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

[ [ "2a", "Title: The Trojan Chicken Study, Minnesota" ], [ "2b", "Passage: This study was reviewed and approved by the University of Iowa's Institutional Review Board and Animal Use and Care Committee." ], [ "2c", "The investigators participated in online human and animal subjects training." ], [ "2d", "Informed consent was sought from participants before they were enrolled." ] ]

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

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

[ [ "3a", "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza" ], [ "3b", "Passage: Students attending the main campus of the university were approached to participate in the study." ], [ "3c", "Two methods were used to identify potential participants." ], [ "3d", "Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate." ], [ "3e", "In the latter half of the study, a snowball approach was used." ], [ "3f", "The snowball approach was adopted due to problems with identifying and recruiting postgraduate students." ], [ "3g", "They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening." ] ]

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

[ "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: The development of antiviral immune responses involves the orchestration of a complex network of innate and adaptive immune cells to promote health over disease. Natural killer cells, plasmacytoid dendritic cells , CD11b and CD8a conventional dendritic cells , B cells, and CD8 T cells have all been demonstrated to be important for the generation of protective immunity to various viral infections . However, how the antiviral defense as a whole is coordinated, and in particular how the functions of different types of immune cells impact the shaping of the global immune response to viruses in vivo, is not thoroughly understood.", "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: To fight viral infections, vertebrates have developed a battery of innate and adaptive immune responses aimed at inhibiting viral replication or at killing infected cells. These responses include the early production of innate antiviral cytokines, especially interferons a and b , and the activation of cytotoxic lymphocytes such as the innate natural killer cells and the adaptive CD8 T cells. While critical for antiviral defense, cytokine or CD8 T cell responses can be detrimental or even fatal to the host when deregulated. Therefore, we need to better understand how the different arms of antiviral immunity are regulated. In particular, NK", "Title: Nanoparticle Vaccines Against Infectious Diseases\nPassage: cells including CD4 + helper T cells secrete different cytokines to modulate the functions of B cells, whereas CD8 + T cells recognize and destroy virally infected cells. Antibodies produced by the B cells can further neutralize the invading microbes or clear infected cell or opsonized pathogens through cell-mediated systems. APCs, in particular dendritic cells and macrophages, migrate through the body to sample, process and present the antigens to T-cells to activate cellular immune responses. These cells express various surface receptors to recognize cognate ligands and danger signals to trigger activation of different signaling pathways that eventually lead to the", "Title: Natural killer cells act as rheostats modulating anti-viral T cells\nPassage: As early as day 6 after medium-dose infection, the proportion and number of interferon-c 1 LCMV-specific CD8 T cells was increased two-to sixfold in mice depleted of NK cells , and antiviral T cells from these mice showed an enhanced ability to co-produce tumour necrosis factor . The number of LCMV epitope NP 396-404 tetramer-binding CD8 T cells in the spleen on day 5 p.i. was increased 4-to 20-fold in NK-cell-depleted mice relative to non-depleted control mice after infection with all doses of virus . The number of virus-specific IFN-c 1 CD4 T cells was also amplified 7-to 20-fold by" ]

[ [ "0a", "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus" ], [ "0b", "Passage: The development of antiviral immune responses involves the orchestration of a complex network of innate and adaptive immune cells to promote health over disease." ], [ "0c", "Natural killer cells, plasmacytoid dendritic cells , CD11b and CD8a conventional dendritic cells , B cells, and CD8 T cells have all been demonstrated to be important for the generation of protective immunity to various viral infections ." ], [ "0d", "However, how the antiviral defense as a whole is coordinated, and in particular how the functions of different types of immune cells impact the shaping of the global immune response to viruses in vivo, is not thoroughly understood." ] ]

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

[ "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: The development of antiviral immune responses involves the orchestration of a complex network of innate and adaptive immune cells to promote health over disease. Natural killer cells, plasmacytoid dendritic cells , CD11b and CD8a conventional dendritic cells , B cells, and CD8 T cells have all been demonstrated to be important for the generation of protective immunity to various viral infections . However, how the antiviral defense as a whole is coordinated, and in particular how the functions of different types of immune cells impact the shaping of the global immune response to viruses in vivo, is not thoroughly understood.", "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: To fight viral infections, vertebrates have developed a battery of innate and adaptive immune responses aimed at inhibiting viral replication or at killing infected cells. These responses include the early production of innate antiviral cytokines, especially interferons a and b , and the activation of cytotoxic lymphocytes such as the innate natural killer cells and the adaptive CD8 T cells. While critical for antiviral defense, cytokine or CD8 T cell responses can be detrimental or even fatal to the host when deregulated. Therefore, we need to better understand how the different arms of antiviral immunity are regulated. In particular, NK", "Title: Nanoparticle Vaccines Against Infectious Diseases\nPassage: cells including CD4 + helper T cells secrete different cytokines to modulate the functions of B cells, whereas CD8 + T cells recognize and destroy virally infected cells. Antibodies produced by the B cells can further neutralize the invading microbes or clear infected cell or opsonized pathogens through cell-mediated systems. APCs, in particular dendritic cells and macrophages, migrate through the body to sample, process and present the antigens to T-cells to activate cellular immune responses. These cells express various surface receptors to recognize cognate ligands and danger signals to trigger activation of different signaling pathways that eventually lead to the", "Title: Natural killer cells act as rheostats modulating anti-viral T cells\nPassage: As early as day 6 after medium-dose infection, the proportion and number of interferon-c 1 LCMV-specific CD8 T cells was increased two-to sixfold in mice depleted of NK cells , and antiviral T cells from these mice showed an enhanced ability to co-produce tumour necrosis factor . The number of LCMV epitope NP 396-404 tetramer-binding CD8 T cells in the spleen on day 5 p.i. was increased 4-to 20-fold in NK-cell-depleted mice relative to non-depleted control mice after infection with all doses of virus . The number of virus-specific IFN-c 1 CD4 T cells was also amplified 7-to 20-fold by" ]

[ [ "1a", "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus" ], [ "1b", "Passage: To fight viral infections, vertebrates have developed a battery of innate and adaptive immune responses aimed at inhibiting viral replication or at killing infected cells." ], [ "1c", "These responses include the early production of innate antiviral cytokines, especially interferons a and b , and the activation of cytotoxic lymphocytes such as the innate natural killer cells and the adaptive CD8 T cells." ], [ "1d", "While critical for antiviral defense, cytokine or CD8 T cell responses can be detrimental or even fatal to the host when deregulated." ], [ "1e", "Therefore, we need to better understand how the different arms of antiviral immunity are regulated." ], [ "1f", "In particular, NK" ] ]

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

[ "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: The development of antiviral immune responses involves the orchestration of a complex network of innate and adaptive immune cells to promote health over disease. Natural killer cells, plasmacytoid dendritic cells , CD11b and CD8a conventional dendritic cells , B cells, and CD8 T cells have all been demonstrated to be important for the generation of protective immunity to various viral infections . However, how the antiviral defense as a whole is coordinated, and in particular how the functions of different types of immune cells impact the shaping of the global immune response to viruses in vivo, is not thoroughly understood.", "Title: Natural Killer Cells Promote Early CD8 T Cell Responses against Cytomegalovirus\nPassage: To fight viral infections, vertebrates have developed a battery of innate and adaptive immune responses aimed at inhibiting viral replication or at killing infected cells. These responses include the early production of innate antiviral cytokines, especially interferons a and b , and the activation of cytotoxic lymphocytes such as the innate natural killer cells and the adaptive CD8 T cells. While critical for antiviral defense, cytokine or CD8 T cell responses can be detrimental or even fatal to the host when deregulated. Therefore, we need to better understand how the different arms of antiviral immunity are regulated. In particular, NK", "Title: Nanoparticle Vaccines Against Infectious Diseases\nPassage: cells including CD4 + helper T cells secrete different cytokines to modulate the functions of B cells, whereas CD8 + T cells recognize and destroy virally infected cells. Antibodies produced by the B cells can further neutralize the invading microbes or clear infected cell or opsonized pathogens through cell-mediated systems. APCs, in particular dendritic cells and macrophages, migrate through the body to sample, process and present the antigens to T-cells to activate cellular immune responses. These cells express various surface receptors to recognize cognate ligands and danger signals to trigger activation of different signaling pathways that eventually lead to the", "Title: Natural killer cells act as rheostats modulating anti-viral T cells\nPassage: As early as day 6 after medium-dose infection, the proportion and number of interferon-c 1 LCMV-specific CD8 T cells was increased two-to sixfold in mice depleted of NK cells , and antiviral T cells from these mice showed an enhanced ability to co-produce tumour necrosis factor . The number of LCMV epitope NP 396-404 tetramer-binding CD8 T cells in the spleen on day 5 p.i. was increased 4-to 20-fold in NK-cell-depleted mice relative to non-depleted control mice after infection with all doses of virus . The number of virus-specific IFN-c 1 CD4 T cells was also amplified 7-to 20-fold by" ]

[ [ "3a", "Title: Natural killer cells act as rheostats modulating anti-viral T cells" ], [ "3b", "Passage: As early as day 6 after medium-dose infection, the proportion and number of interferon-c 1 LCMV-specific CD8 T cells was increased two-to sixfold in mice depleted of NK cells , and antiviral T cells from these mice showed an enhanced ability to co-produce tumour necrosis factor ." ], [ "3c", "The number of LCMV epitope NP 396-404 tetramer-binding CD8 T cells in the spleen on day 5 p.i." ], [ "3d", "was increased 4-to 20-fold in NK-cell-depleted mice relative to non-depleted control mice after infection with all doses of virus ." ], [ "3e", "The number of virus-specific IFN-c 1 CD4 T cells was also amplified 7-to 20-fold by" ] ]

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

[ "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large. It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate. Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender. Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's", "Title: Why language matters: insights and challenges in applying a social determination of health approach in a North-South collaborative research program\nPassage: A comparative analysis of the positive and negative effects of agro-ecological and conventional production systems is underway to consider policy options to promote health equity by ensuring that such factors are considered in food-related decision-making. There are extensive measurement challenges in doing this.", "Title: Australian public health policy in 2003 – 2004\nPassage: the focus on high-visibility programs can demonstrate short-term economic returns.", "Title: Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis\nPassage: on the majority of questions to be rated as 'strong' overall . Greater emphasis was placed upon studies rated as 'strong' or 'moderate' overall within the findings of the review ." ]

[ [ "0a", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study" ], [ "0b", "Passage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large." ], [ "0c", "It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate." ], [ "0d", "Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender." ], [ "0e", "Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's" ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: delivery of vaccine antigens due to their capability to induce robust T cell immune responses . Salmonella is one genus that has been well examined as a vector, building on the extensive research available on the micro-organism's physiology and pathogenesis . There exist several commercial vaccines that are used as anti-Salmonella vaccines in humans and animals . The general strategy for vectoring heterologous antigen is depicted in Fig. 1 . The first clinical trial of a recombinant, which was conducted over 20 years ago using an attenuated Salmonella as a delivery vector, led to the widespread testing of this bacterium", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Salmonella spp. is a Gram-negative bacterium that causes salmonellosis through orofecal routes. As a DNA vaccine carrier, S. enterica serovars Typhimurium is the most widely used Salmonella spp. . This bacterium is suitable for oral administration as its natural infection route. However, it can induce both mucosal and systemic immune responses, activating the humoral and cellular immune systems . As pathogenic bacteria, Salmonella spp. induce the immune response through their lipopolysaccharides and flagellin content on their surface that is recognized as pathogen-associated molecular patterns . Flagellin induces the immune response by binding with Toll-like receptor 5 , whereas LPS binds", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: To summarize, bacterial vectors such as Salmonella and viral vectors such as Ad show great promise as delivery vehicles for heterologous antigens; however, prior exposure to the vector must be considered. By judicious selection of the strain/serotype it will be possible to avoid the negative effects and it may indeed be possible to positively influence the response, particularly for humoral immunity.", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Other bacteria that were developed as DNA vaccine carriers include Listeria monocytogenes , Shigella spp. , and Yersinia enterolica ." ]

[ [ "0a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "0b", "Passage: delivery of vaccine antigens due to their capability to induce robust T cell immune responses ." ], [ "0c", "Salmonella is one genus that has been well examined as a vector, building on the extensive research available on the micro-organism's physiology and pathogenesis ." ], [ "0d", "There exist several commercial vaccines that are used as anti-Salmonella vaccines in humans and animals ." ], [ "0e", "The general strategy for vectoring heterologous antigen is depicted in Fig. 1 ." ], [ "0f", "The first clinical trial of a recombinant, which was conducted over 20 years ago using an attenuated Salmonella as a delivery vector, led to the widespread testing of this bacterium" ] ]

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

[ "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: delivery of vaccine antigens due to their capability to induce robust T cell immune responses . Salmonella is one genus that has been well examined as a vector, building on the extensive research available on the micro-organism's physiology and pathogenesis . There exist several commercial vaccines that are used as anti-Salmonella vaccines in humans and animals . The general strategy for vectoring heterologous antigen is depicted in Fig. 1 . The first clinical trial of a recombinant, which was conducted over 20 years ago using an attenuated Salmonella as a delivery vector, led to the widespread testing of this bacterium", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Salmonella spp. is a Gram-negative bacterium that causes salmonellosis through orofecal routes. As a DNA vaccine carrier, S. enterica serovars Typhimurium is the most widely used Salmonella spp. . This bacterium is suitable for oral administration as its natural infection route. However, it can induce both mucosal and systemic immune responses, activating the humoral and cellular immune systems . As pathogenic bacteria, Salmonella spp. induce the immune response through their lipopolysaccharides and flagellin content on their surface that is recognized as pathogen-associated molecular patterns . Flagellin induces the immune response by binding with Toll-like receptor 5 , whereas LPS binds", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: To summarize, bacterial vectors such as Salmonella and viral vectors such as Ad show great promise as delivery vehicles for heterologous antigens; however, prior exposure to the vector must be considered. By judicious selection of the strain/serotype it will be possible to avoid the negative effects and it may indeed be possible to positively influence the response, particularly for humoral immunity.", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Other bacteria that were developed as DNA vaccine carriers include Listeria monocytogenes , Shigella spp. , and Yersinia enterolica ." ]

[ [ "1a", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System" ], [ "1b", "Passage: Salmonella spp." ], [ "1c", "is a Gram-negative bacterium that causes salmonellosis through orofecal routes." ], [ "1d", "As a DNA vaccine carrier, S. enterica serovars Typhimurium is the most widely used Salmonella spp. ." ], [ "1e", "This bacterium is suitable for oral administration as its natural infection route." ], [ "1f", "However, it can induce both mucosal and systemic immune responses, activating the humoral and cellular immune systems ." ], [ "1g", "As pathogenic bacteria, Salmonella spp." ], [ "1h", "induce the immune response through their lipopolysaccharides and flagellin content on their surface that is recognized as pathogen-associated molecular patterns ." ], [ "1i", "Flagellin induces the immune response by binding with Toll-like receptor 5 , whereas LPS binds" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients . In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV . Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Orf8 orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain fulllength orf8 . However, a 29-nucleotide deletion,", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 ). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: infections and 800 deaths, and Middle East respiratory syndrome CoV which has caused a persistent epidemic in the Arabian Peninsula since 2012 . In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host for SARS-CoV and the dromedary camel for MERS-CoV] before crossing species barriers to infect humans." ]

[ [ "0a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "0b", "Passage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients ." ], [ "0c", "In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV ." ], [ "0d", "Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences." ], [ "0e", "The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase" ] ]

[ "0c", "1c" ]

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients . In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV . Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Orf8 orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain fulllength orf8 . However, a 29-nucleotide deletion,", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 ). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: infections and 800 deaths, and Middle East respiratory syndrome CoV which has caused a persistent epidemic in the Arabian Peninsula since 2012 . In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host for SARS-CoV and the dromedary camel for MERS-CoV] before crossing species barriers to infect humans." ]

[ [ "1a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "1b", "Passage: Orf8 orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses." ], [ "1c", "Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain fulllength orf8 ." ], [ "1d", "However, a 29-nucleotide deletion," ] ]

[ "0c", "1c" ]

[ "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: By prospective design, we mean that respondents are informed in advance of the day that they are requested to record their contacts. 6, 17, 32 In a retrospective design, respondents recall their contacts over a past time period without prior warning or instruction that they would be requested to do so. Of 64 surveys, 29 used a retrospective design and 26 used a prospective design. Only four surveys 6%) used both designs for the purpose of comparison. 10, 17, 50 For five surveys , it was not completely clear whether the study was prospective or retrospective. 20, 24, 30, 48", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: Five surveys used an online respondent-driven method, which can be considered as a snowball or chain sampling technique. 31, 45, 60 Only one survey did not state information on sampling techniques. 34 Finally, three surveys conducted at the general population level used a convenience sample, 29, 44, 50 therefore not relying on a sampling frame. More details on the distribution of sampling schemes based on time and regions are presented in eFigure 3; http://links.lww.com/EDE/B552.", "Title: Tracking social contact networks with online respondent-driven detection: who recruits whom?\nPassage: After completion of the questionnaire, participants were referred to a research website that displayed the latest results . Participants recruited via the first panel who completed the survey had the opportunity to join a raffle for 1 of 10 gift cards of €25. This incentive only slightly increased peer recruitment as was shown in Stein et al. . For details on the software system and information on the 171 nonresponders we also refer the reader to Stein et al. .", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: The prospective design is subject to less recall bias than the retrospective design. This notion can be partly explained by the fact that respondents in the former are informed in advance about which days they will be assigned for reporting their contact information. Furthermore, they are also asked to keep a diary with them and finish reporting before the surveying day is elapsed. Thus, the prospective design requires more commitment from respondents. In return, a prospective design can obtain more reported contacts compared with retrospective design. 17, 50 However, large-scale studies are needed to further confirm these conclusions." ]

[ [ "0a", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections" ], [ "0b", "Passage: By prospective design, we mean that respondents are informed in advance of the day that they are requested to record their contacts." ], [ "0c", "6, 17, 32 In a retrospective design, respondents recall their contacts over a past time period without prior warning or instruction that they would be requested to do so." ], [ "0d", "Of 64 surveys, 29 used a retrospective design and 26 used a prospective design." ], [ "0e", "Only four surveys 6%) used both designs for the purpose of comparison." ], [ "0f", "10, 17, 50 For five surveys , it was not completely clear whether the study was prospective or retrospective." ], [ "0g", "20, 24, 30, 48" ] ]

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

[ "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: By prospective design, we mean that respondents are informed in advance of the day that they are requested to record their contacts. 6, 17, 32 In a retrospective design, respondents recall their contacts over a past time period without prior warning or instruction that they would be requested to do so. Of 64 surveys, 29 used a retrospective design and 26 used a prospective design. Only four surveys 6%) used both designs for the purpose of comparison. 10, 17, 50 For five surveys , it was not completely clear whether the study was prospective or retrospective. 20, 24, 30, 48", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: Five surveys used an online respondent-driven method, which can be considered as a snowball or chain sampling technique. 31, 45, 60 Only one survey did not state information on sampling techniques. 34 Finally, three surveys conducted at the general population level used a convenience sample, 29, 44, 50 therefore not relying on a sampling frame. More details on the distribution of sampling schemes based on time and regions are presented in eFigure 3; http://links.lww.com/EDE/B552.", "Title: Tracking social contact networks with online respondent-driven detection: who recruits whom?\nPassage: After completion of the questionnaire, participants were referred to a research website that displayed the latest results . Participants recruited via the first panel who completed the survey had the opportunity to join a raffle for 1 of 10 gift cards of €25. This incentive only slightly increased peer recruitment as was shown in Stein et al. . For details on the software system and information on the 171 nonresponders we also refer the reader to Stein et al. .", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: The prospective design is subject to less recall bias than the retrospective design. This notion can be partly explained by the fact that respondents in the former are informed in advance about which days they will be assigned for reporting their contact information. Furthermore, they are also asked to keep a diary with them and finish reporting before the surveying day is elapsed. Thus, the prospective design requires more commitment from respondents. In return, a prospective design can obtain more reported contacts compared with retrospective design. 17, 50 However, large-scale studies are needed to further confirm these conclusions." ]

[ [ "1a", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections" ], [ "1b", "Passage: Five surveys used an online respondent-driven method, which can be considered as a snowball or chain sampling technique." ], [ "1c", "31, 45, 60 Only one survey did not state information on sampling techniques." ], [ "1d", "34 Finally, three surveys conducted at the general population level used a convenience sample, 29, 44, 50 therefore not relying on a sampling frame." ], [ "1e", "More details on the distribution of sampling schemes based on time and regions are presented in eFigure 3; http://links.lww.com/EDE/B552." ] ]

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

[ "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: By prospective design, we mean that respondents are informed in advance of the day that they are requested to record their contacts. 6, 17, 32 In a retrospective design, respondents recall their contacts over a past time period without prior warning or instruction that they would be requested to do so. Of 64 surveys, 29 used a retrospective design and 26 used a prospective design. Only four surveys 6%) used both designs for the purpose of comparison. 10, 17, 50 For five surveys , it was not completely clear whether the study was prospective or retrospective. 20, 24, 30, 48", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: Five surveys used an online respondent-driven method, which can be considered as a snowball or chain sampling technique. 31, 45, 60 Only one survey did not state information on sampling techniques. 34 Finally, three surveys conducted at the general population level used a convenience sample, 29, 44, 50 therefore not relying on a sampling frame. More details on the distribution of sampling schemes based on time and regions are presented in eFigure 3; http://links.lww.com/EDE/B552.", "Title: Tracking social contact networks with online respondent-driven detection: who recruits whom?\nPassage: After completion of the questionnaire, participants were referred to a research website that displayed the latest results . Participants recruited via the first panel who completed the survey had the opportunity to join a raffle for 1 of 10 gift cards of €25. This incentive only slightly increased peer recruitment as was shown in Stein et al. . For details on the software system and information on the 171 nonresponders we also refer the reader to Stein et al. .", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections\nPassage: The prospective design is subject to less recall bias than the retrospective design. This notion can be partly explained by the fact that respondents in the former are informed in advance about which days they will be assigned for reporting their contact information. Furthermore, they are also asked to keep a diary with them and finish reporting before the surveying day is elapsed. Thus, the prospective design requires more commitment from respondents. In return, a prospective design can obtain more reported contacts compared with retrospective design. 17, 50 However, large-scale studies are needed to further confirm these conclusions." ]

[ [ "3a", "Title: A Systematic Review of Social Contact Surveys to Inform Transmission Models of Close-contact Infections" ], [ "3b", "Passage: The prospective design is subject to less recall bias than the retrospective design." ], [ "3c", "This notion can be partly explained by the fact that respondents in the former are informed in advance about which days they will be assigned for reporting their contact information." ], [ "3d", "Furthermore, they are also asked to keep a diary with them and finish reporting before the surveying day is elapsed." ], [ "3e", "Thus, the prospective design requires more commitment from respondents." ], [ "3f", "In return, a prospective design can obtain more reported contacts compared with retrospective design." ], [ "3g", "17, 50 However, large-scale studies are needed to further confirm these conclusions." ] ]

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

[ "Title: Efficacy of recombinant human soluble thrombomodulin for the treatment of acute exacerbation of idiopathic pulmonary fibrosis: a single arm, non-randomized prospective clinical trial\nPassage: From the data obtained in the historical untreated comparison group, the standard deviation of the P/F ratio in patients with AE-IPF was presumed to be 50 to estimate the target sample size. In addition, the effect size was also assumed to be 1.0 for the change in the P/F ratio 1 week after the initiation of rhTM administration. Thus, the minimum target sample size was calculated to be 10 patients with a two-sided alpha level of 0.05 and a power of 80 %.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: After each epidemic season, we estimate several groups by numerically calculating fluxes from one state to another. We mainly estimate nine fractions of individuals that are, QIV vaccinees and healthy-HV Q , QIV vaccinees but infected with influenza A virus-V Q I A , TIV vaccinees and healthy-HV T , TIV vaccinees but infected with influenza A virus-V T I A , successful free riders-SFR , failed free riders-FFR A or FFR B . Figure 1 . The layout of the whole dynamical set-up. The vaccine efficacy of TIV vaccine against influenza B virus is assumed e T , which", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: maximum as the corresponding cost is higher; contrarily, TIV vaccinees are seen to reach the highest level for a mid-range of e T , although it starts decreasing with the further increase of e T that arises with the prevalence of free riders. Remarkably, the average payoff of society in case of different costs seems lower than that of the equal cost as the former case imposes a higher financial burden to society.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: vaccine, TIV vaccine or none-that evolve at the end of each season by imitating strategies based on the previous season's experience. We perform a series of numerical simulations by varying vaccination cost, vaccine effectiveness, transmission rates, etc., to depict different scenarios. Our results show that individuals are more inclined to take QIV vaccine whenever both vaccination costs are comparable; however, they prefer TIV vaccine if the cost difference gets higher. Notably, the framework has been validated by the so-called MAS approach." ]

[ [ "1a", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach" ], [ "1b", "Passage: After each epidemic season, we estimate several groups by numerically calculating fluxes from one state to another." ], [ "1c", "We mainly estimate nine fractions of individuals that are, QIV vaccinees and healthy-HV Q , QIV vaccinees but infected with influenza A virus-V Q I A , TIV vaccinees and healthy-HV T , TIV vaccinees but infected with influenza A virus-V T I A , successful free riders-SFR , failed free riders-FFR A or FFR B ." ], [ "1d", "Figure 1 ." ], [ "1e", "The layout of the whole dynamical set-up." ], [ "1f", "The vaccine efficacy of TIV vaccine against influenza B virus is assumed e T , which" ] ]

