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[ "Title: CDC Summary 21 MAR 2020,\nPassage: cases in the United States by age group found that 80% of deaths were among adults 65 years and older with the highest percentage of severe outcomes occurring in people 85 years and older.", "Title: Descriptive study of severe hospitalized cases of laboratory-confirmed influenza during five epidemic seasons (2010–2015)\nPassage: During the 2010-2015 seasons 1400 cases of SHCLCI were recorded, 462 required ICU admission and 167 died: 778 were male. The median age was 61 years . The most-affected age group was the ≥ 65 years age group with 633 cases . The median age of the ≥ 65 years age group was 79 years and the mean age was 78.7 years : 296 were aged ≥ 80 years. Of deaths, 111 occurred in patients aged ≥ 65 years and 55 in patients aged > 80 years .", "Title: Clinical characteristics and outcomes during a severe influenza season in China during 2017–2018\nPassage: in the 14-59 and > 60 groups.", "Title: Global Mortality Impact of the 1957–1959 Influenza Pandemic\nPassage: Age-specific excess mortality rates were highest at both extremes of the age spectrum . However, when excess mortality was compared to baseline mortality rates, the age groups with highest relative burden were 15-24 years , followed by 5-14 years . In contrast, children aged <5 years and seniors aged ≥65 years only experienced a minor elevation over baseline . The sharp mortality elevation in schoolaged children and young adults was consistent throughout Europe , even though the all-age impact of the pandemic on mortality was generally low in this region." ]

[ [ "3a", "Title: Global Mortality Impact of the 1957–1959 Influenza Pandemic" ], [ "3b", "Passage: Age-specific excess mortality rates were highest at both extremes of the age spectrum ." ], [ "3c", "However, when excess mortality was compared to baseline mortality rates, the age groups with highest relative burden were 15-24 years , followed by 5-14 years ." ], [ "3d", "In contrast, children aged <5 years and seniors aged ≥65 years only experienced a minor elevation over baseline ." ], [ "3e", "The sharp mortality elevation in schoolaged children and young adults was consistent throughout Europe , even though the all-age impact of the pandemic on mortality was generally low in this region." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: A single study has examined the ability of MERS-CoV to survive in the environment . Plastic or steel surfaces were inoculated with 10 6 TCID 50 of MERS-CoV at different temperature and relative humidity and virus recovery was attempted in cell culture. At high ambient temperature and low RH MERS-CoV remained viable for 24 h . By comparison, a well known and efficently transmitted respiratory virus, influenza A virus, could not be recovered in culture beyond four hours under any conditions . Aerosol experiments found MERS-CoV viability only decreased 7 % at low RH at 20°C. In comparison, influenza A", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: virus decreased by 95 % . MERS-CoV survival is inferior to that previously demonstrated for SARS-CoV . For context, pathogenic bacteria can remain viable and airborne for 45 min in a coughed aerosol and can spread 4 m. MERS-CoV's ability to remain viable over long time periods gives it the capacity to thoroughly contaminate a room's surfaces when occupied by an infected and symptomatic patient . Whether MERS-CoV can remain adrift and infectious for extended periods remains unknown. Such findings expand our understanding of the possibilities for droplets to transmit respiratory viruses in many settings, including hospital waiting rooms, emergency", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Individual human case studies report long periods of viral shedding, sometimes intermittently and not necessarily linked to the presence of disease symptoms. In one instance, a HCW shed viral RNA for 42 days in the absence of disease . It is an area of high priority to better understand whether such cases are able to infect others. Over three quarters of MERS cases shed viral RNA in their LRT specimens for at least 30 days, while only 30 % of contacts were still shedding RNA in their URT specimens .", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: families and healthcare settings . Clinical pictures of this infection varied from asymptomatic to mild respiratory symptoms to severe respiratory distress and death . Severe ailment can often cause respiratory catastrophes that need mechanical ventilation and support in ICUs across different healthcare settings . Studies have suggested an incubation period of 16 days with a mean of 5-6 days , while the median time until death is 11-13 days among severely ill patients . e gold standard test for the detection of this virus is real-time reverse-transcription polymerase chain reaction assays ." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: A single study has examined the ability of MERS-CoV to survive in the environment ." ], [ "0c", "Plastic or steel surfaces were inoculated with 10 6 TCID 50 of MERS-CoV at different temperature and relative humidity and virus recovery was attempted in cell culture." ], [ "0d", "At high ambient temperature and low RH MERS-CoV remained viable for 24 h ." ], [ "0e", "By comparison, a well known and efficently transmitted respiratory virus, influenza A virus, could not be recovered in culture beyond four hours under any conditions ." ], [ "0f", "Aerosol experiments found MERS-CoV viability only decreased 7 % at low RH at 20°C." ], [ "0g", "In comparison, influenza A" ] ]

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

[ "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: After application of the overlay, plates were monitored periodically using an inverted fluorescence microscope until the first signs of GFP expression were witnessed . From that time forward, a square subset of the center of each well was imaged periodically, using a CellInsight CX5 High Content Screening Platform with a 4X air objective . Microscope settings were held standard across all trials, with exposure time fixed at 0.0006 s for each image. One color channel was imaged, such that images produced show GFP-expressing cells in white and non-GFP-expressing cells in black .", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence\nPassage: Because plaque assays restrict viral transmission neighbor-to-neighbor in two-dimensional cellular space , we were able to track the spread of GFP-expressing virus-infected cells across tissue monolayers via inverted fluorescence microscopy. For each infection trial, we monitored and re-imaged plates for up to 200 hr of observations or until total monolayer destruction, processed resulting images, and generated a time series of the proportion of infectious-cell occupied plate space across the duration of each trial . We used generalized additive models to infer the time course of all cell culture replicates and construct the multi-trial dataset to which we eventually fit our", "Title: Visualizing Viral Infection In Vivo by Multi-Photon Intravital Microscopy\nPassage: express cytoplasmic fluorescent proteins driven e.g., by the chicken β-actin promoter with cytomegalovirus enhancer or human ubiquitin C promoter . Many different mouse lines are available that contain reporter genes for cytoplasmic fluorescent proteins such as EGFP and mCherry . Due to strong and continuous expression rate of the fluorescent proteins long-term tracking of dividing cells without extensive bleaching is possible. In addition, with a superior signal-to-noise ratio visualization of small cellular structures with low cytoplasm content is feasible. Although the approach to adoptively transfer fluorescent cells of interest into donor mice for functional imaging studies is fast and flexible,", "Title: Visualizing Viral Infection In Vivo by Multi-Photon Intravital Microscopy\nPassage: Recently, MP-IVM was used to study the mechanism of retrovirus spread in vivo within secondary lymphoid tissues by visualizing MLV-infected cells and MLV particles directly in living animals. In a first study, in vitro transduced B cells were adoptively transferred into mice for MP-IVM at the popliteal lymph nodes . In contrast to other studies visualizing infected cells expressing cytoplasmic GFP after reporter virus infection, full-length MLV encoding for a capsid fusion with GFP helped to analyze the subcellular distribution of a structural retroviral protein in vivo. MLV Gag-GFP revealed a polarized distribution in static MLV-infected cells indicating the existence" ]

[ [ "1a", "Title: Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence" ], [ "1b", "Passage: Because plaque assays restrict viral transmission neighbor-to-neighbor in two-dimensional cellular space , we were able to track the spread of GFP-expressing virus-infected cells across tissue monolayers via inverted fluorescence microscopy." ], [ "1c", "For each infection trial, we monitored and re-imaged plates for up to 200 hr of observations or until total monolayer destruction, processed resulting images, and generated a time series of the proportion of infectious-cell occupied plate space across the duration of each trial ." ], [ "1d", "We used generalized additive models to infer the time course of all cell culture replicates and construct the multi-trial dataset to which we eventually fit our" ] ]

[ "1b", "1c" ]

[ "Title: Globalization and emerging governance modalities\nPassage: me two conclusions.", "Title: Estimating the number of infections and the impact of non-\nPassage: the appendix, and general limitations presented below in the conclusions.", "Title: Outcome of paediatric intensive care survivors\nPassage: and, therefore, strong conclusive statements difficult.", "Title: Estimating the number of infections and the impact of non-\nPassage: 4 Conclusion and Limitations" ]

[ [ "1a", "Title: Estimating the number of infections and the impact of non-" ], [ "1b", "Passage: the appendix, and general limitations presented below in the conclusions." ] ]

[ "1b", "3b" ]

[ "Title: Globalization and emerging governance modalities\nPassage: me two conclusions.", "Title: Estimating the number of infections and the impact of non-\nPassage: the appendix, and general limitations presented below in the conclusions.", "Title: Outcome of paediatric intensive care survivors\nPassage: and, therefore, strong conclusive statements difficult.", "Title: Estimating the number of infections and the impact of non-\nPassage: 4 Conclusion and Limitations" ]

[ [ "3a", "Title: Estimating the number of infections and the impact of non-" ], [ "3b", "Passage: 4 Conclusion and Limitations" ] ]

[ "1b", "3b" ]

[ "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: should be considered everyone's problem. The recent Zika virus epidemic followed many similar patterns highlighting that we all share the responsibility in responding to infectious outbreaks. Many of the country-level factors, particularly the WHO key indicators were associated with controlling the epidemic. International political and public health leaders should assess the infrastructure of countries affected by communicable diseases.", "Title: Managing emerging transnational public health security threats: lessons learned from the 2014 West African Ebola outbreak\nPassage: This study is subject to certain limitations. Perhaps the most substantial of which is the difficulty to quantify many factors affecting control of the outbreak. For example, the West African people educated their communities, facilitating the change of social practices, such as greetings with physical contact and modifying long-standing traditional burial practices . Education messages on fighting the epidemic were communicated through messaging in radio, billboards, etc.", "Title: Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases\nPassage: Emerging and re-emerging infectious diseases pose some of the greatest health risks to human populations worldwide. Increasingly they are a feature of our time, stoked by changes in human demographics, mobility, land use and climate, and compounded by poor standards of public health in parts of the world . Importantly, new surveillance and intervention strategies are now becoming possible, guided by quantitative interpretation of epidemiological data, potentially strengthening the hand of primary prevention efforts.", "Title: Preventing Emerging and Re-emerging Infections in the Eastern Mediterranean Region: Gaps, Challenges, and Priorities\nPassage: According to the International health regulations of 2005, strengthening or promoting surveillance and response capacities, points of entry capacities, legislation issues, coordination among various national key partners, bio-risk and bio-security and quality management in laboratories are necessary . Strengthening routine vaccination coverage will continue to be the top priority. The Region will focus on improving national managerial capacity and human resource capacity building, empowering decision-making, and supporting countries to reach unreached targets through various evidence-based approaches. Strengthening the monitoring and evaluation systems to use data for action will be among the priority activities. Similarly, strengthening the Regional surveillance networks in" ]

[ [ "3a", "Title: Preventing Emerging and Re-emerging Infections in the Eastern Mediterranean Region: Gaps, Challenges, and Priorities" ], [ "3b", "Passage: According to the International health regulations of 2005, strengthening or promoting surveillance and response capacities, points of entry capacities, legislation issues, coordination among various national key partners, bio-risk and bio-security and quality management in laboratories are necessary ." ], [ "3c", "Strengthening routine vaccination coverage will continue to be the top priority." ], [ "3d", "The Region will focus on improving national managerial capacity and human resource capacity building, empowering decision-making, and supporting countries to reach unreached targets through various evidence-based approaches." ], [ "3e", "Strengthening the monitoring and evaluation systems to use data for action will be among the priority activities." ], [ "3f", "Similarly, strengthening the Regional surveillance networks in" ] ]

[ "3b", "3d" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine. Sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to MERS-CoV transmission chains. However, transmission of MERS-CoV is defined as sporadic , intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact In a household study, 14 of 280 contacts of 26 MERS-CoV positive index patients were RNA or antibody positive; the rate of general transmission, even in outbreaks is around 3 %" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: MERS and SARS have some clinical similarities but they also diverge significantly ." ], [ "0c", "Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities." ], [ "0d", "For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine. Sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to MERS-CoV transmission chains. However, transmission of MERS-CoV is defined as sporadic , intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact In a household study, 14 of 280 contacts of 26 MERS-CoV positive index patients were RNA or antibody positive; the rate of general transmission, even in outbreaks is around 3 %" ]

[ [ "1a", "Title: Host resilience to emerging coronaviruses" ], [ "1b", "Passage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity." ], [ "1c", "The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect." ], [ "1d", "SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 ." ], [ "1e", "Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure ." ], [ "1f", "SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine. Sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to MERS-CoV transmission chains. However, transmission of MERS-CoV is defined as sporadic , intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact In a household study, 14 of 280 contacts of 26 MERS-CoV positive index patients were RNA or antibody positive; the rate of general transmission, even in outbreaks is around 3 %" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs." ], [ "2c", "However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\"." ], [ "2d", "It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\"." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine. Sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to MERS-CoV transmission chains. However, transmission of MERS-CoV is defined as sporadic , intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact In a household study, 14 of 280 contacts of 26 MERS-CoV positive index patients were RNA or antibody positive; the rate of general transmission, even in outbreaks is around 3 %" ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: MERS-CoV was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine." ], [ "3c", "Sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to MERS-CoV transmission chains." ], [ "3d", "However, transmission of MERS-CoV is defined as sporadic , intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact In a household study, 14 of 280 contacts of 26 MERS-CoV positive index patients were RNA or antibody positive; the rate of general transmission, even in outbreaks is around 3 %" ] ]

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

[ "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: The theory of oxidative stress existed since the last 60 years. However, extensive research in the last three decades has clarified myriads of misconceptions and explored leading roles of oxidative stress in the pathogenesis of many viral diseases . A wide range of the reactive species is produced as a result of the metabolic process in the body. These RS can be reactive oxygen species or reactive nitrogen species . Previously, RS were only considered to be toxic compounds: however, recent studies have highlighted their involvements in complex cellular signaling pathways and have improved their importance in several biological systems", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: Owing to the production-dependent oxidative stresses, exploring the molecular mechanisms of ROS production in living organisms is imperative. ROS are primarily produced from the mitochondria, endoplasmic reticulum, plasma membrane, and peroxisomes . Since most of the oxidative processes take place in the mitochondria in an effort to generate energy ), more than 90% of total ROS in eukaryotes is produced by the mitochondria . In the living organisms, most of the consumed oxygen is converted to water in the electron-transport chain by the cytochrome c oxidase without any contribution to ROS production . These ROS include superoxide anion , hydroxyl", "Title: The Role of Na/K-ATPase Signaling in Oxidative Stress Related to Obesity and Cardiovascular Disease\nPassage: There are also several metabolic parameters and complications, which are dysregulated in obesity, and contribute to and amplify oxidative stress. Hyperglycemia induces oxidative stress through activation of the polyol and hexosamine pathways, production of advanced glycation end-products , and increase of diacylglycerol synthesis. Hyperlipidemia induces ROS formation by increasing lipid oxidation and protein carbonylation. Leptin and angiotensin II, both of which are secreted by adipocytes, are inducers of ROS generation. Leptin promotes inflammation and lipid peroxidation, while angiotensin II stimulates AT1R-NADPH oxidases. Dysregulation of all of these metabolic parameters with adipose tissue expansion contributes to oxidative stress . increases selectively", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: complex . This process of ROS production is critical to promote cellular responses . The O 2 − , produced by the immune cells, can lead to the formation of other ROS such as HOCl, H 2 O 2 , peroxynitrite , and OH . The OH radicals are produced from O 2 − by Fenton reaction -). Another possible mechanism is the triggering of ROS production by the virus-induced cytokines. Taken together, ROS may be generated from the activation of XO, NADPH oxidase, lipoxygenases, and cyclooxygenase or from the leakage of electrons from ETC ." ]

[ [ "0a", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections" ], [ "0b", "Passage: The theory of oxidative stress existed since the last 60 years." ], [ "0c", "However, extensive research in the last three decades has clarified myriads of misconceptions and explored leading roles of oxidative stress in the pathogenesis of many viral diseases ." ], [ "0d", "A wide range of the reactive species is produced as a result of the metabolic process in the body." ], [ "0e", "These RS can be reactive oxygen species or reactive nitrogen species ." ], [ "0f", "Previously, RS were only considered to be toxic compounds: however, recent studies have highlighted their involvements in complex cellular signaling pathways and have improved their importance in several biological systems" ] ]

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

[ "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: The theory of oxidative stress existed since the last 60 years. However, extensive research in the last three decades has clarified myriads of misconceptions and explored leading roles of oxidative stress in the pathogenesis of many viral diseases . A wide range of the reactive species is produced as a result of the metabolic process in the body. These RS can be reactive oxygen species or reactive nitrogen species . Previously, RS were only considered to be toxic compounds: however, recent studies have highlighted their involvements in complex cellular signaling pathways and have improved their importance in several biological systems", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: Owing to the production-dependent oxidative stresses, exploring the molecular mechanisms of ROS production in living organisms is imperative. ROS are primarily produced from the mitochondria, endoplasmic reticulum, plasma membrane, and peroxisomes . Since most of the oxidative processes take place in the mitochondria in an effort to generate energy ), more than 90% of total ROS in eukaryotes is produced by the mitochondria . In the living organisms, most of the consumed oxygen is converted to water in the electron-transport chain by the cytochrome c oxidase without any contribution to ROS production . These ROS include superoxide anion , hydroxyl", "Title: The Role of Na/K-ATPase Signaling in Oxidative Stress Related to Obesity and Cardiovascular Disease\nPassage: There are also several metabolic parameters and complications, which are dysregulated in obesity, and contribute to and amplify oxidative stress. Hyperglycemia induces oxidative stress through activation of the polyol and hexosamine pathways, production of advanced glycation end-products , and increase of diacylglycerol synthesis. Hyperlipidemia induces ROS formation by increasing lipid oxidation and protein carbonylation. Leptin and angiotensin II, both of which are secreted by adipocytes, are inducers of ROS generation. Leptin promotes inflammation and lipid peroxidation, while angiotensin II stimulates AT1R-NADPH oxidases. Dysregulation of all of these metabolic parameters with adipose tissue expansion contributes to oxidative stress . increases selectively", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: complex . This process of ROS production is critical to promote cellular responses . The O 2 − , produced by the immune cells, can lead to the formation of other ROS such as HOCl, H 2 O 2 , peroxynitrite , and OH . The OH radicals are produced from O 2 − by Fenton reaction -). Another possible mechanism is the triggering of ROS production by the virus-induced cytokines. Taken together, ROS may be generated from the activation of XO, NADPH oxidase, lipoxygenases, and cyclooxygenase or from the leakage of electrons from ETC ." ]

[ [ "1a", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections" ], [ "1b", "Passage: Owing to the production-dependent oxidative stresses, exploring the molecular mechanisms of ROS production in living organisms is imperative." ], [ "1c", "ROS are primarily produced from the mitochondria, endoplasmic reticulum, plasma membrane, and peroxisomes ." ], [ "1d", "Since most of the oxidative processes take place in the mitochondria in an effort to generate energy ), more than 90% of total ROS in eukaryotes is produced by the mitochondria ." ], [ "1e", "In the living organisms, most of the consumed oxygen is converted to water in the electron-transport chain by the cytochrome c oxidase without any contribution to ROS production ." ], [ "1f", "These ROS include superoxide anion , hydroxyl" ] ]

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

[ "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: The theory of oxidative stress existed since the last 60 years. However, extensive research in the last three decades has clarified myriads of misconceptions and explored leading roles of oxidative stress in the pathogenesis of many viral diseases . A wide range of the reactive species is produced as a result of the metabolic process in the body. These RS can be reactive oxygen species or reactive nitrogen species . Previously, RS were only considered to be toxic compounds: however, recent studies have highlighted their involvements in complex cellular signaling pathways and have improved their importance in several biological systems", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: Owing to the production-dependent oxidative stresses, exploring the molecular mechanisms of ROS production in living organisms is imperative. ROS are primarily produced from the mitochondria, endoplasmic reticulum, plasma membrane, and peroxisomes . Since most of the oxidative processes take place in the mitochondria in an effort to generate energy ), more than 90% of total ROS in eukaryotes is produced by the mitochondria . In the living organisms, most of the consumed oxygen is converted to water in the electron-transport chain by the cytochrome c oxidase without any contribution to ROS production . These ROS include superoxide anion , hydroxyl", "Title: The Role of Na/K-ATPase Signaling in Oxidative Stress Related to Obesity and Cardiovascular Disease\nPassage: There are also several metabolic parameters and complications, which are dysregulated in obesity, and contribute to and amplify oxidative stress. Hyperglycemia induces oxidative stress through activation of the polyol and hexosamine pathways, production of advanced glycation end-products , and increase of diacylglycerol synthesis. Hyperlipidemia induces ROS formation by increasing lipid oxidation and protein carbonylation. Leptin and angiotensin II, both of which are secreted by adipocytes, are inducers of ROS generation. Leptin promotes inflammation and lipid peroxidation, while angiotensin II stimulates AT1R-NADPH oxidases. Dysregulation of all of these metabolic parameters with adipose tissue expansion contributes to oxidative stress . increases selectively", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: complex . This process of ROS production is critical to promote cellular responses . The O 2 − , produced by the immune cells, can lead to the formation of other ROS such as HOCl, H 2 O 2 , peroxynitrite , and OH . The OH radicals are produced from O 2 − by Fenton reaction -). Another possible mechanism is the triggering of ROS production by the virus-induced cytokines. Taken together, ROS may be generated from the activation of XO, NADPH oxidase, lipoxygenases, and cyclooxygenase or from the leakage of electrons from ETC ." ]

[ [ "2a", "Title: The Role of Na/K-ATPase Signaling in Oxidative Stress Related to Obesity and Cardiovascular Disease" ], [ "2b", "Passage: There are also several metabolic parameters and complications, which are dysregulated in obesity, and contribute to and amplify oxidative stress." ], [ "2c", "Hyperglycemia induces oxidative stress through activation of the polyol and hexosamine pathways, production of advanced glycation end-products , and increase of diacylglycerol synthesis." ], [ "2d", "Hyperlipidemia induces ROS formation by increasing lipid oxidation and protein carbonylation." ], [ "2e", "Leptin and angiotensin II, both of which are secreted by adipocytes, are inducers of ROS generation." ], [ "2f", "Leptin promotes inflammation and lipid peroxidation, while angiotensin II stimulates AT1R-NADPH oxidases." ], [ "2g", "Dysregulation of all of these metabolic parameters with adipose tissue expansion contributes to oxidative stress . increases selectively" ] ]

