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2,412 results for “independent”
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Source data for manuscript(De novo protein design with a denoising diffusion network independent of pre-trained structure prediction models)
<p>This respository contains the source data for figure and supplementary figure in manuscript(SCUBA-D).</p>
Data for the manuscript: Historical biogeography of Pomaderris (Rhamnaceae): continental vicariance in Australia and repeated independent dispersals to New Zealand
<p>Gondwanan biogeographic patterns include a combination of old vicariance events following the breakup of the supercontinent, and more recent long-distance dispersals across the southern landmasses. Floristic relationships between Australia and New Zealand have mostly been attributed to recent dispersal events rather than vicariance. We assessed the biogeographic history of Pomaderris (Rhamnaceae), which occurs in both Australia and New Zealand, by constructing a time-calibrated molecular phylogeny to infer (1) phylogenetic relationships and (2) the relative contributions of vicariance and dispersal events in the biogeographic history of the genus. Using hybrid capture and high throughput sequencing, we generated nuclear and plastid data sets to estimate phylogenetic relationships and fossil calibrated divergence time estimates for Pomaderris . BioGeoBEARS and biogeographical stochastic mapping (BSM) were used to assess the ancestral area of the genus and the relative contributions of vicariance vs dispersal, and the directionality of dispersal events. Our analyses indicate that Pomaderris originated in the Oligocene and had a widespread Australian distribution. Vicariance of western and eastern Australian clades coincides with the uplift of the Nullarbor Plain c. 14 Ma, followed by subsequent in-situ and within-biome diversification with little exchange across regions. A rapid radiation of southeastern Australian taxa beginning c. 10 Ma was the source for at least six independent long-distance dispersal events to New Zealand during the Pliocene–Pleistocene. Our study demonstrates the importance of dispersal in explaining not only the current cross-Tasman distributions of Pomaderris, but for the New Zealand flora more broadly. The pattern of multiple independent long-distance dispersal events for Pomaderris , without significant radiation within New Zealand, is congruent with other lowland plant groups, suggesting that this biome has a different evolutionary history compared with the younger alpine flora of New Zealand, which exhibits extensive radiations often following single long distance dispersal events.</p>
Data from: Proximity to parasites reduces host fitness independent of infection in a Drosophila-Macrocheles system
<p>We assayed the longevity and reproductive output of Drosophila nigrospiracula exposed or not exposed to ectoparasitic Macrocheles subbadius accross a mesh barrier. As such we measured the non-consumptive effects (extending the ecology of fear to host-parasite systems) of an ectoparasite on host fecundity and survival. We found that exposure to mites, without infection, caused flies to live shorter lives and produce fewer offspring.</p>
Active sensing in bees through antennal movements is independent of odor molecule (Exemple videos)
<p>Exemple videos demanded by the reviewers to illustrate particular behaviors of the insects or details of the experimental setup. Please see the relevant section in the response document.</p>
Active sensing in bees through antennal movements is independent of odor molecule (Article videos)
<p>Exemple videos referenced in the paper to illustrate particular behaviors of the insects. Please see the relevant section in the supplementary material.</p>
Dataset for Ligand-independent oligomerization of TACI is controlled by the transmembrane domain and regulates proliferation of activated B cells.
<p>This data set provides:</p> <p>a) Details about plasmids used in this study. It is a pdf file, describing expressed sequences and other features of plasmids listed in Supplementary Table 2.</p> <p>b) An Excel file with data used to make graphs of the publication</p>
Independent variation of avian sensitivity to climate change and trait-based adaptive capacity along a tropical elevational gradient
<p>Aim: How species respond to climate change is influenced by their sensitivity to climatic conditions (i.e., their climatic niche) and aspects of their adaptive capacity (e.g., their dispersal ability, ecological niche). To date, it is largely unknown whether and how species' sensitivity to climate change and their adaptive capacity covary. However, understanding this relationship is important to predict the potential consequences of a changing climate for species assemblages. Here, we test how species' sensitivity to climate change and trait-based measures of their ecological adaptive capacity (i) vary along a broad elevational gradient and (ii) covary across a large number of bird species.</p> <p>Location: A Neotropical elevational gradient (300 - 3600 m.a.s.l.) in the Manú biosphere reserve, south‐east Peru.</p> <p>Methods: We focus on 215 frugivorous bird species along a Neotropical elevational gradient. We approximate species' sensitivity to climate change by their climatic niche breadth, based on species occurrences across South America and bioclimatic variables. In addition, we use a trait-based approach to estimate the dispersal ability of species (approximated by their wing pointedness), their dietary niche breadth (approximated by bill width), and their habitat niche breadth (the number of used habitat classes).</p> <p>Results: We found that (i) species' climatic niche breadth increased with elevation, while their trait-based dispersal ability and dietary niche breadth decreased with elevation, and (ii) sensitivity to climate change and trait-based adaptive capacity were not related across species.</p> <p>Main conclusions: These results suggest different mechanisms of how species in lowland and highland assemblages might respond to climate change. The independent variation of species' sensitivity to climate change and their trait-based adaptive capacity suggests that accounting for both dimensions will improve assessments of species' susceptibility to climate change and potential impacts of climate change on diverse species assemblages.</p>
Phylogeny and disparate selection signatures suggest two genetically independent domestication events of pea (Pisum L.)
