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Data supporting the study "An organic crystalline state in ageing atmospheric aerosol proxies: spatially resolved structural changes in levitated fatty acid particles" by Milsom et al. (2021))
<p>Data supporting the figures and findings presented in the study <strong>"An organic crystalline state in ageing atmospheric aerosol proxies: spatially resolved structural changes in levitated fatty acid particles" by Milsom et al. (2021), <em>Atmos. Chem. Phys..</em></strong></p>
Data and software supporting the manuscript 'The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias'
<p>Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions. </p> <p> </p>
Research data supporting "Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment"
<p><em>Research data supporting the publication:</em></p> <p><em>Higgins SG, Nogiwa-Valdez AA, Stevens MM, Considerations for Implementing Electronic Laboratory Notebooks in an Academic Research Environment, Nature Protocols, 2021.</em></p> <p>This repository contains the raw survey data of 172 current and historic electronic laboratory notebook (ELN) software packages.</p> <p>Main files:</p> <ul> <li>"ELN_Review_Higgins_2021_Survey.csv" = raw survey data in 'tidy' data format</li> <li>"ELN_Review_Higgins_2021.Rmd" = an R Markdown File (R Notebook) that takes the survey data as input and produces summary statistics and plots. This file was written using R Studio as the IDE.</li> </ul> <p>Derived files, generated from those above:</p> <ul> <li>"ELN_Review_Higgins_2021.nb.html" = a self-contained HTML file that is automatically generated by R Studio, based on the markdown file. This can be opened in any web browser to allow manual inspection of the code and comments without the need for specialist software. Embedded within this file is also the original markdown script (i.e. a copy of the code in "ELN_Review_Higgins_2021.Rmd")</li> <li>"ELN_Review_Higgins_2021_Lifetimes_Interactive_Figure1.html" = an HTML file generated by the script above via the plotly package. It contains an interactive version of the ELN survey data, allowing the user to hover over the timeline and explore the data.</li> <li>"ELN_Review_Higgins_2021_Timeline.pdf" = static version of ELN timeline, used to generate figure in main manuscript.</li> <li>"ELN_Review_Higgins_2021_Releases-Per-Year.pdf" = static version of number of new ELNs per year, used to generate figure in main manuscript.</li> </ul> <p>This survey was generated from a mixture of primary and secondary sources (see references for secondary sources).</p>
Dataset for paper: A Systematic Literature Review and Recommendations for Ontology-based Support of Digital Forensics
<p>PLEASE, READ THE README.TXT FILE</p> <p>This document describes how to interpret the data and metadata files, and it is licensed under Creative Commons CC BY-NC-AS (https://creativecommons.org/licenses).</p> <p>The file "primary_studies_final_set-DATA.csv" is a CSV file format and contains the raw data extracted from our systematic literature review primary studies. Such data were extracted based on the research questions defined for our study.<br> The file "primary_studies_final_set-METADATA.csv" is a CSV file format and contains the following:<br> - the first row contains two pieces of information: the data type, which might be original or reused;<br> - the second row contains the reused data URL/DOI, which should inform the URL or DOI from which the data was reused, or n/a if the data is original;<br> - the third row contains the date of data generation in the format mm/dd/yyyy;<br> - the fourth row contains 11 elements describing each of the fields of the file "primary_studies_final_set-DATA.csv": the study ID, title, objective, six research questions, and an observation field; and<br> - the fifth row describes the data type of each field of the file "primary_studies_final_set-DATA.csv".<br> The .bib files contain the bibtex entry for the final set of studies.<br> The license.txt file describes the Creative Commons license for this material.</p> <p>We hope you have an excellent read!!</p> <p>Cheers!<br> Thiago, Edson, and Avelino</p>
