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Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This 'SNP skimming' approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test dataset of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size, and epistasis as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives – loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.
Data from: Discrimination of fast click series produced by tagged Risso's dolphins (Grampus griseus) for echolocation or communication
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two types of rapid click-series pulsed sounds, buzzes and burst pulses, were identified as produced by the tagged dolphins and classified using a Gaussian mixture model based on their duration, association with jerk (i.e., rapid change of acceleration), and temporal association with click trains. Buzzes followed regular echolocation clicks and coincided with a strong jerk signal from accelerometers on the tag. They consisted of series averaging 359 ± 210 (mean ± SD) clicks with an increasing repetition rate and relatively low amplitude. Burst pulses consisted of relatively short click series averaging 45 ± 54 clicks with decreasing repetition rate and longer inter-click interval that were less likely to be associated with regular echolocation and the jerk signal. These results suggest that the longer, relatively lower amplitude, jerk-associated buzzes are used in this species to capture prey, mostly during the bottom phase of foraging dives, as seen in other odontocetes. In contrast, the shorter, isolated burst pulses that are generally emitted by the dolphins while at or near the surface are used outside of a direct, known foraging context.
Data from: The metabolic costs of sexual signalling in the chirping katydid Plangia graminea (Serville) (Orthoptera: Tettigoniidae) are context dependent: cumulative costs add up fast
Katydids produce acoustic signals via stridulation which they use to attract conspecific females for mating. However, direct estimates of the metabolic costs of calling to date have produced diverse cost estimates and are limited to only a handful of insect species. In this study, we therefore investigated the metabolic cost of calling in a unstudied sub-Saharan katydid, Plangia graminea. Using wild-caught animals, we measured katydid metabolic rate using standard flow-through respirometry while simultaneously recording the number of calls produced. Overall, the metabolic rate during calling in P. graminea males was 59% higher than the resting metabolic rate (0.443±0.056 vs. 0.279±0.028 CO2 ml g−1 h−1) although highly variable among individuals. While individual call costs were relatively inexpensive (ranging from 0.02–5.4% increase in metabolic rate per call) the individuals with cheaper calls called more often and for longer than those with expensive calls resulting in the former group having significantly greater cumulative costs over a standard amount of time (9.5 h). The metabolic costs of calling are however context dependent since the amount of time spent calling greatly influenced these costs in our trials. A power law function described this relationship between cumulative cost and percentage increase per call (y=130.21x−1.068, R2=0.858); where y=cumulative cost, and x=percentage increase per call. The choice of metric employed for estimating energy costs (i.e. how costs are expressed) also affects the outcome and any interpretation of costs of sexual signalling. For example, the absolute, relative and cumulative metabolic costs of calling yield strongly divergent estimates and any fitness implications depend on the organism's energy budget and the potential trade-offs in allocation of resources that are made as a direct consequence of increased calling effort.
Data from: Males migrate farther than females in a differential migrant: an examination of the fasting endurance hypothesis
Patterns of migration including connectivity between breeding and non-breeding populations and intraspecific variation in the distance travelled are important to study because they can affect individual fitness and population dynamics. Using data from 182 band recoveries across North America and 17 light-level geolocators, we examined the migration patterns of the northern flicker (Colaptes auratus), a migratory woodpecker. This species is unusual among birds because males invest more in parental care than females. Breeding latitude was positively correlated to migration distance because populations in the north appeared to travel farther distances than southern populations to find wintering locations with little snow cover. Connectivity was strong for populations west and east of the Continental Divide. Contrary to the three main hypotheses for intraspecific variation in migration distance, females wintered, on average, farther north than males, although there was overlap throughout their non-breeding range. This pattern contradicts those of other species found to date and is most consistent with the fasting endurance hypothesis if investment in parental care depletes the energy reserves of male flickers more than females. We thus propose a new factor, parental effort, which may influence optimal wintering areas and migration strategies within birds, and encourage future experimental studies to test the relationship between parental care roles and migration strategies of the sexes.
Data from: Nest predation risk and growth strategies of passerine species: grow fast or develop traits to escape risk?
