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[ "Title: Gain-of-Function Research: Ethical Analysis\nPassage: were published in 2012. Advocates of these studies/publications argued that they would improve surveillance of H5N1 in nature and facilitate development of vaccines that might be needed to protect against pandemic strains of the virus. Critics questioned the validity of claims about such benefits and argued that the studies might facilitate creation of biological weapons agents that could kill millions, or possibly even billions, of people.", "Title: Why language matters: insights and challenges in applying a social determination of health approach in a North-South collaborative research program\nPassage: serve as outcome to measure quantitatively. We therefore set out to build the infrastructural capacity, while promoting the use of the material, leaving rigorous evaluation to a future date. Traditional epidemiology would consider this study a failure; however, the research process itself brought together communities, non-governmental organizations, national government and international agencies, serving to raise the level of awareness and conferring some empowerment to serve as a basis for future challenges to detrimental social processes. Table 3 assessed this collaborative research project with respect to the 4 S framework.", "Title: Globalization and Health: developing the journal to advance the field\nPassage: review of all the articles that have been published to date. The purpose of this review was to identify strengths, trends and current gaps in research; highlight opportunities for strengthening existing research; and to propose upcoming areas of research, projected to be of increasing importance over the next ten years.", "Title: Gain-of-Function Research: Ethical Analysis\nPassage: Some argued that publishing studies like these in full detail provided ''recipes'' for especially dangerous potential biological weapons agents to would-be bioterrorists. Many who acknowledged such potential dangers, on the other hand, argued that benefits of publication outweighed risks involved." ]

[ [ "3a", "Title: Gain-of-Function Research: Ethical Analysis" ], [ "3b", "Passage: Some argued that publishing studies like these in full detail provided ''recipes'' for especially dangerous potential biological weapons agents to would-be bioterrorists." ], [ "3c", "Many who acknowledged such potential dangers, on the other hand, argued that benefits of publication outweighed risks involved." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: more selectively, interpreted as indicating their importation along with foreign pilgrims. Over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among Hajj pilgrims. A LRT sample is often not collected for these studies , so false negative findings are a possibility although little is known about the initial site of MERS-CoV infection and replication; it may have been assumed it was the LRT because disease was first noticed there but the URT may be the site of the earliest replication.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is" ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: but close and lengthy exposure appears to be a requirement." ], [ "0c", "The KSA is the focal point of MERS, with the majority of human cases." ], [ "0d", "In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected." ], [ "0e", "However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms." ], [ "0f", "Older males most obviously suffer severe disease and MERS patients often have comorbidities." ], [ "0g", "Compared to severe acute" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: more selectively, interpreted as indicating their importation along with foreign pilgrims. Over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among Hajj pilgrims. A LRT sample is often not collected for these studies , so false negative findings are a possibility although little is known about the initial site of MERS-CoV infection and replication; it may have been assumed it was the LRT because disease was first noticed there but the URT may be the site of the earliest replication.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is" ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: more selectively, interpreted as indicating their importation along with foreign pilgrims." ], [ "1c", "Over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among Hajj pilgrims." ], [ "1d", "A LRT sample is often not collected for these studies , so false negative findings are a possibility although little is known about the initial site of MERS-CoV infection and replication; it may have been assumed it was the LRT because disease was first noticed there but the URT may be the site of the earliest replication." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: more selectively, interpreted as indicating their importation along with foreign pilgrims. Over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among Hajj pilgrims. A LRT sample is often not collected for these studies , so false negative findings are a possibility although little is known about the initial site of MERS-CoV infection and replication; it may have been assumed it was the LRT because disease was first noticed there but the URT may be the site of the earliest replication.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is" ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: a case definition released by the KSA Ministry of Health in June 2015 ." ], [ "2c", "The KSA has been the source of 79 % of human cases." ], [ "2d", "Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions ." ], [ "2e", "Interestingly in June 2015, an outbreak in South Korea followed a similar distribution ." ], [ "2f", "Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia ." ], [ "2g", "Patients often present to a hospital with pneumonia," ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20 % to 40 % of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: more selectively, interpreted as indicating their importation along with foreign pilgrims. Over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among Hajj pilgrims. A LRT sample is often not collected for these studies , so false negative findings are a possibility although little is known about the initial site of MERS-CoV infection and replication; it may have been assumed it was the LRT because disease was first noticed there but the URT may be the site of the earliest replication.", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: a case definition released by the KSA Ministry of Health in June 2015 . The KSA has been the source of 79 % of human cases. Severe MERS is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions . Interestingly in June 2015, an outbreak in South Korea followed a similar distribution . Among laboratory confirmed cases, fever, cough and upper respiratory tract signs and symptoms usually occur first, followed within a week by progressive LRT distress and lymphopaenia . Patients often present to a hospital with pneumonia,", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: Clinically suspected MERS cases may return negative results by RT-rtPCR. Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred . Higher viral loads occur in the LRT compared to the URT. This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease . However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR . This may be due to poor sampling when a cough is" ]

[ [ "3a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "3b", "Passage: Clinically suspected MERS cases may return negative results by RT-rtPCR." ], [ "3c", "Data have shown one or more negative URT samples may be contradicted by further URT sampling or the use of LRT samples, which is preferred ." ], [ "3d", "Higher viral loads occur in the LRT compared to the URT." ], [ "3e", "This fits with the observation that the majority of disease symptoms are reported to manifest as systemic and LRT disease ." ], [ "3f", "However, on occasion, even LRT specimens from MERS cases may initially be negative, only to later become positive by RT-PCR ." ], [ "3g", "This may be due to poor sampling when a cough is" ] ]

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

[ "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: DAMAVER envelope appears as a pear shaped structure in which the homologous model can be fitted. Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution.", "Title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy\nPassage: which of which is slightly bigger than the other. Previous studies that produced recombinant nucleocapsid-like structures showed that expressed VP24 and VP35 both independently associate with NP, but that all three proteins together are necessary to produce ,50 nm diameter helical nucleocapsid-like structures. When VP35, VP30, VP24, and NP were transfected together, approximately 50 nm diameter helical nucleocapsid-like structure was also generated, whereas NP alone generated helical NP-RNA complexes ,20-25 nm in diameter, which were nuclease sensitive . Taken together these results suggest that VP24 and VP35 are the structural components of the bridge located on the periphery of the", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: 24 from which we made the 5′-vRNAp corresponding to the 5′-end and it's 3′ equivalent called 3′-vRNAp . By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct. Similar data had already been published 32 .", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: which the 5′-vRNAp binding site is located between the PA and PB1 subunits 5,6 . The 3′-vRNA, on the other hand, interacts with all three subunits suggesting a sequential vRNAp binding mechanism." ]

[ [ "0a", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5" ], [ "0b", "Passage: DAMAVER envelope appears as a pear shaped structure in which the homologous model can be fitted." ], [ "0c", "Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution." ] ]

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

[ "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: DAMAVER envelope appears as a pear shaped structure in which the homologous model can be fitted. Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution.", "Title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy\nPassage: which of which is slightly bigger than the other. Previous studies that produced recombinant nucleocapsid-like structures showed that expressed VP24 and VP35 both independently associate with NP, but that all three proteins together are necessary to produce ,50 nm diameter helical nucleocapsid-like structures. When VP35, VP30, VP24, and NP were transfected together, approximately 50 nm diameter helical nucleocapsid-like structure was also generated, whereas NP alone generated helical NP-RNA complexes ,20-25 nm in diameter, which were nuclease sensitive . Taken together these results suggest that VP24 and VP35 are the structural components of the bridge located on the periphery of the", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: 24 from which we made the 5′-vRNAp corresponding to the 5′-end and it's 3′ equivalent called 3′-vRNAp . By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct. Similar data had already been published 32 .", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: which the 5′-vRNAp binding site is located between the PA and PB1 subunits 5,6 . The 3′-vRNA, on the other hand, interacts with all three subunits suggesting a sequential vRNAp binding mechanism." ]

[ [ "1a", "Title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy" ], [ "1b", "Passage: which of which is slightly bigger than the other." ], [ "1c", "Previous studies that produced recombinant nucleocapsid-like structures showed that expressed VP24 and VP35 both independently associate with NP, but that all three proteins together are necessary to produce ,50 nm diameter helical nucleocapsid-like structures." ], [ "1d", "When VP35, VP30, VP24, and NP were transfected together, approximately 50 nm diameter helical nucleocapsid-like structure was also generated, whereas NP alone generated helical NP-RNA complexes ,20-25 nm in diameter, which were nuclease sensitive ." ], [ "1e", "Taken together these results suggest that VP24 and VP35 are the structural components of the bridge located on the periphery of the" ] ]

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

[ "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: DAMAVER envelope appears as a pear shaped structure in which the homologous model can be fitted. Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution.", "Title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy\nPassage: which of which is slightly bigger than the other. Previous studies that produced recombinant nucleocapsid-like structures showed that expressed VP24 and VP35 both independently associate with NP, but that all three proteins together are necessary to produce ,50 nm diameter helical nucleocapsid-like structures. When VP35, VP30, VP24, and NP were transfected together, approximately 50 nm diameter helical nucleocapsid-like structure was also generated, whereas NP alone generated helical NP-RNA complexes ,20-25 nm in diameter, which were nuclease sensitive . Taken together these results suggest that VP24 and VP35 are the structural components of the bridge located on the periphery of the", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: 24 from which we made the 5′-vRNAp corresponding to the 5′-end and it's 3′ equivalent called 3′-vRNAp . By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct. Similar data had already been published 32 .", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: which the 5′-vRNAp binding site is located between the PA and PB1 subunits 5,6 . The 3′-vRNA, on the other hand, interacts with all three subunits suggesting a sequential vRNAp binding mechanism." ]

[ [ "2a", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5" ], [ "2b", "Passage: 24 from which we made the 5′-vRNAp corresponding to the 5′-end and it's 3′ equivalent called 3′-vRNAp ." ], [ "2c", "By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct." ], [ "2d", "Similar data had already been published 32 ." ] ]

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

[ "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: DAMAVER envelope appears as a pear shaped structure in which the homologous model can be fitted. Additional envelope volume is visible close to the endonuclease domain, implying that it adopts multiple conformations in solution.", "Title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy\nPassage: which of which is slightly bigger than the other. Previous studies that produced recombinant nucleocapsid-like structures showed that expressed VP24 and VP35 both independently associate with NP, but that all three proteins together are necessary to produce ,50 nm diameter helical nucleocapsid-like structures. When VP35, VP30, VP24, and NP were transfected together, approximately 50 nm diameter helical nucleocapsid-like structure was also generated, whereas NP alone generated helical NP-RNA complexes ,20-25 nm in diameter, which were nuclease sensitive . Taken together these results suggest that VP24 and VP35 are the structural components of the bridge located on the periphery of the", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: 24 from which we made the 5′-vRNAp corresponding to the 5′-end and it's 3′ equivalent called 3′-vRNAp . By thermal shift assay experiments, a 10 °C stabilisation was observed when 5′-vRNAp was added to all the constructs, whereas when 3′-vRNAp was added, the effect was less significant and dependent on the construct. Similar data had already been published 32 .", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5\nPassage: which the 5′-vRNAp binding site is located between the PA and PB1 subunits 5,6 . The 3′-vRNA, on the other hand, interacts with all three subunits suggesting a sequential vRNAp binding mechanism." ]

[ [ "3a", "Title: Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5" ], [ "3b", "Passage: which the 5′-vRNAp binding site is located between the PA and PB1 subunits 5,6 ." ], [ "3c", "The 3′-vRNA, on the other hand, interacts with all three subunits suggesting a sequential vRNAp binding mechanism." ] ]

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

[ "Title: Coinfection and Mortality in Pneumonia-Related Acute Respiratory Distress Syndrome Patients with Bronchoalveolar Lavage: A Prospective Observational Study\nPassage: Of the 142 pathogen-positive patients, 55 had bacterial, 88 had viral, and 81 had fungal pathogens . A total of 55 bacterial pathogens were identified in 42 patients: two pathogens were identified in eight patients, and three pathogens in two patients. Gram-negative bacteria were more common than gram-positive bacteria vs. n ¼ 10 ). The most common gram-negative and gram-positive bacteria were P aeruginosa and methicillinresistant S aureus, respectively. A total of 88 viral pathogens were identified in 82 patients: two pathogens were identified in six patients. The most common virus was CMV, followed by influenza. A total of 81", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: In conclusion, the common respiratory pathogens RSV, influenza A virus, adenovirus, and M pneumoniae were detected in the air and/or on the surfaces of the objects in the rooms occupied by pediatric patients infected with the corresponding pathogen. It cannot be overemphasized that appropriate infection control measures should be strictly implemented when caring for such patients.", "Title: Year in review 2013: critical care - respiratory infections\nPassage: Choi and associates studied the role of viruses in 198 patients with severe pneumonia using RT-PCR and BAL fluid or nasopharyngeal swab . Of the patients, 35.9% had positive bacterial culture, 36.4% had viral infections, and 9.1% had bacterialviral co-infections. Rhinovirus was the most commonly identified virus , followed by parainfluenza virus and human metapneumovirus . Bacterial coinfection was more common with parainfluenza and influenza viruses and less common with respiratory syncitial virus and rhinoviruses. There was no difference in mortality between each group, but of those patients with viral infection, rhinovirus was associated with the highest mortality , followed", "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" ]

[ [ "0a", "Title: Coinfection and Mortality in Pneumonia-Related Acute Respiratory Distress Syndrome Patients with Bronchoalveolar Lavage: A Prospective Observational Study" ], [ "0b", "Passage: Of the 142 pathogen-positive patients, 55 had bacterial, 88 had viral, and 81 had fungal pathogens ." ], [ "0c", "A total of 55 bacterial pathogens were identified in 42 patients: two pathogens were identified in eight patients, and three pathogens in two patients." ], [ "0d", "Gram-negative bacteria were more common than gram-positive bacteria vs. n ¼ 10 )." ], [ "0e", "The most common gram-negative and gram-positive bacteria were P aeruginosa and methicillinresistant S aureus, respectively." ], [ "0f", "A total of 88 viral pathogens were identified in 82 patients: two pathogens were identified in six patients." ], [ "0g", "The most common virus was CMV, followed by influenza." ], [ "0h", "A total of 81" ] ]

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

[ "Title: Coinfection and Mortality in Pneumonia-Related Acute Respiratory Distress Syndrome Patients with Bronchoalveolar Lavage: A Prospective Observational Study\nPassage: Of the 142 pathogen-positive patients, 55 had bacterial, 88 had viral, and 81 had fungal pathogens . A total of 55 bacterial pathogens were identified in 42 patients: two pathogens were identified in eight patients, and three pathogens in two patients. Gram-negative bacteria were more common than gram-positive bacteria vs. n ¼ 10 ). The most common gram-negative and gram-positive bacteria were P aeruginosa and methicillinresistant S aureus, respectively. A total of 88 viral pathogens were identified in 82 patients: two pathogens were identified in six patients. The most common virus was CMV, followed by influenza. A total of 81", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: In conclusion, the common respiratory pathogens RSV, influenza A virus, adenovirus, and M pneumoniae were detected in the air and/or on the surfaces of the objects in the rooms occupied by pediatric patients infected with the corresponding pathogen. It cannot be overemphasized that appropriate infection control measures should be strictly implemented when caring for such patients.", "Title: Year in review 2013: critical care - respiratory infections\nPassage: Choi and associates studied the role of viruses in 198 patients with severe pneumonia using RT-PCR and BAL fluid or nasopharyngeal swab . Of the patients, 35.9% had positive bacterial culture, 36.4% had viral infections, and 9.1% had bacterialviral co-infections. Rhinovirus was the most commonly identified virus , followed by parainfluenza virus and human metapneumovirus . Bacterial coinfection was more common with parainfluenza and influenza viruses and less common with respiratory syncitial virus and rhinoviruses. There was no difference in mortality between each group, but of those patients with viral infection, rhinovirus was associated with the highest mortality , followed", "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" ]

[ [ "1a", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards" ], [ "1b", "Passage: In conclusion, the common respiratory pathogens RSV, influenza A virus, adenovirus, and M pneumoniae were detected in the air and/or on the surfaces of the objects in the rooms occupied by pediatric patients infected with the corresponding pathogen." ], [ "1c", "It cannot be overemphasized that appropriate infection control measures should be strictly implemented when caring for such patients." ] ]

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

[ "Title: Coinfection and Mortality in Pneumonia-Related Acute Respiratory Distress Syndrome Patients with Bronchoalveolar Lavage: A Prospective Observational Study\nPassage: Of the 142 pathogen-positive patients, 55 had bacterial, 88 had viral, and 81 had fungal pathogens . A total of 55 bacterial pathogens were identified in 42 patients: two pathogens were identified in eight patients, and three pathogens in two patients. Gram-negative bacteria were more common than gram-positive bacteria vs. n ¼ 10 ). The most common gram-negative and gram-positive bacteria were P aeruginosa and methicillinresistant S aureus, respectively. A total of 88 viral pathogens were identified in 82 patients: two pathogens were identified in six patients. The most common virus was CMV, followed by influenza. A total of 81", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: In conclusion, the common respiratory pathogens RSV, influenza A virus, adenovirus, and M pneumoniae were detected in the air and/or on the surfaces of the objects in the rooms occupied by pediatric patients infected with the corresponding pathogen. It cannot be overemphasized that appropriate infection control measures should be strictly implemented when caring for such patients.", "Title: Year in review 2013: critical care - respiratory infections\nPassage: Choi and associates studied the role of viruses in 198 patients with severe pneumonia using RT-PCR and BAL fluid or nasopharyngeal swab . Of the patients, 35.9% had positive bacterial culture, 36.4% had viral infections, and 9.1% had bacterialviral co-infections. Rhinovirus was the most commonly identified virus , followed by parainfluenza virus and human metapneumovirus . Bacterial coinfection was more common with parainfluenza and influenza viruses and less common with respiratory syncitial virus and rhinoviruses. There was no difference in mortality between each group, but of those patients with viral infection, rhinovirus was associated with the highest mortality , followed", "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" ]

[ [ "2a", "Title: Year in review 2013: critical care - respiratory infections" ], [ "2b", "Passage: Choi and associates studied the role of viruses in 198 patients with severe pneumonia using RT-PCR and BAL fluid or nasopharyngeal swab ." ], [ "2c", "Of the patients, 35.9% had positive bacterial culture, 36.4% had viral infections, and 9.1% had bacterialviral co-infections." ], [ "2d", "Rhinovirus was the most commonly identified virus , followed by parainfluenza virus and human metapneumovirus ." ], [ "2e", "Bacterial coinfection was more common with parainfluenza and influenza viruses and less common with respiratory syncitial virus and rhinoviruses." ], [ "2f", "There was no difference in mortality between each group, but of those patients with viral infection, rhinovirus was associated with the highest mortality , followed" ] ]

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

[ "Title: Coinfection and Mortality in Pneumonia-Related Acute Respiratory Distress Syndrome Patients with Bronchoalveolar Lavage: A Prospective Observational Study\nPassage: Of the 142 pathogen-positive patients, 55 had bacterial, 88 had viral, and 81 had fungal pathogens . A total of 55 bacterial pathogens were identified in 42 patients: two pathogens were identified in eight patients, and three pathogens in two patients. Gram-negative bacteria were more common than gram-positive bacteria vs. n ¼ 10 ). The most common gram-negative and gram-positive bacteria were P aeruginosa and methicillinresistant S aureus, respectively. A total of 88 viral pathogens were identified in 82 patients: two pathogens were identified in six patients. The most common virus was CMV, followed by influenza. A total of 81", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards\nPassage: In conclusion, the common respiratory pathogens RSV, influenza A virus, adenovirus, and M pneumoniae were detected in the air and/or on the surfaces of the objects in the rooms occupied by pediatric patients infected with the corresponding pathogen. It cannot be overemphasized that appropriate infection control measures should be strictly implemented when caring for such patients.", "Title: Year in review 2013: critical care - respiratory infections\nPassage: Choi and associates studied the role of viruses in 198 patients with severe pneumonia using RT-PCR and BAL fluid or nasopharyngeal swab . Of the patients, 35.9% had positive bacterial culture, 36.4% had viral infections, and 9.1% had bacterialviral co-infections. Rhinovirus was the most commonly identified virus , followed by parainfluenza virus and human metapneumovirus . Bacterial coinfection was more common with parainfluenza and influenza viruses and less common with respiratory syncitial virus and rhinoviruses. There was no difference in mortality between each group, but of those patients with viral infection, rhinovirus was associated with the highest mortality , followed", "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" ]

