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379 results for “data sharing”
Data from: Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations
Following almost 10 years of no reported cases, Guinea worm disease (GWD or dracunculiasis) reemerged in Chad in 2010 with peculiar epidemiological patterns and unprecedented prevalence of infection among non-human hosts, particularly domestic dogs. Since 2014, animal infections with Guinea worms have also been observed in the other three countries with endemic transmission (Ethiopia, Mali, and South Sudan), causing concern and generating interest in the parasites' true taxonomic identity and population genetics. We present the first extensive population genetic data for Guinea worm, investigating mitochondrial and microsatellite variation in adult female worms from both human and non-human hosts in the four endemic countries to elucidate the origins of Chad's current outbreak and possible host-specific differences between parasites. Genetic diversity of Chadian Guinea worms was considerably higher than that of the other three countries, even after controlling for sample size through rarefaction, and demographic analyses are consistent with a large, stable parasite population. Genealogical analyses eliminate the other three countries as possible sources of parasite reintroduction into Chad, and sequence divergence and distribution of genetic variation provide no evidence that parasites in human and non-human hosts are separate species or maintain isolated transmission cycles. Both among and within countries, geographic origin appears to have more influence on parasite population structure than host species. Guinea worm infection in non-human hosts has been occasionally reported throughout the history of the disease, particularly when elimination programs appear to be reaching their end goals. However, no previous reports have evaluated molecular support of the parasite species identity. Our data confirm that Guinea worms collected from non-human hosts in the remaining endemic countries of Africa are Dracunculus medinensis and that the same population of worms infects both humans and dogs in Chad. Our genetic data and the epidemiological evidence suggest that transmission in the Chadian context is currently being maintained by canine hosts.
Data from: Shared decision-making as a cost-containment strategy: US physician reactions from a cross-sectional survey
Objective: To assess US physicians' attitudes towards using shared decision-making (SDM) to achieve cost containment. Design: Cross-sectional mailed survey. Setting: US medical practice. Participants: 3897 physicians were randomly selected from the AMA Physician Masterfile. Of these, 2556 completed the survey. Main outcome measures: Level of enthusiasm for "Promoting better conversations with patients as a means of lowering healthcare costs"; degree of agreement with "Decision support tools that show costs would be helpful in my practice" and agreement with "should promoting SDM be legislated to control overall healthcare costs". Results: Of 2556 respondents (response rate (RR) 65%), two-thirds (67%) were 'very enthusiastic' about promoting SDM as a means of reducing healthcare costs. Most (70%) agreed decision support tools that show costs would be helpful in their practice, but only 24% agreed with legislating SDM to control costs. Compared with physicians with billing-only compensation, respondents with salary compensation were more likely to strongly agree that decision support tools showing costs would be helpful (OR 1.4; 95% CI 1.1 to 1.7). Primary care physicians (vs surgeons, OR 1.4; 95% CI 1.0 to 1.6) expressed more enthusiasm for SDM being legislated as a means to address healthcare costs. Conclusions: Most US physicians express enthusiasm about using SDM to help contain costs. They believe decision support tools that show costs would be useful. Few agree that SDM should be legislated as a means to control healthcare costs.
Data from: Sharing an environment with sick conspecifics alters odors of healthy animals
Body odors change with health status and the odors of sick animals can induce avoidance behaviors in healthy conspecifics. Exposure to sickness odors might also alter the physiology of healthy conspecifics and modify the odors they produce. We hypothesized that exposure to odors of sick (but non-infectious) animals would alter the odors of healthy cage mates. To induce sickness, we injected mice with a bacterial endotoxin, lipopolysaccharide. We used behavioral odor discrimination assays and analytical chemistry techniques followed by predictive classification modeling to ask about differences in volatile odorants produced by two types of healthy mice: those cohoused with healthy conspecifics and those cohoused with sick conspecifics. Mice trained in Y-maze behavioral assays to discriminate between the odors of healthy versus sick mice also discriminated between the odors of healthy mice cohoused with sick conspecifics and odors of healthy mice cohoused with healthy conspecifics. Chemical analyses paired with statistical modeling revealed a parallel phenomenon. Urine volatiles of healthy mice cohoused with sick partners were more likely to be classified as those of sick rather than healthy mice based on discriminant model predictions. Sickness-related odors could have cascading effects on neuroendocrine or immune responses of healthy conspecifics, and could affect individual behaviors, social dynamics, and pathogen spread.
