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1,365 results for “Needs”
Datasets for "Micromonosporaceae Biosynthetic Gene Cluster Diversity Highlights the Need for Broad Spectrum Investigation"
<p>In this data collection is:<br><strong>Data S1</strong>: A folder with all the fasta files, representing the 42 strains (41 <em>Micromonosporaceae</em>, 1 <em>Streptomycetaceae</em>).<br><strong>Data S2</strong>: A folder with all the .gbk files for the BGC regions predicted by antiSMASH v5.1.1. These files were used as inputs for BiG-SCAPE and BiG-SLiCE.<br><strong>Data S3</strong>: A folder with all the .gbk files for the BGC regions predicted by antiSMASH v6.1.0.<br><strong>Data S4</strong>: A folder containing all the Quast outputs for the 42 strains.<br><strong>Data S5</strong>: A folder containing all the BUSCO outputs for the 42 strains. Example scripts are provided for scraping relevant information from the individual BUSCO outputs.<br><strong>Data S6</strong>: A folder containing GTDB (Genome Taxonomy Database) classification results, and species-level grouping results using FastANI (95% cutoff).<br><strong>Data S7</strong>: A folder containing an Interactive Tree of Life (iTOL)-compatible bar chart annotation using antiSMASH v5.1.1 BGC region information.<br><strong>Data S8</strong>: A folder containing a word document that describes the parameters used with Ubuntu WSL (Windows Subsystem for Linux) on the command line for programs antiSMASH v6.1.2, BiG-SCAPE v1.1.2, and BiG-SLiCE v1.1.1. Also included are parameters for MDSC in python. An example script is also provided for batch queries of BGCs against BiG-SLiCE v1.1.1’s pre-processed dataset of ~1.2 million BGCs.<br><strong>Data S9</strong>: A folder containing the BiG-SCAPE visualization of the 38 <em>Micromonosporaceae</em> (post-QC filtering, excluding WMMA1363, WMMB482, WMMB486, and WMMC500) in Cytoscape.<br><strong>Data S10</strong>: A folder containing:<br>The pre-processed dataset of 1.2 million BGCs from BiG-SLiCE.<br>All report folders generated by BiG-SLiCE for the 779 <em>Micromonosporaceae </em>BGCs queried against the 1.2 million BGCs.<br>The results data.db and associated folders for the pre-processed dataset of 1.2 million BGCs.<br><strong>Data S11</strong>: A folder containing the scripts necessary to regenerate the figures and perform independent analyses, and the relevant data used for the analyses.<br><strong>Data S12: </strong>A folder containing the results of the nucleotide blast of WMMA1947.region12's siderophore contig against WMMD1120.region14's siderophore contig.</p> <p><strong>Supplementary Information: </strong>Supplementary Table S1 and Supplementary Figures S1-S181.</p>
The decline of ground-nesting birds in Europe: do we need to manage predation in addition to habitat?
<p>Bird populations are declining globally with losses recorded in many European breeding birds. Habitat management measures have not resulted in a widespread reversal of these declines. We analysed national bird population trends from ten European countries (France, Hungary, Ireland, the Netherlands, Poland, Portugal, Spain, Sweden, Switzerland, and the UK) in relation to the species' nesting strategy ('ground-nesting' or 'other'), Annex I designation ('designated' or 'not designated') and association with agricultural habitats for breeding ('associated' or 'not associated'). For each country in our dataset, we also defined the following factors: farming intensity; predator community complexity; and predator control effort. Our results showed additive effects of nesting strategy, designation, and breeding habitats on the likelihood of population decline. Ground-nesting birds were 86% more likely to decline than birds with other nesting strategies. Annex I designated species of the Birds Directive were 50% less likely to decline than non-designated birds. Birds breeding primarily in agricultural habitats were more likely to decline than birds breeding in other habitats, interactively with farming intensity. Homogenous trends across Europe (i.e., trends in two or more countries that were either not declining in all countries or declining in all countries) indicate that the probability of population decline was related to nesting strategy and breeding habitat, with ground-nesting birds being 15.6 times more likely than other birds to have a declining trend across Europe, and birds nesting in agricultural habitat being 17.8 times more likely than birds nesting in other habitats to have a declining trend across Europe. Our results highlight a widespread challenge, therefore widespread instruments (e.g. legislation, economic policies, agri-environment schemes) will be required to reserve these declines. Ground-nesting species requirements can be complex and multiple strategies will be needed to restore populations including the development of predation management tools.</p>
On the Need to Monitor Continuous Integration Practices: An Empirical Study