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

[ "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: The theory of oxidative stress existed since the last 60 years. However, extensive research in the last three decades has clarified myriads of misconceptions and explored leading roles of oxidative stress in the pathogenesis of many viral diseases . A wide range of the reactive species is produced as a result of the metabolic process in the body. These RS can be reactive oxygen species or reactive nitrogen species . Previously, RS were only considered to be toxic compounds: however, recent studies have highlighted their involvements in complex cellular signaling pathways and have improved their importance in several biological systems", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: Owing to the production-dependent oxidative stresses, exploring the molecular mechanisms of ROS production in living organisms is imperative. ROS are primarily produced from the mitochondria, endoplasmic reticulum, plasma membrane, and peroxisomes . Since most of the oxidative processes take place in the mitochondria in an effort to generate energy ), more than 90% of total ROS in eukaryotes is produced by the mitochondria . In the living organisms, most of the consumed oxygen is converted to water in the electron-transport chain by the cytochrome c oxidase without any contribution to ROS production . These ROS include superoxide anion , hydroxyl", "Title: The Role of Na/K-ATPase Signaling in Oxidative Stress Related to Obesity and Cardiovascular Disease\nPassage: There are also several metabolic parameters and complications, which are dysregulated in obesity, and contribute to and amplify oxidative stress. Hyperglycemia induces oxidative stress through activation of the polyol and hexosamine pathways, production of advanced glycation end-products , and increase of diacylglycerol synthesis. Hyperlipidemia induces ROS formation by increasing lipid oxidation and protein carbonylation. Leptin and angiotensin II, both of which are secreted by adipocytes, are inducers of ROS generation. Leptin promotes inflammation and lipid peroxidation, while angiotensin II stimulates AT1R-NADPH oxidases. Dysregulation of all of these metabolic parameters with adipose tissue expansion contributes to oxidative stress . increases selectively", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections\nPassage: complex . This process of ROS production is critical to promote cellular responses . The O 2 − , produced by the immune cells, can lead to the formation of other ROS such as HOCl, H 2 O 2 , peroxynitrite , and OH . The OH radicals are produced from O 2 − by Fenton reaction -). Another possible mechanism is the triggering of ROS production by the virus-induced cytokines. Taken together, ROS may be generated from the activation of XO, NADPH oxidase, lipoxygenases, and cyclooxygenase or from the leakage of electrons from ETC ." ]

[ [ "3a", "Title: Oxidative Stress in Poultry: Lessons from the Viral Infections" ], [ "3b", "Passage: complex ." ], [ "3c", "This process of ROS production is critical to promote cellular responses ." ], [ "3d", "The O 2 − , produced by the immune cells, can lead to the formation of other ROS such as HOCl, H 2 O 2 , peroxynitrite , and OH ." ], [ "3e", "The OH radicals are produced from O 2 − by Fenton reaction -)." ], [ "3f", "Another possible mechanism is the triggering of ROS production by the virus-induced cytokines." ], [ "3g", "Taken together, ROS may be generated from the activation of XO, NADPH oxidase, lipoxygenases, and cyclooxygenase or from the leakage of electrons from ETC ." ] ]

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

[ "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: of neutral genetic markers has shown that the transmission bottleneck is dependent upon the route of transmission, whether by contact or aerosol transmission . In natural human influenza populations, where modification of the virus is not possible, population genetic methods have been used to analyse bottleneck sizes. Analyses of transmission have employed different approaches, exploiting the observation or non-observation of variant alleles or using changes in allele frequencies to characterise the bottleneck under a model of genetic drift . A recent publication improved this latter model, incorporating the uncertainty imposed upon allele frequencies by the process of within-host growth .", "Title: Insights into the transmission of respiratory infectious diseases through empirical human contact networks\nPassage: In fact, the influenza spreading behavior can be clearly divided into two categories: in the US schools, disease outbreak appears to be relatively strong and early ; in the schools of SCAU, USTB as well as FRPS, a considerably low transmission was observed .", "Title: Transmission Dynamics and Prospects for the Elimination of Canine Rabies\nPassage: Transmission is the most important process underlying infectious disease dynamics , but it is also the least understood. Rates of transmission are usually inferred from population patterns of disease incidence, but populationlevel analyses do not capture between-individual variation in transmission resulting from differences in behaviour, genetics, immune status, and environmental and stochastic factors, which play an important role in determining disease dynamics . Contact tracing has been used to directly measure case-to-case transmission, and applications of the technique to emerging infections such as SARS have generated important insights into disease transmission and control in human populations , but transmission processes", "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: Viral transmission is a critical component of disease and a key factor in viral evolution. In outlining a novel framework for the interpretation of data from viral transmission events we hope to bring a greater clarity to the population genetic theory of how these events operate and a greater power in the interpretation of experimental data, so as to engender a greater understanding of this important topic of research." ]

[ [ "0a", "Title: A novel framework for inferring parameters of transmission from viral sequence data" ], [ "0b", "Passage: of neutral genetic markers has shown that the transmission bottleneck is dependent upon the route of transmission, whether by contact or aerosol transmission ." ], [ "0c", "In natural human influenza populations, where modification of the virus is not possible, population genetic methods have been used to analyse bottleneck sizes." ], [ "0d", "Analyses of transmission have employed different approaches, exploiting the observation or non-observation of variant alleles or using changes in allele frequencies to characterise the bottleneck under a model of genetic drift ." ], [ "0e", "A recent publication improved this latter model, incorporating the uncertainty imposed upon allele frequencies by the process of within-host growth ." ] ]

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

[ "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: of neutral genetic markers has shown that the transmission bottleneck is dependent upon the route of transmission, whether by contact or aerosol transmission . In natural human influenza populations, where modification of the virus is not possible, population genetic methods have been used to analyse bottleneck sizes. Analyses of transmission have employed different approaches, exploiting the observation or non-observation of variant alleles or using changes in allele frequencies to characterise the bottleneck under a model of genetic drift . A recent publication improved this latter model, incorporating the uncertainty imposed upon allele frequencies by the process of within-host growth .", "Title: Insights into the transmission of respiratory infectious diseases through empirical human contact networks\nPassage: In fact, the influenza spreading behavior can be clearly divided into two categories: in the US schools, disease outbreak appears to be relatively strong and early ; in the schools of SCAU, USTB as well as FRPS, a considerably low transmission was observed .", "Title: Transmission Dynamics and Prospects for the Elimination of Canine Rabies\nPassage: Transmission is the most important process underlying infectious disease dynamics , but it is also the least understood. Rates of transmission are usually inferred from population patterns of disease incidence, but populationlevel analyses do not capture between-individual variation in transmission resulting from differences in behaviour, genetics, immune status, and environmental and stochastic factors, which play an important role in determining disease dynamics . Contact tracing has been used to directly measure case-to-case transmission, and applications of the technique to emerging infections such as SARS have generated important insights into disease transmission and control in human populations , but transmission processes", "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: Viral transmission is a critical component of disease and a key factor in viral evolution. In outlining a novel framework for the interpretation of data from viral transmission events we hope to bring a greater clarity to the population genetic theory of how these events operate and a greater power in the interpretation of experimental data, so as to engender a greater understanding of this important topic of research." ]

[ [ "1a", "Title: Insights into the transmission of respiratory infectious diseases through empirical human contact networks" ], [ "1b", "Passage: In fact, the influenza spreading behavior can be clearly divided into two categories: in the US schools, disease outbreak appears to be relatively strong and early ; in the schools of SCAU, USTB as well as FRPS, a considerably low transmission was observed ." ] ]

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

[ "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: of neutral genetic markers has shown that the transmission bottleneck is dependent upon the route of transmission, whether by contact or aerosol transmission . In natural human influenza populations, where modification of the virus is not possible, population genetic methods have been used to analyse bottleneck sizes. Analyses of transmission have employed different approaches, exploiting the observation or non-observation of variant alleles or using changes in allele frequencies to characterise the bottleneck under a model of genetic drift . A recent publication improved this latter model, incorporating the uncertainty imposed upon allele frequencies by the process of within-host growth .", "Title: Insights into the transmission of respiratory infectious diseases through empirical human contact networks\nPassage: In fact, the influenza spreading behavior can be clearly divided into two categories: in the US schools, disease outbreak appears to be relatively strong and early ; in the schools of SCAU, USTB as well as FRPS, a considerably low transmission was observed .", "Title: Transmission Dynamics and Prospects for the Elimination of Canine Rabies\nPassage: Transmission is the most important process underlying infectious disease dynamics , but it is also the least understood. Rates of transmission are usually inferred from population patterns of disease incidence, but populationlevel analyses do not capture between-individual variation in transmission resulting from differences in behaviour, genetics, immune status, and environmental and stochastic factors, which play an important role in determining disease dynamics . Contact tracing has been used to directly measure case-to-case transmission, and applications of the technique to emerging infections such as SARS have generated important insights into disease transmission and control in human populations , but transmission processes", "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: Viral transmission is a critical component of disease and a key factor in viral evolution. In outlining a novel framework for the interpretation of data from viral transmission events we hope to bring a greater clarity to the population genetic theory of how these events operate and a greater power in the interpretation of experimental data, so as to engender a greater understanding of this important topic of research." ]

[ [ "2a", "Title: Transmission Dynamics and Prospects for the Elimination of Canine Rabies" ], [ "2b", "Passage: Transmission is the most important process underlying infectious disease dynamics , but it is also the least understood." ], [ "2c", "Rates of transmission are usually inferred from population patterns of disease incidence, but populationlevel analyses do not capture between-individual variation in transmission resulting from differences in behaviour, genetics, immune status, and environmental and stochastic factors, which play an important role in determining disease dynamics ." ], [ "2d", "Contact tracing has been used to directly measure case-to-case transmission, and applications of the technique to emerging infections such as SARS have generated important insights into disease transmission and control in human populations , but transmission processes" ] ]

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

[ "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: of neutral genetic markers has shown that the transmission bottleneck is dependent upon the route of transmission, whether by contact or aerosol transmission . In natural human influenza populations, where modification of the virus is not possible, population genetic methods have been used to analyse bottleneck sizes. Analyses of transmission have employed different approaches, exploiting the observation or non-observation of variant alleles or using changes in allele frequencies to characterise the bottleneck under a model of genetic drift . A recent publication improved this latter model, incorporating the uncertainty imposed upon allele frequencies by the process of within-host growth .", "Title: Insights into the transmission of respiratory infectious diseases through empirical human contact networks\nPassage: In fact, the influenza spreading behavior can be clearly divided into two categories: in the US schools, disease outbreak appears to be relatively strong and early ; in the schools of SCAU, USTB as well as FRPS, a considerably low transmission was observed .", "Title: Transmission Dynamics and Prospects for the Elimination of Canine Rabies\nPassage: Transmission is the most important process underlying infectious disease dynamics , but it is also the least understood. Rates of transmission are usually inferred from population patterns of disease incidence, but populationlevel analyses do not capture between-individual variation in transmission resulting from differences in behaviour, genetics, immune status, and environmental and stochastic factors, which play an important role in determining disease dynamics . Contact tracing has been used to directly measure case-to-case transmission, and applications of the technique to emerging infections such as SARS have generated important insights into disease transmission and control in human populations , but transmission processes", "Title: A novel framework for inferring parameters of transmission from viral sequence data\nPassage: Viral transmission is a critical component of disease and a key factor in viral evolution. In outlining a novel framework for the interpretation of data from viral transmission events we hope to bring a greater clarity to the population genetic theory of how these events operate and a greater power in the interpretation of experimental data, so as to engender a greater understanding of this important topic of research." ]

[ [ "3a", "Title: A novel framework for inferring parameters of transmission from viral sequence data" ], [ "3b", "Passage: Viral transmission is a critical component of disease and a key factor in viral evolution." ], [ "3c", "In outlining a novel framework for the interpretation of data from viral transmission events we hope to bring a greater clarity to the population genetic theory of how these events operate and a greater power in the interpretation of experimental data, so as to engender a greater understanding of this important topic of research." ] ]

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

[ "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: deoxyribozymes can form from ribonucleotides . Thus, DNA can arise from RNA chemically, without the key protein enzyme, the reverse transcriptase.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: The selected ribozymes were able to replicate, cleave, join, and form peptide bonds. They can polymerize progeny chemically, allow for mutations to occur and can evolve. One molecule serves as catalyst, the other one as substrate. Replication of ribozymes was demonstrated in the test tube . Ribozymes can form peptide bonds between amino acids . Thus, small peptides were available by ribozyme activity. Consequently, an RNA modification has been proposed as peptide nucleic acid , with more stable peptide bonds instead of phosphodiester bonds . Replication of RNA molecules can be performed chemically from RNA without polymerase enzymes. In addition,", "Title: The elusive quest for RNA knots\nPassage: even during the origins of life. The RNA world concept posits a period of time when RNA, or something chemically similar, was responsible for all living processes including heredity and metabolism. RNA-RNA interactions have often been proposed to be critical to maintaining the physical integrity of networks of distinct sequences. Typically these interactions have focused solely on secondary structure interactions, but many environments on an early Earth could have experienced rather extreme temperature fluctuations that could disrupt weak basepairing. More severe entanglements such as knotsbut without covalent bondingwould have been a means to preserve spatial sympatry of RNA network individuals", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: These studies raise the question of how RNA molecules can become longer, if the small polymers become smaller and smaller, replicate faster and outcompete longer ones. This may be overcome by heat flow across an open pore in submerged rocks, which concentrates replicating oligonucleotides from a constant feeding flow and selection for longer strands. This has been described for an increase from 100 to 1,000 nucleotides in vitro. RNA molecules shorter than 75 nucleotides will die out . Could a poor environment lead to an increase of complexity? This could be tested. Ribozymes were shown to grow in size by" ]

[ [ "0a", "Title: Viruses and Evolution – Viruses First?" ], [ "0b", "A Personal Perspective" ], [ "0c", "Passage: deoxyribozymes can form from ribonucleotides ." ], [ "0d", "Thus, DNA can arise from RNA chemically, without the key protein enzyme, the reverse transcriptase." ] ]

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

[ "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: deoxyribozymes can form from ribonucleotides . Thus, DNA can arise from RNA chemically, without the key protein enzyme, the reverse transcriptase.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: The selected ribozymes were able to replicate, cleave, join, and form peptide bonds. They can polymerize progeny chemically, allow for mutations to occur and can evolve. One molecule serves as catalyst, the other one as substrate. Replication of ribozymes was demonstrated in the test tube . Ribozymes can form peptide bonds between amino acids . Thus, small peptides were available by ribozyme activity. Consequently, an RNA modification has been proposed as peptide nucleic acid , with more stable peptide bonds instead of phosphodiester bonds . Replication of RNA molecules can be performed chemically from RNA without polymerase enzymes. In addition,", "Title: The elusive quest for RNA knots\nPassage: even during the origins of life. The RNA world concept posits a period of time when RNA, or something chemically similar, was responsible for all living processes including heredity and metabolism. RNA-RNA interactions have often been proposed to be critical to maintaining the physical integrity of networks of distinct sequences. Typically these interactions have focused solely on secondary structure interactions, but many environments on an early Earth could have experienced rather extreme temperature fluctuations that could disrupt weak basepairing. More severe entanglements such as knotsbut without covalent bondingwould have been a means to preserve spatial sympatry of RNA network individuals", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: These studies raise the question of how RNA molecules can become longer, if the small polymers become smaller and smaller, replicate faster and outcompete longer ones. This may be overcome by heat flow across an open pore in submerged rocks, which concentrates replicating oligonucleotides from a constant feeding flow and selection for longer strands. This has been described for an increase from 100 to 1,000 nucleotides in vitro. RNA molecules shorter than 75 nucleotides will die out . Could a poor environment lead to an increase of complexity? This could be tested. Ribozymes were shown to grow in size by" ]

[ [ "1a", "Title: Viruses and Evolution – Viruses First?" ], [ "1b", "A Personal Perspective" ], [ "1c", "Passage: The selected ribozymes were able to replicate, cleave, join, and form peptide bonds." ], [ "1d", "They can polymerize progeny chemically, allow for mutations to occur and can evolve." ], [ "1e", "One molecule serves as catalyst, the other one as substrate." ], [ "1f", "Replication of ribozymes was demonstrated in the test tube ." ], [ "1g", "Ribozymes can form peptide bonds between amino acids ." ], [ "1h", "Thus, small peptides were available by ribozyme activity." ], [ "1i", "Consequently, an RNA modification has been proposed as peptide nucleic acid , with more stable peptide bonds instead of phosphodiester bonds ." ], [ "1j", "Replication of RNA molecules can be performed chemically from RNA without polymerase enzymes. In addition," ] ]

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

[ "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: deoxyribozymes can form from ribonucleotides . Thus, DNA can arise from RNA chemically, without the key protein enzyme, the reverse transcriptase.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: The selected ribozymes were able to replicate, cleave, join, and form peptide bonds. They can polymerize progeny chemically, allow for mutations to occur and can evolve. One molecule serves as catalyst, the other one as substrate. Replication of ribozymes was demonstrated in the test tube . Ribozymes can form peptide bonds between amino acids . Thus, small peptides were available by ribozyme activity. Consequently, an RNA modification has been proposed as peptide nucleic acid , with more stable peptide bonds instead of phosphodiester bonds . Replication of RNA molecules can be performed chemically from RNA without polymerase enzymes. In addition,", "Title: The elusive quest for RNA knots\nPassage: even during the origins of life. The RNA world concept posits a period of time when RNA, or something chemically similar, was responsible for all living processes including heredity and metabolism. RNA-RNA interactions have often been proposed to be critical to maintaining the physical integrity of networks of distinct sequences. Typically these interactions have focused solely on secondary structure interactions, but many environments on an early Earth could have experienced rather extreme temperature fluctuations that could disrupt weak basepairing. More severe entanglements such as knotsbut without covalent bondingwould have been a means to preserve spatial sympatry of RNA network individuals", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: These studies raise the question of how RNA molecules can become longer, if the small polymers become smaller and smaller, replicate faster and outcompete longer ones. This may be overcome by heat flow across an open pore in submerged rocks, which concentrates replicating oligonucleotides from a constant feeding flow and selection for longer strands. This has been described for an increase from 100 to 1,000 nucleotides in vitro. RNA molecules shorter than 75 nucleotides will die out . Could a poor environment lead to an increase of complexity? This could be tested. Ribozymes were shown to grow in size by" ]

[ [ "3a", "Title: Viruses and Evolution – Viruses First?" ], [ "3b", "A Personal Perspective" ], [ "3c", "Passage: These studies raise the question of how RNA molecules can become longer, if the small polymers become smaller and smaller, replicate faster and outcompete longer ones." ], [ "3d", "This may be overcome by heat flow across an open pore in submerged rocks, which concentrates replicating oligonucleotides from a constant feeding flow and selection for longer strands." ], [ "3e", "This has been described for an increase from 100 to 1,000 nucleotides in vitro." ], [ "3f", "RNA molecules shorter than 75 nucleotides will die out ." ], [ "3g", "Could a poor environment lead to an increase of complexity?" ], [ "3h", "This could be tested." ], [ "3i", "Ribozymes were shown to grow in size by" ] ]

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

[ "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: The case β A > β B leads to infection dominance of influenza A over B virus . This situation can be controlled by TIV vaccine alone as it targets two strains of A virus. Individuals would then mostly prefer TIV vaccine over QIV vaccine as the price of TIV is lower than the price of QIV . As a consequence, we perceive the sensitivity of choosing TIV vaccine only along the direction of C T .", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine . There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines. In split virus vaccines, the virus is disrupted by a detergent. In subunit vaccines, HA and NA have been further purified by removal of other viral components. TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains. TIV efficacy is measured by", "Title: Innate Immune Sensing and Response to Influenza\nPassage: A comparative study of immune response to trivalent inactivated influenza vaccine and live attenuated influenza vaccine using systems biology approach revealed salient common as well as contrasting features between them. While LAIV induced the expression of several interferon-related genes, which are similar to live viral vaccines, the TIV induced a signature composed of genes highly expressed in plasma B cells . For TIV, of the 44 genes identified to accurately predict the outcome of immunization as either high or low antibody titers, one gene-CAMKIV-had no known function in regulating immunity, but was negatively correlated with antibody titers. Consistent with this,", "Title: Evaluation of Approaches to Identify the Targets of Cellular Immunity on a Proteome-Wide Scale\nPassage: For the in vivo evaluation of IVTT products, mice were immunized intramuscularly with 50 mg/100 ml of VR2516 PyCSP DNA vaccine and boosted 3 weeks later with PyCSP IVTT products formulated with 100 ml Aluminium Hydroxide gel adjuvant as follows: A) 15 ml of IVTT reaction ; B) 15 ml of IVTT reaction purified through NI-NTA resin ; C) 15 ml of IVTT reaction purified through MagneHis Protein Purification System ; D) 15 ml of IVTT reaction absorbed in 10 ml of PolybeadH Poly microspheres ; and E) 15 ml of IVTT reaction associated to 10 ml of Protein G" ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine ." ], [ "1c", "There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines." ], [ "1d", "In split virus vaccines, the virus is disrupted by a detergent." ], [ "1e", "In subunit vaccines, HA and NA have been further purified by removal of other viral components." ], [ "1f", "TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains." ], [ "1g", "TIV efficacy is measured by" ] ]

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

[ "Title: Interplay between cost and effectiveness in influenza vaccine uptake: a vaccination game approach\nPassage: The case β A > β B leads to infection dominance of influenza A over B virus . This situation can be controlled by TIV vaccine alone as it targets two strains of A virus. Individuals would then mostly prefer TIV vaccine over QIV vaccine as the price of TIV is lower than the price of QIV . As a consequence, we perceive the sensitivity of choosing TIV vaccine only along the direction of C T .", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The general types of influenza vaccines available in the United States are trivalent inactivated influenza vaccine , quadrivalent influenza vaccine , and live attenuated influenza vaccine . There are three types of inactivated vaccines that include whole virus inactivated, split virus inactivated, and subunit vaccines. In split virus vaccines, the virus is disrupted by a detergent. In subunit vaccines, HA and NA have been further purified by removal of other viral components. TIV is administered intramuscularly and contains three or four inactivated viruses, i.e., two type A strains and one or two type B strains. TIV efficacy is measured by", "Title: Innate Immune Sensing and Response to Influenza\nPassage: A comparative study of immune response to trivalent inactivated influenza vaccine and live attenuated influenza vaccine using systems biology approach revealed salient common as well as contrasting features between them. While LAIV induced the expression of several interferon-related genes, which are similar to live viral vaccines, the TIV induced a signature composed of genes highly expressed in plasma B cells . For TIV, of the 44 genes identified to accurately predict the outcome of immunization as either high or low antibody titers, one gene-CAMKIV-had no known function in regulating immunity, but was negatively correlated with antibody titers. Consistent with this,", "Title: Evaluation of Approaches to Identify the Targets of Cellular Immunity on a Proteome-Wide Scale\nPassage: For the in vivo evaluation of IVTT products, mice were immunized intramuscularly with 50 mg/100 ml of VR2516 PyCSP DNA vaccine and boosted 3 weeks later with PyCSP IVTT products formulated with 100 ml Aluminium Hydroxide gel adjuvant as follows: A) 15 ml of IVTT reaction ; B) 15 ml of IVTT reaction purified through NI-NTA resin ; C) 15 ml of IVTT reaction purified through MagneHis Protein Purification System ; D) 15 ml of IVTT reaction absorbed in 10 ml of PolybeadH Poly microspheres ; and E) 15 ml of IVTT reaction associated to 10 ml of Protein G" ]

