Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

OA eBook Usage Data Use-Cases by Stakeholder Diagram

This image was developed as a part of the "Developing a Data Trust for Open Access Ebook Usage" project funded by The Andrew W. Mellon Foundation. The image summarizes findings of various uses of OA eBook usage data contributed through asynchronous activities and virtual design workshops held with stakeholder groups from 2020-2021. It provides an overview of how publishers, libraries, and book publishing platforms and services use OA book usage data.  Christina Drummond designed and facilitated the virtual processes that generated the input for this image. Ms. Drummond and Kevin Hawkins developed image content. Philemon Eniola designed the graphical layout.

opencc-by-4.0May 2024View details →

Data for "Impact of early visual experience on later usage of color cues"

<div> <div>This repository contains the code and data underlying the paper "Impact of early visual experience on later usage of color cues" (Vogelsang et al., Science, 2024).</div> </div>

dryad36/100

Data from: Vertical niche usage and trait associations in Gabonese amphibians

Tropical forests are vertically complex, and offer unique niche opportunities in the form of resource, climate, and habitat-gradients from the forest floor to the canopy. Rainforest amphibians organize within this vertical space and the highest levels of vertical stratification occur in structurally complex and climatically stable tropical rainforests. Amphibians have diversified into numerous habitat and climatic niches, which has led to the development of a wide variety of morphological, behavioural, physiological, and reproductive traits. However, a lack of data regarding the vertical niche space used by amphibian species has prevented a nuanced analysis of traits and vertical height. We performed 74 ground-to-canopy surveys for amphibians at Baposso Village, Ngounie Province, Gabon, and describe the vertical stratification patterns of the assemblage in terms of richness, abundance, and species specific vertical niche usage. We analyse the relationships between amphibian traits with vertical height using linear mixed effects models, finding strong support that frogs with bigger toes in relation to their length access greater height in the canopy. We also see differences in the vertical heights of species according to their reproductive modes, highlighting the importance of reproductive mode diversity for the vertical stratification of amphibian assemblages.

opencc-zeroMay 2024View details →

opencc-by-4.0Dec 2023View details →

Demo of Impatto: A Static Analyzer for Quantitative Input Data Usage

Impatto is a sound fully-automatic and always-terminating static analysis tool based on the quantitative framework for input data usage properties proposed by Mazzucato (https://hal.science/hal-04339001).Impatto leverages an underlying backward analyzer to compute the set of input-output relations of the program under analysis. This backward analyzer is a parameter of the tool, allowing different kind of analyses such as program or neural network analysis. Furthermore, the choice of the impact definition is also a parameter of the tool to better suit several factors, such as the program structure, the environment, and the intuition of the researcher. GitHub repository at https://github.com/denismazzucato/impatto

opencc-by-4.0Apr 2018View details →

Raw Data for RE18 Data Track (Utilizing Product Usage Data in Communication Services for Evaluating Requirement Offerings)

Title: Raw Data for RE18 Data Track Submitted paper title : Utilizing Product Usage Data in Communication Services for Evaluating Requirement Offerings Submitted paper authors: Ashkan Hemmati, S. M. Didar Al Alam, Chris Carlson

opencc-by-4.0Oct 2019View details →

Data Usage Metrics at Repositories: A Survey

Results of a survey undertaken by the Research Data Alliance Data (RDA) Usage Metrics Working Group during February and March 2019 and presented at the 13th RDA Plenary Meeting in Philadelphia on 3 April 2019.

opencc-by-4.0Nov 2024View details →

Improving the Scalability of DBRepo - Memory Usage Data

Contains the results for the memory usage evaluation of the changes to DBRepo's architecture proposed in the bachelor's thesis "Enabling the Scalability of DBRepo" by Tobias Grantner reported in the unit of bytes. The files are named according to the scheme <code><change>-<state>.csv</code>, where <code><change></code> corresponds to the name of the proposed change to the architecture and <code><state></code> describes whether the system was evaluated before or after the change was implemented.

opencc-by-4.0Nov 2024View details →

Docking data for "The evolution of the SARS-CoV-2 spike protein for differential usage of the host transmembrane serine proteases entry pathway"

