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15,022 results for “differentiation”
Paired differential gene expression and splicing analyses results of 199 baseline vs. case comparisons across 100 datasets
<p>This dataset contains results from paired differential expression and differential splicing analyses as well as gene-set over-representation analysis results for 199 baseline vs. case comparisons across 100 randomly curated datasets with accompanying metadata (<a href="https://doi.org/10.1186/s12915-023-01724-w" target="_blank" rel="noopener">article</a>).<br>All results were computed using the R package <a href="https://github.com/shdam/pairedGSEA">pairedGSEA</a>, which utilized DESeq2 (Love et al., 2014), DEXSeq (Anders et al., 2012), and fgsea (Korotkevich et al., 2019).<br>See limma results here: <a href="https://doi.org/10.5281/zenodo.8162214">https://doi.org/10.5281/zenodo.8162214</a><br><br>Each .RDS file contains a list with four objects: A 'metadata' object with the metadata of the respective raw data, a 'genes' object with gene-level differential splicing and expression results, a 'gene_set' object with over-representation results, and 'experiment' with the experiment title.<br><br>The filenames follow this pattern: "[dataset ID]_[GEO accession number]_[Manually assigned comparison title].RDS".<br><br>All datasets were obtained from a local copy of the ARCHS4 v11 database of transcript counts (Lachmann et al., 2018).</p>
Generation of beta-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids
<p>This repository contains single-cell RNA-sequencing data files (raw FASTQ files generated from Illumina HiSeq sequencing) related to the article entitled "Generation of beta-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids" by Lisa Morisseau et al. (2023) published in the Molecular Omics journal (DOI: 10.1039/d3mo00050h).</p> <p> </p>
DMS measurements dataset for manuscript "Classification of Volatile Organic Compounds by Differential Mobility Spectrometry Based on Continuity of Alpha Curves"
<p>Differential mobility spectrometry dispersion plots collected for the manuscrit "Classification of Volatile Organic Compounds by Differential Mobility Spectrometry Based on Continuity of Alpha Curves". The measurement files are located in the folders that represent certain week and day of measurement. The folders containing measurements are named with the following pattern: [chemical abbreviation]_[dilution rate]. For example "2PEtOH_1o10k" means that the folder contains measurement of 2-phenylethanol diluted with propylene glycol in volumetric proportion 1/10 000. Another example is "nBuOH_1o100" - n-Butanol diluted with propylene glycol in volumetric proportion 1/100. Please find the abbreviations in the article referred.</p> <p>For the first five weeks only 1/100 dilutions were measured. The last two weeks (weeks 6 and 7) 1/10 000 dilutions were measured. However, Carvone 1/100 was measured again on week 6 due to suspicion of faulty measurements during the previous weeks. The faulty measurements were not confirmed, and thus there 25 more samples of Carvone with dilution rate 1/100.</p>
Are you scared yet? Variations to cue components elicits differential prey behavioral responses even when gape limited predators are relatively small.
Anti-predator behavior is often evoked based on measurements of risk calculated from sensory cues emanating from predators independent of physical attack. Yet, the exact sensory indices of cues used in risk assessment remain largely unknown. To examine how different predatory cue indices of information are used in risk assessment, we presented prey with various cues from sublethal gape-limited predators. Rusty crayfish (Faxonius rusticus (Girard, 1852)) were exposed to predatory odors from sublethal-sized largemouth bass (Micropterus salmoides (Lacepède, 1802)) to test effects of changing predator abundance, relative size relationships, and total predator length in flow through mesocosms. Foraging, shelter use, and movement behavior were used to measure cue effects. Foraging time depended jointly upon predator abundance and total predator size (p = 0.030). Specifically, high predator abundance resulted in decreased foraging efforts as gape ratio increased. Similarly, sheltering time depended on the interaction between predator abundance and gape ratio when predator abundance was highest (p = 0.020). Crayfish significantly increased exploration time when gape ratio increased (p = 0.010). Thus, this study shows crayfish can use different indices of predatory cues, namely total predator abundance and relative size ratios, in risk assessment but do so in context-specific ways.