[ [ "2a", "Title: Innate Immune Sensing and Response to Influenza" ], [ "2b", "Passage: A comparative study of immune response to trivalent inactivated influenza vaccine and live attenuated influenza vaccine using systems biology approach revealed salient common as well as contrasting features between them." ], [ "2c", "While LAIV induced the expression of several interferon-related genes, which are similar to live viral vaccines, the TIV induced a signature composed of genes highly expressed in plasma B cells ." ], [ "2d", "For TIV, of the 44 genes identified to accurately predict the outcome of immunization as either high or low antibody titers, one gene-CAMKIV-had no known function in regulating immunity, but was negatively correlated with antibody titers." ], [ "2e", "Consistent with this," ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: One drawback of an Ad5 vector is the potential for preexisting immunity, so alternative adenovirus serotypes have been explored as vectors, particularly non-human and uncommon human serotypes. Non-human adenovirus vectors include those from non-human primates , dogs, sheep, pigs, cows, birds and others . These vectors can infect a variety of cell types, but are generally attenuated in humans avoiding concerns of preexisting immunity. Swine, NHP and bovine adenoviruses expressing H5 HA antigens have been shown to induce immunity comparable to human rAd5-H5 vaccines . Recombinant, replication-defective adenoviruses from low-prevalence serotypes have also been shown to be efficacious. Low prevalence", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Experimental adenovirus-based vaccine vectors are promising alternatives to conventional vaccine platforms. In particular, human adenovirus serotype 5 vectors are well-characterized and are being developed against several infectious disease models including influenza, hepatitis C, dengue and viral hemorrhagic fever viruses . Several candidates have demonstrated unique protective efficacy and can generate robust immune responses in both animal models and clinical trials . Pre-existing immunity against AdHu5 is, however, frequent in the human population and has been associated with undesirable clinical outcomes and the suspension of clinical trials . One promising alternative is the development and evaluation of rare human, chimpanzee, or", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: To obtain AdHu5-HA vaccine, HEK 293 cells were transfected with 10 mg of linearized pAdenoX-HA DNA in calcium phosphate solution and cells were cultured until the appearance of cytopathic effects . Similarly, VR1BL E1 cells were transfected with 10 ug of linearized pFPAV227-HA DNA combined with Lipofectin and cells were cultured until CPE were apparent. Amplified adenoviruses containing cell lysates were harvested, freeze-thawed three times, and purified by CsCl gradients. The integrity of the H05-HA transgene cassette was confirmed through EcoRI restriction digests and by sequencing with multiple primer sets. Total virus particles was determined by OD260 and total infectious", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: points. Although not explored in the current study, previous studies have evaluated the impact of pre-existing immunity to PAV3 and the potential reuse of PAV3-based vectors against different pathogens. Groups of outbred pigs with high PAV3 neutralizing antibody titres were vaccinated with a PAV3-based vaccine and vector re-administration did not result in hepatotoxicity or reduced transgene expression . Doses of 10 13 particles/kg AdHu5 vector can also bypass pre-existing immunity, however, several pathologies including liver damage indicated by elevated transaminase, low platelets count, and lymphocytopenia were observed in nonhuman primates administered similar doses ." ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: One drawback of an Ad5 vector is the potential for preexisting immunity, so alternative adenovirus serotypes have been explored as vectors, particularly non-human and uncommon human serotypes." ], [ "0c", "Non-human adenovirus vectors include those from non-human primates , dogs, sheep, pigs, cows, birds and others ." ], [ "0d", "These vectors can infect a variety of cell types, but are generally attenuated in humans avoiding concerns of preexisting immunity." ], [ "0e", "Swine, NHP and bovine adenoviruses expressing H5 HA antigens have been shown to induce immunity comparable to human rAd5-H5 vaccines ." ], [ "0f", "Recombinant, replication-defective adenoviruses from low-prevalence serotypes have also been shown to be efficacious. Low prevalence" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: One drawback of an Ad5 vector is the potential for preexisting immunity, so alternative adenovirus serotypes have been explored as vectors, particularly non-human and uncommon human serotypes. Non-human adenovirus vectors include those from non-human primates , dogs, sheep, pigs, cows, birds and others . These vectors can infect a variety of cell types, but are generally attenuated in humans avoiding concerns of preexisting immunity. Swine, NHP and bovine adenoviruses expressing H5 HA antigens have been shown to induce immunity comparable to human rAd5-H5 vaccines . Recombinant, replication-defective adenoviruses from low-prevalence serotypes have also been shown to be efficacious. Low prevalence", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Experimental adenovirus-based vaccine vectors are promising alternatives to conventional vaccine platforms. In particular, human adenovirus serotype 5 vectors are well-characterized and are being developed against several infectious disease models including influenza, hepatitis C, dengue and viral hemorrhagic fever viruses . Several candidates have demonstrated unique protective efficacy and can generate robust immune responses in both animal models and clinical trials . Pre-existing immunity against AdHu5 is, however, frequent in the human population and has been associated with undesirable clinical outcomes and the suspension of clinical trials . One promising alternative is the development and evaluation of rare human, chimpanzee, or", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: To obtain AdHu5-HA vaccine, HEK 293 cells were transfected with 10 mg of linearized pAdenoX-HA DNA in calcium phosphate solution and cells were cultured until the appearance of cytopathic effects . Similarly, VR1BL E1 cells were transfected with 10 ug of linearized pFPAV227-HA DNA combined with Lipofectin and cells were cultured until CPE were apparent. Amplified adenoviruses containing cell lysates were harvested, freeze-thawed three times, and purified by CsCl gradients. The integrity of the H05-HA transgene cassette was confirmed through EcoRI restriction digests and by sequencing with multiple primer sets. Total virus particles was determined by OD260 and total infectious", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: points. Although not explored in the current study, previous studies have evaluated the impact of pre-existing immunity to PAV3 and the potential reuse of PAV3-based vectors against different pathogens. Groups of outbred pigs with high PAV3 neutralizing antibody titres were vaccinated with a PAV3-based vaccine and vector re-administration did not result in hepatotoxicity or reduced transgene expression . Doses of 10 13 particles/kg AdHu5 vector can also bypass pre-existing immunity, however, several pathologies including liver damage indicated by elevated transaminase, low platelets count, and lymphocytopenia were observed in nonhuman primates administered similar doses ." ]

[ [ "1a", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model" ], [ "1b", "Passage: Experimental adenovirus-based vaccine vectors are promising alternatives to conventional vaccine platforms." ], [ "1c", "In particular, human adenovirus serotype 5 vectors are well-characterized and are being developed against several infectious disease models including influenza, hepatitis C, dengue and viral hemorrhagic fever viruses ." ], [ "1d", "Several candidates have demonstrated unique protective efficacy and can generate robust immune responses in both animal models and clinical trials ." ], [ "1e", "Pre-existing immunity against AdHu5 is, however, frequent in the human population and has been associated with undesirable clinical outcomes and the suspension of clinical trials ." ], [ "1f", "One promising alternative is the development and evaluation of rare human, chimpanzee, or" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: One drawback of an Ad5 vector is the potential for preexisting immunity, so alternative adenovirus serotypes have been explored as vectors, particularly non-human and uncommon human serotypes. Non-human adenovirus vectors include those from non-human primates , dogs, sheep, pigs, cows, birds and others . These vectors can infect a variety of cell types, but are generally attenuated in humans avoiding concerns of preexisting immunity. Swine, NHP and bovine adenoviruses expressing H5 HA antigens have been shown to induce immunity comparable to human rAd5-H5 vaccines . Recombinant, replication-defective adenoviruses from low-prevalence serotypes have also been shown to be efficacious. Low prevalence", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: Experimental adenovirus-based vaccine vectors are promising alternatives to conventional vaccine platforms. In particular, human adenovirus serotype 5 vectors are well-characterized and are being developed against several infectious disease models including influenza, hepatitis C, dengue and viral hemorrhagic fever viruses . Several candidates have demonstrated unique protective efficacy and can generate robust immune responses in both animal models and clinical trials . Pre-existing immunity against AdHu5 is, however, frequent in the human population and has been associated with undesirable clinical outcomes and the suspension of clinical trials . One promising alternative is the development and evaluation of rare human, chimpanzee, or", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: To obtain AdHu5-HA vaccine, HEK 293 cells were transfected with 10 mg of linearized pAdenoX-HA DNA in calcium phosphate solution and cells were cultured until the appearance of cytopathic effects . Similarly, VR1BL E1 cells were transfected with 10 ug of linearized pFPAV227-HA DNA combined with Lipofectin and cells were cultured until CPE were apparent. Amplified adenoviruses containing cell lysates were harvested, freeze-thawed three times, and purified by CsCl gradients. The integrity of the H05-HA transgene cassette was confirmed through EcoRI restriction digests and by sequencing with multiple primer sets. Total virus particles was determined by OD260 and total infectious", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model\nPassage: points. Although not explored in the current study, previous studies have evaluated the impact of pre-existing immunity to PAV3 and the potential reuse of PAV3-based vectors against different pathogens. Groups of outbred pigs with high PAV3 neutralizing antibody titres were vaccinated with a PAV3-based vaccine and vector re-administration did not result in hepatotoxicity or reduced transgene expression . Doses of 10 13 particles/kg AdHu5 vector can also bypass pre-existing immunity, however, several pathologies including liver damage indicated by elevated transaminase, low platelets count, and lymphocytopenia were observed in nonhuman primates administered similar doses ." ]

[ [ "3a", "Title: A Porcine Adenovirus with Low Human Seroprevalence Is a Promising Alternative Vaccine Vector to Human Adenovirus 5 in an H5N1 Virus Disease Model Passage: points." ], [ "3b", "Although not explored in the current study, previous studies have evaluated the impact of pre-existing immunity to PAV3 and the potential reuse of PAV3-based vectors against different pathogens." ], [ "3c", "Groups of outbred pigs with high PAV3 neutralizing antibody titres were vaccinated with a PAV3-based vaccine and vector re-administration did not result in hepatotoxicity or reduced transgene expression ." ], [ "3d", "Doses of 10 13 particles/kg AdHu5 vector can also bypass pre-existing immunity, however, several pathologies including liver damage indicated by elevated transaminase, low platelets count, and lymphocytopenia were observed in nonhuman primates administered similar doses ." ] ]

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

[ "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: The first three cases detected were reported in France on 24 January 2020 and had onset of symptoms on 17, 19 and 23 January respectively . The first death was reported on 15 February in France. As at 21 February, nine countries had reported cases : Belgium , Finland , France , Germany , Italy , Russia , Spain , Sweden and the UK .", "Title: The origins of the great pandemic\nPassage: A second location, from which the influenza outbreak may first have been reported, is to be found in northern France. Lt J.A.B. Hammond and two colleagues encountered an outbreak of 'purulent bronchitis' in late 1916 and early 1917 at a hospital centre forming part of the British army encampment at Etaples. An initial paper was published by this group in The Lancet in July 1917 . This publication precipitated a rapid follow-up article, also in The Lancet, from an independent military group reporting similar observations at Aldershot, in the south of England . Looking back 2 years later, this second", "Title: Age-Specific Excess Mortality Patterns During the 1918–1920 Influenza Pandemic in Madrid, Spain\nPassage: The name Spanish flu comes from the first news reports of influenza-like-illness in Madrid in the late spring of 1918. However, this pandemic gained its nickname because the first mentions of the virus were published in Spain, where the press faced no censorship during World War I, owing to the country's neutrality . Many people fell ill with respiratory symptoms in May 1918, including King Alfonso XIII, which was well documented in the press . Because respiratory disease outbreaks occurred in neighboring France as early as April 1918, it is likely that the virus was introduced into Spain via Spanish", "Title: Estimating the number of infections and the impact of non-\nPassage: 31. The Local. France bans gatherings of more than 100 people as coronavirus death toll rises -" ]

[ [ "0a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "0b", "Passage: The first three cases detected were reported in France on 24 January 2020 and had onset of symptoms on 17, 19 and 23 January respectively ." ], [ "0c", "The first death was reported on 15 February in France." ], [ "0d", "As at 21 February, nine countries had reported cases : Belgium , Finland , France , Germany , Italy , Russia , Spain , Sweden and the UK ." ] ]

[ "0c" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: or worse, and secondary bacterial infections have been reported ." ], [ "0c", "Disease can progress to acute respiratory distress syndrome and multiorgan system failure ." ], [ "0d", "MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported ." ], [ "0e", "General supportive care is key to managing severe cases . Children under" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers." ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks." ], [ "1c", "Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA." ], [ "1d", "The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die." ], [ "1e", "However the proportion of male deaths from total males with MERS is a similar figure to that for" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: or worse, and secondary bacterial infections have been reported . Disease can progress to acute respiratory distress syndrome and multiorgan system failure . MERS has reportedly killed approximately 35 % of all reported cases, 42 % of cases in the KSA, yet only 19 % of cases in South Korea, where mortality ranged from 7 % among younger age groups to 40 % among those aged 60 years and above ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported . General supportive care is key to managing severe cases . Children under", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The proportion of fatal MERS cases within the KSA compared to outside the KSA, as well as the age, and sex distribution change in different ways when comparing MERS outbreaks. Approximately 43 % of MERS cases in the KSA were fatal betwen 2012 and December 2015 while 21 % died among those occurring outside of the KSA. The total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. However the proportion of male deaths from total males with MERS is a similar figure to that for", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths. 62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47. 63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV. 65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals", "Title: Demographic Variations of MERS-CoV Infection among Suspected and Confirmed Cases: An Epidemiological Analysis of Laboratory-Based Data from Riyadh Regional Laboratory\nPassage: Among confirmed cases, only 25.2% were healthcare workers, whereas around 75% were non-healthcare workers." ]

[ [ "2a", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management" ], [ "2b", "Passage: As of July 2014, the number of confirmed cases of MERS-CoV has exceeded 830, with at least 288 associated deaths." ], [ "2c", "62 The majority of cases have involved patients with comorbidities and are predominately males with a median age of 47." ], [ "2d", "63, 64 Fewer than 25% of patients have reported contact with animals including dromedary camels, which have been shown to be one likely animal reservoir based on sero-positivity and detection of MERS-CoV." ], [ "2e", "65 More than 25% of the infections have been in healthcare workers, and the large number of nosocomial infections is likely due to inadequate infection control in hospitals" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Similarly, MERS-CoV appears to have high severity and low transmissibility. Since 2012, MERS-CoV has caused 2494 reported cases and 858 deaths in 27 countries. MERS-CoV has also caused some rapid outbreaks, mainly in hospitals in Saudi Arabia, Jordan, and South Korea, but estimates of MERS-CoV R0 are less than 1, and thus far it has been contained.5" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: MERS and SARS have some clinical similarities but they also diverge significantly ." ], [ "0c", "Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities." ], [ "0d", "For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Similarly, MERS-CoV appears to have high severity and low transmissibility. Since 2012, MERS-CoV has caused 2494 reported cases and 858 deaths in 27 countries. MERS-CoV has also caused some rapid outbreaks, mainly in hospitals in Saudi Arabia, Jordan, and South Korea, but estimates of MERS-CoV R0 are less than 1, and thus far it has been contained.5" ]

[ [ "1a", "Title: Host resilience to emerging coronaviruses" ], [ "1b", "Passage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity." ], [ "1c", "The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect." ], [ "1d", "SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 ." ], [ "1e", "Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure ." ], [ "1f", "SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Similarly, MERS-CoV appears to have high severity and low transmissibility. Since 2012, MERS-CoV has caused 2494 reported cases and 858 deaths in 27 countries. MERS-CoV has also caused some rapid outbreaks, mainly in hospitals in Saudi Arabia, Jordan, and South Korea, but estimates of MERS-CoV R0 are less than 1, and thus far it has been contained.5" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs." ], [ "2c", "However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\"." ], [ "2d", "It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\"." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS and SARS have some clinical similarities but they also diverge significantly . Defining characteristics include the higher PFC among MERS cases and the higher association between fatal MERS and older males with underlying comorbidities. For the viruses, MERS-CoV has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to SARS-CoV.", "Title: Host resilience to emerging coronaviruses\nPassage: Both SARS-CoV and MERS-CoV are typified by a rapid progression to ARDS, however, there are some distinct differences in the infectivity and pathogenicity. The two viruses have different receptors leading to different cellular tropism, and SARS-CoV is more ubiquitous in the cell type and species it can infect. SARS-CoV uses the ACE2 receptor to gain entry to cells, while MERS-CoV uses the ectopeptidase DPP4 . Unlike SARS-CoV infection, which causes primarily a severe respiratory syndrome, MERS-CoV infection can also lead to kidney failure . SARS-CoV also spreads more rapidly between hosts, while MERS-CoV has been more easily contained, but it", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The 2-3 % prevalence of active MERS-CoV infections is not dissimilar to the hospital-based prevalence of other human CoVs. However, the proportion of deaths among those infected with MERS-CoV is much higher than that known for the HCoVs NL63, HKU1, 229E or OC43 in other countries, and even above that for SARS-CoV; it is not a virus that could reasonably be described as a \"storm in a teacup\". It is the low transmission rate that has prevented worldwide spread, despite many \"opportunities\".", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Similarly, MERS-CoV appears to have high severity and low transmissibility. Since 2012, MERS-CoV has caused 2494 reported cases and 858 deaths in 27 countries. MERS-CoV has also caused some rapid outbreaks, mainly in hospitals in Saudi Arabia, Jordan, and South Korea, but estimates of MERS-CoV R0 are less than 1, and thus far it has been contained.5" ]

[ [ "3a", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus" ], [ "3b", "Passage: Similarly, MERS-CoV appears to have high severity and low transmissibility." ], [ "3c", "Since 2012, MERS-CoV has caused 2494 reported cases and 858 deaths in 27 countries." ], [ "3d", "MERS-CoV has also caused some rapid outbreaks, mainly in hospitals in Saudi Arabia, Jordan, and South Korea, but estimates of MERS-CoV R0 are less than 1, and thus far it has been contained.5" ] ]

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

[ "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals\nPassage: Given the predicted low-titer inoculum driving HIV-1 sexual transmission, a vaccine capable of eliciting antibodies that neutralize a broad spectrum of viral strains could potentially reduce or prevent infection. It has been anticipated that the identification of broadly neutralizing mAbs from HIV-1 infected individuals, and the characterization of their cognate epitopes will be instrumental in the design of immunogens capable of eliciting such a broad neutralizing response . This idea has led to a major international cooperative effort within consortia of laboratories with complementary expertise in human immunology, structural biology and vaccine design .", "Title: Wide Prevalence of Heterosubtypic Broadly Neutralizing Human Anti-Influenza A Antibodies\nPassage: vaccinees , or bone marrow of H5N1-infected ''bird-flu'' survivors . BnAbs with similar properties have also been recovered from immortalized IgGexpressing memory B cells of seasonal vaccinees . An unexpected finding from these studies is the frequent contribution of VH1-69 heavy chain genes to these BnAbs, suggesting that a large fraction of the human naive B cell repertoire has the capability of responding to this conserved epitope . These observations raise additional questions as to whether such BnAbs are present in human serum and at ''protective'' levels, whether they exist as ''natural'' Abs, and/or whether are they generated during the" ]

[ [ "0a", "Title: Techniques to Study Antigen-Specific B Cell Responses" ], [ "0b", "Passage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies ." ], [ "0c", "Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition ." ], [ "0d", "For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer" ] ]

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

[ "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals\nPassage: Given the predicted low-titer inoculum driving HIV-1 sexual transmission, a vaccine capable of eliciting antibodies that neutralize a broad spectrum of viral strains could potentially reduce or prevent infection. It has been anticipated that the identification of broadly neutralizing mAbs from HIV-1 infected individuals, and the characterization of their cognate epitopes will be instrumental in the design of immunogens capable of eliciting such a broad neutralizing response . This idea has led to a major international cooperative effort within consortia of laboratories with complementary expertise in human immunology, structural biology and vaccine design .", "Title: Wide Prevalence of Heterosubtypic Broadly Neutralizing Human Anti-Influenza A Antibodies\nPassage: vaccinees , or bone marrow of H5N1-infected ''bird-flu'' survivors . BnAbs with similar properties have also been recovered from immortalized IgGexpressing memory B cells of seasonal vaccinees . An unexpected finding from these studies is the frequent contribution of VH1-69 heavy chain genes to these BnAbs, suggesting that a large fraction of the human naive B cell repertoire has the capability of responding to this conserved epitope . These observations raise additional questions as to whether such BnAbs are present in human serum and at ''protective'' levels, whether they exist as ''natural'' Abs, and/or whether are they generated during the" ]

[ [ "1a", "Title: Techniques to Study Antigen-Specific B Cell Responses" ], [ "1b", "Passage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies ." ], [ "1c", "Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition ." ], [ "1d", "For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer" ] ]

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

[ "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: For HIV-1, the discovery of broadly neutralizing antibodies that protect against infection across diverse viral isolates has intensified efforts to understand the developmental pathway of the rare B cells that produce these antibodies . Insights into the ontogeny of these rare B cells could allow the design of a step-wise vaccine regimen that stimulates the germ-line precursor to expand and mature to produce circulating bnAbs which could protect against HIV acquisition . For RSV, stabilized versions of the fusion protein in the pre-fusion conformation have led to insights in the B cell's response to infection and has generated potentially safer", "Title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals\nPassage: Given the predicted low-titer inoculum driving HIV-1 sexual transmission, a vaccine capable of eliciting antibodies that neutralize a broad spectrum of viral strains could potentially reduce or prevent infection. It has been anticipated that the identification of broadly neutralizing mAbs from HIV-1 infected individuals, and the characterization of their cognate epitopes will be instrumental in the design of immunogens capable of eliciting such a broad neutralizing response . This idea has led to a major international cooperative effort within consortia of laboratories with complementary expertise in human immunology, structural biology and vaccine design .", "Title: Wide Prevalence of Heterosubtypic Broadly Neutralizing Human Anti-Influenza A Antibodies\nPassage: vaccinees , or bone marrow of H5N1-infected ''bird-flu'' survivors . BnAbs with similar properties have also been recovered from immortalized IgGexpressing memory B cells of seasonal vaccinees . An unexpected finding from these studies is the frequent contribution of VH1-69 heavy chain genes to these BnAbs, suggesting that a large fraction of the human naive B cell repertoire has the capability of responding to this conserved epitope . These observations raise additional questions as to whether such BnAbs are present in human serum and at ''protective'' levels, whether they exist as ''natural'' Abs, and/or whether are they generated during the" ]

[ [ "2a", "Title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals" ], [ "2b", "Passage: Given the predicted low-titer inoculum driving HIV-1 sexual transmission, a vaccine capable of eliciting antibodies that neutralize a broad spectrum of viral strains could potentially reduce or prevent infection." ], [ "2c", "It has been anticipated that the identification of broadly neutralizing mAbs from HIV-1 infected individuals, and the characterization of their cognate epitopes will be instrumental in the design of immunogens capable of eliciting such a broad neutralizing response ." ], [ "2d", "This idea has led to a major international cooperative effort within consortia of laboratories with complementary expertise in human immunology, structural biology and vaccine design ." ] ]

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

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: AP3 had longer half-life than T20. Although T20 has shown efficacy in inhibiting HIV-1 infection, its major weakness lies in its short half-life in plasma . As a result, T20 has to be administered subcutaneously twice daily at 90 mg per dose, often causing serious injection-site reactions 25, 26 . Here, we performed pharmacokinetic studies by intravenous administration of AP3, AP2, and T20, respectively, to SD rat at a dose of 1 mg/kg, in order to compare their in vivo circulation time. As expected, T20 exhibited a shorter half-life and lower AUC from systemic circulation, while AP3 and AP2 demonstrated", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: AP3 had longer half-life than T20. Although T20 has shown efficacy in inhibiting HIV-1 infection, its major weakness lies in its short half-life in plasma . As a result, T20 has to be administered subcutaneously twice daily at 90 mg per dose, often causing serious injection-site reactions 25, 26 . Here, we performed pharmacokinetic studies by intravenous administration of AP3, AP2, and T20, respectively, to SD rat at a dose of 1 mg/kg, in order to compare their in vivo circulation time. As expected, T20 exhibited a shorter half-life and lower AUC from systemic circulation, while AP3 and AP2 demonstrated", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: much higher concentration and longer circulation time . The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model. The pharmacokinetic parameters were calculated with PK Solver. The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 . This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3. Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: much higher concentration and longer circulation time . The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model. The pharmacokinetic parameters were calculated with PK Solver. The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 . This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3. Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries." ]

