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4,489 results for “transitivity”
Host associated transmission favors transition of a commensal toward antagonism
<p>The impacts of host-associated microbes for their hosts varies along a continuum of antagonistic, neutral, and beneficial interactions. Transmission mode is predicted to contribute to transitions along the continuum by altering opportunities for the alignment of host and microbe fitness interests. Under vertical transmission, microbial evolution is tightly coupled to the host environment, which may facilitate fitness alignment. In contrast, environmentally transmitted microbes spend time in the external environment, outside of hosts, partially decoupling their evolution from the host. This decoupling may misalign host and microbe fitness interests, potentially favoring antagonistic microbial traits. Here, we tested whether transmission environment alters microbial evolution by manipulating the interaction between a commensal Serratia marcescens bacteria and their insect host <em>Anasa tristis</em>, which are the primary vector of these bacteria into plants, where they cause disease. We experimentally evolved <em>S. marcescens </em>through several selection environments. The bacteria were passaged between <em>A. tristis </em>hosts, between <em>A. tristis </em>hosts and soil, through soil, or through standard culture media. We observed rapid evolution of virulence toward hosts across treatments when bacterial evolution occurred within the host environment, indicating that direct host-to-host transmission can increase opportunities for microbes to adapt to hosts and evolve antagonistic traits.</p>
Simulation outputs for the manuscript "Snowball Earth transitions from Last Glacial Maximum conditions provide an independent upper limit on Earth's climate sensitivity"
<p>This dataset contains outputs for the simulations shown in the paper "Snowball Earth transitions from Last Glacial Maximum conditions provide an independent upper limit on Earth’s climate sensitivity" by Renoult et al. (submitted). </p> <p>The outputs contain different 2D and 3D variables described in the paper and the file "README.txt".</p>
Gastrointestinal transit time
<p>GI Transit time for a-synuclein<sub>32-46</sub>, CFA-only, PBS immunized HLA mice. GI transit time for a-synuclein<sub>32-46</sub> immunized HLA mice with T cell depletions are included. Corresponds to Figures 2 and 6</p>
Data to D3.1 - Policy design for the transition to circular economy –assessing the inclusion of water and territory in national action plans
<p>This policy paper is part of Project Ô −Demonstration of planning and technology tools for a circular, integrated, and symbiotic use of water, and of WP3 dedicated to the Integrated water management, planning and CE. Itassesses the integration of water and landrelated issues in national CEaction plans of a set of European Union (EU)member states. So far, only two countries associated to the Project Ô demo-sites have a CEaction plan, namely Spain and Italy. This paper also covers a set ofother EU countries enlarging the scope of the analysis.Itis structured into four sections. Section 1 describes the problem and challenges. Section 2 identifies the European policy approach for CEand questions how water and landrelated issues are considered. Section 3 assesses how these concerns have been taken into account in a large set of EU member states CEaction plans. Section 4 suggests a set of policy recommendations for policy design of CEplans regarding water and landrelated issues.</p>
Data from: Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes
<p>Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors), but need not be coupled with access to novel ecological niches.</p>
Real-space observation of ergodicity transitions in artificial spin ice
<p>Coordinate files of every nanomagnet's position and orientation recorded at each moment in time and several temperatures.</p>
model of reconceptualization and analysis of interculturality in the cultural and disruptive transition
<pre>model of reconceptualization and analysis of interculturality in the cultural and disruptive transition</pre>
Characterization of signal and transit peptides based on motif composition and taxon-specific patterns
