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1,774 results for “accelerators”
Quantifying the accelerated diffusion and cost savings of global solar photovoltaic supply chains
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FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity
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Data from: Rapid evolution accelerates plant population spread in fragmented experimental landscapes
Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness—an important control over traits under selection—influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions.
Data from: Model-based acceleration of Look-Locker T1 mapping
Mapping the longitudinal relaxation time T1 has widespread applications in clinical MRI as it promises a quantitative comparison of tissue properties across subjects and scanners. Due to the long scan times of conventional methods, however, the use of quantitative MRI in clinical routine is still very limited. In this work, an acceleration of Inversion-Recovery Look-Locker (IR-LL) T1 mapping is presented. A model-based algorithm is used to iteratively enforce an exponential relaxation model to a highly undersampled radially acquired IR-LL dataset obtained after the application of a single global inversion pulse. Using the proposed technique, a T1 map of a single slice with 1.6mm in-plane resolution and 4mm slice thickness can be reconstructed from data acquired in only 6s. A time-consuming segmented IR experiment was used as gold standard for T1 mapping in this work. In the subsequent validation study, the model-based reconstruction of a single-inversion IR-LL dataset exhibited a T1 difference of less than 2.6% compared to the segmented IR-LL reference in a phantom consisting of vials with T1 values between 200ms and 3000ms. In vivo, the T1 difference was smaller than 5.5% in WM and GM of seven healthy volunteers. Additionally, the T1 values are comparable to standard literature values. Despite the high acceleration, all model-based reconstructions were of a visual quality comparable to fully sampled references. Finally, the reproducibility of the T1 mapping method was demonstrated in repeated acquisitions. In conclusion, the presented approach represents a promising way for fast and accurate T1 mapping using radial IR-LL acquisitions without the need of any segmentation.
Data from: Body acceleration as indicator for walking economy in an ageing population
Background: In adults, walking economy declines with increasing age and negatively influences walking speed. This study aims at detecting determinants of walking economy from body acceleration during walking in an ageing population. Methods: 35 healthy elderly (18 males, age 51 to 83 y, BMI 25.5±2.4 kg/m2) walked on a treadmill. Energy expenditure was measured with indirect calorimetry while body acceleration was sampled at 60Hz with a tri-axial accelerometer (GT3X+, ActiGraph), positioned on the lower back. Walking economy was measured as lowest energy needed to displace one kilogram of body mass for one meter while walking (WCostmin, J/m/kg). Gait features were extracted from the acceleration signal and included in a model to predict WCostmin. Results: On average WCostmin was 2.43±0.42 J/m/kg and correlated significantly with gait rate (r2 = 0.21, p<0.01) and regularity along the frontal (anteroposterior) and lateral (mediolateral) axes (r2 = 0.16, p<0.05 and r2 = 0.12, p<0.05 respectively). Together, the three variables explained 46% of the inter-subject variance (p<0.001) with a standard error of estimate of 0.30 J/m/kg. WCostmin and regularity along the frontal and lateral axes were related to age (WCostmin: r2 = 0.44, p<0.001; regularity: r2 = 0.16, p<0.05 and r2 = 0.12, p<0.05 respectively frontal and lateral). Conclusions: The age associated decline in walking economy is induced by the adoption of an increased gait rate and by irregular body acceleration in the horizontal plane.
Data from: Exposure to males, but not receipt of sex peptide, accelerates functional aging in female fruit flies
Increased exposure to males can affect females negatively, reducing female lifespan and fitness. These costs could derive from increased mating rate and also harassment by males. Additionally, early investment in reproduction can increase the onset or rate of senescence in reproductive traits. Hence, there is a tight link between reproduction and aging. Here, we assess how mating and encounter rate with males impacts declines in female functional traits that are not directly involved in reproduction. In Drosophila melanogaster fruit flies, exposure to males and mating reduces female lifespan through harassment and receipt of seminal proteins, including sex peptide. We manipulated the intensity of female exposure to males and regularly assessed female stress responses and recorded physiological traits over her lifetime. Both mating itself and increased exposure to males accelerates declines in female climbing ability and starvation resistance. However, this is not related to changes in female body mass or fat storage. Moreover, these declines are not driven by the receipt of sex peptide. Our results suggest some synchrony in senescence across traits in response to female exposure to males, however this is not universal, as we did not find this for physiological traits. Synchrony in senescence has been theorised but little supported in the literature. It is clear that aging is a multifaceted trait; to understand environmental impacts on aging rates we must measure more than lifespan, and indeed measure senescence in multiple traits. Specifically, our work shows that we must identify which female traits are sensitive to elevated mating activity to understand the impact of antagonistic interactions between the sexes on female aging patterns.
