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2,326 results for “clusters”
Clusters of interactions common between the Parkinson's disease map and the Ageing map
<p>This set of files was generated using the script demonstrating the use of MINERVA Net repository.</p> <p>The script is available under:</p> <p><a href="https://gitlab.lcsb.uni.lu/minerva/api-scripts/-/blob/master/R/API-minervanet.R">https://gitlab.lcsb.uni.lu/minerva/api-scripts/-/blob/master/R/API-minervanet.R</a></p> <p>The diagrams should be opened with the CellDesigner software (<a href="https://www.celldesigner.org/">https://www.celldesigner.org/</a>).</p>
Analysis of constrained simulations of the Coma cluster and of its surrounding cosmic web
<p>The advent of wide-area spectroscopic galaxy surveys has allowed us to start investigating the properties of the filaments of the cosmic web. How filaments connect to clusters and how these connections impact cluster evolution is a hot topic in astrophysics, of interest for ongoing experiments and future facilities (from both the gas phase perspective, e.g. eROSITA, and the galaxy distribution, e.g. Euclid). The average connectivity (number of connected filaments) of a few observed and simulated clusters has been measured and it has been found that it scales with cluster mass. We applied a cosmic web detection algorithm (DisPerSE) to the Sloan Digital Sky Survey (SDSS) to detect the filaments from the galaxy distribution. We then detected three secure filaments connecting to the Coma cluster. This discovery lead to the developing of a further investigation based on constrained numerical simulations, which allow us to reproduce in detail a portion of the nearby Universe, recreating observed clusters including Coma. We analysed these simulations, with the aim of studying the evolution of the filaments around Coma throughout cosmic history and determining the impact of matter accretion channeled through these structures on the evolution of the Coma cluster. In this talk I will review our previous results and introduce the findings we obtained with the study of our constrained numerical simulations.</p>
Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 1
<p>Part one of the data used for the generation of the article <em>Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.</em></p>
Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 2
<p>Part 2 of data for the article <em>Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.</em></p>
A crowd clustering prediction and captioning technique for public health emergencies
<p>Data set used to implement the project <strong>A crowd clustering prediction and captioning technique for public health emergencies crowd clustering prediction and captioning technique for public health emergencies</strong></p>
Lombardy Cluster Survey Dataset
<p>Dataset del sondaggio presente nel report: "I bisogni in Lombardia dalla voce dei cittadini Report del sondaggio condotto nell’ambito del progetto EU H2020 TRANSFORM"</p> <p>Il report "I bisogni in Lombardia dalla voce dei cittadini Report del sondaggio condotto nell’ambito del progetto EU H2020 TRANSFORM" ha l’obiettivo di raccontare i risultati di una consultazione tramite questionario - condotta in aprile 2021 a cui ha partecipato un campione di mille cittadini residenti in Regione Lombardia, che hanno avuto così la possibilità di esprimere la loro opinione in merito ai bisogni di ricerca e innovazione del territorio lombardo. Il sondaggio è uno dei tasselli di un percorso partecipativo più ampio, organizzato da Fondazione Giannino Bassetti – in dialogo con Regione Lombardia e Finlombarda. La consultazione si è svolta nell’ambito del progetto europeo TRANSFORM, che si pone l’obiettivo di progettare e testare percorsi di coinvolgimento dei cittadini nella governance regionale di ricerca e innovazione.</p>
Open data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters
<p>Original data for publication: Advanced catalyst for CO2 photo-reduction: From controllable product selectivity by architecture engineering to improving charge transfer using stabilized Au clusters, published in Small, 2023.</p> <p>The dataset is organized according to the Figures in the manuscript.</p>
Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study.