Different body components are thought to trade off in their growth and development rates, but the causes for relative prioritization of any trait remains a critical question. Offspring of species at higher risk of predation might prioritize development of locomotor traits that facilitate escaping risky environments over growth of mass. We tested this possibility in 12 altricial passerine species that differed in their risk of nest predation. We found that rates of growth and development of mass, wings, and endothermy increased with nest predation risk across species. In particular, species with higher nest predation risk exhibited relatively faster growth of wings than of mass, fledged with relatively larger wing sizes and smaller mass, and developed endothermy earlier at relatively smaller mass. This differential development can facilitate both escape from predators and survival outside of the nest environment. Tarsus growth was not differentially prioritized with respect to nest predation risk, and instead all species achieved adult tarsus size by age of fledging. We also tested whether different foraging modes (aerial, arboreal, and ground foragers) might explain the variation of differential growth of locomotor modules, but we found that little residual variation was explained. Our results suggest that differences in nest predation risk among species are associated with relative prioritization of body components to facilitate escape from the risky nest environment.
Individual variation in age-dependent reproduction: fast explorers live fast but senesce young?
<p>1. Adaptive integration of life history and behaviour is expected to result in variation in the pace-of-life. Previous work focused on whether "risky" phenotypes live-fast-but-die-young, but reported conflicting support. We posit that individuals exhibiting risky phenotypes may alternatively invest heavily in early-life reproduction but consequently suffer greater reproductive senescence.<br> 2. We used a 7-year longitudinal dataset with >1200 breeding records of >800 female great tits assayed annually for exploratory behaviour to test whether within-individual age-dependency of reproduction varied with exploratory behaviour. We controlled for biasing effects of selective (dis)appearance and within-individual behavioural plasticity.<br> 3. Slower and faster explorers produced moderate-sized clutches when young; faster explorers subsequently showed an increase in clutch size that diminished with age (with moderate support for declines when old), whereas slower explorers produced moderate-sized clutches throughout their lives. There was some evidence that the same pattern characterized annual fledgling success, if so, unpredictable environmental effects diluted personality-related differences in this down-stream reproductive trait.<br> 4. Support for age-related selective appearance was apparent, but only when failing to appreciate within-individual plasticity in reproduction and behaviour.<br> 5. Our study identifies within-individual age-dependent reproduction, and reproductive senescence, as key components of life history strategies that vary between individuals differing in risky behaviour. Future research should thus incorporate age-dependent reproduction in pace-of-life studies.</p>
Data from: Low abundant soil bacteria can be metabolically versatile and fast growing
The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) versus fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 in Billions and billions sold: Pet-feeder crickets (Orthoptera: Gryllidae), commercial cricket farms, an epizootic densovirus, and government regulations make for a potential disaster
FIGURE 6. Fast distance based analysis tree for 16s ribosomal RNA gene. Note total genetic uniformity among 28 individuals of G. locorojo from eight "localities" on three continents. See Appendix A for specimen source data.
Ground magnetic perturbations associated with "Ultra-Fast Kelvin Wave (UFKW) Variations in the Surface Magnetic Field"
<p>The data set is based on the thermosphere-ionosphere-electrodynamics general circulation model (TIEGCM) simulation results and a post-processing 3D ionospheric current and magnetic perturbation calculation, which is used in the publication "Ultra-Fast Kelvin Wave (UFKW) Variations in the Surface Magnetic Field" by Forbes et al. Focus is on an eastward-propagating ultra-fast Kelvin wave (UFKW) packet with periods between 2-4 days and zonal wavenumber s = -1 during DOY 266-281, 2009. Two sets of simulations are provided with different lower boundary (97km) conditions: 1. forced by daily and zonal mean (S0) 2. forced by S0 and 2-7days with s=-1 perturbations with the planetary wave amplitudes increased by a factor of 1.5. For these simulations the solar flux and geomagnetic forcing is held constant. Hourly output is provided of the neutral wind, neutral temperature, and ground magnetic perturbations.</p>