<p>Domestication is considered a model of adaptation that can be used to draw conclusions about the <em>modus operandi</em> of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 <em>Pisum sativum</em> (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild <em>P. sativum</em> revealed five distinct groups with a notable geographic pattern. <em>Pisum abyssinicum</em> clustered unequivocally within the <em>P. sativum</em> complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in <em>P. sativum</em> ssp. <em>sativum</em> and three in <em>P. abyssinicum</em>. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild <em>P. sativum</em> is structured into well-diverged subgroups. Although <em>Pisum sativum</em> ssp<em>. humile</em> is not supported as a taxonomic entity, the so-called 'southern <em>humile</em>' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.</p>
Largely independent effects of top predators, including Amur tigers and humans, on mammal communities in a recovering temperate forest region
<p>Data associated with the manuscript "Largely independent effects of top predators, including Amur tigers and humans, on mammal communities in a recovering temperate forest region"</p>
Data from: Population variation reveals independent selection towards small body size in Chinese Debao pony
Body size, one of the most important quantitative traits under evolutionary scrutiny, varies considerably among species and among populations within species. Revealing the genetic basis underlying this variation is very important, particularly in humans where there is a close relationship with diseases and in domestic animals as the selective patterns are associated with improvements in production traits. The Debao pony is a horse breed with small body size that is unique to China; however, it is unknown whether the size-related candidate genes identified in Western breeds also account for the small body size of the Debao pony. Here, we compared individual horses from the Debao population with other two Chinese horse populations using SNPs identified with the Equine SNP 65 Bead Chip. The previously reported size-related candidate gene HMGA2 showed a significant signature for selection, consistent with its role observed in human populations. More interestingly, we found a candidate gene TBX3, which had not been observed in previous studies on horse body size that displayed the highest differentiation and most significant association, and thus likely is the dominating factor for the small stature of the Debao pony. Further comparison between the Debao pony and other breeds of horses from around the world demonstrated that TBX3 was selected independently in the Debao pony, suggesting that there were multiple origins of small stature in the horse.
The Early Functional Abilities-revised may bridge the gap between the disorder of consciousness and the functional independence scales: evidence from Rasch analysis
<p>Raw data associated with the scientific publication “The Early Functional Abilities-revised may bridge the gap between the disorder of consciousness and the functional independence scales: evidence from Rasch analysis”</p>
Datasets for "Reading Order Independent Metrics for Information Extraction in Handwritten Documents"
<p>This repository includes the five datasets used for our paper entitled <em>Reading Order Independent Metrics for Information Extraction in Handwritten Documents</em>, in which we compare various metrics to evaluate end-to-end information extraction from scanned documents.</p> <h2>Datasets</h2> <p>Five datasets are released following the BIO format:</p> <ul> <li>IAM</li> <li>Simara</li> <li>POPP</li> <li>Esposalles</li> <li>French Military Records</li> </ul> <p>For each dataset, we provide the following data (on test sets):</p> <ul> <li>Ground truth annotations (<code>gt/</code>)</li> <li>Automatic predictions (<code>dan/</code>)</li> <li>Automatic predictions with entities appearing in random order (<code>dan_shuffled/</code>)</li> </ul> <p>The data is organized as follows:</p> <p><code>├── Dataset name/</code><br><code>│ ├── gt/</code><br><code>│ ├── dan/</code><br><code>│ └── dan_shuffled/</code></p> <h2>Metrics</h2> <p>To install the <a href="https://pypi.org/project/ie-eval/"><code>ie-eval</code></a> package, run <code>pip install ie-eval</code>.</p> <p>To compute all metrics on a specific dataset, run:<br><br><code>ie-eval all --label-dir IAM_paragraph/gt/ --prediction-dir IAM_paragraph/dan/</code><br><br></p> <p>To learn more about the various options, use the <code>--help</code> argument or read the <a href="https://ie-eval-ner-metrics-050f40e80b04480e2310d39ad338de778f6bec80e18.pages.teklia.com/">documentation</a>.</p> <p> </p>
Research Data and Code: Evaluating Railway Junction Infrastructure: A Queueing-Based, Timetable-Independent Analysis
<p>Research Data and Code for the publication:</p> <p>Evaluating Railway Junction Infrastructure: A<br>Queueing-Based, Timetable-Independent Analysis</p> <p>In Transportation Research Part C - Emerging Technologies</p> <p>DOI: https://doi.org/10.1016/j.trc.2024.104704</p>
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Supplementary materials for publication Hlanze H. et al. Universal lineage-independent markers of multidrug re-sistance in M. tuberculosis. IJMS 2024.
<p>Drug resistance mutations stat.xlsx - this is an Excel file with data on the statistical evaluation of associations between mutations in protein-coding genes of<em> M. tuberculosis</em> and multidrug resistance;</p> <p>Drug mutation associations for Cytoscape.cys - this is a Cytoscape 3.10.2 dataset with predicted epistatic interactions among global markers of drug resistance in the overall <em>M. tuberculosis </em>population<em>.</em></p>
Evolutionary change is remarkably time independent across scales
Open the record for dataset details and reuse information.
Research productivity in the post-independence period in Portuguese-speaking African countries, a case of Mozambique: Bibliometric analysis of four decades of Health Research and Higher Education
<p>The following datasets were used to build the bibliometric analysis of most productive institutions and frequent keywords in Mozambique.</p>
Adaptive radiation without independent stages of trait evolution in a group of Caribbean anoles
<p>Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a 'stages' model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, belying independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time and historical biogeography, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.</p>
Data of "Efficient and Device-Independent Active Quantum State Certification"
<p>Dataset and analysis code for the manuscript "Efficient and Device-Independent Active Quantum State Certification"</p>
ScienceDex guides
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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.