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    LitCovid-sentences

    {"project":"LitCovid-sentences","denotations":[{"id":"T40","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T41","span":{"begin":5,"end":47},"obj":"Sentence"},{"id":"T42","span":{"begin":48,"end":203},"obj":"Sentence"},{"id":"T43","span":{"begin":204,"end":411},"obj":"Sentence"},{"id":"T44","span":{"begin":412,"end":550},"obj":"Sentence"},{"id":"T45","span":{"begin":551,"end":687},"obj":"Sentence"},{"id":"T46","span":{"begin":688,"end":781},"obj":"Sentence"},{"id":"T47","span":{"begin":782,"end":1092},"obj":"Sentence"},{"id":"T48","span":{"begin":1093,"end":1274},"obj":"Sentence"},{"id":"T49","span":{"begin":1275,"end":1473},"obj":"Sentence"},{"id":"T50","span":{"begin":1474,"end":1602},"obj":"Sentence"},{"id":"T51","span":{"begin":1603,"end":1899},"obj":"Sentence"},{"id":"T52","span":{"begin":1900,"end":2003},"obj":"Sentence"},{"id":"T53","span":{"begin":2004,"end":2165},"obj":"Sentence"},{"id":"T54","span":{"begin":2166,"end":2280},"obj":"Sentence"},{"id":"T55","span":{"begin":2281,"end":2519},"obj":"Sentence"},{"id":"T56","span":{"begin":2520,"end":2649},"obj":"Sentence"},{"id":"T57","span":{"begin":2650,"end":2826},"obj":"Sentence"},{"id":"T58","span":{"begin":2827,"end":3045},"obj":"Sentence"},{"id":"T59","span":{"begin":3046,"end":3214},"obj":"Sentence"},{"id":"T60","span":{"begin":3215,"end":3420},"obj":"Sentence"},{"id":"T61","span":{"begin":3421,"end":3680},"obj":"Sentence"},{"id":"T62","span":{"begin":3681,"end":3806},"obj":"Sentence"},{"id":"T63","span":{"begin":3807,"end":3907},"obj":"Sentence"},{"id":"T64","span":{"begin":3908,"end":4047},"obj":"Sentence"},{"id":"T65","span":{"begin":4048,"end":4232},"obj":"Sentence"},{"id":"T66","span":{"begin":4233,"end":4353},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.1. Pilot Asymptomatic Testing Service (P-ATS)\nThe P-ATS was a pilot programme for SARS2 surveillance conducted in the early phases of the SARS2 pandemic at a semirural campus of a university in the UK. The objective of the programme was to define the baseline SARS-Coronavirus type 2 (SARS-CoV-2) infection rate and seroprevalence in a cohort of university students and staff and to measure changes over time.\nParticipation in P-ATS was on a voluntary basis and aimed to be complementary to the national testing strategy in the United Kingdom (UK). P-ATS was a completely independent initiative within the University to explore the value of SARS-Cov-2 testing in asymptomatic students. National guidelines for actions to be taken by symptomatic students were followed throughout. Any asymptomatic students testing positive in this pilot were advised to undertake a “Pillar 2” test, the results of which would be paramount (the University laboratory testing was a research test only), and hence would feed into the UK National Health Service (NHS) Test and Trace [9] mechanisms, if positive.\nThe P-ATS was offered to all 150 students in their first year (new arrivals in 2020 Cohort 1) as well as 65 final-year students going out into practice rotations in the Autumn term. A select group of 70 university staff who had face-to-face contact with students during the study period were offered the opportunity to join P-ATS if they wished, at any point during the programme.\nThe P-ATS was primarily targeted to students in their first year of study who were living in university accommodation on campus. All first-year students who had arrived in 2020 Cohort 1 were therefore eligible for the P-ATS and were offered the full programme which included a total of 12 PCR tests to be completed weekly over 12 weeks (10 swab tests, and 2 saliva tests) and up to 6 antibody tests from July to October 2020. In addition, a number of students in their final year were invited to join the P-ATS in September 2020. Eligible final-year students were those who were due to start certain 2-week rotation placements that required them to undertake PCR testing prior to attendance. A select number of final year participants therefore participated in the P-ATS between September and October 2020.\nNewly arriving first-year students from 2020 Cohort 1 were accommodated on campus in cluster flats treated as a “household” and attended teaching sessions in “bubbles” through the study period to avoid exposure to larger groups of people. Final-year students mostly lived off campus and attended clinical rotation placements in the community during this year of study. The P-ATS start for eligible final-year students was staggered since they joined at different times according to academic timetabling and the start date of relevant placements. Final-year students joined the programme at different times, had fewer tests offered in total, with some students taking only one test, and others taking more if they changed rotation placement during the study period. Therefore, the total number of tests offered varied between students, although the testing offers and start date were consistent for those who were in their first year. The first- and final-year students who accessed P-ATS, therefore, had a different experience of both the service (with only first years offered the complete programme), and of university life more broadly.\nFor all P-ATS participants, swab, saliva and antibody test kits were collected by P-ATS participants, tests were self-administered and participants deposited samples at dedicated collection points on the university campus with social distancing rules applied.\nThe complete programme consisted of:(a) SARS2-PCR tests offered weekly for the 12-week study period (10× swab and 2× saliva);\n(b) SARS2-antibody tests offered alternate weeks (6 x self-sampled finger-prick dried blood sample).\nIndividuals testing negative were informed by email correspondence to their cohort (indicating that all positive cases had been contacted). Individuals testing positive were personally advised of their result by a clinical virologist, and a central university team was notified so that the student could be safely cared for. This process included notification of Public Health England so that official test, track and trace could take place [9]."}

