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[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host . Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells . In our study, the only patient who recovered from severe infection had higher T-cell counts. Three of the five patients had relatively low T-cell counts when admitted. Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host . Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells . In our study, the only patient who recovered from severe infection had higher T-cell counts. Three of the five patients had relatively low T-cell counts when admitted. Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk", "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: Laboratory findings for the HAdV-7-positive inpatients were also significantly different from those infected by HAdV-3 . Specifically, the HAdV-7-positive inpatients had lower white blood cell count , platelet count . In contrast, hemoglobin and C-reactive protein levels, and the percentages of lymphocytes, neutrophils and positive sputum culture were found to be statistically similar.", "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: Imaging and laboratory data on admission and during hospitalization were collected. White blood cell count > 15,000/ μL was defined as leukocytosis, whereas that < 4000/μL was defined as leukopenia." ]

[ [ "0a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "0b", "Passage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host ." ], [ "0c", "Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells ." ], [ "0d", "In our study, the only patient who recovered from severe infection had higher T-cell counts." ], [ "0e", "Three of the five patients had relatively low T-cell counts when admitted." ], [ "0f", "Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk" ] ]

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

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host . Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells . In our study, the only patient who recovered from severe infection had higher T-cell counts. Three of the five patients had relatively low T-cell counts when admitted. Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host . Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells . In our study, the only patient who recovered from severe infection had higher T-cell counts. Three of the five patients had relatively low T-cell counts when admitted. Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk", "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: Laboratory findings for the HAdV-7-positive inpatients were also significantly different from those infected by HAdV-3 . Specifically, the HAdV-7-positive inpatients had lower white blood cell count , platelet count . In contrast, hemoglobin and C-reactive protein levels, and the percentages of lymphocytes, neutrophils and positive sputum culture were found to be statistically similar.", "Title: Human adenovirus type 7 infection causes a more severe disease than type 3\nPassage: Imaging and laboratory data on admission and during hospitalization were collected. White blood cell count > 15,000/ μL was defined as leukocytosis, whereas that < 4000/μL was defined as leukopenia." ]

[ [ "1a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "1b", "Passage: Recent studies have shown that the immune system plays a crucial role in the clearance of HAdV viremia and survival of the host ." ], [ "1c", "Chen et al. reported that, in the acute phase of HAdV-55 infection, patients with severe disease may have high levels of dendritic cells and Th17 cells ." ], [ "1d", "In our study, the only patient who recovered from severe infection had higher T-cell counts." ], [ "1e", "Three of the five patients had relatively low T-cell counts when admitted." ], [ "1f", "Our results suggest that these three patients may have been relatively immunocompromised and that a lower T-cell count may be a risk" ] ]

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

[ "Title: Gene Knockdowns in Adult Animals: PPMOs and Vivo-Morpholinos\nPassage: Global Therapeutics, the cardiology unit of Cook Medical , is developing PPMO-coated stents for balloon angioplasty using PPMOs from AVI BioPharma Inc. The Morpholino moiety targets c-myc to inhibit proliferation of the vascular endothelial cells, which might otherwise cause restenosis.", "Title: Gene Knockdowns in Adult Animals: PPMOs and Vivo-Morpholinos\nPassage: Typically the highest antiviral efficacies are achieved with pre-infection administration of the PPMO followed by a series of post-infection doses. Recent studies explicitly comparing effects of unmodified Morpholino oligos and PPMOs show that the PPMOs are far more effective in vivo. Viral applications of PPMOs have recently been reviewed so only a few recent papers applying PPMOs to inhibit viruses will be considered here.", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles\nPassage: To assess the replication efficiency of the different vectors, multi-step growth kinetics of cell-associated and released virus were performed following infection at low MOI = 0.03 . Compared to the GFP-encoding control virus MV vac2 -GFP, MVs encompassing the DisOva transgene cassette together with or without MLV gag grew with similar kinetics and reached similar maximum titers as the control virus. Thus, cloning and rescue of both MVs-derived vectors resulted in expression of the inserted antigen in infected cells without impact on viral replication or genetic stability. Antigen-specific cellular immunity against vector and transgene is induced by Ova-presenting MV. To", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles\nPassage: Generation and characterization of recombinant MV vac2 encoding different forms of the Ovaantigen. To was chosen since especially the cellular immune-responses and respective immune-dominant peptides in mice such as used in our studies are well known and can thus considerably support characterization of such responses. For this purpose, Ova was genetically fused to the transmembrane domain of the platelet-derived growth factor receptor giving rise to a membrane-bound extracellular variant that should be readily incorporated into retroviral particles . A recombinant MV encoding DisOva in an additional transcription unit following the P gene in combination with a second, MLV Gag-encoding transgene" ]

[ [ "2a", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles" ], [ "2b", "Passage: To assess the replication efficiency of the different vectors, multi-step growth kinetics of cell-associated and released virus were performed following infection at low MOI = 0.03 ." ], [ "2c", "Compared to the GFP-encoding control virus MV vac2 -GFP, MVs encompassing the DisOva transgene cassette together with or without MLV gag grew with similar kinetics and reached similar maximum titers as the control virus." ], [ "2d", "Thus, cloning and rescue of both MVs-derived vectors resulted in expression of the inserted antigen in infected cells without impact on viral replication or genetic stability." ], [ "2e", "Antigen-specific cellular immunity against vector and transgene is induced by Ova-presenting MV. To" ] ]

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

[ "Title: Gene Knockdowns in Adult Animals: PPMOs and Vivo-Morpholinos\nPassage: Global Therapeutics, the cardiology unit of Cook Medical , is developing PPMO-coated stents for balloon angioplasty using PPMOs from AVI BioPharma Inc. The Morpholino moiety targets c-myc to inhibit proliferation of the vascular endothelial cells, which might otherwise cause restenosis.", "Title: Gene Knockdowns in Adult Animals: PPMOs and Vivo-Morpholinos\nPassage: Typically the highest antiviral efficacies are achieved with pre-infection administration of the PPMO followed by a series of post-infection doses. Recent studies explicitly comparing effects of unmodified Morpholino oligos and PPMOs show that the PPMOs are far more effective in vivo. Viral applications of PPMOs have recently been reviewed so only a few recent papers applying PPMOs to inhibit viruses will be considered here.", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles\nPassage: To assess the replication efficiency of the different vectors, multi-step growth kinetics of cell-associated and released virus were performed following infection at low MOI = 0.03 . Compared to the GFP-encoding control virus MV vac2 -GFP, MVs encompassing the DisOva transgene cassette together with or without MLV gag grew with similar kinetics and reached similar maximum titers as the control virus. Thus, cloning and rescue of both MVs-derived vectors resulted in expression of the inserted antigen in infected cells without impact on viral replication or genetic stability. Antigen-specific cellular immunity against vector and transgene is induced by Ova-presenting MV. To", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles\nPassage: Generation and characterization of recombinant MV vac2 encoding different forms of the Ovaantigen. To was chosen since especially the cellular immune-responses and respective immune-dominant peptides in mice such as used in our studies are well known and can thus considerably support characterization of such responses. For this purpose, Ova was genetically fused to the transmembrane domain of the platelet-derived growth factor receptor giving rise to a membrane-bound extracellular variant that should be readily incorporated into retroviral particles . A recombinant MV encoding DisOva in an additional transcription unit following the P gene in combination with a second, MLV Gag-encoding transgene" ]

[ [ "3a", "Title: Antigen-specific oncolytic MV-based tumor vaccines through presentation of selected tumor-associated antigens on infected cells or virus-like particles" ], [ "3b", "Passage: Generation and characterization of recombinant MV vac2 encoding different forms of the Ovaantigen." ], [ "3c", "To was chosen since especially the cellular immune-responses and respective immune-dominant peptides in mice such as used in our studies are well known and can thus considerably support characterization of such responses." ], [ "3d", "For this purpose, Ova was genetically fused to the transmembrane domain of the platelet-derived growth factor receptor giving rise to a membrane-bound extracellular variant that should be readily incorporated into retroviral particles ." ], [ "3e", "A recombinant MV encoding DisOva in an additional transcription unit following the P gene in combination with a second, MLV Gag-encoding transgene" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: for human sero-surveys. These relied on MERS-CoV-infected cell culture as an antigen source, detecting the presence of human anti-MERS-CoV IgG, IgM or neutralizing antibodies in human samples . No sign of MERS-CoV antibodies was found among 2,400 sera from patients visiting Hospital in Jeddah, from 2010 through 2012, prior to the description of MERS-CoV . Nor did IFA methods detect any sign of prior MERS-CoV infection among a small sample of 130 healthy blood donors from another Hospital in Jeddah . Of 226 slaughterhouse workers, only eight were positive by IFA, and those sera could not be confirmed by virus", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Strategic, widespread sero-surveys of humans using samples collected after 2012 are infrequent. Much of the Arabian Peninsula and all of the Horn of Africa lack baseline data describing the proportion of the community who may have been infected by a MERS-CoV. However, sero-surveys have had widespread use in elucidating the role of DCs as a transmission source for MERS-CoV. Because of the identity shared between DC and human MERS-CoV , serological assays for DC sero-surveys should be transferrable to human screening with minimal re-configuration. Also, no diagnostically relevant variation in neutralization activity have been found from among a range of", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: human sera, a tiered diagnostic process assigned both recombinant IFA and recombinant ELISA positive sera to 'stage 1' seropositivity. A stage 2 seropositive result additionally required a suitably titred PRNT result . The study found 15 sera collected in 2012 to 2013 from 10,009 people in 13 KSA provinces contained MERS-CoV antibodies, but significantly higher proportions in occurred in camel shepherds and slaughterhouse workers . Contemporary surveys are needed.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first sero-survey of livestock living in the Middle East region was conducted during 2012-2013 . DCs were sampled from a mostly Canary Island-born herd and from Omani DCs . A neutralising antibody assay found only 10 % of strongly seropositive Canary Island . b Camel-to-human infections appear to be infrequent, while human-to-human spread of infection is regularly facilitated by poor IPC in healthcare settings where transmission is amplified, accounting for the bulk of cases. There are human MERS cases that do not fall into either category of source and it is unclear if these acquired infection through some entirely" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: for human sero-surveys." ], [ "0c", "These relied on MERS-CoV-infected cell culture as an antigen source, detecting the presence of human anti-MERS-CoV IgG, IgM or neutralizing antibodies in human samples ." ], [ "0d", "No sign of MERS-CoV antibodies was found among 2,400 sera from patients visiting Hospital in Jeddah, from 2010 through 2012, prior to the description of MERS-CoV ." ], [ "0e", "Nor did IFA methods detect any sign of prior MERS-CoV infection among a small sample of 130 healthy blood donors from another Hospital in Jeddah ." ], [ "0f", "Of 226 slaughterhouse workers, only eight were positive by IFA, and those sera could not be confirmed by virus" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: for human sero-surveys. These relied on MERS-CoV-infected cell culture as an antigen source, detecting the presence of human anti-MERS-CoV IgG, IgM or neutralizing antibodies in human samples . No sign of MERS-CoV antibodies was found among 2,400 sera from patients visiting Hospital in Jeddah, from 2010 through 2012, prior to the description of MERS-CoV . Nor did IFA methods detect any sign of prior MERS-CoV infection among a small sample of 130 healthy blood donors from another Hospital in Jeddah . Of 226 slaughterhouse workers, only eight were positive by IFA, and those sera could not be confirmed by virus", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Strategic, widespread sero-surveys of humans using samples collected after 2012 are infrequent. Much of the Arabian Peninsula and all of the Horn of Africa lack baseline data describing the proportion of the community who may have been infected by a MERS-CoV. However, sero-surveys have had widespread use in elucidating the role of DCs as a transmission source for MERS-CoV. Because of the identity shared between DC and human MERS-CoV , serological assays for DC sero-surveys should be transferrable to human screening with minimal re-configuration. Also, no diagnostically relevant variation in neutralization activity have been found from among a range of", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: human sera, a tiered diagnostic process assigned both recombinant IFA and recombinant ELISA positive sera to 'stage 1' seropositivity. A stage 2 seropositive result additionally required a suitably titred PRNT result . The study found 15 sera collected in 2012 to 2013 from 10,009 people in 13 KSA provinces contained MERS-CoV antibodies, but significantly higher proportions in occurred in camel shepherds and slaughterhouse workers . Contemporary surveys are needed.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first sero-survey of livestock living in the Middle East region was conducted during 2012-2013 . DCs were sampled from a mostly Canary Island-born herd and from Omani DCs . A neutralising antibody assay found only 10 % of strongly seropositive Canary Island . b Camel-to-human infections appear to be infrequent, while human-to-human spread of infection is regularly facilitated by poor IPC in healthcare settings where transmission is amplified, accounting for the bulk of cases. There are human MERS cases that do not fall into either category of source and it is unclear if these acquired infection through some entirely" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: human sera, a tiered diagnostic process assigned both recombinant IFA and recombinant ELISA positive sera to 'stage 1' seropositivity." ], [ "2c", "A stage 2 seropositive result additionally required a suitably titred PRNT result ." ], [ "2d", "The study found 15 sera collected in 2012 to 2013 from 10,009 people in 13 KSA provinces contained MERS-CoV antibodies, but significantly higher proportions in occurred in camel shepherds and slaughterhouse workers ." ], [ "2e", "Contemporary surveys are needed." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: for human sero-surveys. These relied on MERS-CoV-infected cell culture as an antigen source, detecting the presence of human anti-MERS-CoV IgG, IgM or neutralizing antibodies in human samples . No sign of MERS-CoV antibodies was found among 2,400 sera from patients visiting Hospital in Jeddah, from 2010 through 2012, prior to the description of MERS-CoV . Nor did IFA methods detect any sign of prior MERS-CoV infection among a small sample of 130 healthy blood donors from another Hospital in Jeddah . Of 226 slaughterhouse workers, only eight were positive by IFA, and those sera could not be confirmed by virus", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Strategic, widespread sero-surveys of humans using samples collected after 2012 are infrequent. Much of the Arabian Peninsula and all of the Horn of Africa lack baseline data describing the proportion of the community who may have been infected by a MERS-CoV. However, sero-surveys have had widespread use in elucidating the role of DCs as a transmission source for MERS-CoV. Because of the identity shared between DC and human MERS-CoV , serological assays for DC sero-surveys should be transferrable to human screening with minimal re-configuration. Also, no diagnostically relevant variation in neutralization activity have been found from among a range of", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: human sera, a tiered diagnostic process assigned both recombinant IFA and recombinant ELISA positive sera to 'stage 1' seropositivity. A stage 2 seropositive result additionally required a suitably titred PRNT result . The study found 15 sera collected in 2012 to 2013 from 10,009 people in 13 KSA provinces contained MERS-CoV antibodies, but significantly higher proportions in occurred in camel shepherds and slaughterhouse workers . Contemporary surveys are needed.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first sero-survey of livestock living in the Middle East region was conducted during 2012-2013 . DCs were sampled from a mostly Canary Island-born herd and from Omani DCs . A neutralising antibody assay found only 10 % of strongly seropositive Canary Island . b Camel-to-human infections appear to be infrequent, while human-to-human spread of infection is regularly facilitated by poor IPC in healthcare settings where transmission is amplified, accounting for the bulk of cases. There are human MERS cases that do not fall into either category of source and it is unclear if these acquired infection through some entirely" ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: The first sero-survey of livestock living in the Middle East region was conducted during 2012-2013 ." ], [ "3c", "DCs were sampled from a mostly Canary Island-born herd and from Omani DCs ." ], [ "3d", "A neutralising antibody assay found only 10 % of strongly seropositive Canary Island ." ], [ "3e", "b Camel-to-human infections appear to be infrequent, while human-to-human spread of infection is regularly facilitated by poor IPC in healthcare settings where transmission is amplified, accounting for the bulk of cases." ], [ "3f", "There are human MERS cases that do not fall into either category of source and it is unclear if these acquired infection through some entirely" ] ]

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

[ "Title: Kinome-Wide siRNA Screening Identifies Src-Enhanced Resistance of Chemotherapeutic Drugs in Triple-Negative Breast Cancer Cells\nPassage: MDA-MB-231 and Hs578T cells were seeded at density of 2 × 10 4 in NanoCulture plates in the presence of 10 nM siRNA. The cells were cultured for 3 days until tumorsphere formation. The tumorsphere were then treated with anticancer drugs for 48 h and stained with Calcein AM and Ethidium homodimer-1 for live and dead cell population, respectively. The cells treated with or without 70% methanol for 30 min were considered as a relative control for all dead or live cells. The live and dead cells were then observed under microscopy and quantitated with Fluoroskan Ascent FL reader as", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: The generation of MDMs has been described in previous studies . Briefly, PBMCs were isolated from human whole blood by density-gradient centrifugation over Histopaque . Monocytes were purified using human CD14-specific microbeads following manufacturer's instructions. CD14 + monocytes were differentiated into MDMs by culturing for 6-7 days with recombinant human macrophage colony-stimulating factor and conditioned medium from KPB-M15 cells . Media were replaced every 2-3 days during the incubation for a total of 6-7 days. The cells were harvested and plated on desired 96-well plates 1 day prior to the drug screen assay. The differentiated MDMs were characterized by flow", "Title: Novel prostate cancer immunotherapy with a DNA-encoded anti-prostate-specific membrane antigen monoclonal antibody\nPassage: To detect cell surface PSMA, tubes of 1.0 × 10 6 LNCaP or TRAMP-C2 cells were washed with phosphate-buffered saline , stained with live/dead fixable violet dead cell stain for 15 min, and then washed twice with FACS buffer . Cells were next incubated for 30 min at room temperature with a 1:4 dilution of day 14 sera from PSMA-DMAb plasmid-injected mice and then washed. Finally, cells were incubated in the dark for 30 min with a 1:100 dilution of PE-conjugated anti-human Fc IgG , followed by a final wash with FACS buffer. Samples were resuspended in 1× stabilizing fixative", "Title: Evaluation of Ultra-Microscopic Changes and Proliferation of Apoptotic Glioblastoma Multiforme Cells Induced by Velogenic Strain of Newcastle Disease Virus AF2240\nPassage: Acridine Orange Double staining DBTRG .05MG cells were stained using propidium iodide and acridine-orange double staining according to standard procedures and examine under a fluorescence microscope N . DBTRG .05MG cells were seeded in 6-well plate and incubated at 37 o C in 5%CO 2 atmosphere. Twenty-four hours later, the medium in each well was removed and replaced with NDV at IC 50 concentration dissolved in the culture medium and incubated at 37 o C in 5%CO 2 atmosphere for 72 hours. After the incubation period, detached cells in the medium were collected and added back to trypsinised adherent cells." ]

[ [ "0a", "Title: Kinome-Wide siRNA Screening Identifies Src-Enhanced Resistance of Chemotherapeutic Drugs in Triple-Negative Breast Cancer Cells" ], [ "0b", "Passage: MDA-MB-231 and Hs578T cells were seeded at density of 2 × 10 4 in NanoCulture plates in the presence of 10 nM siRNA." ], [ "0c", "The cells were cultured for 3 days until tumorsphere formation." ], [ "0d", "The tumorsphere were then treated with anticancer drugs for 48 h and stained with Calcein AM and Ethidium homodimer-1 for live and dead cell population, respectively." ], [ "0e", "The cells treated with or without 70% methanol for 30 min were considered as a relative control for all dead or live cells." ], [ "0f", "The live and dead cells were then observed under microscopy and quantitated with Fluoroskan Ascent FL reader as" ] ]

[ "0a", "0d" ]

[ "Title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009\nPassage: the population of Reunion Island and a Chi2 test was used to analyse differences in age, sex and geographic location. Cumulative incidence rates of infection and seroconversion rates were standardized according to the age structure of the community source).", "Title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009\nPassage: Based on clinical cases reported to the epidemiological surveillance services , it was estimated that 66,915 persons in Reunion Island who consulted a physician were infected by the pH1N1/2009 virus during the 9 weeks of the epidemic, giving a cumulative attack rate of 8.26%. Taking into account those who did not consult a physician, the number of symptomatic infected persons was estimated to 104,067 . In fact, the attack rate of pH1N1/2009 infection in our serosurvey was about 42%-44% at the peak of the antibody response , a figure which is at least 3 to 4 times higher than rates", "Title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009\nPassage: Reunion Island is a French overseas department located in the southwestern Indian Ocean, 700 km east of Madagascar and 200 km southwest of Mauritius. The first imported case of pH1N1/2009v was identified on 5 th July 2009 in a traveller returning from Australia. The first case indicating community transmission was detected on 21 st July . pH1N1/2009v became the predominant circulating influenza virus within four weeks of its first detection, its activity peaked during week 35 and ended at week 38 . Contrary to initial fears, the health care system was not overwhelmed, as morbidity and mortality rates were lower", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012\nPassage: Réunion Island, a French overseas territory with 850,000 inhabitants, is located in the southern hemisphere between Madagascar and Mauritius in the Indian Ocean . The island benefits from a healthcare system similar to mainland France and epidemiological surveillance has been developed by the regional office of the French Institute for Public Health Surveillance , based on the surveillance system of mainland France . Influenza activity generally increases during austral winter, corresponding to summer in Europe . Since 2011, influenza vaccination campaign in Reunion Island starts in April and the vaccine used corresponds to World Health Organization recommendations for the southern" ]

[ [ "3a", "Title: Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012" ], [ "3b", "Passage: Réunion Island, a French overseas territory with 850,000 inhabitants, is located in the southern hemisphere between Madagascar and Mauritius in the Indian Ocean ." ], [ "3c", "The island benefits from a healthcare system similar to mainland France and epidemiological surveillance has been developed by the regional office of the French Institute for Public Health Surveillance , based on the surveillance system of mainland France ." ], [ "3d", "Influenza activity generally increases during austral winter, corresponding to summer in Europe ." ], [ "3e", "Since 2011, influenza vaccination campaign in Reunion Island starts in April and the vaccine used corresponds to World Health Organization recommendations for the southern" ] ]

[ "3b" ]

[ "Title: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification\nPassage: All consensus genome assemblies generated as part of this project were submitted to NCBI's GenBank database . Illumina read data was submitted to NCBI's Short Read Archive under Trace Identifiers SRR513075, SRR513078, SRR513080, SRR513086-87, SRR513092, and SRR527699-726.", "Title: Generation and comparative genomics of synthetic dengue viruses\nPassage: Three DENV cDNA samples were sequenced and analyzed: one of the samples was the wildtype strain, with the WT sequence used as a reference genome for NGS analysis. The two synthetic variants of the virus were synthesized using two different methods . The WT sequence can be found in Additional file 1, section 8. Sequencing libraries were prepared using the INCPM DNA-seq protocol, and sequenced 2 × 150 on an Illumina MiSeq nano v2 PE150. Sequenced reads were mapped to a reference genome using BWA MEM v0.75 . Among all read-pairs with the same alignment, a single representative read was", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study\nPassage: Purified PCR products were sequenced directly. Primer sequences are available upon request. The sequencing reaction was performed by ABI PRISM ® BigDye™ Terminators v3.1 Cycle Sequencing Kit as described previously . The sequences were developed on an automatic ABI PRISM ® 3130 genetic analyzer with 80 cm capillaries. Consensus sequences were generated in SeqScape ® Software v2.5 . Sequence assembly, multiple alignment and alignment trimming were performed with the BioEdit software v.7.0.5 . Distance based neighbor joining phylogenetic trees and character based maximum parsimony trees were generated using the Molecular Evolutionary Genetics Analysis software v.3.1 . Maximum likelihood trees were", "Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers\nPassage: Ultimately, the data set consisted of 686 DNA and RNA libraries, for which 2ˆ100 bp paired end sequencing was performed using the Illumina HiSeq 2000 platform at BGI-Europe, Copenhagen, Denmark. The 686 sequencing libraries thus originated from 252 different cancer samples, 32 non-template controls, and 24 exogenous controls. The distribution of methods, libraries and controls for each sample type is provided in Table S2 . Samples were preferably analysed with multiple methods, thus 165 out of 252 samples were analysed with more than one laboratory method ." ]

