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482 results for “Digital data”
Data from: A survey of digitized data from U.S. fish collections in the iDigBio data aggregator
Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates the aggregation of collections data on a purely voluntary fashion that requires collection staff to consent to sharing of their data. Not all collections are sharing their data with iDigBio, but the data harvested from 38 of the 143 known fish collections in the U.S. that are in iDigBio account for the majority of fish specimens housed in U.S. collections. In the 22 years since publication of the last survey providing information on these 38 collections, 1,219,168 specimen records (lots), 15,225,744 specimens, 3,192 primary types, and 32,868 records of secondary types have been added. This is an increase of 65.1% in the number of cataloged records and an increase of 56.1% in the number of specimens. In addition to providing specimen-based data for research, education, and various outreach activities, data that are accessible via data aggregators can be used to develop accurate, up-to-date reports of information on institutional collections. Such reports present collections data in an organized and accessible fashion and can guide targeted efforts by collections personnel to meet discipline-specific needs and make data more transparent to downstream users. Data from this survey will be updated and published regularly in a dynamic web application that will aid collections staff in communicating collections value while simultaneously giving stakeholders a way to explore collections holdings as they relate to the institutions in which they are housed. It is through this resource that collections will be able to leverage their data against those of similar collections to aid in the procurement of financial and institutional support.
Data from: An Avida-ED digital evolution curriculum for undergraduate biology
We present an inquiry-based curriculum based on the digital evolution platform Avida-ED (http://avida-ed.msu.edu). We designed an instructional sequence and lab book consisting of an introduction to Avida-ED and a set of three lessons focused on specific evolutionary concepts. These served to familiarize students with experimental evolution and Avida-ED. Students then developed independent Avida-ED research projects to test their own questions. Curriculum design and implementation occurred over the course or two semesters, with a pilot implementation in the first semester, followed by curriculum revision and full implementation in the second semester. The curriculum was implemented in an undergraduate Introductory Cell and Molecular Biology course at a major research university. Full implementation of the curriculum in semester two involved the use of Avida-ED mainly in the teaching lab in parallel with a bacterial antibiotic resistance experimental research stream, allowing students to draw connections between Avidian digital evolution and the evolution of antibiotic resistance in microbial populations. After carrying out the introductory exercises, students developed independent Avida-ED projects to test their own research questions, and presented their data to researchers in the NSF-funded BEACON Center for the Study of Evolution in Action. Preliminary results of our studies to assess the impacts of an Avida-ED curriculum indicate a positive effect on student learning of evolutionary concepts, particularly in increasing the level of complexity of student explanations about the random nature of mutation.
Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture
A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness.
Data from: Reconstructing the past: methods and techniques for the digital restoration of fossils
During fossilization, the remains of extinct organisms are subjected to taphonomic and diagenetic processes. As a result, fossils show a variety of preservational artefacts, which can range from small breaks and cracks, disarticulation and fragmentation, to the loss and deformation of skeletal structures and other hard parts. Such artefacts can present a considerable problem, as the preserved morphology of fossils often forms the basis for palaeontological research. Phylogenetic and taxonomic studies, inferences on appearance, ecology and behaviour and functional analyses of fossil organisms strongly rely on morphological information. As a consequence, the restoration of fossil morphology is often a necessary prerequisite for further analyses. Facilitated by recent computational advances, virtual reconstruction and restoration techniques offer versatile tools to restore the original morphology of fossils. Different methodological steps and approaches, as well as software are outlined and reviewed here, and advantages and disadvantages are discussed. Although the complexity of the restorative processes can introduce a degree of interpretation, digitally restored fossils can provide useful morphological information and can be used to obtain functional estimates. Additionally, the digital nature of the restored models can open up possibilities for education and outreach and further research.
