", "SARS-CoV caused 8098 reported cases and 774 deaths in 37 countries before the epidemic was controlled." ], [ "2d", "Control was thought to have been possible because a high proportion of cases were severe, making it easier to rapidly identify and isolate infected individuals." ], [ "2e", "In addition, the virus was present at lower levels in upper airway secretions." ], [ "2f", "There was no secondary transmission in the United States from the 8 imported cases, although" ] ]

[ "2c" ]

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 . On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases . Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 . As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: A novel coronavirus, later named severe acute respiratory syndrome coronavirus 2 , was identified in December 2019 in the city of Wuhan, capital of Hubei Province, China, where cases were first confirmed . During December 2019–February 2020, the number of confirmed cases increased drastically. Model estimates suggested that >75,000 persons were infected by January 25, 2020, and the epidemic had a doubling time of ≈6 days . By the end of January 2020, travel restrictions were implemented for Wuhan and neighboring cities. Nonetheless, the virus spread from Wuhan to other cities in China and outside the country. By February 4,", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public. This event was reported to the World Health Organisation on 31 December . Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine" ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "Passage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 ." ], [ "0c", "On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases ." ], [ "0d", "Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 ." ], [ "0e", "As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region ." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 . On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases . Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 . As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: A novel coronavirus, later named severe acute respiratory syndrome coronavirus 2 , was identified in December 2019 in the city of Wuhan, capital of Hubei Province, China, where cases were first confirmed . During December 2019–February 2020, the number of confirmed cases increased drastically. Model estimates suggested that >75,000 persons were infected by January 25, 2020, and the epidemic had a doubling time of ≈6 days . By the end of January 2020, travel restrictions were implemented for Wuhan and neighboring cities. Nonetheless, the virus spread from Wuhan to other cities in China and outside the country. By February 4,", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public. This event was reported to the World Health Organisation on 31 December . Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine" ]

[ [ "2a", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions," ], [ "2b", "Passage: A novel coronavirus, later named severe acute respiratory syndrome coronavirus 2 , was identified in December 2019 in the city of Wuhan, capital of Hubei Province, China, where cases were first confirmed ." ], [ "2c", "During December 2019–February 2020, the number of confirmed cases increased drastically." ], [ "2d", "Model estimates suggested that >75,000 persons were infected by January 25, 2020, and the epidemic had a doubling time of ≈6 days ." ], [ "2e", "By the end of January 2020, travel restrictions were implemented for Wuhan and neighboring cities." ], [ "2f", "Nonetheless, the virus spread from Wuhan to other cities in China and outside the country." ], [ "2g", "By February 4," ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 . On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases . Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 . As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions,\nPassage: A novel coronavirus, later named severe acute respiratory syndrome coronavirus 2 , was identified in December 2019 in the city of Wuhan, capital of Hubei Province, China, where cases were first confirmed . During December 2019–February 2020, the number of confirmed cases increased drastically. Model estimates suggested that >75,000 persons were infected by January 25, 2020, and the epidemic had a doubling time of ≈6 days . By the end of January 2020, travel restrictions were implemented for Wuhan and neighboring cities. Nonetheless, the virus spread from Wuhan to other cities in China and outside the country. By February 4,", "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public. This event was reported to the World Health Organisation on 31 December . Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine" ]

[ [ "3a", "Title: SARS to novel coronavirus – old lessons and new lessons" ], [ "3b", "Passage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public." ], [ "3c", "This event was reported to the World Health Organisation on 31 December ." ], [ "3d", "Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine" ] ]

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

[ "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: To ensure success in the mission of shutting down the businesses that are still making money and that millions of people live on, the key issue is whether the decision maker and policy maker are aware of the extra dimension , which represents the single option that will result in apparent loss. In this sense, efforts to enhance environmental protection consciousness do, in fact, emphasize that there is an invisible \"green\" dimension. The purpose of thinking green is to make it clear that choosing to \"Chikui\" on an offered dimension that represents exploiting natural resource wealth will gain something on", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures\nPassage: Specifically, Easterners tend to be dialectical when thinking about a situation in a manner that balances the positives and negatives. When things are going well, Easterners might expect a change for the worse, and when things are going badly, they might expect things to get better. This may prepare Easterners for unexpected situations. However, Westerners tend to focus more on one pattern-things will tend to stay as they are, good or bad. This thinking style may lead Westerners to think that things are rather consistent, leading them to concentrate on one side of an issue.", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: The ability to make decisions and carry out effective actions for achieving rewards and avoiding punishments is central to intelligent life . In the real world, many decisions on important life events are to accept or reject an offered single option such as straightening of teeth, admission to college, counterfeit cash, a marriage proposal, a home mortgage, early retirement, or signing away an inheritance.", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures\nPassage: is because if something is expected to change or fluctuate, it would not be taken in the extreme view. Linear thinkers, on the other hand, expect stability, so their thoughts might be grounded more in the extremes . One difference between dialectical and linear thinking styles lies in how people from different cultures view events. Easterners tend to take a more balanced view of negative events compared to Westerners . Indeed, findings suggest that people from dialectical and collectivist cultures make less polarized life quality judgments, whether negative or positive, compared to non-dialectical thinkers and individualist cultures ." ]

[ [ "1a", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures" ], [ "1b", "Passage: Specifically, Easterners tend to be dialectical when thinking about a situation in a manner that balances the positives and negatives." ], [ "1c", "When things are going well, Easterners might expect a change for the worse, and when things are going badly, they might expect things to get better." ], [ "1d", "This may prepare Easterners for unexpected situations." ], [ "1e", "However, Westerners tend to focus more on one pattern-things will tend to stay as they are, good or bad." ], [ "1f", "This thinking style may lead Westerners to think that things are rather consistent, leading them to concentrate on one side of an issue." ] ]

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

[ "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: To ensure success in the mission of shutting down the businesses that are still making money and that millions of people live on, the key issue is whether the decision maker and policy maker are aware of the extra dimension , which represents the single option that will result in apparent loss. In this sense, efforts to enhance environmental protection consciousness do, in fact, emphasize that there is an invisible \"green\" dimension. The purpose of thinking green is to make it clear that choosing to \"Chikui\" on an offered dimension that represents exploiting natural resource wealth will gain something on", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures\nPassage: Specifically, Easterners tend to be dialectical when thinking about a situation in a manner that balances the positives and negatives. When things are going well, Easterners might expect a change for the worse, and when things are going badly, they might expect things to get better. This may prepare Easterners for unexpected situations. However, Westerners tend to focus more on one pattern-things will tend to stay as they are, good or bad. This thinking style may lead Westerners to think that things are rather consistent, leading them to concentrate on one side of an issue.", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: The ability to make decisions and carry out effective actions for achieving rewards and avoiding punishments is central to intelligent life . In the real world, many decisions on important life events are to accept or reject an offered single option such as straightening of teeth, admission to college, counterfeit cash, a marriage proposal, a home mortgage, early retirement, or signing away an inheritance.", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures\nPassage: is because if something is expected to change or fluctuate, it would not be taken in the extreme view. Linear thinkers, on the other hand, expect stability, so their thoughts might be grounded more in the extremes . One difference between dialectical and linear thinking styles lies in how people from different cultures view events. Easterners tend to take a more balanced view of negative events compared to Westerners . Indeed, findings suggest that people from dialectical and collectivist cultures make less polarized life quality judgments, whether negative or positive, compared to non-dialectical thinkers and individualist cultures ." ]

[ [ "3a", "Title: Two Sides of Emotion: Exploring Positivity and Negativity in Six Basic Emotions across Cultures" ], [ "3b", "Passage: is because if something is expected to change or fluctuate, it would not be taken in the extreme view." ], [ "3c", "Linear thinkers, on the other hand, expect stability, so their thoughts might be grounded more in the extremes ." ], [ "3d", "One difference between dialectical and linear thinking styles lies in how people from different cultures view events." ], [ "3e", "Easterners tend to take a more balanced view of negative events compared to Westerners ." ], [ "3f", "Indeed, findings suggest that people from dialectical and collectivist cultures make less polarized life quality judgments, whether negative or positive, compared to non-dialectical thinkers and individualist cultures ." ] ]

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

[ "Title: Performance evaluation of antimicrobial peptide ll-37 and hepcidin and β-defensin-2 secreted by mesenchymal stem cells\nPassage: Hepcidin is bound to plasma alpha-2 macroglobulin . Evidence suggests that other cells may express the hepcidin mRNA at a much lower level than the hepatocytes; the biological significance of the extra hepatic production of hepcidin remains uncertain. Plasma hepcidin is freely treated through glomeruli and in animals with normal kidney activity it quickly passes through the urine. In addition, a part of hepcidin is cleansed through degradation along with ferritin .", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver. Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone . Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention . Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens . Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via", "Title: Relationship between hepcidin and oxidant/antioxidant status in calves with suspected neonatal septicemia\nPassage: Hepcidin is a low molecular weight, antimicrobial peptide hormone and was first discovered in human urine . It is produced by the liver as a firstline response to inflammatory reactions and high Fe concentrations . Hepcidin plays a fundamental role in the regulation of Fe metabolism , which is a part of foundational cellular functions and thus of vital importance. On the other hand, by participating in redox reactions leading to the production of reactive oxygen species , Fe also causes oxidative stress. Therefore, Fe has been regarded as a potentially toxic element to cells . Fe also plays an", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury\nPassage: washed in phosphate-buffered saline and incubated with a polymer horseradish peroxidase-conjugated secondary antibody for one hour. The sections were further incubated with Dako Liquid DAB Large-Volume Substrate-Chromogen System and counterstained with hematoxylin. Negative controls were included in all assays by replacing the rabbit anti-mouse hepcidin antibody with nonimmune rabbit antiserum. The immunostaining was evaluated using an Olympus BX-50 light microscope . The stain density was analyzed using the Image Pro-Plus 6.0 analysis system , and the level of hepcidin was measured as the integral optical density." ]

