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4,489 results for “transitivity”
Data for: Resolving marine–freshwater transitions by diatoms through a fog of gene tree discordance
<p>Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic dataset of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a small set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.</p>
Transition of the mesoscale eddy in the Kuroshio Extension re-circulation gyre in 2019
<p>Transition of the mesoscale cyclonic eddy occurred in the Kuroshio Extension re-circulation gyre (KERG) from June to December 2019. Color shades denote sea surface height (SSH) map (color contours, m). The Kuroshio and Kuroshio Extension (KE) are shown by a sharp southward increase in SSH and the recirculation gyre is illustrated by a high-SSH (>1.6 m) region. The SSH map was generated using E.U. Copernicus Marine Service Information.</p>
Land Water Transition Zone Change Detection - Hydroperiod Maps - WQeMS raster products
<p>Within this dataset, Hydroperiod maps of the Polyphytos open surface water reservoir in Greece and Giaretta reservoir in Italy are available in GeoTIFF raster format. The maps provide information about the total number of days each pixel is inundated within a specific time period.They were generated by the Land Water Transition Zone Change Detection service of the WQeMS project. Each raster file in the dataset is named according to the water body and period during which the processing was performed. Copernicus Sentinel-2 data was utilized for the generation of the inundation maps which were provided as input for the production of the hydroperiod maps.</p>
Land Water Transition Zone Change Detection - Transition Maps between two dates - WQeMS raster products
<p>Within this dataset, land water transition zone maps, which indicate the land-water transition between two instances in time, of the Polyphytos open surface water reservoir in Greece and Giaretta reservoir in Italy, are available in GeoTIFF raster format. The maps depict the transition zones by indicating the change of the pixel status from non-inundated to inundated and vice versa between two provided dates. They were generated by the Land Water Transition Zone Change Detection service of the WQeMS project. Each raster file in the dataset is named according to the water body and the two dates during which the processing was performed. Copernicus Sentinel-2 data was utilized for the generation of the inundation maps on the two dates.</p>
Supplementary materials for "Spanish lower and upper bounded change of state verbs: Focusing on transitive experiencer object verbs", published in Linguistics: An Interdisciplinary Journal of the Language Sciences
<p>Supplementary files are as follows:</p> <ul> <li><strong>R-code_Scalarity.Rmd</strong> contains the R-code in a markdown version of the statistical analysis of the study.</li> <li><strong>R-code_Scalarity.html</strong> displays the R-code_Scalarity.Rmd in an html format.</li> <li><strong>Results_Scalarity.csv</strong> contains the data of the study.</li> </ul> <p>For more details on the description of the data, see the publication: "Spanish lower and upper bounded change of state verbs: Focusing on transitive experiencer object verbs", Linguistics.</p>
Drivers of Forest-Savanna transition
<p>This dataset has the data used in the article titled <strong>"<em><strong>Cu</strong>rrent Forest-Savanna Transition in Northern South America Departs from Typical Climatic Thresholds</em>"</strong> published in the Ecosystems Journal. Further details of variables and data sources are described in the methods section, Table 1, and Supplementary Material of the article.</p> <p> </p>
Data for First-Order Quantum Phase Transition in the Hybrid Metal-Mott Insulator Transition Metal Dichalcogenide 4Hb-TaS2
<p>Data to reproduce the main text figures of the paper "First-Order Quantum Phase Transition in the Hybrid<br> Metal-Mott Insulator Transition Metal Dichalcogenide 4Hb-TaS2" are provided. They are either in the *.txt format or *.fig (matlab figure) format. The *.txt files contain the relevant header information.</p>
Data from: Multispecies interactions shape the transition to multicellularity
<p>This data was collected during the study entitled "Multispecies interactions shape the transition to multicellularity."</p> <p>We explored how interspecific competition shapes the emergence of multicellularity in an experimental system with two yeast species, <em>Saccharomyces cerevisiae</em> and <em>Kluyveromyces lactis</em>, where multicellularity evolves in response to selection for faster settling ability. The experimental design consisted of a 19-day evolution experiment, where cocultures and monocultures of unicellular <em>S. cerevisiae </em>and <em>K. lactis</em> were propagated daily with and without selection for settling (6 replicates each). Cocultures included initial frequencies of 25%, 50%, and 75% <em>K. lactis</em>. Differential growth rates and selection coefficients during the sweep of multicellular <em>K. lactis</em> were calculated, and species frequencies (%) were visualized.