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1,670 results for “FORCE”
Datasets associated with "Improving Small Molecule Force Fields by Identifying and Characterizing Small Molecules with Inconsistent Parameters"
<p>This provides associated datasets for a paper/preprint forthcoming soon, by Ehrman et al., "Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters". A poster describing an earlier portion of the work is available at https://doi.org/10.5281/zenodo.3385278. The AllMolsAllData.csv.gz file provides a Pandas dataframe for the full set of molecules considered, as described in the paper, whereas the 25andunderarchive.tar.gz provides optimized geometries for 265,847 molecules with four or more difference flags.</p>
Cell mechanics measurements in force mapping AFMBioMed Summer school 2020
<p>A 15 min video tutorial to perform AFM cell mechanics measurements in force mapping mode.</p> <p>The video presents:</p> <ul> <li>Preparation of the sample</li> <li>Cantilever coating and calibration </li> <li>Laser alignment and approach</li> <li>How to perform force curves and force maps on living adherent cells</li> </ul>
Slipids-2020 force field for lipid bilayer simulations
<p>Slipids-2020 force field for various lipids<br> -----------------------------------------------------</p> <p>Authors: Joakim Jämbeck, Inna Ermilova, Fredrik Grote, Alexander Lyubartsev<br> Department of Materials and Environmental Chemistry,<br> Stockholm University, Stockholm 10691 Sweden<br> e-mail: alexander.lyubartsev@mmk.su.se<br> 2012 - 2020</p> <p><br> Content:</p> <p>Slipids_2020.ff: directory containing the force field.<br> Included into the Gromacs topology file by: <br> #include "Slipids_2020.ff/forcefield.itp"</p> <p>itp_files: itp files for various lipids<br> boxes: equilibrated configurations for some lipid systems</p> <p>The force field can be used together with the AMBER-family FF for proteins and GAFF for small molecules</p> <p> </p>
Meniscus Matrix Remodeling in Response to Compressive Forces in Dogs
<p>Joint motion and postnatal stress of weight bearing are the principal factors that determine the phenotypical and architectural changes that characterize the maturation process of the meniscus. In this study, the effect of compressive forces on the meniscus will be evaluated in a litter of 12 Dobermann Pinschers, of approximately 2 months of age, euthanized as affected by the quadriceps contracture muscle syndrome of a single limb focusing on extracellular matrix remodeling and cell-extracellular matrix interaction (i.e., meniscal cells maturation, collagen fibers typology and arrangement). The affected limbs were considered as models of continuous compression while the physiologic loaded limbs were considered as controls. The results of this study suggest that a compressive continuous force, applied to the native meniscal cells, triggers an early maturation of the cellular phenotype, at the expense of the proper organization of collagen fibers. Nevertheless, an application of a compressive force could be useful in the engineering process of meniscal tissue in order to induce a faster achievement of the mature cellular phenotype and, consequently, the earlier production of the fundamental extracellular matrix (ECM), in order to improve cellular viability and adhesion of the cells within a hypothetical synthetic scaffold.</p>
Sarcomere length non-uniformities dictate force production along the descending limb of the force-length relation
<p>The force-length relation is one of the most defining features of the sliding filament theory of muscle contraction, and yet a topic of debate in the literature. The force-length relation predicts that the force produced by muscle fibers is directly proportional to the degree of overlap between myosin and actin filaments, but several studies have shown forces that are larger than predicted, especially at long sarcomere lengths. The reason for such discrepancies may be due to technical difficulties – studies have been conducted with muscle fibers, a preparation containing thousands of sarcomeres that makes accurate length measurements challanging. The aim of this study was to directly evaluate force production and sarcomere dynamics in isolated myofibrils and single sarcomeres to enhance our understanding about mechanisms governing