399 research outputs found
Loss of functional diversity through anthropogenic extinctions of island birds is not offset by biotic invasions
Human impacts reshape ecological communities through the extinction and introduction of species. The combined impact of these factors depends on whether non-native species fill the functional roles of extinct species, thus buffering the loss of functional diversity. This question has been difficult to address, because comprehensive information about past extinctions and their traits is generally lacking. We combine detailed information about extinct, extant, and established alien birds to quantify historical changes in functional diversity across nine oceanic archipelagos. We found that alien species often equal or exceed the number of anthropogenic extinctions yet apparently perform a narrower set of functional roles as current island assemblages have undergone a substantial and ubiquitous net loss in functional diversity and increased functional similarity among assemblages. Our results reveal that the introduction of alien species has not prevented anthropogenic extinctions from reducing and homogenizing the functional diversity of native bird assemblages on oceanic archipelagos
Accessible Data Curation and Analytics for International-Scale Citizen Science Datasets
The Covid Symptom Study, a smartphone-based surveillance study on COVID-19
symptoms in the population, is an exemplar of big data citizen science. Over
4.7 million participants and 189 million unique assessments have been logged
since its introduction in March 2020. The success of the Covid Symptom Study
creates technical challenges around effective data curation for two reasons.
Firstly, the scale of the dataset means that it can no longer be easily
processed using standard software on commodity hardware. Secondly, the size of
the research group means that replicability and consistency of key analytics
used across multiple publications becomes an issue. We present ExeTera, an open
source data curation software designed to address scalability challenges and to
enable reproducible research across an international research group for
datasets such as the Covid Symptom Study dataset
Symptom prevalence, duration, and risk of hospital admission in individuals infected with SARS-CoV-2 during periods of omicron and delta variant dominance: a prospective observational study from the ZOE COVID Study
BACKGROUND: The SARS-CoV-2 variant of concern, omicron, appears to be less severe than delta. We aim to quantify the differences in symptom prevalence, risk of hospital admission, and symptom duration among the vaccinated population. METHODS: In this prospective longitudinal observational study, we collected data from participants who were self-reporting test results and symptoms in the ZOE COVID app (previously known as the COVID Symptoms Study App). Eligible participants were aged 16-99 years, based in the UK, with a body-mass index between 15 and 55 kg/m2, had received at least two doses of any SARS-CoV-2 vaccine, were symptomatic, and logged a positive symptomatic PCR or lateral flow result for SARS-CoV-2 during the study period. The primary outcome was the likelihood of developing a given symptom (of the 32 monitored in the app) or hospital admission within 7 days before or after the positive test in participants infected during omicron prevalence compared with those infected during delta prevalence. FINDINGS: Between June 1, 2021, and Jan 17, 2022, we identified 63 002 participants who tested positive for SARS-CoV-2 and reported symptoms in the ZOE app. These patients were matched 1:1 for age, sex, and vaccination dose, across two periods (June 1 to Nov 27, 2021, delta prevalent at >70%; n=4990, and Dec 20, 2021, to Jan 17, 2022, omicron prevalent at >70%; n=4990). Loss of smell was less common in participants infected during omicron prevalence than during delta prevalence (16·7% vs 52·7%, odds ratio [OR] 0·17; 95% CI 0·16-0·19, p<0·001). Sore throat was more common during omicron prevalence than during delta prevalence (70·5% vs 60·8%, 1·55; 1·43-1·69, p<0·001). There was a lower rate of hospital admission during omicron prevalence than during delta prevalence (1·9% vs 2·6%, OR 0·75; 95% CI 0·57-0·98, p=0·03). INTERPRETATION: The prevalence of symptoms that characterise an omicron infection differs from those of the delta SARS-CoV-2 variant, apparently with less involvement of the lower respiratory tract and reduced probability of hospital admission. Our data indicate a shorter period of illness and potentially of infectiousness which should impact work-health policies and public health advice. FUNDING: Wellcome Trust, ZOE, National Institute for Health Research, Chronic Disease Research Foundation, National Institutes of Health, and Medical Research Council
Overview of the CKM Matrix
The current status of the determination of the elements of the
Cabibbo-Kobayashi-Maskawa quark-mixing matrix is reviewed. Tensions in the
global fits are highlighted. Particular attention is paid to progress in, and
prospects for, measurements of CP violation effects.Comment: Proceedings of the Lepton Photon 2011 Conference, to appear in
"Pramana - journal of physics", 17 pages, 13 figure
Common Limitations of Image Processing Metrics:A Picture Story
While the importance of automatic image analysis is continuously increasing,
recent meta-research revealed major flaws with respect to algorithm validation.
