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1,197 results for “FLEXIBILITY”
Protein-protein docking with significant backbone flexibility
<p>The trajectory of a single replica from the protein-protein docking simulation of barnase/barstar system. The movie shows the barnase receptor in surface representation and the barstar ligand in ribbon. The presented replica reached the model with interface RMSD value 1.9 Angstrom from the complex X-ray structure, shown as transparent ribbon. </p>
Data from: Heritable variation in circulating glucocorticoids and endocrine flexibility in a free-living songbird
Phenotypic flexibility is a central way that organisms cope with challenging and changing environments. As endocrine signals mediate many phenotypic traits, heritable variation in hormone levels, or their context-dependent flexibility, could present an important target for selection. Several studies have estimated the heritability of circulating glucocorticoid levels under acute stress conditions, but little is known about the potential for either baseline hormone levels or rapid endocrine flexibility to evolve. Here we assessed the potential for selection to operate on the elevation (circulating hormone levels) and flexibility of glucocorticoid reaction norms to acute restraint stress. Multivariate animal models revealed low but significant heritability in baseline (h2=0.13-0.14) and stress-induced glucocorticoids (h2=0.18), and moderate heritability in glucocorticoid flexibility in response to acute stress (h2=0.38) in free-living juvenile tree swallows (Tachycineta bicolor; n=408). Baseline glucocorticoids were not genetically correlated with either stress-induced glucocorticoids or glucocorticoid flexibility. These findings indicate that baseline glucocorticoids and the acute stress response are distinct traits that can be independently shaped by selection. Microevolutionary changes that influence the expression or flexibility of these endocrine mediators of phenotype may be an important way that populations adapt to changing environments and novel threats.
Self-Organized Construction with Continuous Building Material: Higher Flexibility based on Braided Structures
<p>Paper material.</p>
XGNITIVE: A Flexible Cognitive Architecture for Robots (Experiments)
<p>Dataset of experiments for XGNITIVE: A Flexible Cognitive Architecture for Robots. More information in its repository ( https://github.com/roboticslab-uc3m/xgnitive ).</p>
PART-2: Dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>Complementary file for the attached files<br> Written 24-04-2017<br> by Robert Bleischwitz (modellwerft@freenet.de)</p> <p>General Comments</p> <p>0.) This specific upload contains PART-2 of the full dataset</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload contains PART-2 of the full dataset, including introduction file + membrane-wing case (Load+DIC+PIV measurements) </p>
PART-1: Dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>Complementary file for the attached files<br> Written 24-04-2017<br> by Robert Bleischwitz (modellwerft@freenet.de)</p> <p>General Comments</p> <p>0.) This specific upload contains PART-1 of the full dataset</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload contains PART-1 of the full dataset, including introduction file + rigid flat-plate case (Load+PIV measurements) as reference to membrane wing case (PART-2)</p>
Full dataset for journal: "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect"
<p>0.) Version: 18.May 2017</p> <p>1.) The attached data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (DIC) and planar flow measurements via two side-by-side cameras. </p> <p>3.) More setup and processing details can be found in the paper "On the fluid-structure interaction of flexible membrane wings for MAVs in and out of ground-effect" (2017) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in the Journal of Fluids and Structures (http://www.sciencedirect.com/science/article/pii/S088997461630370X)</p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) file, which give further supporting details how to illustrate the data</p> <p>5.) This specific upload is zipped and contains all necessary files to reconstruct the time-resolved dataset.</p>
Data Supporting: Identification of Nonlinearity Sources in a Flexible Wing
Open the record for dataset details and reuse information.
Data from a flexible framework to assess patterns and drivers of beta diversity across spatial scales
<p><span>The patterns and underlying ecological (e.g., environmental filtering) and </span><span>historical</span><span> (e.g., priority effects) drivers of beta diversity are scale-dependent but generally difficult to distinguish</span> <span>and rarely explored with a sufficiently broad range of spatial scales. We propose a general scale-explicit framework to assess and contrast the patterns and drivers of beta diversity across hierarchical spatial scales ranging from within fine-scale ecoregion-scale to among broad-scale ecoregion-scale. By applying this framework to aquatic macroinvertebrate datasets, we show that beta diversity generally increases with spatial extent.</span> <span>With an increasing spatial extent, beta diversity shifts from being more influenced by environmental filtering to being more influenced by recent historical factors (i.e., past beta diversity). Such recent historical effects may result from past environmental variation rather than priority effects.</span><span> We also found that the small-scale and large-scale environmental drivers act differently on beta diversity across spatial extents. Our research reveals a complex spatial-scale dependence in beta diversity patterns and their drivers and provides a more holistic understanding of beta diversity dynamics. Our framework represents a flexible way to unravel the internal structure of beta diversity across scales by partitioning of entire beta diversity variation into scale-specific differences and may have broad application in community ecology, landscape planning and biodiversity conservation.</span></p>
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
