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2,395 results for “Contrast”
LocScale-EMmerNet deep learning models for contrast optimisation of cryo-EM maps
<p>EMmerNet deep learning models for local optimisation of cryo-EM map contrast using <a href="https://gitlab.tudelft.nl/aj-lab/locscale">LocScale</a>.</p>
Dataset Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere
<p>This dataset is related to the paper "<strong>Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial <em>Pseudomonas </em>in the wheat rhizosphere</strong>" (Garrido-Sanz et al., 2023, doi: 10.1186/s40168-023-01660-5) and contains the data obtained from bacterial competition asays and plant-growth measurements.</p> <p>Sequencing data used in this study has been deposited in the NCBI Sequence Read Archive (RSA) under the BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA948847">PRJNA948847</a>.</p> <p>The R script used to analyze the data generated in the paper is available at <a href="https://github.com/dgarrs/Pprotegens_proliferation_NatComs">GitHub </a>and <a href="https://doi.org/10.5281/zenodo.8322086">Zenodo</a>.</p>
Contrasting effects of landscape composition on crop yield mediated by specialist herbivores
Open the record for dataset details and reuse information.
Data for 'Floral color and family drive contrasting plant-pollinator responses to nutrient enrichment' by Rebecca A. Nelson, Elizabeth T. Borer, and Eric W. Seabloom 2025. Collected in California grasslands 2023 and 2024.
Data for analysis of how flower color and family mediate plant-pollinator response to nutrient enrichment. Data on pollinator visitation and flower abundance were collected in three California grasslands in 2023 and 2024 from a factorial experimental in which combinations of nitrogen, phosphorus, and potassium with micronutrients were applied.
Valuing multiple ecosystem services under contrasting land use scenarios, Grand River Basin (Iowa and Missouri, USA), 2016
This dataset includes spatial and tabular data used to evaluate ecosystem service outcomes under three land-use scenarios (baseline, buffered, and productivity-based) within the Grand River Basin, spanning southwest Iowa and northwest Missouri. The dataset comprises geospatial layers and model inputs for land cover, soil characteristics, and hydrology, as well as outputs from the InVEST modeling suite for nutrient delivery ratio, sediment delivery ratio, carbon storage, and pollinator abundance. It also includes financial data used to estimate the net present value of bioenergy grassland systems, including enterprise budgets and biomass yield assumptions. The scenarios simulate the conversion of cropland to native grassland either adjacent to streams (Buffered) or on low-productivity soils (Productivity-based), and the dataset captures associated changes in land cover, ecosystem service indicators, and potential biomass production. This dataset is intended to support further research and planning related to landscape-scale conservation, ecosystem service valuation, and bioenergy development in agricultural regions.
A micro-environmental dataset exploring shrub-open climate contrasts in Cuyama Valley, California, USA,
A total of 62 Hobo micro-station data logger weather stations were deployed in Cuyama Valley, California drylands on public lands. Each station had 4 channels with two EC5 soil moisture smart sensors and two 12-Bit temperature smart sensors. The sensor arrays were deployed for two years or a total of 24 months. Key ecological variables included microsite, location, vegetation type, and extent of vegetation at each microsite. Temperature sensors were deployed 15 cm above the soil surface under the shrub canopy of Ephedra californica (sheltered from direct sunlight) or at adjacent, open paired-microsites within 1.5m of a focal shrub.Temperatures listed are in degrees Celsius. Soil moisture sensors were inserted into the soil near each temperature probe. The x,y,z columns are the width, perpendicular measure, and height in m respectively of each shrub at those microsites.
Throw trap and electrofishing data collected during 1996–2022 from the Everglades, Florida, United States for the publication "Contrasting invasion histories and effects of three non-native fishes observed with long-term monitoring data"
This dataset was used to analyze the effects of three non-native fishes in the Florida Everglades for a publication in the journal Biological Invasions. The dataset incorporates plot-level mean densities (# of individuals per square meter) of common aquatic animals collected during 1996–2022 from 17 sites across three regions of the Everglades: Taylor Slough, Shark River Slough, and Water Conservation Area 3A. Prey species included are nine common small fishes and three common decapod species (two crayfish species and grass shrimp). The dataset includes throw trap data on three predator taxa: African Jewelfish (Hemichromis letourneuxi), Mayan Cichlids (Mayaheros uruphthalmus), and sunfishes (Lepomis spp.). Annual indices of mean wet season electrofishing catch-per-unit-effort of Asian Swamp Eels (Monopterus albus/javanesis), Mayan Cichlids, sunfishes, and the three other large 'top predator' fishes (Amia calva, Lepisosteus platyrhincus, Micropterus salmoides) are included for plots where electrofishing was performed from 1997-2021. Hydrologic measures used in analyses and R code used to conduct analyses are also included.