[ [ "3a", "Title: Detection of Common Respiratory Viruses and Mycoplasma pneumoniae in Patient-Occupied Rooms in Pediatric Wards" ], [ "3b", "Passage: Viral infections of the respiratory system are very common." ], [ "3c", "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." ], [ "3d", "27 Enterovirus causes herpangina, hand-foot-and-mouth disease, myocarditis, encephalitis, and death." ], [ "3e", "RSV is the most common pathogen of the lower respiratory tract in infants 28 and a common cause of nosocomial infections in pediatric wards." ], [ "3f", "29 Influenza A and B viruses cause seasonal epidemics in Taiwan, especially in winter." ], [ "3g", "30 Adenovirus causes acute respiratory tract infections in children younger than 5 years" ] ]

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

[ "Title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico\nPassage: Fifty randomly selected cases were asked to participate in the study from which 42 accepted participation. All approached controls agreed to participate. In total 126 individuals were recruited. Our drop-out rate was lower than 1% since one participant did not finish the follow-up due to the loss of the assigned GPS logger. Table 1 describes the main characteristics of the subjects in each group. No statistically significant differences were observed in most of variables except in age, since cases were significantly younger than the intradomestic or population controls .", "Title: Drug sales data analysis for outbreak detection of infectious diseases: a systematic literature review\nPassage: Most of the studies were set in the United States , followed by Canada , France , Japan , the Netherlands and England . Only one study was conducted in more than one country .", "Title: Results From a Hypothesis Generating Case-Control Study: Herpes Family Viruses and Schizophrenia Among Military Personnel\nPassage: A total of 180 cases and 532 controls were included in the study population. Eight cases could only be matched to 2 controls. Table 1 shows the distribution of cases and controls by demographic factors. Overall, about 83% were males, 49% were whites, 44% were blacks, over 57% were younger than 25 years, 10% were older than 35 years, about 12% were Hispanic, and over 56% were in the army. Approximately 35% of cases had greater than 3 years of military service.", "Title: A Literature Review and Survey of Childhood Pneumonia Etiology Studies: 2000–2010\nPassage: these, 6 studies were being conducted in Bangladesh; 5 in each of Brazil, India and Nepal; 4 in Indonesia; 3 in each of Kenya, Mozambique, South Africa, the United States, Australia, Thailand and Spain; and 2 in each of Jordan, Guatemala, China and Israel. Two studies reported that they obtained approval to collect postmortem specimens in their protocols, but neither site had collected any postmortem specimens as of March 2011. Additional study characteristics are reported in Supplementary Table 1 ." ]

[ [ "0a", "Title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico" ], [ "0b", "Passage: Fifty randomly selected cases were asked to participate in the study from which 42 accepted participation." ], [ "0c", "All approached controls agreed to participate." ], [ "0d", "In total 126 individuals were recruited." ], [ "0e", "Our drop-out rate was lower than 1% since one participant did not finish the follow-up due to the loss of the assigned GPS logger." ], [ "0f", "Table 1 describes the main characteristics of the subjects in each group." ], [ "0g", "No statistically significant differences were observed in most of variables except in age, since cases were significantly younger than the intradomestic or population controls ." ] ]

[ "0a" ]

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: implemented with the abovementioned conditions. The critical issue that follows is then how limited resources such as antiviral drugs and testkits can be used effectively with those conditions.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: which any policy maker would try to minimize. This is especially true for antiviral drugs, which often represents a hard constraint. Depending on the frequency and proportion of such false positives, proper diagnostic approaches can then be implemented. For instance, when the proportion of false positives is high, such as the case of a high ILI rate, assuming that all patients are pandemic positive would put a strain on the limited drug supplies. Of course, such rates may not be possible to obtain for a novel pandemic strain with no outbreak history. Nonetheless, by not advocating a blanket approach and", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination ." ]

[ [ "0a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "0b", "Passage: The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase." ], [ "0c", "The key limitations of serological testing is the need to collect paired serum samples from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses." ], [ "0d", "The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples." ], [ "0e", "All patients recovered." ] ]

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

[ "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: implemented with the abovementioned conditions. The critical issue that follows is then how limited resources such as antiviral drugs and testkits can be used effectively with those conditions.", "Title: How necessary is a fast testkit for mitigation of pandemic flu?\nPassage: which any policy maker would try to minimize. This is especially true for antiviral drugs, which often represents a hard constraint. Depending on the frequency and proportion of such false positives, proper diagnostic approaches can then be implemented. For instance, when the proportion of false positives is high, such as the case of a high ILI rate, assuming that all patients are pandemic positive would put a strain on the limited drug supplies. Of course, such rates may not be possible to obtain for a novel pandemic strain with no outbreak history. Nonetheless, by not advocating a blanket approach and", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review\nPassage: Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination ." ]

[ [ "3a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "3b", "Passage: Rapid diagnostics plays an important role in disease and outbreak management." ], [ "3c", "The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures." ], [ "3d", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home." ], [ "3e", "Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination ." ] ]

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

[ "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening.", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: The invitees registered themselves as participants on the study's website, via a specially designed interactive voice response telephone service , or by sending in a postal response form. Individuals who stated, in response to the invitation or the first questionnaire , that they were not currently working were excluded due to non-eligibility. After one reminder, the final cohort comprised 2,237 participants. Fig 2 shows the study flow diagram of recruitment, enrolment and follow-up. The study protocol was approved by the Regional Ethics Review Board in Stockholm, Sweden . All participants gave their written informed consent.", "Title: Participant retention practices in longitudinal clinical research studies with high retention rates\nPassage: Of the 19 participating studies, 13 were prospective cohort studies, 5 were RCTs, and 1 was a quasiexperimental study . Included studies had diverse patient populations, including victims of intimate partner violence, persons living with human immunodeficiency virus and acquired immunodeficiency syndrome , survivors of critical illness and other serious illnesses. The target sample size for studies ranged from 255-10,000. Actual sample recruitment at the time of interview ranged from 205 for the Community Aging in Place -Advancing Better Living for Elders study with older adults aging in place to 2528 for the Alzheimer's Disease Anti-Inflammatory Prevention Trial . Though", "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: Should more than a third of the expected household members refuse to participate, the particular household will be excluded from the study. However, this will not apply if members are away from the household for extended periods due to work or school." ]

[ [ "0a", "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza" ], [ "0b", "Passage: Students attending the main campus of the university were approached to participate in the study." ], [ "0c", "Two methods were used to identify potential participants." ], [ "0d", "Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate." ], [ "0e", "In the latter half of the study, a snowball approach was used." ], [ "0f", "The snowball approach was adopted due to problems with identifying and recruiting postgraduate students." ], [ "0g", "They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening." ] ]

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

[ "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening.", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: The invitees registered themselves as participants on the study's website, via a specially designed interactive voice response telephone service , or by sending in a postal response form. Individuals who stated, in response to the invitation or the first questionnaire , that they were not currently working were excluded due to non-eligibility. After one reminder, the final cohort comprised 2,237 participants. Fig 2 shows the study flow diagram of recruitment, enrolment and follow-up. The study protocol was approved by the Regional Ethics Review Board in Stockholm, Sweden . All participants gave their written informed consent.", "Title: Participant retention practices in longitudinal clinical research studies with high retention rates\nPassage: Of the 19 participating studies, 13 were prospective cohort studies, 5 were RCTs, and 1 was a quasiexperimental study . Included studies had diverse patient populations, including victims of intimate partner violence, persons living with human immunodeficiency virus and acquired immunodeficiency syndrome , survivors of critical illness and other serious illnesses. The target sample size for studies ranged from 255-10,000. Actual sample recruitment at the time of interview ranged from 205 for the Community Aging in Place -Advancing Better Living for Elders study with older adults aging in place to 2528 for the Alzheimer's Disease Anti-Inflammatory Prevention Trial . Though", "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: Should more than a third of the expected household members refuse to participate, the particular household will be excluded from the study. However, this will not apply if members are away from the household for extended periods due to work or school." ]

[ [ "1a", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden" ], [ "1b", "Passage: The invitees registered themselves as participants on the study's website, via a specially designed interactive voice response telephone service , or by sending in a postal response form." ], [ "1c", "Individuals who stated, in response to the invitation or the first questionnaire , that they were not currently working were excluded due to non-eligibility." ], [ "1d", "After one reminder, the final cohort comprised 2,237 participants." ], [ "1e", "Fig 2 shows the study flow diagram of recruitment, enrolment and follow-up." ], [ "1f", "The study protocol was approved by the Regional Ethics Review Board in Stockholm, Sweden ." ], [ "1g", "All participants gave their written informed consent." ] ]

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

[ "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening.", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: The invitees registered themselves as participants on the study's website, via a specially designed interactive voice response telephone service , or by sending in a postal response form. Individuals who stated, in response to the invitation or the first questionnaire , that they were not currently working were excluded due to non-eligibility. After one reminder, the final cohort comprised 2,237 participants. Fig 2 shows the study flow diagram of recruitment, enrolment and follow-up. The study protocol was approved by the Regional Ethics Review Board in Stockholm, Sweden . All participants gave their written informed consent.", "Title: Participant retention practices in longitudinal clinical research studies with high retention rates\nPassage: Of the 19 participating studies, 13 were prospective cohort studies, 5 were RCTs, and 1 was a quasiexperimental study . Included studies had diverse patient populations, including victims of intimate partner violence, persons living with human immunodeficiency virus and acquired immunodeficiency syndrome , survivors of critical illness and other serious illnesses. The target sample size for studies ranged from 255-10,000. Actual sample recruitment at the time of interview ranged from 205 for the Community Aging in Place -Advancing Better Living for Elders study with older adults aging in place to 2528 for the Alzheimer's Disease Anti-Inflammatory Prevention Trial . Though", "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: Should more than a third of the expected household members refuse to participate, the particular household will be excluded from the study. However, this will not apply if members are away from the household for extended periods due to work or school." ]

[ [ "2a", "Title: Participant retention practices in longitudinal clinical research studies with high retention rates" ], [ "2b", "Passage: Of the 19 participating studies, 13 were prospective cohort studies, 5 were RCTs, and 1 was a quasiexperimental study ." ], [ "2c", "Included studies had diverse patient populations, including victims of intimate partner violence, persons living with human immunodeficiency virus and acquired immunodeficiency syndrome , survivors of critical illness and other serious illnesses." ], [ "2d", "The target sample size for studies ranged from 255-10,000." ], [ "2e", "Actual sample recruitment at the time of interview ranged from 205 for the Community Aging in Place -Advancing Better Living for Elders study with older adults aging in place to 2528 for the Alzheimer's Disease Anti-Inflammatory Prevention Trial . Though" ] ]

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

[ "Title: Examining the knowledge, attitudes and practices of domestic and international university students towards seasonal and pandemic influenza\nPassage: Students attending the main campus of the university were approached to participate in the study. Two methods were used to identify potential participants. Firstly, the interviewer directly approached a convenience sample of students who were located in the food halls and recreation areas of the university campus and invited them to participate. In the latter half of the study, a snowball approach was used. The snowball approach was adopted due to problems with identifying and recruiting postgraduate students. They constitute a considerably smaller percentage of the total student body, often are enrolled externally and attend classes in the late afternoon/evening.", "Title: Cohort profile: Studies of Work Environment and Disease Epidemiology-Infections (SWEDE-I), a prospective cohort on employed adults in Sweden\nPassage: The invitees registered themselves as participants on the study's website, via a specially designed interactive voice response telephone service , or by sending in a postal response form. Individuals who stated, in response to the invitation or the first questionnaire , that they were not currently working were excluded due to non-eligibility. After one reminder, the final cohort comprised 2,237 participants. Fig 2 shows the study flow diagram of recruitment, enrolment and follow-up. The study protocol was approved by the Regional Ethics Review Board in Stockholm, Sweden . All participants gave their written informed consent.", "Title: Participant retention practices in longitudinal clinical research studies with high retention rates\nPassage: Of the 19 participating studies, 13 were prospective cohort studies, 5 were RCTs, and 1 was a quasiexperimental study . Included studies had diverse patient populations, including victims of intimate partner violence, persons living with human immunodeficiency virus and acquired immunodeficiency syndrome , survivors of critical illness and other serious illnesses. The target sample size for studies ranged from 255-10,000. Actual sample recruitment at the time of interview ranged from 205 for the Community Aging in Place -Advancing Better Living for Elders study with older adults aging in place to 2528 for the Alzheimer's Disease Anti-Inflammatory Prevention Trial . Though", "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: Should more than a third of the expected household members refuse to participate, the particular household will be excluded from the study. However, this will not apply if members are away from the household for extended periods due to work or school." ]

[ [ "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: Should more than a third of the expected household members refuse to participate, the particular household will be excluded from the study." ], [ "3c", "However, this will not apply if members are away from the household for extended periods due to work or school." ] ]

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

[ "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: There are elements with zero genes that fulfill many criteria for early life: ribozymes, catalytic RNAs closely related to viroids. They were recovered in vitro from 10 15 molecules , 220 nucleotides in length, by 10 rounds of selection. Among the many RNA species present in this collection of quasispecies RNAs were catalytically active members, enzymatically active ribozymes. The sequence space for 220-mer RNAs is about 3 × 10 132 .", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even", "Title: Deciphering Biosignatures in Planetary Contexts\nPassage: The different possibilities for the emergence of membranebased compartmentalization have led to a significant research effort to build prebiotically plausible synthetic cell analogues that are capable of mimicking certain aspects of extant life . Analogs demonstrating metabolism, growth, replication, division, and evolution have been devised in the laboratory. These research efforts not only describe plausible options for the earliest forms of life on Earth but also lead to questions of how life can be defined in general terms and pose questions about the kind of compartments and their components that could be considered unambiguous extraterrestrial biosignatures.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: Text: Mycoplasma mycoides by systematic deletion of individual genes resulted in a synthetic minimal genome of 473 genes . Can one consider simpler living entities?" ]

[ [ "0a", "Title: Viruses and Evolution – Viruses First?" ], [ "0b", "A Personal Perspective" ], [ "0c", "Passage: There are elements with zero genes that fulfill many criteria for early life: ribozymes, catalytic RNAs closely related to viroids." ], [ "0d", "They were recovered in vitro from 10 15 molecules , 220 nucleotides in length, by 10 rounds of selection." ], [ "0e", "Among the many RNA species present in this collection of quasispecies RNAs were catalytically active members, enzymatically active ribozymes." ], [ "0f", "The sequence space for 220-mer RNAs is about 3 × 10 132 ." ] ]

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

[ "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: There are elements with zero genes that fulfill many criteria for early life: ribozymes, catalytic RNAs closely related to viroids. They were recovered in vitro from 10 15 molecules , 220 nucleotides in length, by 10 rounds of selection. Among the many RNA species present in this collection of quasispecies RNAs were catalytically active members, enzymatically active ribozymes. The sequence space for 220-mer RNAs is about 3 × 10 132 .", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even", "Title: Deciphering Biosignatures in Planetary Contexts\nPassage: The different possibilities for the emergence of membranebased compartmentalization have led to a significant research effort to build prebiotically plausible synthetic cell analogues that are capable of mimicking certain aspects of extant life . Analogs demonstrating metabolism, growth, replication, division, and evolution have been devised in the laboratory. These research efforts not only describe plausible options for the earliest forms of life on Earth but also lead to questions of how life can be defined in general terms and pose questions about the kind of compartments and their components that could be considered unambiguous extraterrestrial biosignatures.", "Title: Viruses and Evolution – Viruses First? A Personal Perspective\nPassage: Text: Mycoplasma mycoides by systematic deletion of individual genes resulted in a synthetic minimal genome of 473 genes . Can one consider simpler living entities?" ]

[ [ "1a", "Title: Viruses and Evolution – Viruses First?" ], [ "1b", "A Personal Perspective" ], [ "1c", "Passage: DNA-protein world." ], [ "1d", "How far back can we trace their contribution?" ], [ "1e", "Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life." ], [ "1f", "RNA can perform many aspects of life and influences our gene expression until today." ], [ "1g", "The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information." ], [ "1h", "Viruses today are obligatory parasites depending on host cells." ], [ "1i", "Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even" ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: More recently, peptide-displaying phage have been used in attempts to generate therapeutic antibody responses for chronic diseases, cancer, immunotherapy, and immunocontraception. Immunization with phage displaying Alzheimer's disease β-amyloid fibril peptides elicited anti-aggregating antibodies in mice and guinea pigs , possibly reduced amyloid plaque formation in mice , and may have helped maintain cognitive abilities in a transgenic mouse model of Alzheimer's disease ; however, it remains unclear how such antibodies are proposed to cross the blood-brain barrier. Yip et al. found that antibodies raised in mice against an ERBB2/HER2 peptide could inhibit breast-cancer cell proliferation. Phage displaying peptide ligands of", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: More recently, peptide-displaying phage have been used in attempts to generate therapeutic antibody responses for chronic diseases, cancer, immunotherapy, and immunocontraception. Immunization with phage displaying Alzheimer's disease β-amyloid fibril peptides elicited anti-aggregating antibodies in mice and guinea pigs , possibly reduced amyloid plaque formation in mice , and may have helped maintain cognitive abilities in a transgenic mouse model of Alzheimer's disease ; however, it remains unclear how such antibodies are proposed to cross the blood-brain barrier. Yip et al. found that antibodies raised in mice against an ERBB2/HER2 peptide could inhibit breast-cancer cell proliferation. Phage displaying peptide ligands of", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue . Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis . The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue . Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis . The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein." ]

[ [ "2a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "2b", "Passage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue ." ], [ "2c", "Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis ." ], [ "2d", "The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein." ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: More recently, peptide-displaying phage have been used in attempts to generate therapeutic antibody responses for chronic diseases, cancer, immunotherapy, and immunocontraception. Immunization with phage displaying Alzheimer's disease β-amyloid fibril peptides elicited anti-aggregating antibodies in mice and guinea pigs , possibly reduced amyloid plaque formation in mice , and may have helped maintain cognitive abilities in a transgenic mouse model of Alzheimer's disease ; however, it remains unclear how such antibodies are proposed to cross the blood-brain barrier. Yip et al. found that antibodies raised in mice against an ERBB2/HER2 peptide could inhibit breast-cancer cell proliferation. Phage displaying peptide ligands of", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: More recently, peptide-displaying phage have been used in attempts to generate therapeutic antibody responses for chronic diseases, cancer, immunotherapy, and immunocontraception. Immunization with phage displaying Alzheimer's disease β-amyloid fibril peptides elicited anti-aggregating antibodies in mice and guinea pigs , possibly reduced amyloid plaque formation in mice , and may have helped maintain cognitive abilities in a transgenic mouse model of Alzheimer's disease ; however, it remains unclear how such antibodies are proposed to cross the blood-brain barrier. Yip et al. found that antibodies raised in mice against an ERBB2/HER2 peptide could inhibit breast-cancer cell proliferation. Phage displaying peptide ligands of", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue . Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis . The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein.", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue . Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis . The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein." ]

[ [ "3a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "3b", "Passage: a diagnostic and therapeutic reagent for Alzheimer's disease and Parkinson's disease due to the unanticipated ability of the phage to penetrate into brain tissue ." ], [ "3c", "Similarly, phage displaying an immunodominant peptide epitope derived from myelin oligodendrocyte glycoprotein depleted pathogenic demyelinating antibodies in brain tissue in the murine experimental autoimmune encephalomyelitis model of multiple sclerosis ." ], [ "3d", "The advantages of the filamentous phage in this context over traditional antibody-drug or protein-peptide conjugates are its ability to carry very high amounts of drug or peptide, and its ability to access anatomical compartments that cannot generally be reached by systemic administration of a protein." ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "0a", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus" ], [ "0b", "Passage: easy-to- use system ." ], [ "0c", "Our reBmBac system has two major improvements relative to this system." ], [ "0d", "First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene." ], [ "0e", "In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene." ], [ "0f", "Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA." ], [ "0g", "Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "1a", "Title: Antibody Engineering for Pursuing a Healthier Future" ], [ "1b", "Passage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques." ], [ "1c", "Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins ." ], [ "1d", "Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents." ], [ "1e", "However, a variety of recombinant antibodies is needed to interact these hostile antigens." ], [ "1f", "Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "2a", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA" ], [ "2b", "Passage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed )." ], [ "2c", "The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences ." ], [ "2d", "The main advantage of this method is that there are no target limitations and no need for suitable restriction sites." ], [ "2e", "The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: The findings of our study, conducted over a 5-year period at five geographically dispersed sites in the USA, demonstrate that human coronavirus is an important cause of influenza-like illness ranged from 4% to 22%. 14 Additionally, we found HCoV-OC43", "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", "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 [" ]

[ [ "0a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "0b", "Passage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales." ], [ "0c", "There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus ." ], [ "0d", "Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs." ], [ "0e", "CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens." ], [ "0f", "The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000" ] ]

