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773 results for “data science”
Small mammals surveys, 1981 - 1996, Adirondack Long-Term Ecological Monitoring Program Project No. 10 by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York. Environmental Data Initiative
Small mammals are important in forested ecosystems: they are key predators on seeds and invertebrates, provide food for larger predators and act as disease vectors. The objective of this study was to document small mammal abundance and population changes in managed and unmanaged forests of Huntington Wildlife Forest (HWF). Seven sites were sampled from 1981-1996. Fifty traps per site (250 total) were deployed for 4 nights and checked in the mornings. All captured small mammals were identified, sexed, weighed, and measured for reproductive condition, tagged, and brought into the lab for processing. Females with embryos or placental scars were noted in the lab. Over a five-year period, 671 deer mice; 261 woodland jumping mice, 594 southern redbacked voles, 248 short-tailed shrews, 373 masked shrews, 75 smoky shrews and small numbers of other species were captured and sexed/aged. According to Prachar and Sage (1988), weights of deer mice, redbacked voles, woodland jumping mice, short-tailed shrews, masked shrews and smoky shrews differed among years and age classes for 1983-1987. Weights differed between sexes for mice and voles but not shrews. Placental scar/embryo counts of mice and voles did not differ among years, habitats, mammal age classes or sexes. Reproductive rates of shrews exhibited patterns of fluctuation from 1983-1987.
Songbird surveys , 1952 - 1964, 1983 - 2008 Adirondack Long-Term Ecological Monitoring Program Project No. 2 Breeding Birds by Adirondack Ecological Center of the State University of New York College of Environmental Science and Forestry, Newcomb, New York. Environmental Data Initiative.
Study objectives were to (1) Document long-term trends in relative abundance and diversity of breeding forest birds (songbirds) in forest stands with different harvest histories and (2) Identify bird species that can be used as indicators of habitat change or degradation. Declines in neotropical migrants have been linked to changes in habitat quantity and quality across species' range. Songbirds that nest and forage in different habitat types or at different heights in the forest canopy may not be affected equally by forest change or management. We detected breeding songbirds using point-counts at Huntington Wildlife Forest (HWF) in the central Adirondack Mountains of New York during 1983-2000 and modeled on an original songbird point count dataset from Webb et al. (1977). Relative abundance (RA, the number of individual birds/count) was measured in sites with differing management histories, from an unmanaged >300-year-old stand to a stand cut with the shelterwood/overstory removal method just prior to sampling in 1983). Over eighty bird species were detected during the study duration. Songbird ecology and habitat characteristics can be used to understand long-term changes in relative abundance as related to forest change.
Data supplement for Wind Energy Science Paper 'Implementation of the blade element momentum model on a polar grid and its aeroelastic load impact'
<p>Contains the data for most figures in the article, as well as a plotting file written in python that generates the figures.</p>
All site data for Citizen Science (Guildford case study)
<p>The collected data during citizen science activities in Guildford using low-cost sensors.</p>
Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic
<p>This data set contains supplementary material for the paper 'Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic' by Martijn Visser, Nees Jan van Eck, and Ludo Waltman. The data set provides the statistics presented in the figures in the paper.</p>
Data & Open Science analysis of citizen science projects related with pollution
<p>These two spreadsheets contain the analysis done from a Data & Open Science perspective of citizen science projects related with pollution</p>
Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource
Objectives: To analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area. Setting: Retrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018. Participants: Including one eye per patient, 3357 eyes/patients (61% female). Extraction criteria were ≥ 1 ranibizumab or aflibercept injection, entry of "AMD" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database. Main outcome measures: Primary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain. Results: Mean VA gain at one-year and two years were +5.5 (95%CI:5.0,6.0) and +4.9 (95%CI:4.2,5.6) letters respectively. Fifty-four percent of eyes gained ≥5 letters at two years, 63% had stable VA (±≤14 letters), forty-four percent of eyes maintained good VA (≥70 letters). Patients received a mean of 7.7 (95%CI:7.6,7.8) injections during year one and 13.0 (95%CI:12.8,13.2) injections over two years. Younger age, lower baseline VA, and more injections were associated with higher VA gain at two years. Conclusion: This study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.