<p>Ocean warming favors pelagic tunicates, such as salps, that exhibit increasingly frequent and rapid population blooms, impacting trophic dynamics and composition and human marine-dependent activities. Salp blooms are a result of their successful reproductive life history, alternating seasonally between asexual and sexual protogynous (i.e. sequential) hermaphroditic stages. While predicting future salp bloom frequency and intensity relies on an understanding of the transitions during the sexual stage from female through parturition and subsequent sex change to male, these transitions have not been explored at the molecular level. Here we report the development of the first complete genome of S. thompsoni and the North Atlantic sister species S. aspera. Genome and comparative analyses reveal an abundance of repeats and G-quadruplex (G4) motifs, a highly stable secondary structure, distributed throughout both salp genomes, a feature shared with other tunicates that perform alternating sexual-asexual reproductive strategies. Transcriptional analyses across sexual reproductive stages for S. thompsoni revealed genes associated with male sex differentiation and spermatogenesis are expressed as early as birth and before parturition, inconsistent with previous descriptions of sequential sexual differentiation in salps. Our findings suggest salp are poised for reproductive success at birth, increasing the potential for bloom formation as ocean temperatures rise.</p>
Data from: Flexible females: nutritional state influences biparental cooperation in a burying beetle
<p>In species that provide biparental care, there is sexual conflict between parents over how much each should contribute towards caring for their joint offspring. Theoretical models for the resolution of this conflict through behavioral negotiation between parents assume that parents cannot assess their partner's state directly but do so indirectly by monitoring their partner's contribution. Here, we test whether parents can assess their partner's state directly by investigating the effect of nutritional state on cooperation between parents in the burying beetle <em>Nicrophorus vespilloides</em>. We used a two-by-two factorial design, in which a well-fed or food-deprived female was paired with a well-fed or food-deprived male. We found that females adjusted their level of care in response to both their own nutritional state and that of their partner and that these decisions were independent of their partner's contribution. We found no evidence that males responded directly to nutritional state. Males instead responded indirectly based on the contribution of their partner. Our results suggest that parents are able to assess the state of their partner, in contrast to what has been assumed, and that these assessments play an important role in the mediation of sexual conflict between caring parents.</p>
Data from: Consistent seasonal flexibility of the gut and its regions across wild populations of a winter-quiescent fish
<p>Here, we investigated phenotypic flexibility in the size of the gastrointestinal (GI) tract across three northern populations of a winter-dormant warm-water fish, pumpkinseed sunfish (<em>Lepomis gibbosus</em>). The dried masses of all gut regions (stomach, pyloric caeca, intestine) were measured approximately biweekly between January and August 2021. In all populations, pumpkinseed exhibited pronounced structural flexibility in the GI tract, aligned with winter and the timing of reproduction. The dry mass of the GI increased by 1.3- to nearly 2.5-fold in the early spring. The pyloric caeca demonstrated the greatest capacity for flexibility, increasing by up to 3.7-fold prior to reproduction. In all populations, minimum dry GI mass was consistently achieved during winter and mid-summer. This capacity for gut flexibility may represent a novel mechanism for facilitating rapid adaptive responses (e.g., metabolic plasticity) to future environmental change.</p>
Carotenoid skin ornaments as flexible indicators of male foraging behavior in a marine predator: Variation among Mexican colonies of Brown Booby (Sula leucogaster)
<p>Carotenoid-dependent ornaments can reflect animals' diet and foraging behaviors. However, this association should be spatially flexible and variable among populations to account for geographic variation in optimal foraging behaviors. We tested this hypothesis using populations of a marine predator (the brown booby, <em>Sula leucogaster</em>) that forage across a gradient in ocean depth in and near the Gulf of California. Specifically, we quantified green chroma for two skin traits (foot and gular color) and their relationship to foraging location and diet of males, as measured via GPS tracking and stable carbon isotope analysis of blood plasma. Our three focal colonies varied in which foraging attributes were linked to carotenoid-rich ornaments. For gular skin, our data showed a shift from a benthic prey-green skin association in the shallow waters in the north to a pelagic prey-green skin association in the deepest waters to the south. Mean foraging trip duration and distance of the foraging site from the coast also predicted skin coloration in some colonies. Finally, brown booby colonies varied in which trait (foot vs. gular skin color) was associated with foraging metrics. Overall, our results indicate that male ornaments reflect the quality of diet and foraging – information that may help females select mates who are adapted to local foraging conditions and therefore, are likely to provide better parental care. More broadly, our results stress that diet-dependent ornaments are intimately linked to animals' environments and that we cannot assume ornaments or ornament signal content are ubiquitous within species, even when ornaments appear similar among populations. </p>
Data from: Time or distance: flexible coding of Hippocampal cells
