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464 results for “high density”
Improving wheat yield prediction using secondary traits and high-density phenotyping under heat stressed environments
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Litterbag mass and chemistry:FAB 1 : Forests and Biodiversity Experiment - High density diversity
A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of species a
High-density Chemical Cross-linking for Modeling Protein Interactions
<p>Supporting parameters, IMP code and data for Mintseris & Gygi "High-density Chemical Cross-linking for Modeling Protein Interactions" <em>PNAS</em></p> <p><strong>Parameter Files</strong></p> <p>These parameter files were used for running PIXL to produce the data described in the paper</p> <p><strong>Fasta Sequence Databases</strong></p> <p>These sequence databases were used for running PIXL to produce the data described in the paper</p> <p><strong>IMP</strong></p> <p>Code, intermediate data, and final localization densities for IMP proteasome modeling as described in the paper See IMP directory README</p>
On the Fourier Contribution of Strong Current Sheets to the High-Frequency Magnetic Power Spectral Density of the Solar Wind
<p>These two tab-delimited files list the Universal Times at which the WIND spacecraft and the MMS spacecraft encounter strong current sheets in the solar wind.</p>
HLA Class II specificity assessed by high-density peptide microarray interactions
<p>The ability to predict and/or identify MHC binding peptides is an essential component of T cell epitope discovery; something that ultimately should benefit the development of vaccines and immunotherapies. In particular, MHC class I (MHC-I) prediction tools have matured to a point where accurate selection of optimal peptide epitopes is possible for virtually all MHC-I allotypes; in comparison, current MHC class II (MHC-II) predictors are less mature. Since MHC-II restricted CD4+ T cells control and orchestrate most immune responses, this shortcoming severely hampers the development of effective immunotherapies. The ability to generate large panels of peptides and subsequently large bodies of peptide-MHC-II interaction data is key to the solution of this problem; a solution that also will support the improvement of bioinformatics predictors, which critically relies on the availability of large amounts of accurate, diverse and representative data. Here, we have used recombinant HLA-DRB1*01:01 and HLA-DRB1*03:01 molecules to interrogate high-density peptide arrays, <em>in casu</em> containing 70,000 random peptides in triplicates. We demonstrate that the binding data acquired contains systematic and interpretable information reflecting the specificity of the HLA-DR molecules investigated. Collectively, with a cost per peptide reduced to a few cents combined with the flexibility of recombinant HLA technology, this poses an attractive strategy to generate vast bodies of MHC-II binding data at an unprecedented speed and for the benefit of generating peptide-MHC-II binding data as well as improving MHC-II prediction tools.</p>
The High-Latitude Extension of Jupiter's Io Torus: Electron Densities Measured by Juno Waves
<p>This is the supporting data set for the paper by the same title published in AGU JGR Space Physics, <a href="https://doi.org/10.1029/2021JA029195">10.1029/2021JA029195</a></p> <p><strong>Abstract</strong></p> <p>We present Jovian electron densities measured by the Juno Waves instrument at high-latitudes on magnetic field lines threading the Io torus using the first 29 orbits of the Juno mission. We infer electron densities from characteristic frequency cutoffs and resonances in plasma wave spectra. There are often times when more than one of the characteristic frequency of the plasma can be identified, whose consistency provides more credibility to the plasma density estimates. The majority of density measurements are on magnetic field lines threading the Io torus and intersecting Jupiter's ionosphere between Io's M-shell and the auroral main oval, but there is evidence of density dropouts near and within the auroral oval, which may be important in auroral particle acceleration. Sharp density gradients are found near the inner edge of the Io torus region. These observations demonstrate the extension of elevated Io torus densities along field lines to higher latitudes. </p> <p><strong>Key Points</strong></p> <ul> <li>We present Jovian electron densities at high-latitudes on magnetic field lines connected to the Io torus and plasma sheet</li> <li>Sharp density gradients are found near the inner edge of the Io torus M-shell</li> <li>Our densities are consistent with partial electron densities measured by Juno's Jovian Auroral Distributions Experiment</li> </ul>
Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes
Background <p>Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree.</p> Results <p>The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they've been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree.</p> Conclusions <p>We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.</p>
Data from: The arboreal ants of a Neotropical rainforest show high species density and comprise one third of the ant fauna
<p>In tropical rainforests, the ant community can be divided into ground and arboreal faunas. Here we report a thorough sampling of the arboreal ant fauna of La Selva Biological Station, a Neotropical rainforest site. Forty-five canopy fogging samples were centered around large trees. Individual samples harbored an average of 35 ant species, with up to 55 species in a single sample. The fogging samples yielded 163 observed species total, out of a statistically estimated 199 species. We found no relationship between within-sample ant richness and focal tree species, nor were the ant faunas of nearby trees more similar to each other than the faunas of widely spaced trees. Species density was high and beta diversity was low: a single column of vegetation typically harbors at least a fifth of the entire arboreal ant fauna. Considering the entire fauna, based on 23,326 species occurrence records using a wide variety of collecting methods, 182 of 539 observed species (196 of 605, estimated statistically) were entirely arboreal. The arboreal ant fauna is thus about a third of the total La Selva ant fauna, a robust result because inventory completeness was similar for ground and arboreal ants. The taxonomic history of discovery of the species that make up the La Selva fauna reveals no disproportionately large pool of undiscovered ant species in the canopy. The "last biotic frontier" for tropical ants has been the rotten wood, leaf litter, and soil of the forest floor.</p>
Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
<p>The mapping population consists of 166 recombinant inbred lines (RILs) derived from a cross between HD3086 and HI1500.</p> <p><strong>Phenotypic data</strong><br>The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance.</p> <p><strong>Genotypic data</strong><br>DNA was extracted from 21 days old seedlings using CTAB method (Murray and Thompson, 1980). Genomic DNA quality was determined using 0.8% agarose gel electrophoresis with λ DNA as the standard and quantified using nanodrop. The 35K SNP Axiom breeders' array was used for genotyping of parents and the RILs population.</p>
EEAR-Clim: A high density observational dataset of daily precipitation and air temperature for the Extended European Alpine Region
<p>Data, metadata and code for paper published in Earth System Science Data:</p> <p>A high density observational dataset of daily precipitation and air temperature for the Extended Alpine Region</p> <p> </p> <p><strong>Code </strong>(working copy all written in R statistical software): scripts.zip</p> <ul> <li>to read and process data in from different sources</li> <li>to perform intra and inter-stations quality control</li> <li>to perform break detection and homogenization</li> <li>to read results of quality control and homogenization</li> </ul> <p><strong>Data</strong>:</p> <ul> <li>Daily time series of air temperature (mean, minimum and maximum) and precipitation as .zip files, grouped by data provider.</li> <li>Information on column content is provided in separate files "data_readme.txt"</li> <li>about 10000 stations from Italy, France, Switzerland, Austria, Germany, Slovenia, Croatia, Bosnia-Herzegovina, Czech Republic, Slovakia and Hungary</li> <li>Meta data (code, name, longitude, latitude, elevation, measurements availability for each variable, starting date, ending date) in "metadata.zip", including a file for each data provider</li> <li>If you <strong>use the data you agree to adhere to the respective data provider's terms</strong> as listed in "License.pdf"</li> <li>The license terms especially (and additionally to any other terms of the single data providers) include: <strong>Attribution</strong> — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. [from <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>] </li> </ul> <p> </p> <p><strong>Version history:</strong></p> <p>v1.0: initial upload</p> <p>v2.0: update of data policies; addition of France and Croatia time series</p>
Jupyter Notebooks for "Evaluating CephFS Performance vs. Cost on High-Density Commodity Disk Servers" 10.1007/s41781-021-00071-1
<p>Jupyter notebooks used to create plots in article DOI 10.1007/s41781-021-00071-1</p> <p>Title "Evaluating CephFS Performance vs. Cost on High-Density Commodity Disk Servers"</p> <p>Journal "Computing and Software for Big Science"</p>
Cortical Reorganization after Rehabilitation in a Patient with Conduction Aphasia Using High-Density EEG
<p>Conduction aphasia is a language disorder occurred after a left-brain injury. It is characterized<br> by fluent speech production, reading, writing and normal comprehension, while speech repetition is<br> impaired. The aimof this study is to investigate the cortical responses, induced by language activities,<br> in a sub-acute stroke patient affected by conduction aphasia before and after an intensive speech therapy<br> training. The patientwas examined by usingHigh-Density Electroencephalogram(HD-EEG) examination,<br> while was performing language tasks. The patient was evaluated at baseline and after two months<br> after rehabilitative treatment. Our results showed that an intensive rehabilitative process, in sub-acute<br> stroke, could be useful for a good outcome of language deficits. HD-EEG results showed that left<br> parieto-temporol-frontal areas were more activated after 2 months of rehabilitation training compared<br> with baseline. Our results provided evidence that an intensive rehabilitation process could contribute to<br> an inter- and intra-hemispheric reorganization.</p>
Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere
<p>Simulation input files and data sets of "Effect of density gradients on the generation of a highly energetic and strongly collimated proton beam from a laser irradiated Gaussian-shaped Hydrogen microsphere" by A. Bhagawati et al.</p> <p>Simulation code: </p> <p>Picpsi3D, Version 0.1 beta 11<br> (c) Copyright Kartik Patel, L & PTD, BARC<br> </p>
Data for 'Normalization procedure for obtaining the local density of states from high-bias scanning tunneling spectroscopy'
<p>This folder contains all the raw data needed to generate the figures in the paper '<em>Normalization procedure for obtaining the local density of states from high-bias scanning tunneling spectroscopy.</em>' The data are seperated by the figures in which they appear, with a text folder in each folder that contains any relevant additional information. </p>
High-density genomic characterization of native Croatian sheep breeds
<p class="MsoNormal"><span>A recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (F<sub>ROH > 2 Mb</sub>) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds.</span></p>
High-density electrode recordings reveal strong and specific connections between retinal ganglion cells and midbrain neurons.