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

[ "Title: Efficacy of recombinant human soluble thrombomodulin for the treatment of acute exacerbation of idiopathic pulmonary fibrosis: a single arm, non-randomized prospective clinical trial\nPassage: From the data obtained in the historical untreated comparison group, the standard deviation of the P/F ratio in patients with AE-IPF was presumed to be 50 to estimate the target sample size. In addition, the effect size was also assumed to be 1.0 for the change in the P/F ratio 1 week after the initiation of rhTM administration. Thus, the minimum target sample size was calculated to be 10 patients with a two-sided alpha level of 0.05 and a power of 80 %.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: After each epidemic season, we estimate several groups by numerically calculating fluxes from one state to another. We mainly estimate nine fractions of individuals that are, QIV vaccinees and healthy-HV Q , QIV vaccinees but infected with influenza A virus-V Q I A , TIV vaccinees and healthy-HV T , TIV vaccinees but infected with influenza A virus-V T I A , successful free riders-SFR , failed free riders-FFR A or FFR B . Figure 1 . The layout of the whole dynamical set-up. The vaccine efficacy of TIV vaccine against influenza B virus is assumed e T , which", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: maximum as the corresponding cost is higher; contrarily, TIV vaccinees are seen to reach the highest level for a mid-range of e T , although it starts decreasing with the further increase of e T that arises with the prevalence of free riders. Remarkably, the average payoff of society in case of different costs seems lower than that of the equal cost as the former case imposes a higher financial burden to society.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: vaccine, TIV vaccine or none-that evolve at the end of each season by imitating strategies based on the previous season's experience. We perform a series of numerical simulations by varying vaccination cost, vaccine effectiveness, transmission rates, etc., to depict different scenarios. Our results show that individuals are more inclined to take QIV vaccine whenever both vaccination costs are comparable; however, they prefer TIV vaccine if the cost difference gets higher. Notably, the framework has been validated by the so-called MAS approach." ]

[ [ "2a", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach" ], [ "2b", "Passage: maximum as the corresponding cost is higher; contrarily, TIV vaccinees are seen to reach the highest level for a mid-range of e T , although it starts decreasing with the further increase of e T that arises with the prevalence of free riders." ], [ "2c", "Remarkably, the average payoff of society in case of different costs seems lower than that of the equal cost as the former case imposes a higher financial burden to society." ] ]

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

[ "Title: Efficacy of recombinant human soluble thrombomodulin for the treatment of acute exacerbation of idiopathic pulmonary fibrosis: a single arm, non-randomized prospective clinical trial\nPassage: From the data obtained in the historical untreated comparison group, the standard deviation of the P/F ratio in patients with AE-IPF was presumed to be 50 to estimate the target sample size. In addition, the effect size was also assumed to be 1.0 for the change in the P/F ratio 1 week after the initiation of rhTM administration. Thus, the minimum target sample size was calculated to be 10 patients with a two-sided alpha level of 0.05 and a power of 80 %.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: After each epidemic season, we estimate several groups by numerically calculating fluxes from one state to another. We mainly estimate nine fractions of individuals that are, QIV vaccinees and healthy-HV Q , QIV vaccinees but infected with influenza A virus-V Q I A , TIV vaccinees and healthy-HV T , TIV vaccinees but infected with influenza A virus-V T I A , successful free riders-SFR , failed free riders-FFR A or FFR B . Figure 1 . The layout of the whole dynamical set-up. The vaccine efficacy of TIV vaccine against influenza B virus is assumed e T , which", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: maximum as the corresponding cost is higher; contrarily, TIV vaccinees are seen to reach the highest level for a mid-range of e T , although it starts decreasing with the further increase of e T that arises with the prevalence of free riders. Remarkably, the average payoff of society in case of different costs seems lower than that of the equal cost as the former case imposes a higher financial burden to society.", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: vaccine, TIV vaccine or none-that evolve at the end of each season by imitating strategies based on the previous season's experience. We perform a series of numerical simulations by varying vaccination cost, vaccine effectiveness, transmission rates, etc., to depict different scenarios. Our results show that individuals are more inclined to take QIV vaccine whenever both vaccination costs are comparable; however, they prefer TIV vaccine if the cost difference gets higher. Notably, the framework has been validated by the so-called MAS approach." ]

[ [ "3a", "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach" ], [ "3b", "Passage: vaccine, TIV vaccine or none-that evolve at the end of each season by imitating strategies based on the previous season's experience." ], [ "3c", "We perform a series of numerical simulations by varying vaccination cost, vaccine effectiveness, transmission rates, etc., to depict different scenarios." ], [ "3d", "Our results show that individuals are more inclined to take QIV vaccine whenever both vaccination costs are comparable; however, they prefer TIV vaccine if the cost difference gets higher." ], [ "3e", "Notably, the framework has been validated by the so-called MAS approach." ] ]

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

[ "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Acute respiratory infections remain one of the most common major public health threats, accounting for millions of episodes of severe acute lower respiratory infections that result in hospital admissions of otherwise healthy infants and young children worldwide . One-third of the annual deaths occurring in the world are thought to be due to infectious diseases, and respiratory tract infections are responsible for 4 million deaths worldwide each year . According to estimates made by the World Health Organization , pneumonia kills more children worldwide than any other disease, even more than acquired immune deficiency syndrome , malaria and measles combined", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: common cause of significant morbidity, and occasionally mortality, in early childhood. Our current understanding of the epidemiology of early childhood infections is limited by reliance on community-based data from decades ago using low-sensitivity diagnostic methods, and recent studies that primarily focus on severe, hospital-managed disease. 10 11 Much of what we know, especially with newly discovered agents, originates from hospital-based prevalence studies where more than 80% of cases are less than 2 years of age, representing the sickest 2-3% of young children seen. Experience with influenza illustrates how easily disease burden can be underestimated by extrapolating from hospital data. Available", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: For peer review only -http://bmjopen.bmj.com/site/about/guidelines.xhtml 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 and drinking water supplies, good personal hygiene standards, widespread vaccine use, and access to high quality medical care, infectious diseases remain the most common cause of significant morbidity, and occasionally mortality, in early childhood. Our current", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: The highest incidence rates of acute respiratory infections are during the first two years of life where on average infants experience six to eight ARIs each year. 20 Complication rates from acute otitis media and sinusitis are also highest in this age group, 21 while three to five per cent of all infants are hospitalised for viral lower respiratory tract infections, including bronchiolitis, pneumonia, croup, and secondary bacterial pneumonia. 22 There is emerging evidence that infectious insults to the growing and developing lung during early childhood contribute to the pathogenesis of chronic pulmonary disorders in older children and adulthood, such" ]

[ [ "0a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "0b", "Passage: Acute respiratory infections remain one of the most common major public health threats, accounting for millions of episodes of severe acute lower respiratory infections that result in hospital admissions of otherwise healthy infants and young children worldwide ." ], [ "0c", "One-third of the annual deaths occurring in the world are thought to be due to infectious diseases, and respiratory tract infections are responsible for 4 million deaths worldwide each year ." ], [ "0d", "According to estimates made by the World Health Organization , pneumonia kills more children worldwide than any other disease, even more than acquired immune deficiency syndrome , malaria and measles combined" ] ]

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

[ "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Acute respiratory infections remain one of the most common major public health threats, accounting for millions of episodes of severe acute lower respiratory infections that result in hospital admissions of otherwise healthy infants and young children worldwide . One-third of the annual deaths occurring in the world are thought to be due to infectious diseases, and respiratory tract infections are responsible for 4 million deaths worldwide each year . According to estimates made by the World Health Organization , pneumonia kills more children worldwide than any other disease, even more than acquired immune deficiency syndrome , malaria and measles combined", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: common cause of significant morbidity, and occasionally mortality, in early childhood. Our current understanding of the epidemiology of early childhood infections is limited by reliance on community-based data from decades ago using low-sensitivity diagnostic methods, and recent studies that primarily focus on severe, hospital-managed disease. 10 11 Much of what we know, especially with newly discovered agents, originates from hospital-based prevalence studies where more than 80% of cases are less than 2 years of age, representing the sickest 2-3% of young children seen. Experience with influenza illustrates how easily disease burden can be underestimated by extrapolating from hospital data. Available", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: For peer review only -http://bmjopen.bmj.com/site/about/guidelines.xhtml 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 and drinking water supplies, good personal hygiene standards, widespread vaccine use, and access to high quality medical care, infectious diseases remain the most common cause of significant morbidity, and occasionally mortality, in early childhood. Our current", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study\nPassage: The highest incidence rates of acute respiratory infections are during the first two years of life where on average infants experience six to eight ARIs each year. 20 Complication rates from acute otitis media and sinusitis are also highest in this age group, 21 while three to five per cent of all infants are hospitalised for viral lower respiratory tract infections, including bronchiolitis, pneumonia, croup, and secondary bacterial pneumonia. 22 There is emerging evidence that infectious insults to the growing and developing lung during early childhood contribute to the pathogenesis of chronic pulmonary disorders in older children and adulthood, such" ]

[ [ "3a", "Title: Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study" ], [ "3b", "Passage: The highest incidence rates of acute respiratory infections are during the first two years of life where on average infants experience six to eight ARIs each year." ], [ "3c", "20 Complication rates from acute otitis media and sinusitis are also highest in this age group, 21 while three to five per cent of all infants are hospitalised for viral lower respiratory tract infections, including bronchiolitis, pneumonia, croup, and secondary bacterial pneumonia." ], [ "3d", "22 There is emerging evidence that infectious insults to the growing and developing lung during early childhood contribute to the pathogenesis of chronic pulmonary disorders in older children and adulthood, such" ] ]

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

[ "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The Syrian hamster has recently been used as an experimental rodent model for important infectious diseases including Ebola and other viral hemorrhagic fevers . For instance, Syrian hamsters infected with mouseadapted Ebola virus manifest many of the clinical and pathological findings observed in EBOV-infected non-human primates and humans, including systemic viral replication, suppression of the innate immune response, an uncontrolled inflammatory response, and disseminated intravascular coagulation syndrome . The Syrian hamster is emerging as a promising model for leishmaniasis and dyslipidaemia research . The Syrian hamster is also an important animal model in neurosciences research . For instance, this species", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The CHO cell genome is a useful tool for further improving the quality of our Syrian hamster transcriptome annotation for functional genomics work . CHO cells have been used in a variety of genetic, cell biology, and pharmacology studies. They also are the mammalian cell line of choice for producing large quantities of recombinant proteins in large amounts or in or industrial laboratory settings. Although Chinese and Syrian hamsters are phylogenetically distinct within the rodent subfamily Cricetinae , our data confirm that they are more closely related to one another as compared to other muroid rodents.", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The Syrian hamster is becoming an increasingly popular model for a variety of diseases, in particular, diseases known to infect non- Table 3 . Functional enrichment of the mouse genes mapped by our transcriptome assembly. human primates and humans. This Syrian hamster transcriptome discussed here represents a critical step forward in providing the tools necessary for advancing functional genomics in this important animal model.", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: All hamsters were housed in individually ventilated cages . All hamsters are co-housed, unless scientifically justified and approved by the Institutional Animal Care and Use Committee or deemed necessary for veterinary reasons. Housing density is determined by the guidelines outlined in the Guide for the Care and Use of Laboratory Animals and the Association for the Assessment and Accreditation of the Laboratory Animal Care, International . Food and sterile or acidified water were provided ad libitum. Hamster diets were consist of pellets containing a variety of foods such as grains and dried vegetables along with some seeds. Water was provided" ]

[ [ "0a", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome" ], [ "0b", "Passage: The Syrian hamster has recently been used as an experimental rodent model for important infectious diseases including Ebola and other viral hemorrhagic fevers ." ], [ "0c", "For instance, Syrian hamsters infected with mouseadapted Ebola virus manifest many of the clinical and pathological findings observed in EBOV-infected non-human primates and humans, including systemic viral replication, suppression of the innate immune response, an uncontrolled inflammatory response, and disseminated intravascular coagulation syndrome ." ], [ "0d", "The Syrian hamster is emerging as a promising model for leishmaniasis and dyslipidaemia research ." ], [ "0e", "The Syrian hamster is also an important animal model in neurosciences research ." ], [ "0f", "For instance, this species" ] ]

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

[ "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The Syrian hamster has recently been used as an experimental rodent model for important infectious diseases including Ebola and other viral hemorrhagic fevers . For instance, Syrian hamsters infected with mouseadapted Ebola virus manifest many of the clinical and pathological findings observed in EBOV-infected non-human primates and humans, including systemic viral replication, suppression of the innate immune response, an uncontrolled inflammatory response, and disseminated intravascular coagulation syndrome . The Syrian hamster is emerging as a promising model for leishmaniasis and dyslipidaemia research . The Syrian hamster is also an important animal model in neurosciences research . For instance, this species", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The CHO cell genome is a useful tool for further improving the quality of our Syrian hamster transcriptome annotation for functional genomics work . CHO cells have been used in a variety of genetic, cell biology, and pharmacology studies. They also are the mammalian cell line of choice for producing large quantities of recombinant proteins in large amounts or in or industrial laboratory settings. Although Chinese and Syrian hamsters are phylogenetically distinct within the rodent subfamily Cricetinae , our data confirm that they are more closely related to one another as compared to other muroid rodents.", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: The Syrian hamster is becoming an increasingly popular model for a variety of diseases, in particular, diseases known to infect non- Table 3 . Functional enrichment of the mouse genes mapped by our transcriptome assembly. human primates and humans. This Syrian hamster transcriptome discussed here represents a critical step forward in providing the tools necessary for advancing functional genomics in this important animal model.", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome\nPassage: All hamsters were housed in individually ventilated cages . All hamsters are co-housed, unless scientifically justified and approved by the Institutional Animal Care and Use Committee or deemed necessary for veterinary reasons. Housing density is determined by the guidelines outlined in the Guide for the Care and Use of Laboratory Animals and the Association for the Assessment and Accreditation of the Laboratory Animal Care, International . Food and sterile or acidified water were provided ad libitum. Hamster diets were consist of pellets containing a variety of foods such as grains and dried vegetables along with some seeds. Water was provided" ]

[ [ "2a", "Title: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome" ], [ "2b", "Passage: The Syrian hamster is becoming an increasingly popular model for a variety of diseases, in particular, diseases known to infect non- Table 3 ." ], [ "2c", "Functional enrichment of the mouse genes mapped by our transcriptome assembly." ], [ "2d", "human primates and humans." ], [ "2e", "This Syrian hamster transcriptome discussed here represents a critical step forward in providing the tools necessary for advancing functional genomics in this important animal model." ] ]

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

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Information about pre-existing conditions was available for 20 case-patients. Four case-patients had no reported pre-existing conditions or risk factors for severe disease. Pre-existing conditions reported were: morbid obesity/obesity , lung disease , heart disease , pregnancy , diabetes , immunodeficiency , cerebral palsy , prematurity in an infant and genetic disorder . Three case-patients were reported to have more than one pre-existing condition/risk factor. Antiviral therapy was prescribed for 10 case-patients . Antibiotics were prescribed for 10 case-patients . Four case-patients received both antiviral and antibiotic therapy.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Data on pre-existing conditions were reported for seven cases; five had no pre-existing conditions while one was reported to be obese and one had pre-existing cardiac disease. No data on clinical signs e.g. dyspnea etc. were reported for any of the 38 cases.", "Title: Mortality, morbidity and health in developed societies: a review of data sources\nPassage: Studies based on health insurance data can relate to the onset of handicaps, hospital admissions, preventive dental care, etc. Administrative and billing data can be used to study, for example, social inequalities in health or differences in health status between regions. For example, in the USA, Medicare data can be used for comparative effectiveness research on treatments, benefit designs and delivery systems for Medicare beneficiaries , i.e. around 50 million people nationwide . These data permit, for example, national assessments of imaging utilisation and spending for this subpopulation. A French study has used healthcare consumption to compare the health status", "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: the importance of pre-existing conditions such as heart disease and obesity is therefore not possible. Onset dates were estimated by reporting parties where information was not available. Finally, these data relate to a small number of cases." ]

[ [ "0a", "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study" ], [ "0b", "Passage: Information about pre-existing conditions was available for 20 case-patients." ], [ "0c", "Four case-patients had no reported pre-existing conditions or risk factors for severe disease." ], [ "0d", "Pre-existing conditions reported were: morbid obesity/obesity , lung disease , heart disease , pregnancy , diabetes , immunodeficiency , cerebral palsy , prematurity in an infant and genetic disorder ." ], [ "0e", "Three case-patients were reported to have more than one pre-existing condition/risk factor." ], [ "0f", "Antiviral therapy was prescribed for 10 case-patients ." ], [ "0g", "Antibiotics were prescribed for 10 case-patients ." ], [ "0h", "Four case-patients received both antiviral and antibiotic therapy." ] ]

[ "0b", "1b" ]

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Information about pre-existing conditions was available for 20 case-patients. Four case-patients had no reported pre-existing conditions or risk factors for severe disease. Pre-existing conditions reported were: morbid obesity/obesity , lung disease , heart disease , pregnancy , diabetes , immunodeficiency , cerebral palsy , prematurity in an infant and genetic disorder . Three case-patients were reported to have more than one pre-existing condition/risk factor. Antiviral therapy was prescribed for 10 case-patients . Antibiotics were prescribed for 10 case-patients . Four case-patients received both antiviral and antibiotic therapy.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Data on pre-existing conditions were reported for seven cases; five had no pre-existing conditions while one was reported to be obese and one had pre-existing cardiac disease. No data on clinical signs e.g. dyspnea etc. were reported for any of the 38 cases.", "Title: Mortality, morbidity and health in developed societies: a review of data sources\nPassage: Studies based on health insurance data can relate to the onset of handicaps, hospital admissions, preventive dental care, etc. Administrative and billing data can be used to study, for example, social inequalities in health or differences in health status between regions. For example, in the USA, Medicare data can be used for comparative effectiveness research on treatments, benefit designs and delivery systems for Medicare beneficiaries , i.e. around 50 million people nationwide . These data permit, for example, national assessments of imaging utilisation and spending for this subpopulation. A French study has used healthcare consumption to compare the health status", "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: the importance of pre-existing conditions such as heart disease and obesity is therefore not possible. Onset dates were estimated by reporting parties where information was not available. Finally, these data relate to a small number of cases." ]

[ [ "1a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "1b", "Passage: Data on pre-existing conditions were reported for seven cases; five had no pre-existing conditions while one was reported to be obese and one had pre-existing cardiac disease." ], [ "1c", "No data on clinical signs e.g. dyspnea etc. were reported for any of the 38 cases." ] ]

[ "0b", "1b" ]

[ "Title: Estimating the number of infections and the impact of non-\nPassage: current trends continue, there is reason for optimism.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: posterior translates to a reduction in prediction uncertainty. We note that this improvement does not lead to more frequent prediction failure since for both weekly and daily data, the coverage for all targets remains above 90% .", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: associated with earlier availability of the Wikipedia data may still be important.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Much recent research activity has focused on short-and medium-term predictions of influenza activity and the importance of nowcasting 37] . While several previous studies have used similar indirect sources of influenza activity data for forecasting , none of these studies have used daily data or quantified the improvements associated with using these more readily available data sources. Other work has used data with a daily resolution as a basis for forecasting, but these studies have not evaluated the performance over several seasons and do not report gains in prediction performance associated with the higher resolution observation frequency." ]

[ [ "1a", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics" ], [ "1b", "Passage: posterior translates to a reduction in prediction uncertainty." ], [ "1c", "We note that this improvement does not lead to more frequent prediction failure since for both weekly and daily data, the coverage for all targets remains above 90% ." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: current trends continue, there is reason for optimism.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: posterior translates to a reduction in prediction uncertainty. We note that this improvement does not lead to more frequent prediction failure since for both weekly and daily data, the coverage for all targets remains above 90% .", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: associated with earlier availability of the Wikipedia data may still be important.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Much recent research activity has focused on short-and medium-term predictions of influenza activity and the importance of nowcasting 37] . While several previous studies have used similar indirect sources of influenza activity data for forecasting , none of these studies have used daily data or quantified the improvements associated with using these more readily available data sources. Other work has used data with a daily resolution as a basis for forecasting, but these studies have not evaluated the performance over several seasons and do not report gains in prediction performance associated with the higher resolution observation frequency." ]

[ [ "2a", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics" ], [ "2b", "Passage: associated with earlier availability of the Wikipedia data may still be important." ] ]

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

[ "Title: Estimating the number of infections and the impact of non-\nPassage: current trends continue, there is reason for optimism.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: posterior translates to a reduction in prediction uncertainty. We note that this improvement does not lead to more frequent prediction failure since for both weekly and daily data, the coverage for all targets remains above 90% .", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: associated with earlier availability of the Wikipedia data may still be important.", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics\nPassage: Much recent research activity has focused on short-and medium-term predictions of influenza activity and the importance of nowcasting 37] . While several previous studies have used similar indirect sources of influenza activity data for forecasting , none of these studies have used daily data or quantified the improvements associated with using these more readily available data sources. Other work has used data with a daily resolution as a basis for forecasting, but these studies have not evaluated the performance over several seasons and do not report gains in prediction performance associated with the higher resolution observation frequency." ]

[ [ "3a", "Title: Use of daily Internet search query data improves real-time projections of influenza epidemics" ], [ "3b", "Passage: Much recent research activity has focused on short-and medium-term predictions of influenza activity and the importance of nowcasting 37] ." ], [ "3c", "While several previous studies have used similar indirect sources of influenza activity data for forecasting , none of these studies have used daily data or quantified the improvements associated with using these more readily available data sources." ], [ "3d", "Other work has used data with a daily resolution as a basis for forecasting, but these studies have not evaluated the performance over several seasons and do not report gains in prediction performance associated with the higher resolution observation frequency." ] ]

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

[ "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: The prototypical and best-characterised member of the PCSK family is furin/PCSK3. Since it cleaves basic amino acid motifs, it has also been termed PACE . Furin is expressed by the FUR gene on chromosome 15. Although furin is ubiquitously expressed, its mRNA and protein levels vary depending on the cell type and tissue. High levels can be found in salivary glands, liver and bone marrow, whereas muscle cells express relatively low amounts of furin. 9 Three promoters , each harbouring an alternative transcription start site, have been described . However, the respective transcripts differ only in the first untranslated exon", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: Furin is a member of the evolutionarily ancient family of proprotein convertases. Their similarity with bacterial subtilisin and yeast kexin proteases has coined the abbreviation PCSK . Humans encode nine members of this protease family , with PCSK3 representing furin . PCSKs are well known for their ability to activate other cellular proteins. The proteolytic conversion of inactive precursor proteins into bioactive molecules has already been described in the 1960s. 3 However, it took more than 20 years until furin was identified as the first mammalian proprotein convertase. 4, 5 To date, more than 200 cellular substrates of PCSKs have", "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Another mRNA under post-transcriptional regulation by Regnase-1 and Roquin is Furin, which encodes a conserved proprotein convertase crucial in human health and disease. Furin, along with other PCSK family members, is widely implicated in immune regulation, cancer and the entry, maturation or release of a broad array of evolutionarily diverse viruses including human papillomavirus , influenza , Ebola , dengue and human immunodeficiency virus . Here, Braun and Sauter review the roles of furin in these processes, as well as the history and future of furin-targeting therapeutics. 7 They also discuss their recent work revealing how two IFN-cinducible factors exhibit", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: and are therefore predicted to express the same protein. 10 While the P1A and P1B promoters resemble those of constitutively expressed housekeeping genes, the P1 promoter binds the transcription factor C/EBPb and can be trans-activated upon cytokine stimulation. 10 In line with this, IFNc, TGFb, IL-12 and PMA induce furin expression. Upon translation of the mRNA, furin enters the secretory pathway as an inactive proenzyme and is integrated into the ER membrane via its Cterminal transmembrane domain . Like most type I transmembrane proteins, it harbours a short N-terminal signal peptide that is cleaved off cotranslationally. Similar to other proprotein" ]

[ [ "0a", "Title: Furin‐mediated protein processing in infectious diseases and cancer" ], [ "0b", "Passage: The prototypical and best-characterised member of the PCSK family is furin/PCSK3." ], [ "0c", "Since it cleaves basic amino acid motifs, it has also been termed PACE ." ], [ "0d", "Furin is expressed by the FUR gene on chromosome 15." ], [ "0e", "Although furin is ubiquitously expressed, its mRNA and protein levels vary depending on the cell type and tissue." ], [ "0f", "High levels can be found in salivary glands, liver and bone marrow, whereas muscle cells express relatively low amounts of furin." ], [ "0g", "9 Three promoters , each harbouring an alternative transcription start site, have been described ." ], [ "0h", "However, the respective transcripts differ only in the first untranslated exon" ] ]