[ "0c", "3b" ]

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: Species‐specific clinical characteristics of human coronavirus infection among otherwise healthy adolescents and adults\nPassage: The findings of our study, conducted over a 5-year period at five geographically dispersed sites in the USA, demonstrate that human coronavirus is an important cause of influenza-like illness ranged from 4% to 22%. 14 Additionally, we found HCoV-OC43", "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", "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 [" ]

[ [ "3a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "3b", "Passage: Prior to December 2019, 6 CoVs were known to infect human, including 2 αCoV and 4 βCoV (HCoV-OC43 [" ] ]

[ "0c", "3b" ]

[ "Title: CDC Summary 21 MAR 2020,\nPassage: People who get a fever or cough should consider whether they might have COVID-19, depending on where they live, their travel history or other exposures. More than half of the U.S. is seeing some level of community spread of COVID-19. Testing for COVID-19 may be accessed through medical providers or public health departments, but there is no treatment for this virus. Most people have mild illness and are able to recover at home without medical care.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Symptoms at the point of diagnosis were reported for 31 cases. Two cases were asymptomatic and remained so until tested negative. The asymptomatic cases were tested as part of screening following repatriation and during contact tracing respectively. Of the remaining 29, 20 reported fever, 14 reported cough and eight reported weakness. Additional symptoms reported included headaches , sore throat , rhinorrhoea , shortness of breath , myalgia , diarrhoea and nausea . Fever was reported as the sole symptom for nine cases. In 16 of 29 symptomatic cases, the symptoms at diagnosis were consistent with the case definition for acute", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: The 2019-nCoV infected cases have symptoms like fever, fatigue, dry cough, dyspnea etc., with or without nasal congestion, runny nose or other upper respiratory symptoms . Despite the atypical symptoms were reported , Nan-Shan Zhong, the academician of Chinese Academy of Engineering in an exclusive interview with Xinhua News Agency on 28 January 2020, pointed out that fever is still the typical symptom of 2019-nCoV infection.", "Title: CDC Summary 21 MAR 2020,\nPassage: The complete clinical picture with regard to COVID-19 is not fully known. Reported illnesses have ranged from very mild to severe, including illness resulting in death. While information so far suggests that most COVID-19 illness is mild, a reportexternal icon out of China suggests serious illness occurs in 16% of cases. Older people and people of all ages with severe chronic medical conditions — like heart disease, lung disease and diabetes, for example — seem to be at higher risk of developing serious COVID-19 illness. A CDC Morbidity & Mortality Weekly Report that looked at severity of disease among COVID-19" ]

[ [ "0a", "Title: CDC Summary 21 MAR 2020," ], [ "0b", "Passage: People who get a fever or cough should consider whether they might have COVID-19, depending on where they live, their travel history or other exposures." ], [ "0c", "More than half of the U.S. is seeing some level of community spread of COVID-19." ], [ "0d", "Testing for COVID-19 may be accessed through medical providers or public health departments, but there is no treatment for this virus." ], [ "0e", "Most people have mild illness and are able to recover at home without medical care." ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: People who get a fever or cough should consider whether they might have COVID-19, depending on where they live, their travel history or other exposures. More than half of the U.S. is seeing some level of community spread of COVID-19. Testing for COVID-19 may be accessed through medical providers or public health departments, but there is no treatment for this virus. Most people have mild illness and are able to recover at home without medical care.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Symptoms at the point of diagnosis were reported for 31 cases. Two cases were asymptomatic and remained so until tested negative. The asymptomatic cases were tested as part of screening following repatriation and during contact tracing respectively. Of the remaining 29, 20 reported fever, 14 reported cough and eight reported weakness. Additional symptoms reported included headaches , sore throat , rhinorrhoea , shortness of breath , myalgia , diarrhoea and nausea . Fever was reported as the sole symptom for nine cases. In 16 of 29 symptomatic cases, the symptoms at diagnosis were consistent with the case definition for acute", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: The 2019-nCoV infected cases have symptoms like fever, fatigue, dry cough, dyspnea etc., with or without nasal congestion, runny nose or other upper respiratory symptoms . Despite the atypical symptoms were reported , Nan-Shan Zhong, the academician of Chinese Academy of Engineering in an exclusive interview with Xinhua News Agency on 28 January 2020, pointed out that fever is still the typical symptom of 2019-nCoV infection.", "Title: CDC Summary 21 MAR 2020,\nPassage: The complete clinical picture with regard to COVID-19 is not fully known. Reported illnesses have ranged from very mild to severe, including illness resulting in death. While information so far suggests that most COVID-19 illness is mild, a reportexternal icon out of China suggests serious illness occurs in 16% of cases. Older people and people of all ages with severe chronic medical conditions — like heart disease, lung disease and diabetes, for example — seem to be at higher risk of developing serious COVID-19 illness. A CDC Morbidity & Mortality Weekly Report that looked at severity of disease among COVID-19" ]

[ [ "1a", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020" ], [ "1b", "Passage: Symptoms at the point of diagnosis were reported for 31 cases." ], [ "1c", "Two cases were asymptomatic and remained so until tested negative." ], [ "1d", "The asymptomatic cases were tested as part of screening following repatriation and during contact tracing respectively." ], [ "1e", "Of the remaining 29, 20 reported fever, 14 reported cough and eight reported weakness." ], [ "1f", "Additional symptoms reported included headaches , sore throat , rhinorrhoea , shortness of breath , myalgia , diarrhoea and nausea ." ], [ "1g", "Fever was reported as the sole symptom for nine cases." ], [ "1h", "In 16 of 29 symptomatic cases, the symptoms at diagnosis were consistent with the case definition for acute" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: People who get a fever or cough should consider whether they might have COVID-19, depending on where they live, their travel history or other exposures. More than half of the U.S. is seeing some level of community spread of COVID-19. Testing for COVID-19 may be accessed through medical providers or public health departments, but there is no treatment for this virus. Most people have mild illness and are able to recover at home without medical care.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Symptoms at the point of diagnosis were reported for 31 cases. Two cases were asymptomatic and remained so until tested negative. The asymptomatic cases were tested as part of screening following repatriation and during contact tracing respectively. Of the remaining 29, 20 reported fever, 14 reported cough and eight reported weakness. Additional symptoms reported included headaches , sore throat , rhinorrhoea , shortness of breath , myalgia , diarrhoea and nausea . Fever was reported as the sole symptom for nine cases. In 16 of 29 symptomatic cases, the symptoms at diagnosis were consistent with the case definition for acute", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: The 2019-nCoV infected cases have symptoms like fever, fatigue, dry cough, dyspnea etc., with or without nasal congestion, runny nose or other upper respiratory symptoms . Despite the atypical symptoms were reported , Nan-Shan Zhong, the academician of Chinese Academy of Engineering in an exclusive interview with Xinhua News Agency on 28 January 2020, pointed out that fever is still the typical symptom of 2019-nCoV infection.", "Title: CDC Summary 21 MAR 2020,\nPassage: The complete clinical picture with regard to COVID-19 is not fully known. Reported illnesses have ranged from very mild to severe, including illness resulting in death. While information so far suggests that most COVID-19 illness is mild, a reportexternal icon out of China suggests serious illness occurs in 16% of cases. Older people and people of all ages with severe chronic medical conditions — like heart disease, lung disease and diabetes, for example — seem to be at higher risk of developing serious COVID-19 illness. A CDC Morbidity & Mortality Weekly Report that looked at severity of disease among COVID-19" ]

[ [ "2a", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)" ], [ "2b", "Passage: The 2019-nCoV infected cases have symptoms like fever, fatigue, dry cough, dyspnea etc., with or without nasal congestion, runny nose or other upper respiratory symptoms ." ], [ "2c", "Despite the atypical symptoms were reported , Nan-Shan Zhong, the academician of Chinese Academy of Engineering in an exclusive interview with Xinhua News Agency on 28 January 2020, pointed out that fever is still the typical symptom of 2019-nCoV infection." ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: People who get a fever or cough should consider whether they might have COVID-19, depending on where they live, their travel history or other exposures. More than half of the U.S. is seeing some level of community spread of COVID-19. Testing for COVID-19 may be accessed through medical providers or public health departments, but there is no treatment for this virus. Most people have mild illness and are able to recover at home without medical care.", "Title: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020\nPassage: Symptoms at the point of diagnosis were reported for 31 cases. Two cases were asymptomatic and remained so until tested negative. The asymptomatic cases were tested as part of screening following repatriation and during contact tracing respectively. Of the remaining 29, 20 reported fever, 14 reported cough and eight reported weakness. Additional symptoms reported included headaches , sore throat , rhinorrhoea , shortness of breath , myalgia , diarrhoea and nausea . Fever was reported as the sole symptom for nine cases. In 16 of 29 symptomatic cases, the symptoms at diagnosis were consistent with the case definition for acute", "Title: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)\nPassage: The 2019-nCoV infected cases have symptoms like fever, fatigue, dry cough, dyspnea etc., with or without nasal congestion, runny nose or other upper respiratory symptoms . Despite the atypical symptoms were reported , Nan-Shan Zhong, the academician of Chinese Academy of Engineering in an exclusive interview with Xinhua News Agency on 28 January 2020, pointed out that fever is still the typical symptom of 2019-nCoV infection.", "Title: CDC Summary 21 MAR 2020,\nPassage: The complete clinical picture with regard to COVID-19 is not fully known. Reported illnesses have ranged from very mild to severe, including illness resulting in death. While information so far suggests that most COVID-19 illness is mild, a reportexternal icon out of China suggests serious illness occurs in 16% of cases. Older people and people of all ages with severe chronic medical conditions — like heart disease, lung disease and diabetes, for example — seem to be at higher risk of developing serious COVID-19 illness. A CDC Morbidity & Mortality Weekly Report that looked at severity of disease among COVID-19" ]

[ [ "3a", "Title: CDC Summary 21 MAR 2020," ], [ "3b", "Passage: The complete clinical picture with regard to COVID-19 is not fully known." ], [ "3c", "Reported illnesses have ranged from very mild to severe, including illness resulting in death." ], [ "3d", "While information so far suggests that most COVID-19 illness is mild, a reportexternal icon out of China suggests serious illness occurs in 16% of cases." ], [ "3e", "Older people and people of all ages with severe chronic medical conditions — like heart disease, lung disease and diabetes, for example — seem to be at higher risk of developing serious COVID-19 illness." ], [ "3f", "A CDC Morbidity & Mortality Weekly Report that looked at severity of disease among COVID-19" ] ]

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

[ "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis\nPassage: In both of the universities in which this study was conducted there are ethics committees which had been established for the purpose of determining the ethical appropriateness of pharmaceutical trials using humans; since our study involved only the use of a questionnaire and not an experimental drug, we did not apply for approval from either of these ethics committees. Instead, written permission to carry out the study was granted by the dean of the faculty of medicine and by the chief manager of university hospitals. In addition, all of the potential participants were fully informed about the aim and structure", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: What are your plans for obtaining consent? A requirement to inform participants is often seen as being an important way to show respect and promote patient autonomy and welfare. 2) Ensure that consent procedures are acceptable within the study community .", "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis\nPassage: of the study. Furthermore, potential volunteers were all made aware that participation was strictly voluntary and that all of the answers they provide would be done so anonymously.", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: d. How will the consent process be conducted? You may want to consider issues such as: who will consent, where they will do so , will a witness to the consent be required, how much time will be offered to consider whether to be involved? Prior engagement with communities can be a useful way to ensure that the consent process meets local expectations and sensitivities. How will the act of consent be recorded ?" ]

[ [ "0a", "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis" ], [ "0b", "Passage: In both of the universities in which this study was conducted there are ethics committees which had been established for the purpose of determining the ethical appropriateness of pharmaceutical trials using humans; since our study involved only the use of a questionnaire and not an experimental drug, we did not apply for approval from either of these ethics committees." ], [ "0c", "Instead, written permission to carry out the study was granted by the dean of the faculty of medicine and by the chief manager of university hospitals." ], [ "0d", "In addition, all of the potential participants were fully informed about the aim and structure" ] ]

[ "0c", "2c" ]

[ "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis\nPassage: In both of the universities in which this study was conducted there are ethics committees which had been established for the purpose of determining the ethical appropriateness of pharmaceutical trials using humans; since our study involved only the use of a questionnaire and not an experimental drug, we did not apply for approval from either of these ethics committees. Instead, written permission to carry out the study was granted by the dean of the faculty of medicine and by the chief manager of university hospitals. In addition, all of the potential participants were fully informed about the aim and structure", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: What are your plans for obtaining consent? A requirement to inform participants is often seen as being an important way to show respect and promote patient autonomy and welfare. 2) Ensure that consent procedures are acceptable within the study community .", "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis\nPassage: of the study. Furthermore, potential volunteers were all made aware that participation was strictly voluntary and that all of the answers they provide would be done so anonymously.", "Title: Innovations in research ethics governance in humanitarian settings\nPassage: d. How will the consent process be conducted? You may want to consider issues such as: who will consent, where they will do so , will a witness to the consent be required, how much time will be offered to consider whether to be involved? Prior engagement with communities can be a useful way to ensure that the consent process meets local expectations and sensitivities. How will the act of consent be recorded ?" ]

[ [ "2a", "Title: Can \"presumed consent\" justify the duty to treat infectious diseases? An analysis" ], [ "2b", "Passage: of the study." ], [ "2c", "Furthermore, potential volunteers were all made aware that participation was strictly voluntary and that all of the answers they provide would be done so anonymously." ] ]

[ "0c", "2c" ]

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: H7N7). Moreover, we demonstrate in a lethal influenza model with a low pathogenic H7N7 virus virus) and a H1N1pdm influenza virus in C57BL/6 mice that the combined use of both compounds significantly increases survival of infected animals in comparison with both mono-therapies or placebo. Remarkably, this benefit is maintained even when the treatment starts up to 72 hours post infection. CONCLUSION: A nasal spray containing carrageenan and Zanamivir should therefore be tested for prevention and treatment of uncomplicated influenza in clinical trials.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: In summary, the combination of two effective, established mono-therapies resulted in a significantly enhanced survival in lethally H7N7 infected mice. Additionally, the combination therapy was highly efficient in comparison to placebo treatment even after a treatment onset up to 48 hpi." ]

[ [ "0a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model Passage: H7N7)." ], [ "0b", "Moreover, we demonstrate in a lethal influenza model with a low pathogenic H7N7 virus virus) and a H1N1pdm influenza virus in C57BL/6 mice that the combined use of both compounds significantly increases survival of infected animals in comparison with both mono-therapies or placebo." ], [ "0c", "Remarkably, this benefit is maintained even when the treatment starts up to 72 hours post infection." ], [ "0d", "CONCLUSION: A nasal spray containing carrageenan and Zanamivir should therefore be tested for prevention and treatment of uncomplicated influenza in clinical trials." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: H7N7). Moreover, we demonstrate in a lethal influenza model with a low pathogenic H7N7 virus virus) and a H1N1pdm influenza virus in C57BL/6 mice that the combined use of both compounds significantly increases survival of infected animals in comparison with both mono-therapies or placebo. Remarkably, this benefit is maintained even when the treatment starts up to 72 hours post infection. CONCLUSION: A nasal spray containing carrageenan and Zanamivir should therefore be tested for prevention and treatment of uncomplicated influenza in clinical trials.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: In summary, the combination of two effective, established mono-therapies resulted in a significantly enhanced survival in lethally H7N7 infected mice. Additionally, the combination therapy was highly efficient in comparison to placebo treatment even after a treatment onset up to 48 hpi." ]

[ [ "1a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "1b", "Passage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies ." ], [ "1c", "The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi." ], [ "1d", "Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi." ], [ "1e", "This is a remarkable finding since NIs are normally not effective when applied 72 hpi." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: H7N7). Moreover, we demonstrate in a lethal influenza model with a low pathogenic H7N7 virus virus) and a H1N1pdm influenza virus in C57BL/6 mice that the combined use of both compounds significantly increases survival of infected animals in comparison with both mono-therapies or placebo. Remarkably, this benefit is maintained even when the treatment starts up to 72 hours post infection. CONCLUSION: A nasal spray containing carrageenan and Zanamivir should therefore be tested for prevention and treatment of uncomplicated influenza in clinical trials.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: We found that the combination of carrageenan with 3 mg/kg BW/day Zanamivir used for treatment of H7N7 infected mice resulted in significantly enhanced survival of mice in comparison to both mono-therapies . The significantly enhanced survival compared to the placebo treated group was also found after a delayed treatment start 48 hpi. Furthermore, in the H1N1pdm model the combination of carrageenan with 1 mg/kg BW/day Zanamivir showed statistically significant enhanced survival in comparison to placebo treatment even after a treatment start 72 hpi. This is a remarkable finding since NIs are normally not effective when applied 72 hpi.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: virus which has caused more than 175 deaths until October 2014 . Second, they are of special interest for the carrageenan/Zanamivir combination approach. They have shown to differ in in-vitro susceptibility to carrageenan, Zanamivir and the combination thereof . While H1N1pdm was highly sensitive to inhibition by both substances alone, H7N7 required much higher concentrations of carrageenan and Zanamivir, respectively, to achieve similar inhibition efficiencies. Therefore, both virus strains were chosen to further explore the efficiency of the combination therapy in a mouse model.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: In summary, the combination of two effective, established mono-therapies resulted in a significantly enhanced survival in lethally H7N7 infected mice. Additionally, the combination therapy was highly efficient in comparison to placebo treatment even after a treatment onset up to 48 hpi." ]

[ [ "3a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "3b", "Passage: In summary, the combination of two effective, established mono-therapies resulted in a significantly enhanced survival in lethally H7N7 infected mice." ], [ "3c", "Additionally, the combination therapy was highly efficient in comparison to placebo treatment even after a treatment onset up to 48 hpi." ] ]

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

[ "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: ELISA-array. The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use.", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods. The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions. The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate .", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Optimization of the ELISA-array assay", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Antibody arrays for simultaneous multiple antigen quantification are considered the most accurate methods . Liew validated one multiplex ELISA for the detection of 9 antigens; Anderson used microarray ELISA for multiplex detection of antibodies to tumor antigens in breast cancer, and demonstrated that ELISA-based array assays had the broadest dynamic range and lowest sample volume requirements compared with the other assays." ]

[ [ "0a", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses Passage: ELISA-array." ], [ "0b", "The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses." ], [ "0c", "The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs." ], [ "0d", "This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum." ], [ "0e", "The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use." ] ]

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

[ "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: ELISA-array. The ELISA-array assay is based on a \"sandwich\" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that the developed ELISA-array is sensitive and easy to use, which would have potential for clinical use.", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods. The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions. The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate .", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Optimization of the ELISA-array assay", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses\nPassage: Antibody arrays for simultaneous multiple antigen quantification are considered the most accurate methods . Liew validated one multiplex ELISA for the detection of 9 antigens; Anderson used microarray ELISA for multiplex detection of antibodies to tumor antigens in breast cancer, and demonstrated that ELISA-based array assays had the broadest dynamic range and lowest sample volume requirements compared with the other assays." ]

[ [ "1a", "Title: Development of an ELISA-array for simultaneous detection of five encephalitis viruses" ], [ "1b", "Passage: The identical antibodies used in the ELISA-array format were also tested in a conventional ELISA format to determine the difference in sensitivity and specificity of the two methods." ], [ "1c", "The conventional ELISAs were performed at the same time as the ELISA-array assays to ensure similar reaction conditions." ], [ "1d", "The conventional ELISAs were performed in an identical maner to the ELISA-array, except that antibodies were coated at a concentration of 2 μg/mL in PBS , and substrate TMB was used instead of Super Signal ELISA Femto Maximum sensitive substrate ." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Pertussis symptom duration and severity were mild compared with the classic pertussis case presentation. Only 3 of the 17 cases fulfilled the WHO criteria, which requires a minimum of 2 weeks of cough, whoop, or posttussive vomiting . Studies on pertussis in infants have generally been clinic-based, hospital-based, or in an outbreak, which therefore required a certain severity of illness for parents to recognize a need for medical attention . These study designs and passive surveillance efforts therefore may have missed milder pertussis cases . Our study, which required only 1 respiratory symptom for a nasal swab to be collected,", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Although cough, difficulty breathing, and cough with vomit were the most common symptoms, no symptom was present in all B pertussis cases. During an epidemic period in Washington state, among infants <1 year, who had a minimum of 14 days cough plus an additional symptom, 82% had posttussive emesis, 29% had apnea, 26% had whoop, and 42% had cyanosis . A study of US neonates with pertussis showed the symptom prevalence to be 97% for cough, 91% for cyanosis, 58% for apnea, and 3% for fever . Our study found lower or equal symptom prevalence with the exception of fever.", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: respiratory symptom criteria.", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Infant respiratory symptoms were reported by parents, who may have missed signs that might have been observed by a healthcare worker. However, the criteria for collection of the nasal swab were broad and did not require sophisticated clinical skills. However, apnea and cyanosis may have been difficult for parents to identify. Although the criteria for specimen collection changed in year 2, no infant experienced a pertussis-specific symptom in isolation without also having one of the originally specified respiratory symptoms. These data support our assumption that we were unlikely to have missed pertussis cases in year 1 with our less sensitive" ]

