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Data from: The multilayer temporal network of public transport in Great Britain
Despite the widespread availability of information concerning public transport coming from different sources, it is extremely hard to have a complete picture, in particular at a national scale. Here, we integrate timetable data obtained from the United Kingdom open-data program together with timetables of domestic flights, and obtain a comprehensive snapshot of the temporal characteristics of the whole UK public transport system for a week in October 2010. In order to focus on multi-modal aspects of the system, we use a coarse graining procedure and define explicitly the coupling between different transport modes such as connections at airports, ferry docks, rail, metro, coach and bus stations. The resulting weighted, directed, temporal and multilayer network is provided in simple, commonly used formats, ensuring easy access and the possibility of a straightforward use of old or specifically developed methods on this new and extensive dataset.
Data from: A public database of memory and naive B-cell receptor sequences
The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.
Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials
Background: Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications. We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees. Methods and Findings: We used a retrospective cohort of randomized clinical trials (RCTs) based on archived protocols approved by six research ethics committees between 13 January 2000 and 25 November 2003. Only RCTs with industry involvement were eligible. We investigated the documentation of publication agreements in RCT protocols and statements in corresponding journal publications. Of 647 eligible RCT protocols, 456 (70.5%) mentioned an agreement regarding publication of results. Of these 456, 393 (86.2%) documented an industry partner's right to disapprove or at least review proposed manuscripts; 39 (8.6%) agreements were without constraints of publication. The remaining 24 (5.3%) protocols referred to separate agreement documents not accessible to us. Of those 432 protocols with an accessible publication agreement, 268 (62.0%) trials were published. Most agreements documented in the protocol were not reported in the subsequent publication (197/268 [73.5%]). Of 71 agreements reported in publications, 52 (73.2%) were concordant with those documented in the protocol. In 14 of 37 (37.8%) publications in which statements suggested unrestricted publication rights, at least one co-author was an industry employee. In 25 protocol-publication pairs, author statements in publications suggested no constraints, but 18 corresponding protocols documented restricting agreements. Conclusions: Publication agreements constraining academic authors' independence are common. Journal articles seldom report on publication agreements, and, if they do, statements can be discrepant with the trial protocol.
Data from: What is a disease? Perspectives of the public, health professionals, and legislators
Objective: To assess the perception of diseases and the willingness to use public tax revenue for their treatment among relevant stakeholders. Design: A population-based, cross-sectional mailed survey. Setting: Finland Participants: 3 000 laypeople, 1 500 doctors, 1 500 nurses (randomly identified from the databases of the Finnish Population Register, the Finnish Medical Association and the Finnish Nurses Association), and all 200 parliament members. Main outcome measures: Respondents' perspectives on a 5-point Likert scale on two claims on 60 states of being: "[This state of being] is a disease"; and "[This state of being] should be treated with public tax revenue". Results: Of the 6 200 individuals approached, 3 280 (53%) responded. Of the 60 states of being, ≥80% of respondents considered 12 to be diseases (Likert scale responses of "4" and "5") and five not to be diseases (Likert scale responses of "1" and "2"). There was considerable variability in most states, and great variability in ten (≥20% of respondents of all groups considered it a disease and ≥20% rejected as a disease). Doctors were more inclined to consider states of being as diseases than laypeople; nurses and parliament members were intermediate (p<0.001), but all groups showed large variability. Responses to the two claims were very strongly correlated (r = 0.96 [95% CI: 0.94-0.98]; p<0.001). Conclusions: There is large disagreement among the public, health professionals, and legislators regarding the classification of states of being as diseases and whether their management should be publicly funded. Understanding attitudinal differences can help to enlighten social discourse on a number of contentious public policy issues.
Data from: Cooperative investment in public goods is kin directed in communal nests of social birds
The tragedy of the commons predicts social collapse when public goods are jointly exploited by individuals attempting to maximise their fitness at the expense of other social group members. However, animal societies have evolved many times despite this vulnerability to exploitation by selfish individuals. Kin selection offers a solution to this social dilemma, but in large social groups mean relatedness is often low. Sociable weavers (Philetairus socius) live in large colonies that share the benefits of a massive communal nest, which requires individual investment for construction and maintenance. Here, we show that despite low mean kinship within colonies, relatives are spatially and socially clustered and that nest-building males have higher local relatedness to other colony members than do non-building males. Alternative hypotheses received little support, so we conclude that the benefits of the public good are shared with kin and that cooperative investment is, despite the large size and low relatedness of these communities, kin-directed.
Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public and 66 private 0.1‐ha forest plots arrayed across forest age and soil gradients in Guanacaste, Costa Rica. We found that soil fertility appeared to drive the spatial structure of public vs. private ownership; public conservation lands appeared to be non‐randomly located on areas of lower soil fertility. On private lands, areas of crops/pasture appeared to be non‐randomly located on higher soil fertility areas while forests occupied areas of lower soil fertility. We found that forest structure and tree species diversity did not differ significantly between public and private ownership. However, public and private forests differed in tree species composition: 11 percent were more prevalent in public forest and 7 percent were more prevalent in private forest. Swietenia macrophylla, Cedrela odorata, and Astronium graveolens were more prevalent in public forests likely because public forests provide stronger protection for these highly prized timber species. Guazuma ulmifolia was the most abundant tree in private forests likely because this species is widely consumed and dispersed by cattle. Furthermore, some compositional differences appear to result from soil fertility differences due to non‐random placement of public and private land holdings with respect to soil fertility. Land ownership creates a distinctive species composition signature that is likely the result of differences in soil fertility and management between the ownership types. Both biophysical and social variables should be considered to advance understanding of tropical secondary forest structure and biodiversity.
Data from: Using public surveys to reliably and rapidly estimate the distributions of multiple invasive species on the Andaman archipelago
To effectively manage multiple biological invasions, information on their distributions must be generated rapidly and over large spatial scales. Using public surveys in a false-positive occupancy framework, we reliably estimate the distributions of three synanthropic invasive species on the Andaman Islands.
Data from: Incidence and fatality of serious suicide attempts in a predominantly rural population in Shandong, China: a public health surveillance study
Objectives: To estimate the incidence of serious suicide attempts (SSAs, defined as suicide attempts resulting in either death or hospitalisation) and to examine factors associated with fatality among these attempters. Design: A surveillance study of incidence and mortality. Linked data from two public health surveillance systems were analysed. Setting: Three selected counties in Shandong, China. Participants: All residents in the three selected counties. Outcome: measures Incidence rate (per 100 000 person-years) and case fatality rate (%). Methods: Records of suicide deaths and hospitalisations that occurred among residents in selected counties during 2009–2011 (5 623 323 person-years) were extracted from electronic databases of the Disease Surveillance Points (DSP) system and the Injury Surveillance System (ISS) and were linked by name, sex, residence and time of suicide attempt. A multiple logistic regression model was developed to examine the factors associated with a higher or lower fatality rate. Results: The incidence of SSAs was estimated to be 46 (95% CI 44 to 48) per 100 000 person-years, which was 1.5 times higher in rural versus urban areas, slightly higher among females, and increased with age. Among all SSAs, 51% were hospitalised and survived, 9% were hospitalised but later died and 40% died with no hospitalisation. Most suicide deaths (81%) were not hospitalised and most hospitalised SSAs (85%) survived. The fatality rate was 49% overall, but was significantly higher among attempters living in rural areas, who were male, older, with lower education or with a farming occupation. With regard to the method of suicide, fatality was lowest for non-pesticide poisons (7%) and highest for hanging (97%). Conclusions: The incidence of serious suicide attempts is substantially higher in rural areas than in urban areas of China. The risk of death is influenced by the attempter's sex, age, education level, occupation, method used and season of year.
FIGURE 3 in Dating and publication of the Encyclopédie Méthodique (1782- 1832), with special reference to the parts of the Histoire Naturelle and details on the Histoire Naturelle des Insectes
FIGURE 3. Title page of volume 4 of the Histoire Naturelle. Insectes. Panckoucke and Plomteux edition.
