Find research datasets worth reusing

opencc-by-4.0Jan 2021View details →

Data for: Free-Breathing Water, Fat, R2∗ and B0 Field Mapping of the Liver Using Multi-Echo Radial FLASH and Regularized Model-based Reconstruction (MERLOT)

Data for our manuscript with title "Free-Breathing Water, Fat, R2&lowast; and B0 Field Mapping of the Liver Using Multi-Echo Radial FLASH and Regularized Model-based Reconstruction (MERLOT)"

opencc-by-4.0Dec 2020View details →

Map 1 in Discovered online: Hibiscus hareyae sp. nov. of sect. Lilibiscus (Malvaceae), threatened in coastal thicket at Lindi, Tanzania

Map 1. Hibiscus hareyae. Global distribution map.

opencc-by-4.0Jan 2021View details →

Characterizing Technical Debt and Antipatterns in AI-Based Systems: A Systematic Mapping Study

All artifacts related to a systematic mapping study on technical debt and antipatterns in AI-based systems; the data consists of an Excel file (00-all-data.xlsx) which includes a tab for all important constructs plus a separate CSV file per construct: <ul> <li>List of primary studies (01-primary-studies.csv)</li> <li>Established types of technical debt (02-established-td-types.csv)</li> <li>New types of technical debt (03-new-td-types.csv)</li> <li>Affected software quality attributes (04-affected-qas.csv)</li> <li>Identified antipatterns (05-antipatterns.csv)</li> <li>Reported solutions to address technical debt or antipatterns (06-solutions.csv)</li> </ul>

opencc-zeroJan 2021View details →

Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event TEST_EVENT Preliminary

Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event TEST_EVENT Preliminary. A reference to these calculations can be found here: nicepaper

opencc-zeroJan 2021View details →

Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event TEST_EVENT Preliminary

openDec 2020View details →

Surface Water Loss map and Urbanization map

Surface water are severly affected by human activities, and here we defined two novel datasets, both derived from remote sensing data, to investigate the influence of urban areas on the spatial distribution of surface water loss locations across the watersheds in the United States: the Surface Water Loss map and the Urbanization map. The Surface Water Loss map is a binary map that identifies the geographical location of surface water depletion hotspots. It was obtained from the Surface Water Transitions layer of the Global Surface Water dataset (Pekel et al., 2016). Pixels values in the map are as follows: 0 = No surface water loss, 1 = Surface water loss hotspots. The Urbanization map is a binary map that shows the presence of built-up areas. It was generated from the GHS-BUILT layer from the Global Human Settlement dataset (Corbane et al., 2019). Pixels values in the map are as follows: 0 = No urban area, 1 = Urban area. References: Corbane et al. (2019). Automated global delineation of human settlements from 40 years of Landsat satellite data archives. Big Earth Data 3, 140-169, https://doi.org/10.1080/20964471.2019.1625528 Pekel et al. (2016). High-resolution mapping of global surface water and its long-term changes. Nature, 540, 418-422, https://doi.org/10.1038/nature20584

mHealth Mapping

Review of study characteristics and clinical evidence of experimental studies on mHealth apps for the management of major chronic conditions

RWD Mapping

List of RWD sources collected across Europe on hip&knee replacement, TAVI and TMVR, daVinci robot, including details on data features and variables available in the dataset

Excel mapping tools for 2020 zoonoses data reporting

The main objective of the mapping tools is to provide a simple and useable platform for Member states and other reporting countries to map their country-specific standard terminology to that used by EFSA and to enable the production of an XML file for the submission of sample or aggregated-based zoonoses monitoring data via the Data Collection Framework (DCF). The catalogues and the specific hierarchy of each data model (AMR, ESBL, PRV, FBO, AP, DS and SSD2 for Echinococcus multilocularis) are already inserted into each of the specific mapping tool. Specific Excel mapping tools corresponding to each of the seven data models are available. Dynamic or manual version of the tool can be chosen for the first six data models. The Emulti_SSD2_tool can be used to report sample-based results of Echinococcus multilocularis under the Commission Delegated Regulation (EU) 2018/772.