Data from: Land‐sharing potential of large carnivores in human‐modified landscapes of western India
The current Protected Area (PA)network is not sufficient to ensure long-term persistence of wide-ranging carnivore populations.Within India, this is particularly the case for species that inhabit non-forested areas since PAs disproportionately over-represent forested ecosystems. With growing consideration of human-use landscapes as potential habitats for adaptable large carnivores, India provides a model for studying them in densely populated landscapes, where there is little understanding about human-carnivore interactions in shared spaces. Using key informant interviews and an occupancy modeling framework, we assessed the distribution of three large carnivore species, the leopard Panthera pardus, Indian grey wolf Canis lupus pallipes and striped hyena Hyaena hyaena, across a ~89,000 km2 semi-arid multi-use landscape in western India, and quantified ecological drivers of their presence.The three species occupied 57% (leopard), 64% (wolf) and 75% (hyena) of the landscape of which only 2.6% area is protected as national parks or wildlife sanctuaries. Presence of the three carnivores was differentially favored by certain types of agriculture,while populations of domestic livestock supported them in this landscape with low densities of large wild prey. Our results demonstrate the adaptability of large carnivores in human-modified landscapes and we call for an expansion of the current conservation narratives which currently focus on forested protected areas,to include the high potential that anthropogenic landscapes offer as habitats where people and predators can co-adapt and persist.
Data from: Sharing of clinical trial data among trialists: a cross sectional survey
Objective: To investigate clinical trialists' opinions and experiences of sharing of clinical trial data with investigators who are not directly collaborating with the research team. Design and setting: Cross sectional, web based survey. Participants: Clinical trialists who were corresponding authors of clinical trials published in 2010 or 2011 in one of six general medical journals with the highest impact factor in 2011. Main outcome measures: Support for and prevalence of data sharing through data repositories and in response to individual requests, concerns with data sharing through repositories, and reasons for granting or denying requests. Results: Of 683 potential respondents, 317 completed the survey (response rate 46%). In principle, 236 (74%) thought that sharing de-identified data through data repositories should be required, and 229 (72%) thought that investigators should be required to share de-identified data in response to individual requests. In practice, only 56 (18%) indicated that they were required by the trial funder to deposit the trial data in a repository; of these 32 (57%) had done so. In all, 149 respondents (47%) had received an individual request to share their clinical trial data; of these, 115 (77%) had granted and 56 (38%) had denied at least one request. Respondents' most common concerns about data sharing were related to appropriate data use, investigator or funder interests, and protection of research subjects. Conclusions: We found strong support for sharing clinical trial data among corresponding authors of recently published trials in high impact general medical journals who responded to our survey, including a willingness to share data, although several practical concerns were identified.
Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. Results: In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. Conclusions: The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results.
Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
Overview of Research Data Sharing Policies Across Various Scientific Publishers
<p><strong>Context </strong></p><p>With the aim of advancing trust in published research, (scientific) publishers are developing Research Data Sharing Policies for their portfolio. Some publishers have the same policy across all journals. For example for the publishers Frontiers and Springer-Nature, a Data Availability statement is mandatory for all journals in their portfolio. While other publishers have different policy levels depending on the journal (e.g. Elsevier, American Chemical Society). In this list, one will find a short overview of Research Data Sharing Policies across publishers (mostly relevant to the Faculty of Science at Utrecht University).</p><p><strong>Limitations</strong></p><p>The list of publishers does not encompass all scientific publishers. Some Research Data Sharing Policies might be subjected to change.</p>
Replication package for: "P-Hacking, Data Type and Data-Sharing Policy".
