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1,456 results for “parallelism”
Controlled User Study: Usability and Efficiency Evaluation of the Parallel Performance Catalogue Extension for the Palladio-Bench
<p>This repository contains the raw data for the user Study we conduction for the theses of Denis Zaharaive:</p> <p> </p> <p> Controlled User Study: Usability and Efficiency Evaluation of the Parallel Performance Catalogue Extension for the Palladio-Bench</p>
Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation
<p>The accompanying files contain digital data for figures in the article "Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation" by J. R. Myra, S. Ku, D.A. Russell, J. Cheng, I. Keramidas Charidakos, S. E. Parker, R.M. Churchill, and C.S. Chang, submitted to the journal Physics of Plasmas.</p> <p> </p> <p><strong>Abstract</strong></p> <p>Data from the XGC1 gyrokinetic simulation is analyzed to understand the three-dimensional spatial structure and the radial propagation of blob-filaments generated by quasi-steady turbulence in the tokamak edge pedestal and scrape-off layer plasma. Spontaneous toroidal flows vary in the poloidal direction and shear the filaments within a flux surface resulting in a structure that varies in the parallel direction. This parallel structure allows the curvature and grad-B induced polarization charge density to be shorted out via parallel electron motion. As a result, it is found that the blob-filament radial velocity is significantly reduced from estimates which neglect parallel electron kinetics, broadly consistent with experimental observations. Conditions for when this charge shorting effect tends to dominate blob dynamics are derived and compared with the simulation.</p>
Data and code for publication "The role of history and strength of the oceanic forcing in sea level projections from Antarctica with the Parallel Ice Sheet Model"
<p>Data and code underlying the publication <a href="https://tc.copernicus.org/preprints/tc-2019-330/">"The role of history and strength of the oceanic forcing in sea level projections from Antarctica with the Parallel Ice Sheet Model"</a>.</p> <p>Journal: The Cryosphere</p> <p>Authors: <em>Ronja Reese<sup>1*</sup></em><em>, Anders Levermann</em><sup><em>1,2,3</em></sup><em>, Torsten Albrecht</em><sup><em>1</em></sup><em>, Hélène Seroussi<sup>4</sup></em><em>, Ricarda Winkelmann<sup>1,2 </sup></em></p> <p>(1) Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, P.O. Box 60 12 03, D-14412 Potsdam, Germany</p> <p>(2) Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany</p> <p>(3) LDEO, Columbia University, New York, USA</p> <p>(4) Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA</p> <p>(*) email ronja.reese@pik-potsdam.de</p> <p>Abstract:<br> Mass loss from the Antarctic Ice Sheet constitutes the largest uncertainty in projections of future sea level rise. Ocean-driven melting underneath the floating ice shelves and subsequent acceleration of the inland ice streams is the major reason for currently observed mass loss from Antarctica and is expected to become more important in the future. Here we show that for projections of future mass loss from the Antarctic Ice Sheet, it is essential (1) to better constrain the sensitivity of sub-shelf melt rates to ocean warming and (2) to include the historic trajectory of the ice sheet. In particular, we find that while the ice sheet response in simulations using the Parallel Ice Sheet Model is comparable to the median response of models in three Antarctic Ice Sheet Intercomparison projects – initMIP, LARMIP-2 and ISMIP6 – conducted with a range of ice sheet models, the projected 21st century sea level contribution differs significantly depending on these two factors. For the highest emission scenario RCP8.5, this leads to projected ice loss ranging from 1.4 to 4.0 cm of sea level equivalent in the ISMIP6 simulations where the sub-shelf melt sensitivity is comparably low, opposed to a likely range of 9.2 to 35.9 cm using the exact same initial setup, but emulated from the LARMIP-2 experiments with a higher melt sensitivity based on oceanographic studies. Furthermore, using two initial states, one with and one without a previous historic simulation from 1850 to 2014, we show that while differences between the ice sheet configurations in 2015 are marginal, the historic simulation increases the susceptibility of the ice sheet to ocean warming, thereby increasing mass loss from 2015 to 2100 by about 50 %. Our results emphasize that the uncertainty that arises from the forcing is of the same order of magnitude as the ice dynamic response for future sea level projections.</p> <p>Large zip files contain data, small zip file python notebooks for data analysis and PISM code. Please contact ronja.reese@pik-potsdam.de if you have any further questions.</p>
supplementary video for the manuscript "Parallelized manipulation of adherent living cells by magnetic nanoparticles-mediated forces"
<pre><strong>Video S6: Parallelized magnetic control of Hela cells</strong></pre> <pre><strong>Video S7: Parallelized magnetic control of SHSY-5Y cells</strong></pre> <pre><strong>Video S8: Parallelized magnetic control of cortical neurons</strong></pre> <pre><strong>Video S9: Parallelized magnetic control of cortical neurons</strong></pre> <pre><strong>Video S10&S11: Parallelized magnetic control of PC12 cells</strong></pre> <pre><strong>Video S12: Lysosome labeling of Hela cells</strong></pre> <pre><strong>Video S13: Late endosome labeling of Hela cells</strong></pre>
Convergence, parallelism, and function of extreme parietal callus in diverse groups of Cenozoic Gastropoda
We use SEM imaging to examine the shell microstructure of fossil and living species in five families of caenogastropods (Strombidae, Volutidae, Olividae, Pseudolividae, and Ancillariidae) to determine whether parallel or convergent evolution is responsible for the development of a unique caenogastropod trait, the extreme parietal callus. The extreme parietal callus is defined as a substantial thickening of both the spire callus and the callus on the ventral shell surface such that it covers 50% or more of the surface. Caenogastropods as a whole construct EPC convergently, using a variety of low-density, poorly-organized microstructures that are otherwise uncommon in caenogastropod non-callus shell construction. Within clades, however, we see evidence for parallelism in decreased regulation in both the shell and callus microstructure. Low density and poorly-ordered microstructure -- such as used for EPC -- uses less organic scaffolding and is less energetically expensive than normal shell microstructure. This suggests EPC functions to rapidly and inexpensively increase shell thickness and overall body size. Tests of functional ecology suggest that EPC might function both to defend against crushing predation through increased body size and dissipation of forces while aiding in shell orientation of highly-mobile gastropods. These interpretations hinge on the current phylogenetic placement of caenogastropod families, emphasizing the essential contribution of phylogeny when interpreting homoplasy.