Performance metrics are particularly key for meaningful, objective, and
transparent performance assessment and validation of the used automatic
algorithms, but relatively little attention has been given to the practical
pitfalls when using specific metrics for a given image analysis task. These are
typically related to (1) the disregard of inherent metric properties, such as
the behaviour in the presence of class imbalance or small target structures,
(2) the disregard of inherent data set properties, such as the non-independence
of the test cases, and (3) the disregard of the actual biomedical domain
interest that the metrics should reflect. This living dynamically document has
the purpose to illustrate important limitations of performance metrics commonly
applied in the field of image analysis. In this context, it focuses on
biomedical image analysis problems that can be phrased as image-level
classification, semantic segmentation, instance segmentation, or object
detection task. The current version is based on a Delphi process on metrics
conducted by an international consortium of image analysis experts from more
than 60 institutions worldwide.Comment: This is a dynamic paper on limitations of commonly used metrics. The
current version discusses metrics for image-level classification, semantic
segmentation, object detection and instance segmentation. For missing use
cases, comments or questions, please contact [email protected] or
[email protected]. Substantial contributions to this document will be
acknowledged with a co-authorshi
Illness duration and symptom profile in symptomatic UK school-aged children tested for SARS-CoV-2.
BACKGROUND: In children, SARS-CoV-2 infection is usually asymptomatic or causes a mild illness of short duration. Persistent illness has been reported; however, its prevalence and characteristics are unclear. We aimed to determine illness duration and characteristics in symptomatic UK school-aged children tested for SARS-CoV-2 using data from the COVID Symptom Study, one of the largest UK citizen participatory epidemiological studies to date. METHODS: In this prospective cohort study, data from UK school-aged children (age 5-17 years) were reported by an adult proxy. Participants were voluntary, and used a mobile application (app) launched jointly by Zoe Limited and King's College London. Illness duration and symptom prevalence, duration, and burden were analysed for children testing positive for SARS-CoV-2 for whom illness duration could be determined, and were assessed overall and for younger (age 5-11 years) and older (age 12-17 years) groups. Children with longer than 1 week between symptomatic reports on the app were excluded from analysis. Data from symptomatic children testing negative for SARS-CoV-2, matched 1:1 for age, gender, and week of testing, were also assessed. FINDINGS: 258 790 children aged 5-17 years were reported by an adult proxy between March 24, 2020, and Feb 22, 2021, of whom 75 529 had valid test results for SARS-CoV-2. 1734 children (588 younger and 1146 older children) had a positive SARS-CoV-2 test result and calculable illness duration within the study timeframe (illness onset between Sept 1, 2020, and Jan 24, 2021). The most common symptoms were headache (1079 [62·2%] of 1734 children), and fatigue (954 [55·0%] of 1734 children). Median illness duration was 6 days (IQR 3-11) versus 3 days (2-7) in children testing negative, and was positively associated with age (Spearman's rank-order rs 0·19, p<0·0001). Median illness duration was longer for older children (7 days, IQR 3-12) than younger children (5 days, 2-9). 77 (4·4%) of 1734 children had illness duration of at least 28 days, more commonly in older than younger children (59 [5·1%] of 1146 older children vs 18 [3·1%] of 588 younger children; p=0·046). The commonest symptoms experienced by these children during the first 4 weeks of illness were fatigue (65 [84·4%] of 77), headache (60 [77·9%] of 77), and anosmia (60 [77·9%] of 77); however, after day 28 the symptom burden was low (median 2 symptoms, IQR 1-4) compared with the first week of illness (median 6 symptoms, 4-8). Only 25 (1·8%) of 1379 children experienced symptoms for at least 56 days. Few children (15 children, 0·9%) in the negatively tested cohort had symptoms for at least 28 days; however, these children experienced greater symptom burden throughout their illness (9 symptoms, IQR 7·7-11·0 vs 8, 6-9) and after day 28 (5 symptoms, IQR 1·5-6·5 vs 2, 1-4) than did children who tested positive for SARS-CoV-2. INTERPRETATION: Although COVID-19 in children is usually of short duration with low symptom burden, some children with COVID-19 experience prolonged illness duration. Reassuringly, symptom burden in these children did not increase with time, and most recovered by day 56. Some children who tested negative for SARS-CoV-2 also had persistent and burdensome illness. A holistic approach for all children with persistent illness during the pandemic is appropriate. FUNDING: Zoe Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging and Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation, and Alzheimer's Society
The Imaging X-ray Polarimetry Explorer (IXPE): Technical Overview