[ [ "0a", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal" ], [ "0b", "Passage: Pertussis symptom duration and severity were mild compared with the classic pertussis case presentation." ], [ "0c", "Only 3 of the 17 cases fulfilled the WHO criteria, which requires a minimum of 2 weeks of cough, whoop, or posttussive vomiting ." ], [ "0d", "Studies on pertussis in infants have generally been clinic-based, hospital-based, or in an outbreak, which therefore required a certain severity of illness for parents to recognize a need for medical attention ." ], [ "0e", "These study designs and passive surveillance efforts therefore may have missed milder pertussis cases ." ], [ "0f", "Our study, which required only 1 respiratory symptom for a nasal swab to be collected," ] ]

[ "0c" ]

[ "Title: Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay\nPassage: striking examples were shown in Fig. 6 .", "Title: Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay\nPassage: presented approach in diagnostic qPCR was demonstrated on practical examples.", "Title: A broadly neutralizing anti-influenza antibody reveals ongoing capacity of haemagglutinin-specific memory B cells to evolve\nPassage: was also due to decreased dissociation rates, while association rates were equal .", "Title: Model of the pathway of −1 frameshifting: Long pausing\nPassage: and simultaneously provided a consistent explanation of a lot of available independent experimental data." ]

[ [ "1a", "Title: Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay" ], [ "1b", "Passage: presented approach in diagnostic qPCR was demonstrated on practical examples." ] ]

[ "1b" ]

[ "Title: Viral vector-based influenza vaccines\nPassage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types. 184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector. 184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Adenovirus vectors are attractive as vaccine vectors because their genome is very stable and there are a variety of recombinant systems available which can accommodate up to 10 kb of recombinant genetic material . Adenovirus is a non-enveloped virus which is relatively stable and can be formulated for long-term storage at 4 °C, or even storage up to six months at room temperature . Adenovirus vaccines can be grown to high titers, exceeding 10 1° plaque forming units per mL when cultured on 293 or PER.C6 cells , and the virus can be purified by simple methods . Adenovirus vaccines", "Title: Adenovirus flow in host cell networks\nPassage: regard, AdVs are a robust family, composed of more than 100 known serotypes that can infect various vertebrate species including mammals, birds, fish, reptiles and amphibians . To date, there are at least 57 serotypes divided into seven species that can infect humans, causing acute respiratory disease, gastroenteritis, keratoconjunctivits and even obesity . These diseases are generally self-limiting, but severe and deadly infections can occur in immunocompromised hosts . Cell biology studies using optimized tissue culture systems have shown that typical times for producing AdV virions from infected cells ranges from 14 to 19 h depending on serotype , though" ]

[ [ "0a", "Title: Viral vector-based influenza vaccines" ], [ "0b", "Passage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types." ], [ "0c", "184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector." ], [ "0d", "184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview" ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types. 184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector. 184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Adenovirus vectors are attractive as vaccine vectors because their genome is very stable and there are a variety of recombinant systems available which can accommodate up to 10 kb of recombinant genetic material . Adenovirus is a non-enveloped virus which is relatively stable and can be formulated for long-term storage at 4 °C, or even storage up to six months at room temperature . Adenovirus vaccines can be grown to high titers, exceeding 10 1° plaque forming units per mL when cultured on 293 or PER.C6 cells , and the virus can be purified by simple methods . Adenovirus vaccines", "Title: Adenovirus flow in host cell networks\nPassage: regard, AdVs are a robust family, composed of more than 100 known serotypes that can infect various vertebrate species including mammals, birds, fish, reptiles and amphibians . To date, there are at least 57 serotypes divided into seven species that can infect humans, causing acute respiratory disease, gastroenteritis, keratoconjunctivits and even obesity . These diseases are generally self-limiting, but severe and deadly infections can occur in immunocompromised hosts . Cell biology studies using optimized tissue culture systems have shown that typical times for producing AdV virions from infected cells ranges from 14 to 19 h depending on serotype , though" ]

[ [ "1a", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice" ], [ "1b", "Passage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen." ], [ "1c", "Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens ." ], [ "1d", "While these results are encouraging, immunity eventually develops against virus capsid proteins." ], [ "1e", "This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans ." ], [ "1f", "This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan" ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: Recombinant adenoviruses have attractive properties to serve as vaccine vectors: high titer stocks can be grown, genes of interest can easily be inserted into the stable viral genome, long-term storage at 4 degrees is possible and rAd infects a variety of hosts, tissues and cell types. 184 Furthermore, rAd can even induce robust immune responses when administered orally or intra-nasally, potentially bypassing pre-existing immunity against the vector. 184 Finally, even replicationdeficient rAd are known to be immunogenic; adenovirus 5 is a replication-deficient vector that has been evaluated for gene delivery, anti-cancer therapy and as an infectious disease vaccine. An overview", "Title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice\nPassage: The ability of human adenoviruses to induce strong innate and adaptive immune responses makes them powerful adjuvants that facilitate the immune response against an encoded antigen. Recombinant adenoviruses have been shown to elicit significant immune responses to bacterial , viral and tumour-associated antigens . While these results are encouraging, immunity eventually develops against virus capsid proteins. This severely reduces the immunogenicity of adenovirus-based vaccines in mice, , primates and humans . This problem is also significant since a large portion of the Western world has marked levels of anti-adenovirus serotype 5 antibodies and is also prominent in regions of sub-Saharan", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Adenovirus vectors are attractive as vaccine vectors because their genome is very stable and there are a variety of recombinant systems available which can accommodate up to 10 kb of recombinant genetic material . Adenovirus is a non-enveloped virus which is relatively stable and can be formulated for long-term storage at 4 °C, or even storage up to six months at room temperature . Adenovirus vaccines can be grown to high titers, exceeding 10 1° plaque forming units per mL when cultured on 293 or PER.C6 cells , and the virus can be purified by simple methods . Adenovirus vaccines", "Title: Adenovirus flow in host cell networks\nPassage: regard, AdVs are a robust family, composed of more than 100 known serotypes that can infect various vertebrate species including mammals, birds, fish, reptiles and amphibians . To date, there are at least 57 serotypes divided into seven species that can infect humans, causing acute respiratory disease, gastroenteritis, keratoconjunctivits and even obesity . These diseases are generally self-limiting, but severe and deadly infections can occur in immunocompromised hosts . Cell biology studies using optimized tissue culture systems have shown that typical times for producing AdV virions from infected cells ranges from 14 to 19 h depending on serotype , though" ]

[ [ "2a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "2b", "Passage: Adenovirus vectors are attractive as vaccine vectors because their genome is very stable and there are a variety of recombinant systems available which can accommodate up to 10 kb of recombinant genetic material ." ], [ "2c", "Adenovirus is a non-enveloped virus which is relatively stable and can be formulated for long-term storage at 4 °C, or even storage up to six months at room temperature ." ], [ "2d", "Adenovirus vaccines can be grown to high titers, exceeding 10 1° plaque forming units per mL when cultured on 293 or PER.C6 cells , and the virus can be purified by simple methods . Adenovirus vaccines" ] ]

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

[ "Title: Animal lectins: potential receptors for ginseng polysaccharides\nPassage: 1.6.1. P-type lectins P-type lectins are intracellular transmembrane glycoproteins with specificity for mannose-6-phosphate to identify and route lysosomal enzymes to the lysosomal compartment and they have two groups. One is the 43e46 kDa cationdependent M6P receptor which requires Ca 2þ for activity and contains single extracellular domain, followed by a single transmembrane domain . The other is the 275e300 kDa Table 2 A summary of the C-type lectin receptors dealt with in this review insulin-like growth factor II/cation-independent M6P receptor which does not require cation for activity and has a large extracellular domain containing two high-affinity binding sites . The", "Title: Find novel dual-agonist drugs for treating type 2 diabetes by means of cheminformatics\nPassage: G-protein-coupled receptors-grey incident degree analysis and G-protein-coupled receptors -2-layer predictor for identifying G protein-coupled receptors and their types, 25, 26 iLoc-Euk and iLoc-Hum for predicting subcellular localization of eukaryotic and human proteins, 27,28 NR-2L for identifying nuclear receptors and their subfamilies, 29 ProtIdent for identifying proteases and their types, 30 and HIVcleave for predicting human immunodeficiency virus protease cleavage sites in proteins, 31, 32 can provide timely and very useful information, as well as insights for drug development. In addition to the aforementioned approaches, the Virtual Screening technique and Core Hopping technique are also very useful. The former can be", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: fusion and cell-cell fusion are distinct receptor mediated phenomena. The possible contribution of differential glycosylation to these phenotypic differences was evaluated using Western analysis, treatment by glycosylation inhibitors and mutagenesis to remove glycosylation sites.", "Title: Animal lectins: potential receptors for ginseng polysaccharides\nPassage: has the capacity for endocytosis of ligands from the cell surface and serves to turn over IGF by endocytosis, but not CD-MPR ." ]

[ [ "0a", "Title: Animal lectins: potential receptors for ginseng polysaccharides Passage: 1.6.1." ], [ "0b", "P-type lectins P-type lectins are intracellular transmembrane glycoproteins with specificity for mannose-6-phosphate to identify and route lysosomal enzymes to the lysosomal compartment and they have two groups." ], [ "0c", "One is the 43e46 kDa cationdependent M6P receptor which requires Ca 2þ for activity and contains single extracellular domain, followed by a single transmembrane domain ." ], [ "0d", "The other is the 275e300 kDa Table 2 A summary of the C-type lectin receptors dealt with in this review insulin-like growth factor II/cation-independent M6P receptor which does not require cation for activity and has a large extracellular domain containing two high-affinity binding sites . The" ] ]

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

[ "Title: Animal lectins: potential receptors for ginseng polysaccharides\nPassage: 1.6.1. P-type lectins P-type lectins are intracellular transmembrane glycoproteins with specificity for mannose-6-phosphate to identify and route lysosomal enzymes to the lysosomal compartment and they have two groups. One is the 43e46 kDa cationdependent M6P receptor which requires Ca 2þ for activity and contains single extracellular domain, followed by a single transmembrane domain . The other is the 275e300 kDa Table 2 A summary of the C-type lectin receptors dealt with in this review insulin-like growth factor II/cation-independent M6P receptor which does not require cation for activity and has a large extracellular domain containing two high-affinity binding sites . The", "Title: Find novel dual-agonist drugs for treating type 2 diabetes by means of cheminformatics\nPassage: G-protein-coupled receptors-grey incident degree analysis and G-protein-coupled receptors -2-layer predictor for identifying G protein-coupled receptors and their types, 25, 26 iLoc-Euk and iLoc-Hum for predicting subcellular localization of eukaryotic and human proteins, 27,28 NR-2L for identifying nuclear receptors and their subfamilies, 29 ProtIdent for identifying proteases and their types, 30 and HIVcleave for predicting human immunodeficiency virus protease cleavage sites in proteins, 31, 32 can provide timely and very useful information, as well as insights for drug development. In addition to the aforementioned approaches, the Virtual Screening technique and Core Hopping technique are also very useful. The former can be", "Title: Role of receptor polymorphism and glycosylation in syncytium induction and host range variation of ecotropic mouse gammaretroviruses\nPassage: fusion and cell-cell fusion are distinct receptor mediated phenomena. The possible contribution of differential glycosylation to these phenotypic differences was evaluated using Western analysis, treatment by glycosylation inhibitors and mutagenesis to remove glycosylation sites.", "Title: Animal lectins: potential receptors for ginseng polysaccharides\nPassage: has the capacity for endocytosis of ligands from the cell surface and serves to turn over IGF by endocytosis, but not CD-MPR ." ]

[ [ "3a", "Title: Animal lectins: potential receptors for ginseng polysaccharides" ], [ "3b", "Passage: has the capacity for endocytosis of ligands from the cell surface and serves to turn over IGF by endocytosis, but not CD-MPR ." ] ]

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

[ "Title: The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis\nPassage: IL-1 is a polypeptide which has two forms; IL-1α and IL-1β. It is involved in the acutephase response and is accountable for several alterations that are related to the onset of various medical disorders . It is demonstrated recently that higher levels of IL-1β cytokine are strongly associated with surgically treated mycetoma patients, in comparison to those treated without surgery . It is known that IL-1β is a pro-inflammatory cytokine that is involved in cell death coordination . IL-1β cytokine is cleaved into the mature, active form primarily by inflammasome dependent caspase activity . It is possibly that mature IL-1β", "Title: The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis\nPassage: IL-1β, IL-37, and IL-12 were measured in the sera using commercially available enzyme linked immunosorbent assay kits . Serum levels of IL-35 were estimated using a sandwich ELISA commercial kit . Cytokine assays were performed in duplicates according to the manufacturers' protocols. The sensitivity of Human ELISA kits for IL-1β, IL-37, IL-12 and IL-35 cytokines was 0.5 pg/ml.", "Title: The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis\nPassage: IL-37, which is a member of the IL-1 family, has emerged as a potent anti-inflammatory cytokine that suppresses both innate and adaptive immune responses . Its role in human diseases is not completely understood yet . However, the anti-inflammatory properties of IL-37 have been associated with inflammatory diseases, such as systemic lupus erythematosus , and inflammatory bowel disease . It has been reported that IL-37 is negatively associated with pro-inflammatory cytokines such as IL-1β, IL-6, IL-17, TNF-α and IFN-γ in peripheral blood mononuclear cells of patients with degenerative intervertebral discs and Graves' disease . IL-37 protein level in PBMCs and", "Title: The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis\nPassage: IL-35 is a recently identified heterodimeric cytokine which belongs to the IL-12 cytokine family, composed of the subunits of IL-27; β chain Epstein-Barr-virus -induced gene 3 and IL-12α chain p35 . IL-35 is a potent immunosuppressive cytokine produced by B regulatory cells , DCs , and to a lesser extent, by endothelial cells, smooth muscle cells, and monocytes . The biological effect of IL-35 is poorly understood, however IL-35 is recognised as a typical anti-inflammatory cytokine, and the predominant mechanism of suppression is associated with its ability to suppress T cell proliferation and effector functions . Given the direct immunosuppressive" ]

[ [ "0a", "Title: The Role of Interleukin-1 cytokine family (IL-1β, IL-37) and interleukin-12 cytokine family (IL-12, IL-35) in eumycetoma infection pathogenesis" ], [ "0b", "Passage: IL-1 is a polypeptide which has two forms; IL-1α and IL-1β." ], [ "0c", "It is involved in the acutephase response and is accountable for several alterations that are related to the onset of various medical disorders ." ], [ "0d", "It is demonstrated recently that higher levels of IL-1β cytokine are strongly associated with surgically treated mycetoma patients, in comparison to those treated without surgery ." ], [ "0e", "It is known that IL-1β is a pro-inflammatory cytokine that is involved in cell death coordination ." ], [ "0f", "IL-1β cytokine is cleaved into the mature, active form primarily by inflammasome dependent caspase activity ." ], [ "0g", "It is possibly that mature IL-1β" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "0a", "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus" ], [ "0b", "Passage: easy-to- use system ." ], [ "0c", "Our reBmBac system has two major improvements relative to this system." ], [ "0d", "First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene." ], [ "0e", "In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene." ], [ "0f", "Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA." ], [ "0g", "Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "1a", "Title: Antibody Engineering for Pursuing a Healthier Future" ], [ "1b", "Passage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques." ], [ "1c", "Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins ." ], [ "1d", "Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents." ], [ "1e", "However, a variety of recombinant antibodies is needed to interact these hostile antigens." ], [ "1f", "Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "2a", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA" ], [ "2b", "Passage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed )." ], [ "2c", "The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences ." ], [ "2d", "The main advantage of this method is that there are no target limitations and no need for suitable restriction sites." ], [ "2e", "The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based" ] ]

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

[ "Title: A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus\nPassage: easy-to- use system . Our reBmBac system has two major improvements relative to this system. First, the fragment replaced during homologous recombination in our reBmBac system is only a 1.2 kb tet R gene. In contrast, the fragment in bBpGOZA is more than 6 kb, and it contains a miniF replicon and a kan R gene. Second, the CopyControl origin in our system facilitates the large-scale preparation of high-quality reBmBac DNA. Our results over the course of many experiments indicated that the high quality of reBmBac DNA and transfer plasmid DNA are key factors for achieving good recombination results. We", "Title: Antibody Engineering for Pursuing a Healthier Future\nPassage: Similarly, recombinant antibodies have several advantages: bacteria, yeast, plants, or animals can be used to produce antibodies, no need for immunization, and intrinsic properties can be modified easily using mutagenesis techniques. Genetically engineered antibodies have integral characteristics that suit various downstream applications or can be converted into functional whole immunoglobulins . Antibodies exhibit strong immunity to defend against foreign antigens and non-selfagents. However, a variety of recombinant antibodies is needed to interact these hostile antigens. Over the last decade, the use of antibody engineering or recombinant antibody technology has shaped the genetic manipulation of a diverse range of antibody fragments", "Title: Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA\nPassage: Manipulation of BACs using traditional cloning procedures can be difficult and thus a range of methodologies that apply bacterial genetics, including homologous recombination within the E. coli host, have been developed ). The use of homologous recombination allows site-directed mutagenesis of BACs and, by employing a counterselection scheme, specific modifications can be obtained without leaving residual \"foreign\" sequences . The main advantage of this method is that there are no target limitations and no need for suitable restriction sites. The integration of the modified sequence is performed in vivo thereby potentially being more accurate than in vitro approaches like PCR-based", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections\nPassage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous. In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce. 13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ]

[ [ "3a", "Title: DMAb inoculation of synthetic cross reactive antibodies protects against lethal influenza A and B infections" ], [ "3b", "Passage: A distinct approach to antibody immune therapy which would allow for simplicity of production and lower costs, with high stability and ease of deliverability could be advantageous." ], [ "3c", "In this regard, the technology of DNA-encoded protein antigen delivery has specific advantages as demonstrated by recent successes in the DNA vaccine field: plasmid DNA is well-tolerated and nonintegrating, it does not require cold-chain distribution, it can be delivered repeatedly, and it is relatively inexpensive to produce." ], [ "3d", "13 However, to date, the ability to produce substantial levels of protein expression systemically from in vivo delivery of plasmid DNA has not been considered feasible." ] ]

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

[ "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: result from genetic and ethnic differences, but the possibility of the effects of CAM, including KM, cannot be ruled out.", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: were compared. After PS matching, the characteristics of both groups were statistically similar .", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: It should be noted that this paper had several limitations. First, the number of subjects was not sufficient because of data limitations; therefore, we cannot be sure of whether the non-significance of results is due to the absence of a relationship between the groups or to a lack of statistical power. Accordingly, comparative studies with increased duration and number of patients are required to clarify the effects KM on PD. Second, we assessed whether PD and its complications have been wellcontrolled by alternative outcomes-related measures such as the prevalence of hospitalization and annual length of hospitalization after PD diagnosis. Generally,", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: in PD patients ." ]

[ [ "0a", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management" ], [ "0b", "Passage: result from genetic and ethnic differences, but the possibility of the effects of CAM, including KM, cannot be ruled out." ] ]

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

[ "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: result from genetic and ethnic differences, but the possibility of the effects of CAM, including KM, cannot be ruled out.", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: were compared. After PS matching, the characteristics of both groups were statistically similar .", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: It should be noted that this paper had several limitations. First, the number of subjects was not sufficient because of data limitations; therefore, we cannot be sure of whether the non-significance of results is due to the absence of a relationship between the groups or to a lack of statistical power. Accordingly, comparative studies with increased duration and number of patients are required to clarify the effects KM on PD. Second, we assessed whether PD and its complications have been wellcontrolled by alternative outcomes-related measures such as the prevalence of hospitalization and annual length of hospitalization after PD diagnosis. Generally,", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management\nPassage: in PD patients ." ]

[ [ "2a", "Title: Effectiveness of Integrative Therapy for Parkinson’s Disease Management" ], [ "2b", "Passage: It should be noted that this paper had several limitations." ], [ "2c", "First, the number of subjects was not sufficient because of data limitations; therefore, we cannot be sure of whether the non-significance of results is due to the absence of a relationship between the groups or to a lack of statistical power." ], [ "2d", "Accordingly, comparative studies with increased duration and number of patients are required to clarify the effects KM on PD." ], [ "2e", "Second, we assessed whether PD and its complications have been wellcontrolled by alternative outcomes-related measures such as the prevalence of hospitalization and annual length of hospitalization after PD diagnosis. Generally," ] ]