<p>See Readme file. Journal article abstract: "This paper examines the relationship between p-hacking, publication bias, and data-sharing policies. We collect 38,876 test statistics from 1,106 articles published in leading economic journals between 2002--2020. We find that while data-sharing policies increase the provision of data, they do not decrease the extent of p-hacking and publication bias. Similarly, articles that use hard-to-access administrative data or third-party surveys, as compared to those that use easier-to-access (e.g., author-collected) data are not different in their p-hacking and publication extent. Voluntary provision of data by authors on their homepages offers no evidence of reduced p-hacking."</p>
Bike-sharing data Berlin from Nextbike and Call-a-Bike for 2019 and 2022
<p>This includes various data sets used to estimate cycling volume in Berlin. It contains the raw bike-sharing data as well as a routed and cleaned version thereof.</p><p> </p><p>The data is based on free-floating bike-sharing systems and is available in the form of individual trips, for each departure and starting point as well as the respective times at the minute level are known. The bike-sharing data comprises the months of April until December 2019 for the providers Nextbike and Call-a-Bike (provided by City Lab Berlin). Additionally, we web scrap the equivalent data for the months of June until December 2022 from Nextbike (web scraped data).</p><p> </p>
Training data for the shared task Ideology and Power Identification in Parliamentary Debates (2024)
<p>This dataset contains a selection of speeches from <a href="https://www.clarin.eu/parlamint">ParlaMint</a> corpora (version 4.0) as the training set for the shared task on "<a href="https://touche.webis.de/clef24/touche24-web/ideology-and-power-identification-in-parliamentary-debates.html">Ideology and Power Identification in Parliamentary Debates</a>" in <a href="https://clef2024.imag.fr/">CLEF 2024</a>.</p> <p>All files are tab-separated text files with the following fields:</p> <ul> <li>"<em>id</em>" is a unique (arbitrary) ID for each text.</li> <li>"<em>speaker</em>" is a unique (arbitrary) ID for each speaker. There may be multiple speeches from the same speaker.</li> <li>"<em>sex</em>" is the (binary/biological) sex of the speaker. This information is collected from varying sources (typically data published by the respective parliament), and in some cases it may be unspecified or unknown.</li> <li>"<em>text</em>" is the transcribed text of the parliamentary speech. Real examples may include line breaks, and other special sequences escaped or quoted.</li> <li>"<em>text_en</em>" is an automatic English translation of the corresponding text. This field may be empty (obviously) for speeches in English, but the translations may be missing for a small number of non-English speeches as well.</li> <li>"<em>label</em>" is the binary/numeric label. For political orientation, 0 is left and 1 is right. For power identification 0 indicates coalition (or governing party) and 1 indicates opposition.</li> </ul> <p>File names indicate the task and the parliament. We provide data from the following national and regional parliaments.</p> <ul> <li>Austria (at)</li> <li>Bosnia and Herzegovina (ba)</li> <li>Belgium (be)</li> <li>Bulgaria (bg)</li> <li>Czechia (cz)</li> <li>Denmark (dk)</li> <li>Estonia (ee) [only political orientation]</li> <li>Spain (es)</li> <li>Catalonia (es-ct)</li> <li>Galicia (es-ga)</li> <li>Basque Country (es-pv) [only power]</li> <li>Finland (fi)</li> <li>France (fr)</li> <li>Great Britain (gb)</li> <li>Greece (gr)</li> <li>Croatia (hr)</li> <li>Hungary (hu)</li> <li>Iceland (is) [only political orientation]</li> <li>Italy (it)</li> <li>Latvia (lv)</li> <li>The Netherlands (nl)</li> <li>Norway (no) [only political orientation]</li> <li>Poland (pl)</li> <li>Portugal (pt)</li> <li>Serbia (rs)</li> <li>Sweden (se) [only political orientation]</li> <li>Slovenia (si)</li> <li>Turkey (tr)</li> <li>Ukraine (ua)</li> </ul> <p>The number of training instances and the class imbalance differs for each training set. We do not provide a fixed validation split. Please see the <a href="https://touche.webis.de/clef24/touche24-web/ideology-and-power-identification-in-parliamentary-debates.html">shared task website</a> for further description of the data set and the sampling process.</p>
DIPROMATS 2024 - Shared Task 2: few-shot training data for narrative identification