<p>This repository contains all the artifacts and data related to the <strong>On the Need to Monitor Continuous Integration Practices: An Empirical Study</strong>. The folder structure and their entailments are as follows:</p> <ul> <li><strong>data</strong>: Contains .sql files with the dataset collected during the study, which includes all project information retrieved from GitHub. A README.txt file inside the folder explains how to restore the dataset.</li> <li><strong>document_analysis</strong>: Includes the analysis files for specific research questions: <ul> <li>RQ1 subdirectory: Contains the pull request (PR) comments dataset and an Excel file with the analysis data for Research Question 1.</li> <li>RQ3 subdirectory: Contains documentation from CI services and third-party tools analyzed in Research Question 3, along with an Excel file summarizing the analysis data.</li> </ul> </li> <li><strong>scripts</strong>: Provides the R scripts used for data analysis and chart generation.</li> <li><strong>survey</strong>: Includes the collected survey responses and a template of the survey sent to developers.</li> </ul> <p><br>The total size of the repository when decompressed is approximately <strong>8.14 GB</strong>.</p>
Needs-based approaches for representing personal transportation decision-making
<p>Data from a Utah State University research study, "Needs-based approaches for representing personal transportation decision-making". This version includes data from the focus group portion of the study. </p>
Program Determinants of Unmet Need for Family Planning
<p>This data file accompanies a paper submitted for publication in PLOS ONE by Rebecca Rosenberg, John Ross, Karen Hardee and Imelda Zosa-Feranil. The file includes a separate tab for each table and figure in the paper.</p>
Ecological inference using data from accelerometers needs careful protocols
<p>1. Accelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization.</p> <p>2. Using laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA) in human participants, with DBA as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds, using (i) pigeons <i>Columba livia</i> flying in a wind tunnel, with tags mounted simultaneously in two positions, and (ii) back- and<i> </i>tail-mounted tags deployed on wild kittiwakes <i>Rissa tridactyla.</i> Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds <i>Phaethon rubricauda</i> foraging in different seasons.</p> <p>3. Bench tests showed that individual acceleration axes required a two-level correction to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at a range of speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags varying by 9% in pigeons, and tail- and back-mounted tags varying by 13% in kittiwakes. The largest variation occurred between tropicbirds tagged in different seasons, where DBA varied by 25%, which may be due to tag attachment procedures. In general, the tropicbird study highlights the difficulties of attributing changes in signal amplitude to a single factor, when confounding influences tend to covary.</p> <p>4. Accelerometer accuracy, tag placement, and attachment critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that can be executed under field conditions. This should be used prior to deployments and archived with resulting data. We also suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning.</p>
Extended data for "The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing"
<p>Extended data for "The need to reassess single-cell RNA sequencing datasets: the importance of biological sample processing"</p>
Data: Survey of Implemented Mitigation Strategies and Further Needs of the United States Food Industry to Control COVID-19 in the Work Environment in Early 2021
<p>Data set related with the COVID-19 needs assessment study</p>
Can fire-age mosaics really deal with conflicting needs of species? A study using population hotspots of multiple threatened birds
<p> Locations that support high densities of a species ("population hotspots") have a disproportionate influence on species' persistence. In fire-prone ecosystems, managers attempting to promote population hotspots of multiple species must understand how hotspot locations might shift with post-fire succession and how much overlap exists in the locations of population hotspots for multiple species. Mangers are then tasked with resolving fire-management conflicts in overlapping locations.</p> <p>We studied three co-occurring threatened bird species in a fire-prone 'mallee' region of south-eastern Australia. We undertook field surveys for each species (1508 surveys; 540 sites; 9-ha each). We used N-mixture models to determine (a) what factors affect species' density (including post-fire succession); (b) species' population sizes; (c) locations of species' current population hotspots and locations that may become population hotspots in the future as the post-fire successional state changes and (d) the degree of overlap in the current and possible future hotspots of species.</p> <p>We found substantial variation in the densities of the three species across the study area, with roughly half of each species' population occurring in only 20 percent of potential habitat (i.e. population hotspots). All species shared a preference for subtle depressions in the landscape, resulting in substantial overlap in their population hotspots. Two species had contrasting responses to post-fire succession in the subtle depressions. As a result, there was only a narrow post-fire period that supported population hotspots of both species, creating a challenge for fire managers in these shared locations.</p> <p><em>Synthesis and Applications.</em> Many studies make vague recommendations for fire-age mosaics that do not provide managers with the detail they need to implement appropriate fire-age mosaics. By contrast, we explicitly quantify, then balance the conflicting post-fire needs of species in locations that support population hotspots of multiple species. Using this approach, we develop principles to guide the implementation of fire-age mosaics in such locations. This approach represents a step towards applying fire-age mosaic theory to support effective species conservation.</p>
