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ShareScore release 0.7.1
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379 results for “data sharing”
Data from: Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
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Data from: The outcome of shared pollination services is affected by the density and spatial pattern of an attractive neighbour
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Data from: Do intraspecific or interspecific interactions determine responses to predators feeding on a shared size-structured prey community?
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Data from: Land‐sharing potential of large carnivores in human‐modified landscapes of western India
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Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis
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Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
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Data from: Research data sharing: practices and attitudes of geophysicists
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Data from: Food sharing in vampire bats: reciprocal help predicts donations more than relatedness or harassment
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Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?
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Data from: Molecular analysis reveals high compartmentalisation in aphid-primary parasitoid networks and low parasitoid sharing between crop and non-crop habitats.
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Leveraging metrics to drive data sharing at the Science journals
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Data of the article "Journal research data sharing policies: a study of highly-cited journals in neuroscience, physics, and operations research"
<p>The journals’ author guidelines and/or editorial policies were examined on whether they take a stance with regard to the availability of the underlying data of the submitted article. The mere explicated possibility of providing supplementary material along with the submitted article was not considered as a research data policy in the present study. Furthermore, the present article excluded source codes or algorithms from the scope of the paper and thus policies related to them are not included in the analysis of the present article.</p> <p>For selection of journals within the field of neurosciences, Clarivate Analytics’ InCites Journal Citation Reports database was searched using categories of neurosciences and neuroimaging. From the results, journals with the 40 highest Impact Factor (for the year 2017) indicators were extracted for scrutiny of research data policies. Respectively, the selection journals within the field of physics was created by performing a similar search with the categories of physics, applied; physics, atomic, molecular & chemical; physics, condensed matter; physics, fluids & plasmas; physics, mathematical; physics, multidisciplinary; physics, nuclear and physics, particles & fields. From the results, journals with the 40 highest Impact Factor indicators were again extracted for scrutiny. Similarly, the 40 journals representing the field of operations research were extracted by using the search category of operations research and management. </p> <p>Journal-specific data policies were sought from journal specific websites providing journal specific author guidelines or editorial policies. Within the present study, the examination of journal data policies was done in May 2019. The primary data source was journal-specific author guidelines. If journal guidelines explicitly linked to the publisher’s general policy with regard to research data, these were used in the analyses of the present article. If journal-specific research data policy, or lack of, was inconsistent with the publisher’s general policies, the journal-specific policies and guidelines were prioritized and used in the present article’s data. If journals’ author guidelines were not openly available online due to, e.g., accepting submissions on an invite-only basis, the journal was not included in the data of the present article. Also journals that exclusively publish review articles were excluded and replaced with the journal having the next highest Impact Factor indicator so that each set representing the three field of sciences consisted of 40 journals. The final data thus consisted of 120 journals in total. </p> <p>‘Public deposition’ refers to a scenario where researcher deposits data to a public repository and thus gives the administrative role of the data to the receiving repository. ‘Scientific sharing’ refers to a scenario where researcher administers his or her data locally and by request provides it to interested reader. Note that none of the journals examined in the present article required that all data types underlying a submitted work should be deposited into a public data repositories. However, some journals required public deposition of data of specific types. Within the journal research data policies examined in the present article, these data types are well presented by the Springer Nature policy on “Availability of data, materials, code and protocols” (Springer Nature, 2018), that is, DNA and RNA data; protein sequences and DNA and RNA sequencing data; genetic polymorphisms data; linked phenotype and genotype data; gene expression microarray data; proteomics data; macromolecular structures and crystallographic data for small molecules. Furthermore, the registration of clinical trials in a public repository was also considered as a data type in this study. The term <em>specific data types</em> used in the custom coding framework of the present study thus refers to both life sciences data and public registration of clinical trials. These data types have community-endorsed public repositories where deposition was most often mandated within the journals’ research data policies.