<p>Narratives are causally connected sequences of events that are selected and evaluated as meaningful for a particular audience. They make sense of the world by identifying the significance of people, places, objects, and events in time. In international relations, international actors create strategic narratives to “construct a shared meaning of the past, present, and future of international politics to shape the behavior of domestic and international actors”</p> <p>DIPROMATS 2024 Task 2 is a multiclass multilabel classification problem. Given a series of predefined narratives of each international actor, systems must determine which narrative the tweets belong to. Systems will receive the description of each narrative and a few examples of tweets in both languages (English and Spanish) that belong to each of them (few-shot learning). A tweet may be associated with one, several or none of the narratives.</p> <p>These are the few-shot training datasets for Englsih and Spanish.</p> <p>These files don't contain the narratives description. You can find them in the testing dataset:</p> <p>Peñas, A., Fraile-Hernández, J. M., Moral, P., Rodrigo, Á., Deriu, J., Sharma, R., Centeno, R., Rodríguez-García, R., Giedemann, P., & Reyes-Montesinos, J. (2024). DIPROMATS 2024 - Shared Task 2: testing data for narrative identification (1.0.0) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.12663310" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12663310</a></p>
NOOS - Programming skills, notebook environment for sharing data and code
Open the record for dataset details and reuse information.
Data sharing of: Sulfur inventory of the young lunar mantle constrained by experimental sulfide saturation of Chang'e-5 mare basalts and a new sulfur solubility model for silicate melts in equilibrium with sulfides of variable metal–sulfur ratio
<p>Data sharing of: Sulfur inventory of the young lunar mantle constrained by experimental sulfide saturation of Chang’e-5 mare basalts and a new sulfur solubility model for silicate melts in equilibrium with sulfides of variable metal–sulfur ratio</p>
Data of the Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021
<p>This dataset was used in the Shared Task on the Disambiguation of German Verbal Idioms (VID) at <a href="https://konvens2021.phil.hhu.de/">KONVENS 2021</a>. For further details, please refer to the description paper of the shared task:</p> <blockquote> <p>Ehren, Rafael, Timm Lichte, Jakub Waszczuk & Laura Kallmeyer. 2021. Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021. In Proceedings of the Shared Task on the Disambiguation of German Verbal Idioms at KONVENS 2021. <a href="https://doi.org/10.5281/zenodo.5730322">https://doi.org/10.5281/zenodo.5730322</a>. <a href="https://konvens.org/proceedings/2021/index.html">https://konvens.org/proceedings/2021/index.html</a>.</p> </blockquote> <p><strong>Please cite this paper when using the dataset.</strong></p> <p>The content of the zip file is identical to that of the data directory in the <a href="https://github.com/rafehr/vid-disambiguation-sharedtask/tree/3ceb0bb423fa73e70ac018d4e02063ae449b4542">Github repository of the shared task</a>.</p> <p>The dataset consists of 9901 instances of a German VID type or its literal counterpart in context. The set of VID types was pre-selected, thus it constitutes a lexical sample data set. It is a merger of two datasets:</p> <ul> <li><a href="https://www.aclweb.org/anthology/2020.figlang-1.29.pdf">COLF-VID</a> (instances with T*)</li> <li><a href="https://www.aclweb.org/anthology/S13-2007.pdf">German SemEval-2013 task 5b</a> (instances with S*)</li> </ul> <p>The data comes in tsv files and every line has the following format:</p> <pre><code>Instance_ID \t VID_type \t label \t text</code></pre> <p>Consider this example:</p> <pre><code>T890202.28.4077 in wasser fallen figuratively Der Streit ums Hormonfleisch zwischen USA und EG provozierte den Polizeieinsatz . Aber nicht nur der Steakverkauf , auch die Aktionen gegen den Hormonstand , auf die sich Gruppen der Bauernopposition schon vorbereitet hatten , <b>fielen</b> <b>ins</b> <b>Wasser</b> . Die Fleischexporteure der USA wollten ihrerseits die " Grüne Woche " zur " Aufklärung " nutzen .</code></pre> <p>So the first column contains the ID (T890202.28.4077 in the example), the second the VID type (in wasser fallen), the third the label (figuratively) and the fourth the sentence with either the instance of the VID type or its literal counterpart (and two additional context sentences). The parts of the target expression are marked with the <b> tag (<b>fielen</b> <b>ins</b> <b>Wasser</b>). There are four possible labels:</p> <ul> <li>figuratively</li> <li>literally</li> <li>undecidable</li> <li>both</li> </ul> <p>The first two should be self-explanatory. The label undecidable was used by the annotators if it was not possible to disambiguate an instance given the context. The label both was applied when both the literal and the idiomatic readings were active.</p>