Supporting data for manuscript "Geochemical Characterization of Insoluble Particle Clusters in Ice Cores Using Two-dimensional Impurity Imaging"
<p>Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) offers micron-resolution 2D chemical imaging, which has been adapted recently to ice core analysis. The datasets are supporting information for the manuscript "Geochemical Characterization of Insoluble Particle Clusters in Ice Cores Using Two-dimensional Impurity Imaging" accepted for publication at Geochemistry, Geophysics, Geosystems (10.1029/2022GC010595). Measurements were performed at the Ca’Foscari University of Venice, considered as analytes are 23Na, 24Mg, 27Al, 29Si, 43Ca, 56Fe and 88Sr. Background and drift correction as well as image construction were performed using the software HDIP (Teledyne Photon Machines, Bozeman, MT, USA). Impurity maps are acquired as a pattern of lines, without overlap in the direction perpendicular to that of the scan, and without any further spatial interpolation. In a sample of the EGRIP Greenland ice core (from about 1256.95 m depth), maps were obtained over 3 adjacent areas. For each of the maps, for every chemical channel the intensities (in counts, after background and drift correction) are provided as a separate file, named as “ds01_Area1_Na.csv”, etc. These maps were obtained using a 20 µm square spot. This data can be used to obtain the images shown in the manuscript. For the additional map shown as Figure 9 in the manuscript, data were obtained using a LA-ICP-TOFMS for imaging a sample of the last glacial period in the EPICA Dome C (EDC) ice core, bag 1065. The maps were acquired using a 35 µm square spot, with 50% overlap between neighboring pixels to increase the spatial resolution horizontally.</p>
Ecological Niche Models, in 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, of 1508 European Marine Species, developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Native ecological niche models of 1508 European species (894 fish and 614 non fish) developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines, for 2019 and under RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, at 0.5° spatial resolution.</p>
Data supporting: Microscopic observation of two-level systems in a metallic glass model
<p>Dataset of double well potentials sampled from energy landscape exploration of a ternary Lennard-Jones model supporting: "Microscopic observation of two-level systems in a metallic glass model"</p> <p>Thermalised configurations of the ternary Lennard-Jones model are given in the archive (configs.zip) of 1200 atoms at <span class="math-tex">\(T_f\)</span> 0.488, 0.509, 0.558 and 0.617 in the lammps (https://www.lammps.org/) data file format (https://docs.lammps.org/read_data.html).</p> <p>The two datasets each provided as (.zip) archives named dataset1.zip and dataset2.zip</p> <p>Datafiles (.csv) are named nebdf_{:3.3f}_{:05d}.csv where the float is <span class="math-tex">\(T_f\)</span> and the integer is <span class="math-tex">\(\tilde{m}\)</span>. </p> <p>columns of each .csv file are:</p> <p>'transitions', 'forward barriers', 'reverse barriers', 'asymmetry', 'barrier', 'euclidean distance', 'distance along string', 'n_intermediates', 'deltas', 'splittings', 'delta_zeroes', 'gammas', 'PR', 'glass', 'omegas1', 'omegas2', 'omegasts', 'Index 1', 'Index 2', 'Frequency 1>2', 'Frequency 2>1', 'e_1', 'e_2', 'dc', 'Tprep'</p> <p>'glass' is the index of the glassy metabasin sampled</p> <p>omegas1', 'omegas2', 'omegasts' are the curvatures of the minimum energy oaths near the first minimum, second minimum and transition state</p> <p>'e_1', 'e_2' are the energy per atom of the two glass minima </p> <p>'dc' is the typical particle displacement corresponding to <span class="math-tex">\(\sqrt{\dfrac{d^2}{PR}}\)</span></p> <p> </p>
Dataset supporting the paper "Thioetherification of Br-Mercaptobiphenyl Molecules on Au(111). Nano Letters 23, 1350 (2023)"