Code and Data Availability of the manuscript: Mapping tree diversity in the tropical forest region of Chocó-Colombia

Code and Data Availability of the manuscript: Mapping tree diversity in the tropical forest region of Chocó-Colombia In revision at Environmental Research letters.   J. Camilo Fagua1*, Patrick Jantz1, Patrick Burns1, Richard Massey1, Jeiner Y. Buitrago2, Sassan Saatchi3 and Scott J. Goetz1   1 Global Earth Observation & Dynamics of Ecosystems Lab (GEODE), School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University, Flagstaff, Arizona, US.   2 Department of Agronomy, Faculty of Agricultural Sciences, Universidad Nacional de Colombia. Bogota (Colombia).   3 Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA   *Corresponding author: J. Camilo Fagua, School of Informatics, Computing, and Cyber Systems (Building #90) 1295 S. Knoles Dr. Flagstaff, AZ 86011. Email: <a href="mailto:Camilo.Fagua@nau.edu">Camilo.Fagua@nau.edu</a>   1) The files “0_Forest_Structure_maps_in_tif” and “1_Forest_Structure_maps_in_tif” contain seven maps of forest structural metrics for the Chocó region of Colombia in the raster format .tif (a) Canopy height (CH) map: CHOCO_MAP_CH (b) 50th percentile of heights (z_50) map: CHOCO_MAP_z_50 (c) Vertical Canopy Heterogeneity (VCH) map:  CHOCO_MAP_VCH (d) Standard deviation of normalized heights (z_SD) map: CHOCO_MAP_z_SD (e) Horizontal standard deviation of canopy height (CH_ SD):  CHOCO_MAP_CH_SD (f) Horizontal heterogeneity of canopy height (CH_H): CHOCO_MAP_CH_H (g) Rumple Index of canopy height (R_INDEX): CHOCO_MAP_R_INDEX   2) The file “2_Diversity_maps_in_tif” contains five maps of forest structural metrics for the Chocó region of Colombia in the raster format .tif (a) Species richness (Richness): MAPS_MEAN_Richness (b) Shannon’s entropy index (ENS-Shannon): MAPS_MEAN_ENS_shannon (c) Simpson’s concentration index (ENS-Simpson): MAPS_MEAN_ENS_Simpson (d) Shannon diversity index (H): MAPS_MEAN_Shannon (e) Simpson diversity index (D): MAPS_MEAN_Simpson   3) The file “3_LiDAR_processing” contents data and R codes to estimate forest structural metrics from ALS-LiDAR data (.las) in an Amazon moist forest.

opencc-zeroOct 2019View details →

Data from: Retinotopic-like maps of spatial sound in primary 'visual' cortex of blind human echolocators

The functional specialisations of cortical sensory areas were traditionally viewed as being tied to specific modalities. A radically different emerging view is that the brain is organized by task rather than sensory modality, but it has not yet been shown that this applies to primary sensory cortices. Here we report such evidence by showing that primary 'visual' cortex can be adapted to map spatial locations of sound in blind humans who regularly perceive space through sound echoes. Specifically, we objectively quantify the similarity between measured stimulus maps for sound eccentricity and predicted stimulus maps for visual eccentricity in primary 'visual' cortex (using a probabilistic atlas based on cortical anatomy) to find that stimulus maps for sound in expert echolocators are directly comparable to those for vision in sighted people. Furthermore, the degree of this similarity is positively related with echolocation ability. We also rule out explanations based on top-down modulation of brain activity – e.g. through imagery. This result is clear evidence that task-specific organization can extend even to primary sensory cortices, and in this way is pivotal in our reinterpretation of the functional organisation of the human brain.

opencc-zeroFeb 2020View details →

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL-trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II ChIP-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.

opencc-zeroDec 2018View details →

Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice

To investigate the genetic architecture underlying cold tolerance during germination in rice (Oryza sativa), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch's Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The dataset representing the genotype data of 5,185 SNP markers by 257 rice accessions is presented here.

opencc-zeroDec 2015View details →

Data from: Abiotic proxies for predictive mapping of near-shore benthic assemblages: implications for marine spatial planning