[ [ "2a", "Title: Relationship between hepcidin and oxidant/antioxidant status in calves with suspected neonatal septicemia" ], [ "2b", "Passage: Hepcidin is a low molecular weight, antimicrobial peptide hormone and was first discovered in human urine ." ], [ "2c", "It is produced by the liver as a firstline response to inflammatory reactions and high Fe concentrations ." ], [ "2d", "Hepcidin plays a fundamental role in the regulation of Fe metabolism , which is a part of foundational cellular functions and thus of vital importance." ], [ "2e", "On the other hand, by participating in redox reactions leading to the production of reactive oxygen species , Fe also causes oxidative stress." ], [ "2f", "Therefore, Fe has been regarded as a potentially toxic element to cells ." ], [ "2g", "Fe also plays an" ] ]

[ "2b" ]

[ "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns.", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: The general objective of this work is to utilize radio frequency close-proximity sensors to describe and understand the nature of human networks within a low-resource population that have the potential to transmit respiratory infectious diseases. Specifically:", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: were published in 2012. Advocates of these studies/publications argued that they would improve surveillance of H5N1 in nature and facilitate development of vaccines that might be needed to protect against pandemic strains of the virus. Critics questioned the validity of claims about such benefits and argued that the studies might facilitate creation of biological weapons agents that could kill millions, or possibly even billions, of people." ]

[ [ "0a", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households" ], [ "0b", "Passage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level." ], [ "0c", "Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions." ] ]

[ "0a", "0b" ]

[ "Title: Estimating the number of infections and the impact of non-\nPassage: distribution and the initial growth rate of observed deaths. A shorter assumed serial interval results in", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011\nPassage: than the above direct estimate. The shortness of MLE of serial interval is the consequence of many short pairs of infector-infectee reconstructed: One sample of the reconstructed transmission trees for the Hepatitis A outbreak is shown in the left panel of Fig 1. Within this sample tree, the reconstructed infector-infectee pairs have a mean of 7.7 days, which substantially reduces the overall pooled mean. In view of the large amount of infections being asymptomatic , the shortness of the serial interval of reconstructed infector-infectee pairs must have been due to the ignorance of contribution of asymptomatic infections. Hence we regard", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood." ]

[ [ "1a", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011" ], [ "1b", "Passage: than the above direct estimate." ], [ "1c", "The shortness of MLE of serial interval is the consequence of many short pairs of infector-infectee reconstructed: One sample of the reconstructed transmission trees for the Hepatitis A outbreak is shown in the left panel of Fig 1." ], [ "1d", "Within this sample tree, the reconstructed infector-infectee pairs have a mean of 7.7 days, which substantially reduces the overall pooled mean." ], [ "1e", "In view of the large amount of infections being asymptomatic , the shortness of the serial interval of reconstructed infector-infectee pairs must have been due to the ignorance of contribution of asymptomatic infections." ], [ "1f", "Hence we regard" ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: distribution and the initial growth rate of observed deaths. A shorter assumed serial interval results in", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011\nPassage: than the above direct estimate. The shortness of MLE of serial interval is the consequence of many short pairs of infector-infectee reconstructed: One sample of the reconstructed transmission trees for the Hepatitis A outbreak is shown in the left panel of Fig 1. Within this sample tree, the reconstructed infector-infectee pairs have a mean of 7.7 days, which substantially reduces the overall pooled mean. In view of the large amount of infections being asymptomatic , the shortness of the serial interval of reconstructed infector-infectee pairs must have been due to the ignorance of contribution of asymptomatic infections. Hence we regard", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood." ]

[ [ "2a", "Title: Estimation in emerging epidemics: biases and remedies" ], [ "2b", "Passage: value which should be less than the true expected generation time, which is 15." ], [ "2c", "Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed." ], [ "2d", "The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 ." ], [ "2e", "This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: distribution and the initial growth rate of observed deaths. A shorter assumed serial interval results in", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011\nPassage: than the above direct estimate. The shortness of MLE of serial interval is the consequence of many short pairs of infector-infectee reconstructed: One sample of the reconstructed transmission trees for the Hepatitis A outbreak is shown in the left panel of Fig 1. Within this sample tree, the reconstructed infector-infectee pairs have a mean of 7.7 days, which substantially reduces the overall pooled mean. In view of the large amount of infections being asymptomatic , the shortness of the serial interval of reconstructed infector-infectee pairs must have been due to the ignorance of contribution of asymptomatic infections. Hence we regard", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood." ]

[ [ "3a", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic" ], [ "3b", "Passage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated." ], [ "3c", "Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals." ], [ "3d", "The fit using N~4 is the best in terms of the mean likelihood." ] ]

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

[ "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Text: Globally, recent decades have witnessed a growing disjunction, a 'Valley of Death' 1,2 no less, between broadening strides in fundamental biomedical research and their incommensurate reach into the clinic. Plumbing work on research funding and development pipelines through recent changes in the structure of government funding, 2 new public and private joint ventures and specialist undergraduate and postgraduate courses now aim to incorporate pathways to translation at the earliest stages. Reflecting this shift, the number of biomedical research publications targeting 'translational' concepts has increased exponentially, up 1800% between 2003 and 2014 3 and continuing to rise rapidly up to", "Title: Globalization and Health: developing the journal to advance the field\nPassage: In the early years of the journal there was no clear preference for research articles . However from 2011 onwards, research articles accounted for over 50 % of the publications in the journal. Literature reviews were also favoured . Approximately 17 % of papers were classed as highly accessed by the journal's publisher, Bio-Med Central .", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: The number of articles increased exponentially over the period 1965-2017 . Approximately 60% of the articles have been published since 2000.", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: The evolution of RCTs has been an enduring and continuing process . Since the 1970s the publication landscape for RCTs has exhibited an exponential growth. For example, a 1965-2001 bibliometric analysis of the literature identified 369 articles published in 1970 compared to 11,159 published in 2000 . The development of clinical trial registries , the exponential increase in journals publishing trial protocols, results and secondary studies, and growing support for data-sharing policies have created an open research environment of transparency and accountability. Furthermore, the publication of reporting guidelines have served to facilitate the transition between research and reporting to ensure" ]

[ [ "0a", "Title: Frontiers in antiviral therapy and immunotherapy" ], [ "0b", "Passage: Text: Globally, recent decades have witnessed a growing disjunction, a 'Valley of Death' 1,2 no less, between broadening strides in fundamental biomedical research and their incommensurate reach into the clinic." ], [ "0c", "Plumbing work on research funding and development pipelines through recent changes in the structure of government funding, 2 new public and private joint ventures and specialist undergraduate and postgraduate courses now aim to incorporate pathways to translation at the earliest stages." ], [ "0d", "Reflecting this shift, the number of biomedical research publications targeting 'translational' concepts has increased exponentially, up 1800% between 2003 and 2014 3 and continuing to rise rapidly up to" ] ]

[ "0a", "0d" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Abstract: Recently, two coronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, have emerged to cause unusually severe respiratory disease in humans. Currently, there is a lack of effective antiviral treatment options or vaccine available. Given the severity of these outbreaks, and the possibility of additional zoonotic coronaviruses emerging in the near future, the exploration of different treatment strategies is necessary. Disease resilience is the ability of a given host to tolerate an infection, and to return to a state of health. This review focuses on exploring various host resilience mechanisms that could be exploited for treatment", "Title: Host resilience to emerging coronaviruses\nPassage: patients . By understanding risk factors for disease severity we can perhaps predict if a host may be nonresilient and tailor the treatment options appropriately.", "Title: Host resilience to emerging coronaviruses\nPassage: disease tolerant and other patients less tolerant to the viral infection. These factors can serve as a guide to new potential therapies for improved patient care.", "Title: Host resilience to emerging coronaviruses\nPassage: • Host resilience is the ability of a host to tolerate the effects of an infection and return to a state of health." ]

[ [ "0a", "Title: Host resilience to emerging coronaviruses" ], [ "0b", "Passage: Abstract: Recently, two coronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, have emerged to cause unusually severe respiratory disease in humans." ], [ "0c", "Currently, there is a lack of effective antiviral treatment options or vaccine available." ], [ "0d", "Given the severity of these outbreaks, and the possibility of additional zoonotic coronaviruses emerging in the near future, the exploration of different treatment strategies is necessary." ], [ "0e", "Disease resilience is the ability of a given host to tolerate an infection, and to return to a state of health." ], [ "0f", "This review focuses on exploring various host resilience mechanisms that could be exploited for treatment" ] ]