Data from: Responses of sympatric canids to human development revealed through citizen science
<p>Measuring wildlife responses to anthropogenic activities often requires long-term, large-scale datasets that are difficult to collect. This is particularly true for rare or cryptic species, which includes many mammalian carnivores. Citizen science, in which members of the public participate in scientific work, can facilitate collection of large datasets while increasing public awareness of wildlife research and conservation. Hunters provide unique benefits for citizen science given their knowledge and interest in outdoor activities. We examined how anthropogenic changes to land cover impacted relative abundance of two sympatric canids, coyote (<i>Canis latrans</i>) and red fox (<i>Vulpes vulpes</i>) at a large spatial scale. In order to assess how land cover affected canids at this scale, we used citizen science data from bow hunter sighting logs collected throughout New York State, USA, during 2004–2017. We found that the two species had contrasting responses to development, with red foxes positively correlated and coyotes negatively correlated with the percentage of low-density development. Red foxes also responded positively to agriculture, but less so when agricultural habitat was fragmented. Agriculture provides food and denning resources for red foxes, whereas coyotes may select forested areas for denning. Though coyotes and red foxes compete in areas of sympatry, we did not find a relationship between species abundance, likely a consequence of the coarse spatial resolution used. Red foxes may be able to coexist with coyotes by altering their diets and habitat use, or by maintaining territories in small areas between coyote territories. Our study shows the value of citizen science, and particularly hunters, in collection of long-term data across large areas (i.e., the entire state of New York) that otherwise would unlikely be obtained.</p>
Raw data of Call et al. (2020), Journal of Cereal Science 93: 102974
<p>Raw data for the publication "Effects of species and breeding on wheat protein composition" by Call et al. (2020), published in Journal of Cereal Science 93: 102974. ( <a href="https://doi.org/10.1016/j.jcs.2020.102974">https://doi.org/10.1016/j.jcs.2020.102974</a> )</p>
Data for: High-Speed 3D Imaging of Multiphase Systems: Applying SCAPE Microscopy to Analogue Experiments in Volcanology and Earth Sciences
<p>Microscale processes in three-phase suspensions (mixtures of gas, liquids, and solids) can affect the macroscale behavior of the whole suspension. To visualize these small-scale processes at high speed and in 3D, we use a recently developed imaging system: Swept Confocally-Aligned Planar Excitation (SCAPE) microscopy. This dataset contains 3D videos taken with SCAPE microscopy of experiments where different phases interact with each other. Each zipped folder contains raw data and processed data for a single experiment. "Case 1" experiments show CO2 bubbles growing on PMMA (acrylic) particles in sparkling water. The "Case 2" experiment shows water droplets suspended in canola oil and flowing through a porous medium made of packed PMMA particles. "Case 3" experiments show growth of injected air bubbles in particle suspensions (either glass beads in immersion oil, or PMMA particles in a refractive index matched liquid).</p> <p>All scaling parameters are provided in Table 1. "info.txt" files contain metadata for the processed hyperstacks.</p> <p>The experiments provided here are discussed in the following publication:<br> Oppenheimer, J.*, Patel, K.*, Lindoo, A., Hillman, E. M. C., and Lev, E.: High-Speed 3D Imaging of Multiphase Systems: Applying SCAPE Microscopy to Analogue Experiments in Volcanology and Earth Sciences. <em>Geochemistry, Geophysics, Geosystems.</em> (In press, 12/2020)</p> <p><br> </p>
Replication data for: Consumer preference testing of boiled sweetpotato (Ipomoea batatas (L.) Lam.) using crowdsourced citizen science in Ghana and Uganda
<p>Crowdsourced citizen science is an emerging approach in plant sciences. The triadic comparison of technologies (tricot) approach has been successfully utilised by demand-led breeding programmes to identify varieties for dissemination suited to specific geographic and climatic regions. An important feature of this approach is the independent way in which farmers individually evaluate the varieties on their own farms as ‘citizen scientists’. In this study, we adapted this approach to evaluate consumer preferences to boiled sweetpotato (<em>Ipomoea batatas</em> (L.) Lam) roots of 21 advanced breeding materials and varieties in Ghana and 6 released varieties in Uganda. We were specifically interested in evaluating if a more independent style of evaluation (home tasting) would produce results comparable to an approach that involves control over preparation (centralised tasting). We compiled data from 1,433 participants who individually contributed to a home tasting (de-centralised) and a centralised tasting trial in Ghana and Uganda, evaluating overall acceptability, and indicating the reasons for their preferences. Geographic factors showed important contribution to define consumers’ preference to boiled sweetpotato genotypes. Home and centralised tasting approaches gave similar rankings for overall acceptability, which was strongly correlated to taste. In both Ghana and Uganda, it was possible to robustly identify superior sweetpotato genotypes from consumers’ perspectives. Our results indicate that the tricot approach can be successfully applied to consumer preference studies.</p>