[ [ "2a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "2b", "Passage: much higher concentration and longer circulation time ." ], [ "2c", "The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model." ], [ "2d", "The pharmacokinetic parameters were calculated with PK Solver." ], [ "2e", "The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 ." ], [ "2f", "This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3." ], [ "2g", "Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries." ] ]

[ "2e", "3e" ]

[ "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: AP3 had longer half-life than T20. Although T20 has shown efficacy in inhibiting HIV-1 infection, its major weakness lies in its short half-life in plasma . As a result, T20 has to be administered subcutaneously twice daily at 90 mg per dose, often causing serious injection-site reactions 25, 26 . Here, we performed pharmacokinetic studies by intravenous administration of AP3, AP2, and T20, respectively, to SD rat at a dose of 1 mg/kg, in order to compare their in vivo circulation time. As expected, T20 exhibited a shorter half-life and lower AUC from systemic circulation, while AP3 and AP2 demonstrated", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: AP3 had longer half-life than T20. Although T20 has shown efficacy in inhibiting HIV-1 infection, its major weakness lies in its short half-life in plasma . As a result, T20 has to be administered subcutaneously twice daily at 90 mg per dose, often causing serious injection-site reactions 25, 26 . Here, we performed pharmacokinetic studies by intravenous administration of AP3, AP2, and T20, respectively, to SD rat at a dose of 1 mg/kg, in order to compare their in vivo circulation time. As expected, T20 exhibited a shorter half-life and lower AUC from systemic circulation, while AP3 and AP2 demonstrated", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: much higher concentration and longer circulation time . The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model. The pharmacokinetic parameters were calculated with PK Solver. The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 . This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3. Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries.", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy\nPassage: much higher concentration and longer circulation time . The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model. The pharmacokinetic parameters were calculated with PK Solver. The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 . This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3. Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries." ]

[ [ "3a", "Title: Improved Pharmacological and Structural Properties of HIV Fusion Inhibitor AP3 over Enfuvirtide: Highlighting Advantages of Artificial Peptide Strategy" ], [ "3b", "Passage: much higher concentration and longer circulation time ." ], [ "3c", "The pharmacokinetic profiles of AP3 and AP2 fit a non-compartment model." ], [ "3d", "The pharmacokinetic parameters were calculated with PK Solver." ], [ "3e", "The in vivo elimination half-life of AP3 was about 2.8-fold longer than that of T20 ." ], [ "3f", "This result provided the theoretical basis for reducing the injection frequency and dose of the fusion inhibitor, in conjugation with the improved antiviral potency of AP3." ], [ "3g", "Therefore, replacement of T20 with AP3 may significantly reduce injection-site reactions and the drug cost, which would promote the clinical applications of the HIV fusion inhibitor in resource-poor regions or countries." ] ]

[ "2e", "3e" ]

[ "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Dot Blot assays are used to measure protein concentrations semi-quantitatively. It is slightly different from the WBA. Proteins in the sample are not separated by electrophoresis but are spotted directly on a membrane and hybridized with an antibody probe . This technique is cost effective and uses avidin-biotin technology with diaminobenzidine as a chromogen. It is used for the analysis and quantitation of 14-3-3 protein in cerebrospinal fluid samples from cases of Creutzfeldt-Jakob disease , and for disease control of other neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease .", "Title: Protein Reporter Bioassay Systems for the Phenotypic Screening of Candidate Drugs: A Mouse Platform for Anti-Aging Drug Screening\nPassage: technologies allow changes in the localization of GFP-tagged proteins, in response to small molecules, to be detected at the subcellular level in living cells cultured in 384-well plates. Therefore, GFP is suitable as both a reporter of transcriptional activation, and of functional protein translocation in the cell, in response to various stimuli.", "Title: Protein Reporter Bioassay Systems for the Phenotypic Screening of Candidate Drugs: A Mouse Platform for Anti-Aging Drug Screening\nPassage: the blood stream in animals. Some intra-and extracellular reporter gene assays may detect the reporter protein's activity without killing the cells or animals in which the assay is performed. This allows time-course experimentation by sampling of the medium of cultured cells, or the blood plasma of research subjects. As such, report bioassays are potentially suitable for high throughput screening of small molecule drug candidates. Bioassays are used to determine the concentration or biological activity of molecules such as hormones, growth factors, and enzymes. Moreover, they can be used for measuring the effects of candidate drugs on an organism, cultured cells,", "Title: Animal board invited review: advances in proteomics for animal and food sciences\nPassage: second-dimensional molecular sieving by molecular mass . After staining with visible/colorimetric or fluorescent dyes, protein spots are detected and evaluated in abundance by means of dedicated software. Alternatively, modern methods of pre-electrophoretic protein labelling with fluorescent dyes allow direct detection of separated protein spots . Protein spots of interest, usually those that vary in intensity in a treatment-or disease-dependent comparison, are enzymatically digested into peptides. On the basis of their size and fragmentation pattern, subsequent MS analysis attributes them to particular proteins, aided by computer-based search in dedicated large databases." ]

[ [ "0a", "Title: Antibody Engineering for Pursuing a Healthier Future" ], [ "0b", "Passage: Dot Blot assays are used to measure protein concentrations semi-quantitatively." ], [ "0c", "It is slightly different from the WBA." ], [ "0d", "Proteins in the sample are not separated by electrophoresis but are spotted directly on a membrane and hybridized with an antibody probe ." ], [ "0e", "This technique is cost effective and uses avidin-biotin technology with diaminobenzidine as a chromogen." ], [ "0f", "It is used for the analysis and quantitation of 14-3-3 protein in cerebrospinal fluid samples from cases of Creutzfeldt-Jakob disease , and for disease control of other neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease ." ] ]

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

[ "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: containment strategy, usually inefficient 33 . This agrees with the estimate of  in Table 1 , which is not small, implying that isolated individuals still have a high capacity to transmit the virus.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: number and finally be helpful to control the transmission.", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: limit the contact with isolated individuals.", "Title: Transmission of Influenza A in a Student Office Based on Realistic Person-to-Person Contact and Surface Touch Behaviour\nPassage: Many strategies, such as mask wearing , ventilation , hand washing and surface cleaning , can limit the spread of influenza A in a confined room. Wearing a mask can control the spread of disease via the long-range airborne, fomite and close contact routes. A high ventilation rate helps to dilute the virus concentration in the air, and the respiratory dose from the long-range airborne route will be obviously reduced. Hand washing can reduce the infection risk directly via fomites and indirectly via the long-range airborne route because of the lower rate of resuspension from surfaces to the air. The" ]

[ [ "0a", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission" ], [ "0b", "Passage: containment strategy, usually inefficient 33 ." ], [ "0c", "This agrees with the estimate of  in Table 1 , which is not small, implying that isolated individuals still have a high capacity to transmit the virus." ] ]

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

[ "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: containment strategy, usually inefficient 33 . This agrees with the estimate of  in Table 1 , which is not small, implying that isolated individuals still have a high capacity to transmit the virus.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: number and finally be helpful to control the transmission.", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: limit the contact with isolated individuals.", "Title: Transmission of Influenza A in a Student Office Based on Realistic Person-to-Person Contact and Surface Touch Behaviour\nPassage: Many strategies, such as mask wearing , ventilation , hand washing and surface cleaning , can limit the spread of influenza A in a confined room. Wearing a mask can control the spread of disease via the long-range airborne, fomite and close contact routes. A high ventilation rate helps to dilute the virus concentration in the air, and the respiratory dose from the long-range airborne route will be obviously reduced. Hand washing can reduce the infection risk directly via fomites and indirectly via the long-range airborne route because of the lower rate of resuspension from surfaces to the air. The" ]

[ [ "2a", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission" ], [ "2b", "Passage: limit the contact with isolated individuals." ] ]

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

[ "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: containment strategy, usually inefficient 33 . This agrees with the estimate of  in Table 1 , which is not small, implying that isolated individuals still have a high capacity to transmit the virus.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: number and finally be helpful to control the transmission.", "Title: Modeling the effect of comprehensive interventions on Ebola virus transmission\nPassage: limit the contact with isolated individuals.", "Title: Transmission of Influenza A in a Student Office Based on Realistic Person-to-Person Contact and Surface Touch Behaviour\nPassage: Many strategies, such as mask wearing , ventilation , hand washing and surface cleaning , can limit the spread of influenza A in a confined room. Wearing a mask can control the spread of disease via the long-range airborne, fomite and close contact routes. A high ventilation rate helps to dilute the virus concentration in the air, and the respiratory dose from the long-range airborne route will be obviously reduced. Hand washing can reduce the infection risk directly via fomites and indirectly via the long-range airborne route because of the lower rate of resuspension from surfaces to the air. The" ]

[ [ "3a", "Title: Transmission of Influenza A in a Student Office Based on Realistic Person-to-Person Contact and Surface Touch Behaviour" ], [ "3b", "Passage: Many strategies, such as mask wearing , ventilation , hand washing and surface cleaning , can limit the spread of influenza A in a confined room." ], [ "3c", "Wearing a mask can control the spread of disease via the long-range airborne, fomite and close contact routes." ], [ "3d", "A high ventilation rate helps to dilute the virus concentration in the air, and the respiratory dose from the long-range airborne route will be obviously reduced." ], [ "3e", "Hand washing can reduce the infection risk directly via fomites and indirectly via the long-range airborne route because of the lower rate of resuspension from surfaces to the air. The" ] ]

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

[ "Title: Coherence of Influenza Surveillance Data across Different Sources and Age Groups, Beijing, China, 2008-2015\nPassage: Influenza epidemics in temperate latitudes are usually characterized by the dominance of influenza B or one of two subtypes of influenza A, A/H3N2 or A/H1N1. Goldstein et al. found that the epidemic sizes of influenza A/H3N2, A/H1N1, and B infections varied from year to year in temperate regions and discovered that type A was the most virulent of the three types of influenza virus and was associated with seasonal epidemics in temperate regions. Rambaut et al. confirmed that the epidemiological data on influenza A demonstrated an inconsistent seasonal pattern of influenza virus infection across years, with high activity during", "Title: Influenza, evolution, and the next pandemic\nPassage: Influenza A viruses are categorized into two groups. Group 1 includes H1, H2 and H5 subtypes, whereas Group 2 includes H3 and H7 subtypes ). This phylogenetic understanding has informed recent age-specific analyses of mortality patterns before, during and after the 1918 pandemic . Worobey et al. have used a hostspecific molecular clock approach to demonstrate that high mortality in young adults may have been due to childhood exposure to a doubly heterosubtypic putative H3N8 virus that circulated from 1889 to 1900 . They think that young children were protected by childhood exposure to a newly emerged H1variant or N1", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: Novel strains of infl uenza virus arise due to antigenic shifts and drifts. These strains have very different surface glycoproteins which did not exist in human strains before. A pandemic occurs when such a virus emerges in humans with effi cient human to human transmission. As there is very little or no immunity against it, the virus quickly infects a large number of individuals in all age groups. A pandemic has been expected for long and it was feared that H5N1 avian infl uenza virus which caused severe disease in clusters of humans was the most likely candidate virus to", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: virus genes or by animal to human transmission. A pandemic occurs when a new type of infl uenza A virus is introduced in humans that can cause a serious illness and is capable of sustained human to human transmission." ]

[ [ "0a", "Title: Coherence of Influenza Surveillance Data across Different Sources and Age Groups, Beijing, China, 2008-2015" ], [ "0b", "Passage: Influenza epidemics in temperate latitudes are usually characterized by the dominance of influenza B or one of two subtypes of influenza A, A/H3N2 or A/H1N1." ], [ "0c", "Goldstein et al. found that the epidemic sizes of influenza A/H3N2, A/H1N1, and B infections varied from year to year in temperate regions and discovered that type A was the most virulent of the three types of influenza virus and was associated with seasonal epidemics in temperate regions." ], [ "0d", "Rambaut et al. confirmed that the epidemiological data on influenza A demonstrated an inconsistent seasonal pattern of influenza virus infection across years, with high activity during" ] ]

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

[ "Title: Coherence of Influenza Surveillance Data across Different Sources and Age Groups, Beijing, China, 2008-2015\nPassage: Influenza epidemics in temperate latitudes are usually characterized by the dominance of influenza B or one of two subtypes of influenza A, A/H3N2 or A/H1N1. Goldstein et al. found that the epidemic sizes of influenza A/H3N2, A/H1N1, and B infections varied from year to year in temperate regions and discovered that type A was the most virulent of the three types of influenza virus and was associated with seasonal epidemics in temperate regions. Rambaut et al. confirmed that the epidemiological data on influenza A demonstrated an inconsistent seasonal pattern of influenza virus infection across years, with high activity during", "Title: Influenza, evolution, and the next pandemic\nPassage: Influenza A viruses are categorized into two groups. Group 1 includes H1, H2 and H5 subtypes, whereas Group 2 includes H3 and H7 subtypes ). This phylogenetic understanding has informed recent age-specific analyses of mortality patterns before, during and after the 1918 pandemic . Worobey et al. have used a hostspecific molecular clock approach to demonstrate that high mortality in young adults may have been due to childhood exposure to a doubly heterosubtypic putative H3N8 virus that circulated from 1889 to 1900 . They think that young children were protected by childhood exposure to a newly emerged H1variant or N1", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: Novel strains of infl uenza virus arise due to antigenic shifts and drifts. These strains have very different surface glycoproteins which did not exist in human strains before. A pandemic occurs when such a virus emerges in humans with effi cient human to human transmission. As there is very little or no immunity against it, the virus quickly infects a large number of individuals in all age groups. A pandemic has been expected for long and it was feared that H5N1 avian infl uenza virus which caused severe disease in clusters of humans was the most likely candidate virus to", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: virus genes or by animal to human transmission. A pandemic occurs when a new type of infl uenza A virus is introduced in humans that can cause a serious illness and is capable of sustained human to human transmission." ]

[ [ "1a", "Title: Influenza, evolution, and the next pandemic" ], [ "1b", "Passage: Influenza A viruses are categorized into two groups." ], [ "1c", "Group 1 includes H1, H2 and H5 subtypes, whereas Group 2 includes H3 and H7 subtypes )." ], [ "1d", "This phylogenetic understanding has informed recent age-specific analyses of mortality patterns before, during and after the 1918 pandemic ." ], [ "1e", "Worobey et al. have used a hostspecific molecular clock approach to demonstrate that high mortality in young adults may have been due to childhood exposure to a doubly heterosubtypic putative H3N8 virus that circulated from 1889 to 1900 ." ], [ "1f", "They think that young children were protected by childhood exposure to a newly emerged H1variant or N1" ] ]

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

[ "Title: Coherence of Influenza Surveillance Data across Different Sources and Age Groups, Beijing, China, 2008-2015\nPassage: Influenza epidemics in temperate latitudes are usually characterized by the dominance of influenza B or one of two subtypes of influenza A, A/H3N2 or A/H1N1. Goldstein et al. found that the epidemic sizes of influenza A/H3N2, A/H1N1, and B infections varied from year to year in temperate regions and discovered that type A was the most virulent of the three types of influenza virus and was associated with seasonal epidemics in temperate regions. Rambaut et al. confirmed that the epidemiological data on influenza A demonstrated an inconsistent seasonal pattern of influenza virus infection across years, with high activity during", "Title: Influenza, evolution, and the next pandemic\nPassage: Influenza A viruses are categorized into two groups. Group 1 includes H1, H2 and H5 subtypes, whereas Group 2 includes H3 and H7 subtypes ). This phylogenetic understanding has informed recent age-specific analyses of mortality patterns before, during and after the 1918 pandemic . Worobey et al. have used a hostspecific molecular clock approach to demonstrate that high mortality in young adults may have been due to childhood exposure to a doubly heterosubtypic putative H3N8 virus that circulated from 1889 to 1900 . They think that young children were protected by childhood exposure to a newly emerged H1variant or N1", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: Novel strains of infl uenza virus arise due to antigenic shifts and drifts. These strains have very different surface glycoproteins which did not exist in human strains before. A pandemic occurs when such a virus emerges in humans with effi cient human to human transmission. As there is very little or no immunity against it, the virus quickly infects a large number of individuals in all age groups. A pandemic has been expected for long and it was feared that H5N1 avian infl uenza virus which caused severe disease in clusters of humans was the most likely candidate virus to", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: virus genes or by animal to human transmission. A pandemic occurs when a new type of infl uenza A virus is introduced in humans that can cause a serious illness and is capable of sustained human to human transmission." ]

[ [ "2a", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1." ], [ "2b", "Epidemiology and clinical features" ], [ "2c", "Passage: Novel strains of infl uenza virus arise due to antigenic shifts and drifts." ], [ "2d", "These strains have very different surface glycoproteins which did not exist in human strains before." ], [ "2e", "A pandemic occurs when such a virus emerges in humans with effi cient human to human transmission." ], [ "2f", "As there is very little or no immunity against it, the virus quickly infects a large number of individuals in all age groups." ], [ "2g", "A pandemic has been expected for long and it was feared that H5N1 avian infl uenza virus which caused severe disease in clusters of humans was the most likely candidate virus to" ] ]

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

[ "Title: Coherence of Influenza Surveillance Data across Different Sources and Age Groups, Beijing, China, 2008-2015\nPassage: Influenza epidemics in temperate latitudes are usually characterized by the dominance of influenza B or one of two subtypes of influenza A, A/H3N2 or A/H1N1. Goldstein et al. found that the epidemic sizes of influenza A/H3N2, A/H1N1, and B infections varied from year to year in temperate regions and discovered that type A was the most virulent of the three types of influenza virus and was associated with seasonal epidemics in temperate regions. Rambaut et al. confirmed that the epidemiological data on influenza A demonstrated an inconsistent seasonal pattern of influenza virus infection across years, with high activity during", "Title: Influenza, evolution, and the next pandemic\nPassage: Influenza A viruses are categorized into two groups. Group 1 includes H1, H2 and H5 subtypes, whereas Group 2 includes H3 and H7 subtypes ). This phylogenetic understanding has informed recent age-specific analyses of mortality patterns before, during and after the 1918 pandemic . Worobey et al. have used a hostspecific molecular clock approach to demonstrate that high mortality in young adults may have been due to childhood exposure to a doubly heterosubtypic putative H3N8 virus that circulated from 1889 to 1900 . They think that young children were protected by childhood exposure to a newly emerged H1variant or N1", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: Novel strains of infl uenza virus arise due to antigenic shifts and drifts. These strains have very different surface glycoproteins which did not exist in human strains before. A pandemic occurs when such a virus emerges in humans with effi cient human to human transmission. As there is very little or no immunity against it, the virus quickly infects a large number of individuals in all age groups. A pandemic has been expected for long and it was feared that H5N1 avian infl uenza virus which caused severe disease in clusters of humans was the most likely candidate virus to", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1. Epidemiology and clinical features\nPassage: virus genes or by animal to human transmission. A pandemic occurs when a new type of infl uenza A virus is introduced in humans that can cause a serious illness and is capable of sustained human to human transmission." ]

[ [ "3a", "Title: Influenza A: From highly pathogenic H5N1 to pandemic 2009 H1N1." ], [ "3b", "Epidemiology and clinical features" ], [ "3c", "Passage: virus genes or by animal to human transmission." ], [ "3d", "A pandemic occurs when a new type of infl uenza A virus is introduced in humans that can cause a serious illness and is capable of sustained human to human transmission." ] ]

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

[ "Title: Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013)\nPassage: While NMR spectroscopy and X-ray crystallography are the most informative and heavily used methods for understanding protein structure, each has inherent flaws. This is especially evident regarding disordered protein structures, where crystallization requires mostly static structures for diffraction, and NMR is unable to distinguish between different conformational states in an ensemble. Mass spectrometry represents a complementary technique that can be used to generate useful information when examining disordered proteins.", "Title: Murphy's law—if anything can go wrong, it will: Problems in phage electron microscopy\nPassage: Contrast. Poor contrast seems to be a pervasive, if not the main problem of \"digital\" electron microscopy . Indeed, many \"digital\" micrographs are lamentably dark and poorly contrasted. This is not an intrinsic limitation of \"digital\" microscopes or cameras, but rather due to inappropriate parameters or complete misunderstanding of the dynamic signal range during image acquisition.", "Title: Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells\nPassage: To observe thicker samples under cryo-conditions without the need to generate sections, soft X-ray cryo-tomography can be also used , reviewed in ). It is a powerful method that takes advantage of the high penetration power of X-rays without using any fixative or contrasting reagent . Its intermediate resolution in comparison with the high resolution of cryo-ET, has limited its use when fine ultrastructural details are needed. However, 15 nm spatial resolution has been already attained with this method .", "Title: Picornavirus uncoating intermediate captured in atomic detail\nPassage: beamsize of between 0.03 Â 0.03 mm 2 and 0.06 Â 0.07 mm 2 , depending on the size of the crystals. On I24, the X-ray beam was homogenized with a 0.25-mm carbon plate and focused downstream from the crystal. Using 0.1 s exposure times and 100% beam transmission, typically 4-15 useful images could be collected from a crystal ." ]

[ [ "0a", "Title: Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013)" ], [ "0b", "Passage: While NMR spectroscopy and X-ray crystallography are the most informative and heavily used methods for understanding protein structure, each has inherent flaws." ], [ "0c", "This is especially evident regarding disordered protein structures, where crystallization requires mostly static structures for diffraction, and NMR is unable to distinguish between different conformational states in an ensemble." ], [ "0d", "Mass spectrometry represents a complementary technique that can be used to generate useful information when examining disordered proteins." ] ]

[ "0b", "0c" ]

[ "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: respiratory mucosa may also be involved in the protection against the lethal influenza challenges , even though the exact mechanisms remain to be determined further. The immunization with adenovirus vector encoding NP induced both cellular and antibody responses. It has been shown recently that influenza virus-infected cells can be eliminated by anti-M2e IgG-mediated cellular cytotoxicity or phagocytosis since these cells express M2 on their surface after infection . Similarly, the NP-specific antibodies may interact with the viral NP expressed on cell surface of infected cells and mediate cell lysis by antibody-dependent cellular cytotoxicity.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: virus titers at day 5 post-challenge were detected at similar levels in all immunization groups . It is probable that rAd/NP may induce long-lasting innate immunity that contributes complementarily with other specific immune arms to the control of the disease by uncharacterized mechanisms . As a result, the protection may not necessarily correlate with virus titers detected in the lungs upon lethal challenge. Overall, these results indicate that i.n. immunization of rAd/NP can confer complete protection against the lethal homologous virus challenge while allowing competent virus replication to perpetuate even to day 5 post-challenge.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: NP-specific serum IgGs and that PR8-challenge following rAd/NP immunization significantly increases PR8-specific serum IgG levels, compared to that of pre-challenge levels, in intranasally immunized mice, but not in sublingually immunized mice.", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan" ]