[ [ "0a", "Title: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification" ], [ "0b", "Passage: All consensus genome assemblies generated as part of this project were submitted to NCBI's GenBank database ." ], [ "0c", "Illumina read data was submitted to NCBI's Short Read Archive under Trace Identifiers SRR513075, SRR513078, SRR513080, SRR513086-87, SRR513092, and SRR527699-726." ] ]

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

[ "Title: Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification\nPassage: All consensus genome assemblies generated as part of this project were submitted to NCBI's GenBank database . Illumina read data was submitted to NCBI's Short Read Archive under Trace Identifiers SRR513075, SRR513078, SRR513080, SRR513086-87, SRR513092, and SRR527699-726.", "Title: Generation and comparative genomics of synthetic dengue viruses\nPassage: Three DENV cDNA samples were sequenced and analyzed: one of the samples was the wildtype strain, with the WT sequence used as a reference genome for NGS analysis. The two synthetic variants of the virus were synthesized using two different methods . The WT sequence can be found in Additional file 1, section 8. Sequencing libraries were prepared using the INCPM DNA-seq protocol, and sequenced 2 × 150 on an Illumina MiSeq nano v2 PE150. Sequenced reads were mapped to a reference genome using BWA MEM v0.75 . Among all read-pairs with the same alignment, a single representative read was", "Title: The evolution of human influenza A viruses from 1999 to 2006: A complete genome study\nPassage: Purified PCR products were sequenced directly. Primer sequences are available upon request. The sequencing reaction was performed by ABI PRISM ® BigDye™ Terminators v3.1 Cycle Sequencing Kit as described previously . The sequences were developed on an automatic ABI PRISM ® 3130 genetic analyzer with 80 cm capillaries. Consensus sequences were generated in SeqScape ® Software v2.5 . Sequence assembly, multiple alignment and alignment trimming were performed with the BioEdit software v.7.0.5 . Distance based neighbor joining phylogenetic trees and character based maximum parsimony trees were generated using the Molecular Evolutionary Genetics Analysis software v.3.1 . Maximum likelihood trees were", "Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers\nPassage: Ultimately, the data set consisted of 686 DNA and RNA libraries, for which 2ˆ100 bp paired end sequencing was performed using the Illumina HiSeq 2000 platform at BGI-Europe, Copenhagen, Denmark. The 686 sequencing libraries thus originated from 252 different cancer samples, 32 non-template controls, and 24 exogenous controls. The distribution of methods, libraries and controls for each sample type is provided in Table S2 . Samples were preferably analysed with multiple methods, thus 165 out of 252 samples were analysed with more than one laboratory method ." ]

[ [ "1a", "Title: Generation and comparative genomics of synthetic dengue viruses" ], [ "1b", "Passage: Three DENV cDNA samples were sequenced and analyzed: one of the samples was the wildtype strain, with the WT sequence used as a reference genome for NGS analysis." ], [ "1c", "The two synthetic variants of the virus were synthesized using two different methods ." ], [ "1d", "The WT sequence can be found in Additional file 1, section 8." ], [ "1e", "Sequencing libraries were prepared using the INCPM DNA-seq protocol, and sequenced 2 × 150 on an Illumina MiSeq nano v2 PE150." ], [ "1f", "Sequenced reads were mapped to a reference genome using BWA MEM v0.75 ." ], [ "1g", "Among all read-pairs with the same alignment, a single representative read was" ] ]

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

[ "Title: Asymmetry in the Presence of Migration Stabilizes Multistrain Disease Outbreaks\nPassage: Finally, the work discussed here shows a potential effect of human movement between heterogeneous regions. As spatial effects are further studied in epidemic models, it remains to be seen how this phenomenon will extend to more complicated spatial geometries, including more patches and perhaps non-symmetric coupling terms. This work represents a first step towards understanding the role of migration and spatial heterogeneity in dynamical properties of dengue observed in epidemiological data, such as traveling waves of infection in Thailand . Furthermore, because the migration-induced stabilization depends only on the existence of a Hopf bifurcation in the model, it is expected", "Title: Asymmetry in the Presence of Migration Stabilizes Multistrain Disease Outbreaks\nPassage: Bifurcations from steady state to oscillatory behavior can be associated with an increased number of infection cases, particularly if chaotic oscillations occur, as in previous dengue models . Our results suggest that if control strategies in one region are able to generate enough asymmetry, this could lead to a stabilization of the outbreaks, which would have a positive effect on adjacent regions. Asymmetry could be generated in the effective contact rate by mosquito control, which could include reducing mosquito breeding sites , or through new genetic controls which are under development . Asymmetry in the birth rate could be generated", "Title: Asymmetry in the Presence of Migration Stabilizes Multistrain Disease Outbreaks\nPassage: To motivate this result, we diffusively coupled two low dimensional Hopf bifurcations with different characteristic frequencies and analyzed the stability of the steady state. We again saw that coupling between asymmetric systems led to stabilization. This indicates that the stabilization in the epidemic model is a result of the underlying dynamics, rather than the details of the model. We suggest that the stabilization may occur as a result of the two different coupled frequencies generating oscillations that tend to cancel each other because of phase differences. This topic will be studied in more detail in a future work.", "Title: Globalization and emerging governance modalities\nPassage: cannot afford grain. Structural inequalities coupled with civil unrest already produce widespread hunger, malnourishment and famine. An environmental disaster in a large population, most obviously China or India, could have devastating effects within the world system. This, of course, is the great fear environmentalists have for dependence on mono-cropping, species loss, and water management 5 ." ]

[ [ "3a", "Title: Globalization and emerging governance modalities" ], [ "3b", "Passage: cannot afford grain." ], [ "3c", "Structural inequalities coupled with civil unrest already produce widespread hunger, malnourishment and famine." ], [ "3d", "An environmental disaster in a large population, most obviously China or India, could have devastating effects within the world system." ], [ "3e", "This, of course, is the great fear environmentalists have for dependence on mono-cropping, species loss, and water management 5 ." ] ]

[ "3a", "3c" ]

[ "Title: Neutralization Interfering Antibodies: A “Novel” Example of Humoral Immune Dysfunction Facilitating Viral Escape?\nPassage: The S protein of CoVs is inserted in the envelope of the virion mediating binding and fusion events necessary for infection, and it is the major target of the humoral protective immunity . Although the S protein of SARS-CoV shares little aminoacid identity , it shares common structural features with S proteins of the other members of the Coronaviridae family. SARS-S protein is a type I transmembrane glycoprotein of approximately 1,255 amino acids in length and divided into two functional domains: S1 and S2 . In many CoVs, the S protein is cleaved during biogenesis and these two functional domains", "Title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome\nPassage: Previous studies demonstrated that the N-terminal 40 amino acids of the SARS-CoV E protein are important for ion channel formation, and that mutations N15A and V25F ] prevent ion conductivity . In addition, the SARS-CoV 3a protein contains a cysteine-rich domain that is involved in the formation of a homodimer to generate the ion channel . Thus, mutation of the cysteine-rich domain blocks the ion conductivity by the 3a protein . To this end, we substituted amino acids Cys-127, Cys-130, and Cys-133 within the cysteine-rich domain of the SARS-CoV 3a protein with serine to generate a lentivirus expressing the ion", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Spike glycoprotein comprised of S1 and S2 subunits. The S1 subunit contains a signal peptide, followed by an N-terminal domain and receptor-binding domain , while the S2 subunit contains conserved fusion peptide , heptad repeat 1 and 2, transmembrane domain , and cytoplasmic domain . We found that the S2 subunit of 2019-nCoV is highly conserved and shares 99% identity with those of the two bat SARS-like CoVs and human SARS-CoV . Thus the broad spectrum antiviral peptides against S2 would be an important preventive and treatment modality for testing in animal models before clinical trials . Though the S1", "Title: Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides\nPassage: with the potential for the highest in situ binding affinities. These correspond to DENV-2 strain S1 E protein amino acids 41-60, 131-150, 251-270, and 351-370 that were selected for synthesis and antiviral testing ." ]

[ [ "1a", "Title: Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the NLRP3 Inflammasome" ], [ "1b", "Passage: Previous studies demonstrated that the N-terminal 40 amino acids of the SARS-CoV E protein are important for ion channel formation, and that mutations N15A and V25F ] prevent ion conductivity ." ], [ "1c", "In addition, the SARS-CoV 3a protein contains a cysteine-rich domain that is involved in the formation of a homodimer to generate the ion channel ." ], [ "1d", "Thus, mutation of the cysteine-rich domain blocks the ion conductivity by the 3a protein ." ], [ "1e", "To this end, we substituted amino acids Cys-127, Cys-130, and Cys-133 within the cysteine-rich domain of the SARS-CoV 3a protein with serine to generate a lentivirus expressing the ion" ] ]

[ "1b" ]

[ "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial reproduction rate across all 51 outbreaks was 2 with a range of 0 to 38 . About half had an initial R of 1 or less, and over two-thirds had an initial R of 3 or less. The median duration, as measured by number of generations, was 1 with a range of 0 to 9 . About a third did not extend beyond the index generation, and nearly three quarters lasted for 3 or fewer generations. The median outbreak size, as measured by the total number of cases, was 4 with a range of 1 to 134", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial R across the 30 detailed outbreaks was 2 with a range of 0 to 38 . About a third had an initial R of 1 or less, and about two thirds had an initial R of 3 or less. Outbreaks that remained in the community had a lower initial R than those that were hospital based from the first generation . Mixed outbreaks, which generally started in the community and later spread through hospital contacts, had an intermediate initial R . The initial R was smaller when the index case had a typical versus atypical or hemorrhagic", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Outbreaks with greater initial R-values tended to be larger and longer. For example, in outbreaks with an initial R of 5 or less versus more than 5, median values for the total number of cases and generations were 2 versus 23 and 1 versus 2.5 respectively.", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Finally, the outbreak from Kosovo deserves notice because this region is not as developed or as wealthy as most of the other countries studied. This outbreak was the largest identified for this review . Moreover, the hospital and mixed component of this outbreak had the second highest and highest initial reproductive rate, and the hospital component lasted 9 generations . This suggests that a smallpox outbreak in a less developed country with limited resources for healthcare, disease surveillance, and case isolation could be potentially more devastating than a bioterrorist attack in a Western/industrialized country ." ]

[ [ "0a", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II" ], [ "0b", "Passage: The median initial reproduction rate across all 51 outbreaks was 2 with a range of 0 to 38 ." ], [ "0c", "About half had an initial R of 1 or less, and over two-thirds had an initial R of 3 or less." ], [ "0d", "The median duration, as measured by number of generations, was 1 with a range of 0 to 9 ." ], [ "0e", "About a third did not extend beyond the index generation, and nearly three quarters lasted for 3 or fewer generations." ], [ "0f", "The median outbreak size, as measured by the total number of cases, was 4 with a range of 1 to 134" ] ]

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

[ "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial reproduction rate across all 51 outbreaks was 2 with a range of 0 to 38 . About half had an initial R of 1 or less, and over two-thirds had an initial R of 3 or less. The median duration, as measured by number of generations, was 1 with a range of 0 to 9 . About a third did not extend beyond the index generation, and nearly three quarters lasted for 3 or fewer generations. The median outbreak size, as measured by the total number of cases, was 4 with a range of 1 to 134", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial R across the 30 detailed outbreaks was 2 with a range of 0 to 38 . About a third had an initial R of 1 or less, and about two thirds had an initial R of 3 or less. Outbreaks that remained in the community had a lower initial R than those that were hospital based from the first generation . Mixed outbreaks, which generally started in the community and later spread through hospital contacts, had an intermediate initial R . The initial R was smaller when the index case had a typical versus atypical or hemorrhagic", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Outbreaks with greater initial R-values tended to be larger and longer. For example, in outbreaks with an initial R of 5 or less versus more than 5, median values for the total number of cases and generations were 2 versus 23 and 1 versus 2.5 respectively.", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Finally, the outbreak from Kosovo deserves notice because this region is not as developed or as wealthy as most of the other countries studied. This outbreak was the largest identified for this review . Moreover, the hospital and mixed component of this outbreak had the second highest and highest initial reproductive rate, and the hospital component lasted 9 generations . This suggests that a smallpox outbreak in a less developed country with limited resources for healthcare, disease surveillance, and case isolation could be potentially more devastating than a bioterrorist attack in a Western/industrialized country ." ]

[ [ "1a", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II" ], [ "1b", "Passage: The median initial R across the 30 detailed outbreaks was 2 with a range of 0 to 38 ." ], [ "1c", "About a third had an initial R of 1 or less, and about two thirds had an initial R of 3 or less." ], [ "1d", "Outbreaks that remained in the community had a lower initial R than those that were hospital based from the first generation ." ], [ "1e", "Mixed outbreaks, which generally started in the community and later spread through hospital contacts, had an intermediate initial R ." ], [ "1f", "The initial R was smaller when the index case had a typical versus atypical or hemorrhagic" ] ]

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

[ "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial reproduction rate across all 51 outbreaks was 2 with a range of 0 to 38 . About half had an initial R of 1 or less, and over two-thirds had an initial R of 3 or less. The median duration, as measured by number of generations, was 1 with a range of 0 to 9 . About a third did not extend beyond the index generation, and nearly three quarters lasted for 3 or fewer generations. The median outbreak size, as measured by the total number of cases, was 4 with a range of 1 to 134", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: The median initial R across the 30 detailed outbreaks was 2 with a range of 0 to 38 . About a third had an initial R of 1 or less, and about two thirds had an initial R of 3 or less. Outbreaks that remained in the community had a lower initial R than those that were hospital based from the first generation . Mixed outbreaks, which generally started in the community and later spread through hospital contacts, had an intermediate initial R . The initial R was smaller when the index case had a typical versus atypical or hemorrhagic", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Outbreaks with greater initial R-values tended to be larger and longer. For example, in outbreaks with an initial R of 5 or less versus more than 5, median values for the total number of cases and generations were 2 versus 23 and 1 versus 2.5 respectively.", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II\nPassage: Finally, the outbreak from Kosovo deserves notice because this region is not as developed or as wealthy as most of the other countries studied. This outbreak was the largest identified for this review . Moreover, the hospital and mixed component of this outbreak had the second highest and highest initial reproductive rate, and the hospital component lasted 9 generations . This suggests that a smallpox outbreak in a less developed country with limited resources for healthcare, disease surveillance, and case isolation could be potentially more devastating than a bioterrorist attack in a Western/industrialized country ." ]

[ [ "2a", "Title: Transmission patterns of smallpox: systematic review of natural outbreaks in Europe and North America since World War II" ], [ "2b", "Passage: Outbreaks with greater initial R-values tended to be larger and longer." ], [ "2c", "For example, in outbreaks with an initial R of 5 or less versus more than 5, median values for the total number of cases and generations were 2 versus 23 and 1 versus 2.5 respectively." ] ]

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

[ "Title: Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry\nPassage: primer pairs targeting NP and PB2 segments. All primers used in this study had a thymine nucleotide at the 59 end to minimize addition of non-templated adenosines during amplification using Taq polymerase . The sensitivity of each RT-PCR primer pair was determined using known quantities of a synthetic calibrant RNA template as described previously . Each of the primer pairs was sensitive to as few as twenty copies of the calibrant RNA and several primers were sensitive to five copies .", "Title: Multiplex primer prediction software for divergent targets\nPassage: : 1, 100 : 1, 1000 : 1 and 10000 : 1. These correspond to copy number ratios of vaccinia:human genomes of 1. All PCR experiments were analyzed on 3% agarose TBE gels containing ethidum bromide that were purchased from Bio-Rad . Blue juice TM 10Â loading dye was purchased from Invitrogen and diluted to 2Â before use. A 50-bp DNA ladder was purchased from Novagen . For analysis, 15 ml from each separate 25 ml PCR reaction were combined with 2 ml of of loading dye and 15 ml of the loading-dye/product mixture was loaded per well and electrophoresed", "Title: Multiplex primer prediction software for divergent targets\nPassage: acids could be problematic for universal viral priming using primers shorter than 15 bases, particularly for multiplexes of 10 or more primers. Nanda et al. were able to achieve sufficient viral isolation from cell culture samples to allow viral identification using viral PCR with priming sequences as short as pentamers, so the problem of contaminating host nucleic acids for specific, short primer PCR of viruses is not insurmountable. They found specific pentamer PCR to be several logs more sensitive than nonspecific amplification, provided that they purified encapsidated viral nucleic acids prior to PCR. Another method that has been used for", "Title: A novel quantitative PCR mediated by high-fidelity DNA polymerase\nPassage: Oligonucleotides design. Primers were designed using the Primer Premier 5.0 program. Like a TaqMan probe, the HFman probe was designed in general with a fluorophore and a quencher at 5′ and 3′ end, respectively; however, a better form of the HFman probe is to have a 3′ fluorophore and a 5′ quencher. All primers were synthesized commercially by Thermofisher scientific . The detailed information of the primers, TaqMan and HFman probes are shown in Supplementary Tables S1 and S2." ]

[ [ "0a", "Title: Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry" ], [ "0b", "Passage: primer pairs targeting NP and PB2 segments." ], [ "0c", "All primers used in this study had a thymine nucleotide at the 59 end to minimize addition of non-templated adenosines during amplification using Taq polymerase ." ], [ "0d", "The sensitivity of each RT-PCR primer pair was determined using known quantities of a synthetic calibrant RNA template as described previously ." ], [ "0e", "Each of the primer pairs was sensitive to as few as twenty copies of the calibrant RNA and several primers were sensitive to five copies ." ] ]

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

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: naturally occurring pattern following the evolutionary characteristics typical of CoVs, it is highly unlikely that RaTG13 CoV is the immediate source of SARS-CoV-2. The absence of a logical targeted pattern in the new viral sequences and a close relative in a wildlife species are the most revealing signs that SARS-CoV-2 evolved by natural evolution. A search for an intermediate animal host between bats and humans is needed to identify animal CoVs more closely related to human SARS-CoV-2. There is speculation that pangolins might carry CoVs closely related to SARS-CoV-2, but the data to substantiate this is not yet published .", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: Evolution is stepwise and accrues mutations gradually over time, whereas synthetic constructs would typically use a known backbone and introduce logical or targeted changes instead of the randomly occurring mutations that are present in naturally isolated viruses such as bat CoV RaTG13. In our view, there is currently no credible evidence to support the claim that SARS-CoV-2 originated from a laboratory-engineered CoV. It is more likely that SARS-CoV-2 is a recombinant CoV generated in nature between a bat CoV and another coronavirus in an intermediate animal host. More studies are needed to explore this possibility and resolve the natural origin", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: Currently, there are speculations, rumours and conspiracy theories that SARS-CoV-2 is of laboratory origin. Some people have alleged that the human SARS-CoV-2 was leaked directly from a laboratory in Wuhan where a bat CoV was recently reported, which shared ∼96% homology with the SARS-CoV-2 . However, as we know, the human SARS-CoV and intermediate host palm civet SARSlike CoV shared 99.8% homology, with a total of 202 single-nucleotide variations identified across the genome . Given that there are greater than 1,100 nt differences between the human SARS-CoV-2 and the bat RaTG13-CoV , which are distributed throughout the genome in a" ]

[ [ "0a", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2" ], [ "0b", "Passage: naturally occurring pattern following the evolutionary characteristics typical of CoVs, it is highly unlikely that RaTG13 CoV is the immediate source of SARS-CoV-2." ], [ "0c", "The absence of a logical targeted pattern in the new viral sequences and a close relative in a wildlife species are the most revealing signs that SARS-CoV-2 evolved by natural evolution." ], [ "0d", "A search for an intermediate animal host between bats and humans is needed to identify animal CoVs more closely related to human SARS-CoV-2." ], [ "0e", "There is speculation that pangolins might carry CoVs closely related to SARS-CoV-2, but the data to substantiate this is not yet published ." ] ]

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

[ "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: naturally occurring pattern following the evolutionary characteristics typical of CoVs, it is highly unlikely that RaTG13 CoV is the immediate source of SARS-CoV-2. The absence of a logical targeted pattern in the new viral sequences and a close relative in a wildlife species are the most revealing signs that SARS-CoV-2 evolved by natural evolution. A search for an intermediate animal host between bats and humans is needed to identify animal CoVs more closely related to human SARS-CoV-2. There is speculation that pangolins might carry CoVs closely related to SARS-CoV-2, but the data to substantiate this is not yet published .", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: Evolution is stepwise and accrues mutations gradually over time, whereas synthetic constructs would typically use a known backbone and introduce logical or targeted changes instead of the randomly occurring mutations that are present in naturally isolated viruses such as bat CoV RaTG13. In our view, there is currently no credible evidence to support the claim that SARS-CoV-2 originated from a laboratory-engineered CoV. It is more likely that SARS-CoV-2 is a recombinant CoV generated in nature between a bat CoV and another coronavirus in an intermediate animal host. More studies are needed to explore this possibility and resolve the natural origin", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: According to what has been reported , COVID-2019 seems to have similar clinical manifestations to that of the severe acute respiratory syndrome caused by SARS-CoV. The SARS-CoV-2 genome sequence also has ∼80% identity with SARS-CoV, but it is most similar to some bat beta-coronaviruses, with the highest being >96% identity .", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2\nPassage: Currently, there are speculations, rumours and conspiracy theories that SARS-CoV-2 is of laboratory origin. Some people have alleged that the human SARS-CoV-2 was leaked directly from a laboratory in Wuhan where a bat CoV was recently reported, which shared ∼96% homology with the SARS-CoV-2 . However, as we know, the human SARS-CoV and intermediate host palm civet SARSlike CoV shared 99.8% homology, with a total of 202 single-nucleotide variations identified across the genome . Given that there are greater than 1,100 nt differences between the human SARS-CoV-2 and the bat RaTG13-CoV , which are distributed throughout the genome in a" ]