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

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: encoded protein in comparison to native mRNAs . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: be quickly cleared or rendered less competent in its replication so as to blunt any pathological response in the host . The anti-hantavirus innate response can in some cases be attributed to viral interaction as a ligand of TLR-3, but not in others, and in endothelial cells, it appears not to require more than the viral particle itself, even when introduced in replication-incompetent form . Proteins and mRNAs prominently induced by hantaviruses include MxA and IFIT-1 and others including some with known or suspected anti-viral activity. Those hantaviruses, often highly pathogenic strains, that fail to induce a potent antiviral response,", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: are suspected or presumed to have a potent interferon-pathway antagonism mechanism relative to other viruses, a mechanism that acts positively to prevent an effective innate response from forming, at least early in infection . Yet some instances are reported wherein highly pathogenic hantaviruses, such as SNV, are also able to induce expression of interferon-stimulated gene mRNAs, even very early in infection, with ISG proteins, as expected, taking longer to appear in the cell . Anti-interferon activities have also been attributed to the NSs protein that may be elaborated in cells infected by serotypes that encode this protein . Other investigators", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Moreover, it is universally acknowledged that type I IFN responses are essential for hosts to defend against hantaviral infection. Multiple IFN stimulated genes were confirmed to have antihantaviral activity. The interferon-induced MxA protein, a GTPase with extensive antiviral activity, notably against influenza viruses, was reported to inhibit HTNV and PUUV replication in Vero cells . The interferoninduced IFITM3 protein was able to inhibit HTNV infection in both HUVEC and A549 cells by inhibiting virus entry . Several studies have shown that pretreatment with type I IFN could effectively inhibit hantaviral infection. Pretreating endothelial cells with IFNα blocks hantavirus replication, and" ]

[ [ "1a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "1b", "Passage: be quickly cleared or rendered less competent in its replication so as to blunt any pathological response in the host ." ], [ "1c", "The anti-hantavirus innate response can in some cases be attributed to viral interaction as a ligand of TLR-3, but not in others, and in endothelial cells, it appears not to require more than the viral particle itself, even when introduced in replication-incompetent form ." ], [ "1d", "Proteins and mRNAs prominently induced by hantaviruses include MxA and IFIT-1 and others including some with known or suspected anti-viral activity." ], [ "1e", "Those hantaviruses, often highly pathogenic strains, that fail to induce a potent antiviral response," ] ]

[ "1d", "2c" ]

[ "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: encoded protein in comparison to native mRNAs . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: be quickly cleared or rendered less competent in its replication so as to blunt any pathological response in the host . The anti-hantavirus innate response can in some cases be attributed to viral interaction as a ligand of TLR-3, but not in others, and in endothelial cells, it appears not to require more than the viral particle itself, even when introduced in replication-incompetent form . Proteins and mRNAs prominently induced by hantaviruses include MxA and IFIT-1 and others including some with known or suspected anti-viral activity. Those hantaviruses, often highly pathogenic strains, that fail to induce a potent antiviral response,", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens\nPassage: are suspected or presumed to have a potent interferon-pathway antagonism mechanism relative to other viruses, a mechanism that acts positively to prevent an effective innate response from forming, at least early in infection . Yet some instances are reported wherein highly pathogenic hantaviruses, such as SNV, are also able to induce expression of interferon-stimulated gene mRNAs, even very early in infection, with ISG proteins, as expected, taking longer to appear in the cell . Anti-interferon activities have also been attributed to the NSs protein that may be elaborated in cells infected by serotypes that encode this protein . Other investigators", "Title: Vaccines and Therapeutics Against Hantaviruses\nPassage: Moreover, it is universally acknowledged that type I IFN responses are essential for hosts to defend against hantaviral infection. Multiple IFN stimulated genes were confirmed to have antihantaviral activity. The interferon-induced MxA protein, a GTPase with extensive antiviral activity, notably against influenza viruses, was reported to inhibit HTNV and PUUV replication in Vero cells . The interferoninduced IFITM3 protein was able to inhibit HTNV infection in both HUVEC and A549 cells by inhibiting virus entry . Several studies have shown that pretreatment with type I IFN could effectively inhibit hantaviral infection. Pretreating endothelial cells with IFNα blocks hantavirus replication, and" ]

[ [ "2a", "Title: Hantaviruses in the Americas and Their Role as Emerging Pathogens" ], [ "2b", "Passage: are suspected or presumed to have a potent interferon-pathway antagonism mechanism relative to other viruses, a mechanism that acts positively to prevent an effective innate response from forming, at least early in infection ." ], [ "2c", "Yet some instances are reported wherein highly pathogenic hantaviruses, such as SNV, are also able to induce expression of interferon-stimulated gene mRNAs, even very early in infection, with ISG proteins, as expected, taking longer to appear in the cell ." ], [ "2d", "Anti-interferon activities have also been attributed to the NSs protein that may be elaborated in cells infected by serotypes that encode this protein . Other investigators" ] ]

[ "1d", "2c" ]

[ "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies . A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection . Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study.", "Title: Severe novel influenza A (H1N1) infection in cancer patients\nPassage: In our study, we detected bacterial coinfection in seven of the eight patients. The CDC reported that 29% of fatal cases in the United States presented at least one bacterial coinfection . Mauad et al. found evidence of bacterial coinfection in 38% of fatal cases in Sao Paulo.", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: the actual number of cases. The preadmission antibiotic therapy could underestimate the bacterial coinfection rates. Despite these limitations, we identified bacteria coinfection in 28% of our patients.", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection\nPassage: A comparison between H1N1 patients with and without bacterial coinfection is shown in Table 2 . Although 90% of patients were < 50 years old, bacterial coinfection was more frequent in patients > 50 years . The presence of underlying comorbidity provided a suitable niche for bacterial coinfection . Although ICU admissions, mechanical ventilation, renal impairment, mortality and pneumonia were notably higher in patients with bacterial coinfection, they were not statistically significant. Other factors associated with bacterial coinfection in the univariate analysis were development of complications , liver impairment and supplemental oxygen requirement . Out of the 50 patients, 12" ]

[ [ "0a", "Title: Epidemiology and clinical characteristics of hospitalized patients with pandemic influenza A (H1N1) 2009 infections: the effects of bacterial coinfection" ], [ "0b", "Passage: The bacterial coinfection rate of 28% amongst our H1N1 hospitalized patients was higher compared to other studies ." ], [ "0c", "A large laboratory-based study in the United States demonstrated comparable bacterial coinfection rates to our study with similarly very low frequency of viral copathogen detection ." ], [ "0d", "Whilst our finding concurred with several studies that showed H1N1 infections having a predilection for younger patients, patients > 50 years had higher risk of bacterial coinfection in our study." ] ]

[ "0c" ]

[ "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial. Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms . However, in studies of natural infection, it did not significantly affect viral loads or symptom severity .", "Title: Recent developments in antiviral agents against enterovirus 71 infection\nPassage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease . Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes . Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses . X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: All patients with influenza infection were treated with oseltamivir within 24 h of diagnosis. Influenza viral load after receiving treatment was significantly lower for both patients with influenza A and influenza B infections . Ribavirin was administered to 8 patients with RSV infection: 7 patients inhaled ribavirin, and 1 patient received intravenous ribavirin since the patient was on mechanical ventilation . Viral load was significantly reduced after completion of treatment.", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of" ]

[ [ "0a", "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics" ], [ "0b", "Passage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial." ], [ "0c", "Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms ." ], [ "0d", "However, in studies of natural infection, it did not significantly affect viral loads or symptom severity ." ] ]

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

[ "Title: The human viral challenge model: accelerating the evaluation of respiratory antivirals, vaccines and novel diagnostics\nPassage: A Protease inhibitor, rupintrivir thats prevents cleavage of viral proteins required for replication was tested in an HRV challenge trial. Rupintrivir was well tolerated and reduced viral loads and respiratory symptoms . However, in studies of natural infection, it did not significantly affect viral loads or symptom severity .", "Title: Recent developments in antiviral agents against enterovirus 71 infection\nPassage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease . Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes . Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses . X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam", "Title: Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR\nPassage: All patients with influenza infection were treated with oseltamivir within 24 h of diagnosis. Influenza viral load after receiving treatment was significantly lower for both patients with influenza A and influenza B infections . Ribavirin was administered to 8 patients with RSV infection: 7 patients inhaled ribavirin, and 1 patient received intravenous ribavirin since the patient was on mechanical ventilation . Viral load was significantly reduced after completion of treatment.", "Title: Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management\nPassage: Human rhinoviruses usually cause mild acute respiratory infections, but on occasions can also cause more severe respiratory infections, including exacerbations of asthma and COPD. Of 115 Japanese children with asthma, a respiratory virus was detected in 86%, of which HRV or RSV were most common. 79 Ex vivo bronchial epithelial cells from people with asthma are more susceptible to HRV infection, due to deficient induction of IFN-b and IFN-lambda. In a study of 147 asthmatics on inhaled corticosteroid therapy, with a history of virusassociated exacerbations, patients were randomised to 14-day treatment with inhaled IFN-b or placebo within 24 hours of" ]

[ [ "1a", "Title: Recent developments in antiviral agents against enterovirus 71 infection" ], [ "1b", "Passage: A pseudosubstrate, LVLQTM peptide, could inhibit EV-71 infection through binding to the active site of 2A protease ." ], [ "1c", "Rupintrivir is an irreversible peptidomimetic inhibitor of human rhinovirus 3C protease, which reached phase 2 clinical trials with promising outcomes ." ], [ "1d", "Rupintrivir showed significant inhibition of EV-71 infection in vitro and in vivo but with reduced efficacy as compared with human rhinoviruses ." ], [ "1e", "X-ray crystallography of the complex of EV-71 3C protease with rupintrivir revealed that the half-closed S2 sub-site and the size reduced S1′ pocket of EV-71 3C protease limits the access of the rupintrivir's P1′ group which contains a lactam" ] ]

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

[ "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: The chemiluminescent enzyme-linked immunosorbent assay was performed by detecting EBOV with the anti-EBOV VP40 antibody followed by staining with the horseradish peroxidase -conjugated goat anti-mouse secondary antibody . Chemiluminescence was quantified using Pico Chemiluminescent Substrate and a plate reader .", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: In addition to the fluorescent assay, we also implemented a CELIA using an HRP-labeled antibody, which amplified the signal and increased the sensitivity of virus detection. As expected, the CELIA showed an improvement in the quality of data sets compared to the fluorescent assay. S/N ratio and Z' factor were in an acceptable range as early as 24 hpi with the lowest virus input detected at an MOI of 0.1. An EC 50 could also be determined at this time point. At 48 or 72 hpi, the two fluorescent read outs were similar to the chemiluminescent read out.", "Title: A Fluorometric Method of Measuring Carboxypeptidase Activities for Angiotensin II and Apelin-13\nPassage: ELISA-based methods that measure the input of Ang II or the production of Ang-, or both, are available 12, 25 . However, antibody-based assays are intrinsically finicky and the input substrate peptide and the tissue lysate amount have to be carefully optimized to achieve linearity. Even with the best setting, the dynamic range is less than one order of magnitude, as opposed to the three orders of magnitude range achieved by the Ang II phenylalanine assay . The clinical importance of the RAAS in a multitude of diseases underscores the need for techniques to measure enzymatic activities in biological samples,", "Title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters\nPassage: second assay is also well-known and established for measurements of alcohol in food . This assay was miniaturized to microtiter plates. The third assay is a modification of a chromogenic alcohol-oxidase /peroxidase ethanol assay for determination of ethanol in beverages, which normally based on 2,2'-azino-bis as chromogenic substrate . This assay was modified to a luminometric assay by adding luminol instead of a chromogenic substrate. The luminometric measurements should be more sensitive due to photons are released by the detection reaction. For the first time the system was established in a flow system with separated bioreactors by Marschall and Gibson" ]

[ [ "0a", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs" ], [ "0b", "Passage: The chemiluminescent enzyme-linked immunosorbent assay was performed by detecting EBOV with the anti-EBOV VP40 antibody followed by staining with the horseradish peroxidase -conjugated goat anti-mouse secondary antibody ." ], [ "0c", "Chemiluminescence was quantified using Pico Chemiluminescent Substrate and a plate reader ." ] ]

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

[ "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: The chemiluminescent enzyme-linked immunosorbent assay was performed by detecting EBOV with the anti-EBOV VP40 antibody followed by staining with the horseradish peroxidase -conjugated goat anti-mouse secondary antibody . Chemiluminescence was quantified using Pico Chemiluminescent Substrate and a plate reader .", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: In addition to the fluorescent assay, we also implemented a CELIA using an HRP-labeled antibody, which amplified the signal and increased the sensitivity of virus detection. As expected, the CELIA showed an improvement in the quality of data sets compared to the fluorescent assay. S/N ratio and Z' factor were in an acceptable range as early as 24 hpi with the lowest virus input detected at an MOI of 0.1. An EC 50 could also be determined at this time point. At 48 or 72 hpi, the two fluorescent read outs were similar to the chemiluminescent read out.", "Title: A Fluorometric Method of Measuring Carboxypeptidase Activities for Angiotensin II and Apelin-13\nPassage: ELISA-based methods that measure the input of Ang II or the production of Ang-, or both, are available 12, 25 . However, antibody-based assays are intrinsically finicky and the input substrate peptide and the tissue lysate amount have to be carefully optimized to achieve linearity. Even with the best setting, the dynamic range is less than one order of magnitude, as opposed to the three orders of magnitude range achieved by the Ang II phenylalanine assay . The clinical importance of the RAAS in a multitude of diseases underscores the need for techniques to measure enzymatic activities in biological samples,", "Title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters\nPassage: second assay is also well-known and established for measurements of alcohol in food . This assay was miniaturized to microtiter plates. The third assay is a modification of a chromogenic alcohol-oxidase /peroxidase ethanol assay for determination of ethanol in beverages, which normally based on 2,2'-azino-bis as chromogenic substrate . This assay was modified to a luminometric assay by adding luminol instead of a chromogenic substrate. The luminometric measurements should be more sensitive due to photons are released by the detection reaction. For the first time the system was established in a flow system with separated bioreactors by Marschall and Gibson" ]

[ [ "1a", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs" ], [ "1b", "Passage: In addition to the fluorescent assay, we also implemented a CELIA using an HRP-labeled antibody, which amplified the signal and increased the sensitivity of virus detection." ], [ "1c", "As expected, the CELIA showed an improvement in the quality of data sets compared to the fluorescent assay." ], [ "1d", "S/N ratio and Z' factor were in an acceptable range as early as 24 hpi with the lowest virus input detected at an MOI of 0.1." ], [ "1e", "An EC 50 could also be determined at this time point." ], [ "1f", "At 48 or 72 hpi, the two fluorescent read outs were similar to the chemiluminescent read out." ] ]

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

[ "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: The chemiluminescent enzyme-linked immunosorbent assay was performed by detecting EBOV with the anti-EBOV VP40 antibody followed by staining with the horseradish peroxidase -conjugated goat anti-mouse secondary antibody . Chemiluminescence was quantified using Pico Chemiluminescent Substrate and a plate reader .", "Title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs\nPassage: In addition to the fluorescent assay, we also implemented a CELIA using an HRP-labeled antibody, which amplified the signal and increased the sensitivity of virus detection. As expected, the CELIA showed an improvement in the quality of data sets compared to the fluorescent assay. S/N ratio and Z' factor were in an acceptable range as early as 24 hpi with the lowest virus input detected at an MOI of 0.1. An EC 50 could also be determined at this time point. At 48 or 72 hpi, the two fluorescent read outs were similar to the chemiluminescent read out.", "Title: A Fluorometric Method of Measuring Carboxypeptidase Activities for Angiotensin II and Apelin-13\nPassage: ELISA-based methods that measure the input of Ang II or the production of Ang-, or both, are available 12, 25 . However, antibody-based assays are intrinsically finicky and the input substrate peptide and the tissue lysate amount have to be carefully optimized to achieve linearity. Even with the best setting, the dynamic range is less than one order of magnitude, as opposed to the three orders of magnitude range achieved by the Ang II phenylalanine assay . The clinical importance of the RAAS in a multitude of diseases underscores the need for techniques to measure enzymatic activities in biological samples,", "Title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters\nPassage: second assay is also well-known and established for measurements of alcohol in food . This assay was miniaturized to microtiter plates. The third assay is a modification of a chromogenic alcohol-oxidase /peroxidase ethanol assay for determination of ethanol in beverages, which normally based on 2,2'-azino-bis as chromogenic substrate . This assay was modified to a luminometric assay by adding luminol instead of a chromogenic substrate. The luminometric measurements should be more sensitive due to photons are released by the detection reaction. For the first time the system was established in a flow system with separated bioreactors by Marschall and Gibson" ]

[ [ "3a", "Title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters" ], [ "3b", "Passage: second assay is also well-known and established for measurements of alcohol in food ." ], [ "3c", "This assay was miniaturized to microtiter plates." ], [ "3d", "The third assay is a modification of a chromogenic alcohol-oxidase /peroxidase ethanol assay for determination of ethanol in beverages, which normally based on 2,2'-azino-bis as chromogenic substrate ." ], [ "3e", "This assay was modified to a luminometric assay by adding luminol instead of a chromogenic substrate." ], [ "3f", "The luminometric measurements should be more sensitive due to photons are released by the detection reaction." ], [ "3g", "For the first time the system was established in a flow system with separated bioreactors by Marschall and Gibson" ] ]

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

[ "Title: A Global Champion for Health—WHO’s Next?\nPassage: WHO's next Director-General should be a proven leader and advocate, perhaps from a lowincome or middle-income country. The new recruit will be greeted by a full in-tray, and featuring prominently are likely to be the constraints imposed by WHO's current funding mechanisms. A substantial proportion of WHO's existing budget is earmarked for specific projects, leaving the organization with little financial flexibility to respond to unanticipated demands. However, any improved funding mechanism is likely to follow, and be dependent on, organizational reform. According to Kruk, \"WHO is both essential and hamstrung. . .the election of the Director-General should be a moment", "Title: A Global Champion for Health—WHO’s Next?\nPassage: Chan will step down from WHO on June 30, 2017 after more than a decade in the post. The process for choosing WHO's next leader has begun, promising to be protracted and rigorous as befits the importance of the role. Factoring in the many influential stakeholders in the process of appointing Chan's successor, however, transparency of the selection process may be one area unlikely to attract plaudits. Although too soon to speculate about the identity of WHO's next Director-General, it is worth reflecting on what qualities an incoming leader should bring to WHO and how that person might need to", "Title: A Global Champion for Health—WHO’s Next?\nPassage: global body will always be needed to promote, set standards in, and evaluate progress toward better health for people in all countries. The next Director-General will need to heed critics of the organization and craft a process of streamlining and restructuring to produce a new WHO that is demonstrably effective in leading responses to threats to health, and efficient in doing so. As Gostin commented to PLOS Medicine, \"WHO urgently needs a bold reform agenda to fix long-standing problems recognized by every independent group that has evaluated the Organization.\" Political machinations and the enemy within, bureaucracy, are likely to impede", "Title: A Global Champion for Health—WHO’s Next?\nPassage: Instead of electing a new Director-General, Lorenz Von Seidlein of Mahidol University, Thailand, argued that \"the problems. . .are now so deeply ingrained that replacing the WHO with new, more appropriate organizations is the logical solution. . .at a fraction of current cost, free of cumbersome, archaic obligations and entitlements and an ability to respond to new problems.\" This viewpoint is indicative of the strength of feeling that WHO's deficiencies have come to evoke in some of those committed to the cause of improving the health of people in low-income and middle-income countries. But this perception acknowledges that an accountable" ]

[ [ "0a", "Title: A Global Champion for Health—WHO’s Next?" ], [ "0b", "Passage: WHO's next Director-General should be a proven leader and advocate, perhaps from a lowincome or middle-income country." ], [ "0c", "The new recruit will be greeted by a full in-tray, and featuring prominently are likely to be the constraints imposed by WHO's current funding mechanisms." ], [ "0d", "A substantial proportion of WHO's existing budget is earmarked for specific projects, leaving the organization with little financial flexibility to respond to unanticipated demands." ], [ "0e", "However, any improved funding mechanism is likely to follow, and be dependent on, organizational reform." ], [ "0f", "According to Kruk, \"WHO is both essential and hamstrung. ." ], [ "0g", ".the election of the Director-General should be a moment" ] ]