[ "0e", "3b" ]

[ "Title: Host resilience to emerging coronaviruses\nPassage: Abstract: Recently, two coronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, have emerged to cause unusually severe respiratory disease in humans. Currently, there is a lack of effective antiviral treatment options or vaccine available. Given the severity of these outbreaks, and the possibility of additional zoonotic coronaviruses emerging in the near future, the exploration of different treatment strategies is necessary. Disease resilience is the ability of a given host to tolerate an infection, and to return to a state of health. This review focuses on exploring various host resilience mechanisms that could be exploited for treatment", "Title: Host resilience to emerging coronaviruses\nPassage: patients . By understanding risk factors for disease severity we can perhaps predict if a host may be nonresilient and tailor the treatment options appropriately.", "Title: Host resilience to emerging coronaviruses\nPassage: disease tolerant and other patients less tolerant to the viral infection. These factors can serve as a guide to new potential therapies for improved patient care.", "Title: Host resilience to emerging coronaviruses\nPassage: • Host resilience is the ability of a host to tolerate the effects of an infection and return to a state of health." ]

[ [ "3a", "Title: Host resilience to emerging coronaviruses" ], [ "3b", "Passage: • Host resilience is the ability of a host to tolerate the effects of an infection and return to a state of health." ] ]

[ "0e", "3b" ]

[ "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: Flow cytometry of propidium iodide-stained nuclei was performed as described previously . Briefly, PC-3 cells were seeded into 10-cm dishes at a density of 125 0000 cells/well. 24h later, cells were treated with compounds 14 at 100μM as indicated above. DNA content was determined by flow cytometry using a LSRII SORP machine. Rates of cells death were then measured using FlowJo software . 10 6 PC3 cells were inoculated in the flank region of 2-week-old athymic male mice . Tumors were measured weekly and their volume was calculated by the formula length×width×depth×0.5236. When tumors reached 100 mm 3 , mice", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: Cells were transiently transfected the day after seeding with Hsp27 deletion or phosphorylation mutant plasmids as described above, or treated with 14. Transfected cells were then treated with docetaxel in serum-free media for 24h. Cell viability was assessed using 3--2, 5-diphenyl tetrazolium bromide assay for REG, PC-3 and PC-3 RD cells, as previously described . Each assay was performed in triplicate. www.impactjournals.com/oncotarget", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: The human androgen-independent cell line PC-3 were maintained in DMEM media supplemented with 10% fetal bovine serum . The rat colon carcinoma cancer cell line REG was provided by Dr Carmen Garrido and maintained in F10 medium supplemented with 10% FBS. The Human Embryonic Kidney cell line HEK293T was maintained in Dulbecco's Modified Eagle's Medium , supplemented with 10% FBS. All cell lines were cultivated at 37°C in 5% CO 2 . PC-3DR-docetaxel resistant cell line was kindly provided by Dr Martin Gleave and was maintained in culture as previously described.", "Title: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells\nPassage: 3 weeks to construct the prostate cancer model. The mice were anesthetized by 10% chloral hydrate solution , and then the blood samples were collected. Then the mice were sacrificed by cervical dislocation, and the prostate tissues were collected and stored. Animal experiments were approved by the Medical Ethics Committee of Linyi People's Hospital." ]

[ [ "0a", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment" ], [ "0b", "Passage: Flow cytometry of propidium iodide-stained nuclei was performed as described previously ." ], [ "0c", "Briefly, PC-3 cells were seeded into 10-cm dishes at a density of 125 0000 cells/well." ], [ "0d", "24h later, cells were treated with compounds 14 at 100μM as indicated above." ], [ "0e", "DNA content was determined by flow cytometry using a LSRII SORP machine." ], [ "0f", "Rates of cells death were then measured using FlowJo software ." ], [ "0g", "10 6 PC3 cells were inoculated in the flank region of 2-week-old athymic male mice ." ], [ "0h", "Tumors were measured weekly and their volume was calculated by the formula length×width×depth×0.5236." ], [ "0i", "When tumors reached 100 mm 3 , mice" ] ]

[ "0d", "1c" ]

[ "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: Flow cytometry of propidium iodide-stained nuclei was performed as described previously . Briefly, PC-3 cells were seeded into 10-cm dishes at a density of 125 0000 cells/well. 24h later, cells were treated with compounds 14 at 100μM as indicated above. DNA content was determined by flow cytometry using a LSRII SORP machine. Rates of cells death were then measured using FlowJo software . 10 6 PC3 cells were inoculated in the flank region of 2-week-old athymic male mice . Tumors were measured weekly and their volume was calculated by the formula length×width×depth×0.5236. When tumors reached 100 mm 3 , mice", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: Cells were transiently transfected the day after seeding with Hsp27 deletion or phosphorylation mutant plasmids as described above, or treated with 14. Transfected cells were then treated with docetaxel in serum-free media for 24h. Cell viability was assessed using 3--2, 5-diphenyl tetrazolium bromide assay for REG, PC-3 and PC-3 RD cells, as previously described . Each assay was performed in triplicate. www.impactjournals.com/oncotarget", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment\nPassage: The human androgen-independent cell line PC-3 were maintained in DMEM media supplemented with 10% fetal bovine serum . The rat colon carcinoma cancer cell line REG was provided by Dr Carmen Garrido and maintained in F10 medium supplemented with 10% FBS. The Human Embryonic Kidney cell line HEK293T was maintained in Dulbecco's Modified Eagle's Medium , supplemented with 10% FBS. All cell lines were cultivated at 37°C in 5% CO 2 . PC-3DR-docetaxel resistant cell line was kindly provided by Dr Martin Gleave and was maintained in culture as previously described.", "Title: CXCL9 promotes prostate cancer progression through inhibition of cytokines from T cells\nPassage: 3 weeks to construct the prostate cancer model. The mice were anesthetized by 10% chloral hydrate solution , and then the blood samples were collected. Then the mice were sacrificed by cervical dislocation, and the prostate tissues were collected and stored. Animal experiments were approved by the Medical Ethics Committee of Linyi People's Hospital." ]

[ [ "1a", "Title: Targeting Hsp27/eIF4E interaction with phenazine compound: a promising alternative for castration-resistant prostate cancer treatment" ], [ "1b", "Passage: Cells were transiently transfected the day after seeding with Hsp27 deletion or phosphorylation mutant plasmids as described above, or treated with 14." ], [ "1c", "Transfected cells were then treated with docetaxel in serum-free media for 24h." ], [ "1d", "Cell viability was assessed using 3--2, 5-diphenyl tetrazolium bromide assay for REG, PC-3 and PC-3 RD cells, as previously described ." ], [ "1e", "Each assay was performed in triplicate. www.impactjournals.com/oncotarget" ] ]

[ "0d", "1c" ]

[ "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: Viral vector-based influenza vaccines\nPassage: viral vectors can easily be propagated to high virus titers and it is relatively easy to insert genes encoding antigens of choice into the vector. Viral vector technology also allows the production of modified influenza viral antigens in vivo. These modifications can improve the immunogenicity of the influenza viral proteins or alter the specificity of the immune response. In this review, we discuss reports on vectored influenza vaccines and discuss their advantages and disadvantages.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: influenza viruses, while expressed in the context of the vector that can improve immunogenicity. In addition, a vectored vaccine often enables delivery of the vaccine to sites of inductive immunity such as the respiratory tract enabling protection from influenza virus infection. Moreover, the ability to readily manipulate virus vectors to produce novel influenza vaccines may provide the quickest path toward a universal vaccine protecting against all influenza viruses. This review will discuss experimental virus-vectored vaccines for use in humans, comparing them to licensed vaccines and the hurdles faced for licensure of these next-generation influenza virus vaccines.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: helps sustain a durable memory immune response, even augmenting the selection of higher affinity antibody secreting cells. The enhanced memory response is in part linked to the intrinsic augmentation of immunity induced by the vector. Thus, for weaker antigens typical of HA, vectored vaccines have the capacity to overcome real limitations in achieving robust and durable protection." ]

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

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Viral vector-based influenza vaccines\nPassage: viral vectors can easily be propagated to high virus titers and it is relatively easy to insert genes encoding antigens of choice into the vector. Viral vector technology also allows the production of modified influenza viral antigens in vivo. These modifications can improve the immunogenicity of the influenza viral proteins or alter the specificity of the immune response. In this review, we discuss reports on vectored influenza vaccines and discuss their advantages and disadvantages.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: influenza viruses, while expressed in the context of the vector that can improve immunogenicity. In addition, a vectored vaccine often enables delivery of the vaccine to sites of inductive immunity such as the respiratory tract enabling protection from influenza virus infection. Moreover, the ability to readily manipulate virus vectors to produce novel influenza vaccines may provide the quickest path toward a universal vaccine protecting against all influenza viruses. This review will discuss experimental virus-vectored vaccines for use in humans, comparing them to licensed vaccines and the hurdles faced for licensure of these next-generation influenza virus vaccines.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: helps sustain a durable memory immune response, even augmenting the selection of higher affinity antibody secreting cells. The enhanced memory response is in part linked to the intrinsic augmentation of immunity induced by the vector. Thus, for weaker antigens typical of HA, vectored vaccines have the capacity to overcome real limitations in achieving robust and durable protection." ]