Code and data for "Contrasting upper and deep ocean oxygen response to protracted global warming," by Frölicher et al., Global Biogeochemical Cycles, 34, e2020GB006601: https://doi.org/10.1029/2020GB006601
<p>This file contains the data and python/NCL scripts that have been used for the analysis in this paper. </p>
Dataset containing laser speckle-contrast images
<p>Dataset contains laser speckle-contrast images of human skin under various physiological tests (controlled respiration test, breath holding test, venous occlusion test).</p>
Differential associations between nucleotide polymorphisms and physiological traits in Norway spruce (Picea abies Karst.) provenances under contrasting water regimes
<p>Three datasets are provided here, yielded by a study on drought-stressed and control (well-watered) seedlings of Norway spruce (Picea abies Karst.), coming from 5 provenances distributed along a steep altitudinal gradient from 550 to 1,280 m a.s.l. in central Slovakia:</p> <p>1. physiological traits</p> <p>2. double-digest restriction-site associated sequencing data (ddRAD)</p> <p>3. nuclear microsatellite (nSSR) genotypes</p>
Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host
Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.
Dataset on soil hydraulic properties under contrasted plant covers and agricultural practices
<p>Complete dataset on the temporal variation of soil infiltrability along a homogeneous fluvisol, on bare soil or soil planted with two plant species with contrasted root systems (a Malvaceae with a tap-root system and a Poaceae with a fibrous root system), and impacted by three different management practices (burning, mowing, and chemical weeding). An original protocol, based on specific ring infiltrometers, able to measure the temporal dynamics of soil infiltrability was used. This dispositive takes into account the variability of the measurement across space.</p> <p> </p>
Micro-CT image of cell-populated collagen scaffold in the aqueous environment (contrasted with PTA)
<p>A dataset of the collagen scaffold populated with the 3T3 cells scanned in the aqueous environment using Bruker Skyscan 1276 machine (Bruker, Belgium). </p><p><strong>Scaffold production</strong></p><p>The processes of obtaining and working with collagen scaffolds were conducted in an isolated environment under sterile conditions. The collagen sponge matrix was manufactured at the Center for Collagen Innovation within the Institute of Regenerative Medicine at Sechenov University and provided to us for experimental purposes. In order to obtain the collagen, the authors utilized animal-derived materials sourced from the tendons of large horned cattle. To do this, the tendons were cleaned of excess tissues, cut into pieces with a thickness of 0.5-1 cm, and sequentially treated for 12 hours in a 0.5 M NaCl solution. Subsequently, the mass was homogenized in a 0.83 M acetic acid solution. The resulting suspension was hydrolyzed with 0.24% pepsin for 2 days, after which 1 M NaOH was added to adjust the pH to 7.5, halting the hydrolysis process. The suspension was precipitated with a 12% NaCl solution, the resulting precipitate was redissolved in 0.02 M acetic acid, and then dialyzed. To obtain collagen porous matrices (sponges), the obtained solution was neutralized using 0.1 M NaOH until a pH of 7-7.5 was reached, and the resulting suspension was lyophilized at -40°C for 2 days.</p><p>Subsequently, the collagen matrix was cut into cubes with sides measuring 0.5 cm. These cubes were placed in 15 ml test tubes filled with 70% ethyl alcohol for sterilization. The test tubes were then placed on a shaker and left in the refrigerator at +4°C for 24 hours. Afterward, the collagen matrices were removed from the alcohol and rinsed five times with 0.9% NaCl.</p><p>Following the alcohol rinse to confirm the absence of toxicity, an elution test, adapted following the ISO 10993 protocol, was conducted. To obtain collagen cube extracts, they were incubated in a cell culture medium at a volume of 1 ml per sample for 24 hours at 37°C. The 3T3 cell culture was passaged, with 5000 cells seeded in each well of a 96-well plate. After 24 hours, the cells were treated with extract at a volume of 200 µl per well and left in the incubator at 37°C for 24 hours. The following day, extracts were collected, and AlamarBlue reagent (Invitrogen, Waltham, MA, USA) was added according to the manufacturer's instructions to assess the metabolic activity of the cells. Serial dilutions of sodium dodecyl sulfate (SDS) were used as the positive control. Fluorescence intensity was measured using a Victor Nivo spectrofluorimeter (PerkinElmer, Waltham, Massachusetts, USA) at an excitation wavelength of 530 nm and an emission wavelength of 590 nm.