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

[ "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: The prototypical and best-characterised member of the PCSK family is furin/PCSK3. Since it cleaves basic amino acid motifs, it has also been termed PACE . Furin is expressed by the FUR gene on chromosome 15. Although furin is ubiquitously expressed, its mRNA and protein levels vary depending on the cell type and tissue. High levels can be found in salivary glands, liver and bone marrow, whereas muscle cells express relatively low amounts of furin. 9 Three promoters , each harbouring an alternative transcription start site, have been described . However, the respective transcripts differ only in the first untranslated exon", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: Furin is a member of the evolutionarily ancient family of proprotein convertases. Their similarity with bacterial subtilisin and yeast kexin proteases has coined the abbreviation PCSK . Humans encode nine members of this protease family , with PCSK3 representing furin . PCSKs are well known for their ability to activate other cellular proteins. The proteolytic conversion of inactive precursor proteins into bioactive molecules has already been described in the 1960s. 3 However, it took more than 20 years until furin was identified as the first mammalian proprotein convertase. 4, 5 To date, more than 200 cellular substrates of PCSKs have", "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Another mRNA under post-transcriptional regulation by Regnase-1 and Roquin is Furin, which encodes a conserved proprotein convertase crucial in human health and disease. Furin, along with other PCSK family members, is widely implicated in immune regulation, cancer and the entry, maturation or release of a broad array of evolutionarily diverse viruses including human papillomavirus , influenza , Ebola , dengue and human immunodeficiency virus . Here, Braun and Sauter review the roles of furin in these processes, as well as the history and future of furin-targeting therapeutics. 7 They also discuss their recent work revealing how two IFN-cinducible factors exhibit", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: and are therefore predicted to express the same protein. 10 While the P1A and P1B promoters resemble those of constitutively expressed housekeeping genes, the P1 promoter binds the transcription factor C/EBPb and can be trans-activated upon cytokine stimulation. 10 In line with this, IFNc, TGFb, IL-12 and PMA induce furin expression. Upon translation of the mRNA, furin enters the secretory pathway as an inactive proenzyme and is integrated into the ER membrane via its Cterminal transmembrane domain . Like most type I transmembrane proteins, it harbours a short N-terminal signal peptide that is cleaved off cotranslationally. Similar to other proprotein" ]

[ [ "1a", "Title: Furin‐mediated protein processing in infectious diseases and cancer" ], [ "1b", "Passage: Furin is a member of the evolutionarily ancient family of proprotein convertases." ], [ "1c", "Their similarity with bacterial subtilisin and yeast kexin proteases has coined the abbreviation PCSK ." ], [ "1d", "Humans encode nine members of this protease family , with PCSK3 representing furin ." ], [ "1e", "PCSKs are well known for their ability to activate other cellular proteins." ], [ "1f", "The proteolytic conversion of inactive precursor proteins into bioactive molecules has already been described in the 1960s." ], [ "1g", "3 However, it took more than 20 years until furin was identified as the first mammalian proprotein convertase." ], [ "1h", "4, 5 To date, more than 200 cellular substrates of PCSKs have" ] ]

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

[ "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: The prototypical and best-characterised member of the PCSK family is furin/PCSK3. Since it cleaves basic amino acid motifs, it has also been termed PACE . Furin is expressed by the FUR gene on chromosome 15. Although furin is ubiquitously expressed, its mRNA and protein levels vary depending on the cell type and tissue. High levels can be found in salivary glands, liver and bone marrow, whereas muscle cells express relatively low amounts of furin. 9 Three promoters , each harbouring an alternative transcription start site, have been described . However, the respective transcripts differ only in the first untranslated exon", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: Furin is a member of the evolutionarily ancient family of proprotein convertases. Their similarity with bacterial subtilisin and yeast kexin proteases has coined the abbreviation PCSK . Humans encode nine members of this protease family , with PCSK3 representing furin . PCSKs are well known for their ability to activate other cellular proteins. The proteolytic conversion of inactive precursor proteins into bioactive molecules has already been described in the 1960s. 3 However, it took more than 20 years until furin was identified as the first mammalian proprotein convertase. 4, 5 To date, more than 200 cellular substrates of PCSKs have", "Title: Frontiers in antiviral therapy and immunotherapy\nPassage: Another mRNA under post-transcriptional regulation by Regnase-1 and Roquin is Furin, which encodes a conserved proprotein convertase crucial in human health and disease. Furin, along with other PCSK family members, is widely implicated in immune regulation, cancer and the entry, maturation or release of a broad array of evolutionarily diverse viruses including human papillomavirus , influenza , Ebola , dengue and human immunodeficiency virus . Here, Braun and Sauter review the roles of furin in these processes, as well as the history and future of furin-targeting therapeutics. 7 They also discuss their recent work revealing how two IFN-cinducible factors exhibit", "Title: Furin‐mediated protein processing in infectious diseases and cancer\nPassage: and are therefore predicted to express the same protein. 10 While the P1A and P1B promoters resemble those of constitutively expressed housekeeping genes, the P1 promoter binds the transcription factor C/EBPb and can be trans-activated upon cytokine stimulation. 10 In line with this, IFNc, TGFb, IL-12 and PMA induce furin expression. Upon translation of the mRNA, furin enters the secretory pathway as an inactive proenzyme and is integrated into the ER membrane via its Cterminal transmembrane domain . Like most type I transmembrane proteins, it harbours a short N-terminal signal peptide that is cleaved off cotranslationally. Similar to other proprotein" ]

[ [ "2a", "Title: Frontiers in antiviral therapy and immunotherapy" ], [ "2b", "Passage: Another mRNA under post-transcriptional regulation by Regnase-1 and Roquin is Furin, which encodes a conserved proprotein convertase crucial in human health and disease." ], [ "2c", "Furin, along with other PCSK family members, is widely implicated in immune regulation, cancer and the entry, maturation or release of a broad array of evolutionarily diverse viruses including human papillomavirus , influenza , Ebola , dengue and human immunodeficiency virus ." ], [ "2d", "Here, Braun and Sauter review the roles of furin in these processes, as well as the history and future of furin-targeting therapeutics." ], [ "2e", "7 They also discuss their recent work revealing how two IFN-cinducible factors exhibit" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination .", "Title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care\nPassage: is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza . Implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs. 44 Access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact.", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. 7 In a small Irish study , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced. 10 The differences in clinical setting and patient group may explain the smaller decline in our study . Non-PCR-based", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost-benefit analysis should be undertaken." ]

[ [ "0a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: Rapid diagnostics plays an important role in disease and outbreak management." ], [ "0c", "The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures." ], [ "0d", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home." ], [ "0e", "Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination ." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination .", "Title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care\nPassage: is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza . Implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs. 44 Access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact.", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. 7 In a small Irish study , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced. 10 The differences in clinical setting and patient group may explain the smaller decline in our study . Non-PCR-based", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost-benefit analysis should be undertaken." ]

[ [ "1a", "Title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care" ], [ "1b", "Passage: is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza ." ], [ "1c", "Implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs." ], [ "1d", "44 Access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination .", "Title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care\nPassage: is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza . Implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs. 44 Access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact.", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. 7 In a small Irish study , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced. 10 The differences in clinical setting and patient group may explain the smaller decline in our study . Non-PCR-based", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost-benefit analysis should be undertaken." ]

[ [ "2a", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients" ], [ "2b", "Passage: Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs." ], [ "2c", "An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients." ], [ "2d", "7 In a small Irish study , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced." ], [ "2e", "10 The differences in clinical setting and patient group may explain the smaller decline in our study . Non-PCR-based" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination .", "Title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care\nPassage: is clear that rapid identification of pathogens during other outbreaks facilitates rapid treatment and appropriate isolation of patients, leading to improved patient outcomes and potentially slowing the spread of infections such as influenza . Implementation of the first rapid diagnostic tests for influenza was directly associated with reduced length of hospital stay, decreased mortality, and reduced costs. 44 Access to diagnostic tests, early in the course of an outbreak and in hospital laboratories, has a positive public health impact.", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. 7 In a small Irish study , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced. 10 The differences in clinical setting and patient group may explain the smaller decline in our study . Non-PCR-based", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients\nPassage: Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost-benefit analysis should be undertaken." ]

[ [ "3a", "Title: The impact of rapid molecular diagnostic testing for respiratory viruses on outcomes for emergency department patients" ], [ "3b", "Passage: Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system." ], [ "3c", "A formal cost-benefit analysis should be undertaken." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Infectious MERS-CoV added to DC, goat or cow milk and stored at 4°C could be recovered at least 72 h later and, if stored at 22°C, recovery was possible for up to 48 h . MERS-CoV titre decreased somewhat when recovered from milk at 22°C but pasteurization completely ablated MERS-CoV infectivity . In a subsequent study, MERS-CoV RNA was identified in the milk, nasal secretion and faeces of DCs from Qatar .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations . What role maternal camel antibody might play in delaying infection of calves remains unknown . Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection. In contrast to earlier results, slaughterhouse workers who kill both younger and older", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: is an animal of ritual significance after the Hajj pilgrimage . However, MERS-CoV infection frequency is reportedly much lower than is the widespread and frequent habit of eating, drinking and preparing DC products. Daily ingestion of fresh unpasteurized DC milk is common among the desert Bedouin and many others in the KSA. DC urine is also consumed or used for supposed health benefits. Despite camel butchery being a local occupation, neither butchers nor other at-risk groups are identifiable among MERS cases; this may simply be a reporting issue rather than an unexplainable absence of MERS. A small case-control study published", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: positive DC had been infected by a variant of the same virus, harbouring the same distinct pattern of nucleotide polymorphisms. All nine DC in the owner's herd, serially sampled, reacted in a recombinant S1 antigen ELISA, with the two animals that had been RT-rtPCR positive showing a small, verifiable rise in antibody titre . A rise in titre theoretically begins 10 to 21 days after DC infection . The authors suggested that the rise in titre in DC sera which occurred alongside a declining RNA load, while the patient was actively ill and hospitalized, indicated that the DCs were infected" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: Infectious MERS-CoV added to DC, goat or cow milk and stored at 4°C could be recovered at least 72 h later and, if stored at 22°C, recovery was possible for up to 48 h ." ], [ "0c", "MERS-CoV titre decreased somewhat when recovered from milk at 22°C but pasteurization completely ablated MERS-CoV infectivity ." ], [ "0d", "In a subsequent study, MERS-CoV RNA was identified in the milk, nasal secretion and faeces of DCs from Qatar ." ] ]

[ "0b" ]

[ "Title: The origins of the great pandemic\nPassage: In recent years, the question has arisen as to when and where the first case of the influenza pandemic of 1918 may have been detected. At least three locations have been mooted. First, the historian John Barry has suggested that Loring Miner, a physician in rural Kansas, in the USA, encountered cases in the early weeks of 1918 which, while akin to influenza, posed an unusual risk to life . Miner based his diagnosis on the symptomatology involved, and, interestingly, those symptoms did not include heliotrope cyanosis, which, as time drew on, came to be regarded as the tell-tale most", "Title: The origins of the great pandemic\nPassage: Kansas cases no doubt make for a compelling story, but one that has perhaps left a stronger-than-deserved impression that they were the very first cases. Moreover, the noteworthy influenza outbreak at Camp Funston, Kansas, in March 2018, was mild, with many cases but few deaths. This was after New York City already had evidence of very high influenza mortality and increased mortality in young adults . The virus causing those cases in New York City in February presumably predated the March outbreak at Camp Funston. So what happened on this army base in Kansas was not the first large outbreak", "Title: Pandemic (H1N1) 2009 Influenza Community Transmission Was Established in One Australian State When the Virus Was First Identified in North America\nPassage: The first laboratory confirmed case in Victoria was notified on 20 May. Figure 1 shows notified cases by date of onset and location of acquisition until the commencement of the Modified Sustain phase; pandemic phase changes and case identification milestones are also indicated. Only 5% of the first 100 cases in Victoria were imported, and only eight of the 977 cases diagnosed prior to the introduction of the Modified Sustain phase reported a travel history. The first five diagnosed cases reported travel to the Americas: three brothers from one family returned from the US, a visitor from Mexico and another", "Title: The origins of the great pandemic\nPassage: closely associated with the pathogen involved, probably because some victims were asphyxiated by pus blocking their airways. Influenza was not a notifiable disease, but Miner, moved by the morbidity involved, sent off a report to the public health authorities . The significance of the incident, in Barry's view, lies in its timing and location. These deaths in rural Kansas took place in an area only a few hundred miles from a US Army Camp where, a few weeks later, Barry reports, one of the first recorded outbreaks of the pandemic may be said to have occurred." ]

[ [ "0a", "Title: The origins of the great pandemic" ], [ "0b", "Passage: In recent years, the question has arisen as to when and where the first case of the influenza pandemic of 1918 may have been detected." ], [ "0c", "At least three locations have been mooted." ], [ "0d", "First, the historian John Barry has suggested that Loring Miner, a physician in rural Kansas, in the USA, encountered cases in the early weeks of 1918 which, while akin to influenza, posed an unusual risk to life ." ], [ "0e", "Miner based his diagnosis on the symptomatology involved, and, interestingly, those symptoms did not include heliotrope cyanosis, which, as time drew on, came to be regarded as the tell-tale most" ] ]

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

[ "Title: The origins of the great pandemic\nPassage: In recent years, the question has arisen as to when and where the first case of the influenza pandemic of 1918 may have been detected. At least three locations have been mooted. First, the historian John Barry has suggested that Loring Miner, a physician in rural Kansas, in the USA, encountered cases in the early weeks of 1918 which, while akin to influenza, posed an unusual risk to life . Miner based his diagnosis on the symptomatology involved, and, interestingly, those symptoms did not include heliotrope cyanosis, which, as time drew on, came to be regarded as the tell-tale most", "Title: The origins of the great pandemic\nPassage: Kansas cases no doubt make for a compelling story, but one that has perhaps left a stronger-than-deserved impression that they were the very first cases. Moreover, the noteworthy influenza outbreak at Camp Funston, Kansas, in March 2018, was mild, with many cases but few deaths. This was after New York City already had evidence of very high influenza mortality and increased mortality in young adults . The virus causing those cases in New York City in February presumably predated the March outbreak at Camp Funston. So what happened on this army base in Kansas was not the first large outbreak", "Title: Pandemic (H1N1) 2009 Influenza Community Transmission Was Established in One Australian State When the Virus Was First Identified in North America\nPassage: The first laboratory confirmed case in Victoria was notified on 20 May. Figure 1 shows notified cases by date of onset and location of acquisition until the commencement of the Modified Sustain phase; pandemic phase changes and case identification milestones are also indicated. Only 5% of the first 100 cases in Victoria were imported, and only eight of the 977 cases diagnosed prior to the introduction of the Modified Sustain phase reported a travel history. The first five diagnosed cases reported travel to the Americas: three brothers from one family returned from the US, a visitor from Mexico and another", "Title: The origins of the great pandemic\nPassage: closely associated with the pathogen involved, probably because some victims were asphyxiated by pus blocking their airways. Influenza was not a notifiable disease, but Miner, moved by the morbidity involved, sent off a report to the public health authorities . The significance of the incident, in Barry's view, lies in its timing and location. These deaths in rural Kansas took place in an area only a few hundred miles from a US Army Camp where, a few weeks later, Barry reports, one of the first recorded outbreaks of the pandemic may be said to have occurred." ]

[ [ "3a", "Title: The origins of the great pandemic" ], [ "3b", "Passage: closely associated with the pathogen involved, probably because some victims were asphyxiated by pus blocking their airways." ], [ "3c", "Influenza was not a notifiable disease, but Miner, moved by the morbidity involved, sent off a report to the public health authorities ." ], [ "3d", "The significance of the incident, in Barry's view, lies in its timing and location." ], [ "3e", "These deaths in rural Kansas took place in an area only a few hundred miles from a US Army Camp where, a few weeks later, Barry reports, one of the first recorded outbreaks of the pandemic may be said to have occurred." ] ]

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

[ "Title: Enhanced Hygiene Measures and Norovirus Transmission during an Outbreak\nPassage: During the outbreak, the Municipal Health Service assessed the number of new cases from typical gastroenteritis symptoms self-reported by participants and staff. After the jamboree, participants and staff were given a questionnaire asking them to report to the Municipal Health Service whether gastroenteritis had developed within a week after departure. The questionnaire asked the date of symptom onset, symptoms, camp label, and hospital admission.", "Title: Enhanced Hygiene Measures and Norovirus Transmission during an Outbreak\nPassage: On July 29 , the Municipal Health Service \"Hart voor Brabant\" in 's-Hertogenbosch provided advice on enhanced hygiene measures , instructed participants about proper hand hygiene and use of soap pumps and disposable paper towels, and assigned separate toilets for sick participants. In addition, the Municipal Health Service provided guidelines for cleaning toilets and contaminated surfaces with a 1,000-ppm chlorine solution. Sick participants were instructed to go to a fi rst aid tent. Sick participants were not allowed to prepare food until 3 days after their last symptoms. Persons working in the jamboree's fi eld hospital were instructed to wear", "Title: A super-spreading ewe infects hundreds with Q fever at a farmers' market in Germany\nPassage: adults and children was estimated as 20% and 3%, respectively, 25% of cases were hospitalized. The ewe that had lambed as well as 25% of its herd tested positive for C. burnetii antibodies. CONCLUSION: Due to its size and point source nature this outbreak permitted assessment of fundamental, but seldom studied epidemiological parameters. As a consequence of this outbreak, it was recommended that pregnant sheep not be displayed in public during the 3trimester and to test animals in petting zoos regularly for C. burnetii.", "Title: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016\nPassage: bioassay. The C. botulinum strains from 10 cases showed a common profile on fAFLP typing, thereby confirming a link to a common source. All had a recent history of injecting heroin which was obtained either in, or sourced, via Glasgow. The source of infection remains unconfirmed but is thought to be due to contaminated heroin, or cutting agent. There were four deaths, botulism contributing to two. Police Scotland was closely involved in risk management through increased drug seizures throughout the region, reducing the supply of potentially 'contaminated' heroin. Public health measures included; risk communication via distributing postcards widely to PWIDs" ]

[ [ "2a", "Title: A super-spreading ewe infects hundreds with Q fever at a farmers' market in Germany" ], [ "2b", "Passage: adults and children was estimated as 20% and 3%, respectively, 25% of cases were hospitalized." ], [ "2c", "The ewe that had lambed as well as 25% of its herd tested positive for C. burnetii antibodies." ], [ "2d", "CONCLUSION: Due to its size and point source nature this outbreak permitted assessment of fundamental, but seldom studied epidemiological parameters." ], [ "2e", "As a consequence of this outbreak, it was recommended that pregnant sheep not be displayed in public during the 3trimester and to test animals in petting zoos regularly for C. burnetii." ] ]

[ "2e" ]

[ "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky\nPassage: Although the antigenic recycling hypothesis is an attractive explanation of the low 1918-1919 pandemic excess mortality rates among older adults, it is a less parsimonious explanation for younger individuals. Distinct mortality profiles in different regions of the world point to the contribution of distinct factors leading to increased risk among young adults and to protection among seniors. Moreover, the rapid attenuation of the excess mortality risk among young adults by winter 1919 in Kentucky and Scandinavia and by subsequent seasons in New York City and Poland is consistent with a short time scale suggestive of the loss of a pool", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Using mortality data for 1917, we characterized baseline death levels using weekly death rates and a simple, cyclical, Serfling linear regression model . However, this initial attempt to characterize the baseline did not capture a small but noticeable summer mortality peak. To account for this variation, we modified the initial Serfling model with additional parameters, as was done in another study of the 1957 influenza pandemic in Maricopa County, Arizona . The added coefficients in the model account for time and seasonal variations in normal influenza activity, such that the oscillations may be written as: To account for uncertainty in", "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky\nPassage: The atypically young age distribution of influenza-related deaths in the recent 2009 pandemic of influenza A virus subtype H1N1 infection was more reminiscent of the 1918-1919 pandemic than of later pandemics . Comparison of the age-based mortality risk profiles of the 2 pandemics, however, reveals substantial differences, most notably a peak among adults aged 50-64 years in 2009 . These differences lend further support to biological hypotheses that are unique to the 1918 virus and its historical context. Further comparisons of agebased mortality profiles across pandemics putatively associated with antigenic recycling would be interesting but would require mortality data stratified", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Although much progress has been made in uncovering the age-specific mortality patterns of this pandemic in several populations in Latin America , the United States, and Europe , more studies are needed to make sense of the heterogeneous death impact of this pandemic across different populations around the world. For instance, by characterizing and comparing the age-specific excess death rates across pandemic waves during 1918-1920 in different populations, researchers could suggest alternative hypotheses on the drivers of pandemic mortality risk at the time and place more emphasis on less-studied phenomena associated with the pandemic." ]

[ [ "0a", "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky" ], [ "0b", "Passage: Although the antigenic recycling hypothesis is an attractive explanation of the low 1918-1919 pandemic excess mortality rates among older adults, it is a less parsimonious explanation for younger individuals." ], [ "0c", "Distinct mortality profiles in different regions of the world point to the contribution of distinct factors leading to increased risk among young adults and to protection among seniors." ], [ "0d", "Moreover, the rapid attenuation of the excess mortality risk among young adults by winter 1919 in Kentucky and Scandinavia and by subsequent seasons in New York City and Poland is consistent with a short time scale suggestive of the loss of a pool" ] ]

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

[ "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky\nPassage: Although the antigenic recycling hypothesis is an attractive explanation of the low 1918-1919 pandemic excess mortality rates among older adults, it is a less parsimonious explanation for younger individuals. Distinct mortality profiles in different regions of the world point to the contribution of distinct factors leading to increased risk among young adults and to protection among seniors. Moreover, the rapid attenuation of the excess mortality risk among young adults by winter 1919 in Kentucky and Scandinavia and by subsequent seasons in New York City and Poland is consistent with a short time scale suggestive of the loss of a pool", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Using mortality data for 1917, we characterized baseline death levels using weekly death rates and a simple, cyclical, Serfling linear regression model . However, this initial attempt to characterize the baseline did not capture a small but noticeable summer mortality peak. To account for this variation, we modified the initial Serfling model with additional parameters, as was done in another study of the 1957 influenza pandemic in Maricopa County, Arizona . The added coefficients in the model account for time and seasonal variations in normal influenza activity, such that the oscillations may be written as: To account for uncertainty in", "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky\nPassage: The atypically young age distribution of influenza-related deaths in the recent 2009 pandemic of influenza A virus subtype H1N1 infection was more reminiscent of the 1918-1919 pandemic than of later pandemics . Comparison of the age-based mortality risk profiles of the 2 pandemics, however, reveals substantial differences, most notably a peak among adults aged 50-64 years in 2009 . These differences lend further support to biological hypotheses that are unique to the 1918 virus and its historical context. Further comparisons of agebased mortality profiles across pandemics putatively associated with antigenic recycling would be interesting but would require mortality data stratified", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: Although much progress has been made in uncovering the age-specific mortality patterns of this pandemic in several populations in Latin America , the United States, and Europe , more studies are needed to make sense of the heterogeneous death impact of this pandemic across different populations around the world. For instance, by characterizing and comparing the age-specific excess death rates across pandemic waves during 1918-1920 in different populations, researchers could suggest alternative hypotheses on the drivers of pandemic mortality risk at the time and place more emphasis on less-studied phenomena associated with the pandemic." ]

[ [ "2a", "Title: Age- and Sex-Specific Mortality Associated With the 1918–1919 Influenza Pandemic in Kentucky" ], [ "2b", "Passage: The atypically young age distribution of influenza-related deaths in the recent 2009 pandemic of influenza A virus subtype H1N1 infection was more reminiscent of the 1918-1919 pandemic than of later pandemics ." ], [ "2c", "Comparison of the age-based mortality risk profiles of the 2 pandemics, however, reveals substantial differences, most notably a peak among adults aged 50-64 years in 2009 ." ], [ "2d", "These differences lend further support to biological hypotheses that are unique to the 1918 virus and its historical context." ], [ "2e", "Further comparisons of agebased mortality profiles across pandemics putatively associated with antigenic recycling would be interesting but would require mortality data stratified" ] ]

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

[ "Title: A multidimensional classification of public health activity in Australia\nPassage: Factors that influence health status and determine health differentials or health inequalities. They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; physical and social factors, including employment and education, housing quality, the workplace and the wider urban and rural environment; and access to health care .", "Title: Viral factors in influenza pandemic risk assessment\nPassage: host factor or enhance its ability to repel a restriction factor . Recently a host factor, ANP32A, that differs between mammals and flighted birds was shown to be a cofactor of the influenza polymerase, and the species specific difference could explain the inefficient function of avian virus polymerase and the stringent selection for the 627Glu->Lys adaptive mutation in mammals .", "Title: Interrelationship between Climatic, Ecologic, Social, and Cultural Determinants Affecting Dengue Emergence and Transmission in Puerto Rico and Their Implications for Zika Response\nPassage: There are several limitations in this literature review. First, this review was not exhaustive as only extrinsic transmission factors were included in the analysis. Other factors, such as intrinsic factors pertaining to human immunity and the dengue virus , are important to consider in future studies. Second, there is an inherent risk of bias in the studies included in this review since only peer-reviewed studies were included . Third, there is also an inherit level of simplicity in the studies included as they investigated only one or two variables. Many of the included studies are limited by their design .", "Title: A multidimensional classification of public health activity in Australia\nPassage: Factors that influence health status and determine health differentials or health inequalities. They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; the physical and social environment, including housing quality, the workplace and the wider urban and rural environment; and access to health care. 47" ]

[ [ "0a", "Title: A multidimensional classification of public health activity in Australia" ], [ "0b", "Passage: Factors that influence health status and determine health differentials or health inequalities." ], [ "0c", "They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; physical and social factors, including employment and education, housing quality, the workplace and the wider urban and rural environment; and access to health care ." ] ]