<p>Dataset corresponding to theoretical calculations in the paper "Thioetherification of Br-Mercaptobiphenyl Molecules on Au(111). Nano Letters 23, 1350 (2023)" DOI: <a href="https://doi.org/10.1021/acs.nanolett.2c04619">https://doi.org/10.1021/acs.nanolett.2c04619</a></p> <p>List of files:</p> <p>Several folders corresponding to the figures of the paper. They contain:</p> <ul> <li>.dat files: STM images simulated using STMpw (<a href="https://doi.org/10.5281/zenodo.3581159">https://doi.org/10.5281/zenodo.3581159</a>). They can be processed with the programs and scripts in the Utils directory of STMpw.</li> <li>CONTCAR files: relaxed structures in VASP format. They can be visualized with VESTA (<a href="https://jp-minerals.org/vesta/en/">https://jp-minerals.org/vesta/en/</a>).</li> <li>.agr: grace files (<a href="https://plasma-gate.weizmann.ac.il/Grace/">https://plasma-gate.weizmann.ac.il/Grace/</a>).</li> </ul>
Biodiversity Index, in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European Marine Species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Biodiversity Index in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European marine species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution. The Index counts the number of species (among the 1508) potentially present in each 0.5° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
Ecological Niche Models of 96 European Marine Species, for 2019, developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines at 0.1° Resolution
<p>Native ecological niche models of 96 European marine species of particular commercial and conservation interest developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines, for 2019 at 0.1° spatial resolution.</p>
Ensemble Ecological Niche Models and Biodiversity Index for 2019 of 96 European Marine Species based on Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, AquaMaps, and Support Vector Machines at 0.1° Resolution
<p>Ensemble Ecological Niche Models for 2019 of 96 European marine species of particular commercial and conservation interest, based on Ecological Niche Models developed with (i) Artificial Neural Networks, (ii) Maximum Entropy, (iii) Support Vector Machines, and (iv) AquaMaps at 0.1° Resolution. The data report, for each 0.1° cell, how many models (from 0 to 4) overcome a model-specific decision threshold to assess species presence in the cell. A Biodiversity Index is also provided as the count of the number of species (among the 96) potentially present in each 0.1° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
Competence Centres and User Support Centres Landscaping Results
<p>The dataset contains the data collected from the landscaping activity related to the Competence Centre and user support network for the D7.1 Report on Competence Centres landscape and user support activities.</p>
EXAFS and DRIFTS data collected during palladium hydride phase formation in supported palladium nanoparticles
<p>The dataset contains DRIFTS and EXAFS spectra measured under identical conditions at different hydrogen partial pressures with the presence of 0.5% CO in the gas flow. The first line in DRIFTS.dat file is the wavenumber in inverse cm, the following lines are the averaged spectra measured at different conditions. The first line in EXAFS.dat file is the energy in eV, the following lines are the averaged spectra measured at different conditions. File params.dat contain information about the sample temperature (Temperature column), hydrogen partial pressure (H pressure), number of cycle (each experiment was repeated 3 times), and the descriptors of DRIFTS spectra: FWHM, Area (Square) and positions of 8 gaussians, 3 positions of the maxima assigned to On top, Bridged and Hollow geometries of adsorbed CO molecules, and structural descriptors obtained from EXAFS: Pd-Pd interatomic distances (R), coordination numbers (N) and Debye-Waller parameters (ss) with corresponding errors.</p>
Data in support of Primack et al. 2022 Frontiers in Ecology & Environment: Historically excluded groups in ecology are undervalued and poorly treated
Hostile workplaces undermine efforts to make the ecological sciences more inclusive and welcoming. A survey sent to the Ecological Society of America membership and ECOLOG-L listserv subscribers provides a snapshot of a range of workplace experiences in ecology. The results of this survey are published as Primack et al. 2022. Historically excluded groups in ecology are undervalued and poorly treated. Frontiers in Ecology and the Environment. This dataset includes the survey results and code for data analysis.
