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1,221 results for “Aggregators”
A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [Spatial Transcriptomics]
GEO Series GSE270678. Homo sapiens. 72 samples. Type: Other.
PKM2 aggregation drives metabolism reprograming during aging process
GEO Series GSE268773. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
SUMO-targeted ubiquitin ligases (STUbLs) reduce the toxicity and abnormal transcriptional activity associated with a mutant, aggregation-prone fragment of huntingtin
GEO Series GSE115990. Saccharomyces cerevisiae. 11 samples. Type: Expression profiling by high throughput sequencing.
Targeting DNA topoisomerases or checkpoint kinases forces a shift in global protein homeostasis, triggering widespread protein aggregation
GEO Series GSE173940. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
Data for plant aggregation explained by litter traits and litter decomposition
<p>Dataset used in the article "After-life traits and interactions among decomposing litters control during-life aggregation of plant species" in Functional Ecology</p>
Differences in the free energies between the excited states of Abeta40 and Abeta42 monomers encode their aggregation propensities.
<p>The trajectory files (in dcd format) generated for the Abeta40 and Abeta42 monomer sequences using the SOP-IDP model. The data accompanies the publication "Differences in the free energies between the excited states of Abeta40 and Abeta42 monomers encode their aggregation propensities" (doi: https://doi.org/10.1101/2020.02.09.940676) by Debayan Chakraborty, John E. Straub and D. Thirumalai. The scripts for hierarchical clustering, and analysis of ensemble-averaged properties, described in the manuscript are also available. </p>
Aggregated WRF-Chem outputs in "Evaluation of cloud and precipitation response to aerosols in WRF-Chem with satellite observations"
<p>This dataset contains the aggregated output of WRF-Chem simulations by Zhoukun Liu. </p> <p>The "MOR" in file name denotes the data from simulation which used Morrison scheme and "LIN" denotes the data from simulation which used Lin scheme.</p> <p>In "MOR_110km_core.nc" and "LIN_110km_core.nc", the variables are averaged over the cloudy pixels that have the highest 10% of cloud optical thickness in each 110km scene.</p> <p>In "MOR_110km_incloud.nc" and "LIN_110km_incloud.nc", the variables are averaged over all the cloudy pixels in each 110km scene.</p> <p>"MOR_110km_R.nc" and "LIN_110km_R.nc" contains the precipitaiton characteristics from models for each 110km scene. </p> <p> </p>
Replication package for: The Equilibrium Impact of Agricultural Risk on Intermediate Inputs and Aggregate Productivity
<p>The package contains the necessary code and data to reproduce the figures and tables in Donovan (forthcoming), "The Equilibrium Impact of Agricultural Risk on Intermediate Inputs and Aggregate Productivity," Review of Economic Studies. Detailed instructions on accessing the raw data are available in the README file.</p>
Data from: Topological data analysis of biological aggregation models
We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters.
Data from: A telomerase with novel non-canonical roles: TERT controls cellular aggregation and tissue size in Dictyostelium
Telomerase, particularly its main subunit, the reverse transcriptase, TERT, prevents DNA erosion during eukaryotic chromosomal replication, but also has poorly understood non-canonical functions. Here, in the model social amoeba Dictyostelium discoideum, we show that the protein encoded by tert has telomerase-like motifs, and regulates, non-canonically, important developmental processes. Expression levels of wild-type (WT) tert were biphasic, peaking at 8 and 12 h post-starvation, aligning with developmental events, such as the initiation of streaming (~7 h) and mound formation (~10 h). In tert KO mutants, however, aggregation was delayed until 16 h. Large, irregular streams formed, then broke up, forming small mounds. The mound-size defect was not induced when a KO mutant of countin (a master size-regulating gene) was treated with TERT inhibitors, but anti-countin antibodies did rescue size in the tert KO. Although, conditioned medium (CM) from countin mutants failed to rescue size in the tert KO, tert KO CM rescued the countin KO phenotype. These and additional observations indicate that TERT acts upstream of smlA/countin: (i) the observed expression levels of smlA and countin, being respectively lower and higher (than WT) in the tert KO; (ii) the levels of known size-regulation intermediates, glucose (low) and adenosine (high), in the tert mutant, and the size defect's rescue by supplemented glucose or the adenosine-antagonist, caffeine; (iii) the induction of the size defect in the WT by tert KO CM and TERT inhibitors. The tert KO's other defects (delayed aggregation, irregular streaming) were associated with changes to cAMP-regulated processes (e.g. chemotaxis, cAMP pulsing) and their regulatory factors (e.g. cAMP; acaA, carA expression). Overexpression of WT tert in the tert KO rescued these defects (and size), and restored a single cAMP signaling centre. Our results indicate that TERT acts in novel, non-canonical and upstream ways, regulating key developmental events in Dictyostelium.