MCR LTER: Nitrogen source drives differential impacts of nutrients on coral bleaching prevalence, duration, and mortality
Data are from an 18-month field experiment on the fore reef of Moorea, testing how different forms of nitrogen (nitrate vs. urea) impact coral bleaching and mortality during two mild thermal stress events in the Austral summers of 2016 and 2017. These data are associated with a manuscript currently in review at Ecosystems. Tentative mansucript title and author list are: Nitrogen source drives differential impacts of nutrients on coral bleaching prevalence, duration, and mortality Deron E. Burkepile, Andrew A. Shantz, Thomas C. Adam, Katrina S. Munsterman, Kelly E. Speare, Mark C. Ladd, Mallory M. Rice, Shelby McIlroy, Andrew J. Brooks, Russell J. Schmitt, and Sally J. Holbrook These data are part of the NSF project: RAPID: How does nutrient availability alter coral bleaching, mortality, and recovery on Moorea coral reefs? (funded wholly or part by NSF Awards OCE-1619697).
Differentiation of functional networks during long-term memory retrieval in children and adolescents
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Neural Differentiation Tracks Improved Recall of Competing Memories Following Interleaved Study and Retrieval Practice
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Violation Differentiation
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Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism
Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.
Experimental Results for the study "A Modular Hybridization of Particle Swarm Optimization and Differential Evolution"
<p>This repository contains the experiment results and R scripts to analyze the data for the study "A Modular Hybridization of Particle Swarm Optimization andDifferential Evolution", which is accepted in <em>The Genetic and Evolutionary Computation Conference</em> (GECCO) '20 conference: </p> <p>Rick Boks, Hao Wang, and Thomas Bäck. 2020. A Modular Hybridization of Particle Swarm Optimization and Differential Evolution. In <em>Genetic and Evolutionary Computation Conference Companion (GECCO ’20 Companion), July 8–12, 2020, Cancún, Mexico. </em>ACM, New York, NY, USA, 8 pages. <a href="http://https: //doi.org/10.1145/3377929.3398123">https: //doi.org/10.1145/3377929.3398123</a></p> <p>Bibtex:</p> <pre><code class="language-markdown">@inproceedings{BoksWB20, author = {Rick Boks and Hao Wang and Thomas B\"ack}, title = {{A Modular Hybridization of Particle Swarm Optimization and Differential Evolution}}, booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference, {GECCO} 2020, Canc\'un, Mexico, July 8-12, 2020}, publisher = {{ACM}}, year = {2020}, url = {https://doi.org/10.1145/3321707.3321816}, doi = {doi.org/10.1145/3377929.3398123, }</code></pre> <p><strong>Data description:</strong> we benchmarked <strong>800 </strong>different<strong> </strong>hybridizations of the Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms on a well-known continuous black-box problem set called <a href="https://coco.gforge.inria.fr/">COCO/BBOB</a>, which consists of 24 test functions. 30 independent runs are conducted for each algorithm on each problem.</p> <ul> <li>'ERT.csv': a data frame with columns DIM (5D or 20D), funcId (F1-24), algId (algorithm names), target (<span class="math-tex">\(10^{\{-8,-7, \ldots, 1\}}\)</span>), ERT (expected running time), and sd (standard deviation).</li> <li>'raw-data.csv': the running time recorded in each independent run. </li> <li>'analysis.R': the R script that generates ERT tables in the paper.</li> <li>'ecdf.R': the R script that renders the ECDF (empirical cumulative distribution function) plots in the paper.</li> </ul>
Fig. 2 in Can Aurelia (Cnidaria, Scyphozoa) species be differentiated by comparing their scyphistomae and ephyrae?
Fig. 2. Body proportions of polpys (shown as percentage). Error Bars show standard deviation. Abbreviations: see Table 2.
Fig. 1 in Can Aurelia (Cnidaria, Scyphozoa) species be differentiated by comparing their scyphistomae and ephyrae?
Fig. 1. Measurements of: A. Scyphistomae. B. Ephyrae. C. Lappets of an ephyra: the marginal lappet can be divided into rhopalial lappet and lappet stem; also visible are the rhopalial and velar canals. D. Rhopalial lappet and gastric canal forms of ephyrae in this study: 1. Rhopalial lappet forms (i.e. left lappet): (a) pointed spoon-like, (b) round spatula-like, (c) lancet-like and (d) bread knife-like; 2. Rhopalial canal forms: (a) forked, sharp points, (b) club-shaped, forked, sharp points and (c) spade-like; 3. Velar canal forms: (a) spade-like and (b) rhombic. Abbreviations: RH = rhopalium; RhC = rhopalial canal; RL = rhopalial lappet; Sta = statolith; UR = umbrella rim; VC = velar canal. Other abbreviations: see Table 2. Modified after Straehler-Pohl & Jarms (2010).
