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655 results for “constrain”
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
<p>Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet, the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao – an outcrossing, long-lived tree species that is the source of chocolate – to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160 thousand SVs, which together cover eight times more of the genome than SNPs and short indels (125 Mb vs. 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination.<br> Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs on this important local adaptation trait. Beyond revealing new empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao. </p>
Lunar heat flow constrained from Chang'E-2 Microwave Radiometer and Diviner observations at the Moon's south pole
<p>This data repository includes the Chang'E-2 microwave radiometer data which is provided by the Ground Research and Application System of Chinese Lunar Exploration Program.</p>
Fine seismic imaging of the Lianhuashan fault zone, South China, and tectonic implications – Constrained by ambient noise adjoint tomography
<p>The Rayleigh wave group velocity dispersion and the cross-correlation functions used in the study "Fine seismic imaging of the Lianhuashan fault zone, South China, and tectonic implications – Constrained by ambient noise adjoint tomography".</p>
Positive genetic covariance and limited thermal tolerance constrain tropical insect responses to global warming
<p>Tropical ectotherms are particularly vulnerable to global warming because their physiologies are assumed to be adapted to narrow temperature ranges. This study explores three mechanisms potentially constraining thermal adaptation to global warming in tropical insects: 1. tradeoffs in genotypic performance at different temperatures (the jack-of-all-trades hypothesis) 2. positive genetic covariance in performance, with some genotypes performing better than others at viable temperatures (the 'winner and 'loser genotypes hypothesis) or 3. limited genetic variation as the potential result of relaxed selection and the loss of genes associated with responses to extreme temperatures (the gene decay hypothesis). We estimated changes in growth and survival rates at multiple temperatures for three tropical rain forest insect herbivores (<i>Cephaloleia</i> rolled-leaf beetles, Chrysomelidae). We reared 2746 individuals in a full-sibling experimental design, at temperatures known to be experienced by this genus of beetles in nature (<i>i.e.</i>, 10-35°C). Significant genetic covariance was positive for 16 traits, supporting the 'winner and 'loser genotypes hypothesis. Only two traits displayed negative cross-temperature performance correlations. We detected a substantial contribution of genetic variance in traits associated with size and mass (0-44%), but low heritability in plastic traits such as development time (0-6%) or survival (0-4%). Lowland insect populations will most likely decline if current temperatures increase beyond 2°C. It is concerning that local adaption is already lagging behind current temperatures. The consequences of maintaining the current global warming trajectory would be devastating for tropical insects. However, if humans can limit or slow warming, many tropical ectotherms might persist in their current locations, and potentially adapt to warmer temperatures.</p>
Constrained Spherical Deconvolution Tractography Reveals Cerebello-Mammillary Connections in Humans
<p>According to the classical view, the cerebellum has long been confined to motor control physiology; however, it has now become evident that it exerts several non-somatic features other than the coordination of movement and is engaged also in the regulation of cognition and emotion. In a previous diffusion-weighted imaging-constrained spherical deconvolution (CSD) tractography study, we demonstrated the existence of a direct cerebellum-hippocampal pathway, thus reinforcing the hypothesis of the cerebellar role in non-motor domains. However, our understanding of limbic-cerebellar interconnectivity in humans is rather sparse, primarily due to the intrinsic limitation in the acquisition of in vivo tracing. Here, we provided tractographic evidences of connectivity patterns between the cerebellum and mammillary bodies by using whole-brain CSD tractography in 13 healthy subjects. We found both ipsilateral and contralateral connections between the mammillary bodies, cerebellar cortex, and dentate nucleus, in line with previous studies performed in rodents and primates. These pathways could improve our understanding of cerebellar role in several autonomic functions, visuospatial orientation, and memory and may shed new light on neurodegenerative diseases in which clinically relevant impairments in navigational skills or memory may become manifest at early stages.</p>