[ [ "1a", "Title: No credible evidence supporting claims of the laboratory engineering of SARS-CoV-2" ], [ "1b", "Passage: Evolution is stepwise and accrues mutations gradually over time, whereas synthetic constructs would typically use a known backbone and introduce logical or targeted changes instead of the randomly occurring mutations that are present in naturally isolated viruses such as bat CoV RaTG13." ], [ "1c", "In our view, there is currently no credible evidence to support the claim that SARS-CoV-2 originated from a laboratory-engineered CoV." ], [ "1d", "It is more likely that SARS-CoV-2 is a recombinant CoV generated in nature between a bat CoV and another coronavirus in an intermediate animal host." ], [ "1e", "More studies are needed to explore this possibility and resolve the natural origin" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Prior to December 2019, 6 CoVs were known to infect human, including 2 αCoV and 4 βCoV (HCoV-OC43 [", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: infections and 800 deaths, and Middle East respiratory syndrome CoV which has caused a persistent epidemic in the Arabian Peninsula since 2012 . In both of these epidemics, these viruses have likely originated from bats and then jumped into another amplification mammalian host for SARS-CoV and the dromedary camel for MERS-CoV] before crossing species barriers to infect humans.", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: The SARS epidemic began quietly at the turn of the 21st century. In November 2002, a cook in Guangdong Province, China, died from an unidentified illness. He had worked at a restaurant in which meat from wild animals was served. On 27 November 2002 Chinese-language media and internet reports were picked up by Canada's Global Public Health Intelligence Network that indicated a flu-like illness was occurring in China . Unfortunately, the reports were not translated, and China failed to report the occurrence of this illness to the World Health Organization until February 2003. The disease spread to other countries where", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes\nPassage: Text: Coronaviruses belong to the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales. A human coronavirus caused the severe acute respiratory syndrome coronavirus outbreak in 2003. Most recently, an SARS-related CoV was implicated as the etiological agent responsible for the outbreak in Wuhan, central China. This outbreak is estimated to have started on 12th December 2019 and 17,332 laboratory confirmed cases with 361 deaths as of 3rd February 2020 in China . The virus has spread to 23 other countries by travellers from Wuhan . Typical symptoms are fever, malaise, shortness of breath and in severe cases, pneumonia" ]

[ [ "0a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "0b", "Passage: Prior to December 2019, 6 CoVs were known to infect human, including 2 αCoV and 4 βCoV (HCoV-OC43 [" ] ]

[ "0b" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Since that first report, a slow discovery process over the following two to three years revealed a virus that had infected over 90 % of adult dromedary camels in the KSA , also DCs across the Arabian Peninsula and parts of Africa that are a source of DC imports for the KSA . To date, MERS-CoV has not been detected in DCs tested in zoos or herds from other parts of the world . Occasionally, virus is transmitted from infected DCs to exposed humans. Subsequent transmission to other humans requires relatively close and prolonged exposure .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV RNA has also been detected in DC samples, and recovery of infectious virus has also been achieved from DC samples . From some of these, full or majority length genomes of MERS-CoV have been sequenced . DC versions of MERS-CoV were found to be as similar to each other, as were variants detected from different humans over time and across distance." ]

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

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Since that first report, a slow discovery process over the following two to three years revealed a virus that had infected over 90 % of adult dromedary camels in the KSA , also DCs across the Arabian Peninsula and parts of Africa that are a source of DC imports for the KSA . To date, MERS-CoV has not been detected in DCs tested in zoos or herds from other parts of the world . Occasionally, virus is transmitted from infected DCs to exposed humans. Subsequent transmission to other humans requires relatively close and prolonged exposure .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV RNA has also been detected in DC samples, and recovery of infectious virus has also been achieved from DC samples . From some of these, full or majority length genomes of MERS-CoV have been sequenced . DC versions of MERS-CoV were found to be as similar to each other, as were variants detected from different humans over time and across distance." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: Since that first report, a slow discovery process over the following two to three years revealed a virus that had infected over 90 % of adult dromedary camels in the KSA , also DCs across the Arabian Peninsula and parts of Africa that are a source of DC imports for the KSA ." ], [ "2c", "To date, MERS-CoV has not been detected in DCs tested in zoos or herds from other parts of the world ." ], [ "2d", "Occasionally, virus is transmitted from infected DCs to exposed humans." ], [ "2e", "Subsequent transmission to other humans requires relatively close and prolonged exposure ." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: In 2015 two large outbreaks occurred. South Korea was the site of the first large scale outbreak outside the Arabian Peninsula and produced the first cases in both South Korea and China, occurring between May and July 2015. This was closely followed by a distinct outbreak in Ar Riyad province in the KSA which appeared to come under control in early November.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Abstract: The first known cases of Middle East respiratory syndrome , associated with infection by a novel coronavirus , occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia . Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels . MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Since that first report, a slow discovery process over the following two to three years revealed a virus that had infected over 90 % of adult dromedary camels in the KSA , also DCs across the Arabian Peninsula and parts of Africa that are a source of DC imports for the KSA . To date, MERS-CoV has not been detected in DCs tested in zoos or herds from other parts of the world . Occasionally, virus is transmitted from infected DCs to exposed humans. Subsequent transmission to other humans requires relatively close and prolonged exposure .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: MERS-CoV RNA has also been detected in DC samples, and recovery of infectious virus has also been achieved from DC samples . From some of these, full or majority length genomes of MERS-CoV have been sequenced . DC versions of MERS-CoV were found to be as similar to each other, as were variants detected from different humans over time and across distance." ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: MERS-CoV RNA has also been detected in DC samples, and recovery of infectious virus has also been achieved from DC samples ." ], [ "3c", "From some of these, full or majority length genomes of MERS-CoV have been sequenced ." ], [ "3d", "DC versions of MERS-CoV were found to be as similar to each other, as were variants detected from different humans over time and across distance." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Diagnosis is an important component in the overall pandemic management framework. With proper diagnosis, potential flu carriers can be identified before they become symptomatic. Non-pharmaceutical measures such as quarantine and contact tracing can then be activated, thus maximizing the probability of containment .", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Current influenza diagnostic tests, especially when the strains are evolving constantly, vary differently in terms of efficiency, specificity and sensitivity . These factors will impact the intervention policies that should be made during an outbreak. It has been argued that a slow, low throughput laboratorybased diagnostic test, such as immunofluorescence DFA antibody staining and RT-PCR , may not be able to effectively assist pandemic mitigation . Ideally, a rapid PCRbased diagnostic testkit should be able to detect the relevant virus in less than 30 minutes, requiring nothing more than a patient sample, and a portable device to perform extraction and", "Title: Estimating the number of infections and the impact of non-\nPassage: underreporting as well as systematic and country-specific changes in testing.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: both attack rates and costs through the implementation of policies involving full contact tracing and prophylaxis to the contacts will most probably be more significant." ]

[ [ "0a", "Title: How necessary is a fast testkit for mitigation of pandemic flu?" ], [ "0b", "Passage: Diagnosis is an important component in the overall pandemic management framework." ], [ "0c", "With proper diagnosis, potential flu carriers can be identified before they become symptomatic." ], [ "0d", "Non-pharmaceutical measures such as quarantine and contact tracing can then be activated, thus maximizing the probability of containment ." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Diagnosis is an important component in the overall pandemic management framework. With proper diagnosis, potential flu carriers can be identified before they become symptomatic. Non-pharmaceutical measures such as quarantine and contact tracing can then be activated, thus maximizing the probability of containment .", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Current influenza diagnostic tests, especially when the strains are evolving constantly, vary differently in terms of efficiency, specificity and sensitivity . These factors will impact the intervention policies that should be made during an outbreak. It has been argued that a slow, low throughput laboratorybased diagnostic test, such as immunofluorescence DFA antibody staining and RT-PCR , may not be able to effectively assist pandemic mitigation . Ideally, a rapid PCRbased diagnostic testkit should be able to detect the relevant virus in less than 30 minutes, requiring nothing more than a patient sample, and a portable device to perform extraction and", "Title: Estimating the number of infections and the impact of non-\nPassage: underreporting as well as systematic and country-specific changes in testing.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: both attack rates and costs through the implementation of policies involving full contact tracing and prophylaxis to the contacts will most probably be more significant." ]

[ [ "1a", "Title: How necessary is a fast testkit for mitigation of pandemic flu?" ], [ "1b", "Passage: Current influenza diagnostic tests, especially when the strains are evolving constantly, vary differently in terms of efficiency, specificity and sensitivity ." ], [ "1c", "These factors will impact the intervention policies that should be made during an outbreak." ], [ "1d", "It has been argued that a slow, low throughput laboratorybased diagnostic test, such as immunofluorescence DFA antibody staining and RT-PCR , may not be able to effectively assist pandemic mitigation ." ], [ "1e", "Ideally, a rapid PCRbased diagnostic testkit should be able to detect the relevant virus in less than 30 minutes, requiring nothing more than a patient sample, and a portable device to perform extraction and" ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Diagnosis is an important component in the overall pandemic management framework. With proper diagnosis, potential flu carriers can be identified before they become symptomatic. Non-pharmaceutical measures such as quarantine and contact tracing can then be activated, thus maximizing the probability of containment .", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Current influenza diagnostic tests, especially when the strains are evolving constantly, vary differently in terms of efficiency, specificity and sensitivity . These factors will impact the intervention policies that should be made during an outbreak. It has been argued that a slow, low throughput laboratorybased diagnostic test, such as immunofluorescence DFA antibody staining and RT-PCR , may not be able to effectively assist pandemic mitigation . Ideally, a rapid PCRbased diagnostic testkit should be able to detect the relevant virus in less than 30 minutes, requiring nothing more than a patient sample, and a portable device to perform extraction and", "Title: Estimating the number of infections and the impact of non-\nPassage: underreporting as well as systematic and country-specific changes in testing.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: both attack rates and costs through the implementation of policies involving full contact tracing and prophylaxis to the contacts will most probably be more significant." ]

[ [ "2a", "Title: Estimating the number of infections and the impact of non-" ], [ "2b", "Passage: underreporting as well as systematic and country-specific changes in testing." ] ]

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

[ "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Diagnosis is an important component in the overall pandemic management framework. With proper diagnosis, potential flu carriers can be identified before they become symptomatic. Non-pharmaceutical measures such as quarantine and contact tracing can then be activated, thus maximizing the probability of containment .", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: Current influenza diagnostic tests, especially when the strains are evolving constantly, vary differently in terms of efficiency, specificity and sensitivity . These factors will impact the intervention policies that should be made during an outbreak. It has been argued that a slow, low throughput laboratorybased diagnostic test, such as immunofluorescence DFA antibody staining and RT-PCR , may not be able to effectively assist pandemic mitigation . Ideally, a rapid PCRbased diagnostic testkit should be able to detect the relevant virus in less than 30 minutes, requiring nothing more than a patient sample, and a portable device to perform extraction and", "Title: Estimating the number of infections and the impact of non-\nPassage: underreporting as well as systematic and country-specific changes in testing.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: both attack rates and costs through the implementation of policies involving full contact tracing and prophylaxis to the contacts will most probably be more significant." ]

[ [ "3a", "Title: How necessary is a fast testkit for mitigation of pandemic flu?" ], [ "3b", "Passage: both attack rates and costs through the implementation of policies involving full contact tracing and prophylaxis to the contacts will most probably be more significant." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV . However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Is 2019-nCoV infection severe? To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses. However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated. On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: cases are being reported on a daily basis and there is evidence for some human-to-human transmission in China, a number of important questions remain unanswered. For example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease.", "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: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily ." ], [ "0c", "The severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively ." ], [ "0d", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV ." ], [ "0e", "However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV ." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV . However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Is 2019-nCoV infection severe? To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses. However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated. On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: cases are being reported on a daily basis and there is evidence for some human-to-human transmission in China, a number of important questions remain unanswered. For example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease.", "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: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus" ], [ "1b", "Passage: Is 2019-nCoV infection severe?" ], [ "1c", "To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses." ], [ "1d", "However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated." ], [ "1e", "On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China" ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV . However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Is 2019-nCoV infection severe? To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses. However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated. On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: cases are being reported on a daily basis and there is evidence for some human-to-human transmission in China, a number of important questions remain unanswered. For example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease.", "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: Note from the editors: novel coronavirus (2019-nCoV)" ], [ "2b", "Passage: cases are being reported on a daily basis and there is evidence for some human-to-human transmission in China, a number of important questions remain unanswered." ], [ "2c", "For example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV . However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV .", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Is 2019-nCoV infection severe? To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses. However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated. On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China", "Title: Note from the editors: novel coronavirus (2019-nCoV)\nPassage: cases are being reported on a daily basis and there is evidence for some human-to-human transmission in China, a number of important questions remain unanswered. For example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease.", "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" ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: NS4B . It is thus conceivable that inhibitors targeting TMD of NS4B would perturb its function, leading to the suppression of viral RNA replication. In this study, the replacement of Q130 of NS4B with a basic amino acid conferred the resistance effect without suppressing JEV replication, suggesting that position 130 could tolerate a basic amino acid and that the basic amino acid might be involved in the interplay of NS4B with host proteins rather than viral proteins.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: NS4B . It is thus conceivable that inhibitors targeting TMD of NS4B would perturb its function, leading to the suppression of viral RNA replication. In this study, the replacement of Q130 of NS4B with a basic amino acid conferred the resistance effect without suppressing JEV replication, suggesting that position 130 could tolerate a basic amino acid and that the basic amino acid might be involved in the interplay of NS4B with host proteins rather than viral proteins.", "Title: In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1\nPassage: Neuraminidase has become the main target for drug design against influenza virus due to its highly conserved catalytic site and its essential role in influenza virus replication . Oseltamivir is an antiviral drug against neuraminidase that is useful for preventing viral replication in the last stage of the viral live cycle . It directly interacts with the catalytic residues of the neuraminidase catalytic site, while the framework residues stabilize the enzyme structure . Resistance to oseltamivir has already become a widespread phenomenon, and prediction of the neuraminidase structure shows that the resistance could be several times higher than resistance to", "Title: Progress of small molecular inhibitors in the development of anti-influenza virus agents\nPassage: NA is a viral enzyme that is made up of four identical subunits and is anchored to the membrane of the virus . NA plays a key role in the spreading of the virus. The terminal neuraminic acid residues of the glycoproteins of the newly formed virion progeny form glycosidic linkages with the neuraminic acid receptor on the host-cell surface; this glycosidic linkage is cleaved by NA, which thereby assists in the release of the virion progeny from the infected cells . Therefore NA is an attractive target for anti-influenza research, and inhibitors of NA containing a Neu core have" ]

[ [ "2a", "Title: In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1" ], [ "2b", "Passage: Neuraminidase has become the main target for drug design against influenza virus due to its highly conserved catalytic site and its essential role in influenza virus replication ." ], [ "2c", "Oseltamivir is an antiviral drug against neuraminidase that is useful for preventing viral replication in the last stage of the viral live cycle ." ], [ "2d", "It directly interacts with the catalytic residues of the neuraminidase catalytic site, while the framework residues stabilize the enzyme structure ." ], [ "2e", "Resistance to oseltamivir has already become a widespread phenomenon, and prediction of the neuraminidase structure shows that the resistance could be several times higher than resistance to" ] ]

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

[ "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: NS4B . It is thus conceivable that inhibitors targeting TMD of NS4B would perturb its function, leading to the suppression of viral RNA replication. In this study, the replacement of Q130 of NS4B with a basic amino acid conferred the resistance effect without suppressing JEV replication, suggesting that position 130 could tolerate a basic amino acid and that the basic amino acid might be involved in the interplay of NS4B with host proteins rather than viral proteins.", "Title: Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection\nPassage: NS4B . It is thus conceivable that inhibitors targeting TMD of NS4B would perturb its function, leading to the suppression of viral RNA replication. In this study, the replacement of Q130 of NS4B with a basic amino acid conferred the resistance effect without suppressing JEV replication, suggesting that position 130 could tolerate a basic amino acid and that the basic amino acid might be involved in the interplay of NS4B with host proteins rather than viral proteins.", "Title: In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1\nPassage: Neuraminidase has become the main target for drug design against influenza virus due to its highly conserved catalytic site and its essential role in influenza virus replication . Oseltamivir is an antiviral drug against neuraminidase that is useful for preventing viral replication in the last stage of the viral live cycle . It directly interacts with the catalytic residues of the neuraminidase catalytic site, while the framework residues stabilize the enzyme structure . Resistance to oseltamivir has already become a widespread phenomenon, and prediction of the neuraminidase structure shows that the resistance could be several times higher than resistance to", "Title: Progress of small molecular inhibitors in the development of anti-influenza virus agents\nPassage: NA is a viral enzyme that is made up of four identical subunits and is anchored to the membrane of the virus . NA plays a key role in the spreading of the virus. The terminal neuraminic acid residues of the glycoproteins of the newly formed virion progeny form glycosidic linkages with the neuraminic acid receptor on the host-cell surface; this glycosidic linkage is cleaved by NA, which thereby assists in the release of the virion progeny from the infected cells . Therefore NA is an attractive target for anti-influenza research, and inhibitors of NA containing a Neu core have" ]

[ [ "3a", "Title: Progress of small molecular inhibitors in the development of anti-influenza virus agents" ], [ "3b", "Passage: NA is a viral enzyme that is made up of four identical subunits and is anchored to the membrane of the virus ." ], [ "3c", "NA plays a key role in the spreading of the virus." ], [ "3d", "The terminal neuraminic acid residues of the glycoproteins of the newly formed virion progeny form glycosidic linkages with the neuraminic acid receptor on the host-cell surface; this glycosidic linkage is cleaved by NA, which thereby assists in the release of the virion progeny from the infected cells ." ], [ "3e", "Therefore NA is an attractive target for anti-influenza research, and inhibitors of NA containing a Neu core have" ] ]

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

[ "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: The general objective of this work is to utilize radio frequency close-proximity sensors to describe and understand the nature of human networks within a low-resource population that have the potential to transmit respiratory infectious diseases. Specifically:", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns.", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: Significance and potential impact of the study To provide greater insight into social network structures in resource poor settings, we propose to study social contact patterns within schools and households and compare and contrast patterns in the urban and rural setting exhibiting different demographic, economic, and socio-cultural characteristics. This will provide key data for use in transmission dynamic models for common respiratory viral and bacterial infections such as RSV and S. pneumoniae that are the leading cause of childhood morbidity and mortality in the SSA setting. We also seek to answer the question how we can optimize study design to" ]

[ [ "0a", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors" ], [ "0b", "Passage: The general objective of this work is to utilize radio frequency close-proximity sensors to describe and understand the nature of human networks within a low-resource population that have the potential to transmit respiratory infectious diseases. Specifically:" ] ]

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

[ "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: The general objective of this work is to utilize radio frequency close-proximity sensors to describe and understand the nature of human networks within a low-resource population that have the potential to transmit respiratory infectious diseases. Specifically:", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The overall objective of the study was to quantify the efficacy of face masks and/or hand hygiene in reducing transmission of influenza to household contacts at the individual level. Specific objectives of this pilot study were to confirm the feasibility of the study design including the practicability of patient recruitment, randomization and follow-up, the appropriateness of the estimated sample size for a subsequent larger trial in terms of characteristics of local circulating influenza viruses and potential effect sizes, the applicability of the interventions and individual adherence with the interventions.", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: The primary objective of this study was to provide health authorities with evidence-based practical information to guide the development and delivery of key health messages for H1N1 and other health campaigns. The study focused on community responses to key health messages in the 2009 and 2010 H1N1 campaigns.", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors\nPassage: Significance and potential impact of the study To provide greater insight into social network structures in resource poor settings, we propose to study social contact patterns within schools and households and compare and contrast patterns in the urban and rural setting exhibiting different demographic, economic, and socio-cultural characteristics. This will provide key data for use in transmission dynamic models for common respiratory viral and bacterial infections such as RSV and S. pneumoniae that are the leading cause of childhood morbidity and mortality in the SSA setting. We also seek to answer the question how we can optimize study design to" ]

[ [ "3a", "Title: Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors" ], [ "3b", "Passage: Significance and potential impact of the study To provide greater insight into social network structures in resource poor settings, we propose to study social contact patterns within schools and households and compare and contrast patterns in the urban and rural setting exhibiting different demographic, economic, and socio-cultural characteristics." ], [ "3c", "This will provide key data for use in transmission dynamic models for common respiratory viral and bacterial infections such as RSV and S. pneumoniae that are the leading cause of childhood morbidity and mortality in the SSA setting." ], [ "3d", "We also seek to answer the question how we can optimize study design to" ] ]

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

[ "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: meiosis I or II. Aneuploidies and other chromosomal abnormalities are a common cause of birth defects and are associated with significant morbidity and mortality. The spectrum of phenotypes seen in each affected individual is clearly dependant on the particular chromosomal region concerned, although there is still a great deal of variability in the presentation of phenotypes.", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: An example could be Turner syndrome, which is the only whole chromosome monosomy that is viable in humans, with approximately 1 in 2,000 female births having one copy of the X chromosome . In addition to the main features of short stature and ovarian failure, present in almost all cases, there are many other phenotypes that may present, including a short webbed neck, kidney malformations, hearing problems and various learning difficulties, as well as increased risk of type 1 diabetes . It is possible that the extensive copy number variation on the X chromosome-37.8% according to the DGV -may contribute", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: Using Down's Syndrome as an example, an extra copy of chromosome 21 is not sufficient to cause the full range of phenotypes associated with this disorder, as individuals can present with a range of sub-phenotypes. Some features are almost always present, such as the characteristic facial appearance and mental retardation, although these can vary widely in the severity of their presentation . Other features, however, are only present in a fraction of DS cases: for example, congenital heart defects are present in *40% of cases and gastrointestinal defects in *8% of DS . Leukaemia is also common in DS, with", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: an *20% increased risk of acute lymphoblastic leukaemia , and transient myeloproliferative disorder occurring in *10% of DS newborns, of which 10-20% develop acute megakaryoblastic leukaemia before the age of 4 . A detailed knowledge of the genes on the affected chromosome is required to understand the phenotypic effects of aneuploidy. In addition, it is important to determine the overall effects of gene dosage imbalance, which may also be complex. Individuals with partial trisomy 21 resulting from unbalanced chromosomal translocations will only exhibit those features associated with the extra genomic material present. Molecular analysis of these patients enables 'phenotypic mapping'" ]

[ [ "1a", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype" ], [ "1b", "Passage: An example could be Turner syndrome, which is the only whole chromosome monosomy that is viable in humans, with approximately 1 in 2,000 female births having one copy of the X chromosome ." ], [ "1c", "In addition to the main features of short stature and ovarian failure, present in almost all cases, there are many other phenotypes that may present, including a short webbed neck, kidney malformations, hearing problems and various learning difficulties, as well as increased risk of type 1 diabetes ." ], [ "1d", "It is possible that the extensive copy number variation on the X chromosome-37.8% according to the DGV -may contribute" ] ]

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

[ "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: meiosis I or II. Aneuploidies and other chromosomal abnormalities are a common cause of birth defects and are associated with significant morbidity and mortality. The spectrum of phenotypes seen in each affected individual is clearly dependant on the particular chromosomal region concerned, although there is still a great deal of variability in the presentation of phenotypes.", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: An example could be Turner syndrome, which is the only whole chromosome monosomy that is viable in humans, with approximately 1 in 2,000 female births having one copy of the X chromosome . In addition to the main features of short stature and ovarian failure, present in almost all cases, there are many other phenotypes that may present, including a short webbed neck, kidney malformations, hearing problems and various learning difficulties, as well as increased risk of type 1 diabetes . It is possible that the extensive copy number variation on the X chromosome-37.8% according to the DGV -may contribute", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: Using Down's Syndrome as an example, an extra copy of chromosome 21 is not sufficient to cause the full range of phenotypes associated with this disorder, as individuals can present with a range of sub-phenotypes. Some features are almost always present, such as the characteristic facial appearance and mental retardation, although these can vary widely in the severity of their presentation . Other features, however, are only present in a fraction of DS cases: for example, congenital heart defects are present in *40% of cases and gastrointestinal defects in *8% of DS . Leukaemia is also common in DS, with", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: an *20% increased risk of acute lymphoblastic leukaemia , and transient myeloproliferative disorder occurring in *10% of DS newborns, of which 10-20% develop acute megakaryoblastic leukaemia before the age of 4 . A detailed knowledge of the genes on the affected chromosome is required to understand the phenotypic effects of aneuploidy. In addition, it is important to determine the overall effects of gene dosage imbalance, which may also be complex. Individuals with partial trisomy 21 resulting from unbalanced chromosomal translocations will only exhibit those features associated with the extra genomic material present. Molecular analysis of these patients enables 'phenotypic mapping'" ]