Digital Research Data Lifecycle
<p>This "Digital Research Data Lifecycle" diagram was first presented at the Digital Humanities Now Conference (27-29.January.2021), Stockholm University.<br>This diagram is part of the "Exploring the potential of 3D and spectral imaging methods and tools for understanding the past" invited presentation, given by V. Moitinho de Almeida.</p> <p>Further invited speakers: Douglas Biber (Northern Arizona University), Johanna Drucker (UCLA), Béatrice Joyeux-Prunel (University of Geneva), Christof Schöch (Trier University, Kathryn Eccles (University of Oxford), Tuomo Hiippala (University of Helisinki), Mike Kestemont (University of Antwerp), Jane Winters (School of Advanced Study, University of London), Anna Bentkowska-Kafel (King's College London; emerita), Giles Bergel (University of Oxford), Ian Gregory (Lancaster University), Nuria Rodríguez Ortega (University of Málaga). </p> <p>For more information about the Conference, please check: <a href="https://dahj.org/newsblog/dh-now">https://dahj.org/newsblog/dh-now</a></p> <p>Another way of citing this diagram: Moitinho de Almeida, V. (2021). “Digital Research Data Lifecycle”. In: <em>Exploring the potential of 3D and spectral imaging methods and tools for understanding the past</em> (presentation), Digital Humanities Now Conference (27-29.January.2021), Stockholm University. <a href="https://doi.org/10.5281/zenodo.14110887">https://doi.org/10.5281/zenodo.14110887</a></p>
Video Tutorial Resources to Support Student Training in Tidal Data Digitization
<p>These videos serve as supplementary resources to assist students in digitizing high and low tidal points for two specific phases: Phase 1 (2023-2024), focusing on Dublin Port with selected years from the 1970s, and Phase 2 (2024-2025), centred on Kilrush (Training Dataset). These resources complement the paper titled "<em>Evaluating Student Involvement in Ocean Data Digitization Efforts"</em>, providing essential training aimed at improving accuracy and engagement in student-led tidal data digitization projects."</p>
Supplementary digital data for Exposure of Insects to Current Use Pesticide Residues in Soil and Vegetation along Spatial and Temporal Distribution in Agricultural Sites
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Simulation and experimental data of frequency domain and time domain optical signal measurements for optical network digital twins
<p>The dataset contains IQ optical constellation samples for 16-QAM optical connections. Data have been generated both experimentally and through simulations with a MATLAB-based simulator. Different configurations have been simulated: 62 lightpaths having a different number of spans and links and 4 soft-failures affecting a lightpath with increasing failure magnitude.</p>
Digital research data from: Biochar stability in a highly weathered sandy soil under four years of continuous corn production
<p>Biochar is being considered a climate change mitigation tool by increasing soil organic carbon contents (SOC), however, questions remain concerning its longevity in soil. We applied 30,000 kg ha−1 of biochars to plots containing a Goldsboro sandy loam (Fine-loamy, siliceous, sub-active, thermic Aquic Paleudults) and then physically disked all plots. Thereafter, the plots were agronomically managed under 4 years (Y) of continuous corn (Zea Mays, L.) planting. Annually, incremental soil along with corresponding bulk density samples were collected and SOC concentrations were measured in topsoil (down to 23-cm). The biochars were produced from Lodgepole pine (Pinus contorta) chip (PC) and Poultry litter (PL) feedstocks. An untreated Goldsboro soil (0 biochar) served as a control.</p>
Code and Data for Digitization and validation of a chemical synthesis literature database in the ChemPU
<p>Code and data associated with paper. Code can be used for non commerical and academic use. </p>
Supplementary material 1 from: Niehues A, de Visser C, Hagenbeek FA, Karu N, Kindt ASD, Kulkarni P, Pool R, Boomsma DI, van Dongen J, van Gool AJ, `t Hoen PAC (2022) A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object. Research Ideas and Outcomes 8: e94042. https://doi.org/10.3897/rio.8.e94042
Members of the ACTION Consortium
EIAH data model: semantic interoperability between distributed digital repositories
<p>The authors described their information architecture project aimed at improving access to the Encyclopaedia of Iranian architectural history (EIAH) by signalling relationships between concepts and between concepts and documents. The outcome will be presented in a semantic portal or might be used for complex search queries by end users.</p>
Excel file with data from the implementation of "Using a Digital Assistant for learning English language and Geography in Primary Education"
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Data set for article''Digital health intervention in patients undergoing cardiac rehabilitation: systematic review and meta-analysis''
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Data of Building information modelling (BIM), Historic BIM (HBIM), Digital Twins and IoT
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Sample data for tech savvy digital media
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Digital Literacy Data
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Continuous Digital Monitoring of Walking Speed in Frail Elderly Patients: Noninterventional Validation Study and Longitudinal Clinical Trial (Data for interventional clinical trial)
<p>Digital technologies and advanced analytics have drastically improved our ability to capture and interpret health relevant data from patients. However, to date, limited data and results have been published detailing real-world patient compliance, demonstrating accuracy in target indications or examining what novel insights and clinical value can be derived. Here we present novel, digital mobility data from two studies: an independent, non-interventional validation study with elderly, naturally slow walking subjects, and a global, multi-site phase IIb clinical trial involving patients with age-related muscle loss and slow walking speed (sarcopenia). Based on these data, we validate the accuracy of a novel algorithm for capturing in-clinic and real-world gait speed in frail, slow-walking adults. We demonstrate the feasibility of continuous monitoring with a wearable inertial sensor in elderly adults in real-world settings, and propose minimum thresholds for compliance required for robust capture of gait behaviors in this population. We also show how simple, inferred contextual information, describing the length of a given walking bout, can explain some of the variation in real-world gait speed, and use this information to demonstrate for the first time a relationship between in-clinic performance and real-world gait speed behavior. This work lays a foundation for exploration of the clinical relevance and value of such measures and is a first step in building a more complete chain of evidence between standardized physical performance assessment, real-world behavior, and subjective perceptions of mobility, independence and health.</p> <p>This dataset contains data collected during the interventional clinical trial: derived data from raw accelerometry data, and summary performance data.</p> <p>The full dataset, including raw accelerometry data, is available here: <a href="https://mueller-et-al-2019.s3.amazonaws.com/index.html">https://mueller-et-al-2019.s3.amazonaws.com/index.html</a></p>
Data on openness level of digital services trade
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Linked collectors and determiners for: Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation.
Natural history specimen data linked to collectors and determiners held within, "Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904">https://bionomia.net/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904">https://gbif.org/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904</a>. Formatted as a Frictionless Data package.
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.