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LitCovid-PMC-OGER-BB

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":7921,"end":7925},"obj":"Body_part"},{"id":"T2","span":{"begin":7977,"end":7981},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0007356"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0007356"}],"text":"Materials and methods\n\nStudy sites and participants\nThe Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21\nEnrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops). We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.\n\nRecruitment and sampling\nIn each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community. This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.\nParticipants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study. Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study. We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants. At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.\nParticipation in the study was strictly voluntary. Study staff reviewed the information sheet with potential participants and explained the details of the study. This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time. It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.\nFigure 1 Coding themes, subthemes and analysis framework\nFigure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China\n\nData collection and management\nAfter completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I). All interviews were conducted in the local language and audio-recorded without any identifying information. Confidentiality was maintained by conducting the interviews in a private and secure environment. At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.\nField observations were conducted by study staff at each study site concurrently. Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity. The observed information was narrated by study staff and audio-recorded on site.23\nTo enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants. Paper files were scanned electronically and then shredded. All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.\n\nData analysis\nAll interviews and observations were transcribed from the local language into Mandarin and translated into English. All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis. The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori. After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes. Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts. During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding. The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.\nAfter completion of the coding, a code report was generated from MAXQDA. Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).\nTable 1 Demographic characteristics of the study participants\nCharacteristic Participants (n=88)\nFrequency, n %\nGender\nMale 58 66\nFemale 30 34\nAge (y)\n18–30 8 9\n31–50 55 63\n\u003e50 25 28\nProvince\nYunnan 36 41\nGuangxi 25 28\nGuangdong 27 31\nSource of livelihood\nGovernment employee 10 11\nPrivate company employee 7 8\nSchool teacher 5 6\nCash crop production (e.g. fruit tree, bamboo) 23 26\nGrain crop production (e.g. corn, rice) 32 36\nHousehold animal raising for sale 13 15\nDomestic animal farmer 1 1\nWild animal farmer 2 2\nHealth worker 2 2\nConstruction worker 10 11\nNature reserve worker 8 9\nSmall business (e.g. restaurant, grocery store owner) 16 18\nStudent 1 1\nMineworker 1 1\nOther casual or out-migrating work (non-specific) 30 34\nHas worked or work on multiple jobs to make a living 35 40"}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T21","span":{"begin":208,"end":218},"obj":"Disease"},{"id":"T22","span":{"begin":3649,"end":3665},"obj":"Disease"}],"attributes":[{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0025481"}],"text":"Materials and methods\n\nStudy sites and participants\nThe Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21\nEnrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops). We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.\n\nRecruitment and sampling\nIn each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community. This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.\nParticipants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study. Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study. We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants. At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.\nParticipation in the study was strictly voluntary. Study staff reviewed the information sheet with potential participants and explained the details of the study. This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time. It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.\nFigure 1 Coding themes, subthemes and analysis framework\nFigure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China\n\nData collection and management\nAfter completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I). All interviews were conducted in the local language and audio-recorded without any identifying information. Confidentiality was maintained by conducting the interviews in a private and secure environment. At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.\nField observations were conducted by study staff at each study site concurrently. Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity. The observed information was narrated by study staff and audio-recorded on site.23\nTo enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants. Paper files were scanned electronically and then shredded. All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.\n\nData analysis\nAll interviews and observations were transcribed from the local language into Mandarin and translated into English. All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis. The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori. After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes. Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts. During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding. The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.\nAfter completion of the coding, a code report was generated from MAXQDA. Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).\nTable 1 Demographic characteristics of the study participants\nCharacteristic Participants (n=88)\nFrequency, n %\nGender\nMale 58 66\nFemale 30 34\nAge (y)\n18–30 8 9\n31–50 55 63\n\u003e50 25 28\nProvince\nYunnan 36 41\nGuangxi 25 28\nGuangdong 27 31\nSource of livelihood\nGovernment employee 10 11\nPrivate company employee 7 8\nSchool teacher 5 6\nCash crop production (e.g. fruit tree, bamboo) 23 26\nGrain crop production (e.g. corn, rice) 32 36\nHousehold animal raising for sale 13 15\nDomestic animal farmer 1 1\nWild animal farmer 2 2\nHealth worker 2 2\nConstruction worker 10 11\nNature reserve worker 8 9\nSmall business (e.g. restaurant, grocery store owner) 16 18\nStudent 1 1\nMineworker 1 1\nOther casual or out-migrating work (non-specific) 30 34\nHas worked or work on multiple jobs to make a living 35 40"}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T3","span":{"begin":4140,"end":4149},"obj":"Chemical"},{"id":"T4","span":{"begin":5156,"end":5158},"obj":"Chemical"}],"attributes":[{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_27780"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"}],"text":"Materials and methods\n\nStudy sites and participants\nThe Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21\nEnrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops). We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.\n\nRecruitment and sampling\nIn each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community. This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.\nParticipants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study. Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study. We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants. At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.\nParticipation in the study was strictly voluntary. Study staff reviewed the information sheet with potential participants and explained the details of the study. This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time. It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.\nFigure 1 Coding themes, subthemes and analysis framework\nFigure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China\n\nData collection and management\nAfter completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I). All interviews were conducted in the local language and audio-recorded without any identifying information. Confidentiality was maintained by conducting the interviews in a private and secure environment. At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.\nField observations were conducted by study staff at each study site concurrently. Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity. The observed information was narrated by study staff and audio-recorded on site.23\nTo enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants. Paper files were scanned electronically and then shredded. All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.\n\nData analysis\nAll interviews and observations were transcribed from the local language into Mandarin and translated into English. All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis. The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori. After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes. Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts. During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding. The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.\nAfter completion of the coding, a code report was generated from MAXQDA. Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).\nTable 1 Demographic characteristics of the study participants\nCharacteristic Participants (n=88)\nFrequency, n %\nGender\nMale 58 66\nFemale 30 34\nAge (y)\n18–30 8 9\n31–50 55 63\n\u003e50 25 28\nProvince\nYunnan 36 41\nGuangxi 25 28\nGuangdong 27 31\nSource of livelihood\nGovernment employee 10 11\nPrivate company employee 7 8\nSchool teacher 5 6\nCash crop production (e.g. fruit tree, bamboo) 23 26\nGrain crop production (e.g. corn, rice) 32 36\nHousehold animal raising for sale 13 15\nDomestic animal farmer 1 1\nWild animal farmer 2 2\nHealth worker 2 2\nConstruction worker 10 11\nNature reserve worker 8 9\nSmall business (e.g. restaurant, grocery store owner) 16 18\nStudent 1 1\nMineworker 1 1\nOther casual or out-migrating work (non-specific) 30 34\nHas worked or work on multiple jobs to make a living 35 40"}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":1000,"end":1009},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T4","span":{"begin":7311,"end":7321},"obj":"http://purl.obolibrary.org/obo/GO_0065007"}],"text":"Materials and methods\n\nStudy sites and participants\nThe Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21\nEnrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops). We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.\n\nRecruitment and sampling\nIn each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community. This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.\nParticipants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study. Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study. We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants. At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.\nParticipation in the study was strictly voluntary. Study staff reviewed the information sheet with potential participants and explained the details of the study. This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time. It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.