Soil ecotoxicology needs robust biomarkers – a meta-analysis approach to test the robustness of gene expression-based biomarkers for measuring chemical exposure effects in soil invertebrates
<p>Gene expression-based biomarkers are regularly proposed as rapid, sensitive and mechanistically informative tools to identify whether soil invertebrates are experiencing adverse effects due to chemical exposure. However, before biomarkers could be deployed within diagnostic studies, systematic evidence of the robustness of such biomarkers to detect effects is needed. Here, we present an approach for conducting a systematic meta-analysis of the robustness of gene expression-based biomarkers in soil invertebrates.</p> <p>The approach was developed and trialled for two measurements of gene expression commonly proposed as biomarkers in soil ecotoxicology: metallothionein (MT) gene expression in earthworms for metals and heat shock protein 70 (HSP70) gene expression in earthworms for organic chemicals. From a systematic analysis of the published literature, we collected 294 unique gene expression data points and used linear mixed-effect models to assess concentration, exposure duration and species effects on the quantified response.</p> <p>This database provided contains gene-expression data from publications that have used gene expression-based biomakers to study effects of chemical pollutants on soil invertebrates. R scripts are provided that were used to study the patterns of gene expression as reported in accompanying publication. </p> <p>We encourage colleagues in the field to apply this approach to other biomarkers, as such quantitative assessment is a prerequisite to ensuring that the suitability and limitations of proposed biomarkers are known and stated.</p>
Implementing blended learning for clinician teachers: Identifying their needs and its impact on faculty development initiatives
<p>Learning Technologies has been a fast-growing field in Health Professions Education (HPE). Approaches to teaching, learning and assessment has been increasingly influenced by learning technologies which requires HPE teachers to adapt their teaching practices and with that identify areas for professional development. The implementation of blended learning in HPE, has shown improvements in student performance. However, it seems as if there are challenges with the implementation of a blended learning approach and that there might be some needs that clinical teachers have that are not being addressed in order to implement blended learning successfully. We used a qualitative exploratory design to identify clinician teachers' needs. Semi-structured, individual interviews were conducted with a total of eight (n=8) module coordinators in the third year of the MBChB programme, Stellenbosch University, Faculty of Medicine and Health Sciences. Results indicated the need for continuous technical and pedagogical support which refers to a longitudinal faculty development approach. Additionally, faculty development should include the support in structuring and rethinking the blended curriculum, as well as assisting in the clinicians' development in their role and identity as a clinical teacher. These results reveal the importance of faculty development as a targeted longitudinal approach</p>
Supporting Information - Optimizing hydrogen microgrids to facilitate diesel exit and meet the energy needs of remote and northern communities
<p>This file accompanies "Optimizing hydrogen microgrids to facilitate diesel exit and meet the energy needs of remote and northern communities" by Ian Maynard and Ahmed Abdulla.</p> <p>This supporting information contains:</p> <ul> <li>Nomenclature</li> <li>Data inputs</li> <li>Cost ratios used in cost calculations</li> <li>References</li> <li>Optimization results of 40 communities discussed in the paper above</li> </ul>
Dataset behind review manuscript "Macrolitter and microplastics along the East Pacific coasts – a homemade problem needing local solutions"
<p>Dataset containing data on abundance, distribution, composition and sources of marine litter (macrolitter and microplastics) along the East Pacific region, generated by reviewing all the peer-reviewed literature published for the region until December 2023. The results of this literature review are presented in the manuscript "Macrolitter and microplastics along the East Pacific coasts – a homemade problem needing local solutions".</p> <p>All the data extracted from the literature are included in the sheets "MacroData" and "MicroData", corresponding to "macrolitter" and "microplastic" studies, respectively. The sheet "Legend_MacroData&MicroData" contains the metadata for the sheets "MacroData" and "MicroData". All the remaining sheets contain the data utilized for the elaboration of the graphs and figures presented in the manuscript.</p>
Establishing barriers and needs for increased uptake of alternative weed control across Europe: Survey results from the UK, Latvia, France, Italy, Greece, Sweden and Spain.