<p>This is the source file to be use for debugging problems on your own set-up. This files is a good example to both the repository provided for visual processing on the Kremow GitHub:</p> <p>https://github.com/KremkowLab/Axon-on-Neuropixels-in-Kilosort</p> <p>https://github.com/KremkowLab/tangential_recording</p>
High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan
<p>Understanding patterns of genetic structure and adaptive variation in natural populations is crucial for informing conservation and management. Past genetic research using 11 microsatellite loci identified six genetic stocks of lake whitefish (<em>Coregonus clupeaformis</em>) within Lake Michigan, USA. However, ambiguity in genetic stock assignments suggested those neutral microsatellite markers did not provide adequate power for delineating lake whitefish stocks in this system, prompting calls for a genomics approach to investigate stock structure. Here, we generated a dense genomic dataset to characterize population structure and investigate patterns of neutral and adaptive genetic diversity among lake whitefish populations in Lake Michigan. Using Rapture sequencing, we genotyped 829 individuals collected from 17 baseline populations at 197,588 SNP markers after quality filtering. Although the overall pattern of genetic structure was similar to the previous microsatellite study, our genomic data provided several novel insights. Our results indicated a large genetic break between the northwestern and eastern sides of Lake Michigan, and we found a much greater level of population structure on the eastern side compared to the northwestern side. Collectively, we observed five genomic islands of adaptive divergence on five different chromosomes. Each island displayed a different pattern of population structure, suggesting that combinations of genotypes at these adaptive regions are facilitating local adaptation to spatially heterogenous selection pressures. Additionally, we identified a large linkage disequilibrium block of ~8.5 Mb on chromosome 20 that is suggestive of a putative inversion but with a low frequency of the minor haplotype. Our study provides a comprehensive assessment of population structure and adaptive variation that can help inform management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management. </p>
Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation
<p>High-density lipoprotein (HDL) nanoparticles promote endothelial cell (EC) function and suppress inflammation, but their utility in treating EC dysfunction has not been fully explored. Here, we describe a fusion protein named ApoA1-ApoM (A1M) consisting of apolipoprotein A1 (ApoA1), the principal structural protein of HDL that forms lipid nanoparticles, and ApoM, a chaperone for the bioactive lipid sphingosine 1-phosphate (S1P). A1M forms HDL-like particles, binds S1P, and is signaling competent. Molecular dynamic simulations showed that the S1P-bound ApoM moiety in A1M efficiently activated the EC surface receptors. Treatment of human umbilical vein endothelial cells (HUVECs) with A1M-S1P stimulated barrier function either alone or cooperatively with other barrier-enhancing molecules, including the stable prostacyclin analog iloprost, and suppressed cytokine-induced inflammation. A1M-S1P injection into mice during sterile inflammation suppressed neutrophil influx and inflammatory mediator secretion. Moreover, systemic A1M administration led to a sustained increase in circulating HDL-bound S1P and suppressed inflammation in a murine model of LPS-induced endotoxemia. We propose that A1M administration may enhance vascular endothelial barrier function, suppress cytokine storm, and promote resilience of the vascular endothelium.</p>
Dataset for the paper "Ocean wave energy harvesting with high energy density and self-powered monitoring system"
<p>Dataset for the paper "Ocean wave energy harvesting with high energy density and self-powered monitoring system“.</p>
Supplementary Data for "Identifying Promising Metal−Organic Frameworks for Heterogeneous Catalysis via High-Throughput Periodic Density Functional Theory"
<p>Supplementary data to accompany:</p> <p>A.S. Rosen, J.M. Notestein, R.Q. Snurr. "Identifying Promising Metal-Organic Frameworks for Heterogeneous Catalysis via High-Throughput Periodic Density Functional Theory", J. Comput. Chem (2019). DOI: 10.1002/jcc.25787</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.