deviations from the theoretically predicted force-length relation. Contractions at varying sarcomere lengths (SLs) along the plateau (SL=2.25m-2.39m) and the descending limb (SL>2.39m) of the force-length relation were induced by solution switching, and different modes of force measurements were used. Our results show that single sarcomeres and extrapolated forces resemble the theoretical force-length relation closely, while myofibrils with sarcomere length dispersions show an extension of the plateau region and forces elevated above predicted levels. We also found an increase in sarcomere length non-uniformity and slowed rate of force production at long lengths in myofibrils with sarcomeres in series but not in single sarcomere preparations. We conclude that the deviation of the descending limb of the force-length relation obtained from plateau forces is correlated with the degree of sarcomere length non-uniformity and slowed force development.</p>
Amundsen Sea future MAR simulations forced by the CMIP5 multi-model mean
<p><strong>Amundsen Sea future MAR simulation forced by the CMIP5 multi-model mean (RCP8.5)</strong></p> <p>This future simulation is fully described in the following article:</p> <p>Donat-Magnin, M., Jourdain, N. C., Kittel, C., Agosta, C., Amory, C., Gallée, H., Krinner, G., and Chekki, M. Future surface mass balance and surface melt in the Amundsen sector of the West Antarctic Ice Sheet. <em>The Cryosphere</em>.</p> <p>The future is derived from the CMIP5 multi-model mean under the RCP8.5 scenario and covers the 2079-2108 period. The corresponding present-day simulation is available on <a href="http://doi.org/10.5281/zenodo.4308510">http://doi.org/10.5281/zenodo.4308510</a> and was thoroughly evaluated in the following TC paper: <a href="https://doi.org/10.5194/tc-14-229-2020">https://doi.org/10.5194/tc-14-229-2020</a></p> <p>See netcdf metadata for more information. Note that what is called runoff in the outputs is not actually a runoff (into the ocean) but more the net production of liquid water at the surface (which can either form ponds or flow into the ocean).</p> <p>Monthly files provided on MAR grid (see MAR_grid10km.nc). We also provide climatological (2079-2108 average) surface mass balance (SMB), surface melt rates and net liquid water production ("runoff") on a standard 8km WGS84 stereographic grid (see files ending as mean_polar_stereo.nc). Daily snowfall and surface melt rates are provided in ICE*nc.<br> <br> The interpolation to the stereographic grid is done using interpolate_to_std_polar_stereographic.f90. The fields are extrapolated to the ocean grid points so that ice sheet models with various ice-shelf extent can use this dataset.</p> <p>To extrapolate the SMB and surface melt projections to other warming scenarios or period, see eq. (2,3) in Donat-Magnin et al.</p> <p>The following variables are provided:</p> <ul> <li>CC Cloud Cover</li> <li>LHF Latent Heat Flux</li> <li>LWD Long Wave Downward</li> <li>LWU Long Wave Upward</li> <li>QQp Specific Humidity (pressure levels)</li> <li>QQz Specific Humidity (height levels)</li> <li>RH Relative Humidity</li> <li>SHF Sensible Heat Flux</li> <li>SIC Sea ice cover</li> <li>SP Surface Pressure</li> <li>ST Surface Temperature</li> <li>SWD Short Wave Downward</li> <li>SWU Short Wave Upward</li> <li>TI1 Ice/Snow Temperature (snow-layer levels)</li> <li>TTz Temperature (height levels)</li> <li>UUp x-Wind Speed component (pressure levels)</li> <li>UUz x-Wind Speed component (height levels)</li> <li>VVp y-Wind Speed component (pressure levels)</li> <li>VVz y-Wind Speed component (height levels)</li> <li>UVp Horizontal Wind Speed (pressure levels)</li> <li>UVz Horizontal Wind Speed (height levels)</li> <li>ZZp Geopotential Height (pressure levels)</li> <li>mlt Surface melt rate</li> <li>rfz Refreezing rate</li> <li>rnf Rainfall</li> <li>rof "Runoff" (i.e. net production of surface liquid water)</li> <li>sbl Sublimation</li> <li>smb Surface Mass Balance</li> <li>snf Snowfall</li> </ul>
Data-driven subgrid-scale modeling of forced Burgers turbulence using deep learning with generalization to higher Reynolds numbers via transfer learning
<p>These are the data files for use with the codes in https://github.com/envfluids/Burgers_DDP_and_TL.</p>
Data for Multiscale temporal response of salt intrusion to transient river and ocean forcing
