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Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing and Storage
<p>Scanning transmission electron microscopy data related to paper "Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage": <a href="https://doi.org/10.1017/S1431927620001713">https://doi.org/10.1017/S1431927620001713</a></p>
FIGURE 1 in How Fast Could Tyrannosaurus rex Run?
FIGURE 1. IN A FREE-BODY DIAGRAM for a running tyrannosaur, the angles of the leg joints (top) are critical parameters. In addi- tion to the forces and torques produced by leg muscles, external forces (bottom) including the weights of the body (Ƒb), thigh (Ƒt), shank (Ƒs), and metatarsus (Ƒm), as well as the ground reaction force (GRF) that acts a distance R from the toe joint must be incorporated. (Adapted from ref. 6.)
Figure 3 in Tyrannosaurus was not a fast runner
Figure 3 Estimated extensor muscle mass (T, as a percentage of body mass per leg) required to run quickly. Data are from various models and extant species plotted against log(mbody) to illustrate the scaling of T. Larger runners need a larger fraction of their body allocated to extensor muscle mass.Three shades of grey indicate the likelihood of running ability, based on estimated T. Very low estimated T implies a good chance of being a capable runner. Very high estimated T signals little chance of being a capable runner. Intermediate values of estimated T are inconclusive, and running ability in this case depends on the ratio of actual extensor muscle mass to T. Values of T greater than 50% per leg, or greater than 100% in total, are impossible.The solid line represents the case of scaling a chicken isometrically up to 6,000 kg.
Figure 1 in Tyrannosaurus was not a fast runner
Figure 1 Explanation of freebody diagram analysis of body segments. Skeletal illustration modified from ref. 6. The initial Tyrannosaurus model (Trex_1) is shown in right lateral view and (x, y)coordinate space, with the origin located at the toe joint. Pelvic pitch, hip, knee, ankle and toe joint angle definitions are shown (see Supplementary Information). One of the angles is redundant (four angles suffice). The ground reaction force (GRF) is vertical (typical for midstance12–14) and acts at a distance R from the toe joints. The body segment weights (Wb, Wt, Ws and Wm for the trunk, thigh, shank and metatarsus) are also shown. A freebody diagram was used to calculate the internal moments about each joint. For example, about the knee joint (see inset), the moment that knee extensor muscles must generate (Mk) is equal to the ankle contact force (Fa) times its respective moment arm, plus the gravitational moment of the shank segment and the ankle moment (Ma).
FIGURE 2 in How Fast Could Tyrannosaurus rex Run?
FIGURE 2. ESTIMATED EXTENSOR MUSCLE MASS per leg needed to run fast, as a fraction of total body mass. Larger animals need relatively more leg muscle to run. This dependence is illustrated by the solid line, calculated for a chicken scaled up to the size of T. rex. For several models of T. rex anatomy, the estimates (red) all require more leg muscle for running fast than the creature was likely to have had (orange dot). (Adapted from ref. 6.)
FIGURE 1 in How Fast Could Tyrannosaurus rex Run?
FIGURE 1. IN A FREE-BODY DIAGRAM for a running tyrannosaur, the angles of the leg joints (top) are critical parameters. In addi- tion to the forces and torques produced by leg muscles, external forces (bottom) including the weights of the body (Ƒb), thigh (Ƒt), shank (Ƒs), and metatarsus (Ƒm), as well as the ground reaction force (GRF) that acts a distance R from the toe joint must be incorporated. (Adapted from ref. 6.)