\nFigure 1 Coding themes, subthemes and analysis framework\nFigure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China\n\nData collection and management\nAfter completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I). All interviews were conducted in the local language and audio-recorded without any identifying information. Confidentiality was maintained by conducting the interviews in a private and secure environment. At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.\nField observations were conducted by study staff at each study site concurrently. Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity. The observed information was narrated by study staff and audio-recorded on site.23\nTo enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants. Paper files were scanned electronically and then shredded. All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.\n\nData analysis\nAll interviews and observations were transcribed from the local language into Mandarin and translated into English. All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis. The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori. After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes. Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts. During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding. The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.\nAfter completion of the coding, a code report was generated from MAXQDA. Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).\nTable 1 Demographic characteristics of the study participants\nCharacteristic Participants (n=88)\nFrequency, n %\nGender\nMale 58 66\nFemale 30 34\nAge (y)\n18–30 8 9\n31–50 55 63\n\u003e50 25 28\nProvince\nYunnan 36 41\nGuangxi 25 28\nGuangdong 27 31\nSource of livelihood\nGovernment employee 10 11\nPrivate company employee 7 8\nSchool teacher 5 6\nCash crop production (e.g. fruit tree, bamboo) 23 26\nGrain crop production (e.g. corn, rice) 32 36\nHousehold animal raising for sale 13 15\nDomestic animal farmer 1 1\nWild animal farmer 2 2\nHealth worker 2 2\nConstruction worker 10 11\nNature reserve worker 8 9\nSmall business (e.g. restaurant, grocery store owner) 16 18\nStudent 1 1\nMineworker 1 1\nOther casual or out-migrating work (non-specific) 30 34\nHas worked or work on multiple jobs to make a living 35 40"}

LitCovid-sentences

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"32040190-23200502-48103168","span":{"begin":228,"end":230},"obj":"23200502"},{"id":"32040190-28137858-48103169","span":{"begin":338,"end":340},"obj":"28137858"},{"id":"32040190-29614074-48103170","span":{"begin":571,"end":573},"obj":"29614074"},{"id":"32040190-19784865-48103171","span":{"begin":7099,"end":7101},"obj":"19784865"},{"id":"32040190-29486714-48103172","span":{"begin":7546,"end":7548},"obj":"29486714"},{"id":"T27139","span":{"begin":228,"end":230},"obj":"23200502"},{"id":"T66879","span":{"begin":338,"end":340},"obj":"28137858"},{"id":"T82467","span":{"begin":571,"end":573},"obj":"29614074"},{"id":"T88965","span":{"begin":7099,"end":7101},"obj":"19784865"},{"id":"T87475","span":{"begin":7546,"end":7548},"obj":"29486714"}],"text":"Materials and methods\n\nStudy sites and participants\nThe Yunnan, Guangxi and Guangdong provinces in southern China were selected for this study because of their historical importance in the origin of emerging infectious diseases,16 diverse wildlife population within protected forests17 and intensive wildlife farming and trade activities.18 Three sites in rural areas were identified in each province where our previous research had found numerous bat and rodent populations harbouring viruses with pathogenic potential for humans, at sites close to human communities.19–21\nEnrolment criteria for participation in an ethnographic interview in this study included: individuals were residents of the target community, aged ≥18 y, with prior contact with live animals directly (e.g. by raising, hunting, trading or slaughtering live animals) or indirectly (e.g. through animals living in or entering dwellings/crops, bat roosts within roofs, animals invading stored food or crops). We targeted a gender breakdown of 35% of participants being female and aimed to have a diverse sample of participants from different age groups and levels of power and influence in the community.\n\nRecruitment and sampling\nIn each province, project investigators provided a two-day training workshop for study staff from local provincial and city-level Centres for Disease Control and Prevention who spoke the local language and were familiar with the local community. This included a unit on the ethical conduct of human subject research, an in-depth review of the study design and objectives, and comprehensive information on the implementation of observational research, semistructured interviews and notetaking within the context of this study.\nParticipants were identified through key informants and the snowball sampling method because the population size at selected sites and the people who had high-risk contacts with live animals were difficult to elucidate.22 Starting with the key informants, we asked each participant to suggest people who met the inclusion criteria and who might be interested in participating in this study; we then contacted the referrals for potential participation in our study. Local study staff visited potential participants and provided these individuals with the participant information sheet to introduce them to the study. We aimed to obtain a minimum sample size of 20 participants from each of the three provinces, for a total sample size of over 60 participants. At least two field observations of local markets and household environments were conducted at each study site, for a total of 18 observations at a minimum.