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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" ]