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4,489 results for “transitivity”
Data for EUA Trends 2024 - European higher education institutions in times of transition
<p>Since 1999, the EUA Trends reports have consistently mapped developments in the European higher education landscape, by presenting comparative data from the perspective of higher education institutions. In the ninth edition of the European University Association’s long-running series, the Trends 2024 report provides an overview of how European higher education institutions have experienced changes over the past five years, due to higher education reforms, and in the wider context of societal, political, economic and technological changes, marked among others by the implications of Covid-19 pandemic and Russia’s war against Ukraine.</p> <p>Trends 2024 is based on survey data collected in April to July 2023.</p> <p>Responses were gathered from 489 higher education institutions in 46 European higher education systems. The survey was open to all higher education institutions in the European Higher Education Area (EHEA) that provide study programmes in at least one of the three degree cycles (bachelor’s, master’s, doctoral). One response per institution was collected.</p> <p>The survey addressed the higher education institutions’ perspectives and strategies regarding:</p> <p>· The institution and its context</p> <p>· The student life cycle and experience</p> <p>· Learning, teaching and teachers </p> <p>· Inclusion, equity and diversity</p> <p>· Engagement and outreach with society and community </p> <p>· Internationalisation</p> <p>Results of the survey are published in “<a href="https://www.eua.eu/publications/reports/trends-2024.html"><strong>Trends 2024 - European higher education institutions in times of transition</strong></a>”.</p> <p>The following files are available:</p> <ul> <li>Codebook including original questionnaire</li> <li>Dataset</li> </ul>
Fisher zeroes and dynamical quantum phase transitions for two- and three-dimensional models
<p>Data for the publication <em>Fisher zeroes and dynamical quantum phase transitions for two- and three-dimensional models</em>. Included are data for return rates and Fisher zeroes. The names of the data files contain all metadata necessary for specifying the type of data, with a list of the paramters used. For more details on the models and paramters see the article.</p> <ul> <li>Firstly the three models are considered labelled by <em>Kit</em> for the 2D spinless px+ipy topological superconductor, <em>Sq</em> for the 2D spinfull topological superconductor, and <em>3D</em> for the 3D topological insulator.</li> <li>After <em>_N_</em> the system size is written, referring the number of sites along one direction (for finite size calcualtions only).</li> <li><em>RR</em> refers to the return rate. For <em>Kit</em> the columns are $t$, $l(t), $\dot{l}(t)$, $\ddot{l}(t)$. If only two columns exit then there is just $t$, $\dot{l}(t)$. For <em>Sq</em> the columns are $t$, $l(t), $\dot{l}(t)$, $|\lambda_0(t)|$. For <em>3D</em> the columns are $t$, $\dot{l}(t)$, $\ddot{l}(t)$.</li> <li><em>Density</em> refers to the density of Fisher zeroes along the real time axis, with the columns being simply time and density.</li> <li><em>Fisher</em> to Fisher zeroes in the complex plane with <em>kx</em>, etc meaning it is resolved along this momentum direction. The columns are the real and imaginary parts of the complex time argument.</li> <li><em>Critical_k</em> are the critical momenta.</li> <li><em>Critical_k_En</em> lists the energy for each critical momenta in the matching <em>Critical_k </em>file.</li> <li>For <em>Kit</em> the list of quench parameters are 100 times {$\mu_0$, $\Delta_0$, $\mu_1$, $\Delta_1$}.</li> <li>For <em>Sq</em> the list of quench parameters are 100 times {$\nu_0$, \nu_1$, $\mu_0$, $\Delta_0$, $\alpha_0$, $B_0$, $\mu_1$, $\Delta_1$, $\alpha_1$, $B_1$}.</li> <li>For <em>3D</em> the list of quench parameters are 100 times {$v_0$,$w_0$,$v_1$,$w_1$}.</li> <li>For <em>Fisher</em> data <em>branch</em> labels naturally the branch p.</li> <li><em>Zoom</em>, etc, label different zooms in differnet regions, as made explicit by the times inside the files.</li> </ul> <p>This work was supported by the National Science Centre (NCN, Poland) under the grant 2019/35/B/ST3/03625, by the German Research Council (DFG) via the Re- search Unit FOR 2316 and by the National Science and Engineering Resource Council (NSERC) of Canada via the Discovery Grant program.</p>
Data for: Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space
<p>This contains all the TS-DART training results as well as the raw MD simulation data reported in the preprint "Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space".</p>
Figure 1 in Parasites of Moroccan desert Coptodon guineensis (Pisces, Cichlidae): transition and resilience in a simplified hypersaline ecosystem
Figure 1. Map of Morocco indicating the sampling sites.