Input Data for A Fast Surrogate Model for 3D-Earth Glacial Isostatic Adjustment using Tensorflow (v2.8.0) Artificial Neural Networks
<p>Training datasets for the manuscript A Fast Surrogate Model for 3D-Earth Glacial Isostatic Adjustment using Tensorflow (v2.8.0) Artificial Neural Networks. Two separate datasets are contained for training the ANNs: the 3D-spherically-symmetric (SS) rate-of-change of relative sea level (ROCRSL) and the 3D-SS rate of change of radial displacement (ROCRAD) as a function of SS profiles. Two other datasets contain RSL projections from the explicit (i.e. Seakon 3D - Seakon SS + NMSS ) model and the NMSS model, labelled Seakon_plus_NMSS_RSL and NMSS respectively.</p> <p>Filenames denote the structure of the SS profile: </p> <p>???_?.??_??.*.csv = LT_UMV_LMV.*.{csv,nc}<br> </p> <p>LT = elastic lithosphere thickness (km)</p> <p>UMV = upper mantle viscosity (1E21 Pa s)</p> <p>LMV = lower mantle viscosity (1E21 Pa s)</p> <p>i.e. 96_0.5_10.seakon_S40RTS_lr18-SS.rrad.roc.r360x180.P5.density_wSSRRADROC.csv.bz2 has the SS profile</p> <p>96km elastic lithosphere, 0.5E21 Pa s upper mantle viscosity, 10E21 Pa s lower mantle viscosity</p> <p> </p> <p>The columns of the input files are as follows:</p> <p>LT, UMV, LMV, longitude, latitude, time(t=0), ice(t=0), SS_ROC_RSL (t=0), time(t=-1), ice(t=-1), time(t=-2), ice(t=-2), time(t=-3), ice(t=-3), time(t=-4), ice(t=-4), 3D-SS_ROC_RSL(t=0)</p> <p>units for the above are as follows:</p> <p>km, 1E21 Pas, 1E2 Pas, degrees east (0->360), degrees (-180->180), days since 2000, m, mm/year, days since 2000, m, days since 2000, m, days since 2000, m, days since 2000, m, mm/year</p> <p>where 'days since 2000' assumes exactly 365.25 days per year.</p>
Fast wavefront shaping for two-photon brain imaging with multi-patch correction - raw datas
<p>Raw stack images for the main figures of the paper: "Fast wavefront shaping for two-photon brain imaging with multi-patch correction" </p>
Data and code: A fast method to distinguish between fermentative and respiratory metabolisms in single yeast cells
<p>If you have questions, please contact the first autor via the email lauraluzia@gmail.com<br>Link to the bioRxiv preprint -> https://www.biorxiv.org/content/10.1101/2023.06.23.546324v1</p>
Data from: A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions
<p>This repository contains the imaging data (in NIfTI) and analysis code to reproduce the work presented in <em>"A Deep Learning Approach for Fast Muscle Water T2 Mapping with Subject Specific Fat T2 Calibration from Multi-Spin-Echo Acquisitions"</em> by <strong>Marco Barbieri, Melissa T. Hooijmans, Kevin Moulin, Tyler E. Cork, Daniel B. Ennis, Garry E. Gold, Feliks Kogan and Valentina Mazzoli.</strong></p> <p>Citation: "Barbieri, M., Hooijmans, M.T., Moulin, K. <em>et al.</em> A deep learning approach for fast muscle water T2 mapping with subject specific fat T2 calibration from multi-spin-echo acquisitions. <em>Sci Rep</em> 14, 8253 (2024). https://doi.org/10.1038/s41598-024-58812-2"</p> <p>The source code for setting up the Deep Learning application can be found in the GitHub repository https://github.com/barma7/Deep_Learning_for_Muscle_T2_mapping.git</p>
Polyandry and Fast-Z shorebirds
<p>Datasets and R scripts used for the manuscript - <strong>Role-reversed polyandry is associated with faster fast-Z in shorebirds</strong></p>
Single-center, double-blind, randomized, placebo-controlled, single andmultiple dose escalation study to assess safety and tolerability and pharmacokinetics of HRX215 in healthy male volunteers under food and fasting conditions
<p><a name="_Hlk123284665"></a><a name="_Hlk135557103"></a><span><span>Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. </span></span><span><span>Therapies to restore hepatocyte regeneration are lacking, making liver transplantation the only curative option for end stage liver disease. We here report on the structure-based development and characterization (NMR-spectroscopy) of first-in-class small molecule inhibitors of the dual specific kinase MKK4 (MKK4i). MKK4i increased liver regeneration upon hepatectomy in murine and porcine models, allowed for survival of pigs in a lethal 85% hepatectomy model and showed antisteatotic and antifibrotic effects in liver disease mouse models. A first-in-human phase I trial (EudraCT 2021-000193-28) with the clinical candidate HRX215 was conducted and revealed excellent safety and pharmacokinetics. Clinical trials to probe HRX215 for prevention/treatment of liver failure after extensive oncological liver resections or after transplantation of small grafts are warranted.</span></span></p>
Mapping fast DNA polymerase exchange during replication