<p>Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study. Angewandte Chemie, 2023</p>
Photometry and Spectroscopy of a z=9.51 galaxy in the RXJ2129 cluster field
<p>Reduced HST and JWST imaging, plus reduced JWST spectroscopy, of a redshift z=9.51 galaxy that is triply imaged and highly magnified by the RXJ2129 galaxy cluster. </p>
Supplemental data for: Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma
<p><em>Trichoderma</em> is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like <em>Trichoderma</em>, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight <em>Trichoderma</em> genomes representing the full breadth of environmental <em>Trichoderma</em>'s diverse lifestyles and nutritional modes. We generated four new <em>Trichoderma endophyticum</em> genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic <em>Trichoderma</em> genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken into consideration, no particular class of metabolic gene cluster was independently associated with the <em>Trichoderma</em> endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic <em>Trichoderma</em> genomes. Most genomic differences between <em>Trichoderma</em> lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that <em>Trichoderma</em> genomes may be particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to <em>Trichoderma</em>.</p>
Strong lensing mass models for the paper "Model-Independent Mass Reconstruction of the Hubble Frontier Field Clusters with MARS \\ Based on Self-Consistent Strong Lensing Data"
<p><strong>Codes for evaluating multiple image scatters</strong></p> <p>The code "eval_source_scatter.py" generates the source plane scatters for multiple images.</p> <p>In the folder "Image_plane_scatters", there are codes for computing image plane scatters.<br> "lens_rms.py": to find the location of the multiple images in the image plane.<br> "plot_result.py": to plot the result rms scatters.<br> We uploaded our results and code for computing scatters in both the source and the image planes.</p> <p> </p> <p><strong>Results from the MARS algorithm</strong></p> <p>In each folder, there are 'result_fits.fits', 'resut_kappa_w_header.fits', 'deflection_angle_w_header.fits', and 'catalog.txt' files.<br> All kappa and deflection angle maps are scaled to Dds/Ds= 1.</p> <p>"result_fits.fits" contains all parameters produced by MARS and has a size of (140x140 + alpha), where alpha is the number of model redshifts.<br> "result_kappa_w_header.fits" is the 100x100 convergence map.<br> "deflection_angle_w_header.fits" is the 100x100 deflection angle map in the unit of arc second.<br> "catalog.txt" is the multiple image catalog. The positions are given in pixel unit.</p> <p>For more details, readers are referfed to arXiv:2301.08765. Also, feel free to contact us (<a href="mailto:sang6199@yonsei.ac.kr">sang6199@yonsei.ac.kr</a>) if you have any questions.</p> <ul> <li>We found errors in WCS for the fits files and re-uploaded corrected files on 2023-01-27. We thank Jori Liesenborgs for pointing this out.</li> <li>We updated files on 2023-04-06.</li> </ul>
Data from: Evaluation of a community health worker home visit intervention to improve child development in South Africa: A cluster-randomized controlled trial
<p><span>This dataset was collected as part of a</span><span> cluster-randomized controlled trial that evaluated the impact of </span>a home visit intervention on child development<span> in Limpopo Province, South Africa. </span><span>Household survey data were collected at baseline and endline. In a subsample of children, neural function was assessed at a lab at endline and at two interim time points. Primary outcomes were: height-for-age z-scores (HAZ) and stunting; child development scores measured using the Malawi Developmental Assessment Tool (MDAT); absolute electroencephalography (EEG) gamma and total power; relative EEG gamma power; and saccadic reaction time (SRT)—</span>an eye-tracking measure of visual processing speed.</p>
Supplementary materials for: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians
<p><span>Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera <em>Discoglossus</em>, <em>Rana</em>, <em>Lissotriton</em> and <em>Triturus</em> using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species' systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.</span></p>
Neuronal activation in the geomagnetic responsive region Cluster N covaries with nocturnal migratory restlessness in white-throated sparrows
<p>Cluster N is a region of the visual forebrain of nocturnally migrating songbirds that supports the geomagnetic compass of nocturnal migrants. Cluster N expresses immediate-early genes (ZENK), indicating neuronal activation. This neuronal activity has only been recorded at night during the migratory season. Night-to-night variation in Cluster N activity in relation to migratory behaviour has not been previously examined. We tested whether Cluster N is activated only when birds are motivated to migrate and presumably engage their magnetic compass. We measured immediate-early gene activation in Cluster N of white-throated sparrows (<em>Zonotrichia</em> <em>albicollis</em>) in three conditions: daytime, nighttime migratory restless, and nighttime resting. Birds in the nighttime migratory restlessness group had significantly greater numbers of ZENK-labelled cells in Cluster N compared to both the daytime and the nighttime resting groups. Additionally, the degree of migratory restlessness was positively correlated with the number of ZENK-labelled cells in the nighttime migratory restless group. Our study adds to the number of species observed to have neural activation in Cluster N and demonstrates for the first time that immediate early gene activation in Cluster N is correlated with the amount of active migratory behaviour displayed across sampled individuals. We conclude that Cluster N is facultatively regulated by the motivation to migrate, together with nocturnal activity, rather than obligatorily active during the migration season.</p>
Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster
<p>Psychoactive mushrooms in the genus <em>Psilocybe</em> have immense cultural value and have been used for centuries in Mesoamerica. Despite a recent surge in interest in these mushrooms due to emerging evidence that psilocybin, the main psychoactive compound, is a promising therapeutic for a variety of mental illnesses, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five species of <em>Psilocybe</em>, four of which belong to only one of two major clades. We set out to improve the phylogeny for <em>Psilocybe</em> using shotgun sequencing of 71 fungarium specimens, including 23 types, and conducting phylogenomic analysis using 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in <em>Psilocybe</em>, with 4–5 possible horizontal transfers to other mushrooms between 40 and 9mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the cluster that corresponds to a deep split within the genus, possibly consistent with the independent acquisition of the cluster. By mining genomic data beyond markers for phylogenetic inference, we gained novel insights into the evolutionary origins of psilocybin biosynthesis that have implications for understanding the functional role of this powerful chemical and can inform translational applications for human well-being.</p>
Characterisation of night-time outdoor lighting in small urban centres using cluster analysis of remotely sensed light emissions (Dataset)
<p>Data used for the paper "Characterisation of night-time outdoor lighting in small urban centres using cluster analysis of remotely sensed light emissions". </p>
Lattice kinetic Monte Carlo model to simulate RNA polymerase II clusters during stem cell differentiation
<p>This data set includes Python scripts (numerical simulation and analysis) and already generated simulation data for RNA polymerase II clusters during stem cell differentiation. It includes the whole data to recreate panels.</p>
Cluster Interconnectedness maps of COVID-19 spread in India.
<p>This project contains clustered maps from sample data on COVID-19 acquired from the Indian Council of Medical Research. Citation is required if anyone wishes to use the files for additional research. </p>
Technical Land-Sea Spaces. Impacts of the Port Clusterization Phenomenon on coasts, cities and architectures [YouTube Video Version]
<p>Beatrice Moretti lectures on the phenomenon of spatial stretching that is imposing a profound evolution, both formal and institutional, in the sphere of contemporary port cities and regions, by giving first insights about the research methodology oriented in this phase to the definition of a indicator systems of the cluster dimension. The presentation questions the spatial impacts introduced by port clusters in the field of architectural design.</p> <p>[YouTube Video Version]<br> <br> <a href="https://www.iccaua.com/page/conference-brochure">6th International Conference of Contemporary Affairs in Architecture and Urbanism - ICCAUA2023</a><br> Alanya Hamdullah Emin Paşa University, Istanbul (Turkey)<br> Chairman of the Conference:<strong> </strong>Dr. <a href="https://arch.alanyahep.edu.tr/en/akademik-kadro">Hourakhsh A. Nia</a>, AHEP University, Alanya, Antalya, TR.<br> Special Session "Coastal and Maritime Spaces", proposed by The University IUAV, Venice (IT)<br> Chairs: Paolo De Martino and Fabio Carella (IUAV).</p>
Microscopy-based assessment of RNA polymerase II clusters during differentiation of cultured mouse embryonic stem cells
<p>This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of differentiation of cultured mouse embryonic stem cells (mESCs). The cells were induced towards differentiation by either withdrawal of lineage-inhibiting factors (-LIF) or by RHB treatment. Both treatments were carried out in duplicate in independent experiments. Time course data were obtained by collection of cells at 3, 6, 12, 24, and 48 hours following the beginning of induction. Control data from unindexed cells were obtained at 24 and 48 hours. Cells were cultured, treated, collected, and fixed at University Medical Center Göttingen by Yomna Gohar, Priya Kumar, and Carmelo Ferrai. Fixed cells were fluorescently labeled and microscopy images were recorded and analyzed at Karlsruhe Institute of Technology by Lennart Hilbert. </p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>This is the main repository, containing the image analysis scripts alongside the links to the raw image data used in the analysis. The raw data are too large to be stored within this single repository, and therefore can be found at the following additional addresses.</p> <p>Differentiation by withdrawal of lineage-inhibiting factors (-LIF): <a href="https://doi.org/10.5281/zenodo.8013281">10.5281/zenodo.8013281</a></p> <p>Differentiation with addition of RHB for neuronal fate induction (RHB): <a href="https://doi.org/10.5281/zenodo.8013307">10.5281/zenodo.8013307</a></p>
ScienceDex guides
Understand access before you commit
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.