<p>Data used in the paper 'Multiscale temporal response of salt intrusion to transient river and ocean forcing'</p>
Linking Seasonal-to-Interannual Variability of Intermediate Currents in the Southwest Tropical Pacific to Wind Forcing and ENSO
<p>This dataset contains zonal velocity data observed by the mooring at 142E/0,142E,1S,141.4E/1.7S. It is supplementary of the paper "<strong>Linking Seasonal-to-Interannual Variability of Intermediate Currents in the Southwest Tropical Pacific to Wind Forcing and ENSO</strong>" published by the Geophysical Research Letters (https://doi.org/10.1029/2021GL092440). Please let me know if you need any more information.</p>
Aviation contrail cirrus and radiative forcing over Europe for six months in 2020 during COVID-19 compared with 2019: Observations and model results
<p>This file contains supporting information for a manuscript submitted for publication.</p> <p>Aviation contrail cirrus and radiative forcing over Europe for six months in 2020 during COVID-19 compared with 2019: Observations and model results </p> <p>U. Schumann, L. Bugliaro, and C. Voigt</p> <p>Corresponding author: Ulrich Schumann (Ulrich.schumann@dlr.de)</p> <p>For details see the README.txt</p> <p> </p> <p> </p>
Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact with abiotic factors. 2. Here, we develop the use of an ergometer in a novel application to investigate variation in seed traits, specifically the force required for seed abscission and seed terminal velocity, exhibited by seeds from different locations within maternal capitula of the invasive species Carduus nutans (Asteraceae). 3. We find that seeds from the center of capitula are significantly easier to liberate and have slower falling velocities than siblings found near the edge of capitula. When abscission force is positively correlated with terminal velocity, slowly falling, easily abscised seeds are projected to travel much further than the average seed on slow winds. 4. Our experimental and theoretical results, which together show that within-individual variation can strongly affect model projections of species dispersal, have important implications for our broader understanding of population spread rates, the spatial structure of populations, metapopulation connectivity, and gene flow in the landscape.
Data from: Association of work-related stress with mental health problems in a special police force unit
Objectives. Law and order enforcement tasks may expose special force police officers to significant psychosocial risk factors. The aim of this work is to investigate the relationship between job stress and the presence of mental health symptoms while controlling for socio-demographical, occupational and personality variables in special force police officers. Method: At different time points, 292 out of 294 members of the 'VI Reparto Mobile', a special police force engaged exclusively in the enforcement of law and order, responded to our invitation to complete questionnaires for the assessment of personality traits, work-related stress (using the demand-control-support (DCS) and the effort-reward-imbalance (ERI) models), and mental health problems such as depression, anxiety and burnout. Results: Regression analyses showed that lower levels of support and reward and higher levels of effort and overcomittment were associated with higher levels of mental health symptoms. Psychological screening revealed 21 (7.3%) likely cases of mild depression (BDI ≥10). Officers who had experienced a discrepancy between work effort and rewards showed a marked increase in the risk of depression (OR 7.89 95%CI 2.32-26.82) when compared with their counterparts who did not perceive themselves to be in a condition of distress. Conclusions: The findings of this study suggest that self-reported work-related stress may play a role in the development of mental health problems in police officers. The prevalence of mental health symptoms in the cohort investigated here was low, but not negligible in the case of depression. Since special forces police officers have to perform sensitive tasks for which a healthy psychological functioning is needed, the results of this study suggest that steps should be taken to prevent distress and improve the mental well-being of these workers.