[ [ "1a", "Title: Viral vector-based influenza vaccines" ], [ "1b", "Passage: viral vectors can easily be propagated to high virus titers and it is relatively easy to insert genes encoding antigens of choice into the vector." ], [ "1c", "Viral vector technology also allows the production of modified influenza viral antigens in vivo." ], [ "1d", "These modifications can improve the immunogenicity of the influenza viral proteins or alter the specificity of the immune response." ], [ "1e", "In this review, we discuss reports on vectored influenza vaccines and discuss their advantages and disadvantages." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Viral vector-based influenza vaccines\nPassage: viral vectors can easily be propagated to high virus titers and it is relatively easy to insert genes encoding antigens of choice into the vector. Viral vector technology also allows the production of modified influenza viral antigens in vivo. These modifications can improve the immunogenicity of the influenza viral proteins or alter the specificity of the immune response. In this review, we discuss reports on vectored influenza vaccines and discuss their advantages and disadvantages.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: influenza viruses, while expressed in the context of the vector that can improve immunogenicity. In addition, a vectored vaccine often enables delivery of the vaccine to sites of inductive immunity such as the respiratory tract enabling protection from influenza virus infection. Moreover, the ability to readily manipulate virus vectors to produce novel influenza vaccines may provide the quickest path toward a universal vaccine protecting against all influenza viruses. This review will discuss experimental virus-vectored vaccines for use in humans, comparing them to licensed vaccines and the hurdles faced for licensure of these next-generation influenza virus vaccines.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: helps sustain a durable memory immune response, even augmenting the selection of higher affinity antibody secreting cells. The enhanced memory response is in part linked to the intrinsic augmentation of immunity induced by the vector. Thus, for weaker antigens typical of HA, vectored vaccines have the capacity to overcome real limitations in achieving robust and durable protection." ]

[ [ "2a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "2b", "Passage: influenza viruses, while expressed in the context of the vector that can improve immunogenicity." ], [ "2c", "In addition, a vectored vaccine often enables delivery of the vaccine to sites of inductive immunity such as the respiratory tract enabling protection from influenza virus infection." ], [ "2d", "Moreover, the ability to readily manipulate virus vectors to produce novel influenza vaccines may provide the quickest path toward a universal vaccine protecting against all influenza viruses." ], [ "2e", "This review will discuss experimental virus-vectored vaccines for use in humans, comparing them to licensed vaccines and the hurdles faced for licensure of these next-generation influenza virus vaccines." ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: However, before vectored vaccines can be used in the human population they need to satisfy several important criteria. Safety is a major concern, as even a low level of toxicity is unacceptable . Secondly, a vaccine should be inexpensive, so that it can be administered to a large population at minimal cost, and this is particularly important in resource-poor countries . Similar constraints apply to veterinary vaccines, with cost often an even more important consideration. Finally, long-lasting cellular and humoral immune responses to the vectored antigen must be induced following administration of these vaccines, preferably with a single dose .", "Title: Viral vector-based influenza vaccines\nPassage: viral vectors can easily be propagated to high virus titers and it is relatively easy to insert genes encoding antigens of choice into the vector. Viral vector technology also allows the production of modified influenza viral antigens in vivo. These modifications can improve the immunogenicity of the influenza viral proteins or alter the specificity of the immune response. In this review, we discuss reports on vectored influenza vaccines and discuss their advantages and disadvantages.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: influenza viruses, while expressed in the context of the vector that can improve immunogenicity. In addition, a vectored vaccine often enables delivery of the vaccine to sites of inductive immunity such as the respiratory tract enabling protection from influenza virus infection. Moreover, the ability to readily manipulate virus vectors to produce novel influenza vaccines may provide the quickest path toward a universal vaccine protecting against all influenza viruses. This review will discuss experimental virus-vectored vaccines for use in humans, comparing them to licensed vaccines and the hurdles faced for licensure of these next-generation influenza virus vaccines.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: helps sustain a durable memory immune response, even augmenting the selection of higher affinity antibody secreting cells. The enhanced memory response is in part linked to the intrinsic augmentation of immunity induced by the vector. Thus, for weaker antigens typical of HA, vectored vaccines have the capacity to overcome real limitations in achieving robust and durable protection." ]

[ [ "3a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "3b", "Passage: helps sustain a durable memory immune response, even augmenting the selection of higher affinity antibody secreting cells." ], [ "3c", "The enhanced memory response is in part linked to the intrinsic augmentation of immunity induced by the vector." ], [ "3d", "Thus, for weaker antigens typical of HA, vectored vaccines have the capacity to overcome real limitations in achieving robust and durable protection." ] ]

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Childhood pneumonia can also lead to significant morbidity and chronic disease. Early life pneumonia can impair longterm lung health by decreasing lung function . Severe or recurrent pneumonia can have a worse effect on lung function; increasing evidence suggests that chronic obstructive pulmonary disease might be related to early childhood pneumonia . A meta-analysis of the risk of long-term outcomes after childhood pneumonia categorized chronic respiratory sequelae into major and minor groups . The risk of developing at least one of the major sequelae was estimated as 6% after an ambulatory pneumonia event and 14% after an episode of hospitalized", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Childhood pneumonia and clinically severe disease result from a complex interaction of host and environmental risk factors . Because of the effectiveness of pneumococcal conjugate vaccination and Haemophilus influenzae type B conjugate vaccination for prevention of radiologic and clinical pneumonia, incomplete or inadequate vaccination must be considered as a major preventable risk factor for childhood pneumonia. Other risk factors include low birth weight, which is associated with 3.2 times increased odds of severe pneumonia in low-and middle-income countries, and 1.8 times increased odds in high-income countries . Similarly, lack of exclusive breastfeeding for the first 4 months of life increases", "Title: The impact of respiratory viruses on lung health after preterm birth\nPassage: hospitalisation for another respiratory illnesses as well as a more than 4-fold increased risk of subsequent asthma .", "Title: Risk factors for severe acute lower respiratory infections in children – a systematic review and meta-analysis\nPassage: Pneumonia is one of the leading causes of morbidity and mortality globally in young children aged below five years . It is estimated that approximately 156 million cases of pneumonia occur annually in young children, resulting in approximately 1.4 million deaths . Over the past two decades, there were several attempts to investigate an association between various risk factors and pneumonia in young children, but no systematic reviews of published literature assessed the strength of association between the suspected risk factors and pneumonia. In this study, we aimed to assess the quality of available evidence and present summary estimates of" ]

[ [ "0a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "0b", "Passage: Childhood pneumonia can also lead to significant morbidity and chronic disease." ], [ "0c", "Early life pneumonia can impair longterm lung health by decreasing lung function ." ], [ "0d", "Severe or recurrent pneumonia can have a worse effect on lung function; increasing evidence suggests that chronic obstructive pulmonary disease might be related to early childhood pneumonia ." ], [ "0e", "A meta-analysis of the risk of long-term outcomes after childhood pneumonia categorized chronic respiratory sequelae into major and minor groups ." ], [ "0f", "The risk of developing at least one of the major sequelae was estimated as 6% after an ambulatory pneumonia event and 14% after an episode of hospitalized" ] ]

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Childhood pneumonia can also lead to significant morbidity and chronic disease. Early life pneumonia can impair longterm lung health by decreasing lung function . Severe or recurrent pneumonia can have a worse effect on lung function; increasing evidence suggests that chronic obstructive pulmonary disease might be related to early childhood pneumonia . A meta-analysis of the risk of long-term outcomes after childhood pneumonia categorized chronic respiratory sequelae into major and minor groups . The risk of developing at least one of the major sequelae was estimated as 6% after an ambulatory pneumonia event and 14% after an episode of hospitalized", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Childhood pneumonia and clinically severe disease result from a complex interaction of host and environmental risk factors . Because of the effectiveness of pneumococcal conjugate vaccination and Haemophilus influenzae type B conjugate vaccination for prevention of radiologic and clinical pneumonia, incomplete or inadequate vaccination must be considered as a major preventable risk factor for childhood pneumonia. Other risk factors include low birth weight, which is associated with 3.2 times increased odds of severe pneumonia in low-and middle-income countries, and 1.8 times increased odds in high-income countries . Similarly, lack of exclusive breastfeeding for the first 4 months of life increases", "Title: The impact of respiratory viruses on lung health after preterm birth\nPassage: hospitalisation for another respiratory illnesses as well as a more than 4-fold increased risk of subsequent asthma .", "Title: Risk factors for severe acute lower respiratory infections in children – a systematic review and meta-analysis\nPassage: Pneumonia is one of the leading causes of morbidity and mortality globally in young children aged below five years . It is estimated that approximately 156 million cases of pneumonia occur annually in young children, resulting in approximately 1.4 million deaths . Over the past two decades, there were several attempts to investigate an association between various risk factors and pneumonia in young children, but no systematic reviews of published literature assessed the strength of association between the suspected risk factors and pneumonia. In this study, we aimed to assess the quality of available evidence and present summary estimates of" ]