April 2024 Meteorological Analysis for Chios (Chiostown): Transition to Milder Spring Conditions
<h3><strong>April 2024 – Chios (Chiostown)</strong></h3> <p>April 2024 saw a significant increase in temperature and generally mild weather conditions compared to the previous months. The average temperature for the month was <strong>19.3°C</strong>, reflecting the transition from winter to spring.</p> <ul> <li><strong>Highest temperature</strong>: Recorded on <strong>April 15th</strong> at <strong>27.0°C</strong>.</li> <li><strong>Lowest temperature</strong>: Recorded on <strong>April 20th</strong> at <strong>11.7°C</strong>.</li> </ul> <h3>Rainfall</h3> <p>Total rainfall for April was relatively low, with only <strong>28.1 mm</strong> recorded. The highest daily rainfall occurred on <strong>April 20th</strong>, with <strong>36.2 mm</strong>. There were <strong>5 days</strong> with recorded rainfall, but only one day showed significant levels (>20 mm).</p> <h3>Winds</h3> <p>Winds in April were moderate, with an <strong>average wind speed</strong> of around <strong>9.2 km/h</strong>. The strongest winds were recorded on <strong>April 7th</strong> and <strong>April 24th</strong>, with maximum speeds of <strong>53.1 km/h</strong> and <strong>51.5 km/h</strong> respectively. The prevailing wind direction was northerly and north-northeasterly, indicating the influence of cooler air masses from the north.</p> <h3>Conclusion</h3> <p>April 2024 in Chios was characterized by mild spring weather, with gradually increasing temperatures and limited rainfall. Winds remained moderate, with occasional stronger gusts, mostly from northerly directions.</p>
Transitive prediction of small molecule function through alignment of high-content screening resources
<p>This dataset supports the development of CLIP<sup>n</sup>, a contrastive-learning framework designed to align heterogeneous high-content screening (HCS) profile datasets.</p> <p><strong>GitHub link</strong>: https://github.com/AltschulerWu-Lab/CLIPn</p> <h2>Directory Structure</h2> <h3>Data Files</h3> <ul> <li>HCS_datasets.pkl: Contains 13 high-content screening (HCS) datasets from multiple studies across 20 years.</li> <li>Hypoxia.pkl: Contains 8 profile datasets using different assays and treated under diverse hypoxia durations.</li> <li>Expression.pkl: Contains 2 transcriptional profile datasets and 6 image profile datasets for multimodal analysis.</li> </ul> <h3>Folders</h3> <p><strong>raw_profiles</strong>:<br>HCS13/<br>- Contains raw data from 13 high-content screening (HCS) datasets. Each dataset includes meta and feature files. </p> <p>L1000/<br>- CDRP_feature_exp.csv: Raw L1000 expression data from the CDRP dataset.<br>- CDRP_meta_exp.csv: Metadata associated with the CDRP expression data.<br>- LINCS_feature_exp.csv: Raw L1000 expression data from the LINCS dataset.<br>- LINCS_meta_exp.csv: Metadata associated with the LINCS expression data.</p> <p>RxRx3/<br>- RxRx3_feature_final.csv: Profile data from the RxRx3 dataset.<br>- RxRx3_meta_final.csv: Metadata from the RxRx3 dataset.</p> <p>Uncharacterized_compounds/<br>- NCI_cpnData.csv: Feature data for uncharacterized compounds from the NCI dataset.<br>- NCI_cpnInfo.csv: Information about uncharacterized compounds in the NCI dataset.<br>- Prestwick_UTSW_cpnData.csv: Feature data for uncharacterized compounds from the Prestwick UTSW dataset.<br>- Prestwick_UTSW_cpnInfo.csv: Information about uncharacterized compounds from the Prestwick UTSW dataset.</p> <h2><br>Usage</h2> <p><br><br><code>import pickle</code><br><code>with open('data.pkl', 'rb') as f:</code><br><code> data = pickle.load(f)</code></p> <p><code>X = data['X']</code><br><code>y = data['y']</code><br><br></p> <h2>Data Reference</h2> <p><br>For raw datasets from 13 HCS database, data and analysis pipeline for dataset 1 was obtained from https://www.science.org/doi/suppl/10.1126/science.1100709/suppl_file/perlman.som.zip; for datasets 2-3, data were shared by authors; For datasets 4-5, analysis code was downloaded from https://static-content.springer.com/esm/art%3A10.1038%2Fnbt.3419/MediaObjects/41587_2016_BFnbt3419_MOESM21_ESM.zip and data were shared by authors; For datasets 6-7, processed dataset was downloaded from AWS following instructions from https://github.com/carpenter-singh-lab/2022_Haghighi_NatureMethods, and replicate_level_cp_normalized.csv.gz features were used. For project datasets 8-13, datasets and analysis results were downloaded from https://zenodo.org/records/7352487. For RxRx3, dataset was obtained from https://www.rxrx.ai/rxrx3. L1000 transcript datasets were downloaded using the same link as datasets 6-7 and the processed transcript data files (named “replicate_level_l1k.csv”) were used. </p>