\nParticipation in the study was strictly voluntary. Study staff reviewed the information sheet with potential participants and explained the details of the study. This included the voluntary nature of participation, inclusion and exclusion criteria, study implementation processes (e.g. that the interview would be audio-recorded), potential risks and benefits of participation, results sharing and that they could withdraw their participation at any time. It was also explained that an item as a token would be given as appreciation for their participation, which was identified by the study team and appropriate for the context of the study sites.\nFigure 1 Coding themes, subthemes and analysis framework\nFigure 2 Nine study sites in the Yunnan, Guangxi and Guangdong Provinces, Southern China\n\nData collection and management\nAfter completion of the informed consent process, one-on-one semistructured interviews were conducted focusing on the five core themes outlined in the interview guide related to zoonotic disease emergence: human movement, socioeconomics, biosecurity in human environments, human–animal contact and illness, and medical care/treatment and death (Supplementary Data I). All interviews were conducted in the local language and audio-recorded without any identifying information. Confidentiality was maintained by conducting the interviews in a private and secure environment. At the end of the interview, each study participant received a bottle of cooking oil or laundry detergent valued at no more than US$10 as a token of appreciation.\nField observations were conducted by study staff at each study site concurrently. Observations were general and implemented in three settings: (1) local markets where live animals were traded, (2) in and/or around the dwellings of study participants and, if applicable, (3) community centres, to obtain an overview of the study site and the communities, and supplementary data on human-animal interactions and environmental biosecurity. The observed information was narrated by study staff and audio-recorded on site.23\nTo enhance saturation, efforts were made to include a large variety of people with different backgrounds, to conduct a maximized number of interviews during the 8 wk study period in each province and to cover as many themes and subthemes from the interview guide as possible in each interview.24 All data generated, including notes, audio files, digital transcripts and the interviewer checklist, were coded with an alphanumeric ID to preserve the confidentiality of participants. Paper files were scanned electronically and then shredded. All electronic data were encrypted and password-protected, and access was limited to the study staff conducting analyses.\n\nData analysis\nAll interviews and observations were transcribed from the local language into Mandarin and translated into English. All transcripts were imported into MAXQDA release 12 statistical software (VERBI Software, Berlin, Germany) for data management and analysis. The analysis process incorporated both deductive and inductive approaches, and followed a process of initial coding, identification of new themes, primary coding and identification and analysis of emerging themes.25 An initial codebook associated with the five core themes of the interview guide was developed a priori. After a close reading of the transcripts, two authors used the initial codebook to independently code two transcripts in their entirety, making notes on emerging themes and specified subthemes. Subsequently, the two authors adapted the codebook and used the modified codebook to code all of the transcripts. During the coding process, the two authors met when any major new themes or concepts emerged to decide on any necessary revisions to the codebook, until no new themes emerged and no new information was obtained from the coding. The final codebook was restructured with five sections: (1) demographics, (2) biosecurity in human environments, (3) human–animal contact, (4) illness, treatment and death and (5) animal taxa; subthemes were defined under each section.\nAfter completion of the coding, a code report was generated from MAXQDA. Internal reliability was assessed by comparing the coded segments from two authors on the same two transcripts to reach a minimum code interaction rate of 80%.26 A saturation grid was built using the ‘Segment Retrieval’ function in MAXQDA to ensure saturation was reached.27 Coded segments were categorized into protective factors and risk factors based on their known associations with disease transmission, and the analysis was stratified at the individual, community and policy or regulation level.28 At the individual level, both risk and protective factors were analysed in terms of the individuals' knowledge, attitudes and practices to better understand the risk factors for identifying context-based strategies.29 (Figure 1).\nTable 1 Demographic characteristics of the study participants\nCharacteristic Participants (n=88)\nFrequency, n %\nGender\nMale 58 66\nFemale 30 34\nAge (y)\n18–30 8 9\n31–50 55 63\n\u003e50 25 28\nProvince\nYunnan 36 41\nGuangxi 25 28\nGuangdong 27 31\nSource of livelihood\nGovernment employee 10 11\nPrivate company employee 7 8\nSchool teacher 5 6\nCash crop production (e.g. fruit tree, bamboo) 23 26\nGrain crop production (e.g. corn, rice) 32 36\nHousehold animal raising for sale 13 15\nDomestic animal farmer 1 1\nWild animal farmer 2 2\nHealth worker 2 2\nConstruction worker 10 11\nNature reserve worker 8 9\nSmall business (e.g. restaurant, grocery store owner) 16 18\nStudent 1 1\nMineworker 1 1\nOther casual or out-migrating work (non-specific) 30 34\nHas worked or work on multiple jobs to make a living 35 40"}

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