Data from: Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques
A well-covered reference library is crucial for successful identification of species by DNA barcoding. The biggest difficulty in building such a reference library is the lack of materials of organisms. Herbarium collections are potentially an enormous resource of materials. In this study, we demonstrate that it is likely to build such reference libraries using the reconstructed (self-primed PCR amplified) DNA from the herbarium specimens. We used 179 rosaceous specimens to test the effects of DNA reconstruction, 420 randomly sampled specimens to estimate the usable percentage and another 223 specimens of true cherries (Cerasus, Rosaceae) to test the coverage of usable specimens to the species. The barcode rbcLb (the central four-sevenths of rbcL gene) and matK was each amplified in two halves and sequenced on Roche GS 454 FLX+. DNA from the herbarium specimens was typically shorter than 300 bp. DNA reconstruction enabled amplification fragments of 400–500 bp without bringing or inducing any sequence errors. About one-third of specimens in the national herbarium of China (PE) were proven usable after DNA reconstruction. The specimens in PE cover all Chinese true cherry species and 91.5% of vascular species listed in Flora of China. It is very possible to build well-covered reference libraries for DNA barcoding of vascular species in China. As exemplified in this study, DNA reconstruction and DNA-labelled next-generation sequencing can accelerate the construction of local reference libraries. By putting the local reference libraries together, a global library for DNA barcoding becomes closer to reality.
Data from: Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations
The phylogenetic likelihood function is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the phylogenetic likelihood function currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation.
Global acceleration of lake sediment accumulation rates associated with recent human population growth and landuse changes
<p>These datasets include the spatial coordinates and the digitized temporal rates of lake sedimentation expressed as Sediment Accumulation Rates (SAR; mm/year) and Mass Accumulation Rate (MAR; g/cm<sup>2</sup>/year) presented in Baud et al. (2021).</p> <p>Baud, A., Jenny, JP., Francus, P. and Gregory-Eaves, I. Global acceleration of lake sediment accumulation rates associated with recent human population growth and land-use changes. <em>J Paleolimnol</em> (2021). https://doi.org/10.1007/s10933-021-00217-6 </p>
data for "An unbound proline-rich signaling peptide frequently samples cis conformations in Gaussian accelerated molecular dynamics simulations"
<p>Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the <em>cis</em> state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in <em>cis</em>, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the <em>cis </em>conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the <em>cis </em>and <em>trans </em>states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline <em>cis </em>and <em>trans </em>states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in <em>cis</em>, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in <em>trans</em>. The ensemble containing <em>cis</em> prolines also matches more closely to <em>in vitro</em> circular dichroism data than the all-<em>trans</em> ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with <em>in vitro</em> data.</p>
Data from: Overall dynamic body acceleration measures activity differently on large vs small aquatic animals