Data from: The Cumulative Indel Model: fast and accurate statistical evolutionary alignment
Sequence alignment is essential for phylogenetic and molecular evolution inference, as well as in many other areas of bioinformatics and evolutionary biology. Inaccurate alignments can lead to severe biases in most downstream statistical analyses. Statistical alignment based on probabilistic models of sequence evolution addresses these issues by replacing heuristic score functions with evolutionary model-based probabilities. However, score-based aligners and fixed-alignment phylogenetic approaches are still more prevalent than methods based on evolutionary indel models, mostly due to computational convenience. Here, I present new techniques for improving the accuracy and speed of statistical evolutionary alignment. The "cumulative indel model" approximates realistic evolutionary indel dynamics using differential equations. "Adaptive banding" reduces the computational demand of most alignment algorithms without requiring prior knowledge of divergence levels or pseudo-optimal alignments. Using simulations, I show that these methods lead to fast and accurate pairwise alignment inference. Also, I show that it is possible, with these methods, to align and infer evolutionary parameters from a single long synteny block (approximately 530kbp) between the human and chimp genomes. The cumulative indel model and adaptive banding can therefore improve the performance of alignment and phylogenetic methods.
Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities
<p>Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling theory and fast-slow dynamical systems theory, we develop a method for comparing maximum rates of density and phenotypic change estimated from population-level time series data. We apply our method to 30 published empirical studies where changes in morphological traits are caused by evolution, plasticity, or an unknown combination. For every study, the maximum rate of phenotypic change was 0.5 to 2.5 times faster than the maximum rate of change in density. Moreover, there were no systematic differences between systems with different modes of adaptation. Our results show that plasticity and evolution can drive phenotypic change just as fast as changes in densities. We discuss the implications of our results in terms of the strengths of feedbacks between population densities and traits.</p>
Datasets associated with paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off"
<p>This contains 6 data files used in the analysis of the paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off", and one file describing their contents in detail. </p> <p>Kiorboe_and_Hirst_dataset_edited_2020_03_21.csv</p> <p>FoRAGE_dataset_edited_2020_03_21.csv</p> <p>FoRAGE_dataset_taxonomic_info_edited_2020_03_21</p> <p>FoRAGE_dataset_with_outliers_raw.csv</p> <p>Growth_ingestion_dataset_raw.csv</p> <p>Litchman_2007_phytoplankton_Vmax_and_affinity_data.csv<br> </p> <p>The primary contents of these files are compiled parameter estimates of the clearance, ingestion and growth rates of heterotrophic organisms. These have largely been taken from two published data compilations:</p> <p>Kiørboe T, Hirst AG (2014) Shifts in mass scaling of respiration, feeding, and growth rates across life-form transitions in marine pelagic organisms. Am Nat 183(4):E118-30. <a href="https://doi.org/10.1086/675241">https://doi.org/10.1086/675241</a></p> <p>Uiterwaal SF, Lagerstrom IT, Lyon SR, DeLong JP (2018) Data paper: FoRAGE (Functional Responses from Around the Globe in all Ecosystems) database: a compilation of functional responses for consumers and parasitoids. bioRxiv doi: <a href="https://doi.org/10.1101/503334">https://doi.org/10.1101/503334</a> <br> </p> <p>The data files are described in detail in 'Data description.txt'.</p> <p>Scripts to analyse this data can be found at <a href="https://doi.org/10.5281/zenodo.4002083">https://doi.org/10.5281/zenodo.4002083</a> . The paper associated with the data and scripts, will be linked to here when published. </p>
Fast and furious: Early differences in growth rate drive short-term plant dominance and exclusion under eutrophication
<p>1. The reduction of plant diversity following eutrophication threatens many ecosystems worldwide. Yet, the mechanisms by which species are lost following nutrient enrichment are still not completely understood, nor are the details of when such mechanisms act during the growing season, which hampers understanding and the development of mitigation strategies.</p> <p>2. Using a common garden competition experiment, we found that early-season differences in growth rates among five perennial grass species measured in monoculture predicted short-term competitive dominance in pairwise combinations and that the proportion of variance explained was particularly greater under a fertilisation treatment.