<h2>Abstract</h2> <p>Despite extensive studies on DNA replication, the exchange mechanisms of DNA polymerase during replication remain unclear. Existing models propose that this exchange is facilitated by protein partners like helicase. Here we present data, employing a combination of mechanical DNA manipulation and single fluorescent protein observation, that reveal DNA polymerase undergoing rapid and autonomous exchange during replication not coordinated by other proteins. The DNA polymerase shows fast unbinding and rebinding dynamics, displaying a preference for either exonuclease or polymerase activity, or pausing events, during each brief binding event. We also observed a 'memory effect' in DNA polymerase rebinding, i.e., the enzyme tends to preserve its prior activity upon reassociation. This effect, potentially linked to the ssDNA/dsDNA junction's conformation, might play a role in regulating binding preference enabling high processivity amidst rapid protein exchange. Taken together, our findings support an autonomous replication model that includes rapid protein exchange, burst of activity, and a 'memory effect' while moving processively forward. </p> <h2>Data Set Description</h2> <p>The study presents findings on the autonomous exchange mechanisms of DNA polymerase at the replication fork. Employing a combination of mechanical DNA manipulation and single fluorescent protein observation, the research reveals rapid and autonomous exchange of DNA polymerase, independent of protein partners like helicase. It highlights the enzyme's preference for exonuclease or polymerase activity and a 'memory effect' during binding events. In this data repo, we provided all the raw data used to reproduce the findings.</p> <h2>Methodology</h2> <p>The single-molecule experiments were performed at room temperature in a 5-channel microfluidic flow cell using the LUMICKS C-Trap instrument that combines dual optical trapping, confocal microscopy, and microfluidics for single-molecule assays. Data analysis was conducted using Python, Origin, and MATLAB. Detailed methodology and instrument specifications are provided in the associated publication.</p> <h2>File Formats</h2> <ul> <li> <p>All data is obtained from C-trap in .tdms format.</p> </li> </ul> <h2>Usage Notes</h2> <p>The custom-written python scripts used in this study is available at <a href="https://github.com/longfuxu/DNAPolymeraseProject">https://github.com/longfuxu/DNAPolymeraseProject</a>, under the MPL-2.0 license. The repository includes example dataset, example Jupiter notebook, along with a detailed README file for instructions on installation and usage.</p> <h2>Acknowledgments</h2> <p>We thank Seyda Aca and Sandrine D'Haene for assistance with protein purification and DNA construction, Noémie Danné for help with implementing the step-fitting algorithm. We thank Erwin Peterman for critical reading and constructive feedbacks of this manuscript. This work was financially supported by a PhD fellowship from China Scholarship Council (To L.X., funding No. 201704910912), the European Union H2020 Marie-Sklowdowska Curie International Training Network AntiHelix (To G.J.L.W., funding No. 859853), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program MONOCHROME (to G.J.L.W., funding No.883240).</p> <h2>Competing Interest</h2> <p>The combined optical tweezers and fluorescence technologies used in this article are patented and licensed to LUMICKS B.V., in which M.T.J.H., and G.J.L.W. declare a financial interest. All other authors declare that they have no competing interests.</p> <h2>Author Contributions</h2> <p>L.X. and G.J.L.W. conceptualized the research. L.X. prepared protein samples and collected single-molecule data and analyzed data; M.T.J.H. analyzed data; L.X., M.T.J.H. and G.J.L.W. wrote and edited the manuscript; G.J.L.W. supervised the project; the manuscript is read, revised, and confirmed by all the listed authors.</p>
2D Nuclear Fission Pile Animation for Thermal and Fast Neutron Counts for two different pile arrangement configurations.
<p>These animations are obtained from a devised 2D Monte Carlo Neutron Transport Simulator model code written in Python. For the process of a thermal-neutron fission chain reaction these gif animations highlight the neutron count evolution and their respective neutron thermalities over time, for two different grids. The first consists of a chess-board pile arrangement between fuel and moderator cells. The second consists of a concetric ring arrangement pile of width 1. These animations are solely inteded to illustrate the process of the project's simulation and not derive any system-dynamic relationships from. </p>
Data and code for 'Fast and artifact-free excitation multiplexing using synchronized image scanning'
<p>Data and source code for the publication 'Fast and artifact-free excitation multiplexing using synchronized image scanning'.</p>
A New Concept of Air Cooling and Heat Pipe for Electric Vehicles in Fast Discharging
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Advanced hybrid thermal management system for LTO battery module under fast charging
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.