Marine spatial planning (MSP) should assist managers in guiding human activities towards sustainable practices and in minimizing user-conflicts in our oceans. A necessary first step is to quantify spatial patterns of marine assemblages in order to understand the ecosystem's structure, function, and services. However, the large spatial scale, high economic value, and density of human activities in near-shore habitats often makes quantifying this component of marine ecosystems especially daunting. To address this challenge, we developed an assessment method that employs abiotic proxies to rapidly characterize marine assemblages in near-shore benthic environments with relatively high resolution. We evaluated this assessment method along 300 km of the State of Maine's coastal shelf (< 100m depth)—a zone where high densities of buoyed lobster traps typically preclude extensive surveys by towed sampling gear (i.e., otter trawls). During the summer months of 2010-2013, we implemented a stratified-random survey using a small remotely operated vehicle that allowed us to work around lobster buoys and to quantify all benthic megafauna to species. Stratifying by substrate, depth, and coastal water masses, we found that abiotic variables explained a significant portion of variance (37- 59%) in benthic species composition, diversity, biomass and economic value. Generally, the density, diversity, and biomass of assemblages significantly increased with the substrate complexity (i.e., from sand-mud to ledge). The diversity, biomass and economic value of assemblages also decreased significantly with increasing depth. Lastly demersal fish densities, sessile invertebrate densities, species diversity, and assemblage biomass increased from east to west, while the abundance of mobile invertebrates and economic value decreased, corresponding mainly to the contrasting water-mass characteristics of the Maine Coastal Current system (i.e., summertime current direction, speed, and temperature). Integrating modeled predictions with existing GIS layers for abiotic conditions allowed us to scale up important assemblage attributes to define key foundational ecological principles of MSP and to find priority regions where some bottom-disturbing activities would have minimal impact to benthic assemblages. We conclude that abiotic proxies can be strong forcing functions for the assembly of marine communities and therefore useful tools for spatial extrapolations of marine assemblages in congested (heavily used) near-shore habitats.

opencc-zeroDec 2019View details →

Data from: A place-based participatory mapping approach for assessing cultural ecosystem services in urban green space

1. Cultural Ecosystem Services (CES) encompass a range of social, cultural and health benefits to local communities, for example recreation, spirituality, a sense of place and local identity. However, these complex and place-specific CES are often overlooked in rapid land management decisions and assessed using broad, top–down approaches. 2. We use the Toolkit for Ecosystem Service Site-based Assessment (TESSA) to examine a novel approach to rapid assessment of local CES provision using inductive, participatory methods. We combined free-listing and participatory geographic information systems (GIS) techniques to quantify and map perceptions of current CES provision of an urban green space. The results were then statistically compared with those of a proposed alternative scenario with the aim to inform future decision-making. 3. By identifying changes in the spatial hotspots of CES in our study area, we revealed a spatially-specific shift toward positive sentiment regarding several CES under the alternative state with variance across demographic and stakeholder groups. Response aggregations in areas of proposed development reveal previously unknown stakeholder preferences to local decision-makers and highlight potential trade-offs for conservation management. Free-listed responses revealed deeper insight into personal opinion and context. 4. This work serves as a useful case study on how the perceptions and opinions of local people regarding local CES could be accounted for in the future planning of an urban greenspace and how thorough analysis of CES provision is important to fully-inform local-scale conservation and planning for the mutual benefit of local communities and nature.

opencc-zeroDec 2018View details →

Data from: Continent‐scale phenotype mapping using citizen scientists' photographs

