Find research datasets worth reusing

opencc-by-4.0Oct 2019View details →

Selected data from "Small-scale universality in the spectral structure of transitional pipe flows"

Data from Figure 4 and Figure 6 of "Small-scale universality in the spectral structure of transitional pipe flows", Science Advances (2019). Included are spatial spectra normalized with the Kolmogorov scale and viscosity. The collapse of the normalized spectra is indicative of the small-scale universality predicted by Kolmogorov. The data are taken from turbulent and transitional pipe flows at different Re and different positions from the wall from both experiments and simulations (experiments are at the centerline only).

opencc-by-4.0Jul 2024View details →

Flow Cytometry Data from "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing"

This record contains the flow cytometry data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Files are in <a href="https://docs.flowjo.com/flowjo/advanced-features/fj-acs/">Archive Cytometry Standard (ACS) format</a> . Each <code>.acs</code> file is a zip container which holds both the raw <code>.fcs</code> files and a FlowJo workspace (<code>.wsp</code>) file. Keywords in the workspace file identify which primary antibody (<code>primary</code>) was used and which cell genotype (<code>strain</code>) was used for each sample. The workspace also encodes the gating scheme and compensation matrix applied to each sample. Plots in the manuscript are exported from Layout views in the workspace.

opencc-by-4.0Oct 2024View details →

Flow cytometry data and image data -A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice

Open the record for dataset details and reuse information.

opencc-zeroDec 2015View details →

Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.

opencc-zeroDec 2017View details →

Data from: Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea)

Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggests that strong enough divergent selection can overpower gene flow, leading to islands of divergence. However, there are alternative explanations for these patterns. Independent evidence that islands of divergence are due to divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here we present multiple lines of evidence that islands of divergence in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the outcome of divergent selection in the face of gene flow. We analyzed a SNP dataset across the genome to assess the amount of gene flow, resistance to introgression, and patterns of selection on genes resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with gene flow between the species in sympatry. In addition, highly differentiated SNPs were subject to divergent selection. Finally, despite gene flow in sympatry, SNPs that are highly differentiated in allopatry are resistant to homogenization in sympatry. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.

opencc-zeroDec 2017View details →

Data from: Linking beaver dam affected flow dynamics to upstream passage of Arctic grayling

Beaver reintroductions and beaver dam structures are an increasingly utilized ecological tool for rehabilitating degraded streams, yet beaver dams can potentially impact upstream fish migrations. We collected two years of data on Arctic grayling movement through a series of beaver dams in a low gradient mountain stream, utilizing radio-telemetry techniques, to determine how hydrology, dam characteristics, and fish attributes impeded passage and movement rates of spawning grayling. We compared fish movement between a "normal" flow year and a "low" flow year, determined grayling passage probabilities over dams in relation to a suite of factors, and predicted daily movement rates in relation to the number of dams each fish passed and distance between dams during upstream migration to spawning areas. We found that the average passage probability over unbreached beaver dams was 88%, though we found that it fell below 50% at specific dams. Upstream passage of grayling was affected by three main characteristics: 1) temperature 2) breach status and 3) hydrologic linkages that connect sections of stream above and below the dam. Other variables influence passage, but to a lesser degree. Cumulative passage varied with distance upstream and total number of dams passed in low versus normal flow years, while movement rates upstream slowed as fish swam closer to dams. Our findings demonstrate that upstream passage of fish over beaver dams is strongly correlated with hydrologic conditions with moderate controls by dam- and fish-level characteristics. Our results provide a framework that can be applied to reduce barrier effects when and where beaver dams pose a significant threat to the upstream migration of fish populations while maintaining the diverse ecological benefits of beaver activity when dams are not a threat to fish passage.

opencc-by-4.0Jun 2021View details →

VAMONOS - Flow through bridges. Experimental data.