</p><p><strong>Cell seeding</strong></p><p>After confirming the absence of cytotoxic effects, collagen sponges were seeded with the NIH 3T3 cell line at a density of 50,000 cells per sample (cubes of collagen sponge measuring 0.5 cm per side). </p><p><strong>Staining technique</strong></p><p>Fixed specimens in 10% formalin with PBS were washed after 24 hours with distilled water and after that placed in 3% phosphotungstic acid dissolved in distilled water for 24 hours and kept on the rotary shaker at room temperature. After staining, samples were washed and stored in distilled water at 5 °C. </p><p><strong>Image acquisition and reconstruction</strong></p><p>A plastic tube filled with distilled water containing the contrasted sample was placed on the sample holder in a SkyScan 1276 micro-CT (Bruker, Kontich, Belgium) and were scanned at 3 μm voxel resolution with 70 kV voltage and 200 uA source power and an aluminum filter with 1 mm of thickness. The rotation was set to 360° around the vertical axis of the sample, with two middle frames for each 0.2° angle step.</p><p>After scanning, the data were reconstructed using Bruker's NRecon software. During reconstruction, the ring artifact reduction value was set to 20% and the beam hardening correction value to 30%. After that, samples were exported as a series of 16-bit TIFF images which could be opened in the specialized software. </p>
Short and long term impacts of Covid-19 on Older childreN's healTh-Related behAviours, learning and wellbeing STudy (CONTRAST) dataset
<p>The CONTRAST study explored how the Covid-19 (lockdown) restrictions affected lives of older children in the UK, particularly how they have influenced learning, eating, physical and other activities and wellbeing.</p>
Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation
<p>When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (<em>Zonotrichia atricapilla</em>) and the white-crowned sparrow (<em>Zonotrichia leucophrys</em>) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of <em>Z. leucophrys</em>. The two <em>Z. leucophrys</em> subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species <em>Z. leucophrys</em> and <em>Z. atricapilla</em> show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between <em>Z. atricapilla</em> and <em>Z. leucophrys</em> appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.</p>
Contrasting effects of host or local specialization: widespread haemosporidians are host generalist whereas local specialists are locally abundant
<p><strong>Aim: </strong>Despite the wide distribution of many parasites around the globe, the range of individual species varies significantly even among phylogenetically related taxa. Since parasites need suitable hosts to complete their development, parasite geographical and environmental ranges should be limited to communities where their hosts are found. <span><span>Parasites may also suffer from a trade-off between being locally abundant or widely dispersed</span></span>. We hypothesize that the geographical and environmental ranges of parasites are negatively associated to their host specificity and their local abundance.</p> <p><strong>Location: </strong>Worldwide</p> <p><strong>Time period: </strong>2009 to 2021</p> <p><strong>Major taxa studied: </strong>Avian haemosporidian parasites</p> <p><strong>Methods:</strong> We tested these hypotheses using a global database which comprises data on avian haemosporidian parasites from across the world. For each parasite lineage, we computed five metrics: phylogenetic host-range, environmental range, geographical range, and their mean local and total number of observations in the database. Phylogenetic generalized least squares models were ran to evaluate the influence of phylogenetic host-range and total and local abundances on geographical and environmental range. In addition, we analysed separately the two regions with the largest amount of available data: Europe and South America.</p> <p><strong>Results: </strong>We evaluated 401 lineages from 757 localities and observed that generalism (i.e. phylogenetic host range) associates positively to both the parasites' geographical and environmental ranges at global and Europe scales. For South America, generalism only associates with geographical range. Finally, mean local abundance (mean local number of parasite occurrences) was negatively related to geographical and environmental range. This pattern was detected worldwide and in South America, but not in Europe.</p> <p><strong>Main Conclusions:</strong> We demonstrate that parasite specificity is linked to both their geographical and environmental ranges. The fact that locally abundant parasites present restricted ranges, indicates a trade-off between these two traits.<span><span> This trade-off, however, only becomes evident when sufficient heterogeneous host communities are considered.</span></span></p>
EBSD data (with patterns) for indexing of contrast inverted patterns