</p> <p>3. We also examined the role of early-season growth rate in determining the outcome of competition along an experimental nutrient gradient in an alpine meadow. Early differences in growth rate between species predicted short-term competitive dominance under both ambient and fertilized conditions and competitive exclusion under fertilized conditions.</p> <p>4. The results of these two studies suggests that plant species growing faster during the early stage of the growing season gain a competitive advantage over species that initially grow more slowly, and that this advantage is magnified under fertilisation. This finding is consistent with the theory of asymmetric competition for light in which fast-growing species can intercept incident light and hence outcompete and exclude slower-growing (and hence shorter) species. We predict that the current chronic nutrient inputs into many terrestrial ecosystems worldwide will reduce plant diversity and maintain a low biodiversity state by continuously favouring fast-growing species. Biodiversity management strategies should focus on controlling nutrient inputs and reducing the growth of fast-growing species early in the season.</p>
Winner effects and switching assessment strategies facilitate fast and frugal decisions in territorial contests
<p>Animals compete in contests over limited resources, and contestants with greater fighting ability, or resource holding potential (RHP), typically win contests. Contest strategies have evolved to balance contest costs with the benefit of winning resources. Sometimes, contestants decide to leave by estimating their opponent's relative RHP . This strategy (mutual assessment) is cost-effective because it allows weaker opponents to leave contests against formidable opponents before accruing higher costs. However, acquiring reliable information can be costly. Here, we showed that in snapping shrimp contests, contestants assessed relative RHP quickly and costeffectively by assessing their opponent's recent contest success. By staging 26 contests between randomly matched individuals and 24 contests between RHPmatched individuals, we determined that snapping shrimp assessed their opponent's RHP during initial contest phases but no longer assessed relative RHP during escalated phases. Then, after staging 24 contests between individuals with contest experience the day prior, we found that snapping shrimp integrated RHP and recent contest success to make contest decisions. This strategy facilitated fast and accurate judgments when the recent winner was also larger but often resulted in the larger individual retreating when facing a small recent winner. Notably, these systematic biases were corrected when RHP differences were stark. Taken together, our findings demonstrate that by assessing recent contest success early in a contest, snapping shrimp can avoid risky contests. Furthermore, by integrating recent contest success with direct observations of RHP, contestants avoid losing contests prematurely. Similar assessment strategies may be widespread, because they circumvent risky contests while minimizing premature defeats from weaker recent winners.</p>
Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris
Hummingbirds, subsisting almost exclusively on nectar sugar, face extreme challenges to blood sugar regulation. The capacity for transmembrane sugar transport is mediated by the activity of facilitative glucose transporters (GLUTs) and their localisation to the plasma membrane (PM). In this study, we determined the relative protein abundance of GLUT1, GLUT2, GLUT3, and GLUT5 via immunoblot using custom antibodies in whole-tissue and PM fractions of flight-muscle, heart, and liver of ruby-throated hummingbirds (Archilochus colubris). GLUTs examined were detected in nearly all tissues tested. Hepatic GLUT1 was minimally present in whole-tissue and absent in PM fractions. GLUT5 was expressed in flight-muscles at levels comparable to that of their liver, consistent with hummingbird flight-muscles' hypothesised uniquely high fructose-uptake and oxidation capacity. To assess GLUT regulation, we fed ruby-throated hummingbirds 1M sucrose ad libitum for 24 hours followed by either 1 hour of fasting or continued feeding until sampling. We measured relative GLUT abundance and concentrations of circulating sugars. Blood fructose concentration in fasted hummingbirds declined (∼5 mM to ∼0.18 mM), while fructose-transporting GLUT2 and GLUT5 abundance did not change in PM fractions. Blood glucose concentrations remained elevated in fed and fasted hummingbirds (∼30 mM), while glucose-transporting GLUT1 and GLUT3 in flight muscle and liver PM fractions, respectively, declined in fasted birds. Our results suggest that glucose uptake capacity is dynamically reduced in response to fasting, allowing for maintenance of elevated blood glucose levels, while fructose uptake capacity remains constitutively elevated promoting depletion of blood total fructose within the first hour of a fast.