<p><span>Reduced use of chemical herbicides and increased uptake of alternative weed control methods will only occur if there is improved understanding of the current barriers and needs of key stakeholders. An online survey about stakeholders’ perspectives and use of alternative weed control methods was carried out with Farmers, Agronomists, Researchers, Policy makers/advisors in 2023. Key barriers and needs were identified to encourage farmers to adopt sustainable weed control approaches which should guide future work addressing the implementation of Integrated Weed Management. Data consists of returned responses of participants across seven countries involved in the OPER8 project. </span></p> <p><span>The OPER8 Project has received funding from The European Union Horizon 2021 Food, Bioeconomy Natural Resources, Agriculture and Environment Programme under grant agreement 101060591</span></p>
Annotation data needed for FLAMES
<p>Annotation data needed for running FLAMES.</p> <p>All files ending in <strong>.tar.gz <em>must be unpacked before using. <br></em></strong>e.g. using tar -xzvf Annotation_data.tar.gz -C /path/to/extract, where /path/to/extract is the location where you want the files extracted.</p> <p>This page contains the following files:</p> <p><strong>Annotation_data.tar.gz</strong> - This gzipped file contains the data needed for the functional annotation of FLAMES. <br>Please extract the data before running FLAMES,</p> <p><strong>gtex_v8_ts_avg_log2TPM.txt</strong> - This file can be used for generating the tissue-type specific MAGMA results. <br>For a more detailed explanation see github.com/Marijn-Schipper/FLAMES</p> <p><strong>pops_features_full.tar.gz </strong>- This contains the data to recreate PoPS scores as used in the manuscript.</p> <p><strong>pops_features_pathway_naive.tar.gz </strong>- This contains the data to recreate pathway naive PoPS scores as used in the manuscript.</p> <p><strong>pops_features_pathway_FUMA_compatible.gz </strong>- This contains the data to recreate PoPS scores from MAGMA-Z files from ENSEMBL version 1.03-1.10, or FUMA MAGMA results.</p> <p><strong>pops_features_pathway_naive_FUMA_compatible.tar.gz </strong>- This contains the data to recreate pathway naive PoPS scores as used in the manuscript ENSEMBL version 1.03-1.10, or FUMA MAGMA results.<br>NOTE: This will allow for running PoPS on FUMA-generated MAGMA results, but will result in a PoPS score of 0 for genes not included in the original PoPS study. </p>
Data set for: Thema and world needs
<p>In essence, bibliodiversity describes how different communities handle knowledge creation and dissemination. Consequently, the information needs of these communities will also vary. In this article, we will investigate if evidence for this can be found by looking at much downloaded open access books in 100 countries. The subjects of these books are described by the Thema classification, which aims to be global in scope. A clustering algorithm is deployed to find patterns in the combination of classification codes and countries. This will allow us to determine whether the residents of the same region also share an interest in the same topics.</p> <p>When looking at global information needs and open access books, it is obvious that these titles will not just be written in English. The set of books used in this investigation contains text in twenty different languages. The subject classification is however language independent, which allows us to group all of them based on shared subjects. In the next section, we will further explore the Thema classification and bibliodiversity.</p>
A comparison of the present growth pace of the United States infrastructure with the needs of the next decade (2025-2050)
<p><span>The US population relies on crumbling infrastructural facilities needing continual upkeep. As economic activity accelerates with purchasing power projected at more than $34.102 trillion (about $100,000 per person) compared to $16.7 trillion (about $51,000 per person) today, with the US population experiencing rapid growth with a projected population of over 438 million by 2050 compared to 350 million today, infrastructural development will be significantly affected. This study considers how human interactions and recent developments (the Covid-19 outbreak and the development of artificial intelligence) will bring about change in the future demand for infrastructure in the US by 2045.</span></p>
iRECS survey of training needs
<p>Responses to the iRECS project online survey of knowledge gaps and training needs of research ethics committee members and ethics experts</p>
Data file needed for star cluster setup in Phantom smoothed particle hydrodynamics and magnetohydrodynamics code
<p>** this file is automatically downloaded by Phantom when running the starcluster setup **</p> <p>This is a small ascii file containing positions and velocities of stars utilised in the "starcluster" configuration in the Phantom smoothed particle hydrodynamics and magnetohydrodynamics code (<a href="http://adsabs.harvard.edu/abs/2018PASA...35...31P">Price et al. 2018</a>). It is used to set up a collection of N-body particles.</p> <p>The star cluster setup (and the data file) were written by Yann Bernard as part of his PhD thesis at<strong> </strong>Université Grenoble Alpes. The datafile is published here so it can be used in the automated code testing via github actions. </p> <p>The columns are mass, position (x,y,z) and velocity (vx,vy,vz) for all of the stars in the simulation</p>
INVITE: User needs and requirements
<p>This data was collected during the qualitative interview-based survey that was conducted in the framework of INVITE, which aimed at revealing the needs and requirements of prospective users and stakeholders of the OI2 Lab. In particular, a stratified purposeful sampling methodology was employed in order to include diverse OI stakeholders of the quadruple helix (i.e. from businesses and investors in the private sector over to academia and public authorities as well as civil society) and across different regions in Europe. Data in the form of interview transcripts was collected by means of semi-structured interviews and encompass information on the different ways in which OI actors are currently engaged (or not) in OI, various enablers / barriers that appear to be fostering / hindering their participation in OI as well as insights into the perceived knowledge, skills and support that they may need in order to successfully adopt and apply OI.</p>
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.