U.S. household food waste tracking data in support of Li et al. 2023
These data were used to generate the results in the article “Household Food Waste Trending Upwards in the United States: Insights from a National Tracking Survey,” by Ran Li, Yiheng Shu, Kathryn E. Bender & Brian E. Roe, which has been accepted for publication in the Journal of the Agricultural and Applied Economics Association (doi – https://doi.org/10.1002/jaa2.59). The Stata code used to generate results is available from the authors upon request. U.S. residents who participate in consumer panels managed by a commercial vendor were invited by email or text message to participate in a two-part online survey during four waves of data collection: February and March of 2021 (Feb 21 wave, 425 initiated, 361 completed), July and August of 2021 (Jul 21 wave, 606 initiated, 419 completed), December of 2021 and January of 2022 (Dec 21 wave, 760 initiated, 610 completed), and February, March and April of 2022 (Feb 22 wave, 607 initiated, 587 completed), July, August and Septemper of 2022 (Jul 22 wave, 1817 initiated, 1067 completed). We are not able to determine if any respondents participated in multiple waves, i.e., if any of the observations are repeat participants. All participants provided informed consent and received compensation. Inclusion criteria included age 18 years or older and performance of at least half of the household food preparation. No data was collected during major holidays, i.e., the weeks of the Fourth of July (Independence Day), Christmas, or New Years. Recruitment quotas were implemented to ensure sufficient representation by geographical region, race, and age group. Post-hoc sample weights were constructed to reflect population characteristics on age, income and household size. The protocol was approved by the local Internal Review Board. The approach begins with participants completing an initial survey that ends with an announcement that a follow-up survey will arrive in about one week, and that for the next 7 days, participants should pay clo
Northeastern TIME Lakes Dragonfly Mercury and supporting lake geochemistry
We sampled lake water and dragonfly larvae in 74 northeastern US lakes (TIME, or Temporally Integrated Monitoring of Ecosystems, lakes) that are part of the US EPA Long-Term Monitoring Network. The lakes are a statistical population of acid-sensitive lakes, a subset of US EPA EMAP lakes originally sampled in the early 1990s (Stoddard et al. 1996). The TIME lakes are 45 lakes in New York, 43 of which are in the Adirondacks, plus 29 lakes in New England. All lakes were sampled in a late-summer index period during 2012; lake water samples were collected manually from the epilimnion via boat, and dragonfly larvae were collected near shore using dip nets. Major ions, acid-base chemistry, total mercury and methylmercury in lake water, and total mercury and methylmercury in dragonfly larvae were analyzed. GIS analysis of lake watersheds and integration of selected EMAP-derived characteristics provides landscape and some morphometry variables for each lake. Additional annual geochemistry data for the lakes beginning in 1992 (with EMAP sampling) and ending in 2016 are available through US EPA.
UCSB SONGS Mitigation Monitoring: Wetland Performance Standard - Bird Food Chain Support
These data describe annual estimates of the density of feeding birds at four coastal wetlands as part of the SONGS San Dieguito Wetland Restoration monitoring program to track long-term patterns in food chain support provided to birds. This study began in 2012 in the San Dieguito Wetlands and Tijuana Estuary in San Diego County, CA, Carpinteria Salt Marsh in Santa Barbara County, CA, and Point Mugu Lagoon in Ventura County. Beginning in 2024, Tijuana Estuary was replaced with Los Penasquitos Lagoon in San Diego County, CA.
Interagency Ecological Program: Monitoring of water quality, phytoplankton, zooplankton, clams, and Delta Smelt to support the Summer-Fall Suisun Marsh Salinity Control Gates Action 2018-2024
The Suisun Marsh Salinity Control Gates (SMSCG) have the potential to increase low-salinity-zone habitat for endangered Delta Smelt (Hypomesus transpacificus, California Endangered Species Act listed as Endangered, Federal Endangered Species Act listed as Threatened), and to allow them to more frequently occupy Suisun Marsh, especially Montezuma Slough, one of their most important rearing habitats. Operation of the SMSCG in summer and fall to improve Delta Smelt habitat are called for in the Biological Opinion and Incidental Take permit for the Central Valley Project and State Water Project. To support the adaptive management of the action, the California Department of Water Resources and collaborating agencies monitored water quality, phytoplankton, zooplankton, clams, and fishes during the SMSCG management actions in 2018. Monitoring has continued during the summer and fall months of all subsequent years, including both those with and without actions. This data package includes data collected by the Interagency Ecological Program’s (IEP) long-term monitoring programs supplemented with targeted sample collection where existing surveys lacked spatial or temporal coverage. Monitoring during no-action years will be used as a baseline for comparison during action years. This data package will be updated annually.