Fast and accurate estimation of species-specific diversification rates using data augmentation
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring subtle rate variations across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
Data from: Exceptional preservation requires fast biodegradation: the case study of thylacocephalan specimens from La Voulte-sur-Rhône (Callovian, Jurassic, France)
<p>Konservat-Lagerstätten are seen as snapshots of past biodiversity for a given location and time. Yet, processes leading to the exceptional morphological preservation of fossils in these deposits remain incompletely understood. This results in the deficient assessment of taphonomic biases and limits the robustness/relevance of palaeobiological reconstructions. Here, we report the mineralogical characterization of crustacean fossils preserved within carbonate-rich concretions from the Jurassic Konservat-Lagerstätte of La Voulte-sur-Rhône (Ardèche, France). The combination of SEM-EDS, TEM, synchrotron-based XRF, XRD and XANES allows identifying the mineralogical phases composing these fossils (i.e. fluorapatite, Fe-sulfides (pyrite, pyrrhotite) and Mg-calcite) and the surrounding matrix (i.e. Mg-calcite, clays and detrital silicates). Fluorapatite and pyrite (and pyrrhotite) precipitated during decay under anoxic conditions, replacing delicate organic structures and preserving anatomical details. These mineral structures were subsequently consolidated by a Mg-calcite cement. Of note, histologically similar tissues were replaced by the same mineral phases, confirming that 'fossilization [in La Voulte] occurred rapidly enough to be influenced by tissue composition'. Altogether, the present study shows that exceptional preservation requires fast biodegradation, thereby confirming recent experimental evidence.</p>
Data and R Code for publication: Should dispersers be fast learners? Modelling the role of cognition in dispersal
<p><span><span><span><span><span><span><span><span><span><span><span>Both cognitive abilities and dispersal tendencies can vary strongly between individuals. Since cognitive abilities may help dealing with unknown circumstances it is conceivable that </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>dispersers may rely more heavily on learning abilities than residents. However, cognitive abilities are costly and leaving a familiar place might result in losing the advantage of having learned to deal with local conditions. Thus, individuals which invested in learning to cope with local conditions may be more reluctant to leave their natal place. In order to disentangle the complex relationship between dispersal and learning abilities we implemented individual-based simulations. By allowing for developmental plasticity, individuals could either develop a "resident" or "dispersal" cognitive phenotype.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>In line with our expectations, the correlation between learning abilities and dispersal could take any direction, depending how much time individuals had to recoup their investment in cognition. Both, longevity and the timing of dispersal within lifecycles determine the time individuals have to recoup that investment and thus crucially influence this correlation. We therefore suggest that species' life-history will strongly impact the expected cognitive abilities of dispersers, relative to their resident conspecifics, and that cognitive abilities might be an integral part of dispersal syndromes.</span></span></span></span></span></span></span></span></span></span></span></p>
Fast Byzantine SGD (video)
Full video presentation of the paper: Fast Byzantine SGD.<br><br>Appears in Session 2 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
CSR++: A Fast, Scalable, Update-Friendly Graph Data Structure (video)
Full video presentation of the paper: CSR++: A Fast, Scalable, Update-Friendly Graph Data Structure.<br><br>Appears in Session 5 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
The fast and the curious II: performance, personality and metabolism in Karoo bush rats
<p>Personality traits (e.g., activity, exploration, boldness) are frequently correlated with each other and with various other traits of biological importance. According to the performance, allocation, and independent models of energy management, the relationship between personality traits and resting metabolic rate (RMR) is predicted to be either positive, negative, or nil. As for the relationship between personality traits and locomotor performance, the trait compensation and co-specialisation hypotheses respectively predict a positive and negative relationship. To test for associations between personality, metabolism, and performance, we studied a wild population of Karoo bush rat (<i>Myotomys unisulcatus</i>) in South Africa. During summer 2018 we captured 45 individuals (38 females and 7 males) a total of 293 times and repeatedly measured docility (time spent immobile during a bag test), exploration (distance moved