</p> <p>We also completed a 20-day evolution experiment with cocultures of multicellular <em>S. cerevisaie</em> and <em>K. lacti</em>s, with each species beginning as rare, transferred with and without settling (6 replicates each). Differential growth rates during the invasion-from-rare experiment were calculated and visualized.</p> <p>To assess the competitive dynamics of the two species before and after the transition to multicellularity, competition assays were performed, with species’ frequencies determined before and after either 24 hours of growth or 7 minutes of settling when each species began as rare. These assays were repeated for unicellular and multicellular isolates. We also obtained 48-hour growth curves for monocultures and 50% cocultures (10 replicates each) and determined the intrinsic growth rate (r) and carrying capacity (K) for each population. Population densities of each species were also measured before and after 24 hours of growth on each species’ spent media.</p>
Earth's transit spectrum from Macdonald and Cowan (2019)
<p>Earth's transit spectrum from Macdonald and Cowan (2019), constructed from Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) solar occultation data (Hughes et al. 2014). The Atmospheric Chemistry Experiment (ACE), also known as SCISAT, is a Canadian-led mission mainly supported by the Canadian Space Agency. The occultation data used are available at http://www.ace.uwaterloo.ca/atlas.php. </p> <p> </p>
Spatial Data collection for study spatial transition dynamic of Rohingya settlement in Bangladesh: 1st version
<p>Full open access article can be found in: <a href="https://doi.org/10.1016/j.landusepol.2023.106874">https://doi.org/10.1016/j.landusepol.2023.106874</a></p> <p> </p> <p><strong>Full Changelog</strong>: <a href="https://github.com/ssujit/SpatialTransitionDynamic/commits/version">https://github.com/ssujit/SpatialTransitionDynamic/commits/version</a></p>
Data and code for "Revealing the free energy landscape of halide perovskites: Metastability and transition characters in CsPbBr3 and MAPbI3"
<p>This record contains a neuroevolution potential (NEP) model (<code>nep-MAPI-SCAN.txt</code> ) for MAPbI3 used in the linked publication. The model can be used in conjunction with the <a href="https://gpumd.org">GPUMD package</a>. The <a href="https://calorine.materialsmodeling.org">calorine package</a> provides a Python interface to GPUMD.<br> Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP model included here. The <code>demo-for-using-structures-and-model.py</code> script illustrates how to access the structures and model.</p>
Stiffness transitions in new walls post-cell division differ between Marchantia polymorpha gemmae and Arabidopsis thaliana leaves
<p>Plant morphogenesis is governed by the mechanics of the cell wall–a stiff and thin polymeric box that encloses the cells. The cell wall is a highly dynamic composite material. New cell walls are added during cell division. As the cells continue to grow, the properties of cell walls are modulated to undergo significant changes in shape and size without breakage. Spatial and temporal variations in cell wall mechanical properties have been observed. However, how they<br> relate to cell division remains an outstanding question. Here we combine time-lapse imaging with local mechanical measurements via atomic force microscopy to systematically map the cell wall’s age and growth, with their stiffness. We make use of two systems, <em>M. polymorpha</em> gemmae, and <em>A. thaliana</em> leaves. We first characterise the growth and cell division of <em>M. polymorpha</em> gemmae. We then demonstrate that cell division in <em>M. polymorpha</em> gemmae results in<br> the generation of a temporary stiffer and slower growing new wall. In contrast, this transient phenomenon is absent in <em>A. thaliana</em> leaves. We provide evidence that this different temporal behaviour has a direct impact on the local cell geometry via changes in the junction angle. These results are expected to pave the way for developing more realistic plant morphogenetic models and to advance the study into the impact of cell division on tissue growth.</p>
FIGURE 1 in Coexistence of two newt species in a transition zone of range overlap
FIGURE 1 Land use map of the study area in the western part of the department Pas de Calais in the northwest of France (see insert), after Curado et al. (2011) and Arntzen et al. (2017). The small-bodied newt species Lissotriton helveticus and L. vulgaris are frequently syntopic (for data see table 1), but have different strongholds in and outside the 'Dunes de la Slack' and the bomb crater areas, respectively. The partial spatial separation is illustrated by dotted contour lines where L. vulgaris is at 60% (red dots), 50% (purple dots) or 40% (blue dots) of the Lissotriton total. Note the position of the study pond at the species transition.
