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2,225 results for “reversal”
Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
<p>Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the <i>rootstrap</i>, which provides information on the statistical support for any given root position.</p> <p>Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage <a href="http://www.iqtree.org/doc/Rootstrap">http://www.iqtree.org/doc/Rootstrap</a>. In addition, a python script is available at <a href="https://github.com/suhanaser/Rootstrap">https://github.com/suhanaser/Rootstrap</a></p>
High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal
<p>The view genotypic sex determination (GSD) and environmental sex determination (ESD) are mutually exclusive states has been contradicted by the discovery that chromosomal sex and environmental influences can co-exist within the same species, hinting at a continuum of intermediate states. Systems where genes and the environment interact to determine sex present the opportunity for sex reversal to occur, where the phenotypic sex is the opposite of that predicted by their sex chromosome complement. The skink Bassiana duperreyi has XX:XY sex chromosomes with sex reversal of the XX genotype to a male phenotype in response to exposure to cold incubation temperatures. Here we studied the frequency of sex reversal in B. duperreyi in response to climatic variation, using elevation as a surrogate for environmental temperatures. We demonstrate sex reversal for the first time in free-ranging adults of a reptile species with XX/XY sex determination. The highest frequency of sex reversal occurred at the highest elevation location, Mount Ginini (18.64%) and decreases in frequency with elevation. We model the impact of this under Fisher's frequency dependent selection to show that, only at the highest elevations, populations risk the loss of the Y chromosome and a transition to TSD. This study contributes to our understanding of the risks of extinction from climate change in species subject to sex reversal by temperature, and will provide focus for future research to test on-the-ground management strategies to mitigate the effects of climate in local populations.</p> <div> <div> <div class="msocomtxt"> <p class="MsoCommentText"> </p> </div> </div> </div>
Neural Reverse Engineering of Stripped Binaries using Augmented Control Flow Graphs
<p>This dataset and pre-trained models are released as a companion to our OOPSLA '20 publication: "Neural Reverse Engineering of Stripped Binaries using Augmented Control Flow Graphs":</p> <ol> <li>The dataset file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/nero_dataset_binaries.tar.gz?versionId=b943752a-e89e-43c1-b32f-19d4a7420e00">nero_dataset_binaries.tar.gz</a>) is composed from packages of binary executables created by compiling several GNU source-code packages. We used these executables to evaluate our approach as implemented in our prototype "Nero" and compare it to other approaches. All executables contain debug information which serves as the ground truth for the procedure name predictions. The packages are split into three sets: training, validation and test. <ol> <li>The executable file name structure is: "<compiler>-<compiler version>__O<Optimization level(u for default)>__<Package name>[-<optional package version>]__<Executable name>". For example "gcc-5__Ou__cssc__sccs".</li> </ol> </li> <li>The procedure representation file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/procedure_representations.tar.gz?versionId=fef2380c-c869-4a3f-8e32-bc4972dbb219">procedure_representations.tar.gz</a>) contains: <ol> <li>The raw representations for all the binary procedures in the above dataset. Each procedure is represented by one line in the relevant file for each set (training.json, validation.json and test.json) </li> <li>The above representations preprocessed for training.</li> </ol> </li> <li>The pre-trained model file (<a href="https://zenodo.org/api/files/0e98c909-50b4-43e3-8ab2-bb9673eed786/nero_gnn_model.tar.gz">nero_gnn_model.tar.gz</a>) was created using the above preprocessed dataset and contains: <ol> <li>Pre-trained model.</li> <li>Training log.</li> <li>Prediction results log.</li> </ol> </li> </ol> <p>For the code of the "Nero" prototype, and more information about the above artifacts see <a href="https://github.com/tech-srl/Nero">our Github repo</a></p>
Reversible H2 Oxidation and Evolution by Hydrogenase Embedded in a Redox Polymer Film - Original Data
<p>Original data files of the Nature catalysis manuscript submission NATCATAL-20033655A. The data is named according to the corresponding figure captions of teh manuscript main text and the supporting information. A text document lists the figure titles that corresponds to the figure numbers. Fig1, Scheme S1, Scheme S2, FigS 51 are general schemes without any underlying data and are, therefore, not listed here.</p>
Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites
<p>The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (N=835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, STRUCTURE) revealed evidence of historic drainage reversals: Fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific vs. Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of Percichthys trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographic distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.</p>