in an open-field test), sprint speed, and RMR. We found a behavioural syndrome in our population, as more docile individuals covered less distance in the exploration test (<i>r</i>±se=-0.74±0.21). RMR was not correlated with any trait; therefore, the independent energy management model applies in this population. Fast sprinters were less explorative in the novel environment than slow sprinters (<i>r</i>±se=-0.41±0.21), going against the prediction of the phenotypic compensation hypothesis and suggesting co-specialisation of these traits. A similar result was previously observed in two other rodent species, suggesting that exploratory behaviour and locomotor performance may interact in an additive instead of compensatory way. Given the apparent complexity of the links between performance, behaviour, and metabolism, more studies are needed in order to understand their relationships.</p>
STL Fast Decompression Experiment Data for "Standing Shock Prevents Propagation of Sparks in Supersonic Explosive Flows"
<p><strong>Background</strong></p> <p>This data is camera images and pressure gauge and RF antenna voltage traces from rapid decompression shots at the STL shock tube facility. </p> <p>This data is used in figures 1, 2, 3, and 4 and corresponds to the STL shots listed in table S1 of the paper "Standing Shock Prevents Propagation of Sparks in Supersonic Explosive Flows".</p> <p>Electric sparks and explosive flows have long been associated with each other. Flowing dust particles originate charge through contact and separate based on inertia, resulting in strong electric fields supporting sparks. These sparks can cause explosions in dusty environments, especially those rich in carbon, such as coal mines and grain elevators. Recent observations of explosive events in nature and decompression experiments indicate that supersonic flows of explosions may alter the electrical discharge process. Shocks may suppress parts of the hierarchy of the discharge phenomena, such as leaders. In our decompression experiments, a shock tube ejects a flow of gas and particles into an expansion chamber. We imaged an illuminated plume from the decompression of a mixture of argon and <100 mg of diamond particles and observe sparks occurring below the sharp boundary of a condensation cloud. We also performed hydrodynamics simulations of the decompression event that provide insight into the conditions supporting the observed behavior. Simulation results agree closely with the experimentally observed Mach disk shock shape and height. This represents direct evidence that the sparks are sculpted by the outflow. The spatial and temporal scale of the sparks transmit an impression of the shock tube flow, a connection that could enable novel instrumentation to diagnose currently inaccessible supersonic granular phenomena.</p> <p><strong>Accessing Data</strong></p> <p>The prefixes of the filenames correspond to the shot dates and approximate times listed in table S1 of the paper. </p> <p>The "_SA4.zip" and "_SA3.zip" files contains tiff images of the SA4 and SA3 camera frames, respectively. The ".cih" file in each zip lists camera settings in plain text.</p> <p>The "OscilloscopeData.zip" contains files with prefixes corresponding to the shot dates and times listed in table and the diagnostic name. Files ending in ".csv" contain raw data and ".pdf" contain plots of the respective data. For pressure data, 1 V = 100 psi.</p>
Generating fast sparse matrix vector multiplication from a high level generic functional IR
<p>Usage of high-level intermediate representations promises the generation of fast code from a high-level description, improving the productivity of developers while achieving the performance traditionally only reached with low-level programming approaches.</p> <p>High-level IRs come in two flavors:<br> 1) domain-specific IRs designed to express only for a specific application area; or<br> 2) generic high-level IRs that can be used to generate high-performance code across many domains.<br> Developing generic IRs is more challenging but offers the advantage of reusing a common compiler infrastructure various applications.</p> <p>In this paper, we extend a generic high-level IR to enable efficient computation with sparse data structures.<br> Crucially, we encode sparse representation using reusable dense building blocks already present in the high-level IR.<br> We use a form of dependent types to model sparse matrices in CSR format by expressing the relationship between multiple dense arrays explicitly separately storing the length of rows, the column indices, and the non-zero values of the matrix.</p> <p>We demonstrate that we achieve high-performance compared to spare low-level library code using our extended generic high-level code generator.<br> On an Nvidia GPU, we outperform the highly tuned Nvidia cuSparse implementation of SpMV multiplication across 28 sparse matrices of varying sparsity on average by $1.7\times$.</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.