[ [ "2a", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype" ], [ "2b", "Passage: Using Down's Syndrome as an example, an extra copy of chromosome 21 is not sufficient to cause the full range of phenotypes associated with this disorder, as individuals can present with a range of sub-phenotypes." ], [ "2c", "Some features are almost always present, such as the characteristic facial appearance and mental retardation, although these can vary widely in the severity of their presentation ." ], [ "2d", "Other features, however, are only present in a fraction of DS cases: for example, congenital heart defects are present in *40% of cases and gastrointestinal defects in *8% of DS ." ], [ "2e", "Leukaemia is also common in DS, with" ] ]

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

[ "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: meiosis I or II. Aneuploidies and other chromosomal abnormalities are a common cause of birth defects and are associated with significant morbidity and mortality. The spectrum of phenotypes seen in each affected individual is clearly dependant on the particular chromosomal region concerned, although there is still a great deal of variability in the presentation of phenotypes.", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: An example could be Turner syndrome, which is the only whole chromosome monosomy that is viable in humans, with approximately 1 in 2,000 female births having one copy of the X chromosome . In addition to the main features of short stature and ovarian failure, present in almost all cases, there are many other phenotypes that may present, including a short webbed neck, kidney malformations, hearing problems and various learning difficulties, as well as increased risk of type 1 diabetes . It is possible that the extensive copy number variation on the X chromosome-37.8% according to the DGV -may contribute", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: Using Down's Syndrome as an example, an extra copy of chromosome 21 is not sufficient to cause the full range of phenotypes associated with this disorder, as individuals can present with a range of sub-phenotypes. Some features are almost always present, such as the characteristic facial appearance and mental retardation, although these can vary widely in the severity of their presentation . Other features, however, are only present in a fraction of DS cases: for example, congenital heart defects are present in *40% of cases and gastrointestinal defects in *8% of DS . Leukaemia is also common in DS, with", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype\nPassage: an *20% increased risk of acute lymphoblastic leukaemia , and transient myeloproliferative disorder occurring in *10% of DS newborns, of which 10-20% develop acute megakaryoblastic leukaemia before the age of 4 . A detailed knowledge of the genes on the affected chromosome is required to understand the phenotypic effects of aneuploidy. In addition, it is important to determine the overall effects of gene dosage imbalance, which may also be complex. Individuals with partial trisomy 21 resulting from unbalanced chromosomal translocations will only exhibit those features associated with the extra genomic material present. Molecular analysis of these patients enables 'phenotypic mapping'" ]

[ [ "3a", "Title: Implications of copy number variation in people with chromosomal abnormalities: potential for greater variation in copy number state may contribute to variability of phenotype" ], [ "3b", "Passage: an *20% increased risk of acute lymphoblastic leukaemia , and transient myeloproliferative disorder occurring in *10% of DS newborns, of which 10-20% develop acute megakaryoblastic leukaemia before the age of 4 ." ], [ "3c", "A detailed knowledge of the genes on the affected chromosome is required to understand the phenotypic effects of aneuploidy." ], [ "3d", "In addition, it is important to determine the overall effects of gene dosage imbalance, which may also be complex." ], [ "3e", "Individuals with partial trisomy 21 resulting from unbalanced chromosomal translocations will only exhibit those features associated with the extra genomic material present." ], [ "3f", "Molecular analysis of these patients enables 'phenotypic mapping'" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration" ]

[ [ "0a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "0b", "Passage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein ." ], [ "0c", "Among the IFITM family proteins, IFITM5 is unique." ], [ "0d", "Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements ." ], [ "0e", "Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ." ], [ "0f", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration" ]

[ [ "1a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "1b", "Passage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein ." ], [ "1c", "Among the IFITM family proteins, IFITM5 is unique." ], [ "1d", "Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements ." ], [ "1e", "Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ." ], [ "1f", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration" ]

[ [ "2a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "2b", "Passage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice." ], [ "2c", "The conserved residues are highlighted in black." ], [ "2d", "The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 ." ], [ "2e", "The residues unique in IFITM5 are highlighted in gray." ], [ "2f", "The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively." ], [ "2g", "The TM domains were predicted by SOSUI." ], [ "2h", "The aspartates at the C-terminal region in IFITM5 are shown in blue." ], [ "2i", "B) The schematic illustration" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 . The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B) The schematic illustration" ]

[ [ "3a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "3b", "Passage: Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice." ], [ "3c", "The conserved residues are highlighted in black." ], [ "3d", "The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 and IFITM3 ." ], [ "3e", "The residues unique in IFITM5 are highlighted in gray." ], [ "3f", "The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively." ], [ "3g", "The TM domains were predicted by SOSUI." ], [ "3h", "The aspartates at the C-terminal region in IFITM5 are shown in blue." ], [ "3i", "B) The schematic illustration" ] ]

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

[ "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: Community responses to communication campaigns for influenza A (H1N1): a focus group study\nPassage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large. It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate. Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender. Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's", "Title: Estimating the number of infections and the impact of non-\nPassage: 4 Conclusion and Limitations" ]

[ [ "2a", "Title: Community responses to communication campaigns for influenza A (H1N1): a focus group study" ], [ "2b", "Passage: Any conclusions drawn from this study should be considered tentative as the findings cannot be generalised to the population at large." ], [ "2c", "It is not known whether the individuals who chose to participate differed from those who were eligible but chose not to participate." ], [ "2d", "Whilst this study intentionally involved participants with diverse cultural and ethnic backgrounds, and included individuals from vulnerable groups, the sample does not permit conclusions regarding the effect of socio-demographic factors such as age or gender." ], [ "2e", "Further research is needed to explore the complexities involved in the way in which the framing of risk messages impacts on people's" ] ]

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

[ "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case\nPassage: temperature of 40.3uC, had infiltration of lower left lung lobe based on chest radiography, bilateral lower lung moist rales, and substantially reduced oxygen saturation. He was placed on a ventilator and treated with antibiotics, spasmolysis, corticosteroids, and the dissipatation of phlegm and fluids. Despite treatment, the patient presented with function damage of multiple organ on the second day after admission, and died 59 h after admission, and 8 days after the onset of symptoms. Throat swabs were collected and performed RT-PCR and rRT-PCR detection at the day patient died. No antiviral drug treatment was given since the patient died before", "Title: Retrospective diagnosis of a famous historical figure: ontological, epistemic, and ethical considerations\nPassage: original case report was short and did not have all the important elements that I discussed above.", "Title: Severe malaria - a case of fatal Plasmodium knowlesi infection with post-mortem findings: a case report\nPassage: A forty year-old male was brought to the Queen Elizabeth Hospital, Kota Kinabalu, Sabah in a state of collapse. He was unable to give a history himself or to stand. On examination his blood pressure was unrecordable and oxygen saturations were recorded as low.", "Title: Fatal varicella pneumonia in an unvaccinated child with Down Syndrome: a case report\nPassage: The next day, the respiratory condition didn't improve and a new CXR showed an impairment of the spread, and a massive pulmonary hemorrhage. In the absence of recovery of the main indicators of organ perfusion, she was declared dead." ]

[ [ "0a", "Title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case" ], [ "0b", "Passage: temperature of 40.3uC, had infiltration of lower left lung lobe based on chest radiography, bilateral lower lung moist rales, and substantially reduced oxygen saturation." ], [ "0c", "He was placed on a ventilator and treated with antibiotics, spasmolysis, corticosteroids, and the dissipatation of phlegm and fluids." ], [ "0d", "Despite treatment, the patient presented with function damage of multiple organ on the second day after admission, and died 59 h after admission, and 8 days after the onset of symptoms." ], [ "0e", "Throat swabs were collected and performed RT-PCR and rRT-PCR detection at the day patient died." ], [ "0f", "No antiviral drug treatment was given since the patient died before" ] ]

[ "0c", "0d", "0f" ]

[ "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: Viral infections of the respiratory system are very common. In Taiwan, the predominant viruses isolated from patients with respiratory infections are enterovirus, respiratory syncytial virus , influenza A and B viruses, adenovirus, cytomegalovirus, herpes simplex virus-1, and parainfluenza virus. 27 Enterovirus causes herpangina, hand-foot-and-mouth disease, myocarditis, encephalitis, and death. RSV is the most common pathogen of the lower respiratory tract in infants 28 and a common cause of nosocomial infections in pediatric wards. 29 Influenza A and B viruses cause seasonal epidemics in Taiwan, especially in winter. 30 Adenovirus causes acute respiratory tract infections in children younger than 5 years", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: countries . In the developed world, viruses are already the most common pathogens causing diarrhea .", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: Rotavirus infection is the most common cause of viral gastroenteritis among children; however, parents of infected children also often become ill and as a result rotavirus is the second most common cause of gastroenteritis in adults . Studies in human volunteers have shown that infection with rotavirus causes diarrhea, results in shedding of the virus and a rise in antibody anti-virus titer after infection . Additionally, astroviruses infections are common, accounting for about 10% of all sporadic diarrhea cases . Astrovirus has been isolated from diseased people, filtrated and administered to healthy individuals after which in some of the volunteers" ]

[ [ "0a", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards" ], [ "0b", "Passage: Viral infections of the respiratory system are very common." ], [ "0c", "In Taiwan, the predominant viruses isolated from patients with respiratory infections are enterovirus, respiratory syncytial virus , influenza A and B viruses, adenovirus, cytomegalovirus, herpes simplex virus-1, and parainfluenza virus." ], [ "0d", "27 Enterovirus causes herpangina, hand-foot-and-mouth disease, myocarditis, encephalitis, and death." ], [ "0e", "RSV is the most common pathogen of the lower respiratory tract in infants 28 and a common cause of nosocomial infections in pediatric wards." ], [ "0f", "29 Influenza A and B viruses cause seasonal epidemics in Taiwan, especially in winter." ], [ "0g", "30 Adenovirus causes acute respiratory tract infections in children younger than 5 years" ] ]

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

[ "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: Viral infections of the respiratory system are very common. In Taiwan, the predominant viruses isolated from patients with respiratory infections are enterovirus, respiratory syncytial virus , influenza A and B viruses, adenovirus, cytomegalovirus, herpes simplex virus-1, and parainfluenza virus. 27 Enterovirus causes herpangina, hand-foot-and-mouth disease, myocarditis, encephalitis, and death. RSV is the most common pathogen of the lower respiratory tract in infants 28 and a common cause of nosocomial infections in pediatric wards. 29 Influenza A and B viruses cause seasonal epidemics in Taiwan, especially in winter. 30 Adenovirus causes acute respiratory tract infections in children younger than 5 years", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: countries . In the developed world, viruses are already the most common pathogens causing diarrhea .", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: Rotavirus infection is the most common cause of viral gastroenteritis among children; however, parents of infected children also often become ill and as a result rotavirus is the second most common cause of gastroenteritis in adults . Studies in human volunteers have shown that infection with rotavirus causes diarrhea, results in shedding of the virus and a rise in antibody anti-virus titer after infection . Additionally, astroviruses infections are common, accounting for about 10% of all sporadic diarrhea cases . Astrovirus has been isolated from diseased people, filtrated and administered to healthy individuals after which in some of the volunteers" ]

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

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

[ "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: Viral infections of the respiratory system are very common. In Taiwan, the predominant viruses isolated from patients with respiratory infections are enterovirus, respiratory syncytial virus , influenza A and B viruses, adenovirus, cytomegalovirus, herpes simplex virus-1, and parainfluenza virus. 27 Enterovirus causes herpangina, hand-foot-and-mouth disease, myocarditis, encephalitis, and death. RSV is the most common pathogen of the lower respiratory tract in infants 28 and a common cause of nosocomial infections in pediatric wards. 29 Influenza A and B viruses cause seasonal epidemics in Taiwan, especially in winter. 30 Adenovirus causes acute respiratory tract infections in children younger than 5 years", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: countries . In the developed world, viruses are already the most common pathogens causing diarrhea .", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond\nPassage: Rotavirus infection is the most common cause of viral gastroenteritis among children; however, parents of infected children also often become ill and as a result rotavirus is the second most common cause of gastroenteritis in adults . Studies in human volunteers have shown that infection with rotavirus causes diarrhea, results in shedding of the virus and a rise in antibody anti-virus titer after infection . Additionally, astroviruses infections are common, accounting for about 10% of all sporadic diarrhea cases . Astrovirus has been isolated from diseased people, filtrated and administered to healthy individuals after which in some of the volunteers" ]

[ [ "3a", "Title: Viruses Causing Gastroenteritis: The Known, The New and Those Beyond" ], [ "3b", "Passage: Rotavirus infection is the most common cause of viral gastroenteritis among children; however, parents of infected children also often become ill and as a result rotavirus is the second most common cause of gastroenteritis in adults ." ], [ "3c", "Studies in human volunteers have shown that infection with rotavirus causes diarrhea, results in shedding of the virus and a rise in antibody anti-virus titer after infection ." ], [ "3d", "Additionally, astroviruses infections are common, accounting for about 10% of all sporadic diarrhea cases ." ], [ "3e", "Astrovirus has been isolated from diseased people, filtrated and administered to healthy individuals after which in some of the volunteers" ] ]

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

[ "Title: New aspects in the management of pneumonia\nPassage: The main side effects associated with corticosteroids, especially with prolonged use, are hyperglycemia, myopathy, weight gain, brushing, and osteopenia . As well as these side effects, corticosteroids have strong immunosuppressive effects, raising concerns regarding their use in acute infections, despite their potential effect in controlling excessive inflammatory response. The immunosuppressant effect of corticosteroids is related to dose and treatment duration. For example, the use of 40 mg of prednisolone per day for more than 1 week or 20 mg prednisolone or equivalent per day for a month can produce immunosuppression. In acute infection, a low dose for a short period", "Title: New aspects in the management of pneumonia\nPassage: Glucocorticosteroid drugs reproduce effects similar to endogenous cortisol: they have anti-inflammatory activity by switching genes on and off, resulting in a reduction of inflammatory cytokines and chemokines. Corticosteroids have an effect on structural cells of the respiratory tract: they act on epithelial cells by inhibiting transcription factors such as NF-kB, on mucous glands by decreasing mucus secretion, and on smooth muscle cells by increasing β2 receptors .", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: Despite ongoing controversy, glucocorticoids remain the best studied anti-inflammatory strategy in ARDS. There is some evidence to suggest that given early in disease course, intravenous steroids reduce requirement for mechanical ventilation, length of ITU stay and improve oxygenation, with a modest effect on mortality . Such success is, however, only likely to outweigh potential complications in the setting of vigilant surveillance for nosocomial infection and eschewal of neuromuscular blockade due to the potential complications of steroid treatment. Furthermore, it has been suggested that if left to later time points, i.e. >14 days postonset, steroid administration may cause a paradoxical increase", "Title: New aspects in the management of pneumonia\nPassage: may be useful for reducing inflammation and may not cause so much harm by producing immunosuppression. Moreover, a short period of corticosteroid treatment may reduce the risk for side effects." ]

[ [ "0a", "Title: New aspects in the management of pneumonia" ], [ "0b", "Passage: The main side effects associated with corticosteroids, especially with prolonged use, are hyperglycemia, myopathy, weight gain, brushing, and osteopenia ." ], [ "0c", "As well as these side effects, corticosteroids have strong immunosuppressive effects, raising concerns regarding their use in acute infections, despite their potential effect in controlling excessive inflammatory response." ], [ "0d", "The immunosuppressant effect of corticosteroids is related to dose and treatment duration." ], [ "0e", "For example, the use of 40 mg of prednisolone per day for more than 1 week or 20 mg prednisolone or equivalent per day for a month can produce immunosuppression." ], [ "0f", "In acute infection, a low dose for a short period" ] ]

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

[ "Title: New aspects in the management of pneumonia\nPassage: The main side effects associated with corticosteroids, especially with prolonged use, are hyperglycemia, myopathy, weight gain, brushing, and osteopenia . As well as these side effects, corticosteroids have strong immunosuppressive effects, raising concerns regarding their use in acute infections, despite their potential effect in controlling excessive inflammatory response. The immunosuppressant effect of corticosteroids is related to dose and treatment duration. For example, the use of 40 mg of prednisolone per day for more than 1 week or 20 mg prednisolone or equivalent per day for a month can produce immunosuppression. In acute infection, a low dose for a short period", "Title: New aspects in the management of pneumonia\nPassage: Glucocorticosteroid drugs reproduce effects similar to endogenous cortisol: they have anti-inflammatory activity by switching genes on and off, resulting in a reduction of inflammatory cytokines and chemokines. Corticosteroids have an effect on structural cells of the respiratory tract: they act on epithelial cells by inhibiting transcription factors such as NF-kB, on mucous glands by decreasing mucus secretion, and on smooth muscle cells by increasing β2 receptors .", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: Despite ongoing controversy, glucocorticoids remain the best studied anti-inflammatory strategy in ARDS. There is some evidence to suggest that given early in disease course, intravenous steroids reduce requirement for mechanical ventilation, length of ITU stay and improve oxygenation, with a modest effect on mortality . Such success is, however, only likely to outweigh potential complications in the setting of vigilant surveillance for nosocomial infection and eschewal of neuromuscular blockade due to the potential complications of steroid treatment. Furthermore, it has been suggested that if left to later time points, i.e. >14 days postonset, steroid administration may cause a paradoxical increase", "Title: New aspects in the management of pneumonia\nPassage: may be useful for reducing inflammation and may not cause so much harm by producing immunosuppression. Moreover, a short period of corticosteroid treatment may reduce the risk for side effects." ]

[ [ "1a", "Title: New aspects in the management of pneumonia" ], [ "1b", "Passage: Glucocorticosteroid drugs reproduce effects similar to endogenous cortisol: they have anti-inflammatory activity by switching genes on and off, resulting in a reduction of inflammatory cytokines and chemokines." ], [ "1c", "Corticosteroids have an effect on structural cells of the respiratory tract: they act on epithelial cells by inhibiting transcription factors such as NF-kB, on mucous glands by decreasing mucus secretion, and on smooth muscle cells by increasing β2 receptors ." ] ]

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

[ "Title: New aspects in the management of pneumonia\nPassage: The main side effects associated with corticosteroids, especially with prolonged use, are hyperglycemia, myopathy, weight gain, brushing, and osteopenia . As well as these side effects, corticosteroids have strong immunosuppressive effects, raising concerns regarding their use in acute infections, despite their potential effect in controlling excessive inflammatory response. The immunosuppressant effect of corticosteroids is related to dose and treatment duration. For example, the use of 40 mg of prednisolone per day for more than 1 week or 20 mg prednisolone or equivalent per day for a month can produce immunosuppression. In acute infection, a low dose for a short period", "Title: New aspects in the management of pneumonia\nPassage: Glucocorticosteroid drugs reproduce effects similar to endogenous cortisol: they have anti-inflammatory activity by switching genes on and off, resulting in a reduction of inflammatory cytokines and chemokines. Corticosteroids have an effect on structural cells of the respiratory tract: they act on epithelial cells by inhibiting transcription factors such as NF-kB, on mucous glands by decreasing mucus secretion, and on smooth muscle cells by increasing β2 receptors .", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: Despite ongoing controversy, glucocorticoids remain the best studied anti-inflammatory strategy in ARDS. There is some evidence to suggest that given early in disease course, intravenous steroids reduce requirement for mechanical ventilation, length of ITU stay and improve oxygenation, with a modest effect on mortality . Such success is, however, only likely to outweigh potential complications in the setting of vigilant surveillance for nosocomial infection and eschewal of neuromuscular blockade due to the potential complications of steroid treatment. Furthermore, it has been suggested that if left to later time points, i.e. >14 days postonset, steroid administration may cause a paradoxical increase", "Title: New aspects in the management of pneumonia\nPassage: may be useful for reducing inflammation and may not cause so much harm by producing immunosuppression. Moreover, a short period of corticosteroid treatment may reduce the risk for side effects." ]

[ [ "2a", "Title: Key mechanisms governing resolution of lung inflammation" ], [ "2b", "Passage: Despite ongoing controversy, glucocorticoids remain the best studied anti-inflammatory strategy in ARDS." ], [ "2c", "There is some evidence to suggest that given early in disease course, intravenous steroids reduce requirement for mechanical ventilation, length of ITU stay and improve oxygenation, with a modest effect on mortality ." ], [ "2d", "Such success is, however, only likely to outweigh potential complications in the setting of vigilant surveillance for nosocomial infection and eschewal of neuromuscular blockade due to the potential complications of steroid treatment." ], [ "2e", "Furthermore, it has been suggested that if left to later time points, i.e. >14 days postonset, steroid administration may cause a paradoxical increase" ] ]

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

[ "Title: New aspects in the management of pneumonia\nPassage: The main side effects associated with corticosteroids, especially with prolonged use, are hyperglycemia, myopathy, weight gain, brushing, and osteopenia . As well as these side effects, corticosteroids have strong immunosuppressive effects, raising concerns regarding their use in acute infections, despite their potential effect in controlling excessive inflammatory response. The immunosuppressant effect of corticosteroids is related to dose and treatment duration. For example, the use of 40 mg of prednisolone per day for more than 1 week or 20 mg prednisolone or equivalent per day for a month can produce immunosuppression. In acute infection, a low dose for a short period", "Title: New aspects in the management of pneumonia\nPassage: Glucocorticosteroid drugs reproduce effects similar to endogenous cortisol: they have anti-inflammatory activity by switching genes on and off, resulting in a reduction of inflammatory cytokines and chemokines. Corticosteroids have an effect on structural cells of the respiratory tract: they act on epithelial cells by inhibiting transcription factors such as NF-kB, on mucous glands by decreasing mucus secretion, and on smooth muscle cells by increasing β2 receptors .", "Title: Key mechanisms governing resolution of lung inflammation\nPassage: Despite ongoing controversy, glucocorticoids remain the best studied anti-inflammatory strategy in ARDS. There is some evidence to suggest that given early in disease course, intravenous steroids reduce requirement for mechanical ventilation, length of ITU stay and improve oxygenation, with a modest effect on mortality . Such success is, however, only likely to outweigh potential complications in the setting of vigilant surveillance for nosocomial infection and eschewal of neuromuscular blockade due to the potential complications of steroid treatment. Furthermore, it has been suggested that if left to later time points, i.e. >14 days postonset, steroid administration may cause a paradoxical increase", "Title: New aspects in the management of pneumonia\nPassage: may be useful for reducing inflammation and may not cause so much harm by producing immunosuppression. Moreover, a short period of corticosteroid treatment may reduce the risk for side effects." ]

[ [ "3a", "Title: New aspects in the management of pneumonia" ], [ "3b", "Passage: may be useful for reducing inflammation and may not cause so much harm by producing immunosuppression." ], [ "3c", "Moreover, a short period of corticosteroid treatment may reduce the risk for side effects." ] ]