Clinical datasets related DeNoPa olfaction, cerebrospinal fluid readouts and alpha-synuclein seeding aggregation assay
<p>These dataset files are associated with the manuscript: </p> <p>Mollenhauer B*, Li J*, Schade S, Weber S, Trenkwalder C, Concha-Marambio L, Tomlinson JJ, aSCENT-PD Investigators and Schlossmacher MG. <em>Persistent Hyposmia as Surrogate for alpha-Synuclein-Linked Brain Pathology. </em>Submitted 2023</p> <p>3 files:</p> <p>Data dictionary.csv</p> <p>Baseline_cut.csv</p> <p>Time_cut.csv</p> <p>The file "Data dictionary.csv" contains description of the two data files and the variables within.</p> <p>Clinical data used for this study is from the DeNoPa Cohort, led by Dr. Brit Mollenhauer, Department of Neurology, University of Goettingen, Kassel, Germany and the Paracelsus-Elena-Klinik. See references below for additional details.</p> <p>Mollenhauer B, Trautmann E, Sixel-Döring F, Wicke T, Ebentheuer J, Schaumburg M, Lang E, Focke NK, Kumar KR, Lohmann K, Klein C, Schlossmacher MG, Kohnen R, Friede T, Trenkwalder C; DeNoPa Study Group. Nonmotor and diagnostic findings in subjects with de novo Parkinson disease of the DeNoPa cohort. Neurology. 2013 Oct 1;81(14):1226-34. doi: 10.1212/WNL.0b013e3182a6cbd5</p> <p>Concha-Marambio L, Weber S, Farris CM, Dakna M, Lang E, Wicke T, Ma Y, Starke M, Ebentheuer J, Sixel-Döring F, Muntean ML, Schade S, Trenkwalder C, Soto C, Mollenhauer B. Accurate Detection of α-Synuclein Seeds in Cerebrospinal Fluid from Isolated Rapid Eye Movement Sleep Behavior Disorder and Patients with Parkinson's Disease in the DeNovo Parkinson (DeNoPa) Cohort. Mov Disord. 2023 Apr;38(4):567-578. doi: 10.1002/mds.29329</p>
Dataset for publication Eslam El-Seidy, Matteo Sambucci, Mehdi Chougan, Yazeed A. AI-Noaimat, Mazen J. Al-Kheetan, Ilario Biblioteca, Marco Valente, Seyed Hamidreza Ghaffar. (2023). Alkali activated materials with recycled unplasticised polyvinyl chloride aggregates for sand replacement, Construction & Building Materials, doi: https://doi.org/10.1016/j.conbuildmat.2023.134188
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Dataset for publication Eslam El-Seidy, Mehdi Chougan, Matteo Sambucci, Mazen J. Al-Kheetan, Marco Valente, Seyed Hamidreza Ghaffar. (2023). Lightweight alkali-activated materials and ordinary Portland cement composites using recycled polyvinyl chloride and waste glass aggregates to fully replace natural sand. Construction & Building Materials, doi: https://doi.org/10.1016/j.conbuildmat.2023.130399
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Dataset for publication 7. Eslam El-Seidy, Mehdi Chougan, Yazeed A. AI-Noaimat, Mazen J. Al-Kheetan, Seyed Hamidreza Ghaffar. (2024). The impact of waste brick and geo-cement aggregates as sand replacement on the mechanical and durability properties of alkali–activated mortar composites, Results in Engineering, doi: https://doi.org/10.1016/j.rineng.2024.101797
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Arizona Building Aggregated Parameters: Model America v1.0 Data for 146,557 1kmx1km Grid Cells
<p>Oak Ridge National Laboratory (ORNL) has developed the Automatic Building Energy Modeling (AutoBEM) software suite to process multiple types of data, extract building-specific descriptors, generate building energy models, and simulate them on High Performance Computing (HPC) resources. For more information, see AutoBEM-related publications (<a href="https://bit.ly/AutoBEM">bit.ly/AutoBEM</a>).</p> <ul> <li>Building height</li> <li>Building footprint area</li> <li>Building total floor area</li> <li>Height-to-width ratio (height / [longest polygon vertex pair distance]) </li> <li>Number of buildings (ratio of each building type)</li> <li> Street orientation (longest polygon vertex pair's degree)</li> <li>Rooftop area density (total roof area / total cell area)</li> <li>Rooftop area density (total roof area / total cell area)</li> <li>Lambda_p (roof area / total cell area)</li> <li>Lambda_b (surface area of buildings (roof + vertical walls) / total cell area)</li> </ul> <p>Please note that certain parameters include the mean, median, mode, standard deviation, maximum, and minimum values.