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

[ "Title: A Global Champion for Health—WHO’s Next?\nPassage: WHO's next Director-General should be a proven leader and advocate, perhaps from a lowincome or middle-income country. The new recruit will be greeted by a full in-tray, and featuring prominently are likely to be the constraints imposed by WHO's current funding mechanisms. A substantial proportion of WHO's existing budget is earmarked for specific projects, leaving the organization with little financial flexibility to respond to unanticipated demands. However, any improved funding mechanism is likely to follow, and be dependent on, organizational reform. According to Kruk, \"WHO is both essential and hamstrung. . .the election of the Director-General should be a moment", "Title: A Global Champion for Health—WHO’s Next?\nPassage: Chan will step down from WHO on June 30, 2017 after more than a decade in the post. The process for choosing WHO's next leader has begun, promising to be protracted and rigorous as befits the importance of the role. Factoring in the many influential stakeholders in the process of appointing Chan's successor, however, transparency of the selection process may be one area unlikely to attract plaudits. Although too soon to speculate about the identity of WHO's next Director-General, it is worth reflecting on what qualities an incoming leader should bring to WHO and how that person might need to", "Title: A Global Champion for Health—WHO’s Next?\nPassage: global body will always be needed to promote, set standards in, and evaluate progress toward better health for people in all countries. The next Director-General will need to heed critics of the organization and craft a process of streamlining and restructuring to produce a new WHO that is demonstrably effective in leading responses to threats to health, and efficient in doing so. As Gostin commented to PLOS Medicine, \"WHO urgently needs a bold reform agenda to fix long-standing problems recognized by every independent group that has evaluated the Organization.\" Political machinations and the enemy within, bureaucracy, are likely to impede", "Title: A Global Champion for Health—WHO’s Next?\nPassage: Instead of electing a new Director-General, Lorenz Von Seidlein of Mahidol University, Thailand, argued that \"the problems. . .are now so deeply ingrained that replacing the WHO with new, more appropriate organizations is the logical solution. . .at a fraction of current cost, free of cumbersome, archaic obligations and entitlements and an ability to respond to new problems.\" This viewpoint is indicative of the strength of feeling that WHO's deficiencies have come to evoke in some of those committed to the cause of improving the health of people in low-income and middle-income countries. But this perception acknowledges that an accountable" ]

[ [ "3a", "Title: A Global Champion for Health—WHO’s Next?" ], [ "3b", "Passage: Instead of electing a new Director-General, Lorenz Von Seidlein of Mahidol University, Thailand, argued that \"the problems. ." ], [ "3c", ".are now so deeply ingrained that replacing the WHO with new, more appropriate organizations is the logical solution. ." ], [ "3d", ".at a fraction of current cost, free of cumbersome, archaic obligations and entitlements and an ability to respond to new problems.\"" ], [ "3e", "This viewpoint is indicative of the strength of feeling that WHO's deficiencies have come to evoke in some of those committed to the cause of improving the health of people in low-income and middle-income countries." ], [ "3f", "But this perception acknowledges that an accountable" ] ]

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

[ "Title: Improved Global Capacity for Influenza Surveillance\nPassage: objectives and evaluate their influenza surveillance systems' data quality, flexibility, simplicity, stability, acceptability, and utility through training and technical assistance .", "Title: Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals\nPassage: When implementing a national response, the problem to be solved, reduced, changed or prevented must first be understood. Surveillance refers to the systematic collection of outcome-specific data \"…for use in the planning, implementation, and evaluation of public health practice\" . Many countries have no or, at best only very basic, systems of surveillance that provide routine suicide data that is collected systematically and that can inform both programmatic targets for interventions and the development of policy initiatives. Significantly, many countries do not know the key methods used for suicide or the proportion of all suicides who have previously made attempts.", "Title: Steps to a Sustainable Public Health Surveillance Enterprise A Commentary from the International Society for Disease Surveillance\nPassage: 1. Recognize systematic and ongoing public health surveillance as a core public health function that is essential for population health, economic stability, and national security. 2. Create and support funding mechanisms that reinforce enterprise , rather than categorical surveillance infrastructures and activities in order to reduce inefficient silos, leverage resources, and foster synergies. 3. Oppose further cuts to spending for surveillance activities. 4. Invest in surveillance workforce development to build competencies and improve organizational capacity to utilize technological advances in surveillance practice. 5. Advance a rigorous surveillance research and evaluation agenda that will deepen the understanding of community health, identify", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: they target, predictive surveillance efforts are emergent, and there are numerous obstacles, both technical and organizational, that challenge their development." ]

[ [ "0a", "Title: Improved Global Capacity for Influenza Surveillance" ], [ "0b", "Passage: objectives and evaluate their influenza surveillance systems' data quality, flexibility, simplicity, stability, acceptability, and utility through training and technical assistance ." ] ]

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

[ "Title: Improved Global Capacity for Influenza Surveillance\nPassage: objectives and evaluate their influenza surveillance systems' data quality, flexibility, simplicity, stability, acceptability, and utility through training and technical assistance .", "Title: Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals\nPassage: When implementing a national response, the problem to be solved, reduced, changed or prevented must first be understood. Surveillance refers to the systematic collection of outcome-specific data \"…for use in the planning, implementation, and evaluation of public health practice\" . Many countries have no or, at best only very basic, systems of surveillance that provide routine suicide data that is collected systematically and that can inform both programmatic targets for interventions and the development of policy initiatives. Significantly, many countries do not know the key methods used for suicide or the proportion of all suicides who have previously made attempts.", "Title: Steps to a Sustainable Public Health Surveillance Enterprise A Commentary from the International Society for Disease Surveillance\nPassage: 1. Recognize systematic and ongoing public health surveillance as a core public health function that is essential for population health, economic stability, and national security. 2. Create and support funding mechanisms that reinforce enterprise , rather than categorical surveillance infrastructures and activities in order to reduce inefficient silos, leverage resources, and foster synergies. 3. Oppose further cuts to spending for surveillance activities. 4. Invest in surveillance workforce development to build competencies and improve organizational capacity to utilize technological advances in surveillance practice. 5. Advance a rigorous surveillance research and evaluation agenda that will deepen the understanding of community health, identify", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: they target, predictive surveillance efforts are emergent, and there are numerous obstacles, both technical and organizational, that challenge their development." ]

[ [ "1a", "Title: Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals" ], [ "1b", "Passage: When implementing a national response, the problem to be solved, reduced, changed or prevented must first be understood." ], [ "1c", "Surveillance refers to the systematic collection of outcome-specific data \"…for use in the planning, implementation, and evaluation of public health practice\" ." ], [ "1d", "Many countries have no or, at best only very basic, systems of surveillance that provide routine suicide data that is collected systematically and that can inform both programmatic targets for interventions and the development of policy initiatives." ], [ "1e", "Significantly, many countries do not know the key methods used for suicide or the proportion of all suicides who have previously made attempts." ] ]

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

[ "Title: Improved Global Capacity for Influenza Surveillance\nPassage: objectives and evaluate their influenza surveillance systems' data quality, flexibility, simplicity, stability, acceptability, and utility through training and technical assistance .", "Title: Ontology-Based Approach to Social Data Sentiment Analysis: Detection of Adolescent Depression Signals\nPassage: When implementing a national response, the problem to be solved, reduced, changed or prevented must first be understood. Surveillance refers to the systematic collection of outcome-specific data \"…for use in the planning, implementation, and evaluation of public health practice\" . Many countries have no or, at best only very basic, systems of surveillance that provide routine suicide data that is collected systematically and that can inform both programmatic targets for interventions and the development of policy initiatives. Significantly, many countries do not know the key methods used for suicide or the proportion of all suicides who have previously made attempts.", "Title: Steps to a Sustainable Public Health Surveillance Enterprise A Commentary from the International Society for Disease Surveillance\nPassage: 1. Recognize systematic and ongoing public health surveillance as a core public health function that is essential for population health, economic stability, and national security. 2. Create and support funding mechanisms that reinforce enterprise , rather than categorical surveillance infrastructures and activities in order to reduce inefficient silos, leverage resources, and foster synergies. 3. Oppose further cuts to spending for surveillance activities. 4. Invest in surveillance workforce development to build competencies and improve organizational capacity to utilize technological advances in surveillance practice. 5. Advance a rigorous surveillance research and evaluation agenda that will deepen the understanding of community health, identify", "Title: Anticipating the Species Jump: Surveillance for Emerging Viral Threats\nPassage: they target, predictive surveillance efforts are emergent, and there are numerous obstacles, both technical and organizational, that challenge their development." ]

[ [ "2a", "Title: Steps to a Sustainable Public Health Surveillance Enterprise A Commentary from the International Society for Disease Surveillance Passage: 1." ], [ "2b", "Recognize systematic and ongoing public health surveillance as a core public health function that is essential for population health, economic stability, and national security. 2." ], [ "2c", "Create and support funding mechanisms that reinforce enterprise , rather than categorical surveillance infrastructures and activities in order to reduce inefficient silos, leverage resources, and foster synergies. 3." ], [ "2d", "Oppose further cuts to spending for surveillance activities. 4." ], [ "2e", "Invest in surveillance workforce development to build competencies and improve organizational capacity to utilize technological advances in surveillance practice. 5." ], [ "2f", "Advance a rigorous surveillance research and evaluation agenda that will deepen the understanding of community health, identify" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 ). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Orf8 orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain fulllength orf8 . However, a 29-nucleotide deletion,", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients . In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV . Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots." ]

[ [ "0a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "0b", "Passage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 )." ], [ "0c", "As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45." ], [ "0d", "Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV." ], [ "0e", "Based on a secondary structure" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: SARS-CoV that includes the split orf8b , civet SARS-CoV , two bat SARS-related-CoV containing full-length orf8 , 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 ). As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45. Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or Figure 5 ) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes , but this is absent in this novel orf8 of 2019-nCoV. Based on a secondary structure", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Orf8 orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses. Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain fulllength orf8 . However, a 29-nucleotide deletion,", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients . In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV . Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences. The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: The single-stranded RNA genome of the 2019-nCoV was 29891 nucleotides in size, encoding 9860 amino acids. The G + C content was 38%. Similar to other . There are no remarkable differences between the orfs and nsps of 2019-nCoV with those of SARS-CoV . The major distinction between SARSr-CoV and SARS-CoV is in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots." ]

[ [ "2a", "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan" ], [ "2b", "Passage: Bat which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid-and late-phase human patients ." ], [ "2c", "In addition, we have previously identified two bat SARS-related-CoV and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV ." ], [ "2d", "Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences." ], [ "2e", "The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 , the mid-and late-phase" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human. Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: departments, treatment rooms, open intensive care facilities and private patient rooms. The nature and quality of air exchange, circulation and filtration are important variables in risk measurement and reduction as is the use of negative pressure rooms to contain known cases. Droplet spread between humans is considered the mechanism of human-to-human transmission and the need for droplet precautions was emphasized after the Al-Ahsa hospital, the KSA and the South Korean outbreaks . By extrapolation, aerosol-generating events involving DCs should be factored into risk measurement and reduction efforts and messaged using appropriate context. The provision of evidence supporting the best formulation", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: of \"contact\" during these interviews has been defined for one study . Despite this lack of clarity, the WHO consider that evidence linking MERS-CoV transmission between DCs to humans is irrefutable ." ]

[ [ "0a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "0b", "Passage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human." ], [ "0c", "Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings." ], [ "0d", "This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and" ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human. Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: departments, treatment rooms, open intensive care facilities and private patient rooms. The nature and quality of air exchange, circulation and filtration are important variables in risk measurement and reduction as is the use of negative pressure rooms to contain known cases. Droplet spread between humans is considered the mechanism of human-to-human transmission and the need for droplet precautions was emphasized after the Al-Ahsa hospital, the KSA and the South Korean outbreaks . By extrapolation, aerosol-generating events involving DCs should be factored into risk measurement and reduction efforts and messaged using appropriate context. The provision of evidence supporting the best formulation", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: of \"contact\" during these interviews has been defined for one study . Despite this lack of clarity, the WHO consider that evidence linking MERS-CoV transmission between DCs to humans is irrefutable ." ]

[ [ "1a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "1b", "Passage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan." ], [ "1c", "In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards ." ] ]

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

[ "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: It became apparent early on that MERS-CoV spread relatively ineffectively from human-to-human. Despite ongoing and possibly seasonal introduction of virus to the human population via infected DCs and perhaps other animals yet to be identified, the vast majority of MERS-CoV transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. This opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: The first known MERS human-to-human transmission event was one characterized by acute LRT disease in a healthcare setting in Jordan. In stark contrast, a sero-survey of HCW who were sometimes in close and prolonged contact with the first, fatal MERS-CoV case in 2012 , found none of the HCW had seroconverted four months later, despite an absence of eye protection and variable compliance with required PPE standards .", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: departments, treatment rooms, open intensive care facilities and private patient rooms. The nature and quality of air exchange, circulation and filtration are important variables in risk measurement and reduction as is the use of negative pressure rooms to contain known cases. Droplet spread between humans is considered the mechanism of human-to-human transmission and the need for droplet precautions was emphasized after the Al-Ahsa hospital, the KSA and the South Korean outbreaks . By extrapolation, aerosol-generating events involving DCs should be factored into risk measurement and reduction efforts and messaged using appropriate context. The provision of evidence supporting the best formulation", "Title: MERS coronavirus: diagnostics, epidemiology and transmission\nPassage: of \"contact\" during these interviews has been defined for one study . Despite this lack of clarity, the WHO consider that evidence linking MERS-CoV transmission between DCs to humans is irrefutable ." ]

[ [ "2a", "Title: MERS coronavirus: diagnostics, epidemiology and transmission" ], [ "2b", "Passage: departments, treatment rooms, open intensive care facilities and private patient rooms." ], [ "2c", "The nature and quality of air exchange, circulation and filtration are important variables in risk measurement and reduction as is the use of negative pressure rooms to contain known cases." ], [ "2d", "Droplet spread between humans is considered the mechanism of human-to-human transmission and the need for droplet precautions was emphasized after the Al-Ahsa hospital, the KSA and the South Korean outbreaks ." ], [ "2e", "By extrapolation, aerosol-generating events involving DCs should be factored into risk measurement and reduction efforts and messaged using appropriate context." ], [ "2f", "The provision of evidence supporting the best formulation" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: 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", "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: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: SARS: severe acute respiratory syndrome" ]

[ [ "0a", "Title: CDC Summary 21 MAR 2020," ], [ "0b", "Passage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV." ], [ "0c", "All three of these viruses have their origins in bats." ], [ "0d", "The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir." ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: 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", "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: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: SARS: severe acute respiratory syndrome" ]

[ [ "1a", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes" ], [ "1b", "Passage: Text: Coronaviruses belong to the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales." ], [ "1c", "A human coronavirus caused the severe acute respiratory syndrome coronavirus outbreak in 2003." ], [ "1d", "Most recently, an SARS-related CoV was implicated as the etiological agent responsible for the outbreak in Wuhan, central China." ], [ "1e", "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 ." ], [ "1f", "The virus has spread to 23 other countries by travellers from Wuhan ." ], [ "1g", "Typical symptoms are fever, malaise, shortness of breath and in severe cases, pneumonia" ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: 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", "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: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: SARS: severe acute respiratory syndrome" ]

[ [ "2a", "Title: Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review" ], [ "2b", "Passage: The 2019 novel coronavirus , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily ." ], [ "2c", "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 ." ], [ "2d", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV and MERS-CoV ." ], [ "2e", "However, 2019-nCoV has potentially higher transmissibility than both SARS-CoV and MERS-CoV ." ] ]

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

[ "Title: CDC Summary 21 MAR 2020,\nPassage: The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.", "Title: 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", "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: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management\nPassage: SARS: severe acute respiratory syndrome" ]

[ [ "3a", "Title: The Battle Against Coronavirus Disease 2019 (COVID-19): Emergency Management" ], [ "3b", "Passage: SARS: severe acute respiratory syndrome" ] ]

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

[ "Title: An implantable system for long-term assessment of atrial fibrillation substrate in unanesthetized rats exposed to underlying pathological conditions\nPassage: In the elevated plus maze test, there were significant differences between the groups in terms of Supplemental Figure S2 -I shows the mean startle amplitude of rats in response to the 30 startlepulses. There were significant differences between the groups =28.8, p<0.0001). Post hoc Bonferroni test revealed that isolation in both standard cages and in mesh barrier cages significantly increased the mean startle amplitude as compared to controls . Moreover, rats that had been isolated in mesh barrier cages significantly attenuated the hyperarousal response, eliciting a relative decrease in mean startle amplitude compared to the mesh barrier group .", "Title: Milk Lacking α-Casein Leads to Permanent Reduction in Body Size in Mice\nPassage: horizontally positioned pole which was erected slowly to vertical position. Animals falling off before reaching vertical position were recorded. Postural reflex: The animal was placed in an empty observation cage which was then gently shaken 3 times vertically and 3 times horizontally. The presence/absence of the natural reaction to this treatment was recorded.", "Title: Breaking the Waves: Modelling the Potential Impact of Public Health Measures to Defer the Epidemic Peak of Novel Influenza A/H1N1\nPassage: There are a number of possible public health measures that may be used to stop or slow down the spread. Border control has been extensively discussed in this context to delay the international spread of influenza. However, in order to achieve a significant delay, more than 99% of air travel would have to be stopped . As has been shown for SARS, entry screening methods are unlikely to detect more than 10% of imported infections and the positive predictive value of temperature screening is low especially at the beginning of a pandemic . It is therefore inevitable that importation occurs.", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: thus discouraging people from getting out and circulating in the wider population ." ]

[ [ "0a", "Title: An implantable system for long-term assessment of atrial fibrillation substrate in unanesthetized rats exposed to underlying pathological conditions" ], [ "0b", "Passage: In the elevated plus maze test, there were significant differences between the groups in terms of Supplemental Figure S2 -I shows the mean startle amplitude of rats in response to the 30 startlepulses." ], [ "0c", "There were significant differences between the groups =28.8, p<0.0001)." ], [ "0d", "Post hoc Bonferroni test revealed that isolation in both standard cages and in mesh barrier cages significantly increased the mean startle amplitude as compared to controls ." ], [ "0e", "Moreover, rats that had been isolated in mesh barrier cages significantly attenuated the hyperarousal response, eliciting a relative decrease in mean startle amplitude compared to the mesh barrier group ." ] ]

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

[ "Title: Bibliometric analysis of publications on Campylobacter: (2000–2015)\nPassage: attached for those who are interested .", "Title: Outdoor environments and human pathogens in air\nPassage: At the first two meetings, participants were given a topic and asked to prepare a one-page literature review to support their presentations; each topic was assigned to two participants from different disciplines in order to ensure cross-disciplinarity of the discussion. These presentations now form the core of our review, and all the discussions from all the meetings were recorded. We have conducted an extended literature search and review to ensure that the content is representative, comprehensive and connected to the five main areas arranged below.", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: Several limitations exist in our study. First, we characterised the knowledge structures generated by a large number of articles published in major medical journals that are included in the WoS database. However, our results are limited to a subset of all clinical-trial-related articles published in 40 leading medical journals. We suspect that these articles represent those that have great implications for clinical practice and that are relevant to clinical practice guidelines and healthcare regulators. Although the publication production analysed has been drawn from an exhaustive analysis of the biomedical literature, possibly, the search missed some relevant articles . Some reports", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: how the characteristics of the field change over time will be interesting to see." ]

[ [ "2a", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis" ], [ "2b", "Passage: Several limitations exist in our study." ], [ "2c", "First, we characterised the knowledge structures generated by a large number of articles published in major medical journals that are included in the WoS database." ], [ "2d", "However, our results are limited to a subset of all clinical-trial-related articles published in 40 leading medical journals." ], [ "2e", "We suspect that these articles represent those that have great implications for clinical practice and that are relevant to clinical practice guidelines and healthcare regulators." ], [ "2f", "Although the publication production analysed has been drawn from an exhaustive analysis of the biomedical literature, possibly, the search missed some relevant articles . Some reports" ] ]

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

[ "Title: Bibliometric analysis of publications on Campylobacter: (2000–2015)\nPassage: attached for those who are interested .", "Title: Outdoor environments and human pathogens in air\nPassage: At the first two meetings, participants were given a topic and asked to prepare a one-page literature review to support their presentations; each topic was assigned to two participants from different disciplines in order to ensure cross-disciplinarity of the discussion. These presentations now form the core of our review, and all the discussions from all the meetings were recorded. We have conducted an extended literature search and review to ensure that the content is representative, comprehensive and connected to the five main areas arranged below.", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: Several limitations exist in our study. First, we characterised the knowledge structures generated by a large number of articles published in major medical journals that are included in the WoS database. However, our results are limited to a subset of all clinical-trial-related articles published in 40 leading medical journals. We suspect that these articles represent those that have great implications for clinical practice and that are relevant to clinical practice guidelines and healthcare regulators. Although the publication production analysed has been drawn from an exhaustive analysis of the biomedical literature, possibly, the search missed some relevant articles . Some reports", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis\nPassage: how the characteristics of the field change over time will be interesting to see." ]