[ [ "2a", "Title: The impact of respiratory viruses on lung health after preterm birth" ], [ "2b", "Passage: hospitalisation for another respiratory illnesses as well as a more than 4-fold increased risk of subsequent asthma ." ] ]

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

[ "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: Between September 10, 2009 and August 29, 2011, 71,865 body temperatures were electronically recorded by the automatic data logging system and met the inclusion criteria . During the study period, there were 110,465 visits to the emergency department, 37 % of which resulted in admission .", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: The mean body temperature was 98.1°F with a standard deviation of 1.1°F . The median body temperature was 98.0°F with an interquartile range of 97.4-98.7°F . These values are consistent with previous reports is not the mean human body temperature, despite widespread belief ). Overall, 2073 fevers were observed, constituting 2.6 % of the temperature recordings . A mean of 1.0 fevers was measured per thermometer each day .", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: this period : 1.08, range, 1-5), with exceptions for general maintenance. Thermometers were checked, time-stamped measurements were collected, and maintenance was performed on a roughly biweekly basis. Three thermometers were located at triage stations and one was located on a rolling unit. The data-logging thermometers were used as a surrogate to investigate the capabilities of real-time data reporting with networked wireless thermometers.", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: Additional Figure 1 presents the results of applying a Bayesian outbreak detection algorithm to the number of fevers measured in the ED per thermometer. The light blue and dark blue areas show the weekly and daily rates of fevers, respectively. For example, data from the first week of August 2011 show that around 5 fevers were measured per thermometer. The outbreak detection algorithm produces an epidemic threshold that is used to judge whether an outbreak is detected. When the observed fever rates exceed this threshold, an alarm is declared . Using fever rates from the Boston ED, the algorithm successfully" ]

[ [ "0a", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak" ], [ "0b", "Passage: Between September 10, 2009 and August 29, 2011, 71,865 body temperatures were electronically recorded by the automatic data logging system and met the inclusion criteria ." ], [ "0c", "During the study period, there were 110,465 visits to the emergency department, 37 % of which resulted in admission ." ] ]

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

[ "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: Between September 10, 2009 and August 29, 2011, 71,865 body temperatures were electronically recorded by the automatic data logging system and met the inclusion criteria . During the study period, there were 110,465 visits to the emergency department, 37 % of which resulted in admission .", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: The mean body temperature was 98.1°F with a standard deviation of 1.1°F . The median body temperature was 98.0°F with an interquartile range of 97.4-98.7°F . These values are consistent with previous reports is not the mean human body temperature, despite widespread belief ). Overall, 2073 fevers were observed, constituting 2.6 % of the temperature recordings . A mean of 1.0 fevers was measured per thermometer each day .", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: this period : 1.08, range, 1-5), with exceptions for general maintenance. Thermometers were checked, time-stamped measurements were collected, and maintenance was performed on a roughly biweekly basis. Three thermometers were located at triage stations and one was located on a rolling unit. The data-logging thermometers were used as a surrogate to investigate the capabilities of real-time data reporting with networked wireless thermometers.", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak\nPassage: Additional Figure 1 presents the results of applying a Bayesian outbreak detection algorithm to the number of fevers measured in the ED per thermometer. The light blue and dark blue areas show the weekly and daily rates of fevers, respectively. For example, data from the first week of August 2011 show that around 5 fevers were measured per thermometer. The outbreak detection algorithm produces an epidemic threshold that is used to judge whether an outbreak is detected. When the observed fever rates exceed this threshold, an alarm is declared . Using fever rates from the Boston ED, the algorithm successfully" ]

[ [ "1a", "Title: Human temperatures for syndromic surveillance in the emergency department: data from the autumn wave of the 2009 swine flu (H1N1) pandemic and a seasonal influenza outbreak" ], [ "1b", "Passage: The mean body temperature was 98.1°F with a standard deviation of 1.1°F ." ], [ "1c", "The median body temperature was 98.0°F with an interquartile range of 97.4-98.7°F ." ], [ "1d", "These values are consistent with previous reports is not the mean human body temperature, despite widespread belief )." ], [ "1e", "Overall, 2073 fevers were observed, constituting 2.6 % of the temperature recordings ." ], [ "1f", "A mean of 1.0 fevers was measured per thermometer each day ." ] ]

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

[ "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1\nPassage: Text: Without specific interventions, the rate of HIV-1 mother-tochild transmission is approximately 15-45% . UNAIDS estimates that last year alone, more than 400,000 children were infected worldwide, mostly through MTCT and 90% of them lived in sub-Saharan Africa. In the most heavilyaffected countries, such as Zimbabwe, HIV-1 is responsible for one third of all deaths among children under the age of five. MTCT of HIV-1 can occur during pregnancy , delivery or breastfeeding . High maternal viral load, low CD4 cells count, vaginal delivery, low gestational age have all been identified as independent factors associated with MTCT of HIV-1 .", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: The prevalence of HIV among exposed infants can reach up to 45% if left without PMTCT interventions. Nearly two-third of pregnant women living with HIV in the Middle East and North Africa passed the virus onto their infants in the year 2015 alone 10, 11] . In Ethiopia, vertical transmission, which accounted for more than 90% of pediatric HIV, is a very critical issue. Accordingly, HIV related estimates and projections showed that the national estimate of MTCT rate was 25% in 2013 and 17% in 2015. This high magnitude makes HIV/AIDS one of the top priorities of the Health Sector", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: In 2010, UNAIDS estimates that 390,000 children acquired HIV-1-infection worldwide mostly through mother-to-child transmission . Overall transmission rates in the absence of any intervention vary from 12 to 42%. Although antiretroviral therapy can reduce MTCT to as low as 2% , limited access to timely diagnostics and drugs in resource-poor settings blunts the potential impact of this strategy. A better understanding of the mechanisms acting in MTCT of HIV-1 is crucial for the design of interventions other than ART for transmission prevention.", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: Although timely HIV testing of infants is not yet optimal, some strategies and solutions have proven successful, including community-based interventions and support and education of mothers. The Joint United Nations Program on HIV/AIDS 2016-2021 strategy set about ten targets to end the AIDS epidemic by 2030; one of the targets is to make new HIV infections among children zero and improve the health and wellbeing of mothers. The global plan to eliminate new HIV infections among children and improve the health of mothers targets to reduce the MTCT rate to less than 5% among breast feeding population and to less" ]

[ [ "0a", "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1" ], [ "0b", "Passage: Text: Without specific interventions, the rate of HIV-1 mother-tochild transmission is approximately 15-45% ." ], [ "0c", "UNAIDS estimates that last year alone, more than 400,000 children were infected worldwide, mostly through MTCT and 90% of them lived in sub-Saharan Africa." ], [ "0d", "In the most heavilyaffected countries, such as Zimbabwe, HIV-1 is responsible for one third of all deaths among children under the age of five." ], [ "0e", "MTCT of HIV-1 can occur during pregnancy , delivery or breastfeeding ." ], [ "0f", "High maternal viral load, low CD4 cells count, vaginal delivery, low gestational age have all been identified as independent factors associated with MTCT of HIV-1 ." ] ]

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

[ "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1\nPassage: Text: Without specific interventions, the rate of HIV-1 mother-tochild transmission is approximately 15-45% . UNAIDS estimates that last year alone, more than 400,000 children were infected worldwide, mostly through MTCT and 90% of them lived in sub-Saharan Africa. In the most heavilyaffected countries, such as Zimbabwe, HIV-1 is responsible for one third of all deaths among children under the age of five. MTCT of HIV-1 can occur during pregnancy , delivery or breastfeeding . High maternal viral load, low CD4 cells count, vaginal delivery, low gestational age have all been identified as independent factors associated with MTCT of HIV-1 .", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: The prevalence of HIV among exposed infants can reach up to 45% if left without PMTCT interventions. Nearly two-third of pregnant women living with HIV in the Middle East and North Africa passed the virus onto their infants in the year 2015 alone 10, 11] . In Ethiopia, vertical transmission, which accounted for more than 90% of pediatric HIV, is a very critical issue. Accordingly, HIV related estimates and projections showed that the national estimate of MTCT rate was 25% in 2013 and 17% in 2015. This high magnitude makes HIV/AIDS one of the top priorities of the Health Sector", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: In 2010, UNAIDS estimates that 390,000 children acquired HIV-1-infection worldwide mostly through mother-to-child transmission . Overall transmission rates in the absence of any intervention vary from 12 to 42%. Although antiretroviral therapy can reduce MTCT to as low as 2% , limited access to timely diagnostics and drugs in resource-poor settings blunts the potential impact of this strategy. A better understanding of the mechanisms acting in MTCT of HIV-1 is crucial for the design of interventions other than ART for transmission prevention.", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: Although timely HIV testing of infants is not yet optimal, some strategies and solutions have proven successful, including community-based interventions and support and education of mothers. The Joint United Nations Program on HIV/AIDS 2016-2021 strategy set about ten targets to end the AIDS epidemic by 2030; one of the targets is to make new HIV infections among children zero and improve the health and wellbeing of mothers. The global plan to eliminate new HIV infections among children and improve the health of mothers targets to reduce the MTCT rate to less than 5% among breast feeding population and to less" ]