A highly accurate and constrained density functional obtained with differentiable programming
<p>Set of data and codes needed to reproduce the manuscript : "A highly accurate and constrained density functional obtained with differentiable programming"</p>
Data for "Evaluating vertical velocity retrievals from vertical vorticity equation constrained dual-Doppler analysis of real, rapid-scan radar data"
<p>This archive contains data from the Rapid Scanning X-Band Polarimetric (RaXPol) radar, Atmospheric Imaging Radar (AIR), and Shared Mobile Atmospheric Research and Teaching radar (SMART-R) for 4 September 2018 in central Oklahoma. This is a rapid-scan dual-Doppler dataset of a convective storm. RaXPol and AIR were the two radars that can be used for dual-Doppler retrievals and the SMART-R data can be used for verification of vertical velocity.</p> <p>The AIR and RaXPol data have been quality controlled and are provided in cfRadial format. The SMART-R data has not been quality controlled and are available in its raw data format. All data can be read using the Python ARM Radar Toolkit.</p> <p>This dataset was used for the manuscript:</p> <p>Gebauer, J. G., A. Shapiro, C. K. Potvin, N. A. Dahl, M. I. Biggerstaff, and A. A. Alford, 2021: Evaluating vertical velocity retrievals from vertical vorticity equation constrained dual-Doppler analysis of rapid-scan radar data. <em>J. Atmos. Meas. Tech., </em>in review.</p>
Deploying Near Optimal Delay Constrained Paths with Segment-Routing in Massive Scale Networks
<p>Dataset consisting of 5 large topologies used for the evaluation of Best2cop - multi-area version. <br> <br> The topologies themselves are written as a list of edges following the format : <br> <strong>source target delay cost area</strong> <br> "cost" being the IGP cost of the link, and "area", the IGP area to which the edge belongs.</p> <p>Each topology has a descriptive file showcasing some of the network's properties (density, diameter...) as well as an HTML file allowing to see the topology on an actual world map. Note that while we consider the road infrastructure, the links are represented in an abstract fashion for readability purposes.</p> <p> </p>
Constrained Injective Mapping Benchmark
<p>We are glad to release the benchmark dataset in our Siggraph Asia 2021 paper <a href="https://duxingyi-charles.github.io/publication/optimizing-global-injectivity-for-constrained-parameterization/">Optimizing Global Injectivity for Constrained Parameterization</a>. The dataset is used to test various methods on their ability to recover an injective mapping from a non-injective initial mapping while keeping a group of positional constraints in place. The dataset includes <em>1791 </em>triangle mesh examples. Each example consists of an input rest mesh, an initial mesh, several constrained vertices (called handles), and a ground truth injective mapping obtained from the <a href="https://zenodo.org/record/3827969#.YVsE55qZOPp">Locally Injective Mappings Benchmark</a>.</p> <p>For reference, we also share our method's results on the examples in Constrained-Injective-Mappings-Result.zip.</p> <p>We hope that our dataset offers a benchmark for future research in this area.</p>
Figure 3. Strict consensus trees from the constrained analyses. First constrained analysis forcing a in Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria)
Figure 3. Strict consensus trees from the constrained analyses. First constrained analysis forcing a monophyletic Silesauridae apart from the 'traditional ornithischians'. Abbreviations: Aphan, Aphanosauria; Herrer, Herrerasauridae. Silhouettes are based on artwork by Márcio L. Castro, Gabriel Lio, Rodrigo T. Müller, Maurício S. Garcia, John Sibbick and Douglas M. Heman.
Figure 4. Second constrained analysis forcing a in Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria)
Figure 4. Second constrained analysis forcing a monophyletic Ornithoscelida. Abbreviations: Aphan, Aphanosauria; Herrer, Herrerasauridae. Silhouettes are based on artwork by Márcio L. Castro, Gabriel Lio, Rodrigo T. Müller, Maurício S. Garcia, John Sibbick and Douglas M. Heman.