[ [ "3a", "Title: Global mapping of randomised trials related articles published in high-impact-factor medical journals: a cross-sectional analysis" ], [ "3b", "Passage: how the characteristics of the field change over time will be interesting to see." ] ]

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

[ "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: Since there was no data on the proportion of asymptomatic infection of the virus, we simulated the baseline value of proportion of 0.5 . d) Since there was no evidence about the transmissibility of asymptomatic infection, we assumed that the transmissibility of asymptomatic infection was 0.5 times that of symptomatic infection , which was the similar value as influenza . We assumed that the relative shedding rate of A P compared to I P was 0.5. Thus, c = 0.5. e) Since 14 January, 2020, Wuhan City has strengthened the body temperature detection of passengers leaving Wuhan at airports, railway", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011\nPassage: It is well-known that many infections with pathogens such as hepatitis A virus, influenza virus, Mycoplasma pneumoniae, and Mycobacterium tuberculosis are asymptomatic . For an outbreak caused by such pathogen, the only available data are about symptomatic infections or so at least at the early stage of the outbreak. Theoretically we can argue that if the proportion of symptomatic infections remains unchanged over the outbreak and there is no difference in transmissibility between symptomatic and asymptomatic infections, the estimate of R 0 based only on symptomatic cases should give similar results . In this study we test this for a", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: of infectives who could have been asymptomatic transmitters.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: of asymptomatic infection was defined as δ P . The S P will be infected through sufficient contact with W and I P , and the transmission rates were defined as β W and β P , respectively. We also assumed that the transmissibility of A P was κ times that of I P , where 0 ≤ κ ≤ 1." ]

[ [ "0a", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus" ], [ "0b", "Passage: Since there was no data on the proportion of asymptomatic infection of the virus, we simulated the baseline value of proportion of 0.5 ." ], [ "0c", "d) Since there was no evidence about the transmissibility of asymptomatic infection, we assumed that the transmissibility of asymptomatic infection was 0.5 times that of symptomatic infection , which was the similar value as influenza ." ], [ "0d", "We assumed that the relative shedding rate of A P compared to I P was 0.5." ], [ "0e", "Thus, c = 0.5. e) Since 14 January, 2020, Wuhan City has strengthened the body temperature detection of passengers leaving Wuhan at airports, railway" ] ]

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

[ "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: Since there was no data on the proportion of asymptomatic infection of the virus, we simulated the baseline value of proportion of 0.5 . d) Since there was no evidence about the transmissibility of asymptomatic infection, we assumed that the transmissibility of asymptomatic infection was 0.5 times that of symptomatic infection , which was the similar value as influenza . We assumed that the relative shedding rate of A P compared to I P was 0.5. Thus, c = 0.5. e) Since 14 January, 2020, Wuhan City has strengthened the body temperature detection of passengers leaving Wuhan at airports, railway", "Title: Estimating human-to-human transmissibility of hepatitis A virus in an outbreak at an elementary school in China, 2011\nPassage: It is well-known that many infections with pathogens such as hepatitis A virus, influenza virus, Mycoplasma pneumoniae, and Mycobacterium tuberculosis are asymptomatic . For an outbreak caused by such pathogen, the only available data are about symptomatic infections or so at least at the early stage of the outbreak. Theoretically we can argue that if the proportion of symptomatic infections remains unchanged over the outbreak and there is no difference in transmissibility between symptomatic and asymptomatic infections, the estimate of R 0 based only on symptomatic cases should give similar results . In this study we test this for a", "Title: Quantifying social distancing arising from pandemic influenza\nPassage: of infectives who could have been asymptomatic transmitters.", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus\nPassage: of asymptomatic infection was defined as δ P . The S P will be infected through sufficient contact with W and I P , and the transmission rates were defined as β W and β P , respectively. We also assumed that the transmissibility of A P was κ times that of I P , where 0 ≤ κ ≤ 1." ]

[ [ "3a", "Title: A mathematical model for simulating the phase-based transmissibility of a novel coronavirus" ], [ "3b", "Passage: of asymptomatic infection was defined as δ P ." ], [ "3c", "The S P will be infected through sufficient contact with W and I P , and the transmission rates were defined as β W and β P , respectively." ], [ "3d", "We also assumed that the transmissibility of A P was κ times that of I P , where 0 ≤ κ ≤ 1." ] ]

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

[ "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication\nPassage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces . About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease . The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV.", "Title: Isolation and identification of feline calicivirus and feline herpesvirus in Southern Brazil\nPassage: The nasal, oral and conjunctival vias are the natural routes of infection for FCV and FHV-1 . Transmission occurs mainly through direct contact between infected and susceptible cats; however, indirect transmission can also occur in the case of FCV, particularly within a cattery where secretions may contaminate cages, feeding and cleaning utensils or personnel . Reports from cats with URTD have revealed a prevalence ranging among 20-53% for FCV and 10-34% for FHV-1 . In the general healthy cat population from several European countries, USA and Korea, the prevalence of FCV has varied from 15% to 31% whereas values ranging", "Title: Prevalence of feline immunodeficiency virus and feline leukaemia virus in domestic cats in Hungary\nPassage: The point-of-care tests used in this study detect the presence of FeLV p27 antigen and FIV antibodies against p24 antigen . 38, 39 Sensitivity and specificity values were given according to data provided by Zoetis , although slightly different values can be found in some field studies . 40 One drop of EDTA-anticoagulated whole blood was used as per the manufacturer's instructions .", "Title: Exposure of cats to low doses of FeLV: seroconversion as the sole parameter of infection\nPassage: FHV, FPV, FCoV, FIV, hemotropic mycoplasma and presence of FeLV by RT-PCR/PCR as described . The culture was consistently free of the unwanted contaminants. The cat sera were titrated at 4-fold dilutions from 1:4 to 1:256. Samples showing a minimal titre of 1:4 were considered to be FOCMA positive. In addition, samples from week À3 and week 20 p.i. were examined for the presence of antibodies to FeLV gp70, p27 and p15 by Western blot analysis as described ." ]

[ [ "0a", "Title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication" ], [ "0b", "Passage: Study has shown that about 40-80% of cats are detected with FECV shedding in their faeces ." ], [ "0c", "About 12% of these FECV-positive cats have developed immune-mediated fatal FIP disease ." ], [ "0d", "The prevalence of FIP among felines is due to continual cycles of infection and reinfection of FECV and indiscernible clinical symptoms of infected cats with FECV at an early stage before the progressive development of FIPV." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Text: A resurgence of pertussis across age groups has occurred in several countries in recent years . Middle-and high-income countries that use an acellular pertussis vaccine for the primary vaccination series have been particularly affected , and infants and adolescents have experienced the greatest increase . Factors that may contribute to the increased risk of pertussis include rapidly waning immunity from those vaccinated with acellular vaccines , asymptomatic transmission from individuals vaccinated with acellular vaccines , genetic adaption of Bordetella pertussis , vaccination delay or refusal , improved surveillance and laboratory capabilities , and overall increased awareness of the continuing", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: There has been an increase in the incidence of pertussis in the European Union from 2011 onwards . The resurgence of pertussis observed in recent years seems to be a complex but real phenomenon due to a number of reasons, including the use of acellular pertussis vaccines in many locales. Lack of mucosal immune responses after aP vaccine administration favour infection, persistent colonization and transmission of the pathogen. Moreover, earlier waning of protective immunity and the circulation of B. pertussis variants depleted of vaccine-included antigens further favor the increase in pertussis disease . Studies in immunized children have reported that", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: antibody responses and protective immunity wane 3-5 years after immunization with acellular pertussis vaccines, which may reflect poor induction of memory T and/or B cells .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Another etiology is pertussis. In the last decade there has also been a resurgence in pertussis cases, especially in highincome countries . Because pertussis immunity after acellular pertussis vaccination is less long-lasting than immunity after wild-type infection or whole-cell vaccination, many women of child-bearing age have waning pertussis antibody levels. Their infants might therefore be born with low transplacental anti-pertussis immunoglobulin G levels, making them susceptible to pertussis infection before completion of the primary vaccination series . In 2014, more than 40,000 pertussis cases were reported to the Centers for Disease Control and Prevention in the United States; in some" ]

[ [ "0a", "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal" ], [ "0b", "Passage: Text: A resurgence of pertussis across age groups has occurred in several countries in recent years ." ], [ "0c", "Middle-and high-income countries that use an acellular pertussis vaccine for the primary vaccination series have been particularly affected , and infants and adolescents have experienced the greatest increase ." ], [ "0d", "Factors that may contribute to the increased risk of pertussis include rapidly waning immunity from those vaccinated with acellular vaccines , asymptomatic transmission from individuals vaccinated with acellular vaccines , genetic adaption of Bordetella pertussis , vaccination delay or refusal , improved surveillance and laboratory capabilities , and overall increased awareness of the continuing" ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Text: A resurgence of pertussis across age groups has occurred in several countries in recent years . Middle-and high-income countries that use an acellular pertussis vaccine for the primary vaccination series have been particularly affected , and infants and adolescents have experienced the greatest increase . Factors that may contribute to the increased risk of pertussis include rapidly waning immunity from those vaccinated with acellular vaccines , asymptomatic transmission from individuals vaccinated with acellular vaccines , genetic adaption of Bordetella pertussis , vaccination delay or refusal , improved surveillance and laboratory capabilities , and overall increased awareness of the continuing", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: There has been an increase in the incidence of pertussis in the European Union from 2011 onwards . The resurgence of pertussis observed in recent years seems to be a complex but real phenomenon due to a number of reasons, including the use of acellular pertussis vaccines in many locales. Lack of mucosal immune responses after aP vaccine administration favour infection, persistent colonization and transmission of the pathogen. Moreover, earlier waning of protective immunity and the circulation of B. pertussis variants depleted of vaccine-included antigens further favor the increase in pertussis disease . Studies in immunized children have reported that", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: antibody responses and protective immunity wane 3-5 years after immunization with acellular pertussis vaccines, which may reflect poor induction of memory T and/or B cells .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Another etiology is pertussis. In the last decade there has also been a resurgence in pertussis cases, especially in highincome countries . Because pertussis immunity after acellular pertussis vaccination is less long-lasting than immunity after wild-type infection or whole-cell vaccination, many women of child-bearing age have waning pertussis antibody levels. Their infants might therefore be born with low transplacental anti-pertussis immunoglobulin G levels, making them susceptible to pertussis infection before completion of the primary vaccination series . In 2014, more than 40,000 pertussis cases were reported to the Centers for Disease Control and Prevention in the United States; in some" ]

[ [ "1a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "1b", "Passage: There has been an increase in the incidence of pertussis in the European Union from 2011 onwards ." ], [ "1c", "The resurgence of pertussis observed in recent years seems to be a complex but real phenomenon due to a number of reasons, including the use of acellular pertussis vaccines in many locales." ], [ "1d", "Lack of mucosal immune responses after aP vaccine administration favour infection, persistent colonization and transmission of the pathogen." ], [ "1e", "Moreover, earlier waning of protective immunity and the circulation of B. pertussis variants depleted of vaccine-included antigens further favor the increase in pertussis disease ." ], [ "1f", "Studies in immunized children have reported that" ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Text: A resurgence of pertussis across age groups has occurred in several countries in recent years . Middle-and high-income countries that use an acellular pertussis vaccine for the primary vaccination series have been particularly affected , and infants and adolescents have experienced the greatest increase . Factors that may contribute to the increased risk of pertussis include rapidly waning immunity from those vaccinated with acellular vaccines , asymptomatic transmission from individuals vaccinated with acellular vaccines , genetic adaption of Bordetella pertussis , vaccination delay or refusal , improved surveillance and laboratory capabilities , and overall increased awareness of the continuing", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: There has been an increase in the incidence of pertussis in the European Union from 2011 onwards . The resurgence of pertussis observed in recent years seems to be a complex but real phenomenon due to a number of reasons, including the use of acellular pertussis vaccines in many locales. Lack of mucosal immune responses after aP vaccine administration favour infection, persistent colonization and transmission of the pathogen. Moreover, earlier waning of protective immunity and the circulation of B. pertussis variants depleted of vaccine-included antigens further favor the increase in pertussis disease . Studies in immunized children have reported that", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: antibody responses and protective immunity wane 3-5 years after immunization with acellular pertussis vaccines, which may reflect poor induction of memory T and/or B cells .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Another etiology is pertussis. In the last decade there has also been a resurgence in pertussis cases, especially in highincome countries . Because pertussis immunity after acellular pertussis vaccination is less long-lasting than immunity after wild-type infection or whole-cell vaccination, many women of child-bearing age have waning pertussis antibody levels. Their infants might therefore be born with low transplacental anti-pertussis immunoglobulin G levels, making them susceptible to pertussis infection before completion of the primary vaccination series . In 2014, more than 40,000 pertussis cases were reported to the Centers for Disease Control and Prevention in the United States; in some" ]

[ [ "2a", "Title: Vaccination against Paediatric Respiratory Pathogens" ], [ "2b", "Passage: antibody responses and protective immunity wane 3-5 years after immunization with acellular pertussis vaccines, which may reflect poor induction of memory T and/or B cells ." ] ]

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

[ "Title: Population-Based Pertussis Incidence and Risk Factors in Infants Less Than 6 Months in Nepal\nPassage: Text: A resurgence of pertussis across age groups has occurred in several countries in recent years . Middle-and high-income countries that use an acellular pertussis vaccine for the primary vaccination series have been particularly affected , and infants and adolescents have experienced the greatest increase . Factors that may contribute to the increased risk of pertussis include rapidly waning immunity from those vaccinated with acellular vaccines , asymptomatic transmission from individuals vaccinated with acellular vaccines , genetic adaption of Bordetella pertussis , vaccination delay or refusal , improved surveillance and laboratory capabilities , and overall increased awareness of the continuing", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: There has been an increase in the incidence of pertussis in the European Union from 2011 onwards . The resurgence of pertussis observed in recent years seems to be a complex but real phenomenon due to a number of reasons, including the use of acellular pertussis vaccines in many locales. Lack of mucosal immune responses after aP vaccine administration favour infection, persistent colonization and transmission of the pathogen. Moreover, earlier waning of protective immunity and the circulation of B. pertussis variants depleted of vaccine-included antigens further favor the increase in pertussis disease . Studies in immunized children have reported that", "Title: Vaccination against Paediatric Respiratory Pathogens\nPassage: antibody responses and protective immunity wane 3-5 years after immunization with acellular pertussis vaccines, which may reflect poor induction of memory T and/or B cells .", "Title: Community-acquired pneumonia in children — a changing spectrum of disease\nPassage: Another etiology is pertussis. In the last decade there has also been a resurgence in pertussis cases, especially in highincome countries . Because pertussis immunity after acellular pertussis vaccination is less long-lasting than immunity after wild-type infection or whole-cell vaccination, many women of child-bearing age have waning pertussis antibody levels. Their infants might therefore be born with low transplacental anti-pertussis immunoglobulin G levels, making them susceptible to pertussis infection before completion of the primary vaccination series . In 2014, more than 40,000 pertussis cases were reported to the Centers for Disease Control and Prevention in the United States; in some" ]

[ [ "3a", "Title: Community-acquired pneumonia in children — a changing spectrum of disease" ], [ "3b", "Passage: Another etiology is pertussis." ], [ "3c", "In the last decade there has also been a resurgence in pertussis cases, especially in highincome countries ." ], [ "3d", "Because pertussis immunity after acellular pertussis vaccination is less long-lasting than immunity after wild-type infection or whole-cell vaccination, many women of child-bearing age have waning pertussis antibody levels." ], [ "3e", "Their infants might therefore be born with low transplacental anti-pertussis immunoglobulin G levels, making them susceptible to pertussis infection before completion of the primary vaccination series ." ], [ "3f", "In 2014, more than 40,000 pertussis cases were reported to the Centers for Disease Control and Prevention in the United States; in some" ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: Alphaviruses are single-stranded RNA viruses with a positive sense genome of the Togaviridae family. Several alphaviruses are being developed as vaccine vectors, including semliki forest virus , sindbis virus and Venezuelan equine encephalitis . These vectors often are replication deficient replicons that do not encode viral structural proteins, as these regions of the genome are replaced by transgenes of interest. Viral RNAs are self-replicating and are capable of transgene expression at high levels. 98 As an added advantage, when using alphavirus replicons pre-existing immunity to the vector should not pose a problem and multiple sequential vaccinations are a possibility. Furthermore,", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Alphaviruses are positive-sense, single-stranded RNA viruses of the Togaviridae family. A variety of alphaviruses have been developed as vaccine vectors, including Semliki Forest virus , Sindbis virus, Venezuelan equine encephalitis virus, as well as chimeric viruses incorporating portions of SIN and VEE viruses. The replication defective vaccines or replicons do not encode viral structural proteins, having these portions of the genome replaces with transgenic material.", "Title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity\nPassage: for VSRs 26, 27 . Alphaviruses are member of arboviruses containing 27 recognised members 28 with a very wide geographic distribution and several geographical variants on the basis of which they have been classified as Old World and New World viruses 29 . Grouped into seven complexes based on serological cross-reactivity, they infect a variety of host including birds, fishes, mammals including humans and are maintained in natural cycles by transmission between susceptible vectors and vertebrate hosts 30 . Alphaviruses have a single plus-stranded RNA genome encapsulated by capsid proteins. The approx. 12 kb genome consists of two open reading", "Title: Viral vector-based influenza vaccines\nPassage: Another alphaherpesvirus of poultry, turkey herpesvirus has also been extensively studied as influenza vaccine vector in chickens. HVT encoding the HA gene of an A virus afforded protection from infection with various A viruses. Similarly, a recombinant HVT-H7 vaccine protected chickens against infection with the homologous A virus. 125 Since chickens are often vaccinated at very young age , maternal antibodies against the vector or against the protein encoded by the transgene could influence vaccine efficacy. Interestingly, HVT was shown to be immunogenic even in the presence of these maternal antibodies. 126 Marek's disease virus , an alphaherpesvirus closely related" ]

[ [ "0a", "Title: Viral vector-based influenza vaccines" ], [ "0b", "Passage: Alphaviruses are single-stranded RNA viruses with a positive sense genome of the Togaviridae family." ], [ "0c", "Several alphaviruses are being developed as vaccine vectors, including semliki forest virus , sindbis virus and Venezuelan equine encephalitis ." ], [ "0d", "These vectors often are replication deficient replicons that do not encode viral structural proteins, as these regions of the genome are replaced by transgenes of interest." ], [ "0e", "Viral RNAs are self-replicating and are capable of transgene expression at high levels." ], [ "0f", "98 As an added advantage, when using alphavirus replicons pre-existing immunity to the vector should not pose a problem and multiple sequential vaccinations are a possibility. Furthermore," ] ]

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

[ "Title: Viral vector-based influenza vaccines\nPassage: Alphaviruses are single-stranded RNA viruses with a positive sense genome of the Togaviridae family. Several alphaviruses are being developed as vaccine vectors, including semliki forest virus , sindbis virus and Venezuelan equine encephalitis . These vectors often are replication deficient replicons that do not encode viral structural proteins, as these regions of the genome are replaced by transgenes of interest. Viral RNAs are self-replicating and are capable of transgene expression at high levels. 98 As an added advantage, when using alphavirus replicons pre-existing immunity to the vector should not pose a problem and multiple sequential vaccinations are a possibility. Furthermore,", "Title: Virus-Vectored Influenza Virus Vaccines\nPassage: Alphaviruses are positive-sense, single-stranded RNA viruses of the Togaviridae family. A variety of alphaviruses have been developed as vaccine vectors, including Semliki Forest virus , Sindbis virus, Venezuelan equine encephalitis virus, as well as chimeric viruses incorporating portions of SIN and VEE viruses. The replication defective vaccines or replicons do not encode viral structural proteins, having these portions of the genome replaces with transgenic material.", "Title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity\nPassage: for VSRs 26, 27 . Alphaviruses are member of arboviruses containing 27 recognised members 28 with a very wide geographic distribution and several geographical variants on the basis of which they have been classified as Old World and New World viruses 29 . Grouped into seven complexes based on serological cross-reactivity, they infect a variety of host including birds, fishes, mammals including humans and are maintained in natural cycles by transmission between susceptible vectors and vertebrate hosts 30 . Alphaviruses have a single plus-stranded RNA genome encapsulated by capsid proteins. The approx. 12 kb genome consists of two open reading", "Title: Viral vector-based influenza vaccines\nPassage: Another alphaherpesvirus of poultry, turkey herpesvirus has also been extensively studied as influenza vaccine vector in chickens. HVT encoding the HA gene of an A virus afforded protection from infection with various A viruses. Similarly, a recombinant HVT-H7 vaccine protected chickens against infection with the homologous A virus. 125 Since chickens are often vaccinated at very young age , maternal antibodies against the vector or against the protein encoded by the transgene could influence vaccine efficacy. Interestingly, HVT was shown to be immunogenic even in the presence of these maternal antibodies. 126 Marek's disease virus , an alphaherpesvirus closely related" ]