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

[ "Title: A multidimensional classification of public health activity in Australia\nPassage: Factors that influence health status and determine health differentials or health inequalities. They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; physical and social factors, including employment and education, housing quality, the workplace and the wider urban and rural environment; and access to health care .", "Title: Viral factors in influenza pandemic risk assessment\nPassage: host factor or enhance its ability to repel a restriction factor . Recently a host factor, ANP32A, that differs between mammals and flighted birds was shown to be a cofactor of the influenza polymerase, and the species specific difference could explain the inefficient function of avian virus polymerase and the stringent selection for the 627Glu->Lys adaptive mutation in mammals .", "Title: Interrelationship between Climatic, Ecologic, Social, and Cultural Determinants Affecting Dengue Emergence and Transmission in Puerto Rico and Their Implications for Zika Response\nPassage: There are several limitations in this literature review. First, this review was not exhaustive as only extrinsic transmission factors were included in the analysis. Other factors, such as intrinsic factors pertaining to human immunity and the dengue virus , are important to consider in future studies. Second, there is an inherent risk of bias in the studies included in this review since only peer-reviewed studies were included . Third, there is also an inherit level of simplicity in the studies included as they investigated only one or two variables. Many of the included studies are limited by their design .", "Title: A multidimensional classification of public health activity in Australia\nPassage: Factors that influence health status and determine health differentials or health inequalities. They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; the physical and social environment, including housing quality, the workplace and the wider urban and rural environment; and access to health care. 47" ]

[ [ "3a", "Title: A multidimensional classification of public health activity in Australia" ], [ "3b", "Passage: Factors that influence health status and determine health differentials or health inequalities." ], [ "3c", "They include, for example, natural, biological factors, such as age, sex and ethnicity; behaviour and lifestyles, such as smoking, alcohol consumption, diet and physical activity; the physical and social environment, including housing quality, the workplace and the wider urban and rural environment; and access to health care. 47" ] ]

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

[ "Title: Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)\nPassage: Between April 2014 and September 2016, a total of 616 patients with RTI were recruited . The panel diagnosed 516 patients as having a bacterial or a viral infection, encompassing 284 children and 232 adults . The expert panel diagnosed 12 adults as having a non-infectious disease . The reference standard diagnosis was inconclusive for 18 children and 70 adults. In 44% of the children with bacterial and viral RTI had comorbidity and not 'bacterial and viral RTI comorbiditis, most of them had mild diseases . In adults, comorbidity was seen more often and chronic diseases were more diverse .", "Title: Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012–2013: A PCR/Electrospray Ionization Mass Spectrometry Study\nPassage: During the 9-month study period, a total of 267 episodes of acute RTIs from 263 patients were recorded, including 96 episodes at a local clinic and 171 episodes at NCKUH . For convenience, each episode was counted as 1 case. Overall, 123 cases were male patients, and 152 , 60 , and 55 patients were 18 to 39, 40 to 59, and !60 years of age, respectively. Two-hundred and twelve patients presented with upper RTIs , and 55 cases presented with LRTIs. Compared with patients attending the local clinic, patients attending the medical care center were older and had more", "Title: Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012–2013: A PCR/Electrospray Ionization Mass Spectrometry Study\nPassage: To conduct a comprehensive epidemiologic study that included patients with and without comorbidity, we enrolled adults with acute RTIs within 7 days of onset who were treated at a local outpatient clinic of YC hospital or the outpatient or emergency departments of National Cheng-Kung University Hospital , a university-affiliated medical center in southern Taiwan, between October 2012 and June 2013. Acute RTI was defined as the simultaneous occurrence of at least 1 respiratory symptom or sign and at least 1 of the following symptoms: fever, chills, and cough. Lower RTI was defined as the presence of acute RTI and a", "Title: Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)\nPassage: Patient recruitment for this prospective biomarker TTT-study took place in convenience and consecutive series at the ED and wards of secondary and tertiary hospitals in The Netherlands and Israel . For this subgroup analyses, paediatric patients and adult patients , with a suspected upper and/or lower RTI and a maximal disease duration of 8 days, were selected. RTI was defined as presence of two or more of the following signs: tachypnea, cough, nasal flaring, chest retractions, rales, expiratory wheeze and/or decreased breath sounds. For children, WHO age-specific criteria for tachypnea were used . Patients were excluded in case of: previous" ]

[ [ "0a", "Title: Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)" ], [ "0b", "Passage: Between April 2014 and September 2016, a total of 616 patients with RTI were recruited ." ], [ "0c", "The panel diagnosed 516 patients as having a bacterial or a viral infection, encompassing 284 children and 232 adults ." ], [ "0d", "The expert panel diagnosed 12 adults as having a non-infectious disease ." ], [ "0e", "The reference standard diagnosis was inconclusive for 18 children and 70 adults." ], [ "0f", "In 44% of the children with bacterial and viral RTI had comorbidity and not 'bacterial and viral RTI comorbiditis, most of them had mild diseases ." ], [ "0g", "In adults, comorbidity was seen more often and chronic diseases were more diverse ." ] ]

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

[ "Title: Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)\nPassage: Between April 2014 and September 2016, a total of 616 patients with RTI were recruited . The panel diagnosed 516 patients as having a bacterial or a viral infection, encompassing 284 children and 232 adults . The expert panel diagnosed 12 adults as having a non-infectious disease . The reference standard diagnosis was inconclusive for 18 children and 70 adults. In 44% of the children with bacterial and viral RTI had comorbidity and not 'bacterial and viral RTI comorbiditis, most of them had mild diseases . In adults, comorbidity was seen more often and chronic diseases were more diverse .", "Title: Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012–2013: A PCR/Electrospray Ionization Mass Spectrometry Study\nPassage: During the 9-month study period, a total of 267 episodes of acute RTIs from 263 patients were recorded, including 96 episodes at a local clinic and 171 episodes at NCKUH . For convenience, each episode was counted as 1 case. Overall, 123 cases were male patients, and 152 , 60 , and 55 patients were 18 to 39, 40 to 59, and !60 years of age, respectively. Two-hundred and twelve patients presented with upper RTIs , and 55 cases presented with LRTIs. Compared with patients attending the local clinic, patients attending the medical care center were older and had more", "Title: Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012–2013: A PCR/Electrospray Ionization Mass Spectrometry Study\nPassage: To conduct a comprehensive epidemiologic study that included patients with and without comorbidity, we enrolled adults with acute RTIs within 7 days of onset who were treated at a local outpatient clinic of YC hospital or the outpatient or emergency departments of National Cheng-Kung University Hospital , a university-affiliated medical center in southern Taiwan, between October 2012 and June 2013. Acute RTI was defined as the simultaneous occurrence of at least 1 respiratory symptom or sign and at least 1 of the following symptoms: fever, chills, and cough. Lower RTI was defined as the presence of acute RTI and a", "Title: Antibiotic misuse in respiratory tract infections in children and adults—a prospective, multicentre study (TAILORED Treatment)\nPassage: Patient recruitment for this prospective biomarker TTT-study took place in convenience and consecutive series at the ED and wards of secondary and tertiary hospitals in The Netherlands and Israel . For this subgroup analyses, paediatric patients and adult patients , with a suspected upper and/or lower RTI and a maximal disease duration of 8 days, were selected. RTI was defined as presence of two or more of the following signs: tachypnea, cough, nasal flaring, chest retractions, rales, expiratory wheeze and/or decreased breath sounds. For children, WHO age-specific criteria for tachypnea were used . Patients were excluded in case of: previous" ]

[ [ "1a", "Title: Viral Respiratory Tract Infections in Adult Patients Attending Outpatient and Emergency Departments, Taiwan, 2012–2013: A PCR/Electrospray Ionization Mass Spectrometry Study" ], [ "1b", "Passage: During the 9-month study period, a total of 267 episodes of acute RTIs from 263 patients were recorded, including 96 episodes at a local clinic and 171 episodes at NCKUH ." ], [ "1c", "For convenience, each episode was counted as 1 case." ], [ "1d", "Overall, 123 cases were male patients, and 152 , 60 , and 55 patients were 18 to 39, 40 to 59, and !60 years of age, respectively." ], [ "1e", "Two-hundred and twelve patients presented with upper RTIs , and 55 cases presented with LRTIs." ], [ "1f", "Compared with patients attending the local clinic, patients attending the medical care center were older and had more" ] ]

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

[ "Title: The early change of SOFA score as a prognostic marker of 28-day sepsis mortality: analysis through a derivation and a validation cohort\nPassage: non-survivors were done by the Mann-Whitney U test. Breslow-Day's test was used to compare the performance of this cutoff value between the derivation and validation cohorts. A p value lower than 0.05 was considered statistically significant. All p values were twosided. Statistical analyses were performed using SPSS version 25.0 software.", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?\nPassage: In the assessment of item discrimination, the discrimination index was computed by subtracting the mean score of participants in the lower group from the mean value of those in the upper group and dividing it by the maximum possible discrimination. A value of 0.19 or below indicated that the item was subject to improvement . Items with D < 0.19 included items 3, 4, 8, 13, 14, and 15. These six items were eliminated from the scale, thereby reducing the number of items from 24 to 18.", "Title: Interrelationship between Climatic, Ecologic, Social, and Cultural Determinants Affecting Dengue Emergence and Transmission in Puerto Rico and Their Implications for Zika Response\nPassage: Not Applicable because of the study design were disregarded. Each study was then given an overall quality score represented by the quintile range of the percentage of applicable Fink criteria answered in the affirmative. If the study satisfied 80-100% of applicable Fink criteria, it received a quality score of 5, satisfying between 60 and 79% resulting in a score of 4, those between 40 and 59% received a score of 3, those between 20 and 39% received a score of 2, and those between 0 and 19% received a score of 1. A score of 1-2 was considered fair; scores", "Title: Selection of key recommendations for quality indicators describing good quality outbreak response\nPassage: 8 or 9 and >70% of the experts scored in the top tertile, then the recommendation was marked as \"accepted\". If the recommendation had a median <8 and <70% scored in the top tertile, then the recommendation was marked as \"not accepted\" and was excluded. If the recommendation had a median <8 and >70% of the experts scored in the top tertile or the median was 8 or 9 and <70% of the experts scored in the top tertile, then the recommendation was marked as \"to be discussed\"." ]

[ [ "1a", "Title: Suffering a Loss Is Good Fortune: Myth or Reality?" ], [ "1b", "Passage: In the assessment of item discrimination, the discrimination index was computed by subtracting the mean score of participants in the lower group from the mean value of those in the upper group and dividing it by the maximum possible discrimination." ], [ "1c", "A value of 0.19 or below indicated that the item was subject to improvement ." ], [ "1d", "Items with D < 0.19 included items 3, 4, 8, 13, 14, and 15." ], [ "1e", "These six items were eliminated from the scale, thereby reducing the number of items from 24 to 18." ] ]

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

[ "Title: Multiplexed Nucleic Acid Programmable Protein Arrays\nPassage: These results indicate that M-NAPPA can be used for preliminary high throughput screening of novel protein-protein interactions. The screen can then be followed by a verification step using deconvoluted spots via NAPPA to identify the specific proteins that are involved.", "Title: Multiplexed Nucleic Acid Programmable Protein Arrays\nPassage: Third, we showed that M-NAPPA can be used in protein-protein interaction and serological screening studies. The results from M-NAPPA agreed strongly with those observed with non-multiplexed NAPPA . These data indicate that M-NAPPA presents a labor-and cost-effective strategy to initially screen for hits.", "Title: Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples\nPassage: the enteric and respiratory syndromes, for cases of E. coli infection, the PPA was 70% and the NPA was 100%, and for C. perfringens, the PPA was 56% and the NPA was 100%. For respiratory cases, the PPA for Mannheimia haemolytica was 78% and the NPA was 67%, and for Pasteurella multocida, the PPA was 71% and the NPA was 63%. The PPA for Histophilus somni was 100% and the NPA was 70%, and the PPA and NPA for Mycoplasma bovis were both 100%.", "Title: Multiplexed Nucleic Acid Programmable Protein Arrays\nPassage: To test whether M-NAPPA can be used to detect proteomic serological response, we screened ten serum samples from patients with type 1 diabetes that had been previously characterized using NAPPA arrays . A dozen hits were observed with M-NAPPA and NAPPA . Forty-nine of the 53 antigens identified by NAPPA were also detected by M-NAPPA. Four antigens, however, were detected with only one platform . These uncommon discrepancies may be due to variations in surface chemistry, plasmid concentration, printing or array processing." ]

[ [ "2a", "Title: Evaluation of Targeted Next-Generation Sequencing for Detection of Bovine Pathogens in Clinical Samples" ], [ "2b", "Passage: the enteric and respiratory syndromes, for cases of E. coli infection, the PPA was 70% and the NPA was 100%, and for C. perfringens, the PPA was 56% and the NPA was 100%." ], [ "2c", "For respiratory cases, the PPA for Mannheimia haemolytica was 78% and the NPA was 67%, and for Pasteurella multocida, the PPA was 71% and the NPA was 63%." ], [ "2d", "The PPA for Histophilus somni was 100% and the NPA was 70%, and the PPA and NPA for Mycoplasma bovis were both 100%." ] ]

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

[ "Title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis\nPassage: In our patient, hemodynamic investigations using echocardiography and the PICCO system showed hypovolemia with low filling pressures and without any ventricular dysfunction. An elevated amount of extravascular lung water as well as an increased vascular permeability were also observed. This result is confirmed by the chest CT scan findings, showing a large amount of water in the alveoli, in the perivascular and in the pleural space. The pleural effusion was exudative and contained a high quantity of protein which can be explained by a protein leakage rather than by an inflammatory origin.", "Title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis\nPassage: Under normal conditions, the endothelium plays the role of a selective permeable barrier to regulate plasma fluid exchange, as well as molecules and cells trafficking. Disruption of cell junctions, with combination of cell retraction process, lead to the loss of the vascular endothelium barrier function. In such conditions, fluids and proteins infusion are ineffective because of the immediate leakage to the interstitial space with a worsening of the respiratory failure without any efficacy on the hemodynamic state. This mechanism is similar to that reported by Clarkson in 1960 and is explained by a plasma leakage which was also described in", "Title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis\nPassage: In our case, symptoms recorded at admission were compatible with acute infection by hantavirus and required admission to the ICU. The mechanism which may explain the severity of the disease is the tropism of hantavirus for the microvascular endothelial cell . This tropism causes microvascular hyperpermeability with fluid and proteins leakage leading to hypovolemia and to a non cardiogenic pulmonary oedema. Biologically, we observe an increased haematocrit level due to hemoconcentration, and a paradoxical reduced serum Fig. 1 Evolution of the serum protein and hematocrit levels during the first 14 days proteins level secondary to the transfer of proteins from", "Title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis\nPassage: The pathogenesis of capillary leakage remains undefined. Some evidence suggest that hantavirus disease pathogenesis is immunologically mediated by cytotoxic T lymphocytes and other immune cells in target organs producing inflammatory cytokines. Overall, three hypotheses have been reported to explain the mechanism of increased capillary permeability involved in hantavirus infection: a) the attack of infected endothelial cells by virus-specific cytotoxic T lymphocytes , b) TNF-α production by infected monocyte/macrophages and finally c) the direct effect of the virus on the endothelial cell functions . Bradykinin, a potent inflammatory and vasoactive nonapeptide generated by kallikrein at the sites of tissue injury is" ]

[ [ "3a", "Title: Capillary leak-syndrome triggered by Maripa virus in French Guiana: case report and implication for pathogenesis" ], [ "3b", "Passage: The pathogenesis of capillary leakage remains undefined." ], [ "3c", "Some evidence suggest that hantavirus disease pathogenesis is immunologically mediated by cytotoxic T lymphocytes and other immune cells in target organs producing inflammatory cytokines." ], [ "3d", "Overall, three hypotheses have been reported to explain the mechanism of increased capillary permeability involved in hantavirus infection: a) the attack of infected endothelial cells by virus-specific cytotoxic T lymphocytes , b) TNF-α production by infected monocyte/macrophages and finally c) the direct effect of the virus on the endothelial cell functions ." ], [ "3e", "Bradykinin, a potent inflammatory and vasoactive nonapeptide generated by kallikrein at the sites of tissue injury is" ] ]

[ "3d" ]

[ "Title: Temporal trends in the discovery of human viruses\nPassage: is therefore of considerable interest.", "Title: Temporal trends in the discovery of human viruses\nPassage: M. E. J. Woolhouse et al. 2115", "Title: Temporal trends in the discovery of human viruses\nPassage: We confirmed that our model reproduced the observed slight downward trend in the rate of discovery since 1954 and the observed variance in the data from 1954 to 2006 . The distribution of the number of virus species discovered per year shows slight overdispersion which falls within the predicted range . Together, these results support our choice of model, even though we do not explicitly consider heterogeneity in the probability of discovering a given species in any one year or temporal variation in sampling effort, detection techniques and reporting.", "Title: Temporal trends in the discovery of human viruses\nPassage: as analogous to constructing species discovery curves for any subdivision of geographical range or habitat. As we demonstrate below, this approach yields an excellent description of the discovery curve." ]

[ [ "2a", "Title: Temporal trends in the discovery of human viruses" ], [ "2b", "Passage: We confirmed that our model reproduced the observed slight downward trend in the rate of discovery since 1954 and the observed variance in the data from 1954 to 2006 ." ], [ "2c", "The distribution of the number of virus species discovered per year shows slight overdispersion which falls within the predicted range ." ], [ "2d", "Together, these results support our choice of model, even though we do not explicitly consider heterogeneity in the probability of discovering a given species in any one year or temporal variation in sampling effort, detection techniques and reporting." ] ]

[ "2b" ]

[ "Title: Nucleolus: the fascinating nuclear body\nPassage: processing suggests that processing complexes are at least to some extent maintained during mitosis. It is as yet unknown whether migration of the nucleolar processing proteins occurring at the onset of mitosis takes place as a consequence of the arrest of pre-rRNA synthesis or whether it is also regulated. Indeed, it is noticeable that during prophase, the components of the rRNA processing machinery appear to be delocalized before total repression of rDNA transcription occurs, and the most recently synthesized pre-rRNAs accumulate as partially processed 45S pre-rRNAs suggesting that total repression of pre-rRNA processing could occur prior to total repression of", "Title: Nucleolus: the fascinating nuclear body\nPassage: mitosis induces the Wrst events of nucleologenesis. Strikingly, Wbrillarin concentrates in PNBs and rDNA clusters when decrease in CDK1-cyclin B activity overcomes the mitotic repression of RNA pol I transcription , while Nop52 and other GC proteins are recruited later on transcription sites. This late recruitment is under the control of cyclin-dependent kinases since CDK inhibitors block this process . Thus, it seems that recruitment of the processing machinery at the time of nucleolar assembly is a regulated process most probably dependent on cell cycle progression. This provides a physiological situation to investigate the formation, control and dynamics of nuclear", "Title: Nucleolus: the fascinating nuclear body\nPassage: At the beginning of prophase, the components of the pre-rRNA processing machinery do not remain in the vicinity of the rDNAs but become partially distributed over the surface of all the chromosomes . The nucleolar proteins that relocate to the chromosome periphery are components of the DFC and GC of the active nucleolus. In living cells, nucleolar proteins tagged with GFP are concentrated around the chromosomes during mitosis and migrate with the chromosomes . However, the mechanisms maintaining interactions of nucleolar processing proteins with chromosomes during mitosis have not been characterized. The colocalization of the diVerent factors involved in pre-rRNA", "Title: Nucleolus: the fascinating nuclear body\nPassage: The dynamics of the processing nucleolar proteins was analyzed at the transition mitosis/interphase using rapid time-lapse video microscopy . The Wrst detectable assembly of proteins in foci occurred on the surface of the chromosome during telophase , followed by the progressive delivery of proteins to nucleoli ensured by progressive and sequential release of proteins from PNBs . Based on the observations of diVerent Wxed cells, it was concluded that the early processing proteins are recruited Wrst on transcription sites while the majority of the late processing proteins are still in PNBs . This sequence of events was conWrmed in living" ]

[ [ "0a", "Title: Nucleolus: the fascinating nuclear body" ], [ "0b", "Passage: processing suggests that processing complexes are at least to some extent maintained during mitosis." ], [ "0c", "It is as yet unknown whether migration of the nucleolar processing proteins occurring at the onset of mitosis takes place as a consequence of the arrest of pre-rRNA synthesis or whether it is also regulated." ], [ "0d", "Indeed, it is noticeable that during prophase, the components of the rRNA processing machinery appear to be delocalized before total repression of rDNA transcription occurs, and the most recently synthesized pre-rRNAs accumulate as partially processed 45S pre-rRNAs suggesting that total repression of pre-rRNA processing could occur prior to total repression of" ] ]

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

[ "Title: Nucleolus: the fascinating nuclear body\nPassage: processing suggests that processing complexes are at least to some extent maintained during mitosis. It is as yet unknown whether migration of the nucleolar processing proteins occurring at the onset of mitosis takes place as a consequence of the arrest of pre-rRNA synthesis or whether it is also regulated. Indeed, it is noticeable that during prophase, the components of the rRNA processing machinery appear to be delocalized before total repression of rDNA transcription occurs, and the most recently synthesized pre-rRNAs accumulate as partially processed 45S pre-rRNAs suggesting that total repression of pre-rRNA processing could occur prior to total repression of", "Title: Nucleolus: the fascinating nuclear body\nPassage: mitosis induces the Wrst events of nucleologenesis. Strikingly, Wbrillarin concentrates in PNBs and rDNA clusters when decrease in CDK1-cyclin B activity overcomes the mitotic repression of RNA pol I transcription , while Nop52 and other GC proteins are recruited later on transcription sites. This late recruitment is under the control of cyclin-dependent kinases since CDK inhibitors block this process . Thus, it seems that recruitment of the processing machinery at the time of nucleolar assembly is a regulated process most probably dependent on cell cycle progression. This provides a physiological situation to investigate the formation, control and dynamics of nuclear", "Title: Nucleolus: the fascinating nuclear body\nPassage: At the beginning of prophase, the components of the pre-rRNA processing machinery do not remain in the vicinity of the rDNAs but become partially distributed over the surface of all the chromosomes . The nucleolar proteins that relocate to the chromosome periphery are components of the DFC and GC of the active nucleolus. In living cells, nucleolar proteins tagged with GFP are concentrated around the chromosomes during mitosis and migrate with the chromosomes . However, the mechanisms maintaining interactions of nucleolar processing proteins with chromosomes during mitosis have not been characterized. The colocalization of the diVerent factors involved in pre-rRNA", "Title: Nucleolus: the fascinating nuclear body\nPassage: The dynamics of the processing nucleolar proteins was analyzed at the transition mitosis/interphase using rapid time-lapse video microscopy . The Wrst detectable assembly of proteins in foci occurred on the surface of the chromosome during telophase , followed by the progressive delivery of proteins to nucleoli ensured by progressive and sequential release of proteins from PNBs . Based on the observations of diVerent Wxed cells, it was concluded that the early processing proteins are recruited Wrst on transcription sites while the majority of the late processing proteins are still in PNBs . This sequence of events was conWrmed in living" ]

[ [ "1a", "Title: Nucleolus: the fascinating nuclear body" ], [ "1b", "Passage: mitosis induces the Wrst events of nucleologenesis." ], [ "1c", "Strikingly, Wbrillarin concentrates in PNBs and rDNA clusters when decrease in CDK1-cyclin B activity overcomes the mitotic repression of RNA pol I transcription , while Nop52 and other GC proteins are recruited later on transcription sites." ], [ "1d", "This late recruitment is under the control of cyclin-dependent kinases since CDK inhibitors block this process ." ], [ "1e", "Thus, it seems that recruitment of the processing machinery at the time of nucleolar assembly is a regulated process most probably dependent on cell cycle progression." ], [ "1f", "This provides a physiological situation to investigate the formation, control and dynamics of nuclear" ] ]

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

[ "Title: Nucleolus: the fascinating nuclear body\nPassage: processing suggests that processing complexes are at least to some extent maintained during mitosis. It is as yet unknown whether migration of the nucleolar processing proteins occurring at the onset of mitosis takes place as a consequence of the arrest of pre-rRNA synthesis or whether it is also regulated. Indeed, it is noticeable that during prophase, the components of the rRNA processing machinery appear to be delocalized before total repression of rDNA transcription occurs, and the most recently synthesized pre-rRNAs accumulate as partially processed 45S pre-rRNAs suggesting that total repression of pre-rRNA processing could occur prior to total repression of", "Title: Nucleolus: the fascinating nuclear body\nPassage: mitosis induces the Wrst events of nucleologenesis. Strikingly, Wbrillarin concentrates in PNBs and rDNA clusters when decrease in CDK1-cyclin B activity overcomes the mitotic repression of RNA pol I transcription , while Nop52 and other GC proteins are recruited later on transcription sites. This late recruitment is under the control of cyclin-dependent kinases since CDK inhibitors block this process . Thus, it seems that recruitment of the processing machinery at the time of nucleolar assembly is a regulated process most probably dependent on cell cycle progression. This provides a physiological situation to investigate the formation, control and dynamics of nuclear", "Title: Nucleolus: the fascinating nuclear body\nPassage: At the beginning of prophase, the components of the pre-rRNA processing machinery do not remain in the vicinity of the rDNAs but become partially distributed over the surface of all the chromosomes . The nucleolar proteins that relocate to the chromosome periphery are components of the DFC and GC of the active nucleolus. In living cells, nucleolar proteins tagged with GFP are concentrated around the chromosomes during mitosis and migrate with the chromosomes . However, the mechanisms maintaining interactions of nucleolar processing proteins with chromosomes during mitosis have not been characterized. The colocalization of the diVerent factors involved in pre-rRNA", "Title: Nucleolus: the fascinating nuclear body\nPassage: The dynamics of the processing nucleolar proteins was analyzed at the transition mitosis/interphase using rapid time-lapse video microscopy . The Wrst detectable assembly of proteins in foci occurred on the surface of the chromosome during telophase , followed by the progressive delivery of proteins to nucleoli ensured by progressive and sequential release of proteins from PNBs . Based on the observations of diVerent Wxed cells, it was concluded that the early processing proteins are recruited Wrst on transcription sites while the majority of the late processing proteins are still in PNBs . This sequence of events was conWrmed in living" ]