Anonymized Dataset for "Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Genomics"
<p>Anonymous dataset for the paper "Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Genomics." Includes data for simulated, binary prediction, and profile prediction tasks. </p>
Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses
<p>This dataset contains data files and analysis code associated with manuscript entitled "Parallel reverse genetic screening in mutant human cells using transcriptomics".</p> <p>Data files include expression profiles for over 1800 RNA-seq samples and annotations.</p> <p>Analysis files include R scripts to generate summary figures.</p>
A common mechanism for perceptual reversals in motion-induced blindness, the Troxler effect and perceptual filling-in
<p>This is a www.zenodo.org data upload for publication:</p> <p>Devyatko, Appelbaum and Mitroff (2016) A common mechanism for perceptual reversals in motion-induced blindness, the Troxler effect and perceptual filling-in. Perception. </p>
Bit-wise reversible integrations of the Solar System with JANUS
<p>This dataset contains 24 integrations of the Solar System. The integrator is JANUS, a bit-wise reversible algorithm that uses a mix of integer and floating-point arithmetic. The files are Simulation Archives, which can be opened with the REBOUND code. </p>
Supporting data for Shi et al. "Geospace Concussion: Global reversal of ionospheric vertical plasma drift in response to a sudden commencement"
<p>This dataset contains the simulation data supporting the paper titled "Geospace Concussion: Global reversal of ionospheric vertical plasma drift in response to a sudden commencement", submitted by Shi et al., 2022.</p>
Teleseismic reverse time migration image dataset of southwest Japan in "Three-dimensional teleseismic elastic reverse-time migration with deconvolution imaging condition and its application to southwest Japan"
<p>This dataset contains the teleseismic elastic reverse time migration results of southwest Japan used in the manuscript entitled "Three-dimensional teleseismic elastic reverse-time migration with deconvolution imaging condition and its application to southwest Japan". submitted to Journal of Geophysical Research Letters.</p>
Killer prey: Temperature reverses future bacterial predation
<p>Script and datasets for the paper "Killer prey: Temperature reverses future bacterial predation"</p> <p>Prey killer.zip contains the files and code necessary to reproduce the analysis and the figures in the manuscript.<br> • All datasets, as csv files, are in the Data folder together with the README file.<br> • The Figures and Tables folders contain all figures and tables from the manuscript and SI.<br> • prey_killing_predator_script.Rmd is the script used to perform the statistical analyses and create the figures and tables.</p>
Rapid positive response of young trees growth to warming reverses nitrogen loss from subtropical soil
<ol> <li>Global warming is widely expected to alter nitrogen (N) cycling in terrestrial ecosystems by accelerating N transformations in soils. However, it is unclear how warming will affect plant–soil N cycling in subtropical ecosystems.</li> <li>Here, we measured the N transformations including net ammoniation, nitrification, nitrous oxide emissions, and nitrate in soil solution throughout the plant–soil continuum with two years of experimental soil warming (+5 °C) in a young subtropical Chinese fir mesocosm. Seasonal variations of soil and plant (foliage and root) N concentrations and isotopes (δ<sup>15</sup>N), foliar water use efficiency, and arbuscular mycorrhizal colonization rate were measured.</li> <li>Soil warming significantly increased net ammoniation and nitrification of the soil, together with the transient positive response observed in inorganic N of the soil. Warming increased nitrate N fluxes in soil solution and nitrous oxide emissions in the first year but not in the second year, suggesting N losses through leaching and gaseous in the initial period of warming. Warming primarily induced enrichment of <sup>15</sup>N in foliage relative to the soil, which was attributed to the trade-offs of persistent increases in plant N uptake caused by enhanced tree growth and a decrease in N losses with continuous warming.</li> <li>Warming significantly increased arbuscular mycorrhizal colonization and foliar water use efficiency throughout the warming period. These results suggest that young trees' growth and N uptake can rapidly acclimate to warming by mechanisms including increases in plant water use efficiency and mycorrhizal colonization.</li> <li>Our findings highlight that warming accelerates the plant–soil N cycle and promotes young trees' growth and N uptake, which in turn reduces soil N lost from this subtropical ecosystem. Therefore, our study suggests that the competition for N between plants and microbes governs whether subtropical forests are opened or closed N cycle systems under climate warming. We highlight that young trees can still maintain their high productivity in facing future climate warming since warming can improve plant N uptake and reduce N loss from subtropical ecosystems. </li> </ol>
Fig1. Gel electrophoresis 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig1. Gel electrophoresis 2% agarose
Fig2. Gel electrophoresis Agarose 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig2. Gel electrophoresis Agarose 2%.