<p>These files contain data, sequences and supplementary information for the article entitled '<em>Characterization of signal and transit peptides based on motif composition and taxon-specific patterns</em>'.</p> <p><strong>Contents</strong></p> <ol> <li><strong>Raw_data.zip</strong> - contains raw data and sequences downloaded from UniProt and other databases. These files were used to create datasets used for described analyses.</li> <li><strong>Datasets.zip</strong> - presequence and peptide datasets obtained from raw data and used for all subsequent analyses.</li> <li><strong>Motif_analysis_reports_presequences_AMP.zip</strong> - HTML reports with detailed analyses of motif composition of presequences and AMPs</li> <li><strong>Motif_analysis_reports_presequences_encoded.zip</strong> - HTML reports with detailed analyses of motif composition of presequences using reduced alphabets</li> <li><strong>Motif_analysis_reports_presequences_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of presequences for different taxons</li> <li><strong>Motif_analysis_reports_SP_taxonomy.zip</strong> - HTML reports with detailed analyses of motif composition of signal peptides on different taxonomic levels</li> <li><strong>Motif_analysis_reports_presequences_counts.zip </strong> - HTML reports with detailed analyses of motifs occuring more than once in presequences and AMPs</li> </ol> <p> </p> <p><strong>Abstract</strong></p> <p>Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum (ER), and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed a comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.</p>
Transitioning from MODIS to VIIRS Global Water Reservoir Product
<p>The 8-day (VNP28C2/VJ128C2) and monthly (VNP28C3/VJ128C3) VIIRS global water reservoir (GWR) product data are available in the respective folders. While the SNPP (VNP) data is available from 2012-2021, the JPSS1 (VJ1) data is provided from March 2020 to December 2021. Please note that VIIRS (Collection 2) GWR products for the full mission period of SNPP and JPSS-1 will be launched by NASA later this year and will be operational. Hence, VIIRS GWR data for the full-time period in the future can be downloaded from NASA LPDAAC. More information about the VIIRS GWR products will be provided at <a href="https://viirsland.gsfc.nasa.gov/Products/NASA/GWR.html">https://viirsland.gsfc.nasa.gov/Products/NASA/GWR.html</a>.</p>
Two-closures of transitive groups of small degree
<p>This database describes the 2-closures of the transitive permutation groups of degree 2 to 48. It is a supplement to the paper "A census of small Schurian association schemes".</p> <p>The 2-closures for the transitive permutation groups of degree N are contained in the file "TwoClosuresN". Each line of the file contains the list<br> [ id_1, id_2]<br> where:<br> - id_1 is the transitive identification of the permutation group<br> - id_2 is the transitive identification of the corresponding 2-closure</p> <p>In GAP the group G is obtained by TransitiveGroup(N, id_1) and the group H is obtained by TransitiveGroup(N, id_2). The group H is conjugate in S_N to the 2-closure of G.</p>
Original data for "Experimental signatures of the transition from acoustic plasmon to electronic sound in graphene"
<p>This repository contains the original SNOM data and fits to them used in "Experimental signatures of the transition from acoustic plasmon to electronic sound in graphene" by D. Barcons Ruiz et al.<br> - The Raw_data folder contains the original scans recorded with a neaSNOM (neaspec Gmbh) microscope for the two devices in .dump format. <br> These data are easily accesible with Gwyddion. <br> The first part of the filename indicates the date of acquisition and the scanning conditions.<br> The suffix meaning of the individual scans within the raw data folders is:<br> - First element:<br> CT: topography<br> MX: X-harmonic of the mechanical signal (piezo)<br> BX: X-harmonic of the photocurrent signal<br> - Second element:<br> B/F: Backwards/Forward scans<br> - Third element:<br> abs: absolute value<br> arg: phase (-pi to pi)<br> <br> Ex:<br> 2022-02-02_10-48-16_2D-scan_4.25THz_GRp0.1V_GLsweep_m3Vtop1V_B1-B-abs.dump<br> 2022-02-02: date<br> 10-48-16: time<br> 2D-scan: scan type<br> 4.25THz: laser freq.<br> GRp0.1V_GLsweep_m3Vtop1V: scan conditions<br> B1-B-abs: 0th harmonic of the photocurrent signal, backwards trace, absolute value<br> <br> - The folder Figure2 contains the example traces extracted from the scans and shown in Fig.2 of the paper, and the fits to the optical signal, for both device 1 and 2.</p> <p>- The folder Figure3 contains the parameters obtained from the fitting of the plasmon fringes realizad as described in the Supplementary Information for both devices.<br> The real part of the plasmon wavevector is used to calculate the plasmon velocity data appearing in Fig.3 A-B of the paper and constitutes the most important dataset.<br> For every doubt on how to read or interpret these data please refer to the corresponding authors of the paper: <br> Prof. F.H.L. Koppens (frank.koppens@icfo.eu), <br> Dr. Iacopo Torre (iacopo.torre@icfo.eu).</p>
Data of early energy transition in India can achieve deep decarbonization with lower cumulative investments
<p>Data of early energy transition in India can achieve deep decarbonization with lower cumulative investments.</p>