This dataset contains the results from the experimental tests carried out at the hydraulics laboratory of the Civil Engineering School, at University of A Coruña (Spain), as part of the VAMONOS (Vertically-averaged models for non-hydrostatic flows) project (CTM2017-85171-C2-2-R). The aim of the project is the development of enhanced 2D river flow models including additional terms to account for non-hydrostatic pressure and mixed flow conditions around hydraulic structures. This data package includes experimental results on 4 bridge geometries that were tested in an open channel. The experimental facility consists of a 15 m flume with a square cross-section of 0.5 x 0.5 m. Water depths were measured with an automatic positioner on a grid of approximately 117 points. In whole, 32 experimental tests have been carried out under different flow conditions. This dataset is structured in the following pdf documents and folders: <ul> <li>. This file summarizes all the experimental tests.</li> <li>. This file includes information about the experimental facilities, the test conditions and the uploaded files.</li> <li>.pdf. This file includes a 3D representation of the water depths measured in each experimental test.</li> <li>This folder includes the raw data registered in the experimental tests.</li> <li>Matlab_files. This folder contains three Matlab files (.m) that can be used to process the raw data, to plot the results and to generate a document with information about the test.</li> <li>Processed_data. This folder contains, for each structure, a pdf with the structure geometry and a text file per test with the water surface elevations measured.</li> </ul> Those interested in experimental data for the calibration of numerical models or the analysis of empirical discharge rating curves, are suggested to work only with the data included in the folder Processed_data. Further details on the experimental setup are given in the document Data_package_description.pdf.

opencc-by-4.0Dec 2020View details →

Numerical simulation data of a two-dimensional flow around a fixed circular cylinder

Numerical results of a two-dimensional flow past a fixed circular cylinder in the vortex shedding regime. The solver is Cadyf, an in-house fluid-structure interaction code using finite element method (<a href="https://doi.org/10.1016/j.jcp.2008.11.032">doi.org/10.1016/j.jcp.2008.11.032</a>). The Reynolds number is Re = 100. The boundary conditions and numerical integration are described in <a href="https://doi.org/10.1017/jfm.2021.252">doi.org/10.1017/jfm.2021.252</a>. The fixed_cylinder_atRe100 raw file contains the values of the flow velocity, pressure, and node coordinates at each time step. Tables of the results can be extracted using the file processing code in text_flow.py. The Re100_fixe00.reactions raw file contains the values of the total force and torque applied on the cylinder at each time step. Tables of the results can be extracted using the file processing code in reactions_process.py.

opencc-zeroAug 2019View details →

Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic 'landscape' of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.

opencc-zeroDec 2017View details →

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.

opencc-zeroDec 2016View details →

Data from: A test of genomic modularity among life-history adaptations promoting speciation with gene flow

Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or "modularity" among phenotypic traits may reduce constraints and facilitate divergence. Here, we test whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS). Loci genetically associated with diapause termination timing were mainly observed for SNPs mapping to chromosomes 1–3 in the genome, most notably for SNPs displaying higher levels of linkage disequilibrium (LD), likely due to inversions. In contrast, selection on initial diapause intensity affected loci on all five major chromosomes of the genome, specifically those showing low levels of LD. This lack of overlap in genetically associated loci suggests that the two diapause phenotypes are largely modular. On chromosome 2, however, intermediate level LD loci and a subgroup of high LD loci displayed significant negative relationships between initial diapause intensity and diapause termination time. These gene regions on chromosome 2 therefore affected both traits, while most regions were largely independent. Moreover, loci associated with both measured traits also tended to exhibit highly divergent allele frequencies between the host races. Thus, the presence of nonoverlapping genetic modules likely facilitates simultaneous, adaptive divergence for the measured life-history components.