Data from: Climatic forcing of Quaternary deep-sea benthic communities in the North Pacific Ocean
There is a growing evidence that changes in deep-sea benthic ecosystems are modulated by climate changes, but most evidence to date comes from the North Atlantic Ocean. Here we analyze new ostracod and published foraminiferal records for the last 250,000 years on Shatsky Rise in the North Pacific Ocean. Using linear models, we evaluate statistically the ability of environmental drivers (temperature, productivity, and seasonality of productivity) to predict changes in faunal diversity, abundance and composition. These microfossil data show glacial-interglacial shifts in overall abundances and species diversities that are low during glacial intervals and high during interglacials. These patterns replicate those previously documented in the North Atlantic Ocean, suggesting that the climatic forcing of the deep-sea ecosystem is widespread, and possibly global in nature. However, these results also reveal differences with prior studies that probably reflect the isolated nature of Shatsky Rise as a remote oceanic plateau. Ostracod assemblages on Shatsky Rise are highly endemic but of low diversity, consistent with the limited dispersal potential of these animals. Benthic foraminifera, by contrast, have much greater dispersal ability and their assemblages at Shatsky Rise show diversities typical for deep-sea faunas in other regions. Statistical analyses also reveal ostracod–foraminferal differences in relationships between environmental drivers and biotic change. Rarefied diversity is best explained as a hump-shaped function of surface productivity in ostracods, but as having a weak and positive relationship with temperature in foraminifera. Abundance shows a positive relationship with both productivity and seasonality of productivity in foraminifera, and a hump-shaped relationship in ostracods. Finally, species composition in ostracods is influenced by both temperature and productivity, but only a temperature effect is evident in foraminifera. Though complex in detail, the global-scale link between deep-sea ecosystems and Quaternary climate changes underscores the interaction between the physical and biological components of paleoceanographical research to better understand the history of the biosphere.
Data from: Beyond size – morphological predictors of bite force in a diverse insectivorous bat assemblage from Malaysia
1. Bite force is used to investigate feeding performance in a variety of vertebrates. In all taxa studied, bite force is strongly correlated with body and head size. Studies of bite force in bats have largely centred on neotropical species with a particular focus on species that maximize dietary differences. Little is known about the bite force of bats from the Old World tropics, nor of variation in bite force within diverse assemblages of obligate insectivores. Moreover, factors other than size are poorly known but may be important in driving interspecific differences in bite force, and thereby diet. 2. Here, we examine the correlation between morphological variation and bite force of 35 species of insectivorous bats from a single palaeotropical assemblage. We confirmed the overall relationship between size and bite force across species, but found that bite force is predicted more strongly by head length than body mass or forearm length. 3. From the combined action of jaw muscles and muscle-bone mechanisms, bats generate a mechanical advantage that creates pressure during biting. We calculated the size-independent mechanical advantage for each of five mandible lever systems (three delineated by the temporalis muscle and two delineated by the masseter muscle) operating through three function points (molar, canine, and incisor). Size-independent mechanical advantage of the suprazygomatic portion of the temporalis muscle at the molar function point was the only significant predictor of size-independent maximum bite force across all species. 4. Within families, the size-independent mechanical advantage of the superficial portion of the masseter muscle plays a significant role in predicting size-independent maximum bite force in both the Rhinolophidae and Vespertilionidae. For the family Hipposideridae, however, size-independent mechanical advantage showed no role in predicting size-independent maximum bite force, suggesting that size really matters in predicting the maximum bite force capacity for this family.