</p> <p>Three sets of data are provided for 2,555,153 buildings located within the boundary of Arizona in the United States:</p> <ol> <li><strong>Data (3.6MB *.csv) - Arizona 146,557 Grid Cell Locations.</strong></li> <li><strong>Data (15MB *.csv) - Arizona Building Aggregated Parameters Data developed for the Grid Cells.</strong></li> <li><strong>Data (2.5MB *.csv) - Arizona Building Aggregated Parameters Data developed for the Grid Cells (Selected Parameters).</strong></li> </ol> <p>This data is made free and openly available in hopes of stimulating any simulation-informed use case. Data is provided as-is with no warranties, express or implied, regarding fitness for a particular purpose. We wish to thank our sponsors which include Oak Ridge National Laboratory (ORNL), U.S. Dept. of Energy’s (DOE) Building Technologies Office (BTO), Office of Electricity (OE), and Biological and Environmental Research (BER).</p>
Street Spectra aggregated classifications
CSV file containing aggregated classifications for light sources data and metadata.
Data from: Grazer-induced aggregation in diatoms
<p>Data from the paper "Grazer-induced aggregation in diatoms". The paper explores the grazer-induced change in stickiness of different diatoms species. </p> <p>Data includes measurements of stickiness of different diatoms when exposed to grazer cues in different experimental set-ups including duration, dose-response and nutrient-limited experiments. </p>
Silene uralensis aggregate, circumpolar species : dataset, Novaseq Illumina RAW READS SET 2
<p>This dataset includes 16 samples of circumpolar species included in the <em>Silene uralensis</em> aggregate, sensu http://panarcticflora.org/. Forty-eight low copy nuclear genes were enriched with <em>Silene-</em>specific probes. The samples were sequenced with the Novaseq technology from the short read Illumina platform. An excel sheet with samples information is included.</p> <p>Two other datasets are associated to this one, called "Silene uralensis aggregate, circumpolar species : dataset, Novaseq Illumina RAW READS SET 1" on Zenodo 10.5281/zenodo.12699639 and "Silene uralensis aggregate, circumpolar species : dataset, Miseq Illumina RAW READS" on Zenodo 10.5281/zenodo.12688714. These three datasets belong to a study about phylogenetics in the circumpolar <em>Silene uralensis</em> aggregate. </p>
Silene uralensis aggregate, circumpolar species : dataset, Novaseq Illumina RAW READS SET 1
<p>This dataset includes 16 samples of circumpolar species included in the <em>Silene uralensis</em> aggregate, sensu http://panarcticflora.org/. Forty-eight low copy nuclear genes were enriched with <em>Silene-</em>specific probes. The samples were sequenced with the Novaseq technology from the short read Illumina platform. An excel sheet with samples information is included.</p> <p>Two other datasets are associated to this one, called "Silene uralensis aggregate, circumpolar species : dataset, Novaseq Illumina RAW READS SET 2" on Zenodo 10.5281/zenodo.12700012 and "Silene uralensis aggregate, circumpolar species : dataset, Miseq Illumina RAW READS" on Zenodo 10.5281/zenodo.12688714. These three datasets belong to a study about phylogenetics in the circumpolar <em>Silene uralensis</em> aggregate. </p> <div> <div> <div> </div> <div> <div> <div> </div> <div> <p> </p> <p> </p> </div> </div> </div> </div> </div>
Figure 1. A in Record of sleeping aggregation of the solitary aculeate potter wasp Antepipona bipustulata (de Saussure, 1855) (Hymenoptera: Vespidae: Eumeninae) from India
Figure 1. A sleeping aggregate of Antepipona bipustulata (de Saussure) on panicle tips.
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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.