SemEval-2021 Task 12: Learning with Disagreements

Disagreement between coders is ubiquitous in virtually all datasets annotated with human judgements in both natural language processing and computer vision. However, most supervised machine learning methods assume that a single preferred interpretation exists for each item, which is at best an idealization. The aim of the SemEval-2021 shared task on learning with disagreements (Le-Wi-Di) was to provide a unified testing framework for methods for learning from data containing multiple and possibly contradictory annotations covering the best-known datasets containing information about disagreements for interpreting language and classifying images. In this paper we describe the shared task and its results

Caveats in reporting of national vaccine uptake

Funding: EAVE II is supported by the Medical Research Council (MR/R008345/1) with the support of BREATHE - The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. Additional support has been provided through Public Health Scotland and Scottish Government DG Health and Social Care, the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref MC_PC_20058) and the Lifelong Health and Wellbeing study as part of the National Core Studies (MC_PC_20030).Peer reviewe

Severity of omicron variant of concern and effectiveness of vaccine boosters against symptomatic disease in Scotland (EAVE II) : a national cohort study with nested test-negative design

This study is part of the EAVE II project. EAVE II is funded by the MRC (MC_PC_19075) with the support of BREATHE—The Health Data Research Hub for Respiratory Health (MC_PC_19004), which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. This research is part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (MC_PC_20058). Additional support has been provided through Public Health Scotland, the Scottish Government Director General Health and Social Care, and the University of Edinburgh. The original EAVE project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme (11/46/23). The views expressed are those of the authors and not necessarily those of the NIHR, the Department of Health and Social Care, or the UK Government. We thank Dave Kelly from Albasoft (Inverness, UK) for his support with making primary care data available, and Wendy Inglis-Humphrey, Vicky Hammersley, and Laura Brook (University of Edinburgh, Edinburgh, UK) for their support with project management and administration.Peer reviewedPublisher PD

Developing ecosystem service indicators: experiences and lessons learned from sub-global assessments and other initiatives

People depend upon ecosystems to supply a range of services necessary for their survival and well-being. Ecosystem service indicators are critical for knowing whether or not these essential services are being maintained and used in a sustainable manner, thus enabling policy makers to identify the policies and other interventions needed to better manage them. As a result, ecosystem service indicators are of increasing interest and importance to governmental and inter-governmental processes, including amongst others the Convention on Biological Diversity (CBD) and the Aichi Targets contained within its strategic plan for 2011-2020, as well as the emerging Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Despite this growing demand, assessing ecosystem service status and trends and developing robust indicators is o!en hindered by a lack of information and data, resulting in few available indicators. In response, the United Nations Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), together with a wide range of international partners and supported by the Swedish International Biodiversity Programme (SwedBio)*, undertook a project to take stock of the key lessons that have been learnt in developing and using ecosystem service indicators in a range of assessment contexts. The project examined the methodologies, metrics and data sources employed in delivering ecosystem service indicators, so as to inform future indicator development. This report presents the principal results of this project

Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function

ABSTRACT The surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS), creating a permeability barrier against toxic molecules, including many antimicrobials. To assemble LPS on their surface, Gram-negative bacteria must extract newly synthesized LPS from the inner membrane, transport it across the aqueous periplasm, and translocate it across the outer membrane. The LptA to -G proteins assemble into a transenvelope complex that transports LPS from the inner membrane to the cell surface. The Lpt system powers LPS transport from the inner membrane by using a poorly characterized ATP-binding cassette system composed of the ATPase LptB and the transmembrane domains LptFG. Here, we characterize a cluster of residues in the groove region of LptB that is important for controlling LPS transport. We also provide the first functional characterization of LptFG and identify their coupling helices that interact with the LptB groove. Substitutions at conserved residues in these coupling helices compromise both the assembly and function of the LptB2FG complex. Defects in LPS transport conferred by alterations in the LptFG coupling helices can be rescued by changing a residue in LptB that is adjacent to functionally important residues in the groove region. This suppression is achieved by increasing the ATPase activity of the LptB2FG complex. Taken together, these data identify a specific binding site in LptB for the coupling helices of LptFG that is responsible for coupling of ATP hydrolysis by LptB with LptFG function to achieve LPS extraction

Prevalence and risk factors for long COVID among adults in Scotland using electronic health records : a national, retrospective, observational cohort study

Acknowledgements This work was supported by the Chief Scientist Office, grant number COV/LTE/20/15. EAVE II is supported by a grant (MC_PC_19075) from the Medical Research Council; and a grant (MC_PC_19004) from BREATHE–The Health Data Research Hub for Respiratory Health, funded through the UK Research and Innovation Industrial Strategy Challenge Fund. LD was supported by a post-doctoral clinical fellowship from the Asthma UK Centre for Applied Research. SVK acknowledges funding from a NRS Senior Clinical Fellowship (SCAF/15/02), the Medical Research Council (MC_UU_00022/2) and the Scottish Government Chief Scientist Office (SPHSU17). The authors would like to acknowledge the support of Dave Kelly and Lamorna Brown of Albasoft Ltd., and Sharon Kennedy, Mike Birnie, Safraj Shahul Hameed and Elliott Hall of Public Health Scotland for their involvement in obtaining approvals, provisioning, and linking data and the use of the secure analytical platform within the National Safe Haven. Funding Chief Scientist Office (Scotland), Medical Research Council, and BREATHE.Peer reviewe

Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study

Objectives We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation and death during the winter period in Scotland. Design A population-based retrospective cohort analysis Setting Scotland Participants 5.4 million residents in Scotland Main outcome measures Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation. Results Between September 1, 2022 and January 31, 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1,759 in children and 20,525 in adults) in Scotland. Compared to the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR=4.55 95%CI (4.11-5.04)). Compared to 25-29 years old, the risk of ARI hospitalisation was highest amongst the oldest adults aged ≥80 years (7.86 (7.06-8.76)). Adults from more deprived areas (most deprived vs least deprived, 1.64 (1.57-1.72)), with existing health conditions (≥5 vs 0 health conditions, 4.84 (4.53-5.18)) or with history of all-cause emergency admissions (≥6 vs 0 previous emergency admissions 7.53 (5.48-10.35)) were at higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children. Conclusions Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI

BNT162b2 COVID-19 vaccination uptake, safety, effectiveness and waning in children and young people aged 12–17 years in Scotland

This study is part of the EAVE II project. EAVE II is funded by the MRC (MC_PC_19075) with the support of BREATHE—The Health Data Research Hub for Respiratory Health (MC_PC_19004), which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through the Health Data Research UK. This research is part of the Data and Connectivity National Core Study, led by Health Data Research UK in partnership with the Office for National Statistics and funded by UK Research and Innovation (grant ref MC_PC_20058). This work was also supported by The Alan Turing Institute via ‘Towards Turing 2.0’ EPSRC Grant Funding. Additional support has been provided through Public Health Scotland, the Scottish Government Director-General Health and Social Care and the University of Edinburgh. The original EAVE project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme (11/46/23). The views expressed are those of the authors and not necessarily those of the NIHR, the Department of Health and Social Care, or the UK government. We thank Dave Kelly from Albasoft (Inverness, UK) for his support with making primary care data available, and Wendy Inglis-Humphrey, Vicky Hammersley, and Laura Brook (University of Edinburgh, Edinburgh, UK) for their support with project management and administration.Peer reviewedPublisher PD

Risk of winter hospitalisation and death from acute respiratory infections in Scotland : national retrospective cohort study

Funding : This study is funded by the National Institute for Health and Care Research (NIHR). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. This work also benefits from the infrastructure and partnerships assembled by HDR UK, including through the Data and Connectivity National Core Study, funded by UK Research and Innovation [grant ref MC_PC_20058].Objectives  We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland. Design  A population-based retrospective cohort analysis. Setting   Scotland. Participants   5.4 million residents in Scotland. Main outcome measures   Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation. Results   Between September 1, 2022 and January 31, 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1,759 in children and 20,525 in adults) in Scotland. Compared to the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR=4.55 95%CI (4.11-5.04)). Compared to 25-29 years old, the risk of ARI hospitalisation was highest amongst the oldest adults aged ≥80 years (7.86 (7.06-8.76)). Adults from more deprived areas (most deprived vs least deprived, 1.64 (1.57-1.72)), with existing health conditions (≥5 vs 0 health conditions, 4.84 (4.53-5.18)) or with history of all-cause emergency admissions (≥6 vs 0 previous emergency admissions 7.53 (5.48-10.35)) were at higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children. Conclusions   Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.Peer reviewe

Understanding and reporting odds ratios as rate-ratio estimates in case-control studies

Background: We noted that there remains some confusion in the health-science literature on reporting sample odds ratios as estimated rate ratios in case-control studies. Methods: We recap historical literature that definitively answered the question of when sample odds ratios (ORs) from a case-control study are consistent estimators for population rate ratios. We use numerical examples to illustrate the magnitude of the disparity between sample ORs in a case-control study and population rate ratios when sufficient conditions for them to be equal are not satisfied. Results: We stress that in a case-control study, sampling controls from those still at risk at the time of outcome event of the index case is not sufficient for a sample OR to be a consistent estimator for an intelligible rate ratio. In such studies, constancy of the exposure prevalence together with constancy of the hazard ratio (HR) (i.e., the instantaneous rate ratio) over time is sufficient for this result if sampling time is not controlled; if time is controlled, constancy of the HR will suffice. We present numerical examples to illustrate how failure to satisfy these conditions adds a small systematic error to sample ORs as estimates of population rate ratios. Conclusions: We recommend that researchers understand and critically evaluate all conditions used to interpret their estimates as consistent for a population parameter in case-control studies