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: . Pneumonia deaths decreased from 1.8 million in 2000 to 900,000 in 2013 . These data do not reflect the full impact of increasingly widespread use of pneumococcal conjugate vaccine in low-and middle-income countries because the incidence of pneumonia and number of deaths are likely to decrease still further as a result of this widespread intervention .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: The overall burden of childhood pneumonia has been reduced substantially over the last decade, despite an increase in the global childhood population from 605 million in 2000 to 664 million in 2015 . Recent data suggest that there has been a 25% decrease in the incidence of pneumonia, from 0.29 episodes per child year in low-and middle-income countries in 2000, to 0.22 episodes per child year in 2010 . This is substantiated by a 58% decrease in pneumonia-associated disability-adjusted life years between 1990 and 2013, from 186 million to 78 million as estimated in the Global Burden of Disease study", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: The resulting national economic burden is approximately 1 million Euros for pneumococcal meningitis, approximately 209 million Euros for pneumonia, and approximately 293 million Euros , indirect cost , and total cost were significantly higher in pneumonia patients aged 36 months than those aged <36 months . Direct cost of AOM was significantly higher in the patients aged <36 months than those aged 36 months . On the other hand, comparison of costs between genders revealed no difference between the groups .", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: According to the global epidemiological data, more than 90% of pneumonia-related deaths in children under the age of 5 years occur in 40 countries, with the highest mortality rates in India, Pakistan, Bangladesh, and Afghanistan. 7 When intercontinental distribution of pneumonia-related death is evaluated in this age group, sub-Saharan Africa and South Asia show similar distribution. 8 In Turkey, although detailed data about respiratory tract infections are limited, the Turkey Burden of Disease Study conducted between 2002 and 2004 by the Ministry of Health reported that the ratio of disability adjusted life years caused by respiratory tract infections were 13.4%" ]

[ [ "0a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease Passage: ." ], [ "0b", "Pneumonia deaths decreased from 1.8 million in 2000 to 900,000 in 2013 ." ], [ "0c", "These data do not reflect the full impact of increasingly widespread use of pneumococcal conjugate vaccine in low-and middle-income countries because the incidence of pneumonia and number of deaths are likely to decrease still further as a result of this widespread intervention ." ] ]

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

[ "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: . Pneumonia deaths decreased from 1.8 million in 2000 to 900,000 in 2013 . These data do not reflect the full impact of increasingly widespread use of pneumococcal conjugate vaccine in low-and middle-income countries because the incidence of pneumonia and number of deaths are likely to decrease still further as a result of this widespread intervention .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: The overall burden of childhood pneumonia has been reduced substantially over the last decade, despite an increase in the global childhood population from 605 million in 2000 to 664 million in 2015 . Recent data suggest that there has been a 25% decrease in the incidence of pneumonia, from 0.29 episodes per child year in low-and middle-income countries in 2000, to 0.22 episodes per child year in 2010 . This is substantiated by a 58% decrease in pneumonia-associated disability-adjusted life years between 1990 and 2013, from 186 million to 78 million as estimated in the Global Burden of Disease study", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: The resulting national economic burden is approximately 1 million Euros for pneumococcal meningitis, approximately 209 million Euros for pneumonia, and approximately 293 million Euros , indirect cost , and total cost were significantly higher in pneumonia patients aged 36 months than those aged <36 months . Direct cost of AOM was significantly higher in the patients aged <36 months than those aged 36 months . On the other hand, comparison of costs between genders revealed no difference between the groups .", "Title: Economic burden of pneumococcal infections in children under 5 years of age\nPassage: According to the global epidemiological data, more than 90% of pneumonia-related deaths in children under the age of 5 years occur in 40 countries, with the highest mortality rates in India, Pakistan, Bangladesh, and Afghanistan. 7 When intercontinental distribution of pneumonia-related death is evaluated in this age group, sub-Saharan Africa and South Asia show similar distribution. 8 In Turkey, although detailed data about respiratory tract infections are limited, the Turkey Burden of Disease Study conducted between 2002 and 2004 by the Ministry of Health reported that the ratio of disability adjusted life years caused by respiratory tract infections were 13.4%" ]

[ [ "1a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "1b", "Passage: The overall burden of childhood pneumonia has been reduced substantially over the last decade, despite an increase in the global childhood population from 605 million in 2000 to 664 million in 2015 ." ], [ "1c", "Recent data suggest that there has been a 25% decrease in the incidence of pneumonia, from 0.29 episodes per child year in low-and middle-income countries in 2000, to 0.22 episodes per child year in 2010 ." ], [ "1d", "This is substantiated by a 58% decrease in pneumonia-associated disability-adjusted life years between 1990 and 2013, from 186 million to 78 million as estimated in the Global Burden of Disease study" ] ]

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

[ "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: Concerning NRSI combined, 52 meta-analyses included only cohort studies and 5 only prospective cohort studies; 46 meta-analyses combined cohort and case-control studies, and 23 included all types of NRSI. The other 67 meta-analyses included \"observational studies\" , \"prospective and retrospective studies\" , and only \"retrospective studies\" .", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: literature of NRSI is difficult . However, a recent study found that for 32 % of the observational studies registered at ClinicalTrials.gov, unpublished results could be retrieved . In contrast, we found that many meta-analyses assessed reporting bias . Reviewers may have compensated for the absence of searching for grey Only cohort studies 18 34 52 Including also case-control studies 18 28 46 Including all types of NRSI 5 18 23 Other 28 39 67 \"Observational studies\" 6 22 28 \"Prospective and retrospective studies\" 11 12 23 \"Retrospective studies\" 11 5 16 Did not clearly report design for each study", "Title: Comparing the outcomes of different postgraduate year training programs in Taiwan\nPassage: All of the 314 trainees participated in the MCQ exam. They were divided into four groups according to their training program.", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010\nPassage: We received 81 responses to the survey. A total of 65 studies were identified once we removed responses that did not meet our study criteria. Of the 16 studies excluded from analysis, the reasons for exclusion were the following: the study was not a pneumonia etiology study, the study did not include children less than five years of age or multiple responses were received describing the same study. Studies ranged in size from 12 to 27 778 pneumonia patients . Among the 65 pneumonia etiology studies, 41 countries were represented . There were 16 countries that reported multiple studies. Of" ]

[ [ "0a", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review" ], [ "0b", "Passage: Concerning NRSI combined, 52 meta-analyses included only cohort studies and 5 only prospective cohort studies; 46 meta-analyses combined cohort and case-control studies, and 23 included all types of NRSI." ], [ "0c", "The other 67 meta-analyses included \"observational studies\" , \"prospective and retrospective studies\" , and only \"retrospective studies\" ." ] ]

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

[ "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: Concerning NRSI combined, 52 meta-analyses included only cohort studies and 5 only prospective cohort studies; 46 meta-analyses combined cohort and case-control studies, and 23 included all types of NRSI. The other 67 meta-analyses included \"observational studies\" , \"prospective and retrospective studies\" , and only \"retrospective studies\" .", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: literature of NRSI is difficult . However, a recent study found that for 32 % of the observational studies registered at ClinicalTrials.gov, unpublished results could be retrieved . In contrast, we found that many meta-analyses assessed reporting bias . Reviewers may have compensated for the absence of searching for grey Only cohort studies 18 34 52 Including also case-control studies 18 28 46 Including all types of NRSI 5 18 23 Other 28 39 67 \"Observational studies\" 6 22 28 \"Prospective and retrospective studies\" 11 12 23 \"Retrospective studies\" 11 5 16 Did not clearly report design for each study", "Title: Comparing the outcomes of different postgraduate year training programs in Taiwan\nPassage: All of the 314 trainees participated in the MCQ exam. They were divided into four groups according to their training program.", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010\nPassage: We received 81 responses to the survey. A total of 65 studies were identified once we removed responses that did not meet our study criteria. Of the 16 studies excluded from analysis, the reasons for exclusion were the following: the study was not a pneumonia etiology study, the study did not include children less than five years of age or multiple responses were received describing the same study. Studies ranged in size from 12 to 27 778 pneumonia patients . Among the 65 pneumonia etiology studies, 41 countries were represented . There were 16 countries that reported multiple studies. Of" ]

[ [ "1a", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review" ], [ "1b", "Passage: literature of NRSI is difficult ." ], [ "1c", "However, a recent study found that for 32 % of the observational studies registered at ClinicalTrials.gov, unpublished results could be retrieved ." ], [ "1d", "In contrast, we found that many meta-analyses assessed reporting bias ." ], [ "1e", "Reviewers may have compensated for the absence of searching for grey Only cohort studies 18 34 52 Including also case-control studies 18 28 46 Including all types of NRSI 5 18 23 Other 28 39 67 \"Observational studies\" 6 22 28 \"Prospective and retrospective studies\" 11 12 23 \"Retrospective studies\" 11 5 16 Did not clearly report design for each study" ] ]

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

[ "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: Concerning NRSI combined, 52 meta-analyses included only cohort studies and 5 only prospective cohort studies; 46 meta-analyses combined cohort and case-control studies, and 23 included all types of NRSI. The other 67 meta-analyses included \"observational studies\" , \"prospective and retrospective studies\" , and only \"retrospective studies\" .", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: literature of NRSI is difficult . However, a recent study found that for 32 % of the observational studies registered at ClinicalTrials.gov, unpublished results could be retrieved . In contrast, we found that many meta-analyses assessed reporting bias . Reviewers may have compensated for the absence of searching for grey Only cohort studies 18 34 52 Including also case-control studies 18 28 46 Including all types of NRSI 5 18 23 Other 28 39 67 \"Observational studies\" 6 22 28 \"Prospective and retrospective studies\" 11 12 23 \"Retrospective studies\" 11 5 16 Did not clearly report design for each study", "Title: Comparing the outcomes of different postgraduate year training programs in Taiwan\nPassage: All of the 314 trainees participated in the MCQ exam. They were divided into four groups according to their training program.", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010\nPassage: We received 81 responses to the survey. A total of 65 studies were identified once we removed responses that did not meet our study criteria. Of the 16 studies excluded from analysis, the reasons for exclusion were the following: the study was not a pneumonia etiology study, the study did not include children less than five years of age or multiple responses were received describing the same study. Studies ranged in size from 12 to 27 778 pneumonia patients . Among the 65 pneumonia etiology studies, 41 countries were represented . There were 16 countries that reported multiple studies. Of" ]

[ [ "2a", "Title: Comparing the outcomes of different postgraduate year training programs in Taiwan" ], [ "2b", "Passage: All of the 314 trainees participated in the MCQ exam." ], [ "2c", "They were divided into four groups according to their training program." ] ]

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

[ "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: Concerning NRSI combined, 52 meta-analyses included only cohort studies and 5 only prospective cohort studies; 46 meta-analyses combined cohort and case-control studies, and 23 included all types of NRSI. The other 67 meta-analyses included \"observational studies\" , \"prospective and retrospective studies\" , and only \"retrospective studies\" .", "Title: Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review\nPassage: literature of NRSI is difficult . However, a recent study found that for 32 % of the observational studies registered at ClinicalTrials.gov, unpublished results could be retrieved . In contrast, we found that many meta-analyses assessed reporting bias . Reviewers may have compensated for the absence of searching for grey Only cohort studies 18 34 52 Including also case-control studies 18 28 46 Including all types of NRSI 5 18 23 Other 28 39 67 \"Observational studies\" 6 22 28 \"Prospective and retrospective studies\" 11 12 23 \"Retrospective studies\" 11 5 16 Did not clearly report design for each study", "Title: Comparing the outcomes of different postgraduate year training programs in Taiwan\nPassage: All of the 314 trainees participated in the MCQ exam. They were divided into four groups according to their training program.", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010\nPassage: We received 81 responses to the survey. A total of 65 studies were identified once we removed responses that did not meet our study criteria. Of the 16 studies excluded from analysis, the reasons for exclusion were the following: the study was not a pneumonia etiology study, the study did not include children less than five years of age or multiple responses were received describing the same study. Studies ranged in size from 12 to 27 778 pneumonia patients . Among the 65 pneumonia etiology studies, 41 countries were represented . There were 16 countries that reported multiple studies. Of" ]

[ [ "3a", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010" ], [ "3b", "Passage: We received 81 responses to the survey." ], [ "3c", "A total of 65 studies were identified once we removed responses that did not meet our study criteria." ], [ "3d", "Of the 16 studies excluded from analysis, the reasons for exclusion were the following: the study was not a pneumonia etiology study, the study did not include children less than five years of age or multiple responses were received describing the same study." ], [ "3e", "Studies ranged in size from 12 to 27 778 pneumonia patients ." ], [ "3f", "Among the 65 pneumonia etiology studies, 41 countries were represented ." ], [ "3g", "There were 16 countries that reported multiple studies. Of" ] ]

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

[ "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Vaccination against FIPV with an attenuated, temperature-sensitive strain of type II FIPV induces low antibody titre in kittens that have not been exposed to FCoV. However, there is considerable controversy on the safety and efficacy of this vaccine, since the vaccine contains type 2 strain, whereas type 1 viruses are more prevalent in the field . In addition, antibodies against FIPV do not protect infected cats but enhance the infection of monocytes and macrophages via a mechanism known as Antibody-Dependent Enhancement . Besides vaccines, several antiviral drugs such as ribavirin, 2 BioMed Research International interferons, and immunosuppressive drugs have been", "Title: Avipoxviruses: infection biology and their use as vaccine vectors\nPassage: In the poultry industry, prophylactic measures against FWPV are achieved primarily by vaccination with live FWPV or antigenically similar pigeonpox virus strains produced in CEF cells . In the past two decades, numerous outbreaks have been reported in vaccinated flocks, suggesting that vaccines used against the disease were not effective. In the United States a commercial FWPV vaccine was shown to be contaminated with REV and caused lymphoma among broiler chickens . It has been shown that sequences of REV have been integrated into the DNA of FWPV vaccines as well as in field FWPV isolates . The integration site", "Title: Protection against Foot-and-Mouth Disease Virus in Guinea Pigs via Oral Administration of Recombinant Lactobacillus plantarum Expressing VP1\nPassage: Although vaccines have been useful for controlling and even eradicating FMD from parts of the world since the early 1900s, the disease still infects millions of animals each year and remains the main sanitary barrier to the commerce of animals and animal products. Vaccination is the main prophylactic method of preventing FMDV infection. Many types of vaccines have been designed-almost entirely parenterally administered-including inactivated antigen vaccines, live attenuated vaccines, DNA vaccines, empty capsid vaccines and synthetic peptide vaccines . Inactivated virus vaccines can elicit high levels of neutralizing antibodies and offer efficacious protection against homologous serotypes . However, these vaccines", "Title: Viral vector-based influenza vaccines\nPassage: subtype, namely A . 95, 96 Although FPV vector vaccines expressing influenza viral antigens rarely have been used in non-avian species, FPV-HA was capable of inducing antibody responses in cats 97 and afforded protection in pigs when challenged with a lowpathogenic A influenza virus. 67" ]

[ [ "0a", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication" ], [ "0b", "Passage: Vaccination against FIPV with an attenuated, temperature-sensitive strain of type II FIPV induces low antibody titre in kittens that have not been exposed to FCoV." ], [ "0c", "However, there is considerable controversy on the safety and efficacy of this vaccine, since the vaccine contains type 2 strain, whereas type 1 viruses are more prevalent in the field ." ], [ "0d", "In addition, antibodies against FIPV do not protect infected cats but enhance the infection of monocytes and macrophages via a mechanism known as Antibody-Dependent Enhancement ." ], [ "0e", "Besides vaccines, several antiviral drugs such as ribavirin, 2 BioMed Research International interferons, and immunosuppressive drugs have been" ] ]

[ "0a", "0b" ]

[ "Title: Viral vector-based influenza vaccines\nPassage: vaccination.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Similarly, various viral vectors have been successfully tested for their capability to deliver heterologous vaccine antigens, and this generally results in the induction of strong CTL immune responses. In the veterinary field, there are numerous viral vector vaccines that are currently licensed for use in livestock and domesticated animals. These recombinant vaccines are based on both DNA viruses and RNA viruses -based vaccines to be used in horses against West Nile virus] . Based on the safety record in the veterinary field, many viruses have been studied for human use as a vector in vaccine development . Amongst them, YFV", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Other bacteria that were developed as DNA vaccine carriers include Listeria monocytogenes , Shigella spp. , and Yersinia enterolica .", "Title: Viral vector-based influenza vaccines\nPassage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types. 184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector. 184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview" ]

[ [ "1a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "1b", "Passage: Similarly, various viral vectors have been successfully tested for their capability to deliver heterologous vaccine antigens, and this generally results in the induction of strong CTL immune responses." ], [ "1c", "In the veterinary field, there are numerous viral vector vaccines that are currently licensed for use in livestock and domesticated animals." ], [ "1d", "These recombinant vaccines are based on both DNA viruses and RNA viruses -based vaccines to be used in horses against West Nile virus] ." ], [ "1e", "Based on the safety record in the veterinary field, many viruses have been studied for human use as a vector in vaccine development ." ], [ "1f", "Amongst them, YFV" ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: vaccination.", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: Similarly, various viral vectors have been successfully tested for their capability to deliver heterologous vaccine antigens, and this generally results in the induction of strong CTL immune responses. In the veterinary field, there are numerous viral vector vaccines that are currently licensed for use in livestock and domesticated animals. These recombinant vaccines are based on both DNA viruses and RNA viruses -based vaccines to be used in horses against West Nile virus] . Based on the safety record in the veterinary field, many viruses have been studied for human use as a vector in vaccine development . Amongst them, YFV", "Title: Live Bacterial Vectors—A Promising DNA Vaccine Delivery System\nPassage: Other bacteria that were developed as DNA vaccine carriers include Listeria monocytogenes , Shigella spp. , and Yersinia enterolica .", "Title: Viral vector-based influenza vaccines\nPassage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types. 184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector. 184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview" ]

[ [ "3a", "Title: Viral vector-based influenza vaccines" ], [ "3b", "Passage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types." ], [ "3c", "184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector." ], [ "3d", "184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The URT is a less invasive and more convenient sampling site however, and an oropharyngeal and throat swab or a nasopharyngeal aspirate/wash are recommended when URT sampling is to be conducted . Paired sera, collected two to three weeks apart are preferable for serological testing while a single sample is suggested to be sufficient if collected two weeks after onset of disease or a single serum collected during the first 10-12 days if conducting RT-rtPCR . Human urine and stool have been found to contain MERS-CoV RNA 12 to 26 days after symptom onset and are listed as samples that", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: should be considered . In two cases that arrived in the Netherlands, urine was RT-rtPCR negative but faeces was weakly positive and sera were RT-rtPCR positive for five days or more . The finding of MERS-CoV viral RNA in serum provides an avenue for retrospective PCR-based studies if respiratory samples are unavailable . RNAaemia may also correlate with disease severity; signs of virus were cleared from the serum of a recovered patient, yet lingered until the death of another .", "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: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity\nPassage: Unfortunately, in our study, we did not collect stool samples from patients and did not pursue viral RNA in the stool. But we believe the existence of virus RNA in the stool samples from these patients because that a large amount of viral RNA was detected in anal swabs and that viral RNA had also been detected in a case reported from the United States . Also, we didn't collect sputum and bronchoalveolar lavage fluid for virus detection because that the dry coughing characteristic of patients infected with 2019-nCoV prevents producing enough amount of sputum and that bronchoalveolar lavage fluid" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: The URT is a less invasive and more convenient sampling site however, and an oropharyngeal and throat swab or a nasopharyngeal aspirate/wash are recommended when URT sampling is to be conducted ." ], [ "0c", "Paired sera, collected two to three weeks apart are preferable for serological testing while a single sample is suggested to be sufficient if collected two weeks after onset of disease or a single serum collected during the first 10-12 days if conducting RT-rtPCR ." ], [ "0d", "Human urine and stool have been found to contain MERS-CoV RNA 12 to 26 days after symptom onset and are listed as samples that" ] ]

[ "0d", "1c" ]

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The URT is a less invasive and more convenient sampling site however, and an oropharyngeal and throat swab or a nasopharyngeal aspirate/wash are recommended when URT sampling is to be conducted . Paired sera, collected two to three weeks apart are preferable for serological testing while a single sample is suggested to be sufficient if collected two weeks after onset of disease or a single serum collected during the first 10-12 days if conducting RT-rtPCR . Human urine and stool have been found to contain MERS-CoV RNA 12 to 26 days after symptom onset and are listed as samples that", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: should be considered . In two cases that arrived in the Netherlands, urine was RT-rtPCR negative but faeces was weakly positive and sera were RT-rtPCR positive for five days or more . The finding of MERS-CoV viral RNA in serum provides an avenue for retrospective PCR-based studies if respiratory samples are unavailable . RNAaemia may also correlate with disease severity; signs of virus were cleared from the serum of a recovered patient, yet lingered until the death of another .", "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: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity\nPassage: Unfortunately, in our study, we did not collect stool samples from patients and did not pursue viral RNA in the stool. But we believe the existence of virus RNA in the stool samples from these patients because that a large amount of viral RNA was detected in anal swabs and that viral RNA had also been detected in a case reported from the United States . Also, we didn't collect sputum and bronchoalveolar lavage fluid for virus detection because that the dry coughing characteristic of patients infected with 2019-nCoV prevents producing enough amount of sputum and that bronchoalveolar lavage fluid" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: should be considered ." ], [ "1c", "In two cases that arrived in the Netherlands, urine was RT-rtPCR negative but faeces was weakly positive and sera were RT-rtPCR positive for five days or more ." ], [ "1d", "The finding of MERS-CoV viral RNA in serum provides an avenue for retrospective PCR-based studies if respiratory samples are unavailable ." ], [ "1e", "RNAaemia may also correlate with disease severity; signs of virus were cleared from the serum of a recovered patient, yet lingered until the death of another ." ] ]

[ "0d", "1c" ]

[ "Title: Differential Response of Primary Alveolar Type I and Type II Cells to LPS Stimulation\nPassage: The alveolar epithelium is an important component of the innate immune response of the lung. By providing an anatomic barrier that separates the organism from the external environment, the alveolar epithelium serves as a first line of defense against potential inhaled pathogens. While the cells of the innate immune system, such as alveolar macrophages and dendritic cells, harbor the bulk of the responsibility for prompting an immune reaction upon encountering inhaled pathogens, the cells that comprise the alveolar epithelium have also been implicated in aiding to trigger an inflammatory response.", "Title: Epithelial Cells Derived from Swine Bone Marrow Express Stem Cell Markers and Support Influenza Virus Replication In Vitro\nPassage: Bone marrow cell therapy may be effective in conditions that currently lack effective treatment. Stem cells isolated from different anatomic niches of lungs have been shown to differentiate into multiple epithelial cell types following lung injury. Our lab and Wong and colleagues demonstrated the existence of progenitor epithelial cells in the bone marrow of pigs and humans respectively which are capable of differentiating into type I and II pneumocytes suggesting that these cells will be valuable for lung therapies. Functionally, type I pneumocytes are important for gas exchange, water permeability and the regulation of alveolar fluid homeostasis whereas type II", "Title: Epithelial Cells Derived from Swine Bone Marrow Express Stem Cell Markers and Support Influenza Virus Replication In Vitro\nPassage: endotoxin-induced lung injury . Following infusion of BMCs in animal models, these cells have been identified as type I and II alveolar epithelial cells, endothelial cells, fibroblasts, and bronchial epithelial cells . However, precise identity of specific subpopulation of BMCs that engraft in the lung parenchyma and have regenerative potential is still not clear.", "Title: Lung epithelial GM-CSF improves host defense function and epithelial repair in influenza virus pneumonia—a new therapeutic strategy?\nPassage: Myeloid cells like monocytes, macrophages, dendritic cells , and their common precursor cells, summarized as mononuclear phagocytes, are crucial in driving IV clearance . Combining sensor and effector functions of innate immunity, the lung epithelium plays an important role in coordinating, maintaining, and balancing the phagocyte-mediated antiviral host response . The intimate spatial proximity of alveolar macrophages and the tissue-resident DC network with the distal lung epithelium provides an ideal basis for direct cell-cell communication. Mechanisms involved in this cellular crosstalk might represent potential targets for treatment." ]