<p>Acceleration-based proxies for activity and energy expenditure are widely used in bio-logging studies of animal movement and locomotion to explore biomechanical strategies, energetic costs of behaviour, habitat use and the impact of anthropogenic disturbance. The foremost such proxy is Overall Dynamic Body Acceleration (ODBA) along with variants VeDBA and PDBA. This technique, which involves summing the magnitude of high-pass-filtered acceleration signals (the so-called dynamic acceleration) over a reference interval, has been applied to animals as diverse as shags, lobsters, humans and whales. The relationship between ODBA and energy use has been tested empirically on animals small enough to house in laboratory facilities and arguments have been offered for why the method should be generally applicable, however validations on larger animals are scant.</p> <p><span>Here, we examine how body size impacts ODBA and its variants under steady locomotion in large aquatic animals, using cetaceans as model species. To do this, we first develop a simplified mathematical model for the acceleration signals that would be measured by a tag on a swimming animal. We then test this model with empirical data gathered using bio-logging tags on whale species covering nearly an order of magnitude difference in body length from 1.3 m harbour porpoises to 12 m sperm whales.</span></p> <p><span>We show that the motions measured by ODBA can be fundamentally different in small compared to large aquatic animals. Whereas dynamic acceleration in small animals is predominantly due to specific acceleration (i.e., actual accelerative motions generated by muscle action), in larger aquatic animals body rotations (i.e., changes in orientation that accompany swimming and manoeuvring) can dominate the measured acceleration. </span></p> <p><span>As body rotations do not necessarily increase in magnitude as swimming speed increases, ODBA may under-estimate the relative cost of behaviours or responses to disturbance in large aquatic animals. This does not lessen the value of ODBA for small animals, but it raises a caution against uncritical use on larger animals. For large aquatic animals, activity proxies that specifically remove body rotations using gyroscopes or magnetometers may provide more consistent estimates of energy use although these methods are yet to be validated.</span></p>
Figure 5 from: Penev L, Erwin T, Stoev P, Georgiev T (2012) Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys. ZooKeys 251: 1-10. https://doi.org/10.3897/zookeys.251.4516
Figure 5 - Habitus of live Illacme plenipes ♀ with 170 segments and 662 legs. Photo: Marek et al. 2012. ZooKeys: doi: 10.3897/zookeys.241.3831
Figure 4 from: Penev L, Erwin T, Stoev P, Georgiev T (2012) Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys. ZooKeys 251: 1-10. https://doi.org/10.3897/zookeys.251.4516
Figure 4 - Habitus of live Trogloraptor marchingtoni. Photo: Griswold et al. 2012. ZooKeys: doi: 10.3897/zookeys.215.3547
Figure 3 from: Penev L, Erwin T, Stoev P, Georgiev T (2012) Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys. ZooKeys 251: 1-10. https://doi.org/10.3897/zookeys.251.4516
Figure 3 - Figure 3. Habitus of Megalara garuda. Photo: Kimsey and Ohl 2012. ZooKeys: doi: 10.3897/zookeys.177.2475
Figure 1 from: Penev L, Erwin T, Stoev P, Georgiev T (2012) Accelerating innovative publishing in taxonomy and systematics: 250 issues of ZooKeys. ZooKeys 251: 1-10. https://doi.org/10.3897/zookeys.251.4516
Figure 1 - Portraits in life of Paedophryne dekot (A, B) and Paedophryne verrucosa (C, D). Photos: Fred Kraus, 2011. ZooKeys: doi: 10.3897/zookeys.154.1963
Figure 1 from: Doorenweerd C, van Haren M, Schermer M, Pieterse S, van Nieukerken E (2014) A Linnaeus NGTM interactive key to the Lithocolletinae of North-West Europe aimed at accelerating the accumulation of reliable biodiversity data (Lepidoptera, Gracillariidae). ZooKeys 422: 87-101. https://doi.org/10.3897/zookeys.422.7446
Figure 1 - Screenshot of the user interface with different sections indicated. 1 Search by name 2 search by character 3 main window with resulting selection, a more information, links to respective species page on fauna europaea b distinctive characters, becomes visible with a selection of 8 or less c displays species with a similar appearance.