[ [ "2a", "Title: Nucleolus: the fascinating nuclear body" ], [ "2b", "Passage: At the beginning of prophase, the components of the pre-rRNA processing machinery do not remain in the vicinity of the rDNAs but become partially distributed over the surface of all the chromosomes ." ], [ "2c", "The nucleolar proteins that relocate to the chromosome periphery are components of the DFC and GC of the active nucleolus." ], [ "2d", "In living cells, nucleolar proteins tagged with GFP are concentrated around the chromosomes during mitosis and migrate with the chromosomes ." ], [ "2e", "However, the mechanisms maintaining interactions of nucleolar processing proteins with chromosomes during mitosis have not been characterized." ], [ "2f", "The colocalization of the diVerent factors involved in pre-rRNA" ] ]

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

[ "Title: Nucleolus: the fascinating nuclear body\nPassage: processing suggests that processing complexes are at least to some extent maintained during mitosis. It is as yet unknown whether migration of the nucleolar processing proteins occurring at the onset of mitosis takes place as a consequence of the arrest of pre-rRNA synthesis or whether it is also regulated. Indeed, it is noticeable that during prophase, the components of the rRNA processing machinery appear to be delocalized before total repression of rDNA transcription occurs, and the most recently synthesized pre-rRNAs accumulate as partially processed 45S pre-rRNAs suggesting that total repression of pre-rRNA processing could occur prior to total repression of", "Title: Nucleolus: the fascinating nuclear body\nPassage: mitosis induces the Wrst events of nucleologenesis. Strikingly, Wbrillarin concentrates in PNBs and rDNA clusters when decrease in CDK1-cyclin B activity overcomes the mitotic repression of RNA pol I transcription , while Nop52 and other GC proteins are recruited later on transcription sites. This late recruitment is under the control of cyclin-dependent kinases since CDK inhibitors block this process . Thus, it seems that recruitment of the processing machinery at the time of nucleolar assembly is a regulated process most probably dependent on cell cycle progression. This provides a physiological situation to investigate the formation, control and dynamics of nuclear", "Title: Nucleolus: the fascinating nuclear body\nPassage: At the beginning of prophase, the components of the pre-rRNA processing machinery do not remain in the vicinity of the rDNAs but become partially distributed over the surface of all the chromosomes . The nucleolar proteins that relocate to the chromosome periphery are components of the DFC and GC of the active nucleolus. In living cells, nucleolar proteins tagged with GFP are concentrated around the chromosomes during mitosis and migrate with the chromosomes . However, the mechanisms maintaining interactions of nucleolar processing proteins with chromosomes during mitosis have not been characterized. The colocalization of the diVerent factors involved in pre-rRNA", "Title: Nucleolus: the fascinating nuclear body\nPassage: The dynamics of the processing nucleolar proteins was analyzed at the transition mitosis/interphase using rapid time-lapse video microscopy . The Wrst detectable assembly of proteins in foci occurred on the surface of the chromosome during telophase , followed by the progressive delivery of proteins to nucleoli ensured by progressive and sequential release of proteins from PNBs . Based on the observations of diVerent Wxed cells, it was concluded that the early processing proteins are recruited Wrst on transcription sites while the majority of the late processing proteins are still in PNBs . This sequence of events was conWrmed in living" ]

[ [ "3a", "Title: Nucleolus: the fascinating nuclear body" ], [ "3b", "Passage: The dynamics of the processing nucleolar proteins was analyzed at the transition mitosis/interphase using rapid time-lapse video microscopy ." ], [ "3c", "The Wrst detectable assembly of proteins in foci occurred on the surface of the chromosome during telophase , followed by the progressive delivery of proteins to nucleoli ensured by progressive and sequential release of proteins from PNBs ." ], [ "3d", "Based on the observations of diVerent Wxed cells, it was concluded that the early processing proteins are recruited Wrst on transcription sites while the majority of the late processing proteins are still in PNBs ." ], [ "3e", "This sequence of events was conWrmed in living" ] ]

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

[ "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: The premise of this tool is that researchers must be able to exchange and share their results. The development and broad acceptance of common model representation formats such as SBML is a crucial step in that direction, allowing researchers to exchange and build upon each other's work with greater ease and accuracy.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: The vaccine project is a single study project that uses a single influenza-based model of a medium-sized city in the United States. It was developed by the Emory Group headed by Ira Longini. The study consists of six runs generated from a single epidemiological model of disease spread. The main hypothesis behind the vaccine distribution study is to assess whether targeted antiviral prophylaxis , taken prophylactically, is effective in containing influenza. The authors conclude that TAP is nearly as effective as vaccinating 80% of the population, and further, that vaccinating 80% of children less than 19 years of age is", "Title: A Lattice Model for Influenza Spreading\nPassage: In the present model, we simply introduce some very basic rules of social distancing, which are over-imposed to the usual mobility rules during the epidemic. The upgrade of the model in order to include the effects of self-initiated behavioral changes will be discussed in a forthcoming paper.", "Title: Modelling and analysing the coexistence of dual dilemmas in the proactive vaccination game and retroactive treatment game in epidemic viral dynamics\nPassage: The remainder of this paper is organized as follows. The 'Methods and model' section introduces the new model of epidemic vaccination with the antiviral treatment model and demonstrates it schematically. The 'Results and discussion' section validates the proposed model in numerical simulations. Finally, the 'Conclusion' section summarizes and further discusses our findings." ]

[ [ "3a", "Title: Modelling and analysing the coexistence of dual dilemmas in the proactive vaccination game and retroactive treatment game in epidemic viral dynamics" ], [ "3b", "Passage: The remainder of this paper is organized as follows." ], [ "3c", "The 'Methods and model' section introduces the new model of epidemic vaccination with the antiviral treatment model and demonstrates it schematically." ], [ "3d", "The 'Results and discussion' section validates the proposed model in numerical simulations." ], [ "3e", "Finally, the 'Conclusion' section summarizes and further discusses our findings." ] ]

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

[ "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease\nPassage: In addition to RNA Polymerase I, optimal rRNA gene transcription requires a number of accessory factors that facilitate Pol I recruitment, initiation, promoter escape, elongation, termination and re-initiation . Pol I transcription begins with the formation of the preinitiation complex by the upstream binding factor and the TBP-containing complex selectively factor at the rDNA promoter. SL-1 confers promoter sequence specificity by recognizing the core promoter element and it promotes a stable interaction between UBF and the rDNA promoter . In turn, UBF binds the upstream and core promoter elements as a dimer, possibly looping the intervening DNA into a nucleosome", "Title: Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei\nPassage: protein. RanBP10 is a cytoplasmic guanine nucleotide exchange factor that modulates noncentrosomal microtubules involved in mitosis, while cytochrome P450 catalyses diverse reactions in fungal primary and secondary metabolism, and xenobiotic detoxification. As for PM-milR-M2, 20 potential targets were predicted, which include 13 transposon or transposable elements and seven conserved hypothetical proteins.", "Title: Translational profiling of B cells infected with the Epstein-Barr virus reveals 5′ leader ribosome recruitment through upstream open reading frames\nPassage: The out:in ratios were calculated by dividing the number of RPFs mapping within 5 leaders of a transcript by the number of RPFs mapping to the coding region of the transcript including the translation initiation codon . Read coverage was length normalized by nucleotide length of the respective feature . 5 leader:AUG ratios were calculated by dividing the number of RPFs mapping within the 5 leaders of a transcript by the number of RPFs mapping to the start codon of a transcript or non-canonical start codons. Read coverage was length normalized by nucleotide length of the respective feature.", "Title: Translational profiling of B cells infected with the Epstein-Barr virus reveals 5′ leader ribosome recruitment through upstream open reading frames\nPassage: The data provided by the TRPs will allow detailed characterization on the regulation of the translation of any single EBV gene or group of genes that frequently proved to be complex. The BMRF1 and BMRF2 transcripts that extensively overlap with each other and with BMRT3 and BMRT4 transcripts provide one example. BMRF1 and BMRF2 showed a similar number of reads in the TRP of cells treated with cycloheximide . However, the BMRF2 transcript recruited a much lower number of ribosomes than BMRF1 in cells treated with harringtonine . We could confirm by immunostaining that the BMRF2 protein is indeed expressed" ]

[ [ "0a", "Title: Perturbations at the ribosomal genes loci are at the centre of cellular dysfunction and human disease" ], [ "0b", "Passage: In addition to RNA Polymerase I, optimal rRNA gene transcription requires a number of accessory factors that facilitate Pol I recruitment, initiation, promoter escape, elongation, termination and re-initiation ." ], [ "0c", "Pol I transcription begins with the formation of the preinitiation complex by the upstream binding factor and the TBP-containing complex selectively factor at the rDNA promoter." ], [ "0d", "SL-1 confers promoter sequence specificity by recognizing the core promoter element and it promotes a stable interaction between UBF and the rDNA promoter ." ], [ "0e", "In turn, UBF binds the upstream and core promoter elements as a dimer, possibly looping the intervening DNA into a nucleosome" ] ]

[ "0b", "0c" ]

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of tight junction increasing the leakiness further augments the inflammation and exacerbations. In addition, viral infections are usually accompanied with oxidative stress which will further increase the local inflammation in the airway. The dysregulation of inflammation can be further compounded by modulation of miRNAs and epigenetic modification such as DNA methylation and histone modifications that promote dysregulation in inflammation. Finally, the change in the local airway environment and inflammation promotes growth of pathogenic bacteria that may replace the airway microbiome. Furthermore, the inflammatory environment may also disperse upper airway commensals into the lower airway, further causing inflammation and alteration of", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: Affecting approximately 10 % of UK adults, asthma is a common disorder of multi-factorial origins, with research indicating that both genetics and the environment have a significant role to play. In predisposed individuals, 'normal' environmental antigens transmigrate through the airway epithelia and are presented to naïve T cells, which trigger activation of IgE production by B cells. IgE interacts with receptors on the surface of tissue resident mast cells, and further exposure to the antigen results in IgE cross-linkage with cell activation. The resultant mast cell degranulation causes release of mediators including histamine, LTB 4 , IL-8 and IL-10 and", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: of the classical symptoms of chronic airway inflammatory diseases . In addition, the expression of vasodilating factors and fluid homeostatic factors such as angiopoietin-like 4 and bactericidal/permeabilityincreasing fold-containing family member A1 are also associated with viral infections and pneumonia development, which may worsen inflammation in the lower airway Akram et al., 2018) . These factors may serve as targets to prevent viral-induced exacerbations during the management of acute exacerbation of chronic airway inflammatory diseases.", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ]

[ [ "3a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "3b", "Passage: Respiratory viruses primarily infect and replicate within airway epithelial cells ." ], [ "3c", "During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche ." ], [ "3d", "In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells." ], [ "3e", "This eventually results in the resolution of the inflammatory response and clearance of the viral infection ." ], [ "3f", "However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ] ]

[ "3d", "3e" ]

[ "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: and to maintain self-tolerance . T lymphocyte activation culminates with the establishment of the immunological memory, providing the host with T cells more prone and efficient in responding to a reinfection by the same pathogen or upon tumor relapses . Besides, DCs are key players in humoral responses too. Indeed, they directly interact with B cells and indirectly support them by activating CD4 + T cells, leading to humoral memory. All these notions strengthen the idea that DCs represent an optimal target for immunotherapies and vaccines, acting at the interface of innate and adaptive immunity.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: To address this purpose, it is becoming more and more evident that dendritic cells stand out as a potent tool in our hands, being the mediators of cellular and humoral responses . DCs have been discovered in 1973 by R. Steinman and Z. Cohn that divided phagocytic cells in macrophages and DCs on the basis of different effector functions: microbial scavenging activities for macrophages and antigen-presenting function for DCs . Since then, DCs have emerged as the most potent antigen-presenting cells capable of shaping adaptive responses both during infections and cancer. Moreover, the broad spectrum of DCs activation makes them", "Title: Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections\nPassage: . Interestingly, engagement of DCIR on pDCs increases their capacity to present antigen to T lymphocytes. Targeted delivery of vaccine antigens to mouse pDCs via coupling to an anti-SIGLECH antibody also promotes the induction of adaptive immune responses . Thus, the mechanisms that terminate the production of innate cytokines by pDCs during responses to viral type stimuli may not only be in place to prevent the development of a cytokine shock but also to switch pDC functions towards direct activation of adaptive immunity once their initial role in the orchestration of innate immune defenses has been fulfilled.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: DCs educate CD4 + T cells against intracellular bacteria by promoting their polarization into IFN-γ-producing Th type 1 cells. Upon infection by multicellular parasites, DCs, with the help of basophils, polarize CD4 + T cells into Th type 2 cells that produce mainly IL-4. For specialized mucosal and skin immunity, DCs drive the activation of Th type 17 . Thus, polarization of T cells is a crucial event that provides mechanisms specifically orchestrated to restore physiological homeostasis. DCs undergo apoptosis once they have fulfilled their functions. The rapid DC turnover after activation is necessary to avoid excessive T cell activation" ]

[ [ "0a", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines" ], [ "0b", "Passage: and to maintain self-tolerance ." ], [ "0c", "T lymphocyte activation culminates with the establishment of the immunological memory, providing the host with T cells more prone and efficient in responding to a reinfection by the same pathogen or upon tumor relapses ." ], [ "0d", "Besides, DCs are key players in humoral responses too." ], [ "0e", "Indeed, they directly interact with B cells and indirectly support them by activating CD4 + T cells, leading to humoral memory." ], [ "0f", "All these notions strengthen the idea that DCs represent an optimal target for immunotherapies and vaccines, acting at the interface of innate and adaptive immunity." ] ]

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

[ "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: and to maintain self-tolerance . T lymphocyte activation culminates with the establishment of the immunological memory, providing the host with T cells more prone and efficient in responding to a reinfection by the same pathogen or upon tumor relapses . Besides, DCs are key players in humoral responses too. Indeed, they directly interact with B cells and indirectly support them by activating CD4 + T cells, leading to humoral memory. All these notions strengthen the idea that DCs represent an optimal target for immunotherapies and vaccines, acting at the interface of innate and adaptive immunity.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: To address this purpose, it is becoming more and more evident that dendritic cells stand out as a potent tool in our hands, being the mediators of cellular and humoral responses . DCs have been discovered in 1973 by R. Steinman and Z. Cohn that divided phagocytic cells in macrophages and DCs on the basis of different effector functions: microbial scavenging activities for macrophages and antigen-presenting function for DCs . Since then, DCs have emerged as the most potent antigen-presenting cells capable of shaping adaptive responses both during infections and cancer. Moreover, the broad spectrum of DCs activation makes them", "Title: Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections\nPassage: . Interestingly, engagement of DCIR on pDCs increases their capacity to present antigen to T lymphocytes. Targeted delivery of vaccine antigens to mouse pDCs via coupling to an anti-SIGLECH antibody also promotes the induction of adaptive immune responses . Thus, the mechanisms that terminate the production of innate cytokines by pDCs during responses to viral type stimuli may not only be in place to prevent the development of a cytokine shock but also to switch pDC functions towards direct activation of adaptive immunity once their initial role in the orchestration of innate immune defenses has been fulfilled.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: DCs educate CD4 + T cells against intracellular bacteria by promoting their polarization into IFN-γ-producing Th type 1 cells. Upon infection by multicellular parasites, DCs, with the help of basophils, polarize CD4 + T cells into Th type 2 cells that produce mainly IL-4. For specialized mucosal and skin immunity, DCs drive the activation of Th type 17 . Thus, polarization of T cells is a crucial event that provides mechanisms specifically orchestrated to restore physiological homeostasis. DCs undergo apoptosis once they have fulfilled their functions. The rapid DC turnover after activation is necessary to avoid excessive T cell activation" ]

[ [ "1a", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines" ], [ "1b", "Passage: To address this purpose, it is becoming more and more evident that dendritic cells stand out as a potent tool in our hands, being the mediators of cellular and humoral responses ." ], [ "1c", "DCs have been discovered in 1973 by R. Steinman and Z. Cohn that divided phagocytic cells in macrophages and DCs on the basis of different effector functions: microbial scavenging activities for macrophages and antigen-presenting function for DCs ." ], [ "1d", "Since then, DCs have emerged as the most potent antigen-presenting cells capable of shaping adaptive responses both during infections and cancer." ], [ "1e", "Moreover, the broad spectrum of DCs activation makes them" ] ]

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

[ "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: and to maintain self-tolerance . T lymphocyte activation culminates with the establishment of the immunological memory, providing the host with T cells more prone and efficient in responding to a reinfection by the same pathogen or upon tumor relapses . Besides, DCs are key players in humoral responses too. Indeed, they directly interact with B cells and indirectly support them by activating CD4 + T cells, leading to humoral memory. All these notions strengthen the idea that DCs represent an optimal target for immunotherapies and vaccines, acting at the interface of innate and adaptive immunity.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: To address this purpose, it is becoming more and more evident that dendritic cells stand out as a potent tool in our hands, being the mediators of cellular and humoral responses . DCs have been discovered in 1973 by R. Steinman and Z. Cohn that divided phagocytic cells in macrophages and DCs on the basis of different effector functions: microbial scavenging activities for macrophages and antigen-presenting function for DCs . Since then, DCs have emerged as the most potent antigen-presenting cells capable of shaping adaptive responses both during infections and cancer. Moreover, the broad spectrum of DCs activation makes them", "Title: Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections\nPassage: . Interestingly, engagement of DCIR on pDCs increases their capacity to present antigen to T lymphocytes. Targeted delivery of vaccine antigens to mouse pDCs via coupling to an anti-SIGLECH antibody also promotes the induction of adaptive immune responses . Thus, the mechanisms that terminate the production of innate cytokines by pDCs during responses to viral type stimuli may not only be in place to prevent the development of a cytokine shock but also to switch pDC functions towards direct activation of adaptive immunity once their initial role in the orchestration of innate immune defenses has been fulfilled.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: DCs educate CD4 + T cells against intracellular bacteria by promoting their polarization into IFN-γ-producing Th type 1 cells. Upon infection by multicellular parasites, DCs, with the help of basophils, polarize CD4 + T cells into Th type 2 cells that produce mainly IL-4. For specialized mucosal and skin immunity, DCs drive the activation of Th type 17 . Thus, polarization of T cells is a crucial event that provides mechanisms specifically orchestrated to restore physiological homeostasis. DCs undergo apoptosis once they have fulfilled their functions. The rapid DC turnover after activation is necessary to avoid excessive T cell activation" ]

[ [ "2a", "Title: Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections Passage: ." ], [ "2b", "Interestingly, engagement of DCIR on pDCs increases their capacity to present antigen to T lymphocytes." ], [ "2c", "Targeted delivery of vaccine antigens to mouse pDCs via coupling to an anti-SIGLECH antibody also promotes the induction of adaptive immune responses ." ], [ "2d", "Thus, the mechanisms that terminate the production of innate cytokines by pDCs during responses to viral type stimuli may not only be in place to prevent the development of a cytokine shock but also to switch pDC functions towards direct activation of adaptive immunity once their initial role in the orchestration of innate immune defenses has been fulfilled." ] ]

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

[ "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: and to maintain self-tolerance . T lymphocyte activation culminates with the establishment of the immunological memory, providing the host with T cells more prone and efficient in responding to a reinfection by the same pathogen or upon tumor relapses . Besides, DCs are key players in humoral responses too. Indeed, they directly interact with B cells and indirectly support them by activating CD4 + T cells, leading to humoral memory. All these notions strengthen the idea that DCs represent an optimal target for immunotherapies and vaccines, acting at the interface of innate and adaptive immunity.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: To address this purpose, it is becoming more and more evident that dendritic cells stand out as a potent tool in our hands, being the mediators of cellular and humoral responses . DCs have been discovered in 1973 by R. Steinman and Z. Cohn that divided phagocytic cells in macrophages and DCs on the basis of different effector functions: microbial scavenging activities for macrophages and antigen-presenting function for DCs . Since then, DCs have emerged as the most potent antigen-presenting cells capable of shaping adaptive responses both during infections and cancer. Moreover, the broad spectrum of DCs activation makes them", "Title: Plasmacytoid Dendritic Cells and the Control of Herpesvirus Infections\nPassage: . Interestingly, engagement of DCIR on pDCs increases their capacity to present antigen to T lymphocytes. Targeted delivery of vaccine antigens to mouse pDCs via coupling to an anti-SIGLECH antibody also promotes the induction of adaptive immune responses . Thus, the mechanisms that terminate the production of innate cytokines by pDCs during responses to viral type stimuli may not only be in place to prevent the development of a cytokine shock but also to switch pDC functions towards direct activation of adaptive immunity once their initial role in the orchestration of innate immune defenses has been fulfilled.", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines\nPassage: DCs educate CD4 + T cells against intracellular bacteria by promoting their polarization into IFN-γ-producing Th type 1 cells. Upon infection by multicellular parasites, DCs, with the help of basophils, polarize CD4 + T cells into Th type 2 cells that produce mainly IL-4. For specialized mucosal and skin immunity, DCs drive the activation of Th type 17 . Thus, polarization of T cells is a crucial event that provides mechanisms specifically orchestrated to restore physiological homeostasis. DCs undergo apoptosis once they have fulfilled their functions. The rapid DC turnover after activation is necessary to avoid excessive T cell activation" ]

[ [ "3a", "Title: Dendritic Cells in the Cross Hair for the Generation of Tailored Vaccines" ], [ "3b", "Passage: DCs educate CD4 + T cells against intracellular bacteria by promoting their polarization into IFN-γ-producing Th type 1 cells." ], [ "3c", "Upon infection by multicellular parasites, DCs, with the help of basophils, polarize CD4 + T cells into Th type 2 cells that produce mainly IL-4." ], [ "3d", "For specialized mucosal and skin immunity, DCs drive the activation of Th type 17 ." ], [ "3e", "Thus, polarization of T cells is a crucial event that provides mechanisms specifically orchestrated to restore physiological homeostasis." ], [ "3f", "DCs undergo apoptosis once they have fulfilled their functions." ], [ "3g", "The rapid DC turnover after activation is necessary to avoid excessive T cell activation" ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: CHIKV undertakes a complex replication cycle upon host infection , which makes its genome susceptible to mutations . For instance, Ae. aegypti, responsible for epidemics in Kenya, Comoros, and Seychelles, carried CHIKV with an alanine in the 226 position of the E1 gene . However, when the virus struck La Reunion Islands, a decline in population of Ae. aegypti, due to massive dichlorodiphenyltrichloroethane usage and dearth of Ae. albopictus species' www.plosntds.org population, resulted in an ecological pressure, favoring replacement of alanine at position 226 with valine . This mutation allowed CHIKV's secondary vector species, Ae. albopictus, to supplement Ae. aegypti", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Within a year, the E1-A226V mutation was present in La Reunion Island, and Ae. albopictus apparently vectored the large epidemic infecting 34% of La Reunion Island's population . All of the CHIKV strains isolated from Mayotte carried the E1-A226V mutation, and the mutation was also found in Madagascar in 2007 . The E1-A226V mutation was not present at the beginning of the Indian Ocean Islands outbreak . However, more than 90% of later viral strains found there had incorporated the mutation , indicating a genotype switch during the winter season .", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: The E1-A226V mutation also enabled an increase in infectivity of Ae. albopictus when compared to its infectivity of Ae. aegypti , and with several factors taken together, Ae. albopictus has become the new preferred and more lethal vector for CHIKV . In fact, Tsetsarkin et al. found that a Green Fluorescent Protein tagged E1-A226V virus was 100 times more infective to Ae. albopictus than it was to Ae. aegypti . In all the Indian Ocean Islands, Ae. albopictus became the main vector for CHIKV within 1-2 y after CHIKV was introduced to the region .", "Title: Dengue Fever, Hawaii, 2001–2002\nPassage: Ae. albopictus was the vector responsible for the 2001 Hawaii outbreak. Both entomologic surveys support that Ae. albopictus is ubiquitous, often common on all the islands, whereas Ae. aegypti is restricted to a few small foci on the relatively sparsely inhabited island of Hawaii." ]