Data from: Using risk of bias domains to identify opportunities for improvement in food- and nutrition-related research: an evaluation of research type and design, year of publication, and source of funding
Purpose: This retrospective cross-sectional study aimed to identify opportunities for improvement in food and nutrition research by examining risk of bias (ROB) domains. Methods: Rating were extracted from critical appraisal records for 5675 studies used in systematic reviews conducted by three organizations. Variables were as follows: ROB domains defined by the Cochrane Collaboration (Selection, Performance, Detection, Attrition, and Reporting), publication year, research type (intervention or observation) and specific design, funder, and overall quality rating (positive, neutral, or negative). Appraisal instrument questions were mapped to ROB domains. The kappa statistic was used to determine consistency when multiple ROB ratings were available. Binary logistic regression and multinomial logistic regression were used to predict overall quality and ROB domains. Findings: Studies represented a wide variety of research topics (clinical nutrition, food safety, dietary patterns, and dietary supplements) among 15 different research designs with a balance of intervention (49%) and observation (51%) types, published between 1930 and 2015 (64% between 2000-2009). Duplicate ratings (10%) were consistent (k=0.86-0.94). Selection and Performance domain criteria were least likely to be met (57.9% to 60.1%). Selection, Detection, and Performance ROB ratings predicted neutral or negative quality compared to positive quality (p<0.001). Funder, year, and research design were significant predictors of ROB. Some sources of funding predicted increased ROB (p<0.001) for Selection (Interventional: industry only and none/not reported; Observational: other only and none/not reported) and Reporting (Observational: university only and other only). Reduced ROB was predicted by combined and other-only funding for intervention research (p<0.005). Performance ROB domain ratings started significantly improving in 2000; others improved after 1990 (p<0.001). Research designs with higher ROB were nonrandomized intervention and time series designs compared to RCT and prospective cohort designs respectively (p<0.001). Conclusions: Opportunities for improvement in food and nutrition research are in the Selection, Performance, and Detection ROB domains.
pourmalek/covir2: 2.2 public release
<p>2.2 public release</p>
Original Hamilton Ontario Public Water Fountain
Scanned in Hamilton Cemetery Source: Objaverse 1.0 / Sketchfab
Dataset supporting publication entitled: KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome
<p>Supporting dataset for a publication in Genome Biology, entitled</p> <p>"KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome" .</p> <p> </p>
Data and code to accompany the publication: Chemical and Pb isotope composition of phenocrysts from bentonites constrains the chronostratigraphy around the Cretaceous-Paleogene boundary in the Hell Creek region, Montana in G3
<p>EPMA data and analysis for Ikckert et al., 2015</p>
Dataset for the publication "Neutrophilic Bioleaching of Synthetic Covellite – A Model System Combining Experimental Data and Geochemical Modeling"
<p>This dataset contains data, which were used in preparation of the publication "Neutrophilic Bioleaching of Synthetic Covellite – A Model System Combining Experimental Data and Geochemical Modeling"</p>
FIGURE 2 in Publication and dating of the two " Bulletins " of the Société Entomologique de France (1873 1894)
FIGURE 2. First page of issue number 24 of the Bulletin Bimensuel for 1879 (= consecutive issue number 161) showing format for identifying marks of year and issue numbers.
FIGURE 1 in Publication and dating of the two " Bulletins " of the Société Entomologique de France (1873 1894)
FIGURE 1. First page of issue number 24 of the Bulletin Bimensuel for 1876 (= consecutive issue number 90) showing format for identifying marks of year and issue numbers.
FIGURE 10. Dendromonocotyle colorni. A. Male reproductive system. B in Overview of South African Dendromonocotyle (Monogenea: Monocotylidae), with descriptions of 2 new species from stingrays (Dasyatidae) kept in public aquaria
FIGURE 10. Dendromonocotyle colorni. A. Male reproductive system. B. Distal portion of male copulatory organ showing sclerotised accessory flange (af). C. Female reproductive system; note translucent coiled duct (tcd) of vagina. Scale bars = 100μm.
FIGURE 9. Dendromonocotyle colorni. A. Hamulus. B in Overview of South African Dendromonocotyle (Monogenea: Monocotylidae), with descriptions of 2 new species from stingrays (Dasyatidae) kept in public aquaria
FIGURE 9. Dendromonocotyle colorni. A. Hamulus. B. Haptoral papilla showing papillary sclerites (ps) and terminal papillary sclerite (tps). C. Tripartite sclerite (otp) at junction of radial septum and outer-ring septum; papillary sclerites (ps) can also be seen. D. Terminal papillary sclerite (tps). E. Anterior end showing distinct anterolateral gland duct openings (alg). Scale bars: A = 10μm; B = 100μm; C = 50μm; D = 20μm; E = 200μm.
FIGURE 8. Dendromonocotyle colorni. A in Overview of South African Dendromonocotyle (Monogenea: Monocotylidae), with descriptions of 2 new species from stingrays (Dasyatidae) kept in public aquaria
FIGURE 8. Dendromonocotyle colorni. A. Ventral view body-proper, composite. B. Haptor including hamulus (ham). C. Outer ring septal sclerite. D. Septal sclerites. E. Inner-ring tripartite sclerite. F. Outer-ring tripartite sclerite. G. Papillary sclerites. H. Terminal papillary sclerites. I. Hamulus. J. Marginal hooklet. Scale bars: A, B = 500μm; C–J = 10μm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.