Meta-model for Patagonian grass steppe dynamics - library of transition matrices for steppe dynamics under sheep grazing
<p><span>One of the central problems in ecology is how to scale from small-scale observations and experiments to large-scale patterns and processes. One approach to such upscaling is to use dynamic simulation models, but their application to large scales relevant for management is limited by computational costs, and their outputs are difficult to analyse without a systematic strategy. Our general objective is to propose such a strategy. The idea is to approximate the dynamics of detailed simulation models through a set of states, external drivers, and transition matrices, and then use Markov chain and network analysis of the resulting transition matrices to gain insights into the dynamics of the underlying detailed model. We used the individual-based model COIRON, which simulates the dynamics of semiarid grass steppes in Patagonia (Argentina) under alternative grazing management, as example. Our specific objectives are to identify pathways of degradation and rehabilitation, as well as critical grazing thresholds and early-warning vegetation states to guide sustainable grazing management in these steppes. Our results indicate nonlinear effects of stocking rate and grazing season on steppe dynamics. Markov chain analysis suggests benefits of seasonal over continuous grazing at intermediate stocking rates, and network analysis of recovery and degradation trajectories shows that intermediate stocking rates maximize differences between grazing seasons. Finally, our analysis identified specific vegetation states as early warning signals that indicate a high risk of irreversible vegetation changes. Patagonian grass steppes should ideally be managed with multi-paddock grazing at moderate stocking rates around 0.5 sheep·ha<sup>-1</sup>. The transition matrices summarize the relevant key features of the detailed model for larger scales, and applying Markov and network theory provides a systematic strategy to analyse its dynamics to respond to biological questions, both are often difficult to obtain by direct analysis of the detailed model. </span></p>
Probing the long-lived photo-generated charge carriers in transition metal dichalcogenides by time-resolved microwave photoconductivity
<p>Raw data of time resolved microwave conductivity measurements. </p>
First exploration of the runaway greenhouse transition with a GCM
<p>Raw outputs of the Generic-PCM simulations presented in Chaverot et al. (2023).</p> <p>The files are named <em>AA_XWm2.nc</em> where AA is the name of the setup (W01, W1, W10, WCO2, E1, ECO2) and X is the insolation (in W.m<sup>-2</sup>) received by the planet in the simulation. Files corresponding to the dry transition assuming 1bar and 1.5bar of water vapor are named <em>W1_dry1bar_XWm2.nc</em> and <em>W1_dry1.5barXWm2.nc</em> respectively.</p>
3D rendering (left) and 2D orthoslice (rigth) of a virtual longitudinal section in the chorda tendinea insertion into the papillary muscle allowing to visualize the transition from collagen to muscle fibers
<p>The white square on the 3D rendering indicates the region-of-interest shown on the right. At the beginning of the video, the yellow and<br> blue arrows indicated the presence of adipocytes and a vessel filled with blood.</p>
FIGURE 19 in New species of Centris (Xanthemisia) Moure from the Mesoamerican Dominion and the Mexican Transition Zone (Hymenoptera: Apidae)
FIGURE 19. Distribution records for the species of Centris (Xanthemisia) inhabiting the Mexican Transition Zone (purple) and the Mesoamerican Dominion (pine green). The Nearctic Region and the Pacific Dominion are indicated in gray and pink, respectively.
FIGURES 13–16 in New species of Centris (Xanthemisia) Moure from the Mesoamerican Dominion and the Mexican Transition Zone (Hymenoptera: Apidae)
FIGURES 13–16. Centris purhepecha sp. nov. (holotype female). Fig. 13. Head, frontal view (scale bar 2 mm). Fig. 14. Habitus, lateral view (scale bar 5 mm). Fig. 15. Basitibial plates (scale bar 0.5 mm). Fig. 16. Pygidial plate, dorsal view (scale bar 0.5 mm).
FIGURES 17–18 in New species of Centris (Xanthemisia) Moure from the Mesoamerican Dominion and the Mexican Transition Zone (Hymenoptera: Apidae)
FIGURES 17–18. Centris purhepecha sp. nov. (paratype male). Fig. 17. Head, frontal view (scale bar 2 mm). Fig. 18. Habitus, lateral view (scale bar 5 mm).
FIGURES 1–4 in New species of Centris (Xanthemisia) Moure from the Mesoamerican Dominion and the Mexican Transition Zone (Hymenoptera: Apidae)
FIGURES 1–4. Centris jakalteka sp. nov. (holotype female). Fig. 1. Head, frontal view (scale bar 2 mm). Fig. 2. Habitus, lateral view (scale bar 5 mm). Fig. 3. Basitibial plates (scale bar 0.5 mm). Fig. 4. Metasoma, dorsal view (scale bar 1 mm).
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.