Scientists attitudes toward sharing data over time
<p>This data is derived from three previous surveys performed by members of DataONE to gauge scientists' attitudes and practices around data sharing and data management, and also to determine their satisfaction with the resources provided to them for sharing and data management. The data and analysis here are a subset of the questions from those three surveys. A subset of questions from each of the previous surveys was used to assess changes in attitudes towards sharing data and data management over time. The data are also available on <a href="https://github.com/olendorf/scientist_surveys/">Github</a>. Consult the README contained in the ZIP file for usage and other notes.</p>
Supplementary Figure 1: The road to FAIR genomes: a gap analysis of NGS data generation and sharing in the Netherlands
<p><em>Supplementary Figure 1: a flow chart conceptualizing the gap analysis. A generic NGS process diagram was created, based on a commonly used care workflow (Step 1). Next, a questionnaire about the inventory of (meta)data standards and retrieval of gaps was drafted (Step 2), which together with the process diagram was used as a basis for the subsequent interviews (Step 3). In parallel with the first three steps, a short literature review was performed (Step 4). The interviews were processed and current gaps were identified, anonymized and classified (Step 5). Finally, the results are shared with the community through presentations, publications and suggestions for next steps for addressing the identified gaps.</em></p>
Shared Data for De-scattering Deep Neural Network
<p>These images show mouse cortical layer 2/3 pyramidal neurons sparsely labeled with a cell fill (eYFP or mScarlet-I) to visualize the dendritic arbor, including dendritic spines. Cells were imaged in vivo using point-scan two-photon microscopy (PSTPM) and temporal focusing microscopy (TFM). These images were used for training and testing the De-Scattering Deep Neural Network (<a href="https://github.com/eleweiz/DeScattering_NN">https://github.com/eleweiz/DeScattering_NN</a>).</p>
Data from: Whistling shares a common tongue with speech: bioacoustics from real-time MRI of the human vocal tract
Most human communication is carried by modulations of the voice. However, a wide range of cultures has developed alternate forms of communication that make use of a whistled sound source. For example, whistling is used as a highly salient signal for capturing attention, can have iconic cultural meanings such as the cat-call, enact a formal code as in boatswain's calls, or stand as a proxy for speech in whistled languages. We used real-time magnetic resonance imaging to examine the muscular control of whistling to describe a strong association between the shape of the tongue and the whistled frequency. This bioacoustic profile parallels the use of the tongue in vowel production. This is consistent with the role of whistled languages as proxies for spoken languages, in which one of the acoustical features of speech sounds are substituted with a frequency modulated whistle. Furthermore, previous evidence that non-human apes may be capable of learning to whistle from humans suggests that these animals may have similar sensorimotor abilities to those that are used to support speech in humans.
Marine Data Sharing Companion Package
<p>Collection of data from marine data sharing study conducted between January 2022 and June 2022.</p> <p>Contents:</p> <ul> <li>Focus group interview guide</li> <li>Workshop summary of contents</li> <li>Coding categories and subcategories of transcriptions</li> <li>Sample of quotes from participants and their related subcategories</li> </ul> <p>For confidentiality reasons, only summaries and excerpts of the data collected are presented in this package. This content can be used to back up our findings and results w.r.t. marine data sharing, working as a support to the chain of evidence of the findings.</p> <p> </p>
ScienceDex guides
Understand access before you commit
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.