H.J. Andrews Forest Discovery Trail: An interpretation of place based on curriculum of interpretive learning trail and field trip support, 2016
The H.J. Andrews Experimental Forest (HJA) in the Oregon Cascades is one of 24 sites in the Long-Term Ecological Research (LTER) Network. It supports research on forests, streams, and watersheds, and fosters collaborations between ecosystem science, education, natural resource management, and the humanities. The site currently hosts 85 interdisciplinary research projects, as well as experiential training for undergraduate and graduate students. In addition, the HJA runs a vibrant professional development program for teachers. Because much of the HJA’s terrain is steep and occupied with sensitive research materials, middle and high school visits are limited to tours in designated areas. The Discovery Trail was developed in 2011 as a place for visitors (~1800 in 2014) to explore the forest and site research themes from HJA headquarters, but it is not yet amenable to unguided educational exploration. We have designed an interpretive learning trail and field trip support framework for the Discovery Trail. Our primary objective is to educate students about place while guiding them to reflect upon their own relationships with place and personal responsibility for stewardship behavior. Long-term place-based conservation research is woven with creative writing from the HJA writer’s residency program and paired with reflection and creative inquiry. Interactive trail stops enable students to engage the forest from multiple perspectives. The Discovery Trail is wired for intranet wifi and content and assessment will be delivered by digital media (i.e. iPads). We will evaluate conceptual learning according to the Framework for the Next Generation Science Standards, as well as observe affective changes in sense of place, empowerment, and expressions of care or empathy through analysis of student responses to the trail activities. Because conservation attitudes require not just knowledge about systems, but also emotional connections to the material, our learning experience will in
Residential housing segregation and urban tree canopy in 37 US Cities; data in support of Locke et al 2021 in npj Urban Sustainability
Our goal in this paper is to examine whether there are similar patterns in the distribution of tree canopy by Home Owners’ Loan Corporation (HOLC) graded neighborhoods across 37 cities. A pre-print of the paper can be found here: https://osf.io/preprints/socarxiv/97zcs This data packages contains: 1. City-specific file geodatabases with features classes of the HOLC polygons obtained from the Mapping Inequality Project https://dsl.richmond.edu/panorama/redlining/, and tables summarizing tree canopy, and in some cases other land cover classes. 2. An *.R script that replicates all of the analyses, graphs, and tables in the paper. Other double checks, exploratory, and miscellaneous outputs are created by the script too as a bonus. Everything in the paper can be done with the script; additional work outputs are also created. 3. A *.csv file containing city, the HOLC grade, and the percent tree canopy cover. This can be used to create the main findings of the paper and this flat file is provided as an alternative to running the R script to extract information from the geodatabases, combine, and analyze them. The intention is that this file is more widely accessible; the underlying information is the same. Redlining was a racially discriminatory housing policy established by the federal government’s Home Owners’ Loan Corporation (HOLC) during the 1930s. For decades, redlining limited access to homeownership and wealth creation among racial minorities, contributing to a host of adverse social outcomes, including high unemployment, poverty, and residential vacancy, that persist today. While the multigenerational socioeconomic impacts of redlining are increasingly understood, the impacts on urban environments and ecosystems remains unclear. To begin to address this gap, we investigated how the HOLC policy administered 80 years ago may relate to present-day tree canopy at the neighborhood level. Urban trees provide many ecosystem services, mitigate the urban heat island effect
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.