Experimental and observation data used for the paper entitled "Method to constrain the complex refractive index of ambient black carbon aerosol from their observed distribution of the complex forward-scattering amplitude"
<p>The complex forward-scattering amplitude data used for Figure 6 and 7 of the paper entitled "Method to constrain the complex refractive index of ambient black carbon aerosol from their observed distribution of the complex forward-scattering amplitude" by N. Moteki et al.</p>
Toward a Better Understanding of the Global Ocean Copper Distribution and Speciation through a Data-constrained Model
<p>MATLAB codes for a global marine copper model under the AWESOME OCIM framework. </p> <p>Prepared for manuscript submission.</p>
Constrained trait variation by water availability modulates radial growth in evergreen and deciduous Mediterranean oaks
<p>Data supporting the findings of the study "Constrained trait variation by water availability modulates radial growth in two coexisting Mediterranean oaks"</p>
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a in On the first Baryonychinae (Theropoda, Spinosauridae) teeth from South America
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a dentition-based data matrix (tree length = 1318; CI = 0.198; RI = 0.466), Bremer support is displayed below each node; LPUFS specimens (bold) are recovered within the Spinosauridae clade. Theropod silhouette from phylopic.org, see acknowledgements.
Supplemental Data Set for "Constraining Changes in Surface Dust Thickness on Mars Using Diurnal Surface Temperature Observations from EMIRS"
<p>Supporting data set for manuscript "Constraining Changes in Surface Dust Thickness on Mars Using Diurnal Surface Temperature Observations from EMIRS". Provides the binned and averaged EMIRS surface temperatures acquired before and after the January 2022 dust storm for each region of interest to derive changes in surface dust thickness.</p>
Fiber Orientation Estimation from X-ray Dark Field Images of Fiber Reinforced Polymers using Constrained Spherical Deconvolution: Data
<p>The data was simulated in GATEv8.0. The macro's and other files for the simulation can be found in the folders: Sim_50_40, Sim80_60 and Sim90_70. Here, the different files to perform the simulation are given, as well as the output data, found in the folders Flats and Projs (flatfields and projections) in the form of a csv-file. The csv-file contains 5000 rows (one for each image), and each row contains a flattened 450x450 image.</p> <p>The files for visualization of the fiber directions are given in the folder MRtrix. This folder contains the reconstructed scatter magnitudes and their respective directions in a mat-file. On this set of directions the constrained spherical deconvolution is applied using the sf_dirs.mif, sf_mask.mif, sf_response.mif and data.mif files. This returns the orientation density function in each voxel as output (odf_csd_14.mif). An alternative approach is performing a Funk-Radon transform on the coefficients of the scatter function (data_coeffs_10.mif) to obtain odf_frt_10.mif.</p> <p>Using a peak finding algorithm the fiber orientations are extracted from these odf-files and written to peaks_x.mif files, with or without a threshold (10% of largest amplitude).</p>
Dataset and analyses for: Mediolateral foot placement control can be trained: Older adults learn to walk more stable, when ankle moments are constrained
<p>Here you'll find the dataset and analyses belonging to the publication "Mediolateral foot placement control can be trained: Older adults learn to walk more stable, when ankle moments are constrained". Older adults performed 8 sessions of treadmill walking, of which 6 sessions comprised of a training on a shoe constraining ankle moment control (LesSchuh). We evaluated whether participants improved their foot placement control and gait stability as a result of the training. Kinematic data of the feet and thorax were collected.</p> <p>For more detail on the folders' contents please see "Read me.docx".</p>
Fully Constrained Acetabular Liner vs. Dual Mobility Hip Joint in the Surgical Treatment of Metastatic Bone Disease of the Hip
ClinicalTrials.gov study NCT05461313. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Resistance Training and Constrained Induced Movement Therapy on Upper Extremity Motor Recovery and Quality of Life in Sub-acute Stroke Patients
ClinicalTrials.gov study NCT06933147. IPD Sharing: NO. Countries: 1. Publications: 2.
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.