Data from: Designing data science workshops for data-intensive environmental science research
<p>Over the last 20 years, statistics preparation has become vital for a broad range of scientific fields, and statistics coursework has been readily incorporated into undergraduate and graduate programs. However, a gap remains between the computational skills taught in statistics service courses and those required for the use of statistics in scientific research. Ten years after the publication of "Computing in the Statistics Curriculum,'' the nature of statistics continues to change, and computing skills are more necessary than ever for modern scientific researchers. In this paper, we describe research on the design and implementation of a suite of data science workshops for environmental science graduate students, providing students with the skills necessary to retrieve, view, wrangle, visualize, and analyze their data using reproducible tools. These workshops help to bridge the gap between the computing skills necessary for scientific research and the computing skills with which students leave their statistics service courses. Moreover, though targeted to environmental science graduate students, these workshops are open to the larger academic community. As such, they promote the continued learning of the computational tools necessary for working with data, and provide resources for incorporating data science into the classroom.</p>
Data from: Exploratory and confirmatory research in the open science era
<p>1. Applied ecological research is increasingly inspired by the Open Science movement. However, new challenges about how we define our science when biodiversity data is being shared and re-used are not solved. Among these challenges is the risk associated with blurring the distinction between research that mainly seeks to explore patterns with no a-priori articulated hypotheses (exploratory research), and research that explicitly tests a-priori formulated hypotheses (confirmatory research).</p> <p>2. A rapid screening of a random selection of peer-reviewed articles suggests that neither experimental protocols nor hypothesis-testing sensu stricto are common in applied ecological research. In addition, most experiments are carried out on small spatial scales, which contrast with current global policy needs and research trends towards addressing large spatial and temporal scales. This latter trend make it unfeasible for policy to rely mainly on insights gained from experimental research.</p> <p>3. To solve fundamental local, regional and global societal challenges, we need both exploratory and confirmatory research, and the fundamental (but different) role that hypothesis-testing and prediction play in applied ecological research should be revaluated.</p> <p>4. A clearer distinction between exploratory and confirmatory research could be facilitated by allocating journal sections to different types of research; embracing new tools offered by the open science era, such as pre-registration of hypothesis; establishing new systems where post-hoc hypotheses emerging through exploration can also be registered for later testing; and more broad adoption of causal inference methods that foster more structured testing of hypotheses about causal mechanisms from observational biodiversity data.</p> <p>5. Synthesis and applications. To gain the full benefits from the open science era, researchers, funding bodies and journal editors should explicitly consider incentives that encourage openness about methods and approaches, as well as value the full plurality of scientific approaches needed to address questions in conservation science.</p>
Data and Scripts for "Bridging the gap to mesoscale radiation materials science with transient grating spectroscopy"
<p>This release contains all the files required to reproduce the data, figures, and tables in this paper's initial submission as a manuscript. All input files, output files, LAMMPS scripts and atomic configurations, MATLAB data processing scripts, raw plot databases, and plotting scripts can be found here.</p>
Data for Wind Energy Science paper "Modal dynamics of structures with bladed isotropic rotors and its complexity for 2-bladed rotors"
<p>The files are data files with model input and Matlab files with model parameters and function that sets up the block matrices of the dynamic model used in the paper. The Matlab script "test_repo.m" shows how to this function with all input.</p>
Austrian Science Fund (FWF) Publication Cost Data 2016
<p>Following the approach for the datasets in 2013 (http://dx.doi.org/10.6084/m9.figshare.988754), 2014 (https://dx.doi.org/10.6084/m9.figshare.1378610.v14) and 2015 (https://doi.org/10.6084/m9.figshare.3180166), the Austrian Science Fund (FWF) is making the publication costs spent in 2016 (esp. for Open Access) publically available.</p> <p>The dataset includes payments for publications of authors funded by the Austrian Science Fund (FWF) via following programmes:</p> <p>Peer-Reviewed Publications: https://www.fwf.ac.at/en/research-funding/fwf-programmes/peer-reviewed-publications/</p> <p>Stand-Alone Publications: https://www.fwf.ac.at/en/research-funding/fwf-programmes/stand-alone-publications/</p>
Grib and ASCII data, subset ERA-I for shallow water waves Ocean Science study
<p>Specific output from ERA-I reanalysis (wave model component) containing interated parameters, see https://doi.org/10.5194/os-13-1-2017</p>
Glosario: A multilingual glossary for computing and data science terms.