[ [ "1a", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study" ], [ "1b", "Passage: The prevalence of HIV among exposed infants can reach up to 45% if left without PMTCT interventions." ], [ "1c", "Nearly two-third of pregnant women living with HIV in the Middle East and North Africa passed the virus onto their infants in the year 2015 alone 10, 11] ." ], [ "1d", "In Ethiopia, vertical transmission, which accounted for more than 90% of pediatric HIV, is a very critical issue." ], [ "1e", "Accordingly, HIV related estimates and projections showed that the national estimate of MTCT rate was 25% in 2013 and 17% in 2015." ], [ "1f", "This high magnitude makes HIV/AIDS one of the top priorities of the Health Sector" ] ]

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

[ "Title: Functional Genetic Variants in DC-SIGNR Are Associated with Mother-to-Child Transmission of HIV-1\nPassage: Text: Without specific interventions, the rate of HIV-1 mother-tochild transmission is approximately 15-45% . UNAIDS estimates that last year alone, more than 400,000 children were infected worldwide, mostly through MTCT and 90% of them lived in sub-Saharan Africa. In the most heavilyaffected countries, such as Zimbabwe, HIV-1 is responsible for one third of all deaths among children under the age of five. MTCT of HIV-1 can occur during pregnancy , delivery or breastfeeding . High maternal viral load, low CD4 cells count, vaginal delivery, low gestational age have all been identified as independent factors associated with MTCT of HIV-1 .", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: The prevalence of HIV among exposed infants can reach up to 45% if left without PMTCT interventions. Nearly two-third of pregnant women living with HIV in the Middle East and North Africa passed the virus onto their infants in the year 2015 alone 10, 11] . In Ethiopia, vertical transmission, which accounted for more than 90% of pediatric HIV, is a very critical issue. Accordingly, HIV related estimates and projections showed that the national estimate of MTCT rate was 25% in 2013 and 17% in 2015. This high magnitude makes HIV/AIDS one of the top priorities of the Health Sector", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission\nPassage: In 2010, UNAIDS estimates that 390,000 children acquired HIV-1-infection worldwide mostly through mother-to-child transmission . Overall transmission rates in the absence of any intervention vary from 12 to 42%. Although antiretroviral therapy can reduce MTCT to as low as 2% , limited access to timely diagnostics and drugs in resource-poor settings blunts the potential impact of this strategy. A better understanding of the mechanisms acting in MTCT of HIV-1 is crucial for the design of interventions other than ART for transmission prevention.", "Title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study\nPassage: Although timely HIV testing of infants is not yet optimal, some strategies and solutions have proven successful, including community-based interventions and support and education of mothers. The Joint United Nations Program on HIV/AIDS 2016-2021 strategy set about ten targets to end the AIDS epidemic by 2030; one of the targets is to make new HIV infections among children zero and improve the health and wellbeing of mothers. The global plan to eliminate new HIV infections among children and improve the health of mothers targets to reduce the MTCT rate to less than 5% among breast feeding population and to less" ]

[ [ "2a", "Title: Naturally-Occurring Genetic Variants in Human DC-SIGN Increase HIV-1 Capture, Cell-Transfer and Risk of Mother-To-Child Transmission" ], [ "2b", "Passage: In 2010, UNAIDS estimates that 390,000 children acquired HIV-1-infection worldwide mostly through mother-to-child transmission ." ], [ "2c", "Overall transmission rates in the absence of any intervention vary from 12 to 42%." ], [ "2d", "Although antiretroviral therapy can reduce MTCT to as low as 2% , limited access to timely diagnostics and drugs in resource-poor settings blunts the potential impact of this strategy." ], [ "2e", "A better understanding of the mechanisms acting in MTCT of HIV-1 is crucial for the design of interventions other than ART for transmission prevention." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Contact tracing is a non-pharmaceutical social distancing measure for limiting the spread of influenza by identifying people who may have come into contact with an infected person, and giving them prophylaxis or issuing them with quarantine orders. It has been shown theoretically that through contact tracing, major outbreaks can be reduced significantly at a small additional cost . We divided the contacts of each patient into one of the following three categories: household, workplace and friends. When contact tracing for a class has been activated, i.e. the index case is being tested positive for pandemic influenza, all the contacts in", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: Capacity problems may reduce the effectiveness of iterative tracing if effort is directed towards secondary contactees prior to primary contactees; on the other hand, if not quarantine but vaccination is applied, it might be worthwhile to traced contactees of contactees even without diagnostic tests .", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: A relatively easy way to increase the proportion of traced contacts for respiratory pathogens like influenza might be quarantine of households. This can be effective if households are the prime location for spread of the infection; specific models taking into account the contact structures within and between households will be better-suited to study this strategy.", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: However, if the latent period is short, as seen for influenza and possibly FMD, quarantine will occur too late to prevent all infections and more contacts need to be traced." ]

[ [ "1a", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics" ], [ "1b", "Passage: Capacity problems may reduce the effectiveness of iterative tracing if effort is directed towards secondary contactees prior to primary contactees; on the other hand, if not quarantine but vaccination is applied, it might be worthwhile to traced contactees of contactees even without diagnostic tests ." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Contact tracing is a non-pharmaceutical social distancing measure for limiting the spread of influenza by identifying people who may have come into contact with an infected person, and giving them prophylaxis or issuing them with quarantine orders. It has been shown theoretically that through contact tracing, major outbreaks can be reduced significantly at a small additional cost . We divided the contacts of each patient into one of the following three categories: household, workplace and friends. When contact tracing for a class has been activated, i.e. the index case is being tested positive for pandemic influenza, all the contacts in", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: Capacity problems may reduce the effectiveness of iterative tracing if effort is directed towards secondary contactees prior to primary contactees; on the other hand, if not quarantine but vaccination is applied, it might be worthwhile to traced contactees of contactees even without diagnostic tests .", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: A relatively easy way to increase the proportion of traced contacts for respiratory pathogens like influenza might be quarantine of households. This can be effective if households are the prime location for spread of the infection; specific models taking into account the contact structures within and between households will be better-suited to study this strategy.", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: However, if the latent period is short, as seen for influenza and possibly FMD, quarantine will occur too late to prevent all infections and more contacts need to be traced." ]

[ [ "2a", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics" ], [ "2b", "Passage: A relatively easy way to increase the proportion of traced contacts for respiratory pathogens like influenza might be quarantine of households." ], [ "2c", "This can be effective if households are the prime location for spread of the infection; specific models taking into account the contact structures within and between households will be better-suited to study this strategy." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Contact tracing is a non-pharmaceutical social distancing measure for limiting the spread of influenza by identifying people who may have come into contact with an infected person, and giving them prophylaxis or issuing them with quarantine orders. It has been shown theoretically that through contact tracing, major outbreaks can be reduced significantly at a small additional cost . We divided the contacts of each patient into one of the following three categories: household, workplace and friends. When contact tracing for a class has been activated, i.e. the index case is being tested positive for pandemic influenza, all the contacts in", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: Capacity problems may reduce the effectiveness of iterative tracing if effort is directed towards secondary contactees prior to primary contactees; on the other hand, if not quarantine but vaccination is applied, it might be worthwhile to traced contactees of contactees even without diagnostic tests .", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: A relatively easy way to increase the proportion of traced contacts for respiratory pathogens like influenza might be quarantine of households. This can be effective if households are the prime location for spread of the infection; specific models taking into account the contact structures within and between households will be better-suited to study this strategy.", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics\nPassage: However, if the latent period is short, as seen for influenza and possibly FMD, quarantine will occur too late to prevent all infections and more contacts need to be traced." ]

[ [ "3a", "Title: The Effectiveness of Contact Tracing in Emerging Epidemics" ], [ "3b", "Passage: However, if the latent period is short, as seen for influenza and possibly FMD, quarantine will occur too late to prevent all infections and more contacts need to be traced." ] ]

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

[ "Title: Affect of Early Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infections\nPassage: disease . The compliment subunit C5a plays a role in neutrophil recruitment to the mouse lung following IAV infection and may be a potent inducer of hyperoxia-mediated lung injury via recruitment of macrophages, neutrophils, and lymphocytes, and increased expression of IL-6, TNF-α, and MCP-1 occurs . Furthermore, C5a has been shown to increase TGF-β1 in primary human small airway epithelial cells, which could then contribute to the development of fibrosis . Thus, multiple factors could lead to the accumulation of C5a, which could induce inflammation in the lungs of preterm infants. Some of these factors have been proposed targets to", "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Treatment of Paraquat-Induced Lung Injury With an Anti-C5a Antibody: Potential Clinical Application*\nPassage: T he complement system is a pivotal component of innate immune system and bridge of the innate and adaptive immune responses. However, once dysregulated, it can turn against host cells and is involved in numerous diseases and pathologic conditions such as inflammatory diseases, autoimmune diseases, neurodegenerative diseases, and infectious diseases . Complement activation products such as C5a play an important role in mediating proinflammatory activity and regulating modulatory signals . Thus, regulation of complement activation is a promising treatment strategy . Regulating C5a or C5aR has proven beneficial in animal models of transplantation, sepsis, arthritis, and cancer . DOI: 10.1097/CCM.0000000000002950", "Title: New Insights of an Old Defense System: Structure, Function, and Clinical Relevance of the Complement System\nPassage: On a cellular level, it has been shown that C5a effectively interacts with cells and modulates their apoptosis rate. Interestingly, the effects on programmed cell death seem to be cell dependent, with a higher rate of apoptosis in thymocytes but decreased apoptosis in neutrophils . Overall, the C5ainduced changes point toward an enhanced susceptibility toward infections, as well as to a prolonged presence of neutrophils resulting in an exaggerated inflammatory response and host damage." ]