[ [ "0a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "0b", "Passage: CHIKV undertakes a complex replication cycle upon host infection , which makes its genome susceptible to mutations ." ], [ "0c", "For instance, Ae." ], [ "0d", "aegypti, responsible for epidemics in Kenya, Comoros, and Seychelles, carried CHIKV with an alanine in the 226 position of the E1 gene ." ], [ "0e", "However, when the virus struck La Reunion Islands, a decline in population of Ae." ], [ "0f", "aegypti, due to massive dichlorodiphenyltrichloroethane usage and dearth of Ae." ], [ "0g", "albopictus species' www.plosntds.org population, resulted in an ecological pressure, favoring replacement of alanine at position 226 with valine ." ], [ "0h", "This mutation allowed CHIKV's secondary vector species, Ae." ], [ "0i", "albopictus, to supplement Ae. aegypti" ] ]

[ "0d" ]

[ "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: research and requires that researchers reflect upon their own background and position, and how it will affect \"what they choose to investigate, the angle of investigation, the methods judged most adequate for this purpose, the findings considered most appropriate, and the framing and communication of conclusions\" :p483-4. This can entail, for instance, reflecting on how the researcher's status and role may have influenced what the informants disclose and how it is presented to the researcher . We found no explicit discussion of the primary study authors' background or position, including how their studies might have been influenced by these factors,", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Academic researchers are to a great extent driven by the incentives of their profession, which reward publishing papers in peer-reviewed journals, regardless of whether or not the data are used to improve health outcomes. This necessarily influences the communication of results. High-level, multi-country comparisons have proven attractive to the editors of high-profile journals, The Lancet in particular . Publication in these journals in turn imbues academic estimates with a legitimacy that is not shared by data produced at the country level.", "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: We regard this lack of information about and reflection on the context of the studies as a weakness in the studies and connect it to a lack of researcher reflexivity demonstrated by the primary study authors. The authors' contact information indicates that the majority of them held positions at medical faculties and that some of them were Ministry of Health employees. This suggests that they have approached their own study with a public health perspective, focusing on the achievement of herd immunity through patient compliance. The primary study authors' aim of increasing vaccine compliance appears to have influenced their recommendations", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: of homogeneity or assessment of similarity of results across studies was conducted and reported; 9) appropriate weighting of primary studies was conducted; and 10) the author's interpretation of the results were supported by the data . Each criterion is equally weighted and a final methodological score is tallied out of 10. Reviews with an overall rating of eight or more are considered strong, five to seven, moderate, and below four are considered to be weak in methodological quality." ]

[ [ "0a", "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research" ], [ "0b", "Passage: research and requires that researchers reflect upon their own background and position, and how it will affect \"what they choose to investigate, the angle of investigation, the methods judged most adequate for this purpose, the findings considered most appropriate, and the framing and communication of conclusions\" :p483-4." ], [ "0c", "This can entail, for instance, reflecting on how the researcher's status and role may have influenced what the informants disclose and how it is presented to the researcher ." ], [ "0d", "We found no explicit discussion of the primary study authors' background or position, including how their studies might have been influenced by these factors," ] ]

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

[ "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: research and requires that researchers reflect upon their own background and position, and how it will affect \"what they choose to investigate, the angle of investigation, the methods judged most adequate for this purpose, the findings considered most appropriate, and the framing and communication of conclusions\" :p483-4. This can entail, for instance, reflecting on how the researcher's status and role may have influenced what the informants disclose and how it is presented to the researcher . We found no explicit discussion of the primary study authors' background or position, including how their studies might have been influenced by these factors,", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Academic researchers are to a great extent driven by the incentives of their profession, which reward publishing papers in peer-reviewed journals, regardless of whether or not the data are used to improve health outcomes. This necessarily influences the communication of results. High-level, multi-country comparisons have proven attractive to the editors of high-profile journals, The Lancet in particular . Publication in these journals in turn imbues academic estimates with a legitimacy that is not shared by data produced at the country level.", "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: We regard this lack of information about and reflection on the context of the studies as a weakness in the studies and connect it to a lack of researcher reflexivity demonstrated by the primary study authors. The authors' contact information indicates that the majority of them held positions at medical faculties and that some of them were Ministry of Health employees. This suggests that they have approached their own study with a public health perspective, focusing on the achievement of herd immunity through patient compliance. The primary study authors' aim of increasing vaccine compliance appears to have influenced their recommendations", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: of homogeneity or assessment of similarity of results across studies was conducted and reported; 9) appropriate weighting of primary studies was conducted; and 10) the author's interpretation of the results were supported by the data . Each criterion is equally weighted and a final methodological score is tallied out of 10. Reviews with an overall rating of eight or more are considered strong, five to seven, moderate, and below four are considered to be weak in methodological quality." ]

[ [ "1a", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust" ], [ "1b", "Passage: Academic researchers are to a great extent driven by the incentives of their profession, which reward publishing papers in peer-reviewed journals, regardless of whether or not the data are used to improve health outcomes." ], [ "1c", "This necessarily influences the communication of results." ], [ "1d", "High-level, multi-country comparisons have proven attractive to the editors of high-profile journals, The Lancet in particular ." ], [ "1e", "Publication in these journals in turn imbues academic estimates with a legitimacy that is not shared by data produced at the country level." ] ]

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

[ "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: research and requires that researchers reflect upon their own background and position, and how it will affect \"what they choose to investigate, the angle of investigation, the methods judged most adequate for this purpose, the findings considered most appropriate, and the framing and communication of conclusions\" :p483-4. This can entail, for instance, reflecting on how the researcher's status and role may have influenced what the informants disclose and how it is presented to the researcher . We found no explicit discussion of the primary study authors' background or position, including how their studies might have been influenced by these factors,", "Title: In the eye of the beholder: to make global health estimates useful, make them more socially robust\nPassage: Academic researchers are to a great extent driven by the incentives of their profession, which reward publishing papers in peer-reviewed journals, regardless of whether or not the data are used to improve health outcomes. This necessarily influences the communication of results. High-level, multi-country comparisons have proven attractive to the editors of high-profile journals, The Lancet in particular . Publication in these journals in turn imbues academic estimates with a legitimacy that is not shared by data produced at the country level.", "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research\nPassage: We regard this lack of information about and reflection on the context of the studies as a weakness in the studies and connect it to a lack of researcher reflexivity demonstrated by the primary study authors. The authors' contact information indicates that the majority of them held positions at medical faculties and that some of them were Ministry of Health employees. This suggests that they have approached their own study with a public health perspective, focusing on the achievement of herd immunity through patient compliance. The primary study authors' aim of increasing vaccine compliance appears to have influenced their recommendations", "Title: Missing and accounted for: gaps and areas of wealth in the public health review literature\nPassage: of homogeneity or assessment of similarity of results across studies was conducted and reported; 9) appropriate weighting of primary studies was conducted; and 10) the author's interpretation of the results were supported by the data . Each criterion is equally weighted and a final methodological score is tallied out of 10. Reviews with an overall rating of eight or more are considered strong, five to seven, moderate, and below four are considered to be weak in methodological quality." ]

[ [ "2a", "Title: The swine flu vaccine, public attitudes, and researcher interpretations: a systematic review of qualitative research" ], [ "2b", "Passage: We regard this lack of information about and reflection on the context of the studies as a weakness in the studies and connect it to a lack of researcher reflexivity demonstrated by the primary study authors." ], [ "2c", "The authors' contact information indicates that the majority of them held positions at medical faculties and that some of them were Ministry of Health employees." ], [ "2d", "This suggests that they have approached their own study with a public health perspective, focusing on the achievement of herd immunity through patient compliance." ], [ "2e", "The primary study authors' aim of increasing vaccine compliance appears to have influenced their recommendations" ] ]

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

[ "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: and mean or median *Literature estimates show the range of incubation periods consistent with most published estimates and the most frequently stated central tendency for the incubation period; estimates that did not specify a type were assumed to be statements of central tendency. ψObservational studies did not always report a defined number of participants, so a subject count is only reported for experimental studies. . Based on 2,540 observations from 20 observational studies and 15 observations from three experimental studies, we estimate the median incubation period for noroviruses to be 1.2 days with a dispersion of 1.64 . 5% of", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Sartwell and others have shown that the natural logarithm of incubation periods of acute infectious diseases tend to follow a normal distribution; hence the incubation period follows a log-normal distribution specified by the median incubation period and a dispersion factor . In a normal distribution, approximately twothirds of the data fall within one standard deviation of the mean; similarly in a log-normal distribution, approximately two-thirds of cases develop symptoms between median/dispersion and median × dispersion. For each pathogen all observations were pooled together to form a single set of doubly interval censored observations; each data point contained a range of", "Title: The role of heterogeneity in contact timing and duration in network models of influenza spread in schools\nPassage: We assumed that symptom onset of infected individuals occurred later than shedding onset. Specifically, infected individuals entered a symptomatic state after a random, log-normally distributed incubation period with a mean of 1.52 days and a standard deviation of 0.66 . We correlated the latent and incubation period distributions, such that shedding began 0.5-1.2 days before symptom onset. However, under our assumptions for timevarying infectiousness, shedding amounts did not increase to an appreciable level until closer to the time of symptom onset." ]

[ [ "0a", "Title: Incubation periods of viral gastroenteritis: a systematic review" ], [ "0b", "Passage: and mean or median *Literature estimates show the range of incubation periods consistent with most published estimates and the most frequently stated central tendency for the incubation period; estimates that did not specify a type were assumed to be statements of central tendency." ], [ "0c", "ψObservational studies did not always report a defined number of participants, so a subject count is only reported for experimental studies. ." ], [ "0d", "Based on 2,540 observations from 20 observational studies and 15 observations from three experimental studies, we estimate the median incubation period for noroviruses to be 1.2 days with a dispersion of 1.64 . 5% of" ] ]

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

[ "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: and mean or median *Literature estimates show the range of incubation periods consistent with most published estimates and the most frequently stated central tendency for the incubation period; estimates that did not specify a type were assumed to be statements of central tendency. ψObservational studies did not always report a defined number of participants, so a subject count is only reported for experimental studies. . Based on 2,540 observations from 20 observational studies and 15 observations from three experimental studies, we estimate the median incubation period for noroviruses to be 1.2 days with a dispersion of 1.64 . 5% of", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Sartwell and others have shown that the natural logarithm of incubation periods of acute infectious diseases tend to follow a normal distribution; hence the incubation period follows a log-normal distribution specified by the median incubation period and a dispersion factor . In a normal distribution, approximately twothirds of the data fall within one standard deviation of the mean; similarly in a log-normal distribution, approximately two-thirds of cases develop symptoms between median/dispersion and median × dispersion. For each pathogen all observations were pooled together to form a single set of doubly interval censored observations; each data point contained a range of", "Title: The role of heterogeneity in contact timing and duration in network models of influenza spread in schools\nPassage: We assumed that symptom onset of infected individuals occurred later than shedding onset. Specifically, infected individuals entered a symptomatic state after a random, log-normally distributed incubation period with a mean of 1.52 days and a standard deviation of 0.66 . We correlated the latent and incubation period distributions, such that shedding began 0.5-1.2 days before symptom onset. However, under our assumptions for timevarying infectiousness, shedding amounts did not increase to an appreciable level until closer to the time of symptom onset." ]

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

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

[ "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: and mean or median *Literature estimates show the range of incubation periods consistent with most published estimates and the most frequently stated central tendency for the incubation period; estimates that did not specify a type were assumed to be statements of central tendency. ψObservational studies did not always report a defined number of participants, so a subject count is only reported for experimental studies. . Based on 2,540 observations from 20 observational studies and 15 observations from three experimental studies, we estimate the median incubation period for noroviruses to be 1.2 days with a dispersion of 1.64 . 5% of", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Sartwell and others have shown that the natural logarithm of incubation periods of acute infectious diseases tend to follow a normal distribution; hence the incubation period follows a log-normal distribution specified by the median incubation period and a dispersion factor . In a normal distribution, approximately twothirds of the data fall within one standard deviation of the mean; similarly in a log-normal distribution, approximately two-thirds of cases develop symptoms between median/dispersion and median × dispersion. For each pathogen all observations were pooled together to form a single set of doubly interval censored observations; each data point contained a range of", "Title: The role of heterogeneity in contact timing and duration in network models of influenza spread in schools\nPassage: We assumed that symptom onset of infected individuals occurred later than shedding onset. Specifically, infected individuals entered a symptomatic state after a random, log-normally distributed incubation period with a mean of 1.52 days and a standard deviation of 0.66 . We correlated the latent and incubation period distributions, such that shedding began 0.5-1.2 days before symptom onset. However, under our assumptions for timevarying infectiousness, shedding amounts did not increase to an appreciable level until closer to the time of symptom onset." ]

[ [ "2a", "Title: Incubation periods of viral gastroenteritis: a systematic review" ], [ "2b", "Passage: Sartwell and others have shown that the natural logarithm of incubation periods of acute infectious diseases tend to follow a normal distribution; hence the incubation period follows a log-normal distribution specified by the median incubation period and a dispersion factor ." ], [ "2c", "In a normal distribution, approximately twothirds of the data fall within one standard deviation of the mean; similarly in a log-normal distribution, approximately two-thirds of cases develop symptoms between median/dispersion and median × dispersion." ], [ "2d", "For each pathogen all observations were pooled together to form a single set of doubly interval censored observations; each data point contained a range of" ] ]

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

[ "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: and mean or median *Literature estimates show the range of incubation periods consistent with most published estimates and the most frequently stated central tendency for the incubation period; estimates that did not specify a type were assumed to be statements of central tendency. ψObservational studies did not always report a defined number of participants, so a subject count is only reported for experimental studies. . Based on 2,540 observations from 20 observational studies and 15 observations from three experimental studies, we estimate the median incubation period for noroviruses to be 1.2 days with a dispersion of 1.64 . 5% of", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: a) The mean incubation period was 5.2 days : 4.1-7.0) . We set the same value of the incubation period and the latent period in this study. Thus, ω P = ω' P = 0.1923. b) There is a mean 5-day delay from symptom onset to detection/hospitalization of a case . The duration from illness onset to first medical visit for the 45 patients with illness onset before January 1 was estimated to have a mean of 5.8 days . In our model, we set the infectious period of the cases as 5.8 days. Therefore, γ P = 0.1724. c)", "Title: Incubation periods of viral gastroenteritis: a systematic review\nPassage: Sartwell and others have shown that the natural logarithm of incubation periods of acute infectious diseases tend to follow a normal distribution; hence the incubation period follows a log-normal distribution specified by the median incubation period and a dispersion factor . In a normal distribution, approximately twothirds of the data fall within one standard deviation of the mean; similarly in a log-normal distribution, approximately two-thirds of cases develop symptoms between median/dispersion and median × dispersion. For each pathogen all observations were pooled together to form a single set of doubly interval censored observations; each data point contained a range of", "Title: The role of heterogeneity in contact timing and duration in network models of influenza spread in schools\nPassage: We assumed that symptom onset of infected individuals occurred later than shedding onset. Specifically, infected individuals entered a symptomatic state after a random, log-normally distributed incubation period with a mean of 1.52 days and a standard deviation of 0.66 . We correlated the latent and incubation period distributions, such that shedding began 0.5-1.2 days before symptom onset. However, under our assumptions for timevarying infectiousness, shedding amounts did not increase to an appreciable level until closer to the time of symptom onset." ]

[ [ "3a", "Title: The role of heterogeneity in contact timing and duration in network models of influenza spread in schools" ], [ "3b", "Passage: We assumed that symptom onset of infected individuals occurred later than shedding onset." ], [ "3c", "Specifically, infected individuals entered a symptomatic state after a random, log-normally distributed incubation period with a mean of 1.52 days and a standard deviation of 0.66 ." ], [ "3d", "We correlated the latent and incubation period distributions, such that shedding began 0.5-1.2 days before symptom onset." ], [ "3e", "However, under our assumptions for timevarying infectiousness, shedding amounts did not increase to an appreciable level until closer to the time of symptom onset." ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was" ]

[ [ "0a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "0b", "Passage: 2 days ." ], [ "0c", "The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days ." ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was" ]

[ [ "1a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "1b", "Passage: 2 days ." ], [ "1c", "The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days ." ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was" ]

[ [ "2a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "2b", "Passage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission ." ], [ "2c", "Three patients were examined by highresolution computed tomography ." ], [ "2d", "Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients." ], [ "2e", "Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans." ], [ "2f", "Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT ." ], [ "2g", "The mean duration from onset to a single-lobe consolidation on CXRs was" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 2 days . The mean duration from the first positive CXR to bilaterally multilobar lung infiltrates was 4.8 days .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission . Three patients were examined by highresolution computed tomography . Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients. Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans. Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT . The mean duration from onset to a single-lobe consolidation on CXRs was" ]

[ [ "3a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "3b", "Passage: CXRs revealed multiple bilateral lobar or segment consolidation in the lungs of all five patients, and radiographic lesions progressed rapidly after ICU admission ." ], [ "3c", "Three patients were examined by highresolution computed tomography ." ], [ "3d", "Unilateral or bilateral consolidations and infiltrates were found on HRCT scans of all three of these patients." ], [ "3e", "Consolidations within a single lobe or several lobes with a clear border and air bronchogram were the most common findings on HRCT scans." ], [ "3f", "Nodules, patches, pleural effusion, abscess and a cavity were also seen visualized by HRCT ." ], [ "3g", "The mean duration from onset to a single-lobe consolidation on CXRs was" ] ]

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

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Among the fatal cases, cough was the most commonly reported symptom . Other symptoms reported were fever , shortness of breath , muscle pain , headache , vomiting , runny nose , diarrhoea , sneezing and sore throat .", "Title: The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)\nPassage: The most commonly reported symptoms among episodes of disease were respiratory , including coughing, sneezing/runny nose, sore throat and dyspnoea, in decreasing order. Other disease episodes included: fever , headache , body aches , and digestive disorders , including diarrhoea and vomiting/nausea.", "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: As shown in Figure 1 , more than half of the 18 H7N9-infected patients suffered from fever , cough , expectoration , fatigue , poor appetite , dry month , thirst , dyspnea , chest distress , and bitter taste in month . In addition, five patients suffered from hemoptysis and two suffered from dysphoria. Other symptoms such as muscle soreness , aversion to cold , perspiration , pharyngodynia , short breath , deep yellow urine , and cold-limbs also occurred in patients with H7N9 infection.", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: was collected by in-person interview. Participants were then instructed on the use of a daily diary to record the presence/severity of symptoms for 7 days following initial symptom onset. Symptom severity was rated on an ordinal scale from 0 to 3 . Symptom severity scores were quantified using the following five measures: individual symptom score for 20 symptoms, the upper respiratory symptom score, calculated as the sum of severity scores for earache, runny nose, sore throat, and sneezing, the lower respiratory symptom score, calculated as the sum of severity scores for cough, difficulty breathing, hoarseness, and chest discomfort, the gastrointestinal" ]

[ [ "0a", "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study" ], [ "0b", "Passage: Among the fatal cases, cough was the most commonly reported symptom ." ], [ "0c", "Other symptoms reported were fever , shortness of breath , muscle pain , headache , vomiting , runny nose , diarrhoea , sneezing and sore throat ." ] ]

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

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Among the fatal cases, cough was the most commonly reported symptom . Other symptoms reported were fever , shortness of breath , muscle pain , headache , vomiting , runny nose , diarrhoea , sneezing and sore throat .", "Title: The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)\nPassage: The most commonly reported symptoms among episodes of disease were respiratory , including coughing, sneezing/runny nose, sore throat and dyspnoea, in decreasing order. Other disease episodes included: fever , headache , body aches , and digestive disorders , including diarrhoea and vomiting/nausea.", "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: As shown in Figure 1 , more than half of the 18 H7N9-infected patients suffered from fever , cough , expectoration , fatigue , poor appetite , dry month , thirst , dyspnea , chest distress , and bitter taste in month . In addition, five patients suffered from hemoptysis and two suffered from dysphoria. Other symptoms such as muscle soreness , aversion to cold , perspiration , pharyngodynia , short breath , deep yellow urine , and cold-limbs also occurred in patients with H7N9 infection.", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: was collected by in-person interview. Participants were then instructed on the use of a daily diary to record the presence/severity of symptoms for 7 days following initial symptom onset. Symptom severity was rated on an ordinal scale from 0 to 3 . Symptom severity scores were quantified using the following five measures: individual symptom score for 20 symptoms, the upper respiratory symptom score, calculated as the sum of severity scores for earache, runny nose, sore throat, and sneezing, the lower respiratory symptom score, calculated as the sum of severity scores for cough, difficulty breathing, hoarseness, and chest discomfort, the gastrointestinal" ]

[ [ "1a", "Title: The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)" ], [ "1b", "Passage: The most commonly reported symptoms among episodes of disease were respiratory , including coughing, sneezing/runny nose, sore throat and dyspnoea, in decreasing order." ], [ "1c", "Other disease episodes included: fever , headache , body aches , and digestive disorders , including diarrhoea and vomiting/nausea." ] ]

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

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Among the fatal cases, cough was the most commonly reported symptom . Other symptoms reported were fever , shortness of breath , muscle pain , headache , vomiting , runny nose , diarrhoea , sneezing and sore throat .", "Title: The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)\nPassage: The most commonly reported symptoms among episodes of disease were respiratory , including coughing, sneezing/runny nose, sore throat and dyspnoea, in decreasing order. Other disease episodes included: fever , headache , body aches , and digestive disorders , including diarrhoea and vomiting/nausea.", "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: As shown in Figure 1 , more than half of the 18 H7N9-infected patients suffered from fever , cough , expectoration , fatigue , poor appetite , dry month , thirst , dyspnea , chest distress , and bitter taste in month . In addition, five patients suffered from hemoptysis and two suffered from dysphoria. Other symptoms such as muscle soreness , aversion to cold , perspiration , pharyngodynia , short breath , deep yellow urine , and cold-limbs also occurred in patients with H7N9 infection.", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: was collected by in-person interview. Participants were then instructed on the use of a daily diary to record the presence/severity of symptoms for 7 days following initial symptom onset. Symptom severity was rated on an ordinal scale from 0 to 3 . Symptom severity scores were quantified using the following five measures: individual symptom score for 20 symptoms, the upper respiratory symptom score, calculated as the sum of severity scores for earache, runny nose, sore throat, and sneezing, the lower respiratory symptom score, calculated as the sum of severity scores for cough, difficulty breathing, hoarseness, and chest discomfort, the gastrointestinal" ]

[ [ "2a", "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study" ], [ "2b", "Passage: As shown in Figure 1 , more than half of the 18 H7N9-infected patients suffered from fever , cough , expectoration , fatigue , poor appetite , dry month , thirst , dyspnea , chest distress , and bitter taste in month ." ], [ "2c", "In addition, five patients suffered from hemoptysis and two suffered from dysphoria." ], [ "2d", "Other symptoms such as muscle soreness , aversion to cold , perspiration , pharyngodynia , short breath , deep yellow urine , and cold-limbs also occurred in patients with H7N9 infection." ] ]

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

[ "Title: Influenza surveillance in the Pacific Island countries and territories during the 2009 pandemic: an observational study\nPassage: Among the fatal cases, cough was the most commonly reported symptom . Other symptoms reported were fever , shortness of breath , muscle pain , headache , vomiting , runny nose , diarrhoea , sneezing and sore throat .", "Title: The baseline characteristics and interim analyses of the high-risk sentinel cohort of the Vietnam Initiative on Zoonotic InfectiONS (VIZIONS)\nPassage: The most commonly reported symptoms among episodes of disease were respiratory , including coughing, sneezing/runny nose, sore throat and dyspnoea, in decreasing order. Other disease episodes included: fever , headache , body aches , and digestive disorders , including diarrhoea and vomiting/nausea.", "Title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study\nPassage: As shown in Figure 1 , more than half of the 18 H7N9-infected patients suffered from fever , cough , expectoration , fatigue , poor appetite , dry month , thirst , dyspnea , chest distress , and bitter taste in month . In addition, five patients suffered from hemoptysis and two suffered from dysphoria. Other symptoms such as muscle soreness , aversion to cold , perspiration , pharyngodynia , short breath , deep yellow urine , and cold-limbs also occurred in patients with H7N9 infection.", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: was collected by in-person interview. Participants were then instructed on the use of a daily diary to record the presence/severity of symptoms for 7 days following initial symptom onset. Symptom severity was rated on an ordinal scale from 0 to 3 . Symptom severity scores were quantified using the following five measures: individual symptom score for 20 symptoms, the upper respiratory symptom score, calculated as the sum of severity scores for earache, runny nose, sore throat, and sneezing, the lower respiratory symptom score, calculated as the sum of severity scores for cough, difficulty breathing, hoarseness, and chest discomfort, the gastrointestinal" ]

[ [ "3a", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults" ], [ "3b", "Passage: was collected by in-person interview." ], [ "3c", "Participants were then instructed on the use of a daily diary to record the presence/severity of symptoms for 7 days following initial symptom onset." ], [ "3d", "Symptom severity was rated on an ordinal scale from 0 to 3 ." ], [ "3e", "Symptom severity scores were quantified using the following five measures: individual symptom score for 20 symptoms, the upper respiratory symptom score, calculated as the sum of severity scores for earache, runny nose, sore throat, and sneezing, the lower respiratory symptom score, calculated as the sum of severity scores for cough, difficulty breathing, hoarseness, and chest discomfort, the gastrointestinal" ] ]

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: because cases currently being detected and reported would have mostly been infected in mid- to late-January. Average delays between infection and illness onset have been estimated at around 5–6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: cases currently being detected and reported would have mostly been infected in mid-to late-January. Average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: profile online. 3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample. As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. The What was the research question? Investigators adapted the \"Identify, Isolate, Inform\" Tool for use in suspected cases of 2019-nCoV." ]