<p>Analysis of neuronal activity in the hippocampus of behaving animals has revealed cells acting as "Time Cells," which exhibit selective spiking patterns at specific time intervals since a triggering event, and "Distance Cells," which encode the traversal of specific distances. Other neurons exhibit a combination of these features, alongside place selectivity. This study aims to investigate how the task performed by animals during recording sessions influences the formation of these representations. The data used here was originally curated in a treadmill running study conducted by Kraus et al. (2013) in which rats were trained to run at different velocities. The rats were recorded in two trial contexts: a "fixed time" condition, where the animal ran on the treadmill for a predetermined duration before proceeding, and a "fixed distance" condition, where the animal ran a specific distance on the treadmill. Our findings indicate that the type of experimental condition significantly influenced the encoding of hippocampal cells. Specifically, distance-encoding cells dominated in fixed-distance experiments, whereas time-encoding cells dominated in fixed-time experiments. These results underscore the flexible coding capabilities of the hippocampus, which are shaped by over-representation of salient variables associated with reward conditions.</p> <p>Data used in Absramson et al., 2023, "<strong>Time or distance: flexible coding of Hippocampal cells</strong>", originally curated by Kraus et al., Neuron, 78(6), 1090-1101, 2013.</p>
FEater dataset: A molecular fragment dataset to benchmark the robustness of 3D flexible object recognition
<p>This dataset is associated with the work: Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models</p> <pre><code># Original FEater-Single and FEater_Dual dataset. FEater_Single ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 FEater_Dual ├── TestSet_coord.h5 ├── TrainingSet_coord.h5 └── ValidationSet_coord.h5 # Non-redundant baseline dataset FEater_Baseline ├── TestSet_Dual.h5 ├── TestSet_Single.h5 ├── TrainingSet_Dual.h5 └── TrainingSet_Single.h5 # FEater-Single and FEater_Dual in different sample size FEater_Mini200 ├── Mini200_Dual.h5 └── Mini200_Single.h5 FEater_Mini400 ├── Mini400_Dual.h5 └── Mini400_Single.h5 FEater_Mini800 ├── Mini800_Dual.h5 └── Mini800_Single.h5</code></pre> <p>For further details of the usage, please visit the original GitHub repository: <a title="FEater_repo" href="https://github.com/miemiemmmm/FEater" target="_blank" rel="noopener">https://github.com/miemiemmmm/FEater</a></p>
How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study - Second part
<p>Second part of the data deposition for the paper "<strong>How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study</strong>", by Lemmens et al. Part one is availible via <a href="https://doi.org/10.5281/zenodo.13929049">10.5281/zenodo.13929049</a></p>
Behavioral flexibility in solitary foraging ants: how experience, colony size and food distribution shape individual and collective performance
<p>To deal with the unpredictability of available food resources, animals must adjust their behavior to optimize foraging efficiency. Various mechanisms can influence an individual’s food acquisition behaviour, and thus our knowledge of their combined impact on foraging efficiency remains limited. In this study, we conducted laboratory experiments with seven colonies of the solitary foraging ant Dinoponera quadriceps. Foragers were individually observed in semi-controlled experiments where food was offered in aggregated or dispersed distributions. During the experiments, individual participation was voluntary (i.e. ants were free to enter or not the experimental arena), giving us an opportunity to assess internal processes such as motivation. Besides, behavioral traits such as foraging activity, exploration of food patches, and performance were recorded across repeated trials. We found that solitary foragers of D. quadriceps were highly efficient (retrieving food in 77.38% of the trips), especially when exploiting aggregated and abundant food resources. However, individual foraging success declined when more conspecific foragers were present and with longer foraging experience. Foragers increased their exploration levels in environments with larger numbers of dispersed prey items. Individual foraging activity was higher with more experience and in smaller colonies with fewer foragers. Furthermore, foragers and colonies exhibited low but consistent differences in levels of activity, exploration, and success rates. These findings provide a comprehensive view of how different factors combine to give rise to complex behaviors such as foraging. Additionally, they emphasize the importance of individual traits for effective task performance within social groups, an understudied topic.</p>
Data for the paper "Computing MHD equilibria of stellarators with a flexible coordinate frame"
<p>Data for the revised paper "<span>Computing MHD equilibria of stellarators with a </span><span>flexible coordinate frame"</span></p> <p>Thetitle has changed from the submission title: "A generalized Frenet frame for computing MHD equilibria in stellarators"</p> <p>We provide the input and output files for all GVEC simluations presented at the "JOINT VARENNA - LAUSANNE INTERNATIONAL WORKSHOP: THEORY OF FUSION PLASMAS, 2024" and to be published in PPCF.</p> <p>An ipython script that generates the postprocessing /plots is also provided.</p> <p>New content computing the frame from a boundary surface obtained from quasr is now also part of this compilation.</p> <p>See the README.md file for details.</p>
Data from: Evolution of flexible biting in hyperdiverse parasitoid wasps
<p>One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting, but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99 percent of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of freedom and hypothesize their major role in insect diversification. These mandibles are defining features of parasitoid chalcid wasps, one of the most species-rich lineages of insects. The shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps. We reveal a crucial step in insect evolution and highlight the importance of comprehensive studies even of putatively well-known systems.</p>
Conformational ensembles used in "Refining conformational ensembles of flexible proteins against SAXS data; Pesce F. and Lindorff-Larsen K."
<p>Conformational ensembles of Histatin5, Sic1, Tau generated with Flexible-meccano and converted to all-atom models with PULCHRA. TIA-1 ensemble from https://doi.org/10.1371/journal.pcbi.1007870</p> <p>These ensembles have been used for SAXS calculations and reweighting against experimental SAXS data to study the effect of the hydration layer description on the reweighted ensembles.</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.