[ [ "1a", "Title: Virus-Vectored Influenza Virus Vaccines" ], [ "1b", "Passage: Alphaviruses are positive-sense, single-stranded RNA viruses of the Togaviridae family." ], [ "1c", "A variety of alphaviruses have been developed as vaccine vectors, including Semliki Forest virus , Sindbis virus, Venezuelan equine encephalitis virus, as well as chimeric viruses incorporating portions of SIN and VEE viruses." ], [ "1d", "The replication defective vaccines or replicons do not encode viral structural proteins, having these portions of the genome replaces with transgenic material." ] ]

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

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

[ [ "0a", "Title: Silencing airway epithelial cell-derived hepcidin exacerbates sepsis-induced acute lung injury" ], [ "0b", "Passage: Hepcidin is a β-defensin-like antimicrobial peptide that is mainly produced by the liver." ], [ "0c", "Hepcidin not only shows antimicrobial activity against Gram-positive bacteria, Gram-negative bacteria and yeasts, but also functions as a principal iron regulatory hormone ." ], [ "0d", "Hepcidin binds to the iron export protein ferroportin and induces its internalization and degradation, which leads to decreased cellular iron export and increased intracellular iron retention ." ], [ "0e", "Because iron is an essential nutrient for all organisms, hepcidin also restricts the iron available to invading microbes, thereby enhancing the host defense against pathogens ." ], [ "0f", "Furthermore, hepcidin can modulate the lipopolysaccharide -induced acute inflammatory response via" ] ]

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

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

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

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: compared the effect of administration route on filamentous phage immunogenicity. Antibodies are generated against only three major sites on the virion: the surface-exposed N-terminal ∼12 residues of the pVIII monomer lattice ; the N-terminal N1 and N2 domains of pIII ; and bacterial lipopolysaccharide embedded in the phage coat . In mice, serum antibody titers against the phage typically reach 1:10 5 -1:10 6 after 2-3 immunizations, and are maintained for at least 1 year postimmunization . Primary antibody responses against the phage appear to be composed of a mixture of IgM and IgG2b isotypes in C57BL/6 mice, while secondary", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: compared the effect of administration route on filamentous phage immunogenicity. Antibodies are generated against only three major sites on the virion: the surface-exposed N-terminal ∼12 residues of the pVIII monomer lattice ; the N-terminal N1 and N2 domains of pIII ; and bacterial lipopolysaccharide embedded in the phage coat . In mice, serum antibody titers against the phage typically reach 1:10 5 -1:10 6 after 2-3 immunizations, and are maintained for at least 1 year postimmunization . Primary antibody responses against the phage appear to be composed of a mixture of IgM and IgG2b isotypes in C57BL/6 mice, while secondary", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: antibody responses are composed primarily of IgG1 and IgG2b isotypes, with a lesser contribution of IgG2c and IgG3 isotypes . Deletion of the surface-exposed N1 and N2 domains of pIII produces a truncated form of this protein that does not elicit antibodies, but also results in a non-infective phage particle with lower overall immunogenicity .", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: antibody responses are composed primarily of IgG1 and IgG2b isotypes, with a lesser contribution of IgG2c and IgG3 isotypes . Deletion of the surface-exposed N1 and N2 domains of pIII produces a truncated form of this protein that does not elicit antibodies, but also results in a non-infective phage particle with lower overall immunogenicity ." ]

[ [ "0a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "0b", "Passage: compared the effect of administration route on filamentous phage immunogenicity." ], [ "0c", "Antibodies are generated against only three major sites on the virion: the surface-exposed N-terminal ∼12 residues of the pVIII monomer lattice ; the N-terminal N1 and N2 domains of pIII ; and bacterial lipopolysaccharide embedded in the phage coat ." ], [ "0d", "In mice, serum antibody titers against the phage typically reach 1:10 5 -1:10 6 after 2-3 immunizations, and are maintained for at least 1 year postimmunization ." ], [ "0e", "Primary antibody responses against the phage appear to be composed of a mixture of IgM and IgG2b isotypes in C57BL/6 mice, while secondary" ] ]

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

[ "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: compared the effect of administration route on filamentous phage immunogenicity. Antibodies are generated against only three major sites on the virion: the surface-exposed N-terminal ∼12 residues of the pVIII monomer lattice ; the N-terminal N1 and N2 domains of pIII ; and bacterial lipopolysaccharide embedded in the phage coat . In mice, serum antibody titers against the phage typically reach 1:10 5 -1:10 6 after 2-3 immunizations, and are maintained for at least 1 year postimmunization . Primary antibody responses against the phage appear to be composed of a mixture of IgM and IgG2b isotypes in C57BL/6 mice, while secondary", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: compared the effect of administration route on filamentous phage immunogenicity. Antibodies are generated against only three major sites on the virion: the surface-exposed N-terminal ∼12 residues of the pVIII monomer lattice ; the N-terminal N1 and N2 domains of pIII ; and bacterial lipopolysaccharide embedded in the phage coat . In mice, serum antibody titers against the phage typically reach 1:10 5 -1:10 6 after 2-3 immunizations, and are maintained for at least 1 year postimmunization . Primary antibody responses against the phage appear to be composed of a mixture of IgM and IgG2b isotypes in C57BL/6 mice, while secondary", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: antibody responses are composed primarily of IgG1 and IgG2b isotypes, with a lesser contribution of IgG2c and IgG3 isotypes . Deletion of the surface-exposed N1 and N2 domains of pIII produces a truncated form of this protein that does not elicit antibodies, but also results in a non-infective phage particle with lower overall immunogenicity .", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold\nPassage: antibody responses are composed primarily of IgG1 and IgG2b isotypes, with a lesser contribution of IgG2c and IgG3 isotypes . Deletion of the surface-exposed N1 and N2 domains of pIII produces a truncated form of this protein that does not elicit antibodies, but also results in a non-infective phage particle with lower overall immunogenicity ." ]

[ [ "2a", "Title: Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold" ], [ "2b", "Passage: antibody responses are composed primarily of IgG1 and IgG2b isotypes, with a lesser contribution of IgG2c and IgG3 isotypes ." ], [ "2c", "Deletion of the surface-exposed N1 and N2 domains of pIII produces a truncated form of this protein that does not elicit antibodies, but also results in a non-infective phage particle with lower overall immunogenicity ." ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: Text: Coronaviruses are spherical, enveloped, and the largest of positive-strand RNA viruses. They have a wide host range, including birds, farm animals, pets, camels, and bats, in which they primarily cause respiratory and gastrointestinal disease. Belonging to the order Nidovirales, family Coronaviridae, and the subfamily Orthocoronaviridae there are four genera of coronaviruses-Alphacoronavirus, Betacoronavirus, Deltacorona virus, and Gammacoronavirus .", "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: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales." ], [ "0c", "There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus ." ], [ "0d", "Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs." ], [ "0e", "CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens." ], [ "0f", "The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000" ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: Text: Coronaviruses are spherical, enveloped, and the largest of positive-strand RNA viruses. They have a wide host range, including birds, farm animals, pets, camels, and bats, in which they primarily cause respiratory and gastrointestinal disease. Belonging to the order Nidovirales, family Coronaviridae, and the subfamily Orthocoronaviridae there are four genera of coronaviruses-Alphacoronavirus, Betacoronavirus, Deltacorona virus, and Gammacoronavirus .", "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" ]

[ [ "1a", "Title: CDC Summary 21 MAR 2020," ], [ "1b", "Passage: COVID-19 is caused by a coronavirus." ], [ "1c", "Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats." ], [ "1d", "Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus ." ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: Text: Coronaviruses are spherical, enveloped, and the largest of positive-strand RNA viruses. They have a wide host range, including birds, farm animals, pets, camels, and bats, in which they primarily cause respiratory and gastrointestinal disease. Belonging to the order Nidovirales, family Coronaviridae, and the subfamily Orthocoronaviridae there are four genera of coronaviruses-Alphacoronavirus, Betacoronavirus, Deltacorona virus, and Gammacoronavirus .", "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" ]

[ [ "2a", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections" ], [ "2b", "Passage: Text: Coronaviruses are spherical, enveloped, and the largest of positive-strand RNA viruses." ], [ "2c", "They have a wide host range, including birds, farm animals, pets, camels, and bats, in which they primarily cause respiratory and gastrointestinal disease." ], [ "2d", "Belonging to the order Nidovirales, family Coronaviridae, and the subfamily Orthocoronaviridae there are four genera of coronaviruses-Alphacoronavirus, Betacoronavirus, Deltacorona virus, and Gammacoronavirus ." ] ]

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

[ "Title: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan\nPassage: Text: Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales. There are four genera of CoVs, namely, Alphacoronavirus , Betacoronavirus , Deltacoronavirus , and Gammacoronavirus . Evolutionary analyses have shown that bats and rodents are the gene sources of most αCoVs and βCoVs, while avian species are the gene sources of most δCoVs and γCoVs. CoVs have repeatedly crossed species barriers and some have emerged as important human pathogens. The best-known examples include severe acute respiratory syndrome CoV which emerged in China in 2002-2003 to cause a large-scale epidemic with about 8000", "Title: CDC Summary 21 MAR 2020,\nPassage: COVID-19 is caused by a coronavirus. Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus .", "Title: Potential Maternal and Infant Outcomes from (Wuhan) Coronavirus 2019-nCoV Infecting Pregnant Women: Lessons from SARS, MERS, and Other Human Coronavirus Infections\nPassage: Text: Coronaviruses are spherical, enveloped, and the largest of positive-strand RNA viruses. They have a wide host range, including birds, farm animals, pets, camels, and bats, in which they primarily cause respiratory and gastrointestinal disease. Belonging to the order Nidovirales, family Coronaviridae, and the subfamily Orthocoronaviridae there are four genera of coronaviruses-Alphacoronavirus, Betacoronavirus, Deltacorona virus, and Gammacoronavirus .", "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" ]

[ [ "3a", "Title: Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes" ], [ "3b", "Passage: Text: Coronaviruses belong to the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales." ], [ "3c", "A human coronavirus caused the severe acute respiratory syndrome coronavirus outbreak in 2003." ], [ "3d", "Most recently, an SARS-related CoV was implicated as the etiological agent responsible for the outbreak in Wuhan, central China." ], [ "3e", "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 ." ], [ "3f", "The virus has spread to 23 other countries by travellers from Wuhan ." ], [ "3g", "Typical symptoms are fever, malaise, shortness of breath and in severe cases, pneumonia" ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: One approach for a broad antiviral therapy is the creation of a protective physical barrier in the nasal cavity using carrageenan. Carrageenan is a high molecular weight sulfated polymer derived from red seaweed that has been extensively used in food, cosmetic and pharmaceutical industry and is generally recognized as safe by the FDA ). Three main forms of carrageenans are commercially used: kappa, iota and lambda. They differ from each other in the degree of sulfation, solubility and gelling properties . The antiviral mechanism of carrageenan is based on the interference with viral attachment; as a consequence, viral entry is", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: to the broad antiviral effectiveness of carrageenan, patients will receive in parallel a treatment of concomitant viral infections. Therefore, patients will benefit from a decreased probability to develop complications. In consideration of the complications known to accompany an influenza virus illness this combinational therapy meets an urgent medical need.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: cold symptoms than placebo treated patients in the intention-to-treat population . The anti-influenza activity was shown by subgroup analysis of 49 influenza infected patients who benefited from a 3.3 days faster recovery from symptoms. The use of carrageenan nasal spray was associated with a significant reduction of the influenza viral load in nasal fluids and a significant increase in the number of virus free patients within the treatment period of 7 days. In good accordance Prieschl-Grassauer are co-founders of Marinomed Biotechnologie GmbH. Marinomed Biotechnologie GmbH had a role in study design, data collection and analysis, decision to publish, preparation of", "Title: Role of Antioxidants and Natural Products in Inflammation\nPassage: These extracts significantly suppressed paw edema by carrageenan in the 2nd hour at 20 mg/kg and by dextran in the 1st hour at 100 mg/kg, after induction with the phlogistic agents. Besides, it has reduced total leukocytes and neutrophils migration at all different doses tested producing maximum effect at 20 mg/kg and also suppressed the concentrations of proinflammatory cytokines and increased the level of the anti-inflammatory cytokine IL-10 in the peritonitis model . is a well-known functional food and Chinese herbal medicine used to treat various inflammation associated diseases. According to Sogo et al. the active compound, delphinidin 3-sambubioside ," ]

[ [ "0a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "0b", "Passage: One approach for a broad antiviral therapy is the creation of a protective physical barrier in the nasal cavity using carrageenan." ], [ "0c", "Carrageenan is a high molecular weight sulfated polymer derived from red seaweed that has been extensively used in food, cosmetic and pharmaceutical industry and is generally recognized as safe by the FDA )." ], [ "0d", "Three main forms of carrageenans are commercially used: kappa, iota and lambda." ], [ "0e", "They differ from each other in the degree of sulfation, solubility and gelling properties ." ], [ "0f", "The antiviral mechanism of carrageenan is based on the interference with viral attachment; as a consequence, viral entry is" ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: One approach for a broad antiviral therapy is the creation of a protective physical barrier in the nasal cavity using carrageenan. Carrageenan is a high molecular weight sulfated polymer derived from red seaweed that has been extensively used in food, cosmetic and pharmaceutical industry and is generally recognized as safe by the FDA ). Three main forms of carrageenans are commercially used: kappa, iota and lambda. They differ from each other in the degree of sulfation, solubility and gelling properties . The antiviral mechanism of carrageenan is based on the interference with viral attachment; as a consequence, viral entry is", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: to the broad antiviral effectiveness of carrageenan, patients will receive in parallel a treatment of concomitant viral infections. Therefore, patients will benefit from a decreased probability to develop complications. In consideration of the complications known to accompany an influenza virus illness this combinational therapy meets an urgent medical need.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: cold symptoms than placebo treated patients in the intention-to-treat population . The anti-influenza activity was shown by subgroup analysis of 49 influenza infected patients who benefited from a 3.3 days faster recovery from symptoms. The use of carrageenan nasal spray was associated with a significant reduction of the influenza viral load in nasal fluids and a significant increase in the number of virus free patients within the treatment period of 7 days. In good accordance Prieschl-Grassauer are co-founders of Marinomed Biotechnologie GmbH. Marinomed Biotechnologie GmbH had a role in study design, data collection and analysis, decision to publish, preparation of", "Title: Role of Antioxidants and Natural Products in Inflammation\nPassage: These extracts significantly suppressed paw edema by carrageenan in the 2nd hour at 20 mg/kg and by dextran in the 1st hour at 100 mg/kg, after induction with the phlogistic agents. Besides, it has reduced total leukocytes and neutrophils migration at all different doses tested producing maximum effect at 20 mg/kg and also suppressed the concentrations of proinflammatory cytokines and increased the level of the anti-inflammatory cytokine IL-10 in the peritonitis model . is a well-known functional food and Chinese herbal medicine used to treat various inflammation associated diseases. According to Sogo et al. the active compound, delphinidin 3-sambubioside ," ]

[ [ "1a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "1b", "Passage: to the broad antiviral effectiveness of carrageenan, patients will receive in parallel a treatment of concomitant viral infections." ], [ "1c", "Therefore, patients will benefit from a decreased probability to develop complications." ], [ "1d", "In consideration of the complications known to accompany an influenza virus illness this combinational therapy meets an urgent medical need." ] ]

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

[ "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: One approach for a broad antiviral therapy is the creation of a protective physical barrier in the nasal cavity using carrageenan. Carrageenan is a high molecular weight sulfated polymer derived from red seaweed that has been extensively used in food, cosmetic and pharmaceutical industry and is generally recognized as safe by the FDA ). Three main forms of carrageenans are commercially used: kappa, iota and lambda. They differ from each other in the degree of sulfation, solubility and gelling properties . The antiviral mechanism of carrageenan is based on the interference with viral attachment; as a consequence, viral entry is", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: to the broad antiviral effectiveness of carrageenan, patients will receive in parallel a treatment of concomitant viral infections. Therefore, patients will benefit from a decreased probability to develop complications. In consideration of the complications known to accompany an influenza virus illness this combinational therapy meets an urgent medical need.", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model\nPassage: cold symptoms than placebo treated patients in the intention-to-treat population . The anti-influenza activity was shown by subgroup analysis of 49 influenza infected patients who benefited from a 3.3 days faster recovery from symptoms. The use of carrageenan nasal spray was associated with a significant reduction of the influenza viral load in nasal fluids and a significant increase in the number of virus free patients within the treatment period of 7 days. In good accordance Prieschl-Grassauer are co-founders of Marinomed Biotechnologie GmbH. Marinomed Biotechnologie GmbH had a role in study design, data collection and analysis, decision to publish, preparation of", "Title: Role of Antioxidants and Natural Products in Inflammation\nPassage: These extracts significantly suppressed paw edema by carrageenan in the 2nd hour at 20 mg/kg and by dextran in the 1st hour at 100 mg/kg, after induction with the phlogistic agents. Besides, it has reduced total leukocytes and neutrophils migration at all different doses tested producing maximum effect at 20 mg/kg and also suppressed the concentrations of proinflammatory cytokines and increased the level of the anti-inflammatory cytokine IL-10 in the peritonitis model . is a well-known functional food and Chinese herbal medicine used to treat various inflammation associated diseases. According to Sogo et al. the active compound, delphinidin 3-sambubioside ," ]

[ [ "2a", "Title: The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model" ], [ "2b", "Passage: cold symptoms than placebo treated patients in the intention-to-treat population ." ], [ "2c", "The anti-influenza activity was shown by subgroup analysis of 49 influenza infected patients who benefited from a 3.3 days faster recovery from symptoms." ], [ "2d", "The use of carrageenan nasal spray was associated with a significant reduction of the influenza viral load in nasal fluids and a significant increase in the number of virus free patients within the treatment period of 7 days." ], [ "2e", "In good accordance Prieschl-Grassauer are co-founders of Marinomed Biotechnologie GmbH." ], [ "2f", "Marinomed Biotechnologie GmbH had a role in study design, data collection and analysis, decision to publish, preparation of" ] ]

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

[ "Title: Targeting the IL-22/IL-22BP axis enhances tight junctions and reduces inflammation during influenza infection\nPassage: To measure lung leak, the Evan's blue assay was used. Briefly, mice were injected intravenously with a 0.1% sterile solution of Evan's blue dye 30 min prior to sacrifice. The mouse paws and nose turning blue after injection verified dissemination of the dye visually. Evan's blue was measured in the BAL by measuring absorbance at 620 nm on a spectrophotometer.", "Title: Novel protein chip for the detection of antibodies against infectious bronchitis virus\nPassage: demonstrated that when the positive serum was diluted 1:1000, the spot still turned blue . .", "Title: Visible Light-Responsive Platinum-Containing Titania Nanoparticle-Mediated Photocatalysis Induces Nucleotide Insertion, Deletion and Substitution Mutations\nPassage: The blue-white screen was originally developed as a screening technique for rapid and convenient recombinant bacteria detection in vector-based molecular cloning experiments . The method is based on the principle of α-complementation of the β-galactosidase gene lacZ; therefore, the plasmid should contain lacZα , whereas the E. coli strain must contain mutated lacZ with a deleted sequence . Here, the plasmid was transformed into competent host E. coli XL1-blue cells , which were then plated on LB agar plates containing 100 µg/mL ampicillin, 50 g/mL X-gal and 0.1 mM isopropyl β-D-1-thiogalactopyranoside . These plates were then incubated overnight at 37", "Title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children\nPassage: are colored red or blue , with color intensity corresponding to fold change. Modules whose expression was not significantly different are shown as points rather than squares to simplify the diagram." ]

[ [ "0a", "Title: Targeting the IL-22/IL-22BP axis enhances tight junctions and reduces inflammation during influenza infection" ], [ "0b", "Passage: To measure lung leak, the Evan's blue assay was used." ], [ "0c", "Briefly, mice were injected intravenously with a 0.1% sterile solution of Evan's blue dye 30 min prior to sacrifice." ], [ "0d", "The mouse paws and nose turning blue after injection verified dissemination of the dye visually." ], [ "0e", "Evan's blue was measured in the BAL by measuring absorbance at 620 nm on a spectrophotometer." ] ]

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