Field investigations of phenotypic variation in free‐living organisms are often limited in scope owing to time and funding constraints. By collaborating with online communities of amateur naturalists, investigators can greatly increase the amount and diversity of phenotypic data in their analyses while simultaneously engaging with a public audience. Here, we present a method for quantifying phenotypes of individual organisms in citizen scientists' photographs. We then show that our protocol for measuring wing phenotypes from photographs yields accurate measurements in two species of Calopterygid damselflies. Next, we show that, while most observations of our target species were made by members of the large and established community of amateur naturalists at iNaturalist.org, our efforts to increase recruitment through various outreach initiatives were successful. Finally, we present results from two case studies: (1) an analysis of wing pigmentation in male smoky rubyspots (Hetaerina titia) showing previously undocumented geographical variation in a seasonal polyphenism, and (2) an analysis of variation in the relative size of the wing spots of male banded demoiselles (Calopteryx splendens) in Great Britain questioning previously documented evidence for character displacement. Our results demonstrate that our protocol can be used to create high quality phenotypic datasets using citizen scientists' photographs, and, when combined with metadata (e.g., date and location), can greatly broaden the scope of studies of geographical and temporal variation in phenotypes. Our analyses of the recruitment and engagement process also demonstrate that collaborating with an online community of amateur naturalists can be a powerful way to conduct hypothesis‐driven research aiming to elucidate the processes that impact trait evolution at landscape scales.

opencc-zeroMar 2020View details →

Dissecting the genetic basis of variation in Drosophila sleep using a multiparental QTL mapping resource

There is considerable variation in sleep duration, timing and quality in human populations, and sleep dysregulation has been implicated as a risk factor for a range of health problems. Human sleep traits are known to be regulated by genetic factors, but also by an array of environmental and social factors. These uncontrolled, non-genetic effects complicate powerful identification of the loci contributing to sleep directly in humans. The model system, Drosophila melanogaster, exhibits a behavior that shows the hallmarks of mammalian sleep, and here we use a multitiered approach, encompassing high-resolution QTL mapping, expression QTL data, and functional validation with RNAi to investigate the genetic basis of sleep under highly controlled environmental conditions. We measured a battery of sleep phenotypes in >750 genotypes derived from a multiparental mapping panel and identified several, modest-effect QTL contributing to natural variation for sleep. Merging sleep QTL data with a large head transcriptome eQTL mapping dataset from the same population allowed us to refine the list of plausible candidate causative sleep loci. This set includes genes with previously characterized effects on sleep and circadian rhythms, in addition to novel candidates. Finally, we employed adult, nervous system-specific RNAi on the Dopa decarboxylase, dyschronic, and timeless genes, finding significant effects on sleep phenotypes for all three. The genes we resolve are strong candidates to harbor causative, regulatory variation contributing to sleep.

opencc-zeroDec 2017View details →

Data from: Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus

The genomic architecture of barriers to gene exchange during the speciation process is poorly understood. The genomic islands model suggests that loci associated with barriers to gene exchange prevent introgression of nearby genomic regions via linkage disequilibrium. But few analyses of the actual genomic location of non-introgressing loci in closely related species exist. In a previous study Maroja et al. showed that in the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus, 50 non-introgressing loci are localized on two autosomal regions and the X chromosome, but they were not able to map the loci along the X chromosome because they used a male informative cross. Here, we localize the introgressing and non-introgressing loci on the X chromosome and reveal that all X-linked non-introgressing loci are restricted to a 50-cM region with 10 of these loci mapped to a single location. We discuss the implications of this finding to speciation.

opencc-zeroDec 2017View details →

Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge

1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a new approach for mapping fine‐scale thermal heterogeneity. We expected that vegetation would create attenuated microclimates and that the influence of vegetation structure would vary seasonally. We measured shrub volume, horizontal cover, and operative temperature (Te) in a sagebrush‐steppe habitat in Idaho, USA, at 534 microsites across two study sites of approximately 1 km2 each. We modeled relationships between habitat structure and both mean daily maximum temperature (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0001max) and mean diurnal temperature range (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0002) for each study site during summer and winter. Aerial imagery from unmanned aerial systems was used to estimate shrub volume and canopy cover at 1‐m resolution, and we applied the best fit model to map thermal heterogeneity across broader extents. 3. Increasing shrub volume and cover was associated with lower urn:x-wiley:2041210X:media:mee313008:mee313008-math-0003max and (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0004, but strengths of the relationships differed between study sites. There was considerable heterogeneity in availability of thermal refuges across sagebrush‐steppe rangelands that have traditionally been considered relatively homogeneous. 4. This technique can help ecologists and land managers identify critical thermal refuges that large‐scale climate modelling can overlook and thus contribute to an understanding of animal‐habitat relationships under changing climates and land uses.