Data set for reliability-based lift-to-power consumption optimization with an accelerated Kriging model for clapping-wing micro air vehicles
<p>Procedures of the reliability-based lift-to-power consumption optimization with an accelerated Kriging model</p> <p>Step 1: Run the file “LHS.m” to generate initial samples.</p> <p>Step 2: Modify the aerodynamic model according to initial samples (e.g. flapping1_Def.xml, flapping1.bat), and then run the “.bat file” to obtain the original force data.</p> <p>Step 3: Run the file “Kriging.m” to obtain the average lift using a filter.</p> <p>Step 4: Run the file “FW_2.m”, “FW_3.m” to obtain sub-optimal-result.</p> <p>Step 5: Find the new training sample and obtain the eigenvalue of the new training sample.</p> <p>Step 6: Rerun the file “FW_2.m”, “FW_3.m” to obtain sub-optimal-result by reloading the new “.mat” files (e.g. FW_2_41.mat, FW_2_P_20.mat).</p> <p>Step 7: Go to Step 4 until the convergence criteria are satisfied.</p> <p>Step 8: Obtain the optimal result. PS: Other files are function files.</p>
Data and code for "Terrestrial water cycle acceleration-deceleration: Non-binary and space-time divergent"
<p>This dataset provides all data compiled and generated for the manuscript entitled "Terrestrial water cycle acceleration-deceleration: Non-binary and space-time divergent" (manuscript under consideration). This includes the boundaries for 3614 hydrological catchments, the curated data used for analysis and modelling, the developed machine learning model, shapley values and area of applicability results, and data for global extrapolation</p> <p>It also contains the code in a Quarto file ('Code.qmd') and a markdown file ('Code.html') which shows how to access and use the data, and generic sample codes used to generate these results.</p> <p> </p> <p>Code - R session info:</p> <p>R version 4.2.1 (2022-06-23 ucrt)</p> <p>Platform: x86_64-w64-mingw32/x64 (64-bit)</p> <p>Running under: Windows 10 x64 (build 22621)</p> <p>Matrix products: default locale: [1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8 [3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C [5] LC_TIME=Portuguese_Brazil.utf8</p> <p>attached base packages: [1] stats [2] graphics [3] grDevices [4] utils [5] datasets [6] methods [7] base</p> <p>other attached packages: [1] bundle_0.0.0.9200 [2] stacks_1.0.0 [3] bonsai_0.1.0 [4] rules_1.0.0 [5] finetune_0.2.0 [6] yardstick_1.0.0 [7] workflowsets_1.0.0 [8] workflows_1.0.0 [9] tune_1.0.0 [10] tibble_3.1.7 [11] rsample_1.0.0 [12] recipes_1.0.1 [13] purrr_0.3.4 [14] parsnip_1.0.0 [15] modeldata_1.0.0 [16] infer_1.0.2 [17] dials_1.0.0 [18] scales_1.2.0 [19] broom_1.0.0 [20] tidymodels_1.0.0 [21] ggplot2_3.3.6 [22] rnaturalearth_0.1.0 [23] sf_1.0-8 [24] terra_1.6-3 [25] lubridate_1.8.0 [26] stringr_1.4.0 [27] tidyr_1.2.0 [28] dplyr_1.0.9 [29] pacman_0.5.1</p>
Dataset for Phys. Rev. Applied (2023) - Accelerating the heat diffusion: Fast thermal relaxation of a microcantilever
<p><strong>"Fig_step.fig"</strong>: Matlab figures including all the data used to plot figure 3 of the article.</p> <p><strong>"Fig_N1.fig "</strong>: Matlab figures including the data used to plot figure 4 for N=1.</p> <p><strong>"Fig_N2.fig "</strong>: Matlab figures including the data used to plot figure 4 for N=2.</p> <p><strong>"Fig_N3.fig "</strong>: Matlab figures including the data used to plot figure 4 for N=3.</p> <p><strong>"Fig_N4.fig "</strong>: Matlab figures including the data used to plot figure 4 for N=4.</p> <p><strong>"gamman.m "/ "gammansym.m "</strong>: Matlab scripts to compute coefficients gamma_n of the polynomial function F(t).</p> <p><strong>"DisplayData.m "</strong>: Matlab script to display the data of the .mat files 'Data_N1.mat', 'Data_N2.mat', 'Data_N3.mat', and 'Data_N4.mat'.</p> <p><strong>"Fig7a.fig" / "Fig7b.fig"</strong>: Matlab figures including the data used to plot figure 7 of the article</p> <p> </p>
HiPACE++ input scripts for "Temperature effects in plasma-based positron acceleration schemes using electron filaments"
<p>This dataset presents the <a href="https://github.com/Hi-PACE/hipace">HiPACE++</a> input scripts required to re-create the data of the figures in the article "Temperature effects in plasma-based positron acceleration schemes using electron filaments" by S. Diederichs, C. Benedetti, M. Thévenet, A. Sinn, E. Esarey, J. Osterhoff, and C. B. Schroeder.</p>
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.