[ [ "0a", "Title: Affect of Early Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infections" ], [ "0b", "Passage: disease ." ], [ "0c", "The compliment subunit C5a plays a role in neutrophil recruitment to the mouse lung following IAV infection and may be a potent inducer of hyperoxia-mediated lung injury via recruitment of macrophages, neutrophils, and lymphocytes, and increased expression of IL-6, TNF-α, and MCP-1 occurs ." ], [ "0d", "Furthermore, C5a has been shown to increase TGF-β1 in primary human small airway epithelial cells, which could then contribute to the development of fibrosis ." ], [ "0e", "Thus, multiple factors could lead to the accumulation of C5a, which could induce inflammation in the lungs of preterm infants." ], [ "0f", "Some of these factors have been proposed targets to" ] ]

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

[ "Title: Affect of Early Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infections\nPassage: disease . The compliment subunit C5a plays a role in neutrophil recruitment to the mouse lung following IAV infection and may be a potent inducer of hyperoxia-mediated lung injury via recruitment of macrophages, neutrophils, and lymphocytes, and increased expression of IL-6, TNF-α, and MCP-1 occurs . Furthermore, C5a has been shown to increase TGF-β1 in primary human small airway epithelial cells, which could then contribute to the development of fibrosis . Thus, multiple factors could lead to the accumulation of C5a, which could induce inflammation in the lungs of preterm infants. Some of these factors have been proposed targets to", "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Treatment of Paraquat-Induced Lung Injury With an Anti-C5a Antibody: Potential Clinical Application*\nPassage: T he complement system is a pivotal component of innate immune system and bridge of the innate and adaptive immune responses. However, once dysregulated, it can turn against host cells and is involved in numerous diseases and pathologic conditions such as inflammatory diseases, autoimmune diseases, neurodegenerative diseases, and infectious diseases . Complement activation products such as C5a play an important role in mediating proinflammatory activity and regulating modulatory signals . Thus, regulation of complement activation is a promising treatment strategy . Regulating C5a or C5aR has proven beneficial in animal models of transplantation, sepsis, arthritis, and cancer . DOI: 10.1097/CCM.0000000000002950", "Title: New Insights of an Old Defense System: Structure, Function, and Clinical Relevance of the Complement System\nPassage: On a cellular level, it has been shown that C5a effectively interacts with cells and modulates their apoptosis rate. Interestingly, the effects on programmed cell death seem to be cell dependent, with a higher rate of apoptosis in thymocytes but decreased apoptosis in neutrophils . Overall, the C5ainduced changes point toward an enhanced susceptibility toward infections, as well as to a prolonged presence of neutrophils resulting in an exaggerated inflammatory response and host damage." ]

[ [ "1a", "Title: Host resilience to emerging coronaviruses" ], [ "1b", "Passage: Corticosteroids are broadly immunosuppressive and have many physiological effects ." ], [ "1c", "Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections." ], [ "1d", "A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV ." ], [ "1e", "Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection ." ], [ "1f", "Other immunomodulators include celecoxib, mesalazine and eritoran ." ], [ "1g", "Another class of drugs that have been suggested are statins." ], [ "1h", "They act to stabilize the activation of aspects of the innate immune" ] ]

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

[ "Title: Affect of Early Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infections\nPassage: disease . The compliment subunit C5a plays a role in neutrophil recruitment to the mouse lung following IAV infection and may be a potent inducer of hyperoxia-mediated lung injury via recruitment of macrophages, neutrophils, and lymphocytes, and increased expression of IL-6, TNF-α, and MCP-1 occurs . Furthermore, C5a has been shown to increase TGF-β1 in primary human small airway epithelial cells, which could then contribute to the development of fibrosis . Thus, multiple factors could lead to the accumulation of C5a, which could induce inflammation in the lungs of preterm infants. Some of these factors have been proposed targets to", "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Treatment of Paraquat-Induced Lung Injury With an Anti-C5a Antibody: Potential Clinical Application*\nPassage: T he complement system is a pivotal component of innate immune system and bridge of the innate and adaptive immune responses. However, once dysregulated, it can turn against host cells and is involved in numerous diseases and pathologic conditions such as inflammatory diseases, autoimmune diseases, neurodegenerative diseases, and infectious diseases . Complement activation products such as C5a play an important role in mediating proinflammatory activity and regulating modulatory signals . Thus, regulation of complement activation is a promising treatment strategy . Regulating C5a or C5aR has proven beneficial in animal models of transplantation, sepsis, arthritis, and cancer . DOI: 10.1097/CCM.0000000000002950", "Title: New Insights of an Old Defense System: Structure, Function, and Clinical Relevance of the Complement System\nPassage: On a cellular level, it has been shown that C5a effectively interacts with cells and modulates their apoptosis rate. Interestingly, the effects on programmed cell death seem to be cell dependent, with a higher rate of apoptosis in thymocytes but decreased apoptosis in neutrophils . Overall, the C5ainduced changes point toward an enhanced susceptibility toward infections, as well as to a prolonged presence of neutrophils resulting in an exaggerated inflammatory response and host damage." ]

[ [ "2a", "Title: Treatment of Paraquat-Induced Lung Injury With an Anti-C5a Antibody: Potential Clinical Application*" ], [ "2b", "Passage: T he complement system is a pivotal component of innate immune system and bridge of the innate and adaptive immune responses." ], [ "2c", "However, once dysregulated, it can turn against host cells and is involved in numerous diseases and pathologic conditions such as inflammatory diseases, autoimmune diseases, neurodegenerative diseases, and infectious diseases ." ], [ "2d", "Complement activation products such as C5a play an important role in mediating proinflammatory activity and regulating modulatory signals ." ], [ "2e", "Thus, regulation of complement activation is a promising treatment strategy ." ], [ "2f", "Regulating C5a or C5aR has proven beneficial in animal models of transplantation, sepsis, arthritis, and cancer . DOI: 10.1097/CCM.0000000000002950" ] ]

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

[ "Title: Affect of Early Life Oxygen Exposure on Proper Lung Development and Response to Respiratory Viral Infections\nPassage: disease . The compliment subunit C5a plays a role in neutrophil recruitment to the mouse lung following IAV infection and may be a potent inducer of hyperoxia-mediated lung injury via recruitment of macrophages, neutrophils, and lymphocytes, and increased expression of IL-6, TNF-α, and MCP-1 occurs . Furthermore, C5a has been shown to increase TGF-β1 in primary human small airway epithelial cells, which could then contribute to the development of fibrosis . Thus, multiple factors could lead to the accumulation of C5a, which could induce inflammation in the lungs of preterm infants. Some of these factors have been proposed targets to", "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Treatment of Paraquat-Induced Lung Injury With an Anti-C5a Antibody: Potential Clinical Application*\nPassage: T he complement system is a pivotal component of innate immune system and bridge of the innate and adaptive immune responses. However, once dysregulated, it can turn against host cells and is involved in numerous diseases and pathologic conditions such as inflammatory diseases, autoimmune diseases, neurodegenerative diseases, and infectious diseases . Complement activation products such as C5a play an important role in mediating proinflammatory activity and regulating modulatory signals . Thus, regulation of complement activation is a promising treatment strategy . Regulating C5a or C5aR has proven beneficial in animal models of transplantation, sepsis, arthritis, and cancer . DOI: 10.1097/CCM.0000000000002950", "Title: New Insights of an Old Defense System: Structure, Function, and Clinical Relevance of the Complement System\nPassage: On a cellular level, it has been shown that C5a effectively interacts with cells and modulates their apoptosis rate. Interestingly, the effects on programmed cell death seem to be cell dependent, with a higher rate of apoptosis in thymocytes but decreased apoptosis in neutrophils . Overall, the C5ainduced changes point toward an enhanced susceptibility toward infections, as well as to a prolonged presence of neutrophils resulting in an exaggerated inflammatory response and host damage." ]

[ [ "3a", "Title: New Insights of an Old Defense System: Structure, Function, and Clinical Relevance of the Complement System" ], [ "3b", "Passage: On a cellular level, it has been shown that C5a effectively interacts with cells and modulates their apoptosis rate." ], [ "3c", "Interestingly, the effects on programmed cell death seem to be cell dependent, with a higher rate of apoptosis in thymocytes but decreased apoptosis in neutrophils ." ], [ "3d", "Overall, the C5ainduced changes point toward an enhanced susceptibility toward infections, as well as to a prolonged presence of neutrophils resulting in an exaggerated inflammatory response and host damage." ] ]