[ [ "0a", "Title: Differential Response of Primary Alveolar Type I and Type II Cells to LPS Stimulation" ], [ "0b", "Passage: The alveolar epithelium is an important component of the innate immune response of the lung." ], [ "0c", "By providing an anatomic barrier that separates the organism from the external environment, the alveolar epithelium serves as a first line of defense against potential inhaled pathogens." ], [ "0d", "While the cells of the innate immune system, such as alveolar macrophages and dendritic cells, harbor the bulk of the responsibility for prompting an immune reaction upon encountering inhaled pathogens, the cells that comprise the alveolar epithelium have also been implicated in aiding to trigger an inflammatory response." ] ]

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

[ "Title: Differential Response of Primary Alveolar Type I and Type II Cells to LPS Stimulation\nPassage: The alveolar epithelium is an important component of the innate immune response of the lung. By providing an anatomic barrier that separates the organism from the external environment, the alveolar epithelium serves as a first line of defense against potential inhaled pathogens. While the cells of the innate immune system, such as alveolar macrophages and dendritic cells, harbor the bulk of the responsibility for prompting an immune reaction upon encountering inhaled pathogens, the cells that comprise the alveolar epithelium have also been implicated in aiding to trigger an inflammatory response.", "Title: Epithelial Cells Derived from Swine Bone Marrow Express Stem Cell Markers and Support Influenza Virus Replication In Vitro\nPassage: Bone marrow cell therapy may be effective in conditions that currently lack effective treatment. Stem cells isolated from different anatomic niches of lungs have been shown to differentiate into multiple epithelial cell types following lung injury. Our lab and Wong and colleagues demonstrated the existence of progenitor epithelial cells in the bone marrow of pigs and humans respectively which are capable of differentiating into type I and II pneumocytes suggesting that these cells will be valuable for lung therapies. Functionally, type I pneumocytes are important for gas exchange, water permeability and the regulation of alveolar fluid homeostasis whereas type II", "Title: Epithelial Cells Derived from Swine Bone Marrow Express Stem Cell Markers and Support Influenza Virus Replication In Vitro\nPassage: endotoxin-induced lung injury . Following infusion of BMCs in animal models, these cells have been identified as type I and II alveolar epithelial cells, endothelial cells, fibroblasts, and bronchial epithelial cells . However, precise identity of specific subpopulation of BMCs that engraft in the lung parenchyma and have regenerative potential is still not clear.", "Title: Lung epithelial GM-CSF improves host defense function and epithelial repair in influenza virus pneumonia—a new therapeutic strategy?\nPassage: Myeloid cells like monocytes, macrophages, dendritic cells , and their common precursor cells, summarized as mononuclear phagocytes, are crucial in driving IV clearance . Combining sensor and effector functions of innate immunity, the lung epithelium plays an important role in coordinating, maintaining, and balancing the phagocyte-mediated antiviral host response . The intimate spatial proximity of alveolar macrophages and the tissue-resident DC network with the distal lung epithelium provides an ideal basis for direct cell-cell communication. Mechanisms involved in this cellular crosstalk might represent potential targets for treatment." ]

[ [ "3a", "Title: Lung epithelial GM-CSF improves host defense function and epithelial repair in influenza virus pneumonia—a new therapeutic strategy?" ], [ "3b", "Passage: Myeloid cells like monocytes, macrophages, dendritic cells , and their common precursor cells, summarized as mononuclear phagocytes, are crucial in driving IV clearance ." ], [ "3c", "Combining sensor and effector functions of innate immunity, the lung epithelium plays an important role in coordinating, maintaining, and balancing the phagocyte-mediated antiviral host response ." ], [ "3d", "The intimate spatial proximity of alveolar macrophages and the tissue-resident DC network with the distal lung epithelium provides an ideal basis for direct cell-cell communication." ], [ "3e", "Mechanisms involved in this cellular crosstalk might represent potential targets for treatment." ] ]

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

[ "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes. But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures. R is the effectiive number and can include the impact of control measures.", "Title: The Failure of R (0)\nPassage: death rates from the corresponding ODE. Thus, in this case, R 0 does not signal epidemic growth as anticipated from other methods. Roberts noted three fundamental properties commonly attributed to R 0 : that an endemic infection can persist only if R 0 > 1, R 0 provides a direct measure of the control effort required to eliminate the infection, and pathogens evolve to maximise their R 0 value.", "Title: The Failure of R (0)\nPassage: What is urgently needed is a simple, but accurate, measure of disease spread that has a consistent threshold property and which can be understood by nonmathematicians. If R 0 is to be used, it must be accompanied by a declaration of which method was used, which assumptions are underlying the model and evidence that it is actually a threshold, with no backward bifurcation. Without such caveats, the concept of R 0 will continue to fail.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: infection of index cases and the secondary cases they produce. The R0 is a measure of the transmissibility of the strain in the population, and largely determines the proportion of the population that will be infected in a pandemic. The ratio R0/Tg is a measure of an epidemic's rate of growth." ]

[ [ "0a", "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus" ], [ "0b", "Passage: Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes." ], [ "0c", "But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures." ], [ "0d", "R is the effectiive number and can include the impact of control measures." ] ]

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

[ "Title: Preparation for Possible Sustained Transmission of 2019 Novel Coronavirus\nPassage: Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes. But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures. R is the effectiive number and can include the impact of control measures.", "Title: The Failure of R (0)\nPassage: death rates from the corresponding ODE. Thus, in this case, R 0 does not signal epidemic growth as anticipated from other methods. Roberts noted three fundamental properties commonly attributed to R 0 : that an endemic infection can persist only if R 0 > 1, R 0 provides a direct measure of the control effort required to eliminate the infection, and pathogens evolve to maximise their R 0 value.", "Title: The Failure of R (0)\nPassage: What is urgently needed is a simple, but accurate, measure of disease spread that has a consistent threshold property and which can be understood by nonmathematicians. If R 0 is to be used, it must be accompanied by a declaration of which method was used, which assumptions are underlying the model and evidence that it is actually a threshold, with no backward bifurcation. Without such caveats, the concept of R 0 will continue to fail.", "Title: The Model Repository of the Models of Infectious Disease Agent Study\nPassage: infection of index cases and the secondary cases they produce. The R0 is a measure of the transmissibility of the strain in the population, and largely determines the proportion of the population that will be infected in a pandemic. The ratio R0/Tg is a measure of an epidemic's rate of growth." ]

[ [ "3a", "Title: The Model Repository of the Models of Infectious Disease Agent Study" ], [ "3b", "Passage: infection of index cases and the secondary cases they produce." ], [ "3c", "The R0 is a measure of the transmissibility of the strain in the population, and largely determines the proportion of the population that will be infected in a pandemic." ], [ "3d", "The ratio R0/Tg is a measure of an epidemic's rate of growth." ] ]

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: In an analysis of the first 425 confirmed cases of infection, 73% of cases with illness onset between 12 and 22 January reported no exposure to either a wet market or another person with symptoms of a respiratory illness . The lack of reported exposure to another ill person could be attributed to lack of awareness or recall bias, but China's health minister publicly warned that pre-symptomatic transmission could be occurring . Determining the extent to which asymptomatic or pre-symptomatic transmission might be occurring is an urgent priority, because it has direct implications for public health and hospital infection control.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: For our work, we developed a stochastic agent-based pandemic model on a small-scale city. We extended the typical transmission model by adding a pre-symptomatic phase, thus resulting in the SEPIR model. In addition, we further refined the infectious phase into one of the three possible categories-asymptomatic, symptomatic and critical . To capture the constraints imposed by societal norms, such as the different population response patterns during different times of the day, we set the granularity of the time scale to be in terms of hours, rather than days.", "Title: Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting\nPassage: a long history of low numbers of cases. If our missing source of infections was mainly indigenous asymptomatic infections, it would signify that there is an asymptomatic reservoir contributing to onward transmission and that must be controlled to reach elimination. This could be achieved through PCR-based screening and treatment or increased vector control in focal areas. An alternative explanation is that there may be a small number of unreported symptomatic cases or relapse cases which were not reported or detected, which could be indigenous or imported. If due to importation this would further support the need for strong regional cooperation", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: Those under 18 years are a critical group to study in order to tease out the relative roles of susceptibility vs severity as possible underlying causes for the very rare recorded instances of infection in this age group. Are children protected from infection or do they not fall ill after infection? If they are naturally immune, which is unlikely, we should understand why; otherwise, even if they do not show symptoms, it is important to know if they shed the virus. Obviously, the question about virus shedding of those being infected but asymptomatic leads to the crucial question of infectivity." ]

[ [ "0a", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak" ], [ "0b", "Passage: In an analysis of the first 425 confirmed cases of infection, 73% of cases with illness onset between 12 and 22 January reported no exposure to either a wet market or another person with symptoms of a respiratory illness ." ], [ "0c", "The lack of reported exposure to another ill person could be attributed to lack of awareness or recall bias, but China's health minister publicly warned that pre-symptomatic transmission could be occurring ." ], [ "0d", "Determining the extent to which asymptomatic or pre-symptomatic transmission might be occurring is an urgent priority, because it has direct implications for public health and hospital infection control." ] ]

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

[ "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: In an analysis of the first 425 confirmed cases of infection, 73% of cases with illness onset between 12 and 22 January reported no exposure to either a wet market or another person with symptoms of a respiratory illness . The lack of reported exposure to another ill person could be attributed to lack of awareness or recall bias, but China's health minister publicly warned that pre-symptomatic transmission could be occurring . Determining the extent to which asymptomatic or pre-symptomatic transmission might be occurring is an urgent priority, because it has direct implications for public health and hospital infection control.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: For our work, we developed a stochastic agent-based pandemic model on a small-scale city. We extended the typical transmission model by adding a pre-symptomatic phase, thus resulting in the SEPIR model. In addition, we further refined the infectious phase into one of the three possible categories-asymptomatic, symptomatic and critical . To capture the constraints imposed by societal norms, such as the different population response patterns during different times of the day, we set the granularity of the time scale to be in terms of hours, rather than days.", "Title: Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting\nPassage: a long history of low numbers of cases. If our missing source of infections was mainly indigenous asymptomatic infections, it would signify that there is an asymptomatic reservoir contributing to onward transmission and that must be controlled to reach elimination. This could be achieved through PCR-based screening and treatment or increased vector control in focal areas. An alternative explanation is that there may be a small number of unreported symptomatic cases or relapse cases which were not reported or detected, which could be indigenous or imported. If due to importation this would further support the need for strong regional cooperation", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak\nPassage: Those under 18 years are a critical group to study in order to tease out the relative roles of susceptibility vs severity as possible underlying causes for the very rare recorded instances of infection in this age group. Are children protected from infection or do they not fall ill after infection? If they are naturally immune, which is unlikely, we should understand why; otherwise, even if they do not show symptoms, it is important to know if they shed the virus. Obviously, the question about virus shedding of those being infected but asymptomatic leads to the crucial question of infectivity." ]

[ [ "3a", "Title: Epidemiological research priorities for public health control of the ongoing global novel coronavirus (2019-nCoV) outbreak" ], [ "3b", "Passage: Those under 18 years are a critical group to study in order to tease out the relative roles of susceptibility vs severity as possible underlying causes for the very rare recorded instances of infection in this age group." ], [ "3c", "Are children protected from infection or do they not fall ill after infection?" ], [ "3d", "If they are naturally immune, which is unlikely, we should understand why; otherwise, even if they do not show symptoms, it is important to know if they shed the virus." ], [ "3e", "Obviously, the question about virus shedding of those being infected but asymptomatic leads to the crucial question of infectivity." ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Abstract: Chikungunya virus is a mosquito-borne emerging pathogen that has a major health impact in humans and causes fever disease, headache, rash, nausea, vomiting, myalgia, and arthralgia. Indigenous to tropical Africa, recent large outbreaks have been reported in parts of South East Asia and several of its neighboring islands in 2005–07 and in Europe in 2007. Furthermore, positive cases have been confirmed in the United States in travelers returning from known outbreak areas. Currently, there is no vaccine or antiviral treatment. With the threat of an emerging global pandemic, the peculiar problems associated with the more immediate and seasonal epidemics", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: vector similar to the ones observed in Reunion Island .", "Title: Inflammatory Cytokine Expression Is Associated with Chikungunya Virus Resolution and Symptom Severity\nPassage: The Chikungunya virus , an arthropod-borne virus , is a single-stranded positive-sense RNA virus with three genotypes. The virus is of the Alphavirus genus in the Togaviridae family . CHIKV has been shown to infect and be transmitted by Ae. aegyptii and Ae. albopictus mosquitoes. It was identified in East Africa in the early 1950s and since then has caused epidemics in continental Africa, the Indian Ocean region, and countries of Southeast Asia such as India, where since 2006 suspected cases have been estimated to be 1.39 million, and Singapore . The only reported outbreak outside these areas was in" ]

[ [ "0a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "0b", "Passage: Abstract: Chikungunya virus is a mosquito-borne emerging pathogen that has a major health impact in humans and causes fever disease, headache, rash, nausea, vomiting, myalgia, and arthralgia." ], [ "0c", "Indigenous to tropical Africa, recent large outbreaks have been reported in parts of South East Asia and several of its neighboring islands in 2005–07 and in Europe in 2007." ], [ "0d", "Furthermore, positive cases have been confirmed in the United States in travelers returning from known outbreak areas." ], [ "0e", "Currently, there is no vaccine or antiviral treatment." ], [ "0f", "With the threat of an emerging global pandemic, the peculiar problems associated with the more immediate and seasonal epidemics" ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Abstract: Chikungunya virus is a mosquito-borne emerging pathogen that has a major health impact in humans and causes fever disease, headache, rash, nausea, vomiting, myalgia, and arthralgia. Indigenous to tropical Africa, recent large outbreaks have been reported in parts of South East Asia and several of its neighboring islands in 2005–07 and in Europe in 2007. Furthermore, positive cases have been confirmed in the United States in travelers returning from known outbreak areas. Currently, there is no vaccine or antiviral treatment. With the threat of an emerging global pandemic, the peculiar problems associated with the more immediate and seasonal epidemics", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: vector similar to the ones observed in Reunion Island .", "Title: Inflammatory Cytokine Expression Is Associated with Chikungunya Virus Resolution and Symptom Severity\nPassage: The Chikungunya virus , an arthropod-borne virus , is a single-stranded positive-sense RNA virus with three genotypes. The virus is of the Alphavirus genus in the Togaviridae family . CHIKV has been shown to infect and be transmitted by Ae. aegyptii and Ae. albopictus mosquitoes. It was identified in East Africa in the early 1950s and since then has caused epidemics in continental Africa, the Indian Ocean region, and countries of Southeast Asia such as India, where since 2006 suspected cases have been estimated to be 1.39 million, and Singapore . The only reported outbreak outside these areas was in" ]

[ [ "1a", "Title: Chikungunya: A Potentially Emerging Epidemic?" ], [ "1b", "Passage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times ." ], [ "1c", "CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator ." ], [ "1d", "CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures ." ], [ "1e", "The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends" ] ]

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

[ "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Abstract: Chikungunya virus is a mosquito-borne emerging pathogen that has a major health impact in humans and causes fever disease, headache, rash, nausea, vomiting, myalgia, and arthralgia. Indigenous to tropical Africa, recent large outbreaks have been reported in parts of South East Asia and several of its neighboring islands in 2005–07 and in Europe in 2007. Furthermore, positive cases have been confirmed in the United States in travelers returning from known outbreak areas. Currently, there is no vaccine or antiviral treatment. With the threat of an emerging global pandemic, the peculiar problems associated with the more immediate and seasonal epidemics", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: Text: Chikungunya virus , a mosquito-borne pathogen listed by National Institute of Allergy and Infectious Diseases as a Category C Priority Pathogen that causes Chikungunya fever , has been spreading throughout Asia, Africa, and parts of Europe in recent times . CHIKV is an arthropod-borne virus and is transmitted to humans primarily by Aedes aegypti, the infamous yellow fever propagator . CHIKV infection is marked by severe joint pain, contorting its victims into unusual postures . The disease gets its name from the Kimakonde vernacular language of Tanzania and Mozambique, and the word chikungunya means ''that which contorts or bends", "Title: Chikungunya: A Potentially Emerging Epidemic?\nPassage: vector similar to the ones observed in Reunion Island .", "Title: Inflammatory Cytokine Expression Is Associated with Chikungunya Virus Resolution and Symptom Severity\nPassage: The Chikungunya virus , an arthropod-borne virus , is a single-stranded positive-sense RNA virus with three genotypes. The virus is of the Alphavirus genus in the Togaviridae family . CHIKV has been shown to infect and be transmitted by Ae. aegyptii and Ae. albopictus mosquitoes. It was identified in East Africa in the early 1950s and since then has caused epidemics in continental Africa, the Indian Ocean region, and countries of Southeast Asia such as India, where since 2006 suspected cases have been estimated to be 1.39 million, and Singapore . The only reported outbreak outside these areas was in" ]

[ [ "3a", "Title: Inflammatory Cytokine Expression Is Associated with Chikungunya Virus Resolution and Symptom Severity" ], [ "3b", "Passage: The Chikungunya virus , an arthropod-borne virus , is a single-stranded positive-sense RNA virus with three genotypes." ], [ "3c", "The virus is of the Alphavirus genus in the Togaviridae family ." ], [ "3d", "CHIKV has been shown to infect and be transmitted by Ae." ], [ "3e", "aegyptii and Ae. albopictus mosquitoes." ], [ "3f", "It was identified in East Africa in the early 1950s and since then has caused epidemics in continental Africa, the Indian Ocean region, and countries of Southeast Asia such as India, where since 2006 suspected cases have been estimated to be 1.39 million, and Singapore ." ], [ "3g", "The only reported outbreak outside these areas was in" ] ]

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

[ "Title: Clinical characteristics and outcomes in critical patients with hemorrhagic fever with renal syndrome\nPassage: Of the clinical manifestations, agitation, conjunctival hemorrhage, and coma were negatively correlated with the survival outcome . Of the HFRSrelated complications, cardiac failure, ARDS and encephalopathy were negatively correlated with the survival outcome, while ARF was positively correlated with the survival outcome . Of the laboratory parameters, WBC, PT and APTT were negatively correlated with the survival outcome, while Scr was positively correlated with the survival outcome .", "Title: Clinical characteristics and outcomes in critical patients with hemorrhagic fever with renal syndrome\nPassage: Laboratory and imaging results that documented the clinical presentations and outcomes of the critical patients with HFRS complicated by ARDS were analyzed and compared. Biochemical tests of blood samples were performed using an autoanalyzer , including basic metabolic, liver and renal function and glucose tests. Blood clotting functions were tested using hematology analyzers . Chest and abdomen organs were visualized using X-ray radiography and ultrasonography . Computed tomography was performed in some patients. Cardiac function was measured using Cardiofax and ultrasonography . Arterial blood gases were measured using an automatic blood gas system . Hemo cultures were tested using an", "Title: Study on expression of plasma sCD138 in patients with hemorrhagic fever with renal syndrome\nPassage: According to the HFRS criteria of clinical classification , the severity of HFRS was classified into four types: mild, defined as patients who had kidney injury without oliguria and hypotension; moderate, defined as patients who had uremia, effusion , hypotension, hemorrhage , and AKI with typical oliguria; severe, defined as patients who had severe uremia, effusion , hemorrhage , hypotension and AKI with oliguria for ≤5 days or anuria for ≤2 days; and critical, defined as patients who usually had one or more of the following complications compared with the severe patients: refractory shock , visceral hemorrhage, heart failure, pulmonary", "Title: Clinical characteristics and outcomes in critical patients with hemorrhagic fever with renal syndrome\nPassage: The medical charts of 356 typical HFRS patients who were treated in the Center for Infectious Diseases, Tangdu Hospital, between January 2008 and August 2012 were selected randomly and reviewed. The diagnosis of HFRS was made based upon the detection of specific IgM and IgG antibodies to HTNV in acute phase serum specimens by enzyme-linked immunosorbent assay ." ]

[ [ "3a", "Title: Clinical characteristics and outcomes in critical patients with hemorrhagic fever with renal syndrome" ], [ "3b", "Passage: The medical charts of 356 typical HFRS patients who were treated in the Center for Infectious Diseases, Tangdu Hospital, between January 2008 and August 2012 were selected randomly and reviewed." ], [ "3c", "The diagnosis of HFRS was made based upon the detection of specific IgM and IgG antibodies to HTNV in acute phase serum specimens by enzyme-linked immunosorbent assay ." ] ]

[ "3b", "3c" ]

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: The interferon-induced transmembrane protein family is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic loop and extracellular amino-and carboxyl-terminal polypeptide sequences . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans and 7 members in mice . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation , cell-to-cell adhesion , antiviral activity , and bone formation , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: to increase calcium uptake and bone nodule formation . Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 , interferon inducible protein 1 , interferoninduced protein with tetratricopeptide repeats 3 , bmicroglobulin , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity." ]

[ [ "0a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "0b", "Passage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein ." ], [ "0c", "Among the IFITM family proteins, IFITM5 is unique." ], [ "0d", "Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements ." ], [ "0e", "Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ." ], [ "0f", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: The interferon-induced transmembrane protein family is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic loop and extracellular amino-and carboxyl-terminal polypeptide sequences . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans and 7 members in mice . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation , cell-to-cell adhesion , antiviral activity , and bone formation , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: to increase calcium uptake and bone nodule formation . Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 , interferon inducible protein 1 , interferoninduced protein with tetratricopeptide repeats 3 , bmicroglobulin , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity." ]

[ [ "1a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "1b", "Passage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein ." ], [ "1c", "Among the IFITM family proteins, IFITM5 is unique." ], [ "1d", "Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements ." ], [ "1e", "Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ." ], [ "1f", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: The interferon-induced transmembrane protein family is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic loop and extracellular amino-and carboxyl-terminal polypeptide sequences . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans and 7 members in mice . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation , cell-to-cell adhesion , antiviral activity , and bone formation , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: to increase calcium uptake and bone nodule formation . Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 , interferon inducible protein 1 , interferoninduced protein with tetratricopeptide repeats 3 , bmicroglobulin , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity." ]

[ [ "2a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "2b", "Passage: The interferon-induced transmembrane protein family is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic loop and extracellular amino-and carboxyl-terminal polypeptide sequences ." ], [ "2c", "The IFITM proteins are evolutionarily conserved in vertebrates ." ], [ "2d", "Recent genomic research has revealed that there are 5 IFITM members in humans and 7 members in mice ." ], [ "2e", "These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation , cell-to-cell adhesion , antiviral activity , and bone formation , although the detailed functions of IFITM6, 7, and 10 are unknown at present." ], [ "2f", "In particular, IFITM3" ] ]