    LitCovid-PubTator

    {"project":"LitCovid-PubTator","denotations":[{"id":"69","span":{"begin":0,"end":3},"obj":"Gene"},{"id":"74","span":{"begin":84,"end":89},"obj":"Species"},{"id":"75","span":{"begin":140,"end":145},"obj":"Species"},{"id":"76","span":{"begin":287,"end":297},"obj":"Species"},{"id":"77","span":{"begin":299,"end":308},"obj":"Disease"},{"id":"79","span":{"begin":643,"end":653},"obj":"Species"},{"id":"81","span":{"begin":2196,"end":2208},"obj":"Species"},{"id":"83","span":{"begin":2512,"end":2518},"obj":"Species"},{"id":"87","span":{"begin":3435,"end":3447},"obj":"Species"},{"id":"88","span":{"begin":3509,"end":3521},"obj":"Species"},{"id":"89","span":{"begin":3556,"end":3568},"obj":"Species"},{"id":"91","span":{"begin":3721,"end":3726},"obj":"Species"},{"id":"93","span":{"begin":3811,"end":3816},"obj":"Species"}],"attributes":[{"id":"A69","pred":"tao:has_database_id","subj":"69","obj":"Gene:6700"},{"id":"A74","pred":"tao:has_database_id","subj":"74","obj":"Tax:2697049"},{"id":"A75","pred":"tao:has_database_id","subj":"75","obj":"Tax:2697049"},{"id":"A76","pred":"tao:has_database_id","subj":"76","obj":"Tax:2697049"},{"id":"A77","pred":"tao:has_database_id","subj":"77","obj":"MESH:D007239"},{"id":"A79","pred":"tao:has_database_id","subj":"79","obj":"Tax:2697049"},{"id":"A81","pred":"tao:has_database_id","subj":"81","obj":"Tax:9606"},{"id":"A83","pred":"tao:has_database_id","subj":"83","obj":"Tax:9606"},{"id":"A87","pred":"tao:has_database_id","subj":"87","obj":"Tax:9606"},{"id":"A88","pred":"tao:has_database_id","subj":"88","obj":"Tax:9606"},{"id":"A89","pred":"tao:has_database_id","subj":"89","obj":"Tax:9606"},{"id":"A91","pred":"tao:has_database_id","subj":"91","obj":"Tax:2697049"},{"id":"A93","pred":"tao:has_database_id","subj":"93","obj":"Tax:2697049"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.1. Pilot Asymptomatic Testing Service (P-ATS)\nThe P-ATS was a pilot programme for SARS2 surveillance conducted in the early phases of the SARS2 pandemic at a semirural campus of a university in the UK. The objective of the programme was to define the baseline SARS-Coronavirus type 2 (SARS-CoV-2) infection rate and seroprevalence in a cohort of university students and staff and to measure changes over time.\nParticipation in P-ATS was on a voluntary basis and aimed to be complementary to the national testing strategy in the United Kingdom (UK). P-ATS was a completely independent initiative within the University to explore the value of SARS-Cov-2 testing in asymptomatic students. National guidelines for actions to be taken by symptomatic students were followed throughout. Any asymptomatic students testing positive in this pilot were advised to undertake a “Pillar 2” test, the results of which would be paramount (the University laboratory testing was a research test only), and hence would feed into the UK National Health Service (NHS) Test and Trace [9] mechanisms, if positive.\nThe P-ATS was offered to all 150 students in their first year (new arrivals in 2020 Cohort 1) as well as 65 final-year students going out into practice rotations in the Autumn term. A select group of 70 university staff who had face-to-face contact with students during the study period were offered the opportunity to join P-ATS if they wished, at any point during the programme.\nThe P-ATS was primarily targeted to students in their first year of study who were living in university accommodation on campus. All first-year students who had arrived in 2020 Cohort 1 were therefore eligible for the P-ATS and were offered the full programme which included a total of 12 PCR tests to be completed weekly over 12 weeks (10 swab tests, and 2 saliva tests) and up to 6 antibody tests from July to October 2020. In addition, a number of students in their final year were invited to join the P-ATS in September 2020. Eligible final-year students were those who were due to start certain 2-week rotation placements that required them to undertake PCR testing prior to attendance. A select number of final year participants therefore participated in the P-ATS between September and October 2020.\nNewly arriving first-year students from 2020 Cohort 1 were accommodated on campus in cluster flats treated as a “household” and attended teaching sessions in “bubbles” through the study period to avoid exposure to larger groups of people. Final-year students mostly lived off campus and attended clinical rotation placements in the community during this year of study. The P-ATS start for eligible final-year students was staggered since they joined at different times according to academic timetabling and the start date of relevant placements. Final-year students joined the programme at different times, had fewer tests offered in total, with some students taking only one test, and others taking more if they changed rotation placement during the study period. Therefore, the total number of tests offered varied between students, although the testing offers and start date were consistent for those who were in their first year. The first- and final-year students who accessed P-ATS, therefore, had a different experience of both the service (with only first years offered the complete programme), and of university life more broadly.\nFor all P-ATS participants, swab, saliva and antibody test kits were collected by P-ATS participants, tests were self-administered and participants deposited samples at dedicated collection points on the university campus with social distancing rules applied.\nThe complete programme consisted of:(a) SARS2-PCR tests offered weekly for the 12-week study period (10× swab and 2× saliva);\n(b) SARS2-antibody tests offered alternate weeks (6 x self-sampled finger-prick dried blood sample).\nIndividuals testing negative were informed by email correspondence to their cohort (indicating that all positive cases had been contacted). Individuals testing positive were personally advised of their result by a clinical virologist, and a central university team was notified so that the student could be safely cared for. This process included notification of Public Health England so that official test, track and trace could take place [9]."}