[ [ "0a", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection" ], [ "0b", "Passage: respiratory mucosa may also be involved in the protection against the lethal influenza challenges , even though the exact mechanisms remain to be determined further." ], [ "0c", "The immunization with adenovirus vector encoding NP induced both cellular and antibody responses." ], [ "0d", "It has been shown recently that influenza virus-infected cells can be eliminated by anti-M2e IgG-mediated cellular cytotoxicity or phagocytosis since these cells express M2 on their surface after infection ." ], [ "0e", "Similarly, the NP-specific antibodies may interact with the viral NP expressed on cell surface of infected cells and mediate cell lysis by antibody-dependent cellular cytotoxicity." ] ]

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

[ "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: respiratory mucosa may also be involved in the protection against the lethal influenza challenges , even though the exact mechanisms remain to be determined further. The immunization with adenovirus vector encoding NP induced both cellular and antibody responses. It has been shown recently that influenza virus-infected cells can be eliminated by anti-M2e IgG-mediated cellular cytotoxicity or phagocytosis since these cells express M2 on their surface after infection . Similarly, the NP-specific antibodies may interact with the viral NP expressed on cell surface of infected cells and mediate cell lysis by antibody-dependent cellular cytotoxicity.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: virus titers at day 5 post-challenge were detected at similar levels in all immunization groups . It is probable that rAd/NP may induce long-lasting innate immunity that contributes complementarily with other specific immune arms to the control of the disease by uncharacterized mechanisms . As a result, the protection may not necessarily correlate with virus titers detected in the lungs upon lethal challenge. Overall, these results indicate that i.n. immunization of rAd/NP can confer complete protection against the lethal homologous virus challenge while allowing competent virus replication to perpetuate even to day 5 post-challenge.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: NP-specific serum IgGs and that PR8-challenge following rAd/NP immunization significantly increases PR8-specific serum IgG levels, compared to that of pre-challenge levels, in intranasally immunized mice, but not in sublingually immunized mice.", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan" ]

[ [ "1a", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection" ], [ "1b", "Passage: virus titers at day 5 post-challenge were detected at similar levels in all immunization groups ." ], [ "1c", "It is probable that rAd/NP may induce long-lasting innate immunity that contributes complementarily with other specific immune arms to the control of the disease by uncharacterized mechanisms ." ], [ "1d", "As a result, the protection may not necessarily correlate with virus titers detected in the lungs upon lethal challenge." ], [ "1e", "Overall, these results indicate that i.n." ], [ "1f", "immunization of rAd/NP can confer complete protection against the lethal homologous virus challenge while allowing competent virus replication to perpetuate even to day 5 post-challenge." ] ]

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

[ "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: respiratory mucosa may also be involved in the protection against the lethal influenza challenges , even though the exact mechanisms remain to be determined further. The immunization with adenovirus vector encoding NP induced both cellular and antibody responses. It has been shown recently that influenza virus-infected cells can be eliminated by anti-M2e IgG-mediated cellular cytotoxicity or phagocytosis since these cells express M2 on their surface after infection . Similarly, the NP-specific antibodies may interact with the viral NP expressed on cell surface of infected cells and mediate cell lysis by antibody-dependent cellular cytotoxicity.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: virus titers at day 5 post-challenge were detected at similar levels in all immunization groups . It is probable that rAd/NP may induce long-lasting innate immunity that contributes complementarily with other specific immune arms to the control of the disease by uncharacterized mechanisms . As a result, the protection may not necessarily correlate with virus titers detected in the lungs upon lethal challenge. Overall, these results indicate that i.n. immunization of rAd/NP can confer complete protection against the lethal homologous virus challenge while allowing competent virus replication to perpetuate even to day 5 post-challenge.", "Title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection\nPassage: NP-specific serum IgGs and that PR8-challenge following rAd/NP immunization significantly increases PR8-specific serum IgG levels, compared to that of pre-challenge levels, in intranasally immunized mice, but not in sublingually immunized mice.", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan" ]

[ [ "3a", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice" ], [ "3b", "Passage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen." ], [ "3c", "Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens ." ], [ "3d", "While these results are encouraging, immunity eventually develops against virus capsid proteins." ], [ "3e", "This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans ." ], [ "3f", "This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan" ] ]

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

[ "Title: Estimation in emerging epidemics: biases and remedies\nPassage: The exact relationship between the generation time G and serial interval S is thus model-dependent, but it always holds that they have the same mean. As for the variances, nothing can be said in complete generality. However, for all existing models we are aware of, it holds that V ! V, with equality requiring rather specific assumptions. So, except in specific cases, the observed serial interval distribution will be a biased estimate of the generation time distribution and will have a larger variance. The quantitative effects of using a distribution with equal mean but larger variance than the true one", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: The estimated serial interval distributions and credible intervals are shown in Figure 5 for the two different values of j, along with kernel density plots for the mean serial intervals. In the original analysis a Weibull distribution was fitted and is shown for comparison; the estimated mean serial interval was 3:6 days . From the serial interval distributions we estimate the mean serial interval to be 3:6 days assuming j~2 and 3:8 days assuming j~4. The mean likelihood of the j~4 fit is approximately three times that of the j~2 fit. Figure 6 shows the expected number of serial interval", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ]

[ [ "0a", "Title: Estimation in emerging epidemics: biases and remedies" ], [ "0b", "Passage: The exact relationship between the generation time G and serial interval S is thus model-dependent, but it always holds that they have the same mean." ], [ "0c", "As for the variances, nothing can be said in complete generality." ], [ "0d", "However, for all existing models we are aware of, it holds that V !" ], [ "0e", "V, with equality requiring rather specific assumptions." ], [ "0f", "So, except in specific cases, the observed serial interval distribution will be a biased estimate of the generation time distribution and will have a larger variance." ], [ "0g", "The quantitative effects of using a distribution with equal mean but larger variance than the true one" ] ]

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

[ "Title: Estimation in emerging epidemics: biases and remedies\nPassage: The exact relationship between the generation time G and serial interval S is thus model-dependent, but it always holds that they have the same mean. As for the variances, nothing can be said in complete generality. However, for all existing models we are aware of, it holds that V ! V, with equality requiring rather specific assumptions. So, except in specific cases, the observed serial interval distribution will be a biased estimate of the generation time distribution and will have a larger variance. The quantitative effects of using a distribution with equal mean but larger variance than the true one", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: The estimated serial interval distributions and credible intervals are shown in Figure 5 for the two different values of j, along with kernel density plots for the mean serial intervals. In the original analysis a Weibull distribution was fitted and is shown for comparison; the estimated mean serial interval was 3:6 days . From the serial interval distributions we estimate the mean serial interval to be 3:6 days assuming j~2 and 3:8 days assuming j~4. The mean likelihood of the j~4 fit is approximately three times that of the j~2 fit. Figure 6 shows the expected number of serial interval", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ]

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

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

[ "Title: Estimation in emerging epidemics: biases and remedies\nPassage: The exact relationship between the generation time G and serial interval S is thus model-dependent, but it always holds that they have the same mean. As for the variances, nothing can be said in complete generality. However, for all existing models we are aware of, it holds that V ! V, with equality requiring rather specific assumptions. So, except in specific cases, the observed serial interval distribution will be a biased estimate of the generation time distribution and will have a larger variance. The quantitative effects of using a distribution with equal mean but larger variance than the true one", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: The estimated serial interval distributions and credible intervals are shown in Figure 5 for the two different values of j, along with kernel density plots for the mean serial intervals. In the original analysis a Weibull distribution was fitted and is shown for comparison; the estimated mean serial interval was 3:6 days . From the serial interval distributions we estimate the mean serial interval to be 3:6 days assuming j~2 and 3:8 days assuming j~4. The mean likelihood of the j~4 fit is approximately three times that of the j~2 fit. Figure 6 shows the expected number of serial interval", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ]

[ [ "2a", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic" ], [ "2b", "Passage: The estimated serial interval distributions and credible intervals are shown in Figure 5 for the two different values of j, along with kernel density plots for the mean serial intervals." ], [ "2c", "In the original analysis a Weibull distribution was fitted and is shown for comparison; the estimated mean serial interval was 3:6 days ." ], [ "2d", "From the serial interval distributions we estimate the mean serial interval to be 3:6 days assuming j~2 and 3:8 days assuming j~4." ], [ "2e", "The mean likelihood of the j~4 fit is approximately three times that of the j~2 fit." ], [ "2f", "Figure 6 shows the expected number of serial interval" ] ]

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

[ "Title: Estimation in emerging epidemics: biases and remedies\nPassage: The exact relationship between the generation time G and serial interval S is thus model-dependent, but it always holds that they have the same mean. As for the variances, nothing can be said in complete generality. However, for all existing models we are aware of, it holds that V ! V, with equality requiring rather specific assumptions. So, except in specific cases, the observed serial interval distribution will be a biased estimate of the generation time distribution and will have a larger variance. The quantitative effects of using a distribution with equal mean but larger variance than the true one", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: interval is most sensitive to the mean exposed period, 1=s, and thus this is more accurately estimated. Although the parameter estimates from the three models are different, the estimated serial interval distributions corresponding to mean parameter estimates are all very similar , thus so are the mean serial intervals. The fit using N~4 is the best in terms of the mean likelihood.", "Title: Estimating a Markovian Epidemic Model Using Household Serial Interval Data from the Early Phase of an Epidemic\nPassage: The estimated serial interval distributions and credible intervals are shown in Figure 5 for the two different values of j, along with kernel density plots for the mean serial intervals. In the original analysis a Weibull distribution was fitted and is shown for comparison; the estimated mean serial interval was 3:6 days . From the serial interval distributions we estimate the mean serial interval to be 3:6 days assuming j~2 and 3:8 days assuming j~4. The mean likelihood of the j~4 fit is approximately three times that of the j~2 fit. Figure 6 shows the expected number of serial interval", "Title: Estimation in emerging epidemics: biases and remedies\nPassage: value which should be less than the true expected generation time, which is 15. Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed. The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 . This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ]

[ [ "3a", "Title: Estimation in emerging epidemics: biases and remedies" ], [ "3b", "Passage: value which should be less than the true expected generation time, which is 15." ], [ "3c", "Theory again predicts that the backward generation time should have mean 12.57, which is not far from what is observed." ], [ "3d", "The variance of the true generation time is 75 and both variance estimates from the simulation samples tend to be much less, somewhat above 50 ." ], [ "3e", "This also leads to the useful conclusion that serial intervals are affected by the same \"contraction\" as generation times when ascertained \"backwards\", at least in the chosen parameter setting." ] ]

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

[ "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus\nPassage: The use of statins, angiotensin II receptor blockers and angiotensin converting enzyme inhibitors has been proposed to regulate the IAV-induced cytokine storm in severe infections . Retrospective studies conducted separately in Mexico, Netherlands, UK and USA reported an association of reduced IAV-related pneumonia and lower case fatality due to lower respiratory tract IAV infections with statin treatment . However, this association was contested in two additional studies that found no benefit of statin treatment on IAVinduced disease burden . This uncertainty regarding the IAV therapeutic potential of these widely used compounds warrants further investigations at the basic science level and", "Title: Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations\nPassage: acute respiratory disease syndrome associated with sepsis . In contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin-8, and interferon-γ, and therefore inhibit influenza A virus replication . Further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely.", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: 5-7 days postinfection . In the past decade, it has been increasingly recognised that as well as reducing lipid burden and modifying cardiovascular disease, HMG Co-A reductase inhibitors have hitherto unappreciated anti-inflammatory effects that are potentially harnessable for management of inflammatory disease. A recent trial suggested that atorvastatin reduced cough severity in stable bronchiectasis with associated increase in apoptotic neutrophils seen in sputum, and there is renewed interest in their role in modulating acute inflammatory conditions . A recent systematic review examined a number of studies exploring the role of statins in CAP and concluded that they modulate neutrophil response," ]

[ [ "0a", "Title: Host resilience to emerging coronaviruses" ], [ "0b", "Passage: Corticosteroids are broadly immunosuppressive and have many physiological effects ." ], [ "0c", "Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections." ], [ "0d", "A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV ." ], [ "0e", "Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection ." ], [ "0f", "Other immunomodulators include celecoxib, mesalazine and eritoran ." ], [ "0g", "Another class of drugs that have been suggested are statins." ], [ "0h", "They act to stabilize the activation of aspects of the innate immune" ] ]

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

[ "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus\nPassage: The use of statins, angiotensin II receptor blockers and angiotensin converting enzyme inhibitors has been proposed to regulate the IAV-induced cytokine storm in severe infections . Retrospective studies conducted separately in Mexico, Netherlands, UK and USA reported an association of reduced IAV-related pneumonia and lower case fatality due to lower respiratory tract IAV infections with statin treatment . However, this association was contested in two additional studies that found no benefit of statin treatment on IAVinduced disease burden . This uncertainty regarding the IAV therapeutic potential of these widely used compounds warrants further investigations at the basic science level and", "Title: Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations\nPassage: acute respiratory disease syndrome associated with sepsis . In contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin-8, and interferon-γ, and therefore inhibit influenza A virus replication . Further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely.", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: 5-7 days postinfection . In the past decade, it has been increasingly recognised that as well as reducing lipid burden and modifying cardiovascular disease, HMG Co-A reductase inhibitors have hitherto unappreciated anti-inflammatory effects that are potentially harnessable for management of inflammatory disease. A recent trial suggested that atorvastatin reduced cough severity in stable bronchiectasis with associated increase in apoptotic neutrophils seen in sputum, and there is renewed interest in their role in modulating acute inflammatory conditions . A recent systematic review examined a number of studies exploring the role of statins in CAP and concluded that they modulate neutrophil response," ]

[ [ "1a", "Title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus" ], [ "1b", "Passage: The use of statins, angiotensin II receptor blockers and angiotensin converting enzyme inhibitors has been proposed to regulate the IAV-induced cytokine storm in severe infections ." ], [ "1c", "Retrospective studies conducted separately in Mexico, Netherlands, UK and USA reported an association of reduced IAV-related pneumonia and lower case fatality due to lower respiratory tract IAV infections with statin treatment ." ], [ "1d", "However, this association was contested in two additional studies that found no benefit of statin treatment on IAVinduced disease burden ." ], [ "1e", "This uncertainty regarding the IAV therapeutic potential of these widely used compounds warrants further investigations at the basic science level and" ] ]

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

[ "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus\nPassage: The use of statins, angiotensin II receptor blockers and angiotensin converting enzyme inhibitors has been proposed to regulate the IAV-induced cytokine storm in severe infections . Retrospective studies conducted separately in Mexico, Netherlands, UK and USA reported an association of reduced IAV-related pneumonia and lower case fatality due to lower respiratory tract IAV infections with statin treatment . However, this association was contested in two additional studies that found no benefit of statin treatment on IAVinduced disease burden . This uncertainty regarding the IAV therapeutic potential of these widely used compounds warrants further investigations at the basic science level and", "Title: Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations\nPassage: acute respiratory disease syndrome associated with sepsis . In contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin-8, and interferon-γ, and therefore inhibit influenza A virus replication . Further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely.", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: 5-7 days postinfection . In the past decade, it has been increasingly recognised that as well as reducing lipid burden and modifying cardiovascular disease, HMG Co-A reductase inhibitors have hitherto unappreciated anti-inflammatory effects that are potentially harnessable for management of inflammatory disease. A recent trial suggested that atorvastatin reduced cough severity in stable bronchiectasis with associated increase in apoptotic neutrophils seen in sputum, and there is renewed interest in their role in modulating acute inflammatory conditions . A recent systematic review examined a number of studies exploring the role of statins in CAP and concluded that they modulate neutrophil response," ]

[ [ "2a", "Title: Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations" ], [ "2b", "Passage: acute respiratory disease syndrome associated with sepsis ." ], [ "2c", "In contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin-8, and interferon-γ, and therefore inhibit influenza A virus replication ." ], [ "2d", "Further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely." ] ]

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

[ "Title: Host resilience to emerging coronaviruses\nPassage: Corticosteroids are broadly immunosuppressive and have many physiological effects . Several recent studies have suggested that other compounds could be useful in increasing host resilience to viral lung infections. A recent paper demonstrates that topoisomerase I can protect against inflammation-induced death from a variety of viral infections including IAV . Blockade of C5a complement signaling has also been suggested as a possible option in decreasing inflammation during IAV infection . Other immunomodulators include celecoxib, mesalazine and eritoran . Another class of drugs that have been suggested are statins. They act to stabilize the activation of aspects of the innate immune", "Title: Response Modifiers: Tweaking the Immune Response Against Influenza A Virus\nPassage: The use of statins, angiotensin II receptor blockers and angiotensin converting enzyme inhibitors has been proposed to regulate the IAV-induced cytokine storm in severe infections . Retrospective studies conducted separately in Mexico, Netherlands, UK and USA reported an association of reduced IAV-related pneumonia and lower case fatality due to lower respiratory tract IAV infections with statin treatment . However, this association was contested in two additional studies that found no benefit of statin treatment on IAVinduced disease burden . This uncertainty regarding the IAV therapeutic potential of these widely used compounds warrants further investigations at the basic science level and", "Title: Statin Treatment and Mortality: Propensity Score-Matched Analyses of 2007–2008 and 2009–2010 Laboratory-Confirmed Influenza Hospitalizations\nPassage: acute respiratory disease syndrome associated with sepsis . In contrast, a recent in vitro study showed that statin treatment can protect host cells against influenzainduced inflammation by reducing the production of tumor necrosis factor-α, interleukin-8, and interferon-γ, and therefore inhibit influenza A virus replication . Further studies to evaluate the effect of immunomodulatory agents in reducing influenza-related complications may still be warranted, but they may be better suited for settings where these drugs are not used widely.", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: 5-7 days postinfection . In the past decade, it has been increasingly recognised that as well as reducing lipid burden and modifying cardiovascular disease, HMG Co-A reductase inhibitors have hitherto unappreciated anti-inflammatory effects that are potentially harnessable for management of inflammatory disease. A recent trial suggested that atorvastatin reduced cough severity in stable bronchiectasis with associated increase in apoptotic neutrophils seen in sputum, and there is renewed interest in their role in modulating acute inflammatory conditions . A recent systematic review examined a number of studies exploring the role of statins in CAP and concluded that they modulate neutrophil response," ]

[ [ "3a", "Title: Key mechanisms governing resolution of lung inflammation" ], [ "3b", "Passage: 5-7 days postinfection ." ], [ "3c", "In the past decade, it has been increasingly recognised that as well as reducing lipid burden and modifying cardiovascular disease, HMG Co-A reductase inhibitors have hitherto unappreciated anti-inflammatory effects that are potentially harnessable for management of inflammatory disease." ], [ "3d", "A recent trial suggested that atorvastatin reduced cough severity in stable bronchiectasis with associated increase in apoptotic neutrophils seen in sputum, and there is renewed interest in their role in modulating acute inflammatory conditions ." ], [ "3e", "A recent systematic review examined a number of studies exploring the role of statins in CAP and concluded that they modulate neutrophil response," ] ]

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

[ "Title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity\nPassage: Currently, one urgent and critical challenge is to treat infected patients and save their lives. Several studies have roughly described the overall clinical features of 2019-nCoV patients . However, the more specific and classified clinical characteristics of the infected patients still require further investigation, particularly for those with severe symptoms, which is roughly estimated to be approximately 15-20 percent of totally confirmed cases based on the local data in our hospital. Clinically, for those severe patients, the main symptoms of 2019-nCoV pneumonia are fever, decreased white blood cell and lymphocyte count, increased C reaction protein and abnormally expressed cytokines .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Those with one of the following pathogenic evidence is the confirmed case: positive for the 2019-nCoV by the real-time PCR test for nucleic acid in respiratory or blood samples . 2) viral gene sequencing shows highly homogeneity to the known 2019-nCoV in respiratory or blood samples .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted .", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: There are eleven studies that focus on SARS-CoV diagnostic testing . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity ." ]

[ [ "0a", "Title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity" ], [ "0b", "Passage: Currently, one urgent and critical challenge is to treat infected patients and save their lives." ], [ "0c", "Several studies have roughly described the overall clinical features of 2019-nCoV patients ." ], [ "0d", "However, the more specific and classified clinical characteristics of the infected patients still require further investigation, particularly for those with severe symptoms, which is roughly estimated to be approximately 15-20 percent of totally confirmed cases based on the local data in our hospital." ], [ "0e", "Clinically, for those severe patients, the main symptoms of 2019-nCoV pneumonia are fever, decreased white blood cell and lymphocyte count, increased C reaction protein and abnormally expressed cytokines ." ] ]

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

[ "Title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity\nPassage: Currently, one urgent and critical challenge is to treat infected patients and save their lives. Several studies have roughly described the overall clinical features of 2019-nCoV patients . However, the more specific and classified clinical characteristics of the infected patients still require further investigation, particularly for those with severe symptoms, which is roughly estimated to be approximately 15-20 percent of totally confirmed cases based on the local data in our hospital. Clinically, for those severe patients, the main symptoms of 2019-nCoV pneumonia are fever, decreased white blood cell and lymphocyte count, increased C reaction protein and abnormally expressed cytokines .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Those with one of the following pathogenic evidence is the confirmed case: positive for the 2019-nCoV by the real-time PCR test for nucleic acid in respiratory or blood samples . 2) viral gene sequencing shows highly homogeneity to the known 2019-nCoV in respiratory or blood samples .", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: Throughout the period of home care, healthcare personnel should perform regular follow-up through face-to-face visits or phone interviews to follow the progress of symptoms and, if necessary, specific diagnostic tests should be conducted .", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: There are eleven studies that focus on SARS-CoV diagnostic testing . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test and serological test showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity ." ]

[ [ "1a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "1b", "Passage: Those with one of the following pathogenic evidence is the confirmed case: positive for the 2019-nCoV by the real-time PCR test for nucleic acid in respiratory or blood samples ." ], [ "1c", "2) viral gene sequencing shows highly homogeneity to the known 2019-nCoV in respiratory or blood samples ." ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids covalently attached to certain cysteine residues via a thioester linkage . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity,", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids covalently attached to certain cysteine residues via a thioester linkage . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity,", "Title: The intracellular dynamic of protein palmitoylation\nPassage: but, instead, likely inhibits membrane binding by blocking palmitoylation. This phosphoregulation of palmitoylation might be relevant to many palmitoylated peripheral proteins and could represent a mechanism to promote a shift toward the depalmitoylated state of a protein in the absence of active depalmitoylation. Negatively charged phosphate groups are likely to inhibit palmitoylation of neighboring cysteines by interfering with membrane interactions before palmitoylation .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction" ]

[ [ "2a", "Title: The intracellular dynamic of protein palmitoylation" ], [ "2b", "Passage: but, instead, likely inhibits membrane binding by blocking palmitoylation." ], [ "2c", "This phosphoregulation of palmitoylation might be relevant to many palmitoylated peripheral proteins and could represent a mechanism to promote a shift toward the depalmitoylated state of a protein in the absence of active depalmitoylation." ], [ "2d", "Negatively charged phosphate groups are likely to inhibit palmitoylation of neighboring cysteines by interfering with membrane interactions before palmitoylation ." ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids covalently attached to certain cysteine residues via a thioester linkage . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity,", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids covalently attached to certain cysteine residues via a thioester linkage . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity,", "Title: The intracellular dynamic of protein palmitoylation\nPassage: but, instead, likely inhibits membrane binding by blocking palmitoylation. This phosphoregulation of palmitoylation might be relevant to many palmitoylated peripheral proteins and could represent a mechanism to promote a shift toward the depalmitoylated state of a protein in the absence of active depalmitoylation. Negatively charged phosphate groups are likely to inhibit palmitoylation of neighboring cysteines by interfering with membrane interactions before palmitoylation .", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction" ]