The dataset includes predicted complexes of the SARS-CoV-2 Spike protein (specifically at the S2' cleavage site) with Hepsin and TMPRSS2 proteins. It contains data on three variants: Wuhan, Delta, and Omicron BA.1. Compressed folders: -357596-DeltaHepsin.tgz -357597-DeltaTMPRSS2.tgz -360039-WuhanHepsin.tgz -360042-TMPRSSWuhan.tgz -392981-TMPRSS-BA1_all.tgz -392982-Hepsin-BA-all.tgz Each compressed folder contains the following: -Initial structures in pdb format -Output complexes in pdb format -Clusters in pdb format -Protocols -Parameters -Scoring files   Protein-protein docking  Molecular docking between the SARS-CoV-2 S protein of Wuhan, Delta (PDB: 7W92, [DOI: 10.1038/s41467-022-28528-w]), and BA.1 (PDB: 7XO5, [DOI: 10.1038/s41422-022-00672-4]) and the human proteases TMPRSS2 (PDB: 8HD8, [DOI: 10.1038/s41467-023-42527-5]) and Hepsin (PDB: 1Z8G, [DOI: 10.1042/BJ20041955]) was performed using the HADDOCK v2.5-2024.03 webserver ([DOI: 10.1021/ja026939x], [DOI: 10.1016/j.jmb.2015.09.014]). Missing loops in the protein structures were reconstructed using Modeller v10.5 ([DOI: 10.1006/jmbi.1993.1626]). Every heteroatom was removed from the reference structures. The relaxed atomistic coordinates for each S protein variant were derived via all-atom molecular dynamics (MD) simulations. These simulations were performed using AMBER22 with the FF19SB force fields and the pmemd.cuda module for enhanced performance ([DOI: 10.1021/acs.jcim.3c01153], [DOI: 10.1021/jz501780a], [DOI:10.1021/ct400314y]). For the Wuhan variant the S protein was retrieved from our previous modeling study [DOI: 10.1039/D0NR03969A] where for Delta and BA.1, ecah S protein was placed in a dodecahedral box, extending 20 Å beyond the solute in every cartesian direction, and solvated with the four-site OPC water model ([DOI: 10.1021/jz501780a]). The systems were neutralized with counterions, specifically one Cl− ion for the Delta variant and three Cl- ions for the BA.1 variant. To remove local clashes, a geometric optimization was performed using the steepest descent algorithm for 5000 cycles. The MD equilibration process consisted of several stages. First, temperature equilibration in the NVT ensemble was performed by gradually increasing the temperature through steps of 150, 200, 250, 300, and finally 310 K, each lasting 200 ps. During this phase, position restraints were applied to the heavy atoms of the proteins, with progressively decreasing spring constants of 5.0, 4.0, 3.0, and 1.0 kcal mol−1 Å−2, facilitating gradual relaxation. This was followed by a 1 ns equilibration at 310 K in the NPT ensemble without restraints. For production MD, the simulations were run in the NPT ensemble with periodic boundary conditions and Particle Mesh Ewald (PME) method ([DOI: 10.1063/5.0040966], [DOI: 10.1021/ct9001015]) using a grid spacing of 1.0 Å for long-range electrostatics. Non-bonded interactions were modeled with a Lennard-Jones potential using a 9Å cutoff. Temperature control was maintained using Langevin dynamics ([DOI: 10.1021/ct800573m]) with a collision frequency of 4.0 ps−1, and pressure control was managed by the Monte Carlo barostat ([DOI: 10.1016/j.cplett.2003.12.039]) with a 2.0 ps relaxation time at 1 bar. Bond constraints on hydrogen atoms were applied using the SHAKE algorithm ([DOI: 10.1016/0021-9991(77)90098-5]), and the hydrogen mass repartitioning scheme was applied via ParmEd ([DOI: 10.1371/journal.pcbi.1005659]), enabling a 4 fs integration time step ([DOI: 10.1021/ct5010406]). Each protein complex was simulated for a total of 20 ns. For the Wuhan variant, the 3D coordinates were retrieved from [DOI: 10.5281/zenodo.3817446]. The active interaction region on the spike protein was defined as the cleavage site (residues P809-R815). For TMPRSS2 and Hepsin, the active sites were defined based on their catalytic residues: H296, D345, D435, S441, S460, and G462 for TMPRSS2, and H203, D257, D347, A348, and S353 for Hepsin. These specific regions were selected to guide the docking process and maximize biologically relevant interactions. Docking clusters were analyzed by selecting those with the lowest interaction energies for further structural analysis. To evaluate binding accuracy, native contacts between the S protein and proteases were computed using the contact map analysis based on the OV+rCSU method ([DOI: 10.12693/APhysPolA.145.S9, 10.1021/acs.jctc.6b00986]), which allows for a precise identification of critical stabilizing interactions, both specific and non-specifics. High-frequency contacts, defined as those appearing in over 70% of the generated models, were highlighted as key determinants of protein-protein recognition, providing insight into the most stable and consistent interactions across docking configurations.