Dataset for the manuscript "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5
<p>Dataset for publication "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5, https://doi.org/10.1126/sciadv.adj4883.</p> <p>The details corresponding to the dataset of the figures are given in a readme file in the corresponding folders.</p>
Dataset (I.) related to publication: PIP4K2C inhibition reverses autophagic flux arrest induced by SARS-CoV-2
<p>MD simulation data (PIKfyve simulations) related to publication: </p> <p>Karim, M., Mishra, M., Lo, CW. <em>et al.</em> PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. <em>Nat Commun</em> <strong>16</strong>, 6397 (2025). https://doi.org/10.1038/s41467-025-61759-1</p> <ul> <li>The .zip files contain raw Desmond simulation trajectories of PIKfyve in complex with RMC-113 [18 replicas; each 4 us] (-out.cms files and trajectories).</li> </ul> <p> </p>
Pole Reversals and Delta Q Dynamics: A MEFI-Based Multiscale Analysis
<p>This study examines the phenomena of geomagnetic pole reversals through the Modified Einstein</p> <p>Field Interaction (MEFI) framework. By exploring Delta Q stabilization, resonance deviations, and</p> <p>their global impacts, the study demonstrates MEFI's potential as a universal model. This journal</p> <p>entry provides visual evidence and simulations to highlight the quantum, geophysical, and societal</p> <p>effects of pole reversals, underscoring MEFI?s predictive power.</p>
Data and Weights for Reverse Homology
<p>Training data, weights, and classification datasets for "Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning". </p> <p><strong>Training data:</strong></p> <ul> <li>scer_idr_homologues and human_idr_homologues contain a zip file of the fasta files of IDR homologues used to train the yeast and human model, respectively. Note that these fasta files are aligned, but we strip away the alignment symbol "-" before input into our model. disprot_idr_homologues contain a zip file of IDR homologues corresponding to the DisProt database.</li> <li>human_protein_alignments contains fasta files for the full proteins containing these IDRs</li> </ul> <p><strong>Weights:</strong></p> <ul> <li>scer_idr_model and human_idr_model contain a zip file of the weights for the yeast and human model respectively, which can be loaded into the model files at github.com/alexxijielu/reverse_homology. Likewise, disprot_idr_model contains a zip file of our model trained on DisProt IDRs exclusively.</li> </ul> <p><strong>Logo Websites:</strong></p> <ul> <li>scer_idr_logo_website, human_idr_logo_website, and disprot_idr_logo_website contain a zip file of an HTML file for the yeast, human, and DisProt model respectively, showing sequence logos of the features learned by each model and their enrichments.</li> </ul> <p><strong>Features:</strong></p> <ul> <li>human_idr_features contains the raw feature activations for all human IDRs in our human model. (We didn't include this file in the supplementary for the paper due to size.) </li> </ul> <p><strong>Classification datasets:</strong></p> <ul> <li>IDR_classification_datasets contains datasets used in our benchmarks. These datasets are encoded as binary csv matrixes. cdc28_classification contains IDRs labeled as Cdc28 phosphorylation sites, mitochondrial_targeting_classification contains IDRs labeled as mitochondrial targeting signals, evosig_cluster_classification contains IDRs labeled by clusters assigned in previous computational work by Zarin <em>et al</em>. eLife 2019, and go_SLIM_classification contains proteins labeled by GO Slim annotations. </li> </ul>
Big Five Inventory scores for University Students with relevant item scores reversed.
<ul> <li>First Year (n = 97, cohort 6). Sample details, 55% Male, 45% Female; age profile, typically 18-19*; 94% UK, 6% international. </li> <li>Final Year (n = 44, cohort 7): Sample details: 41% Male, 59% Female; age profile 20-35, m = 22.3; 84% UK, 16% international. </li> <li>Masters (n = 51, cohort 8): Sample details: 43% Male, 57% Female; age profile 20-36, m = 24.3; 49% UK, 51% international. </li> </ul>
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.