Fig. 4 in Can Aurelia (Cnidaria, Scyphozoa) species be differentiated by comparing their scyphistomae and ephyrae?
Fig. 4. Linear Discriminant Analysis based on the morphology. A. Scyphistomae (17 cultures) of Aurelia congeners. B. Ephyrae (7 of the 17 cultures) of Aurelia congeners. In each case, cultures can be distinguished from one another by different symbols and corresponding numbers (see legend).
Fig. 3 in Can Aurelia (Cnidaria, Scyphozoa) species be differentiated by comparing their scyphistomae and ephyrae?
Fig. 3. Body proportions of ephyrae (shown as percentages). Error bars show standard deviation. Abbreviations: see Table 2.
Convolutional Neural Net (CNN) models for epigenomic landscapes in epidermal differentiation - Basset architecture, classification and regression
<p>Deep learning models trained on epigenomic landscapes in keratinocyte differentiation. The models are Basset convolutional neural networks (Kelley, et al 2016). The dataset used to train these models can be found at https://doi.org/10.5281/zenodo.4062509. The file `nn.ggr.models.basset.clf.tar.gz` contains 10 cross-validated models that were pretrained using ENCODE-Roadmap trained model weights as initialization weights and also 10 cross-validated models that were initialized with random weights. Similarly, the file `nn.ggr.models.basset.regr.tar.gz` contains 10 cross-validated models that were pretrained using the classification model weights as initialization weights and also 10 cross-validated models that were initialized with random weights.</p>
Data accompanying the manuscript "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies"
<p>Dataset for figures 2, A6 and A8 for the manuscript: "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies." The dataset contains the optimal protocols for Majorana transport in both the Kitaev Chain model as well as the Proximity Coupled Semiconduncting Nanowire model obtained with Differentiable Programming and Natural Evolution Strategies. Also the Simulated Annealing (SA) optimal protocols for the Kitaev chain are included.</p>
Differentiation of human monocytes into macrophages (RNA-seq, Salmon 1.4.0, GENCODE 36)
<p>RNA-seq of differentiation of human monocytes into macrophages as described in:</p> <p>Phanstiel et al "Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development" Molecular Cell, Volume 67, Issue 6, 2017, Pages 1037-1048.e6.</p> <p>https://doi.org/10.1016/j.molcel.2017.08.006</p> <p>See publication for full author list.</p> <p>Data from publication was reprocessed by Michael Love. Paired end reads were quantified with Salmon 1.4.0 and GENCODE 36 human transcripts.</p>
Data from: Differential patterns of floristic phylogenetic diversity across a post-glacial landscape
<p>Abstract: Aim: In this study, we explored spatial patterns of phylogenetic diversity and endemism in the flora of Norway and tested hypothesized post-glacial environmental drivers of phylogenetic diversity, including temperature, precipitation, edaphic factors, and time since glacial retreat.<br> <br> Location: Norway.<br> <br> Taxon: Vascular plants (Trachaeophyta).<br> <br> Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.<br> <br> Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.<br> <br> Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.</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: Differential impact of severe drought on infant mortality in two sympatric neotropical primates
<p>Extreme climate events can have important consequences for the dynamics of natural populations, and severe droughts are predicted to become more common and intense due to climate change. We analysed infant mortality in relation to drought in two primate species (white-faced capuchins, <i>Cebus capucinus imitator,</i> and Geoffroy's spider monkeys, <i>Ateles geoffroyi</i>) in a tropical dry forest in north-western Costa Rica. Our survival analyses combine several rare and valuable long-term data sets, including long-term primate life-history, landscape-scale fruit abundance, food-tree mortality, and climate conditions. Infant capuchins showed a threshold mortality response to drought, with exceptionally high mortality during a period of intense drought, but not during periods of moderate water shortage. In contrast, spider monkey females stopped reproducing during severe drought, and the mortality of infant spider monkeys peaked later during a period of low fruit abundance and high food-tree mortality linked to the drought. These divergent patterns implicate differing physiology, behaviour, or associated factors in shaping species-specific drought responses. Our findings link predictions about the Earth's changing climate to environmental influences on primate mortality risk and thereby improve our understanding of how the increasing severity and frequency of droughts will affect the dynamics and conservation of wild primates.</p>
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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.