<p><code>glosario</code> is an open-source glossary of terms used in data science that is available online and also as a library in both <a href="https://github.com/carpentries/glosario-r/">R</a> and <a href="https://github.com/carpentries/glosario-py/">Python</a>. By adding glossary keys to a lesson’s metadata, authors can indicate what the lesson teaches, what learners ought to know before they start, and where they can go to find that knowledge. Authors can also use the library’s functions to insert consistent hyperlinks for terms and definitions in their lessons in any of several languages. The master copy of the glossary lives in the <code>glossary.yml</code> file. </p>
Data from: Diversifying large-scale participatory science: The efficacy of engagement through facilitator organizations
<p class="MsoNormal"><span>Large-scale, scientist-led, participatory science (citizen science) projects often engage primarily participants who are White, wealthy, and well-educated. Calls to diversify contributory projects are increasingly common, but little research has evaluated the efficacy of suggested strategies for diversification. We engaged participants in Crowd the Tap through facilitator organizations like Historically Black Colleges and Universities (HBCUs), predominantly White institutions (PWI), high school science classrooms, and corporate volunteer programs. Crowd the Tap is a contributory project focused on identifying and addressing lead contamination in household drinking water in the United States. We investigated how participant diversity with respect to race, ethnicity, and homeownership (a proxy for income) differed between participation facilitated through a partner organization and in unfacilitated participation in which participants came to the project independently. We were also interested in which facilitators were most effective at increasing participant diversity. White and wealthy participants were overrepresented in unfacilitated participation. Facilitation helped increase engagement of people of color, especially Black households, and lower-income households. High schools were particularly effective at engaging Hispanic or Latino participants and HBCUs were important for engaging Black households. Ultimately, our results suggest that engagement through facilitator organizations may be an effective means of engaging diverse participants in large-scale projects. Our results have important implications for the field of participatory science as we seek to identify evidence-based strategies for diversifying project participants. </span></p>
Citizen science data reveals altitudinal movement and seasonal ecosystem use by hummingbirds in the Andes Mountains
Ensuring connectivity is crucial to protect landscapes but it requires knowledge about how animals use ecosystems throughout the year. However, animal movements remain largely unknown in biodiversity hotspots, even for species that fulfill key ecological roles, as is the case of hummingbirds in the Andes. In the complex topography of mountain slopes, movement of these avian pollinators may occur either between habitat patches with asynchronous plant blooms or across ecosystems that are located within same elevation bands or along altitudinal gradients. Here, we used two decades (2000-2020) of records from citizen science data and boosted regression trees to predict monthly distributions for 55 hummingbird species in the Andes. We identified shifts in altitudinal distribution between contiguous months and calculated changes in the proportion of predicted distributions occupied by ecosystem types. Our findings reveal substantial altitudinal movement and differences in the proportion of ecosystem types utilized throughout the year that had not been previously reported for several species. Yet the magnitude of altitudinal and ecosystem shifts varies between hummingbird clades, and in some cases changes in the proportion of ecosystem types within estimated distributions occurs with little variation in altitude. All ecosystems across the Andes show temporal changes in hummingbird occurrence, but these are higher in natural landscapes compared to croplands or urban areas. Finally, we used phylogenetic logistic regression to test whether altitudinal and ecosystem shifts affect population trends. We found that higher ecosystem seasonality is more strongly associated with decreasing populations in comparison to altitudinal shifts. Altogether, our study reveals complex patterns of movement in hummingbirds and highlights the importance of ecological connectivity across different ecosystem types. More generally, it demonstrates the opportunity of using citizen science data to increase understanding about species' seasonal occurrences so that landscapes can be better managed to protect animal movement.
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.