</p> <p>The term ‘location’ refers to whether the journal’s data policy provides suggestions or requirements for the repositories or services used to share the underlying data of the submitted works. A mere general reference to ‘public repositories’ was not considered a location suggestion, but only references to individual repositories and services. The category of ‘immediate release of data’ examines whether the journals’ research data policy addresses the timing of publication of the underlying data of submitted works. Note that even though the journals may only encourage public deposition of the data, the editorial processes could be set up so that it leads to either publication of the research data or the research data metadata in conjunction to publishing of the submitted work.<em> </em></p> <p> </p>
Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
<p>Gene flow has tremendous importance on local adaptation, by influencing the fate of <i>de novo</i> mutations, maintaining standing genetic variation, and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of evolutionary mechanisms impending or favoring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (<i>Mallotus villosus</i>). We first assembled a 490 Mbp draft genome of <i>M. villosus</i> to map our RAD sequence reads. Then, we used a large dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they likely diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within each lineage, our analyses provided evidence for large <i>N</i><sub><i>e</i></sub> and high gene flow among spawning sites. Within the NWA lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that, both shared polymorphism among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.</p>
Data from: Snakeskin gourami (Trichopodus pectoralis) exhibits XX/XY sex determination and putative young Y chromosome shares sex chromosomal linkage homologies with those of amniotes
<p class="CxSpFirst"><span>Snakeskin gourami (<i>Trichopodus pectoralis</i>) is one of the most common air-breathing freshwater fish of the Indochina peninsula. It has a high meat yield and is one of the top five aquaculture freshwater fish in Thailand. However, it takes 2–3<b> </b>years for adults to reach sexual maturity. Snakeskin gourami is not externally sexually dimorphic and its sex determination remains unknown, complicating many aspects of broodstock management including sex manipulation. Understanding the sex determination system will contribute significantly towards full-scale commercialization. By characterizing the sex determination system in snakeskin gourami using cytogenetic approaches and Diversity Arrays Technology, we identified sex-specific loci in 16 phenotypic sex assignments of snakeskin gourami. Of the 39 loci present in all males, 4<b> </b>male-linked loci reached the criteria of moderately sex-linked loci (70:30; males:females and 80:20; males:females). By contrast, only one female-linked locus was detected from moderately sex-linked loci. This suggests that snakeskin gourami exhibits an XX/XY sex determination mode. No different chromosomal patterns were observed in karyotype, C-banding, and microsatellite repeat fluorescence <i>in situ</i> hybridization mapping between males and females, and no male-specific loci of 100:0 (males:females) were observed in snakeskin gourami. This suggests that the putative Y chromosome is young and the non-recombination region is very cryptic. A total of<b> </b>10.26% male-linked loci were involved with the sex developmental pathway in vertebrates and 5.13% showed partial homology with several amniote sex chromosomal linkages. Surprisingly, the hypothesis of an ancestral amniote super-sex chromosome with overlaps of partial sex chromosomal linkages was also found in teleosts. This approach provides a solid baseline to reveal the sex determination mechanism<b> </b>and identify potential sex determination regions in teleosts, allowing further investigation of genetic improvements in snakeskin gourami.</span></p>
Raw data belonged to the study: The sharing of research data facing the COVID-19 pandemic
<p>Raw data belonged to the study: "The sharing of research data facing the COVID-19 pandemic"</p>
Data from: Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology.
Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e. linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, by examining populations adapting to the same niche we did not find evidence that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments.
The sharing of research raw data in journals indexed in the Reproductive Biology JCR category
<p><a href="https://zenodo.org/record/2384871">Raw data belonged to the study of use and sharing of raw research data in the Journal Citation Reports' Reproductive Biology Category</a>.</p>
Code and data sharing for manuscript titled "Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2"
<p>Code and data sharing for manuscript titled "Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2".</p>
Data and Code for "Limitation by a shared mutualist promotes coexistence of multiple competing partners"
<p>Code for the ecological model (.R file) and data (.xlsx file) presented in Hammarlund et al. "Limitation by a shared mutualist promotes coexistence of multiple competing partners."</p>
COVID-19-data-sharing
<p>COVID-19-data-sharing</p>
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.