opencc-by-4.0Jul 2021View details →

A concept for FAIR clinical medication data usage - From care to research with OMOP: literature list of OHDSI studies

This list of papers has been reviewed for the usage of drug data and to answer the question on what drug level the study was done.  We checked whether drug ingredient level or drug component with dose and unit was required for the studies.

dryad36/100

Data from: Vertical niche usage and trait associations in Gabonese amphibians

Open the record for dataset details and reuse information.

publicMay 2024View details →

opencc-by-4.0Dec 2019View details →

Training data for "Differential exon usage analysis"

In RNA-Seq, we usually want to know the differentially expressed genes, as explained in several Galaxy Training Material tutorials. Sometimes,the question is more "which exons are differentially expressed". The process to identify differentially expressed exons is really similar to the one for differentially expressed genes. In this tutorial, we identify exons regulated by the Pasilla gene using RNA-Seq data from <a href="https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#brooks2011conservation">Brooks et al. 2011</a>.

opencc-zeroDec 2016View details →

Data from: Exploring temporal patterning of psychological skills usage during the week leading up to competition: lessons for developing intervention programmes

Background and purpose: Although sport psychology literature focuses on psychological skills use to promote proficiency, it is still puzzling that current research has focused on psychological skills use only during competition. There remains a scarcity of empirical evidence to support the timing, and content of psychological skill application during the time preceding competition. This study examined the extent to which psychological skills usage are dynamic or stable over a 7-day pre-competitive period and whether any natural learning experiences might have accounted for the acquisition of these skills across gender and skill level. Methods and results: Ninety elite and semi-elite table tennis players completed the Test of Performance Strategies (TOPS) at three different periods (7 days, 2 days, 1hour) before competition. A MANOVA repeated measures with follow-up analyses revealed significant multivariate main effects for only skill level and time-to-competition with no interactions. Specifically, elite (international) athletes reported more usage than semi-elite (national) counterparts for self-talk, imagery and relaxation respectively. Time-to-competition effects showed imagery use decreased steadily across the three time points while reported usage of relaxation were almost at the same level on two time points (7 days and 1 hour) but decreased 2 days before competition. Conclusions: Findings suggest an implementation of formalized and periodized psychological skills training programs over continuous training cycles. This may foster a positive long-term athletes' psychological state prior to the onset of competition.

opencc-zeroDec 2016View details →

Data from: Usage of unscheduled hospital care by homeless individuals in Dublin, Ireland: a cross-sectional study

Objectives: Homeless people lack a secure, stable place to live, and experience higher rates of serious illness than the housed population. Studies, mainly from the US, have reported increased use of unscheduled health care by homeless individuals. We compared the use of unscheduled ED and inpatient care between housed and homeless hospital patients in a high-income European setting. Setting: A large university teaching hospital serving the south inner city in Dublin, Ireland. Patient data is collected on an electronic patient record within the hospital. Participants: We carried out an observational cross-sectional study using data on all ED visits (n=47,174) and all unscheduled admissions under the general medical take (n=7,031) in 2015. Primary and Secondary Outcome Measures: The address field of the hospital's electronic patient record was used to identify patients living in emergency accommodation or rough sleeping (hereafter referred to as homeless). Data on demographic details, length of stay and diagnoses was extracted. Results: In comparison to housed individuals in the hospital catchment area, homeless individuals had higher rates of ED attendance (0.16 attendances per person/annum vs 3.0 attendances per person/annum respectively) and inpatient bed days (0.3 bed days per person/annum vs 4.4 bed days per person/annum. The rate of leaving ED before assessment was higher in homeless individuals (40% of ED attendances vs 15% of ED attendances in housed individuals). The mean age of homeless medical inpatients was 44.19 (95% CI 42.98-45.40), whereas that of housed patients was 61.20 (95% CI 60.72-61.68). Homeless patients were more likely to terminate an inpatient admission against medical advice (15% of admissions vs 2% of admissions in homeless individuals). Conclusion: Homeless patients represent a significant proportion of ED attendees and medical inpatients. In contrast to housed patients, the bulk of usage of unscheduled care by homeless people occurs in individuals younger than 65.

opencc-zeroDec 2018View details →

Data from: Habitat usage of Daubenton's bat (Myotis daubentonii), common pipistrelle (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) in a North Wales upland river catchment