[ [ "3a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "3b", "Passage: In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells." ], [ "3c", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid ." ], [ "3d", "The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated." ], [ "3e", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A ." ], [ "3f", "The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: MVA as a leading viral-vectored candidate vaccine.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: magnitude of the antigen-specific effector functions . MVA is also a potent activator of early innate immune responses further enhancing adaptive immune responses . Between early smallpox vaccine development and more recent vaccine vector development, MVA has undergone extensive safety testing and shown to be attenuated in severely immunocompromised animals and safe for use in children, adults, elderly, and immunocompromised persons. With extensive pre-clinical data, recombinant MVA vaccines expressing influenza antigens have been tested in clinical trials and been shown to be safe and immunogenic in humans . These results combined with data from other clinical and pre-clinical studies support", "Title: Viral vector-based influenza vaccines\nPassage: MVA holds great promise as a vaccine vector and was initially shown to be a promising influenza vaccine in 1994 by Sutter et al. 37 This vaccine was engineered to express the HA and nucleoprotein gene from influenza virus A/PR/8/34. In addition, recombinant MVA expressing other proteins from various influenza strains were generated and tested in animal models.", "Title: Viral vector-based influenza vaccines\nPassage: various subtypes of influenza A virus. This vaccination regimen proved immunogenic in pigs, but the protective potential was not tested in this species. 58 An MVA-NPCM1 vaccine was subsequently tested in phase 1/2a clinical trials and was shown to induce virus-specific CD8 C T-cells in humans and protect from experimental challenge infection with an A virus. 58, 60, 61 Furthermore, this vaccination regimen was again shown to be safe and immunogenic in the elderly, 62 and could be co-administered with TIV. 63 Universal influenza vaccines on basis of MVA Because of the variable nature of influenza viruses and the extensive" ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: magnitude of the antigen-specific effector functions ." ], [ "1c", "MVA is also a potent activator of early innate immune responses further enhancing adaptive immune responses ." ], [ "1d", "Between early smallpox vaccine development and more recent vaccine vector development, MVA has undergone extensive safety testing and shown to be attenuated in severely immunocompromised animals and safe for use in children, adults, elderly, and immunocompromised persons." ], [ "1e", "With extensive pre-clinical data, recombinant MVA vaccines expressing influenza antigens have been tested in clinical trials and been shown to be safe and immunogenic in humans ." ], [ "1f", "These results combined with data from other clinical and pre-clinical studies support" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: MVA as a leading viral-vectored candidate vaccine.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: magnitude of the antigen-specific effector functions . MVA is also a potent activator of early innate immune responses further enhancing adaptive immune responses . Between early smallpox vaccine development and more recent vaccine vector development, MVA has undergone extensive safety testing and shown to be attenuated in severely immunocompromised animals and safe for use in children, adults, elderly, and immunocompromised persons. With extensive pre-clinical data, recombinant MVA vaccines expressing influenza antigens have been tested in clinical trials and been shown to be safe and immunogenic in humans . These results combined with data from other clinical and pre-clinical studies support", "Title: Viral vector-based influenza vaccines\nPassage: MVA holds great promise as a vaccine vector and was initially shown to be a promising influenza vaccine in 1994 by Sutter et al. 37 This vaccine was engineered to express the HA and nucleoprotein gene from influenza virus A/PR/8/34. In addition, recombinant MVA expressing other proteins from various influenza strains were generated and tested in animal models.", "Title: Viral vector-based influenza vaccines\nPassage: various subtypes of influenza A virus. This vaccination regimen proved immunogenic in pigs, but the protective potential was not tested in this species. 58 An MVA-NPCM1 vaccine was subsequently tested in phase 1/2a clinical trials and was shown to induce virus-specific CD8 C T-cells in humans and protect from experimental challenge infection with an A virus. 58, 60, 61 Furthermore, this vaccination regimen was again shown to be safe and immunogenic in the elderly, 62 and could be co-administered with TIV. 63 Universal influenza vaccines on basis of MVA Because of the variable nature of influenza viruses and the extensive" ]

[ [ "2a", "Title: Viral vector-based influenza vaccines" ], [ "2b", "Passage: MVA holds great promise as a vaccine vector and was initially shown to be a promising influenza vaccine in 1994 by Sutter et al. 37 This vaccine was engineered to express the HA and nucleoprotein gene from influenza virus A/PR/8/34." ], [ "2c", "In addition, recombinant MVA expressing other proteins from various influenza strains were generated and tested in animal models." ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: MVA as a leading viral-vectored candidate vaccine.", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: magnitude of the antigen-specific effector functions . MVA is also a potent activator of early innate immune responses further enhancing adaptive immune responses . Between early smallpox vaccine development and more recent vaccine vector development, MVA has undergone extensive safety testing and shown to be attenuated in severely immunocompromised animals and safe for use in children, adults, elderly, and immunocompromised persons. With extensive pre-clinical data, recombinant MVA vaccines expressing influenza antigens have been tested in clinical trials and been shown to be safe and immunogenic in humans . These results combined with data from other clinical and pre-clinical studies support", "Title: Viral vector-based influenza vaccines\nPassage: MVA holds great promise as a vaccine vector and was initially shown to be a promising influenza vaccine in 1994 by Sutter et al. 37 This vaccine was engineered to express the HA and nucleoprotein gene from influenza virus A/PR/8/34. In addition, recombinant MVA expressing other proteins from various influenza strains were generated and tested in animal models.", "Title: Viral vector-based influenza vaccines\nPassage: various subtypes of influenza A virus. This vaccination regimen proved immunogenic in pigs, but the protective potential was not tested in this species. 58 An MVA-NPCM1 vaccine was subsequently tested in phase 1/2a clinical trials and was shown to induce virus-specific CD8 C T-cells in humans and protect from experimental challenge infection with an A virus. 58, 60, 61 Furthermore, this vaccination regimen was again shown to be safe and immunogenic in the elderly, 62 and could be co-administered with TIV. 63 Universal influenza vaccines on basis of MVA Because of the variable nature of influenza viruses and the extensive" ]

[ [ "3a", "Title: Viral vector-based influenza vaccines" ], [ "3b", "Passage: various subtypes of influenza A virus." ], [ "3c", "This vaccination regimen proved immunogenic in pigs, but the protective potential was not tested in this species." ], [ "3d", "58 An MVA-NPCM1 vaccine was subsequently tested in phase 1/2a clinical trials and was shown to induce virus-specific CD8 C T-cells in humans and protect from experimental challenge infection with an A virus." ], [ "3e", "58, 60, 61 Furthermore, this vaccination regimen was again shown to be safe and immunogenic in the elderly, 62 and could be co-administered with TIV." ], [ "3f", "63 Universal influenza vaccines on basis of MVA Because of the variable nature of influenza viruses and the extensive" ] ]

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

[ "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: detailed analysis of B cell subsets with pathogenic potential in humans could lead to a better understanding of how to prevent and treat autoimmune diseases.", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: detailed analysis of B cell subsets with pathogenic potential in humans could lead to a better understanding of how to prevent and treat autoimmune diseases.", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus . Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens . Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice . The study of autoantigen-specific B cells and a", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus . Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens . Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice . The study of autoantigen-specific B cells and a" ]

[ [ "2a", "Title: Techniques to Study Antigen-Specific B Cell Responses" ], [ "2b", "Passage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus ." ], [ "2c", "Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens ." ], [ "2d", "Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice ." ], [ "2e", "The study of autoantigen-specific B cells and a" ] ]

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

[ "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: detailed analysis of B cell subsets with pathogenic potential in humans could lead to a better understanding of how to prevent and treat autoimmune diseases.", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: detailed analysis of B cell subsets with pathogenic potential in humans could lead to a better understanding of how to prevent and treat autoimmune diseases.", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus . Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens . Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice . The study of autoantigen-specific B cells and a", "Title: Techniques to Study Antigen-Specific B Cell Responses\nPassage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus . Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens . Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice . The study of autoantigen-specific B cells and a" ]

[ [ "3a", "Title: Techniques to Study Antigen-Specific B Cell Responses" ], [ "3b", "Passage: The study of B cell responses has not only informed vaccine design but has also advanced our understanding of antibodymediated autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus ." ], [ "3c", "Up to 20% of mature, naïve B cells have receptors with the capacity to bind self-antigens ." ], [ "3d", "Although these cells are potentially pathogenic, the deletion of B cells with high affinity to self-antigen through apoptosis, anergy of B cells with low affinity to self-antigen, and the absence of T cell help combine together to protect against autoimmune disease in mice ." ], [ "3e", "The study of autoantigen-specific B cells and a" ] ]

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

[ "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: Of the 29 swabs received, 18 had a corresponding research swab that was positive for a respiratory pathogen. Seven corresponding self-swabs were concordant with the positive research swabs for influenza, and eight corresponding self-swabs were concordant with the research swab for noninfluenza pathogens . The kappa statistic between research and self-swab was 0.84. There were no differences in demographic variables, including education level or days between drop-off and receipt of swabs, among participants whose self-and research-staff obtained swabs correlated versus those whose swabs did not correlate . Of the self-swab samples that had a corresponding positive research swab, the longest", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: the self-swab using the research swab as the gold standard was assessed. All analyses were conducted using SPSS Statistics V22.0 .", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: To assess feasibility, we determined the proportion of households agreeing to perform the self-swab, the proportion returning the swab, and the number of days elapsed between when the participants received the kit and when the swab arrived in the laboratory. All swabs obtained by research staff were analyzed by a commercially available multiplex reverse transcription polymerase chain reaction assay according to the manufacturer's instructions . The assay has a limit of detection of 1-200 tissue culture infective dose 50/mL for influenza, and an LOD of 4-30,000 TCID50/mL for non-influenza viral pathogens, of which only rhinovirus/enterovirus has an LOD of more", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population\nPassage: mailer that followed the US Postal Service guidelines for biological substances. 9 Participants were advised that if the swab was not sent the day it was obtained, it should be stored in the refrigerator. The research staff followed up by telephone the next day to confirm that the self-swab was obtained and sent. Each participant obtaining the self-swab received a round-trip New York City MetroCard when the specimen was received." ]

[ [ "2a", "Title: Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population" ], [ "2b", "Passage: To assess feasibility, we determined the proportion of households agreeing to perform the self-swab, the proportion returning the swab, and the number of days elapsed between when the participants received the kit and when the swab arrived in the laboratory." ], [ "2c", "All swabs obtained by research staff were analyzed by a commercially available multiplex reverse transcription polymerase chain reaction assay according to the manufacturer's instructions ." ], [ "2d", "The assay has a limit of detection of 1-200 tissue culture infective dose 50/mL for influenza, and an LOD of 4-30,000 TCID50/mL for non-influenza viral pathogens, of which only rhinovirus/enterovirus has an LOD of more" ] ]

[ "2c" ]

[ "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public. This event was reported to the World Health Organisation on 31 December . Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: Text: The situation has continued to evolve rapidly since then and just a few weeks later, as at 23 January, 614 laboratory-confirmed cases and 17 deaths have been reported including some cases detected outside mainland China . Meanwhile, on 7 January 2020, the novel coronavirus, currently named 2019-nCoV, was officially announced as the causative agent by Chinese authorities . In order to support public health action, viral genome sequences were released by Chinese researchers on 10 January and 2 days later, four further sequences were also made available on the Global Initiative on Sharing All Influenza Data . While more", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 . On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases . Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 . As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir." ]

[ [ "1a", "Title: Note from the editors: novel coronavirus (2019-nCoV)" ], [ "1b", "Passage: Text: The situation has continued to evolve rapidly since then and just a few weeks later, as at 23 January, 614 laboratory-confirmed cases and 17 deaths have been reported including some cases detected outside mainland China ." ], [ "1c", "Meanwhile, on 7 January 2020, the novel coronavirus, currently named 2019-nCoV, was officially announced as the causative agent by Chinese authorities ." ], [ "1d", "In order to support public health action, viral genome sequences were released by Chinese researchers on 10 January and 2 days later, four further sequences were also made available on the Global Initiative on Sharing All Influenza Data . While more" ] ]

[ "1c", "2c" ]

[ "Title: SARS to novel coronavirus – old lessons and new lessons\nPassage: Text: On 29 December 2019 clinicians in a hospital in Wuhan City, China noticed a clustering of cases of unusual pneumonia with an apparent link to a market that sells live fish, poultry and animals to the public. This event was reported to the World Health Organisation on 31 December . Within 4 weeks, by 26 January 2020, the causative organism had been identified as a novel coronavirus, the genome of the virus had been sequenced and published, reverse transcription polymerase chain reaction tests had been developed, the WHO R&D Blueprint had been activated to accelerate diagnostics, therapeutics and vaccine", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: Text: The situation has continued to evolve rapidly since then and just a few weeks later, as at 23 January, 614 laboratory-confirmed cases and 17 deaths have been reported including some cases detected outside mainland China . Meanwhile, on 7 January 2020, the novel coronavirus, currently named 2019-nCoV, was officially announced as the causative agent by Chinese authorities . In order to support public health action, viral genome sequences were released by Chinese researchers on 10 January and 2 days later, four further sequences were also made available on the Global Initiative on Sharing All Influenza Data . While more", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: A cluster of pneumonia of unknown origin was identified in Wuhan, China, in December 2019 . On 12 January 2020, Chinese authorities shared the sequence of a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 isolated from some clustered cases . Since then, the disease caused by SARS-CoV-2 has been named coronavirus disease 2019 . As at 21 February 2020, the virus had spread rapidly mostly within China but also to 28 other countries, including in the World Health Organization European Region .", "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir." ]

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

[ "1c", "2c" ]

[ "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods. The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions. The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate .", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Antigen binding was performed in PBS at 37°C for 2 h, followed by washing 3 times. Incubation of ELISA plates with biotinylated detecting antibody cocktails was performed in PBS at 37°C for 2 h. After washing, specific binding of the detecting antibodies was reported by streptavidin-HRP and stained with Super Signal ELISA Femto Maximum sensitive substrate . Visualization of the plate was performed in AE 1000 cool CCD image analyzer. The signal intensity and background of each spot was read out and recorded with \"Monster\"software. The positive signals were defined as a signal value > 400 and a signal value", "Title: Evaluation of Diagnostic Performance of Three Indirect Enzyme-Linked Immunosorbent Assays for the Detection of IgG Antibodies to Ebola Virus in Human Sera\nPassage: All reagents were added to the immunoplates at a volume of 100 µL/well unless otherwise stated. Passive adsorption onto ELISA plates was performed at 4 • C overnight and all subsequent incubations were performed at 37 • C in a humidified chamber for 1 h. Following coating, plates were washed 3 times with 300 µL of PBS containing 0.1% Tween 20; the same washing procedure followed each subsequent stage of I-ELISAs. Plates were blocked with 200 µL 10% non-fat milk powder in PBS. After incubation, plates were washed, and control and test sera diluted 1:400 in 2% non-fat milk powder", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: ELISA-array. The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use." ]

[ [ "0a", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses" ], [ "0b", "Passage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods." ], [ "0c", "The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions." ], [ "0d", "The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate ." ] ]

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

[ "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods. The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions. The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate .", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Antigen binding was performed in PBS at 37°C for 2 h, followed by washing 3 times. Incubation of ELISA plates with biotinylated detecting antibody cocktails was performed in PBS at 37°C for 2 h. After washing, specific binding of the detecting antibodies was reported by streptavidin-HRP and stained with Super Signal ELISA Femto Maximum sensitive substrate . Visualization of the plate was performed in AE 1000 cool CCD image analyzer. The signal intensity and background of each spot was read out and recorded with \"Monster\"software. The positive signals were defined as a signal value > 400 and a signal value", "Title: Evaluation of Diagnostic Performance of Three Indirect Enzyme-Linked Immunosorbent Assays for the Detection of IgG Antibodies to Ebola Virus in Human Sera\nPassage: All reagents were added to the immunoplates at a volume of 100 µL/well unless otherwise stated. Passive adsorption onto ELISA plates was performed at 4 • C overnight and all subsequent incubations were performed at 37 • C in a humidified chamber for 1 h. Following coating, plates were washed 3 times with 300 µL of PBS containing 0.1% Tween 20; the same washing procedure followed each subsequent stage of I-ELISAs. Plates were blocked with 200 µL 10% non-fat milk powder in PBS. After incubation, plates were washed, and control and test sera diluted 1:400 in 2% non-fat milk powder", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: ELISA-array. The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use." ]

[ [ "1a", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses" ], [ "1b", "Passage: Antigen binding was performed in PBS at 37°C for 2 h, followed by washing 3 times." ], [ "1c", "Incubation of ELISA plates with biotinylated detecting antibody cocktails was performed in PBS at 37°C for 2 h. After washing, specific binding of the detecting antibodies was reported by streptavidin-HRP and stained with Super Signal ELISA Femto Maximum sensitive substrate ." ], [ "1d", "Visualization of the plate was performed in AE 1000 cool CCD image analyzer." ], [ "1e", "The signal intensity and background of each spot was read out and recorded with \"Monster\"software." ], [ "1f", "The positive signals were defined as a signal value > 400 and a signal value" ] ]

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

[ "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods. The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions. The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate .", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Antigen binding was performed in PBS at 37°C for 2 h, followed by washing 3 times. Incubation of ELISA plates with biotinylated detecting antibody cocktails was performed in PBS at 37°C for 2 h. After washing, specific binding of the detecting antibodies was reported by streptavidin-HRP and stained with Super Signal ELISA Femto Maximum sensitive substrate . Visualization of the plate was performed in AE 1000 cool CCD image analyzer. The signal intensity and background of each spot was read out and recorded with \"Monster\"software. The positive signals were defined as a signal value > 400 and a signal value", "Title: Evaluation of Diagnostic Performance of Three Indirect Enzyme-Linked Immunosorbent Assays for the Detection of IgG Antibodies to Ebola Virus in Human Sera\nPassage: All reagents were added to the immunoplates at a volume of 100 µL/well unless otherwise stated. Passive adsorption onto ELISA plates was performed at 4 • C overnight and all subsequent incubations were performed at 37 • C in a humidified chamber for 1 h. Following coating, plates were washed 3 times with 300 µL of PBS containing 0.1% Tween 20; the same washing procedure followed each subsequent stage of I-ELISAs. Plates were blocked with 200 µL 10% non-fat milk powder in PBS. After incubation, plates were washed, and control and test sera diluted 1:400 in 2% non-fat milk powder", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: ELISA-array. The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use." ]

[ [ "3a", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses Passage: ELISA-array." ], [ "3b", "The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses." ], [ "3c", "The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs." ], [ "3d", "This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum." ], [ "3e", "The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use." ] ]

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

[ "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Among 148 patients diagnosed with dengue infection patients aged ≤18 years), 64 were dengue fever without warning signs, 77 were dengue fever with warning signs, and 7 were severe dengue, based on 2009 WHO case definitions . An individual patient might have received more than one The mean time lapse from onset of symptoms to ER presentation was 3.7 ± 1.8 days, and the mean fever duration was 4.0 ± 2.3 days. The 3 most common symptoms other than fever in dengue patients were malaise , rashes , and joint pain . Marked thrombocytopenia and leukopenia were found in 109", "Title: A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania\nPassage: Male enrollment was more common than female enrollment. The median age of enrollment was 23 years . The most common presenting complaints, other than fever, were headache , lethargy , cough , and vomiting . Of all enrolled participants, 116 were admitted for inpatient care and treatment . Patient-level data, inclusive of particular clinical and epidemiologic data as well as diagnostic results, are included in a supplemental file .", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Of 526 patients aged ≤18 years) influenza infections, 447 were 2009 pandemic H1N1 and 79 were seasonal H3N2. The mean interval between onset of illness and the patient's arrival at the ER was 1.7 ± 1.2 days, and the mean fever duration was 2.8 ± 1.6 days. Besides fever, the 3 most common symptoms were cough , rhinorrhea , and sore throat . Mild thrombocytopenia was detected in 38 of the 238 patients with an available peripheral platelet count. Of 364 patients receiving oseltamivir, 107 started therapy >48 h after illness onset. The 3 most common influenza-associated complications were pneumonia", "Title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania\nPassage: The most common presenting complaints, other than fever, were headache , cough and abdominal pain . The mean axillary temperature was 38.4˚C which was consistent across all age groups. Given similarity in fever distributions among younger children, older children and adults, we could define fever tertiles of all enrolled febrile participants, defined as mild fever , moderate fever , and severe fever . Each tertile comprised approximately 33% of all enrolled participants." ]

[ [ "0a", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room" ], [ "0b", "Passage: Among 148 patients diagnosed with dengue infection patients aged ≤18 years), 64 were dengue fever without warning signs, 77 were dengue fever with warning signs, and 7 were severe dengue, based on 2009 WHO case definitions ." ], [ "0c", "An individual patient might have received more than one The mean time lapse from onset of symptoms to ER presentation was 3.7 ± 1.8 days, and the mean fever duration was 4.0 ± 2.3 days." ], [ "0d", "The 3 most common symptoms other than fever in dengue patients were malaise , rashes , and joint pain ." ], [ "0e", "Marked thrombocytopenia and leukopenia were found in 109" ] ]

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

[ "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Among 148 patients diagnosed with dengue infection patients aged ≤18 years), 64 were dengue fever without warning signs, 77 were dengue fever with warning signs, and 7 were severe dengue, based on 2009 WHO case definitions . An individual patient might have received more than one The mean time lapse from onset of symptoms to ER presentation was 3.7 ± 1.8 days, and the mean fever duration was 4.0 ± 2.3 days. The 3 most common symptoms other than fever in dengue patients were malaise , rashes , and joint pain . Marked thrombocytopenia and leukopenia were found in 109", "Title: A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania\nPassage: Male enrollment was more common than female enrollment. The median age of enrollment was 23 years . The most common presenting complaints, other than fever, were headache , lethargy , cough , and vomiting . Of all enrolled participants, 116 were admitted for inpatient care and treatment . Patient-level data, inclusive of particular clinical and epidemiologic data as well as diagnostic results, are included in a supplemental file .", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Of 526 patients aged ≤18 years) influenza infections, 447 were 2009 pandemic H1N1 and 79 were seasonal H3N2. The mean interval between onset of illness and the patient's arrival at the ER was 1.7 ± 1.2 days, and the mean fever duration was 2.8 ± 1.6 days. Besides fever, the 3 most common symptoms were cough , rhinorrhea , and sore throat . Mild thrombocytopenia was detected in 38 of the 238 patients with an available peripheral platelet count. Of 364 patients receiving oseltamivir, 107 started therapy >48 h after illness onset. The 3 most common influenza-associated complications were pneumonia", "Title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania\nPassage: The most common presenting complaints, other than fever, were headache , cough and abdominal pain . The mean axillary temperature was 38.4˚C which was consistent across all age groups. Given similarity in fever distributions among younger children, older children and adults, we could define fever tertiles of all enrolled febrile participants, defined as mild fever , moderate fever , and severe fever . Each tertile comprised approximately 33% of all enrolled participants." ]

[ [ "1a", "Title: A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania" ], [ "1b", "Passage: Male enrollment was more common than female enrollment." ], [ "1c", "The median age of enrollment was 23 years ." ], [ "1d", "The most common presenting complaints, other than fever, were headache , lethargy , cough , and vomiting ." ], [ "1e", "Of all enrolled participants, 116 were admitted for inpatient care and treatment ." ], [ "1f", "Patient-level data, inclusive of particular clinical and epidemiologic data as well as diagnostic results, are included in a supplemental file ." ] ]