Data from: Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
<p><b>Background:</b> Recent increases in understanding the ecological and evolutionary roles of microbial communities has underscored their importance for their hosts' biology. Yet, little is known about gut microbiota dynamics during early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of extremely young adaptive radiations of Nicaraguan Midas cichlid fish (<i>Amphilophus</i> cf. <i>citrinellus</i>) from two crater lakes to test the hypothesis that parallel divergence in trophic ecology is associated with parallel changes of the gut microbiota.</p> <p><b>Results:</b> Bacterial communities of the water and guts were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Across individuals of the same crater lake, differentiation in trophic ecology was associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across two crater lakes, we could not detect evidence for parallel changes of the gut microbiota associated with trophic ecology.</p> <p><b>Conclusions:</b> Similar cases of non-parallelism have been observed in other recently diverged fish species and might be explained by a lack of clearly differentiated niches during early stages of ecological diversification.</p>
Parallel responses of species diversity and functional diversity to changes in patch size are driven by distinct processes
1. Do species and functional trait diversity respond similarly to deterministic and random processes? Theory predicts that the contributions of random and deterministic processes to species diversity depend on patch size. Smaller patches are more strongly influenced by random sampling effects, by having fewer individuals, as well as ecological drift, which propagates the effects of small samples through stochastic birth and death processes. These random processes decrease species richness and increase compositional differences among small patches. Larger patches are predicted to be more deterministically assembled, with greater species richness and greater predictability of composition for a particular environment. The consequences of patch size for the diversity of functional traits, however, are poorly understood. Species diversity may be a poor proxy for functional diversity due to trait redundancies among species, making it unclear how random and deterministic processes alter functional diversity within patches of differing size, and how these differences scale up to determine among-patch functional diversity. 2. We report a novel experimental study of species and functional diversity across spatial scales. We manipulated patch area in an experimental plant metacommunity and used a nested sampling design to distinguish the effects of deterministic processes, ecological drift, and sampling effects on species and functional trait diversity. 3. Our study revealed a pervasive influence of ecological drift and sampling effects on diversity, with distinct influences on functional traits and species composition within and among patches. Overall, drift and sampling effects caused a 2- to 3-fold decrease in the importance of deterministic processes in small fragments. Species and functional diversity showed similar patterns with patch size: larger patches had greater within-patch (alpha) diversity and lower among-patch (beta) diversity, consistent with theory. However, our nested sampling design revealed that sampling effects (i.e. the size of the sample area) largely determined alpha species diversity and beta functional diversity, while ecological drift had a stronger influence on alpha functional diversity and beta species diversity. 4. Synthesis. The compositions of species and functional diversity in a community are influenced by distinct processes, resulting in divergent spatial scaling of species and their traits within patches and across landscapes.