Distributions of Daubenton's bat (Myotis daubentonii), common pipistrelle, (Pipistrellus pipistrellus), and soprano pipistrelle (Pipistrellus pygmaeus) were investigated along and altitudinal gradient of the Lledr River, Conwy, North Wales, and presence assessed in relation to the water surface condition, presence/absence of bank‐side trees, and elevation. Ultrasound recordings of bats made on timed transects in summer 1999 were used to quantify habitat usage. All species significantly preferred smooth water sections of the river with trees on either one or both banks; P. pygmaeus also preferred smooth water with no trees. Bats avoided rough and cluttered water areas, as rapids may generate high‐frequency echolocation‐interfering noise and cluttered areas present obstacles to flight. In lower river regions, detections of bats reflected the proportion of suitable habitat available. At higher elevations, sufficient habitat was available; however, bats were likely restricted due to other factors such as a less predictable food source. This study emphasizes the importance of riparian habitat, bank‐side trees, and smooth water as foraging habitat for bats in marginal upland areas until a certain elevation, beyond which bats in these areas likely cease to forage. These small‐scale altitudinal differences in habitat selection should be factored in when designing future bat distribution studies and taken into consideration by conservation planners when reviewing habitat requirements of these species in Welsh river valleys, and elsewhere within the United Kingdom.

opencc-by-4.0Nov 2023View details →

HPCG Power Usage Data Set

Node-level power samples for the HPCG benchmark workload running on 96 nodes of the Mutrino HPC system at Sandia.

opencc-zeroOct 2021View details →

The value of increased spatial resolution of pesticide usage data for assessing risk to endangered species: Data, notebooks, and results

Decision makers often cite data quality as a limitation in environmental management. Value of information approaches evaluates the benefit of new data collection for management outcomes. Pesticide exposure risk assessment for endangered species is one context where data limitations may affect decisions and a value of information type approach could be useful for identifying optimal data quality and resolution. Under the U.S. Federal Insecticide, Fungicide and Rodenticide Act, the U.S. Environmental Protection Agency (EPA) is responsible for registering pesticides before they can be sold and regularly reviewing pesticides. Section 7 of the Endangered Species Act requires that the EPA consider potential impacts of pesticides to listed endangered species and critical habitats in this process, and for the Services—U.S. Fish and Wildlife Service and National Marine Fisheries Service—to complete a formal Section 7 consultation if the EPA deems it necessary. The current process is time‐intensive, lacks transparency and confidence among stakeholders, and leaves hundreds of unreviewed pesticides on the market. Increasing the resolution of pesticide usage data could address these concerns by improving estimated overlaps between species ranges and pesticide usage. Thus, we evaluated the relative importance of different resolutions of pesticide usage data for assessing expected carbaryl exposure to endangered plant species endemic to California. We found that spatially explicit, township resolution usage data (~36 mile2) excluded 33% of terrestrial plants (55/168) and 51% their critical habitats (27/53) from requiring a Section 7 consultation, while coarser resolution data excluded none. In contrast, the EPA's biological evaluation for carbaryl only excludes 4% of terrestrial plants (nationally) from requiring formal Section 7 consultation. This suggests high‐resolution data could increase pesticide review efficiency and decrease the amount of time pesticides remain on the market without a formal evaluation.

opencc-by-4.0Apr 2021View details →

OA eBook Usage Data Analytics Reporting Service Business Model Canvas

This initial business model canvas was created to inform technical and governance roadmap discussions pertaining to the dashboard and analytics elements of the Developing a Data Trust for Open Access Ebook Usage project.

opencc-by-4.0Apr 2021View details →

OA eBook Usage Data Exchange Network Business Model Canvas

This initial business model canvas was created to inform technical and governance roadmap discussions pertaining to the data exchange elements of the Developing a Data Trust for Open Access Ebook Usage project.

opencc-by-4.0Oct 2023View details →

OA Book Usage Data Trust Business Model Canvas - 2023 Discussion Draft

Despite the "Business Model Canvas" (BMC) monikor, this diagram presents sustainability-model elements related to a not-for-profit International Data Space focused on open access book usage data exchange. This diagram was inspired by an initial 2021 draft version created by Murphy et al (<a href="https://doi.org/10.5281/zenodo.6227423" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.6227423</a>) and includes information known in 2023 by OA Book Usage Data Trust project team members. The BMC diagram organizes and presents information about potential partners, activites, resources, value propositions, relationships, outreach, and users alongside anticipated costs and potential cost recovery mechanisms.  This work was made possible through the "OAeBU Data Trust: Advancing to Launch by Developing IDS Governance Building Blocks" project grant funded by The Mellon Foundation.