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

[ "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Among 148 patients diagnosed with dengue infection patients aged ≤18 years), 64 were dengue fever without warning signs, 77 were dengue fever with warning signs, and 7 were severe dengue, based on 2009 WHO case definitions . An individual patient might have received more than one The mean time lapse from onset of symptoms to ER presentation was 3.7 ± 1.8 days, and the mean fever duration was 4.0 ± 2.3 days. The 3 most common symptoms other than fever in dengue patients were malaise , rashes , and joint pain . Marked thrombocytopenia and leukopenia were found in 109", "Title: A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania\nPassage: Male enrollment was more common than female enrollment. The median age of enrollment was 23 years . The most common presenting complaints, other than fever, were headache , lethargy , cough , and vomiting . Of all enrolled participants, 116 were admitted for inpatient care and treatment . Patient-level data, inclusive of particular clinical and epidemiologic data as well as diagnostic results, are included in a supplemental file .", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Of 526 patients aged ≤18 years) influenza infections, 447 were 2009 pandemic H1N1 and 79 were seasonal H3N2. The mean interval between onset of illness and the patient's arrival at the ER was 1.7 ± 1.2 days, and the mean fever duration was 2.8 ± 1.6 days. Besides fever, the 3 most common symptoms were cough , rhinorrhea , and sore throat . Mild thrombocytopenia was detected in 38 of the 238 patients with an available peripheral platelet count. Of 364 patients receiving oseltamivir, 107 started therapy >48 h after illness onset. The 3 most common influenza-associated complications were pneumonia", "Title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania\nPassage: The most common presenting complaints, other than fever, were headache , cough and abdominal pain . The mean axillary temperature was 38.4˚C which was consistent across all age groups. Given similarity in fever distributions among younger children, older children and adults, we could define fever tertiles of all enrolled febrile participants, defined as mild fever , moderate fever , and severe fever . Each tertile comprised approximately 33% of all enrolled participants." ]

[ [ "2a", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room" ], [ "2b", "Passage: Of 526 patients aged ≤18 years) influenza infections, 447 were 2009 pandemic H1N1 and 79 were seasonal H3N2." ], [ "2c", "The mean interval between onset of illness and the patient's arrival at the ER was 1.7 ± 1.2 days, and the mean fever duration was 2.8 ± 1.6 days." ], [ "2d", "Besides fever, the 3 most common symptoms were cough , rhinorrhea , and sore throat ." ], [ "2e", "Mild thrombocytopenia was detected in 38 of the 238 patients with an available peripheral platelet count." ], [ "2f", "Of 364 patients receiving oseltamivir, 107 started therapy >48 h after illness onset." ], [ "2g", "The 3 most common influenza-associated complications were pneumonia" ] ]

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

[ "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Among 148 patients diagnosed with dengue infection patients aged ≤18 years), 64 were dengue fever without warning signs, 77 were dengue fever with warning signs, and 7 were severe dengue, based on 2009 WHO case definitions . An individual patient might have received more than one The mean time lapse from onset of symptoms to ER presentation was 3.7 ± 1.8 days, and the mean fever duration was 4.0 ± 2.3 days. The 3 most common symptoms other than fever in dengue patients were malaise , rashes , and joint pain . Marked thrombocytopenia and leukopenia were found in 109", "Title: A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania\nPassage: Male enrollment was more common than female enrollment. The median age of enrollment was 23 years . The most common presenting complaints, other than fever, were headache , lethargy , cough , and vomiting . Of all enrolled participants, 116 were admitted for inpatient care and treatment . Patient-level data, inclusive of particular clinical and epidemiologic data as well as diagnostic results, are included in a supplemental file .", "Title: Use of simple clinical and laboratory predictors to differentiate influenza from dengue and other febrile illnesses in the emergency room\nPassage: Of 526 patients aged ≤18 years) influenza infections, 447 were 2009 pandemic H1N1 and 79 were seasonal H3N2. The mean interval between onset of illness and the patient's arrival at the ER was 1.7 ± 1.2 days, and the mean fever duration was 2.8 ± 1.6 days. Besides fever, the 3 most common symptoms were cough , rhinorrhea , and sore throat . Mild thrombocytopenia was detected in 38 of the 238 patients with an available peripheral platelet count. Of 364 patients receiving oseltamivir, 107 started therapy >48 h after illness onset. The 3 most common influenza-associated complications were pneumonia", "Title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania\nPassage: The most common presenting complaints, other than fever, were headache , cough and abdominal pain . The mean axillary temperature was 38.4˚C which was consistent across all age groups. Given similarity in fever distributions among younger children, older children and adults, we could define fever tertiles of all enrolled febrile participants, defined as mild fever , moderate fever , and severe fever . Each tertile comprised approximately 33% of all enrolled participants." ]

[ [ "3a", "Title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania" ], [ "3b", "Passage: The most common presenting complaints, other than fever, were headache , cough and abdominal pain ." ], [ "3c", "The mean axillary temperature was 38.4˚C which was consistent across all age groups." ], [ "3d", "Given similarity in fever distributions among younger children, older children and adults, we could define fever tertiles of all enrolled febrile participants, defined as mild fever , moderate fever , and severe fever ." ], [ "3e", "Each tertile comprised approximately 33% of all enrolled participants." ] ]

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

[ "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: Estimating the number of infections and the impact of non-\nPassage: before testing became widespread.", "Title: Severe influenza cases in paediatric intensive care units in Germany during the pre-pandemic seasons 2005 to 2008\nPassage: Underlying chronic medical conditions were reported in 11 children, whereby 7 of these had more than Information about the influenza vaccination status was available from 17 patients; none had been vaccinated against influenza. Out of the 11 children from risk groups with chronic underlying disease the vaccination status was not available in 2 patients, and 1 child was < 6 months of age and therefore too young to be immunized." ]

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

[ "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: Estimating the number of infections and the impact of non-\nPassage: before testing became widespread.", "Title: Severe influenza cases in paediatric intensive care units in Germany during the pre-pandemic seasons 2005 to 2008\nPassage: Underlying chronic medical conditions were reported in 11 children, whereby 7 of these had more than Information about the influenza vaccination status was available from 17 patients; none had been vaccinated against influenza. Out of the 11 children from risk groups with chronic underlying disease the vaccination status was not available in 2 patients, and 1 child was < 6 months of age and therefore too young to be immunized." ]

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

[ "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: Estimating the number of infections and the impact of non-\nPassage: before testing became widespread.", "Title: Severe influenza cases in paediatric intensive care units in Germany during the pre-pandemic seasons 2005 to 2008\nPassage: Underlying chronic medical conditions were reported in 11 children, whereby 7 of these had more than Information about the influenza vaccination status was available from 17 patients; none had been vaccinated against influenza. Out of the 11 children from risk groups with chronic underlying disease the vaccination status was not available in 2 patients, and 1 child was < 6 months of age and therefore too young to be immunized." ]

[ [ "3a", "Title: Severe influenza cases in paediatric intensive care units in Germany during the pre-pandemic seasons 2005 to 2008" ], [ "3b", "Passage: Underlying chronic medical conditions were reported in 11 children, whereby 7 of these had more than Information about the influenza vaccination status was available from 17 patients; none had been vaccinated against influenza." ], [ "3c", "Out of the 11 children from risk groups with chronic underlying disease the vaccination status was not available in 2 patients, and 1 child was < 6 months of age and therefore too young to be immunized." ] ]

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

[ "Title: Non-specific Effect of Vaccines: Immediate Protection against Respiratory Syncytial Virus Infection by a Live Attenuated Influenza Vaccine\nPassage: Respiratory viral infections, caused by influenza virus, respiratory syncytial virus , human parainfluenza viruses , and coronaviruses, remain a global public health concern . WHO has acknowledged the magnitude of this problem and has highlighted the need for research focused on the prevention of respiratory viral infections. However, except for influenza virus, there are no authorized vaccines available for the prevention of emerging/re-emerging respiratory viral infections . Vaccination is based on the adaptive immune responses that provide protection against a specific pathogen. Safe and controlled activation of the immune system results in a specific memory in the vaccinated hosts and", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Ongoing studies could identify effective candidates. An active instrument against infection is needed since RSV infection can cause serious complications in infants, young children and the elderly.", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: ARIs are extremely common in children, especially those under 5 years old. They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood. For some of the responsible pathogens, vaccines are available. This review focuses on the most recent data about vaccines against respiratory pathogens. The use of influenza, pneumococcal, pertussis and measles vaccines is essential to reduce ARIs burden. Vaccination coverage rates must be improved to achieve the full benefits of these vaccines. Recently, advances in the knowledge of RSV virus biology and immunology as well as the development of new techniques to generate vaccine", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Despite a consensus on the need for an RSV vaccine, there is no licensed product available yet, mainly due to the early age of infection, the capacity of RSV to evade innate immunity, and the failure of RSV-induced adaptive immunity to prevent re-infection . Several clinical trials are now ongoing to assess the safety and effectiveness of different RSV vaccine candidates . Owing to the substantial burden of RSV disease worldwide, RSV vaccine continues to be a necessity for most infants, children and also the elderly. The ideal vaccine should produce long-lasting immunity characterized by a robust Th1-mediated response and" ]

[ [ "0a", "Title: Non-specific Effect of Vaccines: Immediate Protection against Respiratory Syncytial Virus Infection by a Live Attenuated Influenza Vaccine" ], [ "0b", "Passage: Respiratory viral infections, caused by influenza virus, respiratory syncytial virus , human parainfluenza viruses , and coronaviruses, remain a global public health concern ." ], [ "0c", "WHO has acknowledged the magnitude of this problem and has highlighted the need for research focused on the prevention of respiratory viral infections." ], [ "0d", "However, except for influenza virus, there are no authorized vaccines available for the prevention of emerging/re-emerging respiratory viral infections ." ], [ "0e", "Vaccination is based on the adaptive immune responses that provide protection against a specific pathogen." ], [ "0f", "Safe and controlled activation of the immune system results in a specific memory in the vaccinated hosts and" ] ]

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

[ "Title: Non-specific Effect of Vaccines: Immediate Protection against Respiratory Syncytial Virus Infection by a Live Attenuated Influenza Vaccine\nPassage: Respiratory viral infections, caused by influenza virus, respiratory syncytial virus , human parainfluenza viruses , and coronaviruses, remain a global public health concern . WHO has acknowledged the magnitude of this problem and has highlighted the need for research focused on the prevention of respiratory viral infections. However, except for influenza virus, there are no authorized vaccines available for the prevention of emerging/re-emerging respiratory viral infections . Vaccination is based on the adaptive immune responses that provide protection against a specific pathogen. Safe and controlled activation of the immune system results in a specific memory in the vaccinated hosts and", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Ongoing studies could identify effective candidates. An active instrument against infection is needed since RSV infection can cause serious complications in infants, young children and the elderly.", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: ARIs are extremely common in children, especially those under 5 years old. They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood. For some of the responsible pathogens, vaccines are available. This review focuses on the most recent data about vaccines against respiratory pathogens. The use of influenza, pneumococcal, pertussis and measles vaccines is essential to reduce ARIs burden. Vaccination coverage rates must be improved to achieve the full benefits of these vaccines. Recently, advances in the knowledge of RSV virus biology and immunology as well as the development of new techniques to generate vaccine", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Despite a consensus on the need for an RSV vaccine, there is no licensed product available yet, mainly due to the early age of infection, the capacity of RSV to evade innate immunity, and the failure of RSV-induced adaptive immunity to prevent re-infection . Several clinical trials are now ongoing to assess the safety and effectiveness of different RSV vaccine candidates . Owing to the substantial burden of RSV disease worldwide, RSV vaccine continues to be a necessity for most infants, children and also the elderly. The ideal vaccine should produce long-lasting immunity characterized by a robust Th1-mediated response and" ]

[ [ "1a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "1b", "Passage: Ongoing studies could identify effective candidates." ], [ "1c", "An active instrument against infection is needed since RSV infection can cause serious complications in infants, young children and the elderly." ] ]

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

[ "Title: Non-specific Effect of Vaccines: Immediate Protection against Respiratory Syncytial Virus Infection by a Live Attenuated Influenza Vaccine\nPassage: Respiratory viral infections, caused by influenza virus, respiratory syncytial virus , human parainfluenza viruses , and coronaviruses, remain a global public health concern . WHO has acknowledged the magnitude of this problem and has highlighted the need for research focused on the prevention of respiratory viral infections. However, except for influenza virus, there are no authorized vaccines available for the prevention of emerging/re-emerging respiratory viral infections . Vaccination is based on the adaptive immune responses that provide protection against a specific pathogen. Safe and controlled activation of the immune system results in a specific memory in the vaccinated hosts and", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Ongoing studies could identify effective candidates. An active instrument against infection is needed since RSV infection can cause serious complications in infants, young children and the elderly.", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: ARIs are extremely common in children, especially those under 5 years old. They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood. For some of the responsible pathogens, vaccines are available. This review focuses on the most recent data about vaccines against respiratory pathogens. The use of influenza, pneumococcal, pertussis and measles vaccines is essential to reduce ARIs burden. Vaccination coverage rates must be improved to achieve the full benefits of these vaccines. Recently, advances in the knowledge of RSV virus biology and immunology as well as the development of new techniques to generate vaccine", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Despite a consensus on the need for an RSV vaccine, there is no licensed product available yet, mainly due to the early age of infection, the capacity of RSV to evade innate immunity, and the failure of RSV-induced adaptive immunity to prevent re-infection . Several clinical trials are now ongoing to assess the safety and effectiveness of different RSV vaccine candidates . Owing to the substantial burden of RSV disease worldwide, RSV vaccine continues to be a necessity for most infants, children and also the elderly. The ideal vaccine should produce long-lasting immunity characterized by a robust Th1-mediated response and" ]

[ [ "2a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "2b", "Passage: ARIs are extremely common in children, especially those under 5 years old." ], [ "2c", "They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood." ], [ "2d", "For some of the responsible pathogens, vaccines are available." ], [ "2e", "This review focuses on the most recent data about vaccines against respiratory pathogens." ], [ "2f", "The use of influenza, pneumococcal, pertussis and measles vaccines is essential to reduce ARIs burden." ], [ "2g", "Vaccination coverage rates must be improved to achieve the full benefits of these vaccines." ], [ "2h", "Recently, advances in the knowledge of RSV virus biology and immunology as well as the development of new techniques to generate vaccine" ] ]

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

[ "Title: Non-specific Effect of Vaccines: Immediate Protection against Respiratory Syncytial Virus Infection by a Live Attenuated Influenza Vaccine\nPassage: Respiratory viral infections, caused by influenza virus, respiratory syncytial virus , human parainfluenza viruses , and coronaviruses, remain a global public health concern . WHO has acknowledged the magnitude of this problem and has highlighted the need for research focused on the prevention of respiratory viral infections. However, except for influenza virus, there are no authorized vaccines available for the prevention of emerging/re-emerging respiratory viral infections . Vaccination is based on the adaptive immune responses that provide protection against a specific pathogen. Safe and controlled activation of the immune system results in a specific memory in the vaccinated hosts and", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Ongoing studies could identify effective candidates. An active instrument against infection is needed since RSV infection can cause serious complications in infants, young children and the elderly.", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: ARIs are extremely common in children, especially those under 5 years old. They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood. For some of the responsible pathogens, vaccines are available. This review focuses on the most recent data about vaccines against respiratory pathogens. The use of influenza, pneumococcal, pertussis and measles vaccines is essential to reduce ARIs burden. Vaccination coverage rates must be improved to achieve the full benefits of these vaccines. Recently, advances in the knowledge of RSV virus biology and immunology as well as the development of new techniques to generate vaccine", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: Despite a consensus on the need for an RSV vaccine, there is no licensed product available yet, mainly due to the early age of infection, the capacity of RSV to evade innate immunity, and the failure of RSV-induced adaptive immunity to prevent re-infection . Several clinical trials are now ongoing to assess the safety and effectiveness of different RSV vaccine candidates . Owing to the substantial burden of RSV disease worldwide, RSV vaccine continues to be a necessity for most infants, children and also the elderly. The ideal vaccine should produce long-lasting immunity characterized by a robust Th1-mediated response and" ]

[ [ "3a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "3b", "Passage: Despite a consensus on the need for an RSV vaccine, there is no licensed product available yet, mainly due to the early age of infection, the capacity of RSV to evade innate immunity, and the failure of RSV-induced adaptive immunity to prevent re-infection ." ], [ "3c", "Several clinical trials are now ongoing to assess the safety and effectiveness of different RSV vaccine candidates ." ], [ "3d", "Owing to the substantial burden of RSV disease worldwide, RSV vaccine continues to be a necessity for most infants, children and also the elderly." ], [ "3e", "The ideal vaccine should produce long-lasting immunity characterized by a robust Th1-mediated response and" ] ]

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

[ "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: due to lack of a translatable research model .", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: glands was variable, the number of mother ferrets was always three ferrets per time point. Feces from infant ferrets were collected at the time of anal temperature collection. Each feces was placed directly in RLT buffer or placed directly at -80°C from the animals' anus to avoid surface contamination. Samples were stored in -80°C before processing for viral loads or RNA. Samples for RNA were either placed in RNA later or homogenized in TRIzol . Sample aliquots for histopathology were stored in formalin until processing.", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: As the mothers of inoculated infants began to display clinical signs of influenza including temperature increases, weight loss, and mortality, we went on to analyze the upper and lower respiratory tracts of the infants and their mothers to determine virus transmission and pathogenesis. Viral burden in infant NW was first detected Day 1 post-infant-inoculation . The NW of nursing-mothers were positive for influenza virus Day 3 post-infant-inoculation. Viral titers remained high in mother NW Day 6-7 at more than 6 TCID 50 /ml . Residual virus persisted in the mothers' NW by Day 10 . Virus transmission between adult ferrets", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: We next determined if transmission of the virus from infants to mother led to lower respiratory tract infection. Examination of viral titers in the lower respiratory tract of the mothers found virus levels above 6 TCID 50 /ml in both the trachea and lungs post-infant-inoculation in 2 out of 3 mothers investigated . H&E staining of mother lungs revealed delayed, airway-localized inflammation . Day 3/4 post-infant-inoculation, mother lungs showed areas of minimal infiltrating leukocytes . Increased leukocyte infiltration was observed Day 7 post-infant-inoculation where sites of inflammation were dense in mononuclear cells with lymphocyte-like morphology. Infected mother lungs were compared" ]

[ [ "1a", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses" ], [ "1b", "Passage: glands was variable, the number of mother ferrets was always three ferrets per time point." ], [ "1c", "Feces from infant ferrets were collected at the time of anal temperature collection." ], [ "1d", "Each feces was placed directly in RLT buffer or placed directly at -80°C from the animals' anus to avoid surface contamination." ], [ "1e", "Samples were stored in -80°C before processing for viral loads or RNA." ], [ "1f", "Samples for RNA were either placed in RNA later or homogenized in TRIzol ." ], [ "1g", "Sample aliquots for histopathology were stored in formalin until processing." ] ]

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

[ "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: due to lack of a translatable research model .", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: glands was variable, the number of mother ferrets was always three ferrets per time point. Feces from infant ferrets were collected at the time of anal temperature collection. Each feces was placed directly in RLT buffer or placed directly at -80°C from the animals' anus to avoid surface contamination. Samples were stored in -80°C before processing for viral loads or RNA. Samples for RNA were either placed in RNA later or homogenized in TRIzol . Sample aliquots for histopathology were stored in formalin until processing.", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: As the mothers of inoculated infants began to display clinical signs of influenza including temperature increases, weight loss, and mortality, we went on to analyze the upper and lower respiratory tracts of the infants and their mothers to determine virus transmission and pathogenesis. Viral burden in infant NW was first detected Day 1 post-infant-inoculation . The NW of nursing-mothers were positive for influenza virus Day 3 post-infant-inoculation. Viral titers remained high in mother NW Day 6-7 at more than 6 TCID 50 /ml . Residual virus persisted in the mothers' NW by Day 10 . Virus transmission between adult ferrets", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: We next determined if transmission of the virus from infants to mother led to lower respiratory tract infection. Examination of viral titers in the lower respiratory tract of the mothers found virus levels above 6 TCID 50 /ml in both the trachea and lungs post-infant-inoculation in 2 out of 3 mothers investigated . H&E staining of mother lungs revealed delayed, airway-localized inflammation . Day 3/4 post-infant-inoculation, mother lungs showed areas of minimal infiltrating leukocytes . Increased leukocyte infiltration was observed Day 7 post-infant-inoculation where sites of inflammation were dense in mononuclear cells with lymphocyte-like morphology. Infected mother lungs were compared" ]

[ [ "2a", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses" ], [ "2b", "Passage: As the mothers of inoculated infants began to display clinical signs of influenza including temperature increases, weight loss, and mortality, we went on to analyze the upper and lower respiratory tracts of the infants and their mothers to determine virus transmission and pathogenesis." ], [ "2c", "Viral burden in infant NW was first detected Day 1 post-infant-inoculation ." ], [ "2d", "The NW of nursing-mothers were positive for influenza virus Day 3 post-infant-inoculation." ], [ "2e", "Viral titers remained high in mother NW Day 6-7 at more than 6 TCID 50 /ml ." ], [ "2f", "Residual virus persisted in the mothers' NW by Day 10 ." ], [ "2g", "Virus transmission between adult ferrets" ] ]

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

[ "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: due to lack of a translatable research model .", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: glands was variable, the number of mother ferrets was always three ferrets per time point. Feces from infant ferrets were collected at the time of anal temperature collection. Each feces was placed directly in RLT buffer or placed directly at -80°C from the animals' anus to avoid surface contamination. Samples were stored in -80°C before processing for viral loads or RNA. Samples for RNA were either placed in RNA later or homogenized in TRIzol . Sample aliquots for histopathology were stored in formalin until processing.", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: As the mothers of inoculated infants began to display clinical signs of influenza including temperature increases, weight loss, and mortality, we went on to analyze the upper and lower respiratory tracts of the infants and their mothers to determine virus transmission and pathogenesis. Viral burden in infant NW was first detected Day 1 post-infant-inoculation . The NW of nursing-mothers were positive for influenza virus Day 3 post-infant-inoculation. Viral titers remained high in mother NW Day 6-7 at more than 6 TCID 50 /ml . Residual virus persisted in the mothers' NW by Day 10 . Virus transmission between adult ferrets", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses\nPassage: We next determined if transmission of the virus from infants to mother led to lower respiratory tract infection. Examination of viral titers in the lower respiratory tract of the mothers found virus levels above 6 TCID 50 /ml in both the trachea and lungs post-infant-inoculation in 2 out of 3 mothers investigated . H&E staining of mother lungs revealed delayed, airway-localized inflammation . Day 3/4 post-infant-inoculation, mother lungs showed areas of minimal infiltrating leukocytes . Increased leukocyte infiltration was observed Day 7 post-infant-inoculation where sites of inflammation were dense in mononuclear cells with lymphocyte-like morphology. Infected mother lungs were compared" ]