[ [ "0a", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak" ], [ "0b", "Passage: because cases currently being detected and reported would have mostly been infected in mid- to late-January." ], [ "0c", "Average delays between infection and illness onset have been estimated at around 5–6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average ." ] ]

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: because cases currently being detected and reported would have mostly been infected in mid- to late-January. Average delays between infection and illness onset have been estimated at around 5–6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: cases currently being detected and reported would have mostly been infected in mid-to late-January. Average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: profile online. 3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample. As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. The What was the research question? Investigators adapted the \"Identify, Isolate, Inform\" Tool for use in suspected cases of 2019-nCoV." ]

[ [ "1a", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak" ], [ "1b", "Passage: cases currently being detected and reported would have mostly been infected in mid-to late-January." ], [ "1c", "Average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average ." ] ]

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: because cases currently being detected and reported would have mostly been infected in mid- to late-January. Average delays between infection and illness onset have been estimated at around 5–6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: cases currently being detected and reported would have mostly been infected in mid-to late-January. Average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: profile online. 3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample. As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. The What was the research question? Investigators adapted the \"Identify, Isolate, Inform\" Tool for use in suspected cases of 2019-nCoV." ]

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

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: because cases currently being detected and reported would have mostly been infected in mid- to late-January. Average delays between infection and illness onset have been estimated at around 5–6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: cases currently being detected and reported would have mostly been infected in mid-to late-January. Average delays between infection and illness onset have been estimated at around 5-6 days, with an upper limit of around 11-14 days , and delays from illness onset to laboratory confirmation added a further 10 days on average .", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: hospitalization, and ultimately die. 22 Early predictions for incubation time are between 2 and 14 days, based on data from similar coronaviruses. The 14-day criterion for epidemiological risk assumes the longest estimated incubation time. 23 In addition, the World Health Organization has created its own interim case definition. 24", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus\nPassage: profile online. 3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample. As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths. 2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin. The What was the research question? Investigators adapted the \"Identify, Isolate, Inform\" Tool for use in suspected cases of 2019-nCoV." ]

[ [ "3a", "Title: 2019-nCoV: The Identify-Isolate-Inform (3I) Tool Applied to a Novel Emerging Coronavirus" ], [ "3b", "Passage: profile online." ], [ "3c", "3, 4 Additionally, on January 28, 2020, an Australian laboratory reported growing the virus from a patient sample." ], [ "3d", "As of January 30, 2020, there have been at least 9,776 persons infected and 213 verified deaths." ], [ "3e", "2 These numbers are likely underestimates due to the limited information available regarding incubation time, transmissibility, and virus origin." ], [ "3f", "The What was the research question?" ], [ "3g", "Investigators adapted the \"Identify, Isolate, Inform\" Tool for use in suspected cases of 2019-nCoV." ] ]

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

[ "Title: The epidemiological and public health research response to 2009 pandemic influenza A(H1N1): experiences from Hong Kong\nPassage: The government subsequently ordered 3 million doses of pH1N1 vaccine for the local population of 7 million, and began distribution in December 2009. However, pH1N1 vaccine uptake was low, with <250 000 doses administered mainly to the elderly and healthcare workers. A subsequent longitudinal study found that intention to receive vaccine was an unreliable predictor of subsequent vaccine uptake. 44 Among healthcare workers, a study conducted in May 2009 found around 50% of survey respondents willing to receive pH1N1 vaccine. 45 Another study of community nurses in June 2009 found only 27% reporting willingness to receive pH1N1 vaccine. 40 Uptake", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: with students, teachers were more likely to answer the above questions Table 3 and Table 4 ). Regarding the A/H1N1vaccination, 69.9% respondents believed that the occurrence rate of adverse reactions caused by A/H1N1 vaccination was fairly low and they were not afraid of taking up vaccination. Most residents thought that the state's vaccination strategy was reasonable.", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: to the state's prior vaccination strategy for population at high risk such as students, teachers, healthcare workers and people with chronic disease, as well as the confusion between seasonal flu vaccine and A/H1N1 vaccine in residents. People who couldn't access the A/H1N1 vaccine may take up seasonal flu vaccine as preventive behaviors. The A/ H1N1 vaccine was not available in China until the middle of September 2009. All populations at high risk above three years old were invited for vaccination free of charge . A survey among 868 European travelers showed 14.2% participants were vaccinated against pandemic influenza A/H1N1 ,", "Title: Pandemic (H1N1) 2009 among Quarantined Close Contacts, Beijing, People’s Republic of China\nPassage: have worked to some extent at the beginning but were outpaced by local transmission ; the percentage of locally acquired infections ranged from <10% in June 2009 to >80% in September 2009 ." ]

[ [ "0a", "Title: The epidemiological and public health research response to 2009 pandemic influenza A(H1N1): experiences from Hong Kong" ], [ "0b", "Passage: The government subsequently ordered 3 million doses of pH1N1 vaccine for the local population of 7 million, and began distribution in December 2009." ], [ "0c", "However, pH1N1 vaccine uptake was low, with <250 000 doses administered mainly to the elderly and healthcare workers." ], [ "0d", "A subsequent longitudinal study found that intention to receive vaccine was an unreliable predictor of subsequent vaccine uptake." ], [ "0e", "44 Among healthcare workers, a study conducted in May 2009 found around 50% of survey respondents willing to receive pH1N1 vaccine." ], [ "0f", "45 Another study of community nurses in June 2009 found only 27% reporting willingness to receive pH1N1 vaccine. 40 Uptake" ] ]

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

[ "Title: The epidemiological and public health research response to 2009 pandemic influenza A(H1N1): experiences from Hong Kong\nPassage: The government subsequently ordered 3 million doses of pH1N1 vaccine for the local population of 7 million, and began distribution in December 2009. However, pH1N1 vaccine uptake was low, with <250 000 doses administered mainly to the elderly and healthcare workers. A subsequent longitudinal study found that intention to receive vaccine was an unreliable predictor of subsequent vaccine uptake. 44 Among healthcare workers, a study conducted in May 2009 found around 50% of survey respondents willing to receive pH1N1 vaccine. 45 Another study of community nurses in June 2009 found only 27% reporting willingness to receive pH1N1 vaccine. 40 Uptake", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: with students, teachers were more likely to answer the above questions Table 3 and Table 4 ). Regarding the A/H1N1vaccination, 69.9% respondents believed that the occurrence rate of adverse reactions caused by A/H1N1 vaccination was fairly low and they were not afraid of taking up vaccination. Most residents thought that the state's vaccination strategy was reasonable.", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: to the state's prior vaccination strategy for population at high risk such as students, teachers, healthcare workers and people with chronic disease, as well as the confusion between seasonal flu vaccine and A/H1N1 vaccine in residents. People who couldn't access the A/H1N1 vaccine may take up seasonal flu vaccine as preventive behaviors. The A/ H1N1 vaccine was not available in China until the middle of September 2009. All populations at high risk above three years old were invited for vaccination free of charge . A survey among 868 European travelers showed 14.2% participants were vaccinated against pandemic influenza A/H1N1 ,", "Title: Pandemic (H1N1) 2009 among Quarantined Close Contacts, Beijing, People’s Republic of China\nPassage: have worked to some extent at the beginning but were outpaced by local transmission ; the percentage of locally acquired infections ranged from <10% in June 2009 to >80% in September 2009 ." ]

[ [ "1a", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey" ], [ "1b", "Passage: with students, teachers were more likely to answer the above questions Table 3 and Table 4 )." ], [ "1c", "Regarding the A/H1N1vaccination, 69.9% respondents believed that the occurrence rate of adverse reactions caused by A/H1N1 vaccination was fairly low and they were not afraid of taking up vaccination." ], [ "1d", "Most residents thought that the state's vaccination strategy was reasonable." ] ]

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

[ "Title: The epidemiological and public health research response to 2009 pandemic influenza A(H1N1): experiences from Hong Kong\nPassage: The government subsequently ordered 3 million doses of pH1N1 vaccine for the local population of 7 million, and began distribution in December 2009. However, pH1N1 vaccine uptake was low, with <250 000 doses administered mainly to the elderly and healthcare workers. A subsequent longitudinal study found that intention to receive vaccine was an unreliable predictor of subsequent vaccine uptake. 44 Among healthcare workers, a study conducted in May 2009 found around 50% of survey respondents willing to receive pH1N1 vaccine. 45 Another study of community nurses in June 2009 found only 27% reporting willingness to receive pH1N1 vaccine. 40 Uptake", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: with students, teachers were more likely to answer the above questions Table 3 and Table 4 ). Regarding the A/H1N1vaccination, 69.9% respondents believed that the occurrence rate of adverse reactions caused by A/H1N1 vaccination was fairly low and they were not afraid of taking up vaccination. Most residents thought that the state's vaccination strategy was reasonable.", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey\nPassage: to the state's prior vaccination strategy for population at high risk such as students, teachers, healthcare workers and people with chronic disease, as well as the confusion between seasonal flu vaccine and A/H1N1 vaccine in residents. People who couldn't access the A/H1N1 vaccine may take up seasonal flu vaccine as preventive behaviors. The A/ H1N1 vaccine was not available in China until the middle of September 2009. All populations at high risk above three years old were invited for vaccination free of charge . A survey among 868 European travelers showed 14.2% participants were vaccinated against pandemic influenza A/H1N1 ,", "Title: Pandemic (H1N1) 2009 among Quarantined Close Contacts, Beijing, People’s Republic of China\nPassage: have worked to some extent at the beginning but were outpaced by local transmission ; the percentage of locally acquired infections ranged from <10% in June 2009 to >80% in September 2009 ." ]

[ [ "2a", "Title: Knowledge, Attitudes and Practices (KAP) related to the Pandemic (H1N1) 2009 among Chinese General Population: a Telephone Survey" ], [ "2b", "Passage: to the state's prior vaccination strategy for population at high risk such as students, teachers, healthcare workers and people with chronic disease, as well as the confusion between seasonal flu vaccine and A/H1N1 vaccine in residents." ], [ "2c", "People who couldn't access the A/H1N1 vaccine may take up seasonal flu vaccine as preventive behaviors." ], [ "2d", "The A/ H1N1 vaccine was not available in China until the middle of September 2009." ], [ "2e", "All populations at high risk above three years old were invited for vaccination free of charge ." ], [ "2f", "A survey among 868 European travelers showed 14.2% participants were vaccinated against pandemic influenza A/H1N1 ," ] ]

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

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

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

[ "0b" ]

[ "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: six individual IgG surfaces, five titrated concentrations of antigen in 2-fold dilutions were simultaneously injected in the horizontal direction. The binding interactions were monitored over a 10-min association period and a 45-min dissociation period using a high flow rate of 40 l/min. The last channel was injected with PBS/Tween/EDTA for reference subtraction. The surfaces were regenerated with two 18-s pulses of glycine, pH 1.5, at 100 l/min in both horizontal and vertical directions to allow the capture of different serum IgGs for kinetic binding measurements.", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: 90% at 6.5-7.5 min and finally to 0% at 8 -10 min. After chromatographic separation, the sample entered the Orbitrap Fusion TM mass spectrometer operated in positive electrospray ionization mode. The employed method included activated types of collision-induced dissociation and electron transfer dissociation when identifying control peptides, using a resolution of 120,000, a minimum signal of 5000, an isolation width of 3.0, and a normalized collision energy of 30.0 V. The S-lens radiofrequency level was set at 60%. For peptide identification, the data were collected in profile mode for the full MS scan and in centroid mode for the collision-induced", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: Deuterium Exchange-Using the H/D-X PAL TM robotic system , samples containing IgGs incubated with human IL-13 were added to a D 2 O-containing buffer, and the reactions were subsequently quenched at consistent times and temperatures using an automated sample run list. Two separate sample compartments were used for each experiment. One compartment was kept at 20°C for D 2 O labeling , and the other was maintained at 4°C for reaction quenching. After the samples were prepared, they were transferred into Chromacol screen top vials and stored in individual positions within the 4°C sample compartments. A work list was written", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: concentrations showed that the sensitivity of the method was ϳ31 ng of antigen-specific IgG per l of serum. This high sensitivity can facilitate the detection of less abundant IgGs exhibiting unique epitopes, maximizing the diversity of antibodies that can be recovered. After establishing the highly sensitive SPR and HDX LC/MS methods for detecting antigen-specific antibodies in serum, we tested their performance using sera from immunized mice. Nine serum samples collected from various strains of mice, which were immunized with human IL-13 using different protocols, were analyzed with these methods in a \"proof-of-concept\" study. These samples were previously classified as binders" ]

[ [ "0a", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses" ], [ "0b", "Passage: six individual IgG surfaces, five titrated concentrations of antigen in 2-fold dilutions were simultaneously injected in the horizontal direction." ], [ "0c", "The binding interactions were monitored over a 10-min association period and a 45-min dissociation period using a high flow rate of 40 l/min." ], [ "0d", "The last channel was injected with PBS/Tween/EDTA for reference subtraction." ], [ "0e", "The surfaces were regenerated with two 18-s pulses of glycine, pH 1.5, at 100 l/min in both horizontal and vertical directions to allow the capture of different serum IgGs for kinetic binding measurements." ] ]

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

[ "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: six individual IgG surfaces, five titrated concentrations of antigen in 2-fold dilutions were simultaneously injected in the horizontal direction. The binding interactions were monitored over a 10-min association period and a 45-min dissociation period using a high flow rate of 40 l/min. The last channel was injected with PBS/Tween/EDTA for reference subtraction. The surfaces were regenerated with two 18-s pulses of glycine, pH 1.5, at 100 l/min in both horizontal and vertical directions to allow the capture of different serum IgGs for kinetic binding measurements.", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: 90% at 6.5-7.5 min and finally to 0% at 8 -10 min. After chromatographic separation, the sample entered the Orbitrap Fusion TM mass spectrometer operated in positive electrospray ionization mode. The employed method included activated types of collision-induced dissociation and electron transfer dissociation when identifying control peptides, using a resolution of 120,000, a minimum signal of 5000, an isolation width of 3.0, and a normalized collision energy of 30.0 V. The S-lens radiofrequency level was set at 60%. For peptide identification, the data were collected in profile mode for the full MS scan and in centroid mode for the collision-induced", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: Deuterium Exchange-Using the H/D-X PAL TM robotic system , samples containing IgGs incubated with human IL-13 were added to a D 2 O-containing buffer, and the reactions were subsequently quenched at consistent times and temperatures using an automated sample run list. Two separate sample compartments were used for each experiment. One compartment was kept at 20°C for D 2 O labeling , and the other was maintained at 4°C for reaction quenching. After the samples were prepared, they were transferred into Chromacol screen top vials and stored in individual positions within the 4°C sample compartments. A work list was written", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: concentrations showed that the sensitivity of the method was ϳ31 ng of antigen-specific IgG per l of serum. This high sensitivity can facilitate the detection of less abundant IgGs exhibiting unique epitopes, maximizing the diversity of antibodies that can be recovered. After establishing the highly sensitive SPR and HDX LC/MS methods for detecting antigen-specific antibodies in serum, we tested their performance using sera from immunized mice. Nine serum samples collected from various strains of mice, which were immunized with human IL-13 using different protocols, were analyzed with these methods in a \"proof-of-concept\" study. These samples were previously classified as binders" ]

[ [ "1a", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses" ], [ "1b", "Passage: 90% at 6.5-7.5 min and finally to 0% at 8 -10 min." ], [ "1c", "After chromatographic separation, the sample entered the Orbitrap Fusion TM mass spectrometer operated in positive electrospray ionization mode." ], [ "1d", "The employed method included activated types of collision-induced dissociation and electron transfer dissociation when identifying control peptides, using a resolution of 120,000, a minimum signal of 5000, an isolation width of 3.0, and a normalized collision energy of 30.0 V. The S-lens radiofrequency level was set at 60%." ], [ "1e", "For peptide identification, the data were collected in profile mode for the full MS scan and in centroid mode for the collision-induced" ] ]

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

[ "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: six individual IgG surfaces, five titrated concentrations of antigen in 2-fold dilutions were simultaneously injected in the horizontal direction. The binding interactions were monitored over a 10-min association period and a 45-min dissociation period using a high flow rate of 40 l/min. The last channel was injected with PBS/Tween/EDTA for reference subtraction. The surfaces were regenerated with two 18-s pulses of glycine, pH 1.5, at 100 l/min in both horizontal and vertical directions to allow the capture of different serum IgGs for kinetic binding measurements.", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: 90% at 6.5-7.5 min and finally to 0% at 8 -10 min. After chromatographic separation, the sample entered the Orbitrap Fusion TM mass spectrometer operated in positive electrospray ionization mode. The employed method included activated types of collision-induced dissociation and electron transfer dissociation when identifying control peptides, using a resolution of 120,000, a minimum signal of 5000, an isolation width of 3.0, and a normalized collision energy of 30.0 V. The S-lens radiofrequency level was set at 60%. For peptide identification, the data were collected in profile mode for the full MS scan and in centroid mode for the collision-induced", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: Deuterium Exchange-Using the H/D-X PAL TM robotic system , samples containing IgGs incubated with human IL-13 were added to a D 2 O-containing buffer, and the reactions were subsequently quenched at consistent times and temperatures using an automated sample run list. Two separate sample compartments were used for each experiment. One compartment was kept at 20°C for D 2 O labeling , and the other was maintained at 4°C for reaction quenching. After the samples were prepared, they were transferred into Chromacol screen top vials and stored in individual positions within the 4°C sample compartments. A work list was written", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: concentrations showed that the sensitivity of the method was ϳ31 ng of antigen-specific IgG per l of serum. This high sensitivity can facilitate the detection of less abundant IgGs exhibiting unique epitopes, maximizing the diversity of antibodies that can be recovered. After establishing the highly sensitive SPR and HDX LC/MS methods for detecting antigen-specific antibodies in serum, we tested their performance using sera from immunized mice. Nine serum samples collected from various strains of mice, which were immunized with human IL-13 using different protocols, were analyzed with these methods in a \"proof-of-concept\" study. These samples were previously classified as binders" ]

[ [ "2a", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses" ], [ "2b", "Passage: Deuterium Exchange-Using the H/D-X PAL TM robotic system , samples containing IgGs incubated with human IL-13 were added to a D 2 O-containing buffer, and the reactions were subsequently quenched at consistent times and temperatures using an automated sample run list." ], [ "2c", "Two separate sample compartments were used for each experiment." ], [ "2d", "One compartment was kept at 20°C for D 2 O labeling , and the other was maintained at 4°C for reaction quenching." ], [ "2e", "After the samples were prepared, they were transferred into Chromacol screen top vials and stored in individual positions within the 4°C sample compartments." ], [ "2f", "A work list was written" ] ]

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

[ "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: six individual IgG surfaces, five titrated concentrations of antigen in 2-fold dilutions were simultaneously injected in the horizontal direction. The binding interactions were monitored over a 10-min association period and a 45-min dissociation period using a high flow rate of 40 l/min. The last channel was injected with PBS/Tween/EDTA for reference subtraction. The surfaces were regenerated with two 18-s pulses of glycine, pH 1.5, at 100 l/min in both horizontal and vertical directions to allow the capture of different serum IgGs for kinetic binding measurements.", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: 90% at 6.5-7.5 min and finally to 0% at 8 -10 min. After chromatographic separation, the sample entered the Orbitrap Fusion TM mass spectrometer operated in positive electrospray ionization mode. The employed method included activated types of collision-induced dissociation and electron transfer dissociation when identifying control peptides, using a resolution of 120,000, a minimum signal of 5000, an isolation width of 3.0, and a normalized collision energy of 30.0 V. The S-lens radiofrequency level was set at 60%. For peptide identification, the data were collected in profile mode for the full MS scan and in centroid mode for the collision-induced", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: Deuterium Exchange-Using the H/D-X PAL TM robotic system , samples containing IgGs incubated with human IL-13 were added to a D 2 O-containing buffer, and the reactions were subsequently quenched at consistent times and temperatures using an automated sample run list. Two separate sample compartments were used for each experiment. One compartment was kept at 20°C for D 2 O labeling , and the other was maintained at 4°C for reaction quenching. After the samples were prepared, they were transferred into Chromacol screen top vials and stored in individual positions within the 4°C sample compartments. A work list was written", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses\nPassage: concentrations showed that the sensitivity of the method was ϳ31 ng of antigen-specific IgG per l of serum. This high sensitivity can facilitate the detection of less abundant IgGs exhibiting unique epitopes, maximizing the diversity of antibodies that can be recovered. After establishing the highly sensitive SPR and HDX LC/MS methods for detecting antigen-specific antibodies in serum, we tested their performance using sera from immunized mice. Nine serum samples collected from various strains of mice, which were immunized with human IL-13 using different protocols, were analyzed with these methods in a \"proof-of-concept\" study. These samples were previously classified as binders" ]

[ [ "3a", "Title: Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses" ], [ "3b", "Passage: concentrations showed that the sensitivity of the method was ϳ31 ng of antigen-specific IgG per l of serum." ], [ "3c", "This high sensitivity can facilitate the detection of less abundant IgGs exhibiting unique epitopes, maximizing the diversity of antibodies that can be recovered." ], [ "3d", "After establishing the highly sensitive SPR and HDX LC/MS methods for detecting antigen-specific antibodies in serum, we tested their performance using sera from immunized mice." ], [ "3e", "Nine serum samples collected from various strains of mice, which were immunized with human IL-13 using different protocols, were analyzed with these methods in a \"proof-of-concept\" study." ], [ "3f", "These samples were previously classified as binders" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: An epithelial-centric alarmin pathway around IL-25, IL-33 and thymic stromal lymphopoietin , and their interaction with group 2 innate lymphoid cells has also recently been identified . IL-25, IL-33 and TSLP are type 2 inflammatory cytokines expressed by the epithelial cells upon injury to the epithelial barrier . ILC2s are a group of lymphoid cells lacking both B and T cell receptors but play a crucial role in secreting type 2 cytokines to perpetuate type 2 inflammation when activated . In the event of viral infection, cell death and injury to the epithelial barrier will also induce the expression of", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: T H 2-high endotype is initiated directly via IL-25 and IL-33 released by epithelial cells or indirectly via stimulation of innate lymphocytes type 2 . A third initiation pathway acts via TSLP stimulation of dendritic cells, which attenuate T H 2 polarisation. Neither TSLP, IL33 nor IL23 impairs airway epithelial barrier . T H 2 and ILC2 cells recruit eosinophils, and, via induction of B cells, also mast cells and basophils. Thus, T H 2-high endotype is characterised by enrichment of eosinophils, basophils and mast cells . The accumulation of these immune cells results in a typical chemokine pattern, called", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: factor and monocyte chemotractant protein 1 . The response to proteolytically active allergens involves storeoperated Ca 2+ entry in epithelial cells , and it should be noted that bacterial exotoxins also activate store-operated Ca 2+ entry . Other factors, which belong to dangerassociated molecular patterns , like adenosine , prostaglandin or histamine , initiate IL-1β, IL-6, IL-8 and GM-CSF production and release. Further, stimuli for chemokine release from airway epithelial cells are inhaled air pollutants and cold . More recent investigations revealed airway epithelial cells as a source of IL-25, IL-33 and thymic stromal lymphopoieitin . This subset of cytokines", "Title: Cytokines IL-17 and IL-22 in the host response to infection\nPassage: including those that encode proteins involved in tissue inflammation, immunosurveillance and homeostasis . By eliciting various innate defense mechanisms from epithelial cells, IL-22 is essential for host defense at mucosal surfaces against extracellular pathogens such as bacteria and yeast . In general, IL-22 acts to strengthen epithelial barrier functions and is involved in tissue homeostasis as well as in tissue repair and wound healing. However, excessive or prolonged production of IL-22 can cause pathology, such as psoriasis-like skin inflammation ." ]

[ [ "0a", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium" ], [ "0b", "Passage: An epithelial-centric alarmin pathway around IL-25, IL-33 and thymic stromal lymphopoietin , and their interaction with group 2 innate lymphoid cells has also recently been identified ." ], [ "0c", "IL-25, IL-33 and TSLP are type 2 inflammatory cytokines expressed by the epithelial cells upon injury to the epithelial barrier ." ], [ "0d", "ILC2s are a group of lymphoid cells lacking both B and T cell receptors but play a crucial role in secreting type 2 cytokines to perpetuate type 2 inflammation when activated ." ], [ "0e", "In the event of viral infection, cell death and injury to the epithelial barrier will also induce the expression of" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: An epithelial-centric alarmin pathway around IL-25, IL-33 and thymic stromal lymphopoietin , and their interaction with group 2 innate lymphoid cells has also recently been identified . IL-25, IL-33 and TSLP are type 2 inflammatory cytokines expressed by the epithelial cells upon injury to the epithelial barrier . ILC2s are a group of lymphoid cells lacking both B and T cell receptors but play a crucial role in secreting type 2 cytokines to perpetuate type 2 inflammation when activated . In the event of viral infection, cell death and injury to the epithelial barrier will also induce the expression of", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: T H 2-high endotype is initiated directly via IL-25 and IL-33 released by epithelial cells or indirectly via stimulation of innate lymphocytes type 2 . A third initiation pathway acts via TSLP stimulation of dendritic cells, which attenuate T H 2 polarisation. Neither TSLP, IL33 nor IL23 impairs airway epithelial barrier . T H 2 and ILC2 cells recruit eosinophils, and, via induction of B cells, also mast cells and basophils. Thus, T H 2-high endotype is characterised by enrichment of eosinophils, basophils and mast cells . The accumulation of these immune cells results in a typical chemokine pattern, called", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: factor and monocyte chemotractant protein 1 . The response to proteolytically active allergens involves storeoperated Ca 2+ entry in epithelial cells , and it should be noted that bacterial exotoxins also activate store-operated Ca 2+ entry . Other factors, which belong to dangerassociated molecular patterns , like adenosine , prostaglandin or histamine , initiate IL-1β, IL-6, IL-8 and GM-CSF production and release. Further, stimuli for chemokine release from airway epithelial cells are inhaled air pollutants and cold . More recent investigations revealed airway epithelial cells as a source of IL-25, IL-33 and thymic stromal lymphopoieitin . This subset of cytokines", "Title: Cytokines IL-17 and IL-22 in the host response to infection\nPassage: including those that encode proteins involved in tissue inflammation, immunosurveillance and homeostasis . By eliciting various innate defense mechanisms from epithelial cells, IL-22 is essential for host defense at mucosal surfaces against extracellular pathogens such as bacteria and yeast . In general, IL-22 acts to strengthen epithelial barrier functions and is involved in tissue homeostasis as well as in tissue repair and wound healing. However, excessive or prolonged production of IL-22 can cause pathology, such as psoriasis-like skin inflammation ." ]

