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13,117 results for “Maps”
Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)
<p><span><span>Mung bean (<i>Vigna radiata</i> L.) quality is dependent on seed chemical composition, which in turn determines the benefits of mung bean consumption for human health. While rich in a range of nutritional components, such as protein, macro- and micro- nutrients, carbohydrates and vitamins, mung bean remains less well studied than other legume crops. Mung bean genomics and genetic resources are relatively sparse. To further improve nutritional levels of mung bean grain requires genome-wide marker system tools. The objectives of this research were to develop these tools and conduct nutrient analysis in order to 1) identify single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) and to 2) perform genome-wide association studies (GWAS) for levels of calcium, iron, potassium, manganese, phosphorous, sulfur, and zinc in mung bean grain produced over two years of field experiment. A total of 112 GWAS models were explored using 6,486 high quality SNPs discovered in 92 cultivated mung bean accessions chosen from USDA core collection that represented 13 countries. The data obtained allowed for the identification of 43 associated SNPs and 20 main genomic regions that explained on average 22 % of the overall variation in seed macro- and micro- nutrients concentration on the basis of a multiple-year analysis. Most of the regions discovered in this study provide valuable candidate gene to use in future breeding of new varieties of mung bean with novel nutritional properties. Identification of the <a>underlying genes</a> will help to reveal the genetic control of mung bean seed nutritional property. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) in the species <i>V</i>. <i>radiata</i>, including wide and narrow crosses with / between cultivated and wild mung bean.</span></span></p>
Weekly depth to groundwater space-time maps for a shallow aquifer in rural Colombia
<p>The following dataset is related to the paper: Integrating community science research and space-time mapping to determine depth to groundwater in a remote rural region. It contains the results of the modeling approach that combines space-time depth to groundwater values with probabilistic depth to groundwater data. </p> <p> </p> <p><strong>Abstract [From the paper]:</strong></p> <p>We show how Community Science Research, an approach in which research projects are built with active community participation, added essential descriptive information to a statistical model to represent groundwater levels of a shallow aquifer located in Colombia. The community collected depth to groundwater during an extreme wet year and an average year in the watershed's middle-low-elevation areas. We used the data to map depth to groundwater using three statistical models, each with different configurations. Depth to groundwater is better represented by the model that incorporates qualitative data into quantitative observations. We map the probability of shallow depth to groundwater to identify how the aquifer responds to precipitation and show that in the wet year, the area of shallow depth to groundwater considerably increases compared to the average year. This difference implies that after the watershed receives an excess in precipitation, its flow regulation capacity can decrease, which is further threatened by local land-use activities. </p>
Annual 30-m land use/land cover maps of China for 1980–2015 from the integration of AVHRR, MODIS and Landsat data using the BFAST algorithm
<p>This package supplements the following paper entitled “Annual 30-m land use/land cover maps of China for 1980–2015 from the integration of AVHRR, MODIS and Landsat data using the BFAST algorithm” published with Science China Earth Sciences.</p>
Device-Free Localization & Identification Using Sub-GHz Passive Radio Mapping
<p>This dataset contains signal strength measurements from radio frequency communication links formed between 15 transceivers which were installed in a ~42 m<sup>2</sup> office environment. These measurements were performed when 1 of 6 possible single stationary human individuals was present in the environment at 1 of 15 possible locations. Communication occurred on both the 433 MHz & 868 MHz frequency bands using the DASH7 Alliance Protocol (D7A).</p>
APPENDIX Locality details for Murina mapped in Figs. 1 and 2a. Details for the remaining species in Fig. 2 are given in the text in A review of tube-nosed bats (Murina) from Laos with a description of two new species
APPENDIX Locality details for Murina mapped in Figs. 1 and 2a. Details for the remaining species in Fig. 2 are given in the text
"The evolutionary history of Neandertal and Denisovan Y chromosomes" - hg20 mapping of the capture data
<p>This archive contains the alignments of all individuals captured with the 6.9 Mb array mapped to GRCh38/hg20. See the project's GitHub repository for more information: <a href="https://www.github.com/bodkan/archaic-ychr">https://www.github.com/bodkan/archaic-ychr</a>.</p>
Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea
Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction-site associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, some of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
Hooded crow genome assembly (PacBio long reads + BioNano optical maps + DoveTail HiC maps)
<p>Structural variation (SV) is an important component of mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.</p>
Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection
Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) in wheat. It is the most important leaf blotch pathogen in Norwegian spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility have been identified. Some of these QTL are the result of underlying gene-for-gene interactions involving necrotrophic effectors (NEs) and corresponding sensitivity (Snn) genes. A collection of diverse spring wheat lines was evaluated for SNB resistance/susceptibility over seven growing seasons in the field. In addition, wheat seedlings were inoculated and infiltrated with culture filtrates (CFs) from four single spore isolates and infiltrated with semi-purified NEs (SnToxA, SnTox1 and SnTox3) under greenhouse conditions. In adult plants, the most stable SNB resistance QTL were located on 2B, 2D, 4A, 4B, 5A, 6B, 7A and 7B. The QTL on 2D was effective most years in the field. At the seedling stage, the most significant QTL after inoculation were located on 1A, 1B, 3A, 4B, 5B, 6B, 7A and 7B. The QTL on 3A and 6B were significant both after inoculation and CF infiltration, indicating the presence of novel NE-Snn interactions. The QTL on 4B and 7A were significant in both seedlings and adult plants. Correlations between SnToxA sensitivity and disease severity in the field were significant. To our knowledge, this is the first genome wide association mapping study (GWAS) to investigate SNB resistance at the adult plant stage under field conditions.