Dataset for 'Warmer Oceans may Accelerate the Marine-to-Land Transition of a West Greenland Outlet Glacier'
<p>Monthly hydrographic records from 2008-2023, collected from the standard station GF10 (64°36.6N, 51°57.5 W; maximum depth: 576 m) as part of Greenland Climate Research Centre “Long-term standard hydrographic fjord research program”. Note that the date values reflect the last day of each month, not necessarily the date that the measurements were obtained.</p> <p>Please cite this reference if dataset were used in any way.</p> <p>Correspondence to John Mortensen at jomo@natur.gl</p>
Data for "Ultrafast Excitonic Transitions in Enantiopure and Racemic Squaraine Thin Films"
<p>Here we present the raw data and data processing files for the paper entitled "Ultrafast Excitonic Transitions in Enantiopure and Racemic Squaraine Thin Films", which is published in Aggregate.</p>
An automated sensitive approach for measuring whole gut transit time
Background <p>Commonly used methods to measure whole gut transit time in rodents have yet to combine high sensitivity, objectivity and automation. We have developed a novel method using oral gavage of non-toxic fluorescent dye particles and their detection by fluorescence imaging to enable unbiased automated detection of gut transit time simultaneously in 8 cages.</p> Methods <p>Naïve mice (n=20) were gavaged with a 4.4% suspension of fluorescent dye in CMC in 3 groups on 2 occasions. Each group was imaged in 8 cages at 5-minute intervals using blue LEDs for illumination and a Sony full-frame mirrorless camera with a green band-pass emission filter. Custom Matlab code counted the number of fluorescent boli per cage post-hoc and provided graphical and spreadsheet output. Boli counts across a wide range of parameters were compared to blind assessments by an experimenter.</p> Results <p>Fluorescent boli were detected with high sensitivity, while unstained boli were readily rejected. All cages showed no fluorescent boli for the first ~20 frames (120 minutes), after which many cages gradually show a rise to 1-6 fluorescent boli. The mean time to first fluorescent bolus in each session was 264±141 and 223±81 minutes post-gavage, with no within subject consistency. There was high correlation between automated scores and that of experimenter (r=0.95±0.02), being robust to parameter changes.</p> Conclusions & Inferences <p>This novel approach provides a reliable, automatic and low-cost method of measuring gastrointestinal transit time in mice.</p>
Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system
<p>Mating systems of haploid species such as fungi, algae, and bryophytes are either heterothallic (self-incompatible) with two sex phenotypes (male and female, or mating type <i>minus</i> and <i>plus</i> in isogamous species) or homothallic (self-compatible) with only a bisexual phenotype producing zygotes within a clone. The anisogamous volvocine green alga <i>Pleodorina starrii</i> is a haploid species previously reported to have a heterothallic mating system. Here, we found that two additional culture strains originating from the same water system of <i>P. starrii</i> were taxonomically identified as <i>P. starrii</i> and produced male and female gametes and zygotes within a clone (bisexual). Sequences of rapidly evolving plastid genome regions were identical between the bisexual and unisexual (male or female) <i>P. starrii</i> strains. Intercrossings between the bisexual and unisexual strains demonstrated normal thick-walled zygotes and high survivability of F1 strains. Thus, these strains belong to the same biological species. <i>P. starrii</i> has a new haploid mating system that is unique in having three sex phenotypes; namely, male, female, and bisexual. Genetic analyses suggested the existence of autosomal "bisexual factor" locus independent of volvocine male and female determining regions. The present findings increase our understanding of the initial evolutionary step of transition from heterothallism to homothallism.</p>
Data from: Convergent changes in gene expression associated with repeated transitions between hummingbird and bee pollinated flowers