[ [ "1a", "Title: Tight junctions in pulmonary epithelia during lung inflammation" ], [ "1b", "Passage: T H 2-high endotype is initiated directly via IL-25 and IL-33 released by epithelial cells or indirectly via stimulation of innate lymphocytes type 2 ." ], [ "1c", "A third initiation pathway acts via TSLP stimulation of dendritic cells, which attenuate T H 2 polarisation." ], [ "1d", "Neither TSLP, IL33 nor IL23 impairs airway epithelial barrier ." ], [ "1e", "T H 2 and ILC2 cells recruit eosinophils, and, via induction of B cells, also mast cells and basophils." ], [ "1f", "Thus, T H 2-high endotype is characterised by enrichment of eosinophils, basophils and mast cells ." ], [ "1g", "The accumulation of these immune cells results in a typical chemokine pattern, called" ] ]

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

[ "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: An epithelial-centric alarmin pathway around IL-25, IL-33 and thymic stromal lymphopoietin , and their interaction with group 2 innate lymphoid cells has also recently been identified . IL-25, IL-33 and TSLP are type 2 inflammatory cytokines expressed by the epithelial cells upon injury to the epithelial barrier . ILC2s are a group of lymphoid cells lacking both B and T cell receptors but play a crucial role in secreting type 2 cytokines to perpetuate type 2 inflammation when activated . In the event of viral infection, cell death and injury to the epithelial barrier will also induce the expression of", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: T H 2-high endotype is initiated directly via IL-25 and IL-33 released by epithelial cells or indirectly via stimulation of innate lymphocytes type 2 . A third initiation pathway acts via TSLP stimulation of dendritic cells, which attenuate T H 2 polarisation. Neither TSLP, IL33 nor IL23 impairs airway epithelial barrier . T H 2 and ILC2 cells recruit eosinophils, and, via induction of B cells, also mast cells and basophils. Thus, T H 2-high endotype is characterised by enrichment of eosinophils, basophils and mast cells . The accumulation of these immune cells results in a typical chemokine pattern, called", "Title: Tight junctions in pulmonary epithelia during lung inflammation\nPassage: factor and monocyte chemotractant protein 1 . The response to proteolytically active allergens involves storeoperated Ca 2+ entry in epithelial cells , and it should be noted that bacterial exotoxins also activate store-operated Ca 2+ entry . Other factors, which belong to dangerassociated molecular patterns , like adenosine , prostaglandin or histamine , initiate IL-1β, IL-6, IL-8 and GM-CSF production and release. Further, stimuli for chemokine release from airway epithelial cells are inhaled air pollutants and cold . More recent investigations revealed airway epithelial cells as a source of IL-25, IL-33 and thymic stromal lymphopoieitin . This subset of cytokines", "Title: Cytokines IL-17 and IL-22 in the host response to infection\nPassage: including those that encode proteins involved in tissue inflammation, immunosurveillance and homeostasis . By eliciting various innate defense mechanisms from epithelial cells, IL-22 is essential for host defense at mucosal surfaces against extracellular pathogens such as bacteria and yeast . In general, IL-22 acts to strengthen epithelial barrier functions and is involved in tissue homeostasis as well as in tissue repair and wound healing. However, excessive or prolonged production of IL-22 can cause pathology, such as psoriasis-like skin inflammation ." ]

[ [ "2a", "Title: Tight junctions in pulmonary epithelia during lung inflammation" ], [ "2b", "Passage: factor and monocyte chemotractant protein 1 ." ], [ "2c", "The response to proteolytically active allergens involves storeoperated Ca 2+ entry in epithelial cells , and it should be noted that bacterial exotoxins also activate store-operated Ca 2+ entry ." ], [ "2d", "Other factors, which belong to dangerassociated molecular patterns , like adenosine , prostaglandin or histamine , initiate IL-1β, IL-6, IL-8 and GM-CSF production and release." ], [ "2e", "Further, stimuli for chemokine release from airway epithelial cells are inhaled air pollutants and cold ." ], [ "2f", "More recent investigations revealed airway epithelial cells as a source of IL-25, IL-33 and thymic stromal lymphopoieitin ." ], [ "2g", "This subset of cytokines" ] ]

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

[ "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: ASSUR calculated each plot were equally weighted and the average of these parameters were calculated for each target microbe. These averages were then pooled and re-averaged based on the sample type and also for all three sample types and these values used to rank developers in terms of ASSUR.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: at the PATH laboratory and the Applied Biosystems 7500 Fast system at the CDC laboratory.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: for each ASSUR radial data point were equally weighted and the averaged data within each plot was calculated as compared to optimal ASSUR plot values of 1.0 . The developers were ranked for each of the three sample panels and overall via the average of the pooled values for both targets per sample panel and for all six targets for overall. The developers were ranked in ascending order. The ranking of the developers based upon sensitivity and specificity only is provided in parentheses; FLU, influenza A, MTB, M. tuberculosis; SP, sputum; MS2, male specific bacteriophage; SPN, S. pneumoniae; BL, blood,", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: was tested in triplicate via the CDC real time RT-PCR protocols for the corresponding microbial NAs , and the C t values shared with the PATH laboratory for subsequent analyses." ]

[ [ "0a", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings" ], [ "0b", "Passage: ASSUR calculated each plot were equally weighted and the average of these parameters were calculated for each target microbe." ], [ "0c", "These averages were then pooled and re-averaged based on the sample type and also for all three sample types and these values used to rank developers in terms of ASSUR." ] ]

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

[ "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: ASSUR calculated each plot were equally weighted and the average of these parameters were calculated for each target microbe. These averages were then pooled and re-averaged based on the sample type and also for all three sample types and these values used to rank developers in terms of ASSUR.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: at the PATH laboratory and the Applied Biosystems 7500 Fast system at the CDC laboratory.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: for each ASSUR radial data point were equally weighted and the averaged data within each plot was calculated as compared to optimal ASSUR plot values of 1.0 . The developers were ranked for each of the three sample panels and overall via the average of the pooled values for both targets per sample panel and for all six targets for overall. The developers were ranked in ascending order. The ranking of the developers based upon sensitivity and specificity only is provided in parentheses; FLU, influenza A, MTB, M. tuberculosis; SP, sputum; MS2, male specific bacteriophage; SPN, S. pneumoniae; BL, blood,", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: was tested in triplicate via the CDC real time RT-PCR protocols for the corresponding microbial NAs , and the C t values shared with the PATH laboratory for subsequent analyses." ]

[ [ "2a", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings" ], [ "2b", "Passage: for each ASSUR radial data point were equally weighted and the averaged data within each plot was calculated as compared to optimal ASSUR plot values of 1.0 ." ], [ "2c", "The developers were ranked for each of the three sample panels and overall via the average of the pooled values for both targets per sample panel and for all six targets for overall." ], [ "2d", "The developers were ranked in ascending order." ], [ "2e", "The ranking of the developers based upon sensitivity and specificity only is provided in parentheses; FLU, influenza A, MTB, M. tuberculosis; SP, sputum; MS2, male specific bacteriophage; SPN, S. pneumoniae; BL, blood," ] ]

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

[ "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: ASSUR calculated each plot were equally weighted and the average of these parameters were calculated for each target microbe. These averages were then pooled and re-averaged based on the sample type and also for all three sample types and these values used to rank developers in terms of ASSUR.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: at the PATH laboratory and the Applied Biosystems 7500 Fast system at the CDC laboratory.", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: for each ASSUR radial data point were equally weighted and the averaged data within each plot was calculated as compared to optimal ASSUR plot values of 1.0 . The developers were ranked for each of the three sample panels and overall via the average of the pooled values for both targets per sample panel and for all six targets for overall. The developers were ranked in ascending order. The ranking of the developers based upon sensitivity and specificity only is provided in parentheses; FLU, influenza A, MTB, M. tuberculosis; SP, sputum; MS2, male specific bacteriophage; SPN, S. pneumoniae; BL, blood,", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings\nPassage: was tested in triplicate via the CDC real time RT-PCR protocols for the corresponding microbial NAs , and the C t values shared with the PATH laboratory for subsequent analyses." ]

[ [ "3a", "Title: Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings" ], [ "3b", "Passage: was tested in triplicate via the CDC real time RT-PCR protocols for the corresponding microbial NAs , and the C t values shared with the PATH laboratory for subsequent analyses." ] ]

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

[ "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities. It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs. Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases . Some DUSPs are also known as MAPK phosphatases . Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family. The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities. It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs. Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases . Some DUSPs are also known as MAPK phosphatases . Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family. The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Innate immune response protects the host from MTB infection by secretion of cytokines including TNF-α in immune cells. Meanwhile, MAPK is one of the critical proteins in the regulation of immunity and cytokine expression. Since MAPK is regulated by MKP-1 in response to LPS and the activation of MAPK is important in BCGinduced cytokine expression, we hypothesize that MKP-1 plays a critical role in the immune regulation of BCG in human monocytes. We examined the involvement of MKP-1 in BCG-induced MAPK activation and its consequent cytokine expression. Here, we present evidences that MKP-1 plays an unexpected role in the regulation", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Innate immune response protects the host from MTB infection by secretion of cytokines including TNF-α in immune cells. Meanwhile, MAPK is one of the critical proteins in the regulation of immunity and cytokine expression. Since MAPK is regulated by MKP-1 in response to LPS and the activation of MAPK is important in BCGinduced cytokine expression, we hypothesize that MKP-1 plays a critical role in the immune regulation of BCG in human monocytes. We examined the involvement of MKP-1 in BCG-induced MAPK activation and its consequent cytokine expression. Here, we present evidences that MKP-1 plays an unexpected role in the regulation" ]

[ [ "0a", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1" ], [ "0b", "Passage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities." ], [ "0c", "It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs." ], [ "0d", "Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases ." ], [ "0e", "Some DUSPs are also known as MAPK phosphatases ." ], [ "0f", "Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family." ], [ "0g", "The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component" ] ]

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

[ "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities. It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs. Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases . Some DUSPs are also known as MAPK phosphatases . Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family. The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities. It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs. Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases . Some DUSPs are also known as MAPK phosphatases . Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family. The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Innate immune response protects the host from MTB infection by secretion of cytokines including TNF-α in immune cells. Meanwhile, MAPK is one of the critical proteins in the regulation of immunity and cytokine expression. Since MAPK is regulated by MKP-1 in response to LPS and the activation of MAPK is important in BCGinduced cytokine expression, we hypothesize that MKP-1 plays a critical role in the immune regulation of BCG in human monocytes. We examined the involvement of MKP-1 in BCG-induced MAPK activation and its consequent cytokine expression. Here, we present evidences that MKP-1 plays an unexpected role in the regulation", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1\nPassage: Innate immune response protects the host from MTB infection by secretion of cytokines including TNF-α in immune cells. Meanwhile, MAPK is one of the critical proteins in the regulation of immunity and cytokine expression. Since MAPK is regulated by MKP-1 in response to LPS and the activation of MAPK is important in BCGinduced cytokine expression, we hypothesize that MKP-1 plays a critical role in the immune regulation of BCG in human monocytes. We examined the involvement of MKP-1 in BCG-induced MAPK activation and its consequent cytokine expression. Here, we present evidences that MKP-1 plays an unexpected role in the regulation" ]

[ [ "1a", "Title: A novel anti-mycobacterial function of mitogen-activated protein kinase phosphatase-1" ], [ "1b", "Passage: Since MAPKs are activated by phosphorylation, dephosphorylation of MAPKs seems to be an efficient process to inactivate their activities." ], [ "1c", "It can be achieved by specific protein kinase phosphatases which can remove the phosphate group from MAPKs." ], [ "1d", "Examples of these phosphatases include tyrosine phosphatases, serine/threonine phosphatases, and dual-specificity phosphatases ." ], [ "1e", "Some DUSPs are also known as MAPK phosphatases ." ], [ "1f", "Currently, there are at least 10 MKPs identified, while MKP-1 is the most studied member of the family." ], [ "1g", "The regulatory role of MKP-1 on cytokine induction is best demonstrated by MKP-1 knockout macrophages in response to lipopolysaccharide , a cell wall component" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "0a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "0b", "Passage: All patients had HAdV-55 viremia." ], [ "0c", "In four of the five patients, it was first detected in endotracheal aspirate samples." ], [ "0d", "The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days ." ], [ "0e", "Virus DNA copies in ETAs were determined for all patients during their ICU stay." ], [ "0f", "The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient." ], [ "0g", "The viral load became negative in the only patient who survived." ], [ "0h", "In the four patients who did not survive, DNA" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "1a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "1b", "Passage: All patients had HAdV-55 viremia." ], [ "1c", "In four of the five patients, it was first detected in endotracheal aspirate samples." ], [ "1d", "The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days ." ], [ "1e", "Virus DNA copies in ETAs were determined for all patients during their ICU stay." ], [ "1f", "The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient." ], [ "1g", "The viral load became negative in the only patient who survived." ], [ "1h", "In the four patients who did not survive, DNA" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "2a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "2b", "Passage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included." ], [ "2c", "All five patients were immunocompetent young men with a median age of 32 years." ], [ "2d", "The mean time from onset to dyspnea was 5 days." ], [ "2e", "Arterial blood gas analysis at ICU admission revealed profound hypoxia." ], [ "2f", "Mean partial oxygen pressure/fraction of inspired oxygen was 58.1." ], [ "2g", "Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively." ], [ "2h", "The viral load was higher than 1 × 10 copies in three patients and was" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: All patients had HAdV-55 viremia. In four of the five patients, it was first detected in endotracheal aspirate samples. The time between initial ETA sample collection of adenoviruses and positive results for HAdV-55 nucleic acid in the blood was 1 to 10 days . Virus DNA copies in ETAs were determined for all patients during their ICU stay. The viral load was higher than 1 × 10 8 copies in three patients and 1 × 10 4 in one patient. The viral load became negative in the only patient who survived. In the four patients who did not survive, DNA", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: five consecutive patients with severe ARDS with confirmed HAdV-55 infection were included. All five patients were immunocompetent young men with a median age of 32 years. The mean time from onset to dyspnea was 5 days. Arterial blood gas analysis at ICU admission revealed profound hypoxia. Mean partial oxygen pressure/fraction of inspired oxygen was 58.1. Mean durations from onset to a single-lobe consolidation shown on chest X-rays and, from the first positive CXR to bilateral multilobar lung infiltrates, were 2 days and 4.8 days, respectively. The viral load was higher than 1 × 10 copies in three patients and was", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: 1 × 10 in one patient. It was negative in the only patient who survived. The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively. Four patients received venovenous ECMO. Four of the five patients died despite receiving appropriate respiratory support. CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men. Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS. Viral load monitoring may help predict disease severity and outcome. The" ]

[ [ "3a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "3b", "Passage: 1 × 10 in one patient." ], [ "3c", "It was negative in the only patient who survived." ], [ "3d", "The mean duration for noninvasive positive pressure ventilation failure and IMV failure were 30.8 hours and 6.2 days, respectively." ], [ "3e", "Four patients received venovenous ECMO." ], [ "3f", "Four of the five patients died despite receiving appropriate respiratory support." ], [ "3g", "CONCLUSIONS: HAdV-55 may cause severe ARDS in immunocompetent young men." ], [ "3h", "Persistent high fever, dyspnea and rapid progression to respiratory failure within 2 weeks, together with bilateral consolidations and infiltrates, are the most frequent clinical manifestations of HAdV-55-induced severe ARDS." ], [ "3i", "Viral load monitoring may help predict disease severity and outcome. The" ] ]

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

[ "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling\nPassage: Weekly respiratory virus identifications from September 1999 to August 2006 were obtained from the Respiratory Virus Detection Surveillance System , Public Health Agency of Canada . The RVDSS collects, collates, and reports weekly data from participating laboratories on the number of tests performed and the number of specimens confirmed positive for influenza, respiratory syncytial virus , para-influenza virus , and adenovirus. Specimens are generally submitted to laboratories by clinicians in the course of clinical care, and by clinicians participating in one of our national influenza surveillance programs, ). Indicators of influenza activity are reported year round on a weekly basis", "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling\nPassage: to the FluWatch program. The RVDSS is supplemented by case reports of influenza positive cases . From the case reports, influenza A was confirmed in all age groups and sporadic cases were confirmed in the off-season months of June through September. Infants and children under the age of 5 years accounted for 25% of the influenza A positive tests, and persons over the age 65 years another 35%. Unfortunately, FluWatch surveillance data does not provide the total number of tests by age. Testing practices are known to be varied . The predominant testing methods used for influenza detection varied considerably", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: In our study, leukocyte count was used as an indicator of inclusion criteria and it probably affected the positive rate. Viruses not considered in the study, for example coronaviruses, would underestimate the positive rate. Most studies showed that RSV or HRV was the most prevalent viruses in children with viral respiratory tract infection. 1 In this study, IAV was the most frequently detected respiratory virus, followed by RSV and HRV. IAV outbreak in 2009 could explain this shift. Data showed that about 60% of IAV infections were detected during the outbreak period. Studies showed that the H1N1 outbreak could change", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: Our study showed that RSV and HRV were the two most viruses involved in multiple infection, followed by IAV and PIVs, regardless of IAV infection in the H1N1 outbreak period. It was difficult to explain the variations of coinfection patterns based only on seasonal distribution. A recent study suggested that co-infection patterns were not random and certain pathogens had higher frequency of coinfection. 41 As molecular assays only detect nucleic acid and positive result does not mean the presence of the pathogen, when studying co-infection patterns of respiratory viruses, the ability to differentiate the real causative pathogens needs to be" ]

[ [ "0a", "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling" ], [ "0b", "Passage: Weekly respiratory virus identifications from September 1999 to August 2006 were obtained from the Respiratory Virus Detection Surveillance System , Public Health Agency of Canada ." ], [ "0c", "The RVDSS collects, collates, and reports weekly data from participating laboratories on the number of tests performed and the number of specimens confirmed positive for influenza, respiratory syncytial virus , para-influenza virus , and adenovirus." ], [ "0d", "Specimens are generally submitted to laboratories by clinicians in the course of clinical care, and by clinicians participating in one of our national influenza surveillance programs, )." ], [ "0e", "Indicators of influenza activity are reported year round on a weekly basis" ] ]

[ "0c", "1c" ]

[ "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling\nPassage: Weekly respiratory virus identifications from September 1999 to August 2006 were obtained from the Respiratory Virus Detection Surveillance System , Public Health Agency of Canada . The RVDSS collects, collates, and reports weekly data from participating laboratories on the number of tests performed and the number of specimens confirmed positive for influenza, respiratory syncytial virus , para-influenza virus , and adenovirus. Specimens are generally submitted to laboratories by clinicians in the course of clinical care, and by clinicians participating in one of our national influenza surveillance programs, ). Indicators of influenza activity are reported year round on a weekly basis", "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling\nPassage: to the FluWatch program. The RVDSS is supplemented by case reports of influenza positive cases . From the case reports, influenza A was confirmed in all age groups and sporadic cases were confirmed in the off-season months of June through September. Infants and children under the age of 5 years accounted for 25% of the influenza A positive tests, and persons over the age 65 years another 35%. Unfortunately, FluWatch surveillance data does not provide the total number of tests by age. Testing practices are known to be varied . The predominant testing methods used for influenza detection varied considerably", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: In our study, leukocyte count was used as an indicator of inclusion criteria and it probably affected the positive rate. Viruses not considered in the study, for example coronaviruses, would underestimate the positive rate. Most studies showed that RSV or HRV was the most prevalent viruses in children with viral respiratory tract infection. 1 In this study, IAV was the most frequently detected respiratory virus, followed by RSV and HRV. IAV outbreak in 2009 could explain this shift. Data showed that about 60% of IAV infections were detected during the outbreak period. Studies showed that the H1N1 outbreak could change", "Title: A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China\nPassage: Our study showed that RSV and HRV were the two most viruses involved in multiple infection, followed by IAV and PIVs, regardless of IAV infection in the H1N1 outbreak period. It was difficult to explain the variations of coinfection patterns based only on seasonal distribution. A recent study suggested that co-infection patterns were not random and certain pathogens had higher frequency of coinfection. 41 As molecular assays only detect nucleic acid and positive result does not mean the presence of the pathogen, when studying co-infection patterns of respiratory viruses, the ability to differentiate the real causative pathogens needs to be" ]

[ [ "1a", "Title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling" ], [ "1b", "Passage: to the FluWatch program." ], [ "1c", "The RVDSS is supplemented by case reports of influenza positive cases ." ], [ "1d", "From the case reports, influenza A was confirmed in all age groups and sporadic cases were confirmed in the off-season months of June through September." ], [ "1e", "Infants and children under the age of 5 years accounted for 25% of the influenza A positive tests, and persons over the age 65 years another 35%." ], [ "1f", "Unfortunately, FluWatch surveillance data does not provide the total number of tests by age." ], [ "1g", "Testing practices are known to be varied ." ], [ "1h", "The predominant testing methods used for influenza detection varied considerably" ] ]

[ "0c", "1c" ]

[ "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae\nPassage: Five of the novel viruses identified in this study were assigned to established genera. Two of these, KOOLV and YATV, clustered within the existing Ephemerovirus clade, and possessed the characteristic genome organization of ephemeroviruses, including a non-structural glycoprotein gene followed by a viroporin Newly proposed genera are indicated by a † symbol. Cytorhabdovirus, novirhabdovirus and nucleorhabdovirus outgroup sequences were excluded from the tree as they were too divergent to establish a reliable rooting. The tree is therefore rooted arbitrarily on one of two basal clades that comprise viruses isolated from mosquitoes.", "Title: Serious Invasive Saffold Virus Infections in Children, 2009\nPassage: During the past few years, intensive searches for new viruses, using conventional virologic methods and metagenomics, have resulted in the discovery of several new viruses. During the past decade, the family Picornaviridae has grown as the number of recognized genera has increased from 6 to 12 ; the numbers of species, types, and subtypes have increased even more. However, only viruses from 3 genera have been fi rmly established as being capable of causing clinically signifi cant disease in humans. Viruses from other genera have so far been detected only in noninvasively collected human sample material such as fecal and", "Title: Mimiviridae, Marseilleviridae, and virophages as emerging human pathogens causing healthcare-associated infections\nPassage: , , . In 2007, a first member of the Marseilleviridae family also related to NCLDVs, Acanthamoeba polyphaga marseillevirus , was isolated from water collected from a cooling tower in Paris, France, using a method based on Acanthamoeba polyphaga culture . This virus was named in honor of its amoebal host and of the name of the French city, Marseille, where it was discovered . The Marseillevirus was characterized by a 368-kb genome, 457 genes, and a minimum of 49 proteins . Furthermore, the first member of the second branch of Mimiviridae family, Cafeteria roenbergensis virus , was described in", "Title: Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts\nPassage: We also detected a sequence related to the large segment of members of the family Bunyaviridae in adult culicine mosquitoes. The contig contained a single long ORF that showed greatest similarity to members of the genus Phlebovirus, and the currently unclassified GOUV which was originally detected in specimens of the mosquito genera Anopheles , Culex and Uranotaenia in West Africa. Here, we provide evidence for a related novel virus from mosquitoes collected in France. Further field studies are necessary to allow the potential full isolation of this strain, which considering its divergence from GOUV, may constitute a novel genus within" ]

[ [ "0a", "Title: Evolution of Genome Size and Complexity in the Rhabdoviridae" ], [ "0b", "Passage: Five of the novel viruses identified in this study were assigned to established genera." ], [ "0c", "Two of these, KOOLV and YATV, clustered within the existing Ephemerovirus clade, and possessed the characteristic genome organization of ephemeroviruses, including a non-structural glycoprotein gene followed by a viroporin Newly proposed genera are indicated by a † symbol." ], [ "0d", "Cytorhabdovirus, novirhabdovirus and nucleorhabdovirus outgroup sequences were excluded from the tree as they were too divergent to establish a reliable rooting." ], [ "0e", "The tree is therefore rooted arbitrarily on one of two basal clades that comprise viruses isolated from mosquitoes." ] ]

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