The Imaging X-ray Polarimetry Explorer (IXPE) will expand the information space for study of cosmic sources, by adding linear polarization to the properties (time, energy, and position) observed in x-ray astronomy. Selected in 2017 January as a NASA Astrophysics Small Explorer (SMEX) mission, IXPE will be launched into an equatorial orbit in 2021. The IXPE mission will provide scientifically meaningful measurements of the x-ray polarization of a few dozen sources in the 2-8 keV band, including polarization maps of several x-ray-bright extended sources and phase-resolved polarimetry of many bright pulsating x-ray sources
Understanding metric-related pitfalls in image analysis validation
Validation metrics are key for the reliable tracking of scientific progress
and for bridging the current chasm between artificial intelligence (AI)
research and its translation into practice. However, increasing evidence shows
that particularly in image analysis, metrics are often chosen inadequately in
relation to the underlying research problem. This could be attributed to a lack
of accessibility of metric-related knowledge: While taking into account the
individual strengths, weaknesses, and limitations of validation metrics is a
critical prerequisite to making educated choices, the relevant knowledge is
currently scattered and poorly accessible to individual researchers. Based on a
multi-stage Delphi process conducted by a multidisciplinary expert consortium
as well as extensive community feedback, the present work provides the first
reliable and comprehensive common point of access to information on pitfalls
related to validation metrics in image analysis. Focusing on biomedical image
analysis but with the potential of transfer to other fields, the addressed
pitfalls generalize across application domains and are categorized according to
a newly created, domain-agnostic taxonomy. To facilitate comprehension,
illustrations and specific examples accompany each pitfall. As a structured
body of information accessible to researchers of all levels of expertise, this
work enhances global comprehension of a key topic in image analysis validation.Comment: Shared first authors: Annika Reinke, Minu D. Tizabi; shared senior
authors: Paul F. J\"ager, Lena Maier-Hei
Effect of a Perioperative, Cardiac Output-Guided Hemodynamic Therapy Algorithm on Outcomes Following Major Gastrointestinal Surgery A Randomized Clinical Trial and Systematic Review
Importance: small trials suggest that postoperative outcomes may be improved by the use of cardiac output monitoring to guide administration of intravenous fluid and inotropic drugs as part of a hemodynamic therapy algorithm.Objective: to evaluate the clinical effectiveness of a perioperative, cardiac output–guided hemodynamic therapy algorithm.Design, setting, and participants: OPTIMISE was a pragmatic, multicenter, randomized, observer-blinded trial of 734 high-risk patients aged 50 years or older undergoing major gastrointestinal surgery at 17 acute care hospitals in the United Kingdom. An updated systematic review and meta-analysis were also conducted including randomized trials published from 1966 to February 2014.Interventions: patients were randomly assigned to a cardiac output–guided hemodynamic therapy algorithm for intravenous fluid and inotrope (dopexamine) infusion during and 6 hours following surgery (n=368) or to usual care (n=366).Main outcomes and measures: the primary outcome was a composite of predefined 30-day moderate or major complications and mortality. Secondary outcomes were morbidity on day 7; infection, critical care–free days, and all-cause mortality at 30 days; all-cause mortality at 180 days; and length of hospital stay.Results: baseline patient characteristics, clinical care, and volumes of intravenous fluid were similar between groups. Care was nonadherent to the allocated treatment for less than 10% of patients in each group. The primary outcome occurred in 36.6% of intervention and 43.4% of usual care participants (relative risk [RR], 0.84 [95% CI, 0.71-1.01]; absolute risk reduction, 6.8% [95% CI, ?0.3% to 13.9%]; P?=?.07). There was no significant difference between groups for any secondary outcomes. Five intervention patients (1.4%) experienced cardiovascular serious adverse events within 24 hours compared with none in the usual care group. Findings of the meta-analysis of 38 trials, including data from this study, suggest that the intervention is associated with fewer complications (intervention, 488/1548 [31.5%] vs control, 614/1476 [41.6%]; RR, 0.77 [95% CI, 0.71-0.83]) and a nonsignificant reduction in hospital, 28-day, or 30-day mortality (intervention, 159/3215 deaths [4.9%] vs control, 206/3160 deaths [6.5%]; RR, 0.82 [95% CI, 0.67-1.01]) and mortality at longest follow-up (intervention, 267/3215 deaths [8.3%] vs control, 327/3160 deaths [10.3%]; RR, 0.86 [95% CI, 0.74-1.00]).Conclusions and relevance: in a randomized trial of high-risk patients undergoing major gastrointestinal surgery, use of a cardiac output–guided hemodynamic therapy algorithm compared with usual care did not reduce a composite outcome of complications and 30-day mortality. However, inclusion of these data in an updated meta-analysis indicates that the intervention was associated with a reduction in complication rate
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