FIGURE 2 in Coexistence of two newt species in a transition zone of range overlap
FIGURE 2 Dynamics of the adult newt breeding populations in the study pond, with percentage values over the 1975–2021 period for Ichthyosaura alpestris (black), Lissotroton helveticus (blue) and L. vulgaris (red), with open dots for samples and solid dots for population size estimates (see also tables 2 and 3). Years without observations are marked by open rectangles. The asterisk indicates a hypothetical frequency, on the assumption that the L. helveticus cohort that in March 1986 fell prone to a late freezing event (details see text) would have made it to the breeding population.
Energy transition matrix
<p>This table accompanies the SAPEA evidence review report published with the DOI 10.26356/energytransition. It is Table 5 of that report. For contextual information and accompanying descriptions, see the report.</p> <p>This table is based on a literature review.</p>
Microscopic defect dynamics during a brittle-to-ductile transition
<p>Description of Data employed in “<em>Microscopic defect dynamics during a brittle-to-ductile transition</em>”-</p> <p>The data reported in Table S.1 of PNAS paper is as follows :</p> <ol> <li>All raw data [mechanical synchronized with ultrasonic probes ] are in .mat files.</li> <li>The data includes both strain, stress, P-velocityand waveforms of passive sensor in the point of strain-stress also are provided . All data are in 2ns time-resolution –</li> <li>AE_CAT_xxx includes all information recorded during test in Paterson rig. The data are synchronized with pulsing (active) and passive excitations based on simple off-line synchronized matching ;</li> <li>The index the AE_CAT_xxx table doe have a corresponding waveforms due to an AE in M_xxx</li> <li>UM_XXX are based on table S1 and does have full strain-stress data set.</li> <li>Dist_xx_yy is distance measurement calculated based on DTW algorithm between each pair of tests</li> </ol> <p>Feel free to request [ hoghaff@mit.edu or <a href="mailto:mpec@mit.edu">mpec@mit.edu</a>] further information regarding our methods of analysis the data or obtaining the waves in Paterson rig. </p> <p>**Apart of the presented data in the paper , we repeated each test at least twice to be confident about our results in particular ultra-high frequency AEs and the strain-stress history. Feel free to request data independently from corresponding authors.</p>
Dataset for "Universal scaling of the dynamic BKT transition in quenched 2D Bose gases"
<p>This repository contains data and numerical simulation code for Sunami et. al., "Universal scaling of the dynamic BKT transition in quenched 2D Bose gases".</p> <p>The data is stored in the format of hdf5 (Hierarchical Data Format), which can be read from standard programming environment such as python (h5py), matlab (`h5read`), and many others.</p> <p>Numerical simulation scripts consist of functions.c, MonteCarloSampling.cpp and phase12_den_sample_time.cpp. Please see the section for numerical simulation in the Supplementary Material.</p> <p>The description for each hdf5 file in this repository is provided in readme.txt.</p>
Strain, Young's modulus, and structural transition of EuTiO3 thin films probed by micro-mechanical methods (Dataset)
<p>Datafiles of the Article "Strain, Young’s modulus, and structural transition of EuTiO3 thin films probed by micro-mechanical methods (Dataset)"</p>
Parties' Ideological Positions on the Digital Transition to Platform Societies: Dataset
<p>The dataset showcases an original classification of the ideological positions on the digital transition to platform societies by 29 parties in 4 Western European countries. The codebook details the definition of the coding units. The coding files illustrates how the paragraphs are sorted into the indicators' scores. </p>
Research data of "Quantum resonant optical bistability with a narrow atomic transition: bistability phase diagram in the bad cavity regime"
<p>The data set includes the matlab programs, measured data and drawings used for the figures in D Rivero et al 2023 New J. Phys. 25 093053</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.