<p>Data needed to reproduce results from paper:</p> <p>Grzegorz Cios, Aimo Winkelmann, Gert Nolze, Tomasz Tokarski, Benedykt R. Jany, Piotr Bała,<br>EBSD and TKD analyses using inverted contrast Kikuchi diffraction patterns and alternative measurement geometries,<br>Ultramicroscopy, 2024, 114055, ISSN 0304-3991,<br>https://doi.org/10.1016/j.ultramic.2024.114055.<br>(https://www.sciencedirect.com/science/article/pii/S0304399124001347)</p> <p><br>Abstract: Electron backscatter diffraction (EBSD) patterns can exhibit Kikuchi bands with inverted contrast due to anomalous absorption. This can be observed, for example, on samples with nanoscale topography, in case of a low tilt backscattering geometry, or for transmission Kikuchi diffraction (TKD) on thicker samples. Three examples are discussed where contrast-inverted physics-based simulated master patterns have been applied to find the correct crystal orientation. As first EBSD example, self-assembled gold nanostructures made of Au fcc and Au hcp phases on single-crystal germanium were investigated. Gold covered about 12% of the mapped area, with only two thirds being successfully interpreted using standard Hough-based indexing. The remaining third was solved by brute force indexing using a contrast-inverted master pattern. The second EBSD example deals with maps collected at a non-tilted surface instead of the commonly used 70° tilted one. As TKD example, a jet-polished foil made of duplex stainless steel 2205 was examined. The thin part close to the hole edge producing normal-contrast patterns were standard indexed. The areas of the foil that become thicker with increasing distance from the edge of the hole produce contrast-inverted patterns. They covered three times the evaluable area and were successfully processed using the contrast-inverted master pattern. In the last example, inverted patterns collected at a non-tiled sample were mathematically inverted to normal contrast, and Hough/Radon-based indexing was successfully applied.<br>Keywords: EBSD; TKD; Contrast inversion; Topography; Kikuchi diffraction</p>
Dataset related to article "Performance of dual-energy subtraction in contrast-enhanced mammography for three different manufacturers: a phantom study"
<p><span>The dataset provided here contains the raw data used in the study discussed in this article. The primary objective of the study was to conduct a comparative analysis of the performance of dual energy subtraction (DES) images acquired using contrast-enhanced mammography (CEM) systems produced by three different manufacturers. The comparison, facilitated by a CEM-specific phantom, focused on the assessment of radiation dose and image quality.</span></p> <p><span>Composed of three separate CSV files, the dataset is structured as follows:</span></p> <p><span>1) "Dose-related data": This file provides exposure parameters (including A/F combination, tube voltage and exposure) and the corresponding mean glandular dose (MGD for low-energy (LE) and high-energy (HE) images. Data are given for each CEM system and automatic exposure mode (AEC).</span></p> <p><span>2) "CNR-related data": Encapsulated in this file are data extracted from the phantom DES images. These include measurements of the mean pixel value (MPV) for each iodinated contrast detail, as well as the MPV and standard deviation (SD) for the surrounding background. These data were used to calculate the contrast-to-noise ratio (CNR) for the iodinated contrast details.</span></p> <p><span>3) “Residual CNR data”: This file includes MPV and SD data extracted from phantom DES images, which were useful for calculating the residual CNR after cancellation of the normal background tissue by the DES algorithm.</span></p>
Figure 7 in Looks can be deceiving: contrasting temperature characteristics of two morphologically similar kelp species co-occurring in the Arctic
Figure 7: Effect of temperature on the relative abundance of different ontogenetic stages during gametogenesis of Laminaria digitata (left) and Hedophyllum nigripes (right) in a temperature gradient after seven days (above) and 14 days (below; mean of n = 3–4; SD not shown for clarity). Only the most developed stage was counted per female gametophyte. †All gametophytes died.
Figure 6 in Looks can be deceiving: contrasting temperature characteristics of two morphologically similar kelp species co-occurring in the Arctic
Figure 6: Sex ratio (female:male) of gametophytes of Laminaria digitata (left) and Hedophyllum nigripes (right) after 14 days in temperature gradients between 0 and 25 °C (L. digitata) and 22 °C (H. nigripes) (n = 4, mean ± SD). Different letters denote significant differences among temperatures within each species (L. digitata: Kruskal–Wallis test with multiple p-value comparison; H. nigripes: one-way ANOVA with Tukey's post hoc test). Please note that the marked deviation from an expected initial 50:50 ratio was due to applied seeding methods. †All gametophytes died.
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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.