Data from: A multi-decade dataset of monthly beach profile surveys and inshore wave forcing at Narrabeen, Australia
Long-term observational datasets that record and quantify variability, changes and trends in beach morphology at sandy coastlines together with the accompanying wave climate are rare. A monthly beach profile survey program commenced in April 1976 at Narrabeen located on Sydney's Northern Beaches in southeast Australia is one of just a handful of sites worldwide where on-going and uninterrupted beach monitoring now spans multiple decades. With the Narrabeen survey program reaching its 40-year milestone in April 2016, it is timely that free and unrestricted use of these data be facilitated to support the next advances in beach erosion-recovery modelling. The archived dataset detailed here includes the monthly subaerial profiles, available bathymetry for each survey transect extending seawards to 20 m water depth, and time-series of ocean astronomical tide and inshore wave forcing at 10 m water depths, the latter corresponding to the location of individual survey transects. In addition, on-going access to the results of the continuing monthly survey program is described.
Data from: Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen
The Pleistocene climatic fluctuations had a huge impact on all life-forms, and various hypotheses regarding the survival of organisms during glacial periods have been postulated. In the European Alps, evidence has been found in support of refugia outside the ice shield (massifs de refuge) acting as sources for postglacial recolonisation of inner-Alpine areas. In contrast, evidence for survival on nunataks, ice-free areas above the glacier, remains scarce. Here, we combine multivariate genetic analyses with ecological niche models (ENMs) through multiple timescales to elucidate the history of alpine Megabunus harvestmen throughout the ice ages, a genus that comprises eight high altitude endemics. ENMs suggest two types of refugia throughout the Last Glacial Maximum, inner-Alpine survival on nunataks for four species and peripheral refugia for further four species. In some geographic regions, the patterns of genetic variation are consistent with long-distance dispersal out of massifs de refuge, repeatedly coupled with geographic parthenogenesis. In other regions, long-term persistence in nunataks may dominate the patterns of genetic divergence. Overall, our results suggest that glacial cycles contributed to allopatric diversification in Alpine Megabunus, both within and at the margins of the ice shield. These findings exemplify the power of ENM projections coupled with genetic analyses to identify hypotheses about the position and number of glacial refugia and thus to evaluate the role of Pleistocene glaciations in driving species-specific responses of recolonisation or persistence that may have contributed to observed patterns of biodiversity.
Data from: Rapid diversification of sexual signals in Hawaiian Nesosydne planthoppers (Hemiptera: Delphacidae): the relative role of neutral and selective forces
Changes in sexual signals have the potential to promote rapid divergence and reproductive isolation among populations of animals. Thus, identifying processes contributing to variation in signals is key to understanding the drivers of speciation. However, it is difficult to identify the processes initiating changes in signals in empirical systems because (1) the demographic history of populations under study is usually unclear, and (2) there is no unified hypothesis-testing framework for evaluating the simultaneous contribution of multiple processes. A unique system for study in the Hawaiian Islands, the planthopper species Nesosydne chambersi, offers a clear demographic context to disentangle these factors. By measuring variation in male vibratory sexual signals across different genetic populations on the island of Hawaii, we found that that multiple signal traits varied significantly between populations. We developed a mixed modelling framework to simultaneously test competing hypotheses about which processes contribute to changes in signal traits: genetic drift, sensory drive or reproductive character displacement. Our findings suggest that signal divergence proceeds along different axes for different signal traits under the influence of both neutral and selective processes. They are the first, to our knowledge, to document the relative importance of multiple processes on divergence in sexual signals.
Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats
Maximum bite force is an important metric of feeding performance that defines the dietary ecology of many vertebrates. In mammals, theoretical analyses and empirical studies suggest a trade-off between maximum bite force and gape at behavioural and evolutionary scales; in vivo bite force is expected to decrease at wide gapes, and cranial morphologies that enable high mechanical advantage are thought to have a lower ability to generate high bite forces at wide gapes, and vice versa. However, very few studies have confirmed these relationships in free-ranging mammals. This study uses an ecologically diverse sample of bats to document the variation in bite force with respect to gape angle, and applies three-dimensional models of the feeding apparatus to identify the major morphological and biomechanical predictors of the gape-bite force relationship. In vivo and model data corroborated that bite force decreases significantly at wide gapes across species, but there is substantial intraspecific variation in the data obtained from live bats. Results from biomechanical models, analysed within a phylogenetic framework, revealed that species with larger temporalis muscles, higher temporalis stretch factors and high mechanical advantages experience a steeper reduction in bite force with increasing gape. These trends are illustrated by short-faced durophagous frugivores. The results from this study suggest that gape-mediated changes in bite force can be explained both by behavioural effects and cranial morphology, and that these links are relevant for functional analyses of mammal dietary ecology.