[ [ "3a", "Title: Influenza Transmission in the Mother-Infant Dyad Leads to Severe Disease, Mammary Gland Infection, and Pathogenesis by Regulating Host Responses" ], [ "3b", "Passage: We next determined if transmission of the virus from infants to mother led to lower respiratory tract infection." ], [ "3c", "Examination of viral titers in the lower respiratory tract of the mothers found virus levels above 6 TCID 50 /ml in both the trachea and lungs post-infant-inoculation in 2 out of 3 mothers investigated ." ], [ "3d", "H&E staining of mother lungs revealed delayed, airway-localized inflammation ." ], [ "3e", "Day 3/4 post-infant-inoculation, mother lungs showed areas of minimal infiltrating leukocytes ." ], [ "3f", "Increased leukocyte infiltration was observed Day 7 post-infant-inoculation where sites of inflammation were dense in mononuclear cells with lymphocyte-like morphology." ], [ "3g", "Infected mother lungs were compared" ] ]

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

[ "Title: Recent Advances in the Diagnosis and Treatment of Influenza Pneumonia\nPassage: Annual immunization is the most important preventive measure . However, two classes of antiviral drugs are available and play an important role in the treatment and prevention of influenza : the neuraminidase inhibitors , oseltamivir and zanamivir, which are active against both influenza A and B viruses; and the M2 inhibitors, amantadine and rimantadine, which are active against all influenza A strains, but have no activity against influenza B viruses. In general, the duration for therapy with an NI is 5 days, and with the M2 inhibitors is three to 5 days.", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: A number of monoclonal and polyclonal antibodies, targeted against a variety of influenza viral proteins, are also in development . Similarly, convalescent plasma has shown potential benefit in the treatment of severe influenza, and further trials are underway . Another area of intense interest is the modification of the host antiviral response to influenza virus infection. There are ongoing preclinical and clinical studies of a variety of other immunomodulatory agents for treatment of influenza, including celecoxib , statins, etanercept, pioglitazone, azithromycin , and interferons .", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Although neuraminidase inhibitors are currently recommended for antiviral treatment of influenza in hospitalized patients based on observational studies, including in critically ill patients, there are a number of novel strategies and products for treating influenza in various stages of development. One approach under investigation is triple-combination antiviral drug therapy, which combines amantadine, ribavirin, and oseltamivir for treatment of influenza in critically ill and high-risk patients. Unfortunately, studies to date have not shown a benefit of TCAD over oseltamivir monotherapy . Several novel antiviral compounds are in various stages of investigation, including small-molecule polymerase inhibitors such as pimodivir and favipiravir ." ]

[ [ "0a", "Title: Recent Advances in the Diagnosis and Treatment of Influenza Pneumonia" ], [ "0b", "Passage: Annual immunization is the most important preventive measure ." ], [ "0c", "However, two classes of antiviral drugs are available and play an important role in the treatment and prevention of influenza : the neuraminidase inhibitors , oseltamivir and zanamivir, which are active against both influenza A and B viruses; and the M2 inhibitors, amantadine and rimantadine, which are active against all influenza A strains, but have no activity against influenza B viruses." ], [ "0d", "In general, the duration for therapy with an NI is 5 days, and with the M2 inhibitors is three to 5 days." ] ]

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

[ "Title: Recent Advances in the Diagnosis and Treatment of Influenza Pneumonia\nPassage: Annual immunization is the most important preventive measure . However, two classes of antiviral drugs are available and play an important role in the treatment and prevention of influenza : the neuraminidase inhibitors , oseltamivir and zanamivir, which are active against both influenza A and B viruses; and the M2 inhibitors, amantadine and rimantadine, which are active against all influenza A strains, but have no activity against influenza B viruses. In general, the duration for therapy with an NI is 5 days, and with the M2 inhibitors is three to 5 days.", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: A number of monoclonal and polyclonal antibodies, targeted against a variety of influenza viral proteins, are also in development . Similarly, convalescent plasma has shown potential benefit in the treatment of severe influenza, and further trials are underway . Another area of intense interest is the modification of the host antiviral response to influenza virus infection. There are ongoing preclinical and clinical studies of a variety of other immunomodulatory agents for treatment of influenza, including celecoxib , statins, etanercept, pioglitazone, azithromycin , and interferons .", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Although neuraminidase inhibitors are currently recommended for antiviral treatment of influenza in hospitalized patients based on observational studies, including in critically ill patients, there are a number of novel strategies and products for treating influenza in various stages of development. One approach under investigation is triple-combination antiviral drug therapy, which combines amantadine, ribavirin, and oseltamivir for treatment of influenza in critically ill and high-risk patients. Unfortunately, studies to date have not shown a benefit of TCAD over oseltamivir monotherapy . Several novel antiviral compounds are in various stages of investigation, including small-molecule polymerase inhibitors such as pimodivir and favipiravir ." ]

[ [ "1a", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment" ], [ "1b", "Passage: A number of monoclonal and polyclonal antibodies, targeted against a variety of influenza viral proteins, are also in development ." ], [ "1c", "Similarly, convalescent plasma has shown potential benefit in the treatment of severe influenza, and further trials are underway ." ], [ "1d", "Another area of intense interest is the modification of the host antiviral response to influenza virus infection." ], [ "1e", "There are ongoing preclinical and clinical studies of a variety of other immunomodulatory agents for treatment of influenza, including celecoxib , statins, etanercept, pioglitazone, azithromycin , and interferons ." ] ]

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

[ "Title: Recent Advances in the Diagnosis and Treatment of Influenza Pneumonia\nPassage: Annual immunization is the most important preventive measure . However, two classes of antiviral drugs are available and play an important role in the treatment and prevention of influenza : the neuraminidase inhibitors , oseltamivir and zanamivir, which are active against both influenza A and B viruses; and the M2 inhibitors, amantadine and rimantadine, which are active against all influenza A strains, but have no activity against influenza B viruses. In general, the duration for therapy with an NI is 5 days, and with the M2 inhibitors is three to 5 days.", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: A number of monoclonal and polyclonal antibodies, targeted against a variety of influenza viral proteins, are also in development . Similarly, convalescent plasma has shown potential benefit in the treatment of severe influenza, and further trials are underway . Another area of intense interest is the modification of the host antiviral response to influenza virus infection. There are ongoing preclinical and clinical studies of a variety of other immunomodulatory agents for treatment of influenza, including celecoxib , statins, etanercept, pioglitazone, azithromycin , and interferons .", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Although neuraminidase inhibitors are currently recommended for antiviral treatment of influenza in hospitalized patients based on observational studies, including in critically ill patients, there are a number of novel strategies and products for treating influenza in various stages of development. One approach under investigation is triple-combination antiviral drug therapy, which combines amantadine, ribavirin, and oseltamivir for treatment of influenza in critically ill and high-risk patients. Unfortunately, studies to date have not shown a benefit of TCAD over oseltamivir monotherapy . Several novel antiviral compounds are in various stages of investigation, including small-molecule polymerase inhibitors such as pimodivir and favipiravir ." ]

[ [ "2a", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment" ], [ "2b", "Passage: Treatment of severe influenza presents multiple challenges." ], [ "2c", "The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset ." ], [ "2d", "Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes ." ], [ "2e", "NAIs and baloxavir have activity against both influenza A and B viruses." ], [ "2f", "Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses." ], [ "2g", "Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated" ] ]

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

[ "Title: Recent Advances in the Diagnosis and Treatment of Influenza Pneumonia\nPassage: Annual immunization is the most important preventive measure . However, two classes of antiviral drugs are available and play an important role in the treatment and prevention of influenza : the neuraminidase inhibitors , oseltamivir and zanamivir, which are active against both influenza A and B viruses; and the M2 inhibitors, amantadine and rimantadine, which are active against all influenza A strains, but have no activity against influenza B viruses. In general, the duration for therapy with an NI is 5 days, and with the M2 inhibitors is three to 5 days.", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: A number of monoclonal and polyclonal antibodies, targeted against a variety of influenza viral proteins, are also in development . Similarly, convalescent plasma has shown potential benefit in the treatment of severe influenza, and further trials are underway . Another area of intense interest is the modification of the host antiviral response to influenza virus infection. There are ongoing preclinical and clinical studies of a variety of other immunomodulatory agents for treatment of influenza, including celecoxib , statins, etanercept, pioglitazone, azithromycin , and interferons .", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Treatment of severe influenza presents multiple challenges. The mainstay of therapy for patients with influenza is initiation of antiviral medication as soon as possible after illness onset . Currently available FDAapproved antiviral medications include neuraminidase inhibitors ; cap-dependent endonuclease inhibitor ; and adamantanes . NAIs and baloxavir have activity against both influenza A and B viruses. Adamantanes only have activity against influenza A viruses and are not recommended for treatment of influenza due to widespread resistance among currently circulating strains of seasonal influenza A viruses. Notably, FDA-approved antiviral medications for treatment of influenza are approved for early treatment of uncomplicated", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment\nPassage: Although neuraminidase inhibitors are currently recommended for antiviral treatment of influenza in hospitalized patients based on observational studies, including in critically ill patients, there are a number of novel strategies and products for treating influenza in various stages of development. One approach under investigation is triple-combination antiviral drug therapy, which combines amantadine, ribavirin, and oseltamivir for treatment of influenza in critically ill and high-risk patients. Unfortunately, studies to date have not shown a benefit of TCAD over oseltamivir monotherapy . Several novel antiviral compounds are in various stages of investigation, including small-molecule polymerase inhibitors such as pimodivir and favipiravir ." ]

[ [ "3a", "Title: Influenza virus-related critical illness: prevention, diagnosis, treatment" ], [ "3b", "Passage: Although neuraminidase inhibitors are currently recommended for antiviral treatment of influenza in hospitalized patients based on observational studies, including in critically ill patients, there are a number of novel strategies and products for treating influenza in various stages of development." ], [ "3c", "One approach under investigation is triple-combination antiviral drug therapy, which combines amantadine, ribavirin, and oseltamivir for treatment of influenza in critically ill and high-risk patients." ], [ "3d", "Unfortunately, studies to date have not shown a benefit of TCAD over oseltamivir monotherapy ." ], [ "3e", "Several novel antiviral compounds are in various stages of investigation, including small-molecule polymerase inhibitors such as pimodivir and favipiravir ." ] ]

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

[ "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: Influenza vaccination is the primary strategy to prevent influenza-related morbidity and mortality, especially for older adults, who are at higher risk of severe outcomes . In this age group, influenza vaccines are 24-63% effective in preventing laboratory-confirmed influenza . Due to frequent changes in circulating virus strains, annual vaccination is recommended.", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: It remains unclear whether true vaccine interference is occurring from repeated vaccination or whether the differences between studies are an artefact of residual confounding . Individuals may be more inclined to be vaccinated for the first time if they were infected by influenza in the prior season. Vaccine responses may be enhanced with recent prior infection , such that those who were vaccinated repeatedly may appear to have lower VE. However, measuring immunity arising from previous infection is challenging . In addition, while pooling of multiple seasons can increase statistical power, it can mask important variation at the individual season", "Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice\nPassage: Influenza A virus is a seasonal virus which affects 32,000 individuals in the US and 600,000 worldwide each year . Those at most risk from complications include young children, pregnant women, asthma sufferers, immune compromised individuals and the elderly. The elderly account for up to 80% of hospitalisations and 95% of influenza associated mortality . To help reduce these severe outcomes, public health authorities recommend that individuals over 65 should receive yearly influenza vaccination. However, several clinical trials and cohort studies have reported low rates of vaccine efficacy in the elderly, as judged by statistically significant reductions in influenza associated", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: However, the impact of repeated vaccination on vaccine effectiveness is uncertain. A randomised trial conducted in the 1970s at a British boarding school found higher influenza incidence among students who had received multiple previous vaccines than among those who received only the current season's vaccine . Results from a larger RCT among adults in the 1980s did not lead to the same conclusion . Based on the antigenic distance hypothesis put forth by Smith et al., negative or positive interference can result from prior season vaccination depending on differences in the antigenic distances between prior and current vaccine strains and" ]

[ [ "0a", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada" ], [ "0b", "Passage: Influenza vaccination is the primary strategy to prevent influenza-related morbidity and mortality, especially for older adults, who are at higher risk of severe outcomes ." ], [ "0c", "In this age group, influenza vaccines are 24-63% effective in preventing laboratory-confirmed influenza ." ], [ "0d", "Due to frequent changes in circulating virus strains, annual vaccination is recommended." ] ]

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

[ "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: Influenza vaccination is the primary strategy to prevent influenza-related morbidity and mortality, especially for older adults, who are at higher risk of severe outcomes . In this age group, influenza vaccines are 24-63% effective in preventing laboratory-confirmed influenza . Due to frequent changes in circulating virus strains, annual vaccination is recommended.", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: It remains unclear whether true vaccine interference is occurring from repeated vaccination or whether the differences between studies are an artefact of residual confounding . Individuals may be more inclined to be vaccinated for the first time if they were infected by influenza in the prior season. Vaccine responses may be enhanced with recent prior infection , such that those who were vaccinated repeatedly may appear to have lower VE. However, measuring immunity arising from previous infection is challenging . In addition, while pooling of multiple seasons can increase statistical power, it can mask important variation at the individual season", "Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice\nPassage: Influenza A virus is a seasonal virus which affects 32,000 individuals in the US and 600,000 worldwide each year . Those at most risk from complications include young children, pregnant women, asthma sufferers, immune compromised individuals and the elderly. The elderly account for up to 80% of hospitalisations and 95% of influenza associated mortality . To help reduce these severe outcomes, public health authorities recommend that individuals over 65 should receive yearly influenza vaccination. However, several clinical trials and cohort studies have reported low rates of vaccine efficacy in the elderly, as judged by statistically significant reductions in influenza associated", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: However, the impact of repeated vaccination on vaccine effectiveness is uncertain. A randomised trial conducted in the 1970s at a British boarding school found higher influenza incidence among students who had received multiple previous vaccines than among those who received only the current season's vaccine . Results from a larger RCT among adults in the 1980s did not lead to the same conclusion . Based on the antigenic distance hypothesis put forth by Smith et al., negative or positive interference can result from prior season vaccination depending on differences in the antigenic distances between prior and current vaccine strains and" ]

[ [ "1a", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada" ], [ "1b", "Passage: It remains unclear whether true vaccine interference is occurring from repeated vaccination or whether the differences between studies are an artefact of residual confounding ." ], [ "1c", "Individuals may be more inclined to be vaccinated for the first time if they were infected by influenza in the prior season." ], [ "1d", "Vaccine responses may be enhanced with recent prior infection , such that those who were vaccinated repeatedly may appear to have lower VE." ], [ "1e", "However, measuring immunity arising from previous infection is challenging ." ], [ "1f", "In addition, while pooling of multiple seasons can increase statistical power, it can mask important variation at the individual season" ] ]

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

[ "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: Influenza vaccination is the primary strategy to prevent influenza-related morbidity and mortality, especially for older adults, who are at higher risk of severe outcomes . In this age group, influenza vaccines are 24-63% effective in preventing laboratory-confirmed influenza . Due to frequent changes in circulating virus strains, annual vaccination is recommended.", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: It remains unclear whether true vaccine interference is occurring from repeated vaccination or whether the differences between studies are an artefact of residual confounding . Individuals may be more inclined to be vaccinated for the first time if they were infected by influenza in the prior season. Vaccine responses may be enhanced with recent prior infection , such that those who were vaccinated repeatedly may appear to have lower VE. However, measuring immunity arising from previous infection is challenging . In addition, while pooling of multiple seasons can increase statistical power, it can mask important variation at the individual season", "Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice\nPassage: Influenza A virus is a seasonal virus which affects 32,000 individuals in the US and 600,000 worldwide each year . Those at most risk from complications include young children, pregnant women, asthma sufferers, immune compromised individuals and the elderly. The elderly account for up to 80% of hospitalisations and 95% of influenza associated mortality . To help reduce these severe outcomes, public health authorities recommend that individuals over 65 should receive yearly influenza vaccination. However, several clinical trials and cohort studies have reported low rates of vaccine efficacy in the elderly, as judged by statistically significant reductions in influenza associated", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: However, the impact of repeated vaccination on vaccine effectiveness is uncertain. A randomised trial conducted in the 1970s at a British boarding school found higher influenza incidence among students who had received multiple previous vaccines than among those who received only the current season's vaccine . Results from a larger RCT among adults in the 1980s did not lead to the same conclusion . Based on the antigenic distance hypothesis put forth by Smith et al., negative or positive interference can result from prior season vaccination depending on differences in the antigenic distances between prior and current vaccine strains and" ]

[ [ "2a", "Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice" ], [ "2b", "Passage: Influenza A virus is a seasonal virus which affects 32,000 individuals in the US and 600,000 worldwide each year ." ], [ "2c", "Those at most risk from complications include young children, pregnant women, asthma sufferers, immune compromised individuals and the elderly." ], [ "2d", "The elderly account for up to 80% of hospitalisations and 95% of influenza associated mortality ." ], [ "2e", "To help reduce these severe outcomes, public health authorities recommend that individuals over 65 should receive yearly influenza vaccination." ], [ "2f", "However, several clinical trials and cohort studies have reported low rates of vaccine efficacy in the elderly, as judged by statistically significant reductions in influenza associated" ] ]

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

[ "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: Influenza vaccination is the primary strategy to prevent influenza-related morbidity and mortality, especially for older adults, who are at higher risk of severe outcomes . In this age group, influenza vaccines are 24-63% effective in preventing laboratory-confirmed influenza . Due to frequent changes in circulating virus strains, annual vaccination is recommended.", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: It remains unclear whether true vaccine interference is occurring from repeated vaccination or whether the differences between studies are an artefact of residual confounding . Individuals may be more inclined to be vaccinated for the first time if they were infected by influenza in the prior season. Vaccine responses may be enhanced with recent prior infection , such that those who were vaccinated repeatedly may appear to have lower VE. However, measuring immunity arising from previous infection is challenging . In addition, while pooling of multiple seasons can increase statistical power, it can mask important variation at the individual season", "Title: CpG Improves Influenza Vaccine Efficacy in Young Adult but Not Aged Mice\nPassage: Influenza A virus is a seasonal virus which affects 32,000 individuals in the US and 600,000 worldwide each year . Those at most risk from complications include young children, pregnant women, asthma sufferers, immune compromised individuals and the elderly. The elderly account for up to 80% of hospitalisations and 95% of influenza associated mortality . To help reduce these severe outcomes, public health authorities recommend that individuals over 65 should receive yearly influenza vaccination. However, several clinical trials and cohort studies have reported low rates of vaccine efficacy in the elderly, as judged by statistically significant reductions in influenza associated", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada\nPassage: However, the impact of repeated vaccination on vaccine effectiveness is uncertain. A randomised trial conducted in the 1970s at a British boarding school found higher influenza incidence among students who had received multiple previous vaccines than among those who received only the current season's vaccine . Results from a larger RCT among adults in the 1980s did not lead to the same conclusion . Based on the antigenic distance hypothesis put forth by Smith et al., negative or positive interference can result from prior season vaccination depending on differences in the antigenic distances between prior and current vaccine strains and" ]

[ [ "3a", "Title: The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: a test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada" ], [ "3b", "Passage: However, the impact of repeated vaccination on vaccine effectiveness is uncertain." ], [ "3c", "A randomised trial conducted in the 1970s at a British boarding school found higher influenza incidence among students who had received multiple previous vaccines than among those who received only the current season's vaccine ." ], [ "3d", "Results from a larger RCT among adults in the 1980s did not lead to the same conclusion ." ], [ "3e", "Based on the antigenic distance hypothesis put forth by Smith et al., negative or positive interference can result from prior season vaccination depending on differences in the antigenic distances between prior and current vaccine strains and" ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly" ]

[ [ "0a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "0b", "Passage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy." ], [ "0c", "Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations." ], [ "0d", "For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes ." ], [ "0e", "Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development." ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy. Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations. For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes . Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Although our understanding of the immune response against the filamentous phage pales in comparison to classical model antigens such as ovalbumin, recent work has begun to shed light on the immune mechanisms activated in response to phage vaccination . The phage particle is immunogenic without adjuvant in all species tested to date, including mice , rats , rabbits , guinea pigs , fish , non-human primates , and humans . Various routes of immunization have been employed, including oral administration as well as subcutaneous , intraperitoneal , intramuscular , intravenous , and intradermal injection ; no published study has directly" ]

[ [ "1a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "1b", "Passage: an anti-IgE antibody elicited antibodies that bound purified IgE molecules , which may be useful in allergy immunotherapy." ], [ "1c", "Several strategies for phage-based contraceptive vaccines have been proposed for control of animal populations." ], [ "1d", "For example, immunization with phage displaying follicle-stimulating hormone peptides on pVIII elicited antibodies that impaired the fertility of mice and ewes ." ], [ "1e", "Phage displaying or chemically Rubinchik and Chow conjugated to sperm antigen peptides or peptide mimics and gonadotropin-releasing hormone are also in development." ] ]

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

[ "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: The recent SARS epidemic vividly demonstrates how the economic infrastructure and dense population of Asia facilitate the rapid international spread of disease. The combination of large primate reservoirs, prevalent humanprimate contact, a growing immunocompromised population, and advanced infrastructure in Asia increases the likelihood of a primateborne zoonosis emerging on this continent.", "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: than any other context.", "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: mucosal splashes with saliva from primates are likely mechanisms of transmission .", "Title: Transmission Potential of Chikungunya Virus and Control Measures: The Case of Italy\nPassage: the generation interval probability distribution function and the number of gonotrophic cycles of the mosquito. This method can not be applied in our study, as the undertaken control measures have contributed to alter the gonotrophic cycles of the mosquito in a indeterminable manner. We found that the probability of observing a major outbreak after the introduction of an index case depends on the ratio of mosquitoes to humans and was estimated to be in the range of 32%-76%. These results confirm the high risk to Europe of tropical vector-borne diseases as a consequence of globalization, which has been modifying the" ]

[ [ "0a", "Title: Primate-to-Human Retroviral Transmission in Asia" ], [ "0b", "Passage: The recent SARS epidemic vividly demonstrates how the economic infrastructure and dense population of Asia facilitate the rapid international spread of disease." ], [ "0c", "The combination of large primate reservoirs, prevalent humanprimate contact, a growing immunocompromised population, and advanced infrastructure in Asia increases the likelihood of a primateborne zoonosis emerging on this continent." ] ]

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

[ "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: The recent SARS epidemic vividly demonstrates how the economic infrastructure and dense population of Asia facilitate the rapid international spread of disease. The combination of large primate reservoirs, prevalent humanprimate contact, a growing immunocompromised population, and advanced infrastructure in Asia increases the likelihood of a primateborne zoonosis emerging on this continent.", "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: than any other context.", "Title: Primate-to-Human Retroviral Transmission in Asia\nPassage: mucosal splashes with saliva from primates are likely mechanisms of transmission .", "Title: Transmission Potential of Chikungunya Virus and Control Measures: The Case of Italy\nPassage: the generation interval probability distribution function and the number of gonotrophic cycles of the mosquito. This method can not be applied in our study, as the undertaken control measures have contributed to alter the gonotrophic cycles of the mosquito in a indeterminable manner. We found that the probability of observing a major outbreak after the introduction of an index case depends on the ratio of mosquitoes to humans and was estimated to be in the range of 32%-76%. These results confirm the high risk to Europe of tropical vector-borne diseases as a consequence of globalization, which has been modifying the" ]

[ [ "2a", "Title: Primate-to-Human Retroviral Transmission in Asia" ], [ "2b", "Passage: mucosal splashes with saliva from primates are likely mechanisms of transmission ." ] ]

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