<p>Transcriptomic data for 6 Gesneriaceae species (<strong><em>Nemathanthus albus </em>-NA-,<em> N. fritchii </em>-NF-<em>, Sinningia eumorpha </em>-SE-<em>, S. magnifica </em>-SM-<em>, Vanhouttea calcarata </em>-VC-<em>, Paliavana tenuiflora </em>-PV-</strong>), presented in "Convergent changes in gene expression associated with repeated transitions between hummingbird and bee pollinated flowers". For each species, transcriptomes were obtained from RNA collected from flowers at three different developmental stages.</p> <p>The following files are availables:</p> <p><strong>Trimmed_Species_Trinity.fasta:</strong> Transcriptome assembly of the species in fasta format. The transcriptomes were obtained from RNA-Seq (Illumina paired-end reads) of three different floral developmental stages. For more information, please refer to the publication.</p> <p><strong>ORF_AllSpecies_Pep.fasta</strong>: Predicted protein sequences for each transcript of each species.</p> <p><strong>ORF_AllSpecies_CDS.fasta</strong>: Predicted coding sequences (CDS) for each transcript of each species.</p> <p><strong>BLASTP_allgenes6species.FINAL.txt</strong>: Blastp annotation for each transcript of each species.</p> <p><strong>BLASTX_allgenes6species.FINAL.txt: </strong>Blastx annotation for each transcript of each species.</p> <p><strong>groups.txt </strong>: Orthologous groups (OG) between the six species obtained with OrthoMCL. For more information, please refer to the publication.</p> <p><strong>1to1_OG.txt</strong>: Obtained single-copy orthologs (1-to-1 orthologous groups) between the six species</p> <p><strong>OG_and_genes.txt : </strong>link between orthologous groups and genes ID for each species.</p> <p>For more information, please refer to the publication.</p>
Data from: Transitions between phases of genomic differentiation during stick-insect speciation
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genic speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation.
Supporting data for: Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition
<p><span><span><span><span><span><span><span><span><span><span><span>The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (South-West France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which likely played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.</span></span></span></span></span></span></span></span></span></span></span></p>
Data for "Observation of a Superradiant Quantum Phase Transition in an Intracavity Degenerate Fermi Gas"
<p>This dataset is corresponding to the article "Observation of Superradiant Quantum Phase Transition in an Intracavity Degenerate Fermi Gas".</p>
Quantum coherent spin-electric control in a molecular nanomagnet at clock transitions. Open data set
<p>Data supporting the related publication.</p>
Figure 9 in An assemblage of early Oligocene lizards (Squamata) from the locality of Boutersem (Belgium), with comments on the Eocene-Oligocene transition
Figure 9. Necrosaurus sp., osteoderm, IRSNB R 250, previously BOU-AR-28-RS, dorsal view.
Figure 7 in An assemblage of early Oligocene lizards (Squamata) from the locality of Boutersem (Belgium), with comments on the Eocene-Oligocene transition
Figure 7. Necrosaurus sp., fragment of maxilla, IRSNB R 248, previously BOU-AR-33-RS, medial view.
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration
<p>Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. We created a single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 88 publicly available single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting dataset includes more than 365,000 cells and spans a wide range of ages, injury, and repair conditions. Together, these data enabled identification of the predominant cell types in skeletal muscle, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro/adipogenic progenitors defined by functional roles, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem cell quiescence to myofiber maturation and identified rare, transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. We also used the integrated dataset to explore ligand-receptor co-expression patterns and identify dynamic cell-cell interactions in muscle injury response. We provide a public web tool to enable interactive exploration and visualization of the data. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.</p>
Molecular Dynamics Simulation on the Effect of Transition Metal Binding to the N-Terminal Fragment of Amyloid-β
<p>Molecular dynamics trajectories in PDB format for 3x Cu-Aβ, 3x Zn-Aβ and 9x Fe-Aβ<strong> </strong>simulations.</p>
Photoluminescence study of interband transitions in few-layer, pseudomorphic, and strain-unbalanced Ge/GeSi multiple quantum wells - Dataset
<p>Relevant PL data (as txt files) for the publication </p> <p><a href="https://arxiv.org/ct?url=https%3A%2F%2Fdx.doi.org%2F10.1103%252FPhysRevB.98.195310&v=88200607">10.1103/PhysRevB.98.195310</a></p>
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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.