Data from: Does diet drive the evolution of head shape and bite force in chameleons of the genus Bradypodion?
The head is a complex integrated system that is implicated in many vital functions. As such, its morphology is impacted by different and sometimes conflicting demands. Consequently, head shape varies greatly depending on the environment and dietary ecology of an organism. Moreover, given its role in territory defence and mating in lizards, it is also subjected to strong sexual selection in these animals. We investigated the relationships between head shape, bite performance and diet in 14 of the 17 extant Bradypodion species to determine whether variation in diet can explain the observed diversity in bite force and head shape in this genus. We also evaluate differences between sexes in terms of the relationships between head shape, bite force and diet and predict tighter relationships in females given that the head in this sex is principally under natural selection. Our results show that there is indeed a correlation between head shape, diet and bite force, but the direction and magnitude are sex-dependent. Whereas we observed a correlation between absolute bite force and head shape in both sexes, size-corrected bite force was correlated with mandible and quadrate shape in females only. Despite strong correlations between bite force and prey hardness, and between prey hardness and head shape, we did not find any relationship between head shape and prey evasiveness. These data suggest that the cranial system in chameleons of the genus Bradypodion evolves under natural selection for the ability to eat large or hard prey. Moreover, significant differences in the ecomorphological relationships between the two sexes suggest that sexual selection plays a role in driving the evolution of bite force and head shape. These data suggest that ecomorphological relationships may be sex-dependent.
Data from: FEATHER: automated analysis of force spectroscopy unbinding and unfolding data via a Bayesian algorithm
Single-molecule force spectroscopy (SMFS) provides a powerful tool to explore the dynamics and energetics of individual proteins, protein-ligand interactions, and nucleic acid structures. In the canonical assay, a force probe is retracted at constant velocity to induce a mechanical unfolding/unbinding event. Next, two energy landscape parameters, the zero-force dissociation rate constant (ko) and the distance to the transition state (Δx‡), are deduced by analyzing the most probable rupture force as a function of the loading rate, the rate of change in force. Analyzing the shape of the rupture force distribution reveals additional biophysical information, such as the height of the energy barrier (ΔG‡). Accurately quantifying such distributions requires high-precision characterization of the unfolding events and significantly larger data sets. Yet, identifying events in SMFS data is often done in a manual or semiautomated manner and is obscured by the presence of noise. Here, we introduce, to our knowledge, a new algorithm, FEATHER (force extension analysis using a testable hypothesis for event recognition), to automatically identify the locations of unfolding/unbinding events in SMFS records and thereby deduce the corresponding rupture force and loading rate. FEATHER requires no knowledge of the system under study, does not bias data interpretation toward the dominant behavior of the data, and has two easy-to-interpret, user-defined parameters. Moreover, it is a linear algorithm, so it scales well for large data sets. When analyzing a data set from a polyprotein containing both mechanically labile and robust domains, FEATHER featured a 30-fold improvement in event location precision, an eightfold improvement in a measure of the accuracy of the loading rate and rupture force distributions, and a threefold reduction of false positives in comparison to two representative reference algorithms. We anticipate FEATHER being leveraged in more complex analysis schemes, such as the segmentation of complex force-extension curves for fitting to worm-like chain models and extended in future work to data sets containing both unfolding and refolding transitions.
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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.
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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.