Dataset for formation of amorphous materials causes parallel brittle-viscous flow of crustal rocks: Experiments on quartz – feldspar aggregates
<p>Mechanical and microstructural data saved as .mat data files together with scripts used for plotting saved as .m filed (MATLAB). Experiments are described in Pec and Al Nasser, JGR, 2021.</p>
Shared, modular chromosome rearrangements enable parallel adaptation in a marine fish
Genomic architecture and standing variation can play a key role in ecological adaptation, and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behaviour in regional analyses. However, the degree of parallelism , the extent of independent inheritance, and functional distinctiveness of these rearrangements remains poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangement with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures have likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
Parallel text dataset for Neural Machine Translation (French -> Fongbe, French -> Ewe)
<p>This A Multilingual Dataset for Machine Translation from French to Ewe and fongbe, languages respectively from Togo and Benin</p> <p>This is a contribution with the AI4D initiative</p> <p>It contains 70k+ parallel sentences that have been annotated for Neural Machine Translation and sentence classification tasks.</p>
An iterative process for efficient optimisation of parameters in geoscientific models: a demonstration using the Parallel Ice Sheet Model (PISM) version 0.7.3
<p>Physical processes within geoscientific models are sometimes described by simplified schemes known as parameterisations. The values of the parameters within these schemes can be poorly constrained by theory or observation. Uncertainty in the parameter values translates into uncertainty in the outputs of the models. Proper quantification of the uncertainty in model predictions therefore requires a systematic approach for sampling parameter space. In this study, we develop a simple and efficient approach to identify regions of multi-dimensional parameter space that are consistent with observations. Using the Parallel Ice Sheet Model to simulate the present-day state of the Antarctic Ice Sheet, we find that co-dependencies between parameters preclude the identification of a single optimal set of parameter values. Approaches such as large ensemble modelling are therefore required in order to generate model predictions that incorporate proper quantification of the uncertainty arising from the parameterisation of physical processes.</p>
- Superior volsella straight, not swollen at apex; anal point parallel–sided to point........................................................................................... C. parallelus Yan, Tang et Wang, 2005 (Palaearctic) in A new species of the genus Cryptotendipes Beck et Beck, 1969 (Diptera Chironomidae) from India, with a world key to the males and tentative phylogenetic relationship
- Superior volsella straight, not swollen at apex; anal point parallel–sided to point........................................................................................... C. parallelus Yan, Tang et Wang, 2005 (Palaearctic)
Parallel molecular mechanisms for enzyme temperature adaptation
<p><span>The mechanisms that underly the adaptation enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Herein, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis</span><span> and we establish the underlying physical mechanisms</span><span>. </span>This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature in 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation. We assess the properties of these residues, molecular interactions and interaction networks that appear to underly temperature adaptation.</p>
Data from: Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback
Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.
Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids
The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case are blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through "hybrid parallel speciation". Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new "nyererei-like" and "pundamilia-like" species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the 'all at once' taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing 'chirosurveillance' and conservation strategies.
Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance
<p>CRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR-Cas9 screens using <i>TP53</i> wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and <i>TP53</i> knockout human retinal pigment epithelial cells using a focused dual guide RNA library targeting 852 DDR-associated genes. Our work demonstrates that although functional p53 status negatively affects identification of significantly depleted genes, optimal screen design can nevertheless enable robust screen performance. Through analysis of our own and published screen data, we highlight key factors for successful screens in both wild-type and p53-deficient cells.</p>
Data from: Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore
Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67-K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric-Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome-wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long-term separation among population clusters.
Data from: Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution
The fossils assigned to the tetrapod stem group document the evolution of terrestrial vertebrates from lobe-finned fishes. During the past 18 years the phylogenetic structure of this stem group has remained remarkably stable, even when accommodating new discoveries such as the earliest known stem tetrapod Tungsenia and the elpistostegid (fish–tetrapod intermediate) Tiktaalik. Here we present a large lobe-finned fish from the Late Devonian period of China that disrupts this stability. It combines characteristics of rhizodont fishes (supposedly a basal branch in the stem group, distant from tetrapods) with derived elpistostegid-like and tetrapod-like characters. This mélange of characters may reflect either detailed convergence between rhizodonts and elpistostegids plus tetrapods, under a phylogenetic scenario deduced from Bayesian inference analysis, or a previously unrecognized close relationship between these groups, as supported by maximum parsimony analysis. In either case, the overall result reveals a substantial increase in homoplasy in the tetrapod stem group. It also suggests that ecological diversity and biogeographical provinciality in the tetrapod stem group have been underestimated.
Data from: Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage
Disjunct distributions have intrigued biologists for centuries. Investigating these biogeographic patterns provides insight into speciation and biodiversity at multiple spatial and phylogenetic scales. Some disjunctions have been intensively studied, yet others have been largely overlooked and remain poorly understood. Among the lesser-known disjunction patterns is that between the mountain ranges of western North America. Flora and fauna endemic to the mountains of this region provide important systems for investigating causes and results of disjunctions, given the relatively recent geological formation of this area and the intense climatic fluctuations that have occurred since its formation. In Micranthes (Saxifragaceae), which has high rates of montane endemism, two species, M. bryophora and M. tolmiei, show this biogeographical pattern. By reconstructing a time-calibrated phylogeny based on 518 low-copy nuclear markers and including multiple populations of each species from the Coast Ranges, Cascades, Sierra Nevada, and Rocky Mountains, this study provides a biogeographical and temporal framework for the evolution of Micranthes in western North America. Strongly supported east-west differentiated clades are recovered for M. bryophora and M. tolmiei in both maximum likelihood and coalescent-based species tree reconstructions. Biogeographic analysis suggests different patterns of dispersal for both taxa and the dating analyses recovered contrasting ages for each clade. Due to both the different geographic patterns and the timing of the initial diversification of each taxon corresponding to different geologic and climatic events, the disjunction patterns shown for these taxa are suggested to be an example of biogeographical pseudocongruence.
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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.
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.