Data from: Mapping Tasmania's cultural landscapes: using habitat suitability modelling of archaeological sites as a landscape history tool
Aim: Understanding past distributions of people across the landscape is key to understanding how people used, affected and related to the natural environment. Here we use habitat suitability modelling to represent the landscape distribution of Tasmanian Aboriginal archaeological sites and assess the implications for patterns of past human activity. Location: Tasmania, Australia Methods: We developed a RandomForest 'habitat suitability' model of site records in the Tasmanian Aboriginal Heritage Register. We applied a best-effort bias correction, considered 31 predictor variables relating to climate, topography and resource proximity, and used a variable selection procedure to optimise the final model. Model uncertainty was assessed via bootstrapping and we ran an analogous MAXENT model as a cross-validation exercise. Results: The results from the RandomForest and MAXENT models are highly congruent. The strongest environmental predictors of site occurrence include distance to coast, elevation, soil clay content, topographic roughness and distance to inland water. The highest habitat suitability scores are distributed across a wide range of environments in central, northern and eastern Tasmania, including coastal areas, inland water body margins, and forests and savannas in the drier parts of Tasmania. With the exception of coastal areas much of western Tasmania has low habitat suitability scores, consistent with theories of low-density Holocene Tasmanian Aboriginal settlement in this region. Main conclusions: Our modelling suggests Tasmanian Aboriginal people occupied a heterogeneity of habitats but targeted coastal areas around the whole island, and drier, less steep, and/or open forest and savanna environments in the central lowlands. The western interior was identified as being rarely used by Aboriginal people in the Holocene, with the exception of isolated pockets of habitat; yet whether this is a true reflection of Aboriginal resource use demands increased archaeological surveys, particularly in the Tasmanian Wilderness World Heritage Area.
Domain-specific Language for Data-driven Design Time Analyses and Result Mappings for Logic Programs - Data Set
<p>This data set contains additional information to the master thesis of Sebastian Hahner. This includes the prototypical implementation of the domain-specific language (DSL) as well as sample scenarios and mapping results.</p>
QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)
<p><span>Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of sulfur phytotoxicity in melon. One major (qSulf-1) and two minor (qSulf-8 and qSulf-12) QTL were associated with sulfur tolerance in the population. <a name="_Hlk40443716">The development of Kompetitive Allele-Specific PCR (KASP) markers developed across qSulf-1 decreased the QTL interval from 239 kb (cotyledons) and 157 kb (leaves) to 97 kb (both tissues). </a>The markers were validated for linkage to sulfur tolerance in a set of melon cultivars. These KASP markers can be incorporated into melon breeding programs for introgression of sulfur tolerance into elite melon germplasm.</span></p> <p> </p> <p> </p>
Map of growing stock volume of Russian forests for the year 2014
<p>The data products consist of two layers that include estimates of<br> 1. growing stock volume (GSV, unit: m3/ha) for the year 2014 (raster data set)<br> Definition: volume of all living trees more than 6 cm in diameter at breast height measured over bark from ground to a top stem diameter of 0 cm. Excludes: branches, twigs, foliage, flowers, seeds, stump and roots.<br> 2. per-pixel of growing stock volume uncertainty expressed as standard error in m3/ha (raster data set)</p> <p>The maps have a spatial resolution of 3.2 arc sec (ca 0.5 ha for Russia).</p> <p>The GSV estimates were obtained by calibration of two remote sensing-based maps with ca 8000 ground plots from the National Forest Inventory:<br> • The global GlobBiomass map of GSV (Santoro, 2018; Santoro et al., 2020) is based on synthetic aperture radar (SAR) observations acquired around the year 2010 and has a spatial resolution of 100m, units m³ ha<sup>-1</sup>.<br> • The global Climate Change Initiative (CCI) Biomass map of AGB (Santoro and Cartus, 2019) is also based on SAR data, acquired in 2017 and has a spatial resolution of 100m, units t ha<sup>-1</sup>.</p> <p>The methodology, input data and software are published here:</p> <p>Schepaschenko, D., Moltchanova, E., Fedorov, S. <em>et al.</em> Russian forest sequesters substantially more carbon than previously reported. <em>Sci Rep</em> <strong>11, </strong>12825 (2021). https://doi.org/10.1038/s41598-021-92152-9 </p>
The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets