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

[ "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like protein . Among the IFITM family proteins, IFITM5 is unique. Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins , while IFITM1-3 proteins share ~ 85% similarity with each", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: The interferon-induced transmembrane protein family is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic loop and extracellular amino-and carboxyl-terminal polypeptide sequences . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans and 7 members in mice . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation , cell-to-cell adhesion , antiviral activity , and bone formation , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells\nPassage: to increase calcium uptake and bone nodule formation . Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 , interferon inducible protein 1 , interferoninduced protein with tetratricopeptide repeats 3 , bmicroglobulin , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity." ]

[ [ "3a", "Title: Role of S-Palmitoylation on IFITM5 for the Interaction with FKBP11 in Osteoblast Cells" ], [ "3b", "Passage: to increase calcium uptake and bone nodule formation ." ], [ "3c", "Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator complex ." ], [ "3d", "When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 , interferon inducible protein 1 , interferoninduced protein with tetratricopeptide repeats 3 , bmicroglobulin , and MHC class I antigen gene." ], [ "3e", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity." ] ]

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

[ "Title: A New Model for Hendra Virus Encephalitis in the Mouse\nPassage: bats have been identified as the reservoir host , however epidemiological evidence does not support direct bat to human transmission. Horses have been an intermediate host in the transmission of disease to humans in all cases. There are as yet no readily available effective therapies or prophylaxis for HeV infection, either for use in humans or other susceptible animals.", "Title: Molecular Phylogeny of Hantaviruses Harbored by Insectivorous Bats in Côte d’Ivoire and Vietnam\nPassage: Mammalian reservoirs of zoonotic viruses typically do not display host restrictions within a given taxonomic order. Also, infection is usually chronic, persistent and subclinical. For example, rodents of multiple genera and species, belonging to four subfamilies in the order Rodentia, serve as reservoirs of hantaviruses in Eurasia, Africa and the Americas and do not exhibit clinical disease or survival disadvantage. In addition, recently, hantaviruses exhibiting far greater genetic diversity have been detected in healthy-appearing shrews and moles representing many genera in six subfamilies within the order Soricomorpha in Eurasia, Africa and North America. Similarly, as mentioned earlier, bat species belonging", "Title: Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France\nPassage: Hantaviruses are emerging zoonotic pathogens distributed worldwide except in Antarctica . They may cause two severe pathologies in humans: hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome . Viruses of the genus Hantavirus are exceptions within the Bunyaviridae family, in being directly transmitted via aerosols ofsmall mammals excreta with no role for arthropod vectors . Although a growing diversity of hantaviruses has been discovered over the last decade in insectivores and bats , up to now, only rodent-borne hantaviruses have been shown at the origin of human diseases. Hantaviruses are small, enveloped viruses, possessing a tri-segmented RNA genome of", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Hantavirus is a virus transmitted mainly by rodent animals, mainly through urine, feces, and saliva and the aerosols produced by them, but rarely by the bites of infected animals . In recent years, the infection rate of hantavirus has increased in China and Europe . Hantavirus disease has turned out to be a newly identified but not a \"new\" disease in Germany . The clinical presentations may vary according to viral strains prevalence in different regions. In Asia, hantavirus infection by Hantan virus and Seoul virus targets mainly the human kidney and causes hemorrhagic fever with renal syndrome . In" ]

[ [ "1a", "Title: Molecular Phylogeny of Hantaviruses Harbored by Insectivorous Bats in Côte d’Ivoire and Vietnam" ], [ "1b", "Passage: Mammalian reservoirs of zoonotic viruses typically do not display host restrictions within a given taxonomic order." ], [ "1c", "Also, infection is usually chronic, persistent and subclinical." ], [ "1d", "For example, rodents of multiple genera and species, belonging to four subfamilies in the order Rodentia, serve as reservoirs of hantaviruses in Eurasia, Africa and the Americas and do not exhibit clinical disease or survival disadvantage." ], [ "1e", "In addition, recently, hantaviruses exhibiting far greater genetic diversity have been detected in healthy-appearing shrews and moles representing many genera in six subfamilies within the order Soricomorpha in Eurasia, Africa and North America." ], [ "1f", "Similarly, as mentioned earlier, bat species belonging" ] ]

[ "1d", "3b" ]

[ "Title: A New Model for Hendra Virus Encephalitis in the Mouse\nPassage: bats have been identified as the reservoir host , however epidemiological evidence does not support direct bat to human transmission. Horses have been an intermediate host in the transmission of disease to humans in all cases. There are as yet no readily available effective therapies or prophylaxis for HeV infection, either for use in humans or other susceptible animals.", "Title: Molecular Phylogeny of Hantaviruses Harbored by Insectivorous Bats in Côte d’Ivoire and Vietnam\nPassage: Mammalian reservoirs of zoonotic viruses typically do not display host restrictions within a given taxonomic order. Also, infection is usually chronic, persistent and subclinical. For example, rodents of multiple genera and species, belonging to four subfamilies in the order Rodentia, serve as reservoirs of hantaviruses in Eurasia, Africa and the Americas and do not exhibit clinical disease or survival disadvantage. In addition, recently, hantaviruses exhibiting far greater genetic diversity have been detected in healthy-appearing shrews and moles representing many genera in six subfamilies within the order Soricomorpha in Eurasia, Africa and North America. Similarly, as mentioned earlier, bat species belonging", "Title: Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France\nPassage: Hantaviruses are emerging zoonotic pathogens distributed worldwide except in Antarctica . They may cause two severe pathologies in humans: hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome . Viruses of the genus Hantavirus are exceptions within the Bunyaviridae family, in being directly transmitted via aerosols ofsmall mammals excreta with no role for arthropod vectors . Although a growing diversity of hantaviruses has been discovered over the last decade in insectivores and bats , up to now, only rodent-borne hantaviruses have been shown at the origin of human diseases. Hantaviruses are small, enveloped viruses, possessing a tri-segmented RNA genome of", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Hantavirus is a virus transmitted mainly by rodent animals, mainly through urine, feces, and saliva and the aerosols produced by them, but rarely by the bites of infected animals . In recent years, the infection rate of hantavirus has increased in China and Europe . Hantavirus disease has turned out to be a newly identified but not a \"new\" disease in Germany . The clinical presentations may vary according to viral strains prevalence in different regions. In Asia, hantavirus infection by Hantan virus and Seoul virus targets mainly the human kidney and causes hemorrhagic fever with renal syndrome . In" ]

[ [ "3a", "Title: Vaccines and Therapeutics Against Hantaviruses" ], [ "3b", "Passage: Hantavirus is a virus transmitted mainly by rodent animals, mainly through urine, feces, and saliva and the aerosols produced by them, but rarely by the bites of infected animals ." ], [ "3c", "In recent years, the infection rate of hantavirus has increased in China and Europe ." ], [ "3d", "Hantavirus disease has turned out to be a newly identified but not a \"new\" disease in Germany ." ], [ "3e", "The clinical presentations may vary according to viral strains prevalence in different regions." ], [ "3f", "In Asia, hantavirus infection by Hantan virus and Seoul virus targets mainly the human kidney and causes hemorrhagic fever with renal syndrome . In" ] ]

[ "1d", "3b" ]

[ "Title: Characterization of Influenza A Virus Infection in Mouse Pulmonary Stem/Progenitor Cells\nPassage: Influenza virus can cause acute and severe respiratory diseases. According to the WHO, about 3-5 million people are severely infected with influenza virus, and among those, 290,000-650,000 people die annually , 2017). Compared to most seasonal influenza viruses, pandemic influenza viruses prefer to infect lower respiratory airways and often cause severe lung disease, such as pneumonia and acute respiratory distress syndrome . The lower respiratory tract consists of the trachea, bronchi, bronchioles, and alveoli. Alveoli are the ends of the respiratory tree and act as the basic units of ventilation of the lung. The alveoli consist of an epithelial layer", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ]

[ [ "1a", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC" ], [ "1b", "Passage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx." ], [ "1c", "The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells." ], [ "1d", "Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule" ] ]

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

[ "Title: Characterization of Influenza A Virus Infection in Mouse Pulmonary Stem/Progenitor Cells\nPassage: Influenza virus can cause acute and severe respiratory diseases. According to the WHO, about 3-5 million people are severely infected with influenza virus, and among those, 290,000-650,000 people die annually , 2017). Compared to most seasonal influenza viruses, pandemic influenza viruses prefer to infect lower respiratory airways and often cause severe lung disease, such as pneumonia and acute respiratory distress syndrome . The lower respiratory tract consists of the trachea, bronchi, bronchioles, and alveoli. Alveoli are the ends of the respiratory tree and act as the basic units of ventilation of the lung. The alveoli consist of an epithelial layer", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ]

[ [ "2a", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC" ], [ "2b", "Passage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx." ], [ "2c", "The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells." ], [ "2d", "Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule" ] ]

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

[ "Title: Characterization of Influenza A Virus Infection in Mouse Pulmonary Stem/Progenitor Cells\nPassage: Influenza virus can cause acute and severe respiratory diseases. According to the WHO, about 3-5 million people are severely infected with influenza virus, and among those, 290,000-650,000 people die annually , 2017). Compared to most seasonal influenza viruses, pandemic influenza viruses prefer to infect lower respiratory airways and often cause severe lung disease, such as pneumonia and acute respiratory distress syndrome . The lower respiratory tract consists of the trachea, bronchi, bronchioles, and alveoli. Alveoli are the ends of the respiratory tree and act as the basic units of ventilation of the lung. The alveoli consist of an epithelial layer", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC\nPassage: Inoculation of RV happens either directly on the nasal mucosa or via the eye conjunctiva where it is transported via the lacrymal duct to the nasal cavity, and then on to the nasopharynx. The airway epithelium is the primary site of infection of RV and it was shown in studies of both natural and experimentally-induced cold that viral RNA cannot be detected in the subepithelial layer, only in epithelial cells. Most RV-A and -B utilize intercellular adhesion molecule -1 as cell entry receptor and the others alternatively bind low density lipoprotein receptor , whereas RV-C utilizes a different receptor molecule", "Title: Respiratory Viral Infections in Exacerbation of Chronic Airway Inflammatory Diseases: Novel Mechanisms and Insights From the Upper Airway Epithelium\nPassage: Respiratory viruses primarily infect and replicate within airway epithelial cells . During the replication process, the cells release antiviral factors and cytokines that alter local airway inflammation and airway niche . In a healthy airway, the inflammation normally leads to type 1 inflammatory responses consisting of activation of an antiviral state and infiltration of antiviral effector cells. This eventually results in the resolution of the inflammatory response and clearance of the viral infection . However, in a chronically inflamed airway, the responses against the virus may be impaired or aberrant, causing sustained inflammation and erroneous infiltration, resulting in the exacerbation" ]

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

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

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Hantavirus infections became a concern in the Americas after the description of an outbreak of acute respiratory distress occurred in the Four Corners area in 1993 . The newly recognized disease, hantavirus cardiopulmonary syndrome, HCPS , was linked to infection by the newly-discovered Sin Nombre virus , and the rodent Peromyscus maniculatus was identified as the reservoir . However, hantavirus infections have a much longer history. A review of ancient Chinese writings, dating back to approximately 960 AD, revealed descriptions closely resembling hemorrhagic fever with renal syndrome , the syndrome caused by Old World hantaviruses . During the twentieth century,", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: of human hantavirus infections in Central America. In South America, the first largest identified outbreak occurred in the Chaco region in northwestern Paraguay during 1995-1996. Seventeen individuals were identified with SNV antibody or were antigen positive out of 52 suspected cases . Major outbreaks due to ANDV occurred in 1996 in southern Argentina ; in southern Chile clusters of patients presented with hantavirus illness in 1997 . In Brazil, the first outbreak was identified in the Brazilian Amazon in 2000, and involved small villages that resulted in a 13.3% prevalence of those tested .", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Hantaviruses are horizontally transmitted between rodents and are not transmitted by arthropods . Spillover infection to nonhuman mammals usually results in no onward transmission, but if humans are infected may result in high morbidity and mortality . During the spring of 1993, an outbreak of patients with HCPS due to SNV occurred in the Four Corners states resulting in more than 60% case-fatality among the initial cases, many involving members of the Navajo tribe . In Panama, an outbreak was reported during 1999-2000 in Los Santos, and 12 cases where identified with three fatalities . This represented the first report", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: cases of acute febrile disease with renal compromise were described from several Eurasian countries and Japan, often in association with military engagements . HFRS as a distinct syndrome, however, was first brought to the attention of western medicine in association with an outbreak that occurred among United Nations troops during the Korean conflict between 1951 and 1954, where more than 3,200 soldiers were afflicted . It took more than two decades until the etiologic agent, Hantaan virus , was isolated from the striped field mouse Apodemus agrarius, detected in part by the binding of antibodies from patient serum samples to" ]

[ [ "0a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "0b", "Passage: Hantavirus infections became a concern in the Americas after the description of an outbreak of acute respiratory distress occurred in the Four Corners area in 1993 ." ], [ "0c", "The newly recognized disease, hantavirus cardiopulmonary syndrome, HCPS , was linked to infection by the newly-discovered Sin Nombre virus , and the rodent Peromyscus maniculatus was identified as the reservoir ." ], [ "0d", "However, hantavirus infections have a much longer history." ], [ "0e", "A review of ancient Chinese writings, dating back to approximately 960 AD, revealed descriptions closely resembling hemorrhagic fever with renal syndrome , the syndrome caused by Old World hantaviruses ." ], [ "0f", "During the twentieth century," ] ]

[ "0b", "2d" ]

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Hantavirus infections became a concern in the Americas after the description of an outbreak of acute respiratory distress occurred in the Four Corners area in 1993 . The newly recognized disease, hantavirus cardiopulmonary syndrome, HCPS , was linked to infection by the newly-discovered Sin Nombre virus , and the rodent Peromyscus maniculatus was identified as the reservoir . However, hantavirus infections have a much longer history. A review of ancient Chinese writings, dating back to approximately 960 AD, revealed descriptions closely resembling hemorrhagic fever with renal syndrome , the syndrome caused by Old World hantaviruses . During the twentieth century,", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: of human hantavirus infections in Central America. In South America, the first largest identified outbreak occurred in the Chaco region in northwestern Paraguay during 1995-1996. Seventeen individuals were identified with SNV antibody or were antigen positive out of 52 suspected cases . Major outbreaks due to ANDV occurred in 1996 in southern Argentina ; in southern Chile clusters of patients presented with hantavirus illness in 1997 . In Brazil, the first outbreak was identified in the Brazilian Amazon in 2000, and involved small villages that resulted in a 13.3% prevalence of those tested .", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: Hantaviruses are horizontally transmitted between rodents and are not transmitted by arthropods . Spillover infection to nonhuman mammals usually results in no onward transmission, but if humans are infected may result in high morbidity and mortality . During the spring of 1993, an outbreak of patients with HCPS due to SNV occurred in the Four Corners states resulting in more than 60% case-fatality among the initial cases, many involving members of the Navajo tribe . In Panama, an outbreak was reported during 1999-2000 in Los Santos, and 12 cases where identified with three fatalities . This represented the first report", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: cases of acute febrile disease with renal compromise were described from several Eurasian countries and Japan, often in association with military engagements . HFRS as a distinct syndrome, however, was first brought to the attention of western medicine in association with an outbreak that occurred among United Nations troops during the Korean conflict between 1951 and 1954, where more than 3,200 soldiers were afflicted . It took more than two decades until the etiologic agent, Hantaan virus , was isolated from the striped field mouse Apodemus agrarius, detected in part by the binding of antibodies from patient serum samples to" ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: Hantaviruses are horizontally transmitted between rodents and are not transmitted by arthropods ." ], [ "2c", "Spillover infection to nonhuman mammals usually results in no onward transmission, but if humans are infected may result in high morbidity and mortality ." ], [ "2d", "During the spring of 1993, an outbreak of patients with HCPS due to SNV occurred in the Four Corners states resulting in more than 60% case-fatality among the initial cases, many involving members of the Navajo tribe ." ], [ "2e", "In Panama, an outbreak was reported during 1999-2000 in Los Santos, and 12 cases where identified with three fatalities ." ], [ "2f", "This represented the first report" ] ]

[ "0b", "2d" ]

[ "Title: Old World camels in a modern world – a balancing act between conservation and genetic improvement\nPassage: Female and male reproductive performances according to camel type were traced in three Indian dromedary populations . Several parameters, like conception rate, first service conception rate, percentage of infertile females, average number of services required per fertile female, pregnancy rate, sperm morphology and motility, and testosterone profiling, were shown to exhibit inter-type variability. The latest study on pregnancy and parturition in over 2100 dromedaries from six different breeds/ecotypes showed that the season and the female camel were the most important determinants of variation in gestation length and calf birth weight. Seasonal changes were independent of nutritional factors but associated with", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations . What role maternal camel antibody might play in delaying infection of calves remains unknown . Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection. In contrast to earlier results, slaughterhouse workers who kill both younger and older", "Title: Old World camels in a modern world – a balancing act between conservation and genetic improvement\nPassage: representing seven different populations over a 5-year period, showing a strong influence of the respective dromedary types on all parameters. Furthermore, the milking performance of three Saudi dromedary types managed under the same conditions during a 10-month lactation period showed that camels achieved peak yields at the fourth month of lactation, whereas the total lactation yield and milk composition varied among the three populations .", "Title: Old World camels in a modern world – a balancing act between conservation and genetic improvement\nPassage: In some countries, mainly young males up to two years old are slaughtered for meat, whereas in other regions adults are preferred . These preferences have led to different fattening systems: extensive, pastoral fattening mainly used for adults, e.g. in Somalia and Ethiopia; and intensive fattening with feedlots for young camels as practised, for example, in Saudi Arabia, United Arab Emirates and Tunisia." ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: Camel calving season occurs in the winter months and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve DC populations ." ], [ "1c", "What role maternal camel antibody might play in delaying infection of calves remains unknown ." ], [ "1d", "Juvenile DCs appear to host active infection more often than adult DCs and thus the sacrificial slaughter of DCs, which must be five years of age or older , may not be accompanied by significant risk of exposure to infection." ], [ "1e", "In contrast to earlier results, slaughterhouse workers who kill both younger and older" ] ]

[ "1b" ]

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Our study results suggest that the following may be clinical features of ARDS caused by HAdV-55: persistent high fever, rapid progression of dyspnea, need for mechanical ventilation support, elevated AST level and rapid progression from unilateral infiltrates to bilateral consolidations. These clinical features are highly similar to those of ARDS caused by other types of HAdV described in previous reports .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Our study results suggest that the following may be clinical features of ARDS caused by HAdV-55: persistent high fever, rapid progression of dyspnea, need for mechanical ventilation support, elevated AST level and rapid progression from unilateral infiltrates to bilateral consolidations. These clinical features are highly similar to those of ARDS caused by other types of HAdV described in previous reports .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS. Viral load monitoring may help predict disease severity and patient outcome. The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients. HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS. Viral load monitoring may help predict disease severity and patient outcome. The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients. HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support." ]

[ [ "2a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "2b", "Passage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS." ], [ "2c", "Viral load monitoring may help predict disease severity and patient outcome." ], [ "2d", "The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients." ], [ "2e", "HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support." ] ]

[ "2b", "3b" ]

[ "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Our study results suggest that the following may be clinical features of ARDS caused by HAdV-55: persistent high fever, rapid progression of dyspnea, need for mechanical ventilation support, elevated AST level and rapid progression from unilateral infiltrates to bilateral consolidations. These clinical features are highly similar to those of ARDS caused by other types of HAdV described in previous reports .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: Our study results suggest that the following may be clinical features of ARDS caused by HAdV-55: persistent high fever, rapid progression of dyspnea, need for mechanical ventilation support, elevated AST level and rapid progression from unilateral infiltrates to bilateral consolidations. These clinical features are highly similar to those of ARDS caused by other types of HAdV described in previous reports .", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS. Viral load monitoring may help predict disease severity and patient outcome. The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients. HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support.", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study\nPassage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS. Viral load monitoring may help predict disease severity and patient outcome. The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients. HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support." ]

[ [ "3a", "Title: Emergent severe acute respiratory distress syndrome caused by adenovirus type 55 in immunocompetent adults in 2013: a prospective observational study" ], [ "3b", "Passage: together with bilateral consolidations and infiltrates at the same time, are the most frequent clinical manifestations of severe HAdV-55induced ARDS." ], [ "3c", "Viral load monitoring may help predict disease severity and patient outcome." ], [ "3d", "The NPPV and IMV failure rates were very high, and ECMO may be the last support method for this group of patients." ], [ "3e", "HAdV-55-induced severe ARDS has a very high mortality rate despite appropriate respiratory support." ] ]

[ "2b", "3b" ]

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Recently, Esvelt et al. developed a novel strategy for directed evolution of filamentous phage-displayed proteins, called phage-assisted continuous evolution , which allows multiple rounds of evolution per day with little experimental intervention. The authors engineered M13 phage to encode an exogenous protein , whose functional activity triggers gene III expression from an accessory plasmid; variants of the exogenous protein arise by random mutagenesis during phage replication, the rate of which can be increased by inducible expression of error-prone DNA polymerases. By supplying limiting amounts of receptive E. coli cells to the engineered phage variants, Esvelt et al. elegantly linked phage", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Recently, Esvelt et al. developed a novel strategy for directed evolution of filamentous phage-displayed proteins, called phage-assisted continuous evolution , which allows multiple rounds of evolution per day with little experimental intervention. The authors engineered M13 phage to encode an exogenous protein , whose functional activity triggers gene III expression from an accessory plasmid; variants of the exogenous protein arise by random mutagenesis during phage replication, the rate of which can be increased by inducible expression of error-prone DNA polymerases. By supplying limiting amounts of receptive E. coli cells to the engineered phage variants, Esvelt et al. elegantly linked phage", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution . The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface. First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII. Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution . The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface. First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII. Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis" ]

[ [ "2a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "2b", "Passage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution ." ], [ "2c", "The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface." ], [ "2d", "First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII." ], [ "2e", "Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis" ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Recently, Esvelt et al. developed a novel strategy for directed evolution of filamentous phage-displayed proteins, called phage-assisted continuous evolution , which allows multiple rounds of evolution per day with little experimental intervention. The authors engineered M13 phage to encode an exogenous protein , whose functional activity triggers gene III expression from an accessory plasmid; variants of the exogenous protein arise by random mutagenesis during phage replication, the rate of which can be increased by inducible expression of error-prone DNA polymerases. By supplying limiting amounts of receptive E. coli cells to the engineered phage variants, Esvelt et al. elegantly linked phage", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Recently, Esvelt et al. developed a novel strategy for directed evolution of filamentous phage-displayed proteins, called phage-assisted continuous evolution , which allows multiple rounds of evolution per day with little experimental intervention. The authors engineered M13 phage to encode an exogenous protein , whose functional activity triggers gene III expression from an accessory plasmid; variants of the exogenous protein arise by random mutagenesis during phage replication, the rate of which can be increased by inducible expression of error-prone DNA polymerases. By supplying limiting amounts of receptive E. coli cells to the engineered phage variants, Esvelt et al. elegantly linked phage", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution . The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface. First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII. Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution . The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface. First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII. Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis" ]