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

[ "Title: Modeling the impact of quarantine during an outbreak of Ebola virus disease\nPassage: To show that all solutions of the model The result below follows from the above analyses.", "Title: Model answers or trivial pursuits? The role of mathematical models in influenza pandemic preparedness planning\nPassage: for showing the effect of mixing in school on earlier transmission to households. The island's school was closed on 31 January. 60 McVernon et al.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: .", "Title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam\nPassage: the fact that in all waves and places the BRT model found the spatial autocorrelation term to have the highest rank of influence. As expected, the relative influence of the autocorrelation term at the national level was higher than at the delta levels . In the GLMM models we found the Akaike Information Criterion using the entire set of 14 variables to be much lower than the AICs of a GLMM model without fixed effects. This indicated that though clustering effects were significant, our theory driven predictor variables improved model performance." ]

[ [ "0a", "Title: Modeling the impact of quarantine during an outbreak of Ebola virus disease" ], [ "0b", "Passage: To show that all solutions of the model The result below follows from the above analyses." ] ]

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

[ "Title: Modeling the impact of quarantine during an outbreak of Ebola virus disease\nPassage: To show that all solutions of the model The result below follows from the above analyses.", "Title: Model answers or trivial pursuits? The role of mathematical models in influenza pandemic preparedness planning\nPassage: for showing the effect of mixing in school on earlier transmission to households. The island's school was closed on 31 January. 60 McVernon et al.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: .", "Title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam\nPassage: the fact that in all waves and places the BRT model found the spatial autocorrelation term to have the highest rank of influence. As expected, the relative influence of the autocorrelation term at the national level was higher than at the delta levels . In the GLMM models we found the Akaike Information Criterion using the entire set of 14 variables to be much lower than the AICs of a GLMM model without fixed effects. This indicated that though clustering effects were significant, our theory driven predictor variables improved model performance." ]

[ [ "1a", "Title: Model answers or trivial pursuits?" ], [ "1b", "The role of mathematical models in influenza pandemic preparedness planning" ], [ "1c", "Passage: for showing the effect of mixing in school on earlier transmission to households." ], [ "1d", "The island's school was closed on 31 January." ], [ "1e", "60 McVernon et al." ] ]

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

[ "Title: Modeling the impact of quarantine during an outbreak of Ebola virus disease\nPassage: To show that all solutions of the model The result below follows from the above analyses.", "Title: Model answers or trivial pursuits? The role of mathematical models in influenza pandemic preparedness planning\nPassage: for showing the effect of mixing in school on earlier transmission to households. The island's school was closed on 31 January. 60 McVernon et al.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: .", "Title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam\nPassage: the fact that in all waves and places the BRT model found the spatial autocorrelation term to have the highest rank of influence. As expected, the relative influence of the autocorrelation term at the national level was higher than at the delta levels . In the GLMM models we found the Akaike Information Criterion using the entire set of 14 variables to be much lower than the AICs of a GLMM model without fixed effects. This indicated that though clustering effects were significant, our theory driven predictor variables improved model performance." ]

[ [ "3a", "Title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam" ], [ "3b", "Passage: the fact that in all waves and places the BRT model found the spatial autocorrelation term to have the highest rank of influence." ], [ "3c", "As expected, the relative influence of the autocorrelation term at the national level was higher than at the delta levels ." ], [ "3d", "In the GLMM models we found the Akaike Information Criterion using the entire set of 14 variables to be much lower than the AICs of a GLMM model without fixed effects." ], [ "3e", "This indicated that though clustering effects were significant, our theory driven predictor variables improved model performance." ] ]

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

[ "Title: The 1918 Influenza Pandemic: Looking Back, Looking Forward\nPassage: In commemoration of the centennial of the 1918 pandemic, the American Journal of Epidemiology has convened a collection of 12 articles that further illuminate the epidemiology of that pandemic and consider whether we would be more prepared if an equally deadly influenza virus were to emerge today. Five of the 12 articles touch on the origins of the 1918 pandemic virus, addressing the role of swine as mixing vessels in this and other pandemic events , the age-specific mortality patterns of the pandemic , and prior population immunity . Others include reports on geographic and social heterogeneities in the pandemic", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The early 20th century was a time of dramatic changes in human use of domestic animals . After centuries of influenza epizootics in equines, the 20th century marked a rapid decline in use of horses for urban transport and farm work. Just as declining densities of horses were breaking the episodic cycles of equine influenza in urban areas, a trend toward high-intensity livestock production was underway . In addition to representing one of the greatest disease events in human history, the Spanish flu pandemic may also mark a turning point in the ecology of influenza and the increasing importance of", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian ." ]

[ [ "0a", "Title: The 1918 Influenza Pandemic: Looking Back, Looking Forward" ], [ "0b", "Passage: In commemoration of the centennial of the 1918 pandemic, the American Journal of Epidemiology has convened a collection of 12 articles that further illuminate the epidemiology of that pandemic and consider whether we would be more prepared if an equally deadly influenza virus were to emerge today." ], [ "0c", "Five of the 12 articles touch on the origins of the 1918 pandemic virus, addressing the role of swine as mixing vessels in this and other pandemic events , the age-specific mortality patterns of the pandemic , and prior population immunity ." ], [ "0d", "Others include reports on geographic and social heterogeneities in the pandemic" ] ]

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

[ "Title: The 1918 Influenza Pandemic: Looking Back, Looking Forward\nPassage: In commemoration of the centennial of the 1918 pandemic, the American Journal of Epidemiology has convened a collection of 12 articles that further illuminate the epidemiology of that pandemic and consider whether we would be more prepared if an equally deadly influenza virus were to emerge today. Five of the 12 articles touch on the origins of the 1918 pandemic virus, addressing the role of swine as mixing vessels in this and other pandemic events , the age-specific mortality patterns of the pandemic , and prior population immunity . Others include reports on geographic and social heterogeneities in the pandemic", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The early 20th century was a time of dramatic changes in human use of domestic animals . After centuries of influenza epizootics in equines, the 20th century marked a rapid decline in use of horses for urban transport and farm work. Just as declining densities of horses were breaking the episodic cycles of equine influenza in urban areas, a trend toward high-intensity livestock production was underway . In addition to representing one of the greatest disease events in human history, the Spanish flu pandemic may also mark a turning point in the ecology of influenza and the increasing importance of", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian ." ]

[ [ "1a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "1b", "Passage: The early 20th century was a time of dramatic changes in human use of domestic animals ." ], [ "1c", "After centuries of influenza epizootics in equines, the 20th century marked a rapid decline in use of horses for urban transport and farm work." ], [ "1d", "Just as declining densities of horses were breaking the episodic cycles of equine influenza in urban areas, a trend toward high-intensity livestock production was underway ." ], [ "1e", "In addition to representing one of the greatest disease events in human history, the Spanish flu pandemic may also mark a turning point in the ecology of influenza and the increasing importance of" ] ]

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

[ "Title: The 1918 Influenza Pandemic: Looking Back, Looking Forward\nPassage: In commemoration of the centennial of the 1918 pandemic, the American Journal of Epidemiology has convened a collection of 12 articles that further illuminate the epidemiology of that pandemic and consider whether we would be more prepared if an equally deadly influenza virus were to emerge today. Five of the 12 articles touch on the origins of the 1918 pandemic virus, addressing the role of swine as mixing vessels in this and other pandemic events , the age-specific mortality patterns of the pandemic , and prior population immunity . Others include reports on geographic and social heterogeneities in the pandemic", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: The early 20th century was a time of dramatic changes in human use of domestic animals . After centuries of influenza epizootics in equines, the 20th century marked a rapid decline in use of horses for urban transport and farm work. Just as declining densities of horses were breaking the episodic cycles of equine influenza in urban areas, a trend toward high-intensity livestock production was underway . In addition to representing one of the greatest disease events in human history, the Spanish flu pandemic may also mark a turning point in the ecology of influenza and the increasing importance of", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: However, to our knowledge, there is no evidence of sustained onward transmission of the 1918 pandemic virus outside of North America, where the virus sustained long-term circulation in pigs and became established as the \"classical\" H1N1 swine influenza virus lineage , which continues to circulate in North American and has been introduced into Asian swine.", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis\nPassage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic . In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian ." ]

[ [ "3a", "Title: Origins of the 1918 Pandemic: Revisiting the Swine “Mixing Vessel” Hypothesis" ], [ "3b", "Passage: Overall, the most parsimonious explanation is that the genes of the 1918 virus transmitted largely from birds to humans at the start of the pandemic, and from humans to swine once the pandemic was widespread in humans, with no role played by swine in the origins of the human pandemic ." ], [ "3c", "In addition to Koen, there is a reference to an infection with influenzalike disease in swine near the China-Russia border during the second global wave of the pandemic during October 1918 and an independent description of influenza in European swine in 1918 by Altmann Aladar, a Hungarian veterinarian ." ] ]

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