<p>High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (<em>Entosphenus tridentatus</em>) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations likely explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent datasets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.</p>
Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology
<p>Tropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on ecological applications of these methods. We also discuss key considerations for tropical ecologists looking to use rainfall metrics that better align with hypothesized biological or ecological mechanisms or that more effectively describe rainfall variability in the systems we study, and provide a toolkit (R scripts and gridded datasets) to do so. We argue that incorporating more sophisticated approaches to quantify rainfall variability into study design and statistical analyses will enhance our understanding of past, ongoing, and future changes in tropical ecosystems. </p>
Biocuration - mapping resources and needs - Underlying Data
<p>A variety of teams and individuals are involved in biocuration worldwide. However, they may not self-identify as biocurators <em>per se</em>, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the ELIXIR Training Platform launched an Implementation Study in order to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development. To achieve the goals of the study we carried out a global survey about the nature of biocuration work, the tools and resources that are used, training that has been received and additional training needs. To examine these topics in more detail we ran workshop-based discussions at ISB Biocuration Conference<strong> </strong>2019 and the ELIXIR All Hands Meeting 2019. We also had guided conversations with selected people from the EMBL-European Bioinformatics Institute.</p> <p>The following files represent the underlying data for this study:</p> <ul> <li> <p>Pilot survey questions.docx (questionnaire sent to staff of Wellcome Genome Campus)</p> </li> <li> <p>Questions to guide conversations with biocurators.docx (conversation guide outlines the type of questions to be asked)</p> </li> <li> <p>Global survey questions.docx (globally disseminated questionnaire revised on the basis of the pilot survey)</p> </li> <li> <p>Themed summary of the responses given in the guided conversations – deidentified.docx (de-identified outcomes of the guided conversations)</p> <ul> <li> <p>Information that may lead to the identification of respondents has been redacted.</p> </li> </ul> </li> <li> <p>Global_survey_deidentified.xlsx (de-identified responses to the global survey)</p> <ul> <li> <p>This file includes de-identified responses to the survey questions. Responses that may lead to the identification of respondents have been redacted. Free text responses to questions 6, 14 and 15 have been categorised into tasks, topics and skills, respectively. </p> </li> </ul> </li> <li> <p>Bar graphs of global survey.xlsx (quantitative responses to multiple choice questions in the global survey. For some questions, respondents could choose more than one option)</p> </li> <li> <p>Tools and resources.xlsx (Tools and resources used for biocuration work and listed by the respondents of the global survey)</p> </li> <li> <p>Biocuration training course list.xlsx (formal training courses listed by respondents of the global survey)</p> </li> </ul> <p> </p>
AI-Derived West Nile Virus Determinants Maps - 2018 Europe - Data
<p>Data for AI-Derived West Nile Virus Determinants Maps</p> <p>2018 Europe</p> <ol> <li>Original (nominal value) data</li> <li>SHAP-derived effect data </li> </ol>
Comprehensive Risk and Emergency Management Conceptual Design and Map (Response Process Big Picture)
<p>Comprehensive Risk and Emergency Management Conceptual Design and Map helps to have an insight about Risk and Emergency Planning and Management Process to better act.</p> <p>Response Process Big Picture</p>
Learning to plan with uncertain topological maps: Dataset
<p>Dataset for training and evaluation of neural path planning algorithms, for the paper "Learning to Plan with Uncertain Topological Maps"</p> <p><a href="https://arxiv.org/abs/2007.05270">https://arxiv.org/abs/2007.05270</a></p>
Data for: Model-Based Reconstruction for Simultaneous Multi-Slice T1 Mapping using Single-Shot Inversion-Recovery Radial FLASH
<p>Magnetic Resonance Imaging measurement data used in our paper about "Model-based reconstruction for simultaneous multi-slice T1 mapping using single-shot inversion-recovery radial FLASH" (DOI: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.28497">10.1002/mrm.28497</a>). The data is provided in a file format used by the BART toolbox (DOI: <a href="http://doi.org/10.5281/zenodo.592960">10.5281/zenodo.592960</a>).</p>
ScienceDex guides
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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.