[ [ "3a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "3b", "Passage: Because of their large population sizes, short generation times, small genome sizes and ease of manipulation, various filamentous and non-filamentous bacteriophages have been used as models of experimental evolution ." ], [ "3c", "The filamentous phage has additional practical uses in protein engineering and directed protein evolution, due to its unique tolerance of genetic modifications that allow biomolecules to be displayed on the virion surface." ], [ "3d", "First and foremost among these applications is in vitro affinity maturation of antibody fragments displayed on pIII." ], [ "3e", "Libraries of variant Fabs and single chain antibodies can be generated via random or sitedirected mutagenesis and selected on the basis" ] ]

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

[ "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: The trial commenced recruiting patients in February 2013 and by the end of May 2014 had recruited 357 patients. Two interim analyses were made by an independent data monitoring and ethics committee, as predetermined, and on both occasions, it was concluded that the trial was being conducted well, and should continue. An investigators' meeting was held in Vietnam to develop the collaborative network, share best-practice qualities, discuss recruitment strategies, and consider opportunities for substudies.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The 8-week pilot study will take place from January to April 2007. The exact starting and stopping dates of patient recruitment will not be fixed in advance. Recruitment will begin after the start of the annual influenza peak season has been confirmed by the Department of Microbiology, HKU, and will continue until the prespecified sample size is reached. The 39-week main study will take place from January to September 2008.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Event-driven stopping of the trial after 247 observed deaths is not foreseen even if this should occur prior to recruiting 880 patients. Thus, the study will be conservatively powered if the study mortality is larger than 30%. For example, if overall mortality was around 50% and 412 deaths were observed during the study, power would increase to 95% for a true hazard ratio of 0.7 and to 83% for a true hazard ratio of 0.75.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Selected study members will be trained on how to enter all clinical data as source information from the CRFs and from laboratory source documents into an Internet-based computerised dataentry system called CliRes hosted by OUCRU Viet Nam. Data entry will occur simultaneously, as data are being generated during the trial as soon as possible after the information is generated. Data may be manually entered or scanned and electronically uploaded, dependent on available software. Source documents and electronic data will be verified according to the Trial Monitoring Plan." ]

[ [ "0a", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial" ], [ "0b", "Passage: The trial commenced recruiting patients in February 2013 and by the end of May 2014 had recruited 357 patients." ], [ "0c", "Two interim analyses were made by an independent data monitoring and ethics committee, as predetermined, and on both occasions, it was concluded that the trial was being conducted well, and should continue." ], [ "0d", "An investigators' meeting was held in Vietnam to develop the collaborative network, share best-practice qualities, discuss recruitment strategies, and consider opportunities for substudies." ] ]

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

[ "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: The trial commenced recruiting patients in February 2013 and by the end of May 2014 had recruited 357 patients. Two interim analyses were made by an independent data monitoring and ethics committee, as predetermined, and on both occasions, it was concluded that the trial was being conducted well, and should continue. An investigators' meeting was held in Vietnam to develop the collaborative network, share best-practice qualities, discuss recruitment strategies, and consider opportunities for substudies.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The 8-week pilot study will take place from January to April 2007. The exact starting and stopping dates of patient recruitment will not be fixed in advance. Recruitment will begin after the start of the annual influenza peak season has been confirmed by the Department of Microbiology, HKU, and will continue until the prespecified sample size is reached. The 39-week main study will take place from January to September 2008.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Event-driven stopping of the trial after 247 observed deaths is not foreseen even if this should occur prior to recruiting 880 patients. Thus, the study will be conservatively powered if the study mortality is larger than 30%. For example, if overall mortality was around 50% and 412 deaths were observed during the study, power would increase to 95% for a true hazard ratio of 0.7 and to 83% for a true hazard ratio of 0.75.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Selected study members will be trained on how to enter all clinical data as source information from the CRFs and from laboratory source documents into an Internet-based computerised dataentry system called CliRes hosted by OUCRU Viet Nam. Data entry will occur simultaneously, as data are being generated during the trial as soon as possible after the information is generated. Data may be manually entered or scanned and electronically uploaded, dependent on available software. Source documents and electronic data will be verified according to the Trial Monitoring Plan." ]

[ [ "2a", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial" ], [ "2b", "Passage: Event-driven stopping of the trial after 247 observed deaths is not foreseen even if this should occur prior to recruiting 880 patients." ], [ "2c", "Thus, the study will be conservatively powered if the study mortality is larger than 30%." ], [ "2d", "For example, if overall mortality was around 50% and 412 deaths were observed during the study, power would increase to 95% for a true hazard ratio of 0.7 and to 83% for a true hazard ratio of 0.75." ] ]

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

[ "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: The trial commenced recruiting patients in February 2013 and by the end of May 2014 had recruited 357 patients. Two interim analyses were made by an independent data monitoring and ethics committee, as predetermined, and on both occasions, it was concluded that the trial was being conducted well, and should continue. An investigators' meeting was held in Vietnam to develop the collaborative network, share best-practice qualities, discuss recruitment strategies, and consider opportunities for substudies.", "Title: Preliminary Findings of a Randomized Trial of Non-Pharmaceutical Interventions to Prevent Influenza Transmission in Households\nPassage: The 8-week pilot study will take place from January to April 2007. The exact starting and stopping dates of patient recruitment will not be fixed in advance. Recruitment will begin after the start of the annual influenza peak season has been confirmed by the Department of Microbiology, HKU, and will continue until the prespecified sample size is reached. The 39-week main study will take place from January to September 2008.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Event-driven stopping of the trial after 247 observed deaths is not foreseen even if this should occur prior to recruiting 880 patients. Thus, the study will be conservatively powered if the study mortality is larger than 30%. For example, if overall mortality was around 50% and 412 deaths were observed during the study, power would increase to 95% for a true hazard ratio of 0.7 and to 83% for a true hazard ratio of 0.75.", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial\nPassage: Selected study members will be trained on how to enter all clinical data as source information from the CRFs and from laboratory source documents into an Internet-based computerised dataentry system called CliRes hosted by OUCRU Viet Nam. Data entry will occur simultaneously, as data are being generated during the trial as soon as possible after the information is generated. Data may be manually entered or scanned and electronically uploaded, dependent on available software. Source documents and electronic data will be verified according to the Trial Monitoring Plan." ]

[ [ "3a", "Title: CryptoDex: A randomised, double-blind, placebo-controlled phase III trial of adjunctive dexamethasone in HIV-infected adults with cryptococcal meningitis: study protocol for a randomised control trial" ], [ "3b", "Passage: Selected study members will be trained on how to enter all clinical data as source information from the CRFs and from laboratory source documents into an Internet-based computerised dataentry system called CliRes hosted by OUCRU Viet Nam." ], [ "3c", "Data entry will occur simultaneously, as data are being generated during the trial as soon as possible after the information is generated." ], [ "3d", "Data may be manually entered or scanned and electronically uploaded, dependent on available software." ], [ "3e", "Source documents and electronic data will be verified according to the Trial Monitoring Plan." ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and strains of circulating viruses. Also, because PCR was used for viral detection, the study was limited to detection of viruses in the primer sets. Given that these are the most up-to-date and common viruses, this approach was deemed sufficient for this initial investigation.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ]

[ [ "0a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "0b", "Passage: We also compared and contrasted the clinical and community results." ], [ "0c", "Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample." ], [ "0d", "These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community." ], [ "0e", "Together they infected 94% of clinical subjects, and 7% in the community ." ], [ "0f", "The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples." ], [ "0g", "However a different strain, coronavirus OC 229" ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and strains of circulating viruses. Also, because PCR was used for viral detection, the study was limited to detection of viruses in the primer sets. Given that these are the most up-to-date and common viruses, this approach was deemed sufficient for this initial investigation.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ]

[ [ "1a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "1b", "Passage: and 5 of quadruple." ], [ "1c", "Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects ." ], [ "1d", "Coronavirus OC43 was the most common virus detected in community members ." ], [ "1e", "A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community." ], [ "1f", "This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of" ] ]

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

[ "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: We also compared and contrasted the clinical and community results. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses found in the clinical sample. These three infections resulted in 41 viruses detected in 15 subjects clinically, and eight infections detected in five people in the community. Together they infected 94% of clinical subjects, and 7% in the community . The most common virus detected in community samples was Coronavirus OC43; this virus was detected in 13.3% people in the community and not in any of the clinical samples. However a different strain, coronavirus OC 229", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and 5 of quadruple. Parainfluenza virus 4, respiratory syncytial virus B and enterovirus were the most common viruses in the clinical sample; present in 93.8% of clinical subjects, and 6.7% of community subjects . Coronavirus OC43 was the most common virus detected in community members . A different strain, Coronavirus OC 229 E/NL63 was detected among subjects from the clinic and not detected in the community. This pilot study provides evidence that data from the community can potentially represent different information than that sourced clinically, suggesting the need for community surveillance to enhance public health efforts and scientific understanding of", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: and strains of circulating viruses. Also, because PCR was used for viral detection, the study was limited to detection of viruses in the primer sets. Given that these are the most up-to-date and common viruses, this approach was deemed sufficient for this initial investigation.", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria\nPassage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria. RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria. Nasal swabs were collected and tested using polymerase chain reaction. The majority of subjects were under 6 years old, of whom 46 were infected . A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ]

[ [ "3a", "Title: Etiology of respiratory tract infections in the community and clinic in Ilorin, Nigeria" ], [ "3b", "Passage: Abstract: OBJECTIVE: Recognizing increasing interest in community disease surveillance globally, the goal of this study was to investigate whether respiratory viruses circulating in the community may be represented through clinical surveillance in Nigeria." ], [ "3c", "RESULTS: Children were selected via convenience sampling from communities and a tertiary care center during spring 2017 in Ilorin, Nigeria." ], [ "3d", "Nasal swabs were collected and tested using polymerase chain reaction." ], [ "3e", "The majority of subjects were under 6 years old, of whom 46 were infected ." ], [ "3f", "A total of 33 of the 91 subjects had one or more respiratory tract virus; there were 10 cases of triple infection" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The NYVAC vector is a highly attenuated vaccinia virus strain. NYVAC is replication-restricted; however, it grows in chick embryo fibroblasts and Vero cells enabling vaccine-scale production. In non-permissive cells, critical late structural proteins are not produced stopping replication at the immature virion stage . NYVAC is very attenuated and considered safe for use in humans of all ages; however, it predominantly induces a CD4 + T cell response which is different compared to MVA . Both MVA and NYVAC provoke robust humoral responses, and can be delivered mucosally to induce mucosal antibody responses . There has been only limited exploration", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern. Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population. While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains. This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: . Intriguingly, NYVAC may have an advantage for use as an influenza vaccine vector, because immunization with this vector induces weaker vaccine-specific immune responses compared to other poxvirus vaccines, a feature that may address the concerns surrounding preexisting immunity .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: was the first to be licensed for use in humans, where the cDNAs encoding the envelope proteins of YFV were replaced with the corresponding genes of an attenuated Japanese encephalitis virus strain, SA14-14-2 . Poxviruses are also studied extensively as candidate vectors for human use, among which attenuated derivatives of vaccinia virus and New York attenuated vaccinia virus NYVAC strains] are the most promising vectors . They are ideal candidate vectors due to their large DNA-packing capacity and their thermal and genetic stability . The NYVAC vector has been shown to induce CD4 + T cell-dominant responses, and MVA induces" ]

[ [ "0a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "0b", "Passage: The NYVAC vector is a highly attenuated vaccinia virus strain." ], [ "0c", "NYVAC is replication-restricted; however, it grows in chick embryo fibroblasts and Vero cells enabling vaccine-scale production." ], [ "0d", "In non-permissive cells, critical late structural proteins are not produced stopping replication at the immature virion stage ." ], [ "0e", "NYVAC is very attenuated and considered safe for use in humans of all ages; however, it predominantly induces a CD4 + T cell response which is different compared to MVA ." ], [ "0f", "Both MVA and NYVAC provoke robust humoral responses, and can be delivered mucosally to induce mucosal antibody responses ." ], [ "0g", "There has been only limited exploration" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The NYVAC vector is a highly attenuated vaccinia virus strain. NYVAC is replication-restricted; however, it grows in chick embryo fibroblasts and Vero cells enabling vaccine-scale production. In non-permissive cells, critical late structural proteins are not produced stopping replication at the immature virion stage . NYVAC is very attenuated and considered safe for use in humans of all ages; however, it predominantly induces a CD4 + T cell response which is different compared to MVA . Both MVA and NYVAC provoke robust humoral responses, and can be delivered mucosally to induce mucosal antibody responses . There has been only limited exploration", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern. Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population. While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains. This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: . Intriguingly, NYVAC may have an advantage for use as an influenza vaccine vector, because immunization with this vector induces weaker vaccine-specific immune responses compared to other poxvirus vaccines, a feature that may address the concerns surrounding preexisting immunity .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: was the first to be licensed for use in humans, where the cDNAs encoding the envelope proteins of YFV were replaced with the corresponding genes of an attenuated Japanese encephalitis virus strain, SA14-14-2 . Poxviruses are also studied extensively as candidate vectors for human use, among which attenuated derivatives of vaccinia virus and New York attenuated vaccinia virus NYVAC strains] are the most promising vectors . They are ideal candidate vectors due to their large DNA-packing capacity and their thermal and genetic stability . The NYVAC vector has been shown to induce CD4 + T cell-dominant responses, and MVA induces" ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern." ], [ "1c", "Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population." ], [ "1d", "While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains." ], [ "1e", "This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use" ] ]

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

[ "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: The NYVAC vector is a highly attenuated vaccinia virus strain. NYVAC is replication-restricted; however, it grows in chick embryo fibroblasts and Vero cells enabling vaccine-scale production. In non-permissive cells, critical late structural proteins are not produced stopping replication at the immature virion stage . NYVAC is very attenuated and considered safe for use in humans of all ages; however, it predominantly induces a CD4 + T cell response which is different compared to MVA . Both MVA and NYVAC provoke robust humoral responses, and can be delivered mucosally to induce mucosal antibody responses . There has been only limited exploration", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: While there is strong safety and efficacy data for use of NYVAC or MVA-vectored influenza vaccines, preexisting immunity remains a concern. Although the smallpox vaccination campaign has resulted in a population of poxvirus-naï ve people, the initiation of an MVA or NYVAC vaccination program for HIV, influenza or other pathogens will rapidly reduce this susceptible population. While there is significant interest in development of pox-vectored influenza virus vaccines, current influenza vaccination strategies rely upon regular immunization with vaccines matched to circulating strains. This would likely limit the use and/or efficacy of poxvirus-vectored influenza virus vaccines for regular and seasonal use", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: . Intriguingly, NYVAC may have an advantage for use as an influenza vaccine vector, because immunization with this vector induces weaker vaccine-specific immune responses compared to other poxvirus vaccines, a feature that may address the concerns surrounding preexisting immunity .", "Title: Pre-existing immunity against vaccine vectors – friend or foe?\nPassage: was the first to be licensed for use in humans, where the cDNAs encoding the envelope proteins of YFV were replaced with the corresponding genes of an attenuated Japanese encephalitis virus strain, SA14-14-2 . Poxviruses are also studied extensively as candidate vectors for human use, among which attenuated derivatives of vaccinia virus and New York attenuated vaccinia virus NYVAC strains] are the most promising vectors . They are ideal candidate vectors due to their large DNA-packing capacity and their thermal and genetic stability . The NYVAC vector has been shown to induce CD4 + T cell-dominant responses, and MVA induces" ]

[ [ "3a", "Title: Pre-existing immunity against vaccine vectors – friend or foe?" ], [ "3b", "Passage: was the first to be licensed for use in humans, where the cDNAs encoding the envelope proteins of YFV were replaced with the corresponding genes of an attenuated Japanese encephalitis virus strain, SA14-14-2 ." ], [ "3c", "Poxviruses are also studied extensively as candidate vectors for human use, among which attenuated derivatives of vaccinia virus and New York attenuated vaccinia virus NYVAC strains] are the most promising vectors ." ], [ "3d", "They are ideal candidate vectors due to their large DNA-packing capacity and their thermal and genetic stability ." ], [ "3e", "The NYVAC vector has been shown to induce CD4 + T cell-dominant responses, and MVA induces" ] ]

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

[ "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: Human adenoviral vector-based vaccines expressing HIV-1 or SIV antigens have been shown to induce potent HIV-1 or SIV-specific T-cell responses in the periphery and at mucosal sites . However, vaccination regimens using a replication-defective adenovirus serotype 5 vector , alone or in prime-boost with DNA, did not reduce HIV-1 acquisition rates or set-point viral loads in clinical trials . Both CD4 + and CD8 + T-cell responses were detected in the vaccinees, with a predominance of CD8 + T-cell responses. Whether the insufficient magnitude, functionality or breadth of the vaccine-induced cellular immune responses participated in the failure of the Ad5", "Title: Comparison of Heterologous Prime-Boost Strategies against Human Immunodeficiency Virus Type 1 Gag Using Negative Stranded RNA Viruses\nPassage: Like many infectious diseases that have had significant impact on the human population, a vaccine against HIV is critically needed. Along with humoral immunity, CD8 + T cells have been shown to be important in the control of HIV . Cellular immunity induced in the Ad5-STEP trial failed to protect individuals from HIV, resulting in more people from the vaccine group acquiring infection compared to the placebo . Part of the problem was thought to be the presence of preexisting immunity against the vector . The NSVs used in this study were chosen, because few individuals have preexisting immunity.", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: vaccine to provide demonstrable protection against HIV-1 infection remains unclear. In particular, in the 'STEP' clinical trial, pre-existing Ad5-specific antibody titers appeared to have negatively impacted the HIV-1-specific CD8 + T-cell responder rate after vaccination .", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: While no F4/AS01-induced CD8 + T-cell responses were observed in our experiments in the NHP model , such responses were observed in CB6F1 mice. After vaccination, HIV-1 specific cytokine-expressing CD4 + and/or CD8 + T cells were detected in each compartment assessed, with the highest frequencies found in the genital tract mucosa . No CD4 + or CD8 + T-cell responses were detected in the control group." ]

[ [ "0a", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques" ], [ "0b", "Passage: Human adenoviral vector-based vaccines expressing HIV-1 or SIV antigens have been shown to induce potent HIV-1 or SIV-specific T-cell responses in the periphery and at mucosal sites ." ], [ "0c", "However, vaccination regimens using a replication-defective adenovirus serotype 5 vector , alone or in prime-boost with DNA, did not reduce HIV-1 acquisition rates or set-point viral loads in clinical trials ." ], [ "0d", "Both CD4 + and CD8 + T-cell responses were detected in the vaccinees, with a predominance of CD8 + T-cell responses." ], [ "0e", "Whether the insufficient magnitude, functionality or breadth of the vaccine-induced cellular immune responses participated in the failure of the Ad5" ] ]

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

[ "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: Human adenoviral vector-based vaccines expressing HIV-1 or SIV antigens have been shown to induce potent HIV-1 or SIV-specific T-cell responses in the periphery and at mucosal sites . However, vaccination regimens using a replication-defective adenovirus serotype 5 vector , alone or in prime-boost with DNA, did not reduce HIV-1 acquisition rates or set-point viral loads in clinical trials . Both CD4 + and CD8 + T-cell responses were detected in the vaccinees, with a predominance of CD8 + T-cell responses. Whether the insufficient magnitude, functionality or breadth of the vaccine-induced cellular immune responses participated in the failure of the Ad5", "Title: Comparison of Heterologous Prime-Boost Strategies against Human Immunodeficiency Virus Type 1 Gag Using Negative Stranded RNA Viruses\nPassage: Like many infectious diseases that have had significant impact on the human population, a vaccine against HIV is critically needed. Along with humoral immunity, CD8 + T cells have been shown to be important in the control of HIV . Cellular immunity induced in the Ad5-STEP trial failed to protect individuals from HIV, resulting in more people from the vaccine group acquiring infection compared to the placebo . Part of the problem was thought to be the presence of preexisting immunity against the vector . The NSVs used in this study were chosen, because few individuals have preexisting immunity.", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: vaccine to provide demonstrable protection against HIV-1 infection remains unclear. In particular, in the 'STEP' clinical trial, pre-existing Ad5-specific antibody titers appeared to have negatively impacted the HIV-1-specific CD8 + T-cell responder rate after vaccination .", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: While no F4/AS01-induced CD8 + T-cell responses were observed in our experiments in the NHP model , such responses were observed in CB6F1 mice. After vaccination, HIV-1 specific cytokine-expressing CD4 + and/or CD8 + T cells were detected in each compartment assessed, with the highest frequencies found in the genital tract mucosa . No CD4 + or CD8 + T-cell responses were detected in the control group." ]

[ [ "1a", "Title: Comparison of Heterologous Prime-Boost Strategies against Human Immunodeficiency Virus Type 1 Gag Using Negative Stranded RNA Viruses" ], [ "1b", "Passage: Like many infectious diseases that have had significant impact on the human population, a vaccine against HIV is critically needed." ], [ "1c", "Along with humoral immunity, CD8 + T cells have been shown to be important in the control of HIV ." ], [ "1d", "Cellular immunity induced in the Ad5-STEP trial failed to protect individuals from HIV, resulting in more people from the vaccine group acquiring infection compared to the placebo ." ], [ "1e", "Part of the problem was thought to be the presence of preexisting immunity against the vector ." ], [ "1f", "The NSVs used in this study were chosen, because few individuals have preexisting immunity." ] ]

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

[ "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: Human adenoviral vector-based vaccines expressing HIV-1 or SIV antigens have been shown to induce potent HIV-1 or SIV-specific T-cell responses in the periphery and at mucosal sites . However, vaccination regimens using a replication-defective adenovirus serotype 5 vector , alone or in prime-boost with DNA, did not reduce HIV-1 acquisition rates or set-point viral loads in clinical trials . Both CD4 + and CD8 + T-cell responses were detected in the vaccinees, with a predominance of CD8 + T-cell responses. Whether the insufficient magnitude, functionality or breadth of the vaccine-induced cellular immune responses participated in the failure of the Ad5", "Title: Comparison of Heterologous Prime-Boost Strategies against Human Immunodeficiency Virus Type 1 Gag Using Negative Stranded RNA Viruses\nPassage: Like many infectious diseases that have had significant impact on the human population, a vaccine against HIV is critically needed. Along with humoral immunity, CD8 + T cells have been shown to be important in the control of HIV . Cellular immunity induced in the Ad5-STEP trial failed to protect individuals from HIV, resulting in more people from the vaccine group acquiring infection compared to the placebo . Part of the problem was thought to be the presence of preexisting immunity against the vector . The NSVs used in this study were chosen, because few individuals have preexisting immunity.", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: vaccine to provide demonstrable protection against HIV-1 infection remains unclear. In particular, in the 'STEP' clinical trial, pre-existing Ad5-specific antibody titers appeared to have negatively impacted the HIV-1-specific CD8 + T-cell responder rate after vaccination .", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques\nPassage: While no F4/AS01-induced CD8 + T-cell responses were observed in our experiments in the NHP model , such responses were observed in CB6F1 mice. After vaccination, HIV-1 specific cytokine-expressing CD4 + and/or CD8 + T cells were detected in each compartment assessed, with the highest frequencies found in the genital tract mucosa . No CD4 + or CD8 + T-cell responses were detected in the control group." ]

[ [ "2a", "Title: Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques" ], [ "2b", "Passage: vaccine to provide demonstrable protection against HIV-1 infection remains unclear." ], [ "2c", "In particular, in the 'STEP' clinical trial, pre-existing Ad5-specific antibody titers appeared to have negatively impacted the HIV-1-specific CD8 + T-cell responder rate after vaccination ." ] ]

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