Supporting data for the article "Continuing invariant solutions towards the turbulent flow"

Supporting data for the article "Continuing invariant solutions towards the turbulent flow": numerical code and computed invariant solutions

Density-driven flow experiment data

This data is the measured flux of MEG in sand through image processing technique. The experiment is designed to recover the density-driven instability and following convection process in the geological CO2 storage.

opencc-zeroAug 2021View details →

Optic flow and odometry data from intelrealsense camera

Insects rely on the perception of image motion, or optic flow, to estimate their velocity relative to nearby objects. This information provides important sensory input for avoiding obstacles. However, certain behaviors, such as estimating the absolute distance to a landing target, accurately measuring absolute distance travelled, and estimating the ambient wind speed require decoupling optic flow into its component parts: absolute ground velocity and distance to nearby objects. Behavioral experiments suggest that insects perform these calculations, but their mechanism for doing so remains unknown. Here we present a novel algorithm that combines the geometry of dynamic forward motion with known features of insect visual processing to provide a hypothesis for how insects might \textit{directly} estimate absolute ground velocity from a combination of optic flow and acceleration information. Our robotics-inspired-biology approach reveals three critical requirements. First, absolute ground velocity can only be directly estimated from optic flow during times of active acceleration and deceleration. Second, spatial pooling of optic flow across a receptive field helps to alleviate the effects of noise and/or low resolution visual systems. Third, averaging velocity estimates from multiple receptive fields further helps to reject noise. Our algorithm provides a hypothesis for how insects might estimate absolute velocity from vision during active maneuvers, and also provides a theoretical framework for designing fast analog circuitry for efficient state estimation that can be applied to insect-sized robots.

Flow cytometry data of "The impact of storage on extracellular vesicles: a systematic study" experiments

Flow cytometry raw data acquired for the pubblication of "The impact of storage on extracellular vesicles: a systematic study"

ARRIVE Questionnaire, CONSORT Check-list and Flow Diagram + TGO, TGP, HEMOGRAMA AND OSTEOREGENERATIVE DATA - Paper: "Biological performance of a bioabsorbable Poly (L-Lactic Acid) produced in polymerization unit: in vivo studies"

The data in excel refer to 3 types of experimental analysis: 1- Hepatocyte transaminase studies for animals at 6 and 9 months post implantation, implanted with PLLA and not implanted with PLLA. 2- Hemogram studies for animals 6 and 9 months after implantation, implanted with PLLA and not implanted with PLLA. These data are divided in 2 files, one file for animals of 6 months and another file for animals of 9 months 3- Bone lesion regeneration area study for animals 6 and 9 months after implantation, implanted with PLLA and not implanted with PLLA. 4- File for CONSORT Checklist 5-  File for ARRIVE questionnaire 6- File for Flow Diagram

opencc-zeroSep 2021View details →

Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity

Carcinus maenas is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing. Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R). Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.

opencc-by-4.0Oct 2021View details →

Rock-magnetic, paleomagnetic and multimethod paleointensity data from an upper Miocene lava flow sequence from São Vicente (Cape Verde)

The folder “Praia Grande Paleomagnetism Data.zip” contains paleomagnetic thermal and alternating field demagnetisation data obtained on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Data are in .txt format with the extension .rs3. Columns are separated by empty spaces. Data can be visualised and analysed with the Remasoft software (Chadima and Hrouda, 2006). The folder “Praia Grande rock magnetism Data.zip” contains data in .txt format of IRM acquisition curves (extension .irm), hysteresis curves (extension .hys), backfield curves (extension .coe) and thermomagnetic magnetisation versus temperature curves (extension .rmp) obtained on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Columns are separated by tabs. Data can be visualised and analysed with the RockMagAnalyzer 1.0 software (Leonhardt, 2006). The folder “Praia Grande Thellier-Coe Data.zip”contains paleointensity determination data obtained with the Thellier-Coe method on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Data are in .txt format with the extension .tdt separated by tabs. Data can be visualised and analysed with the ThellierTool software (Leonhardt et al.,2004). The folder “Praia Grande Multispecimen.zip” contains paleointensity determination data on upper Miocene volcanic rocks from São Vicente (Cape Verde) obtained with the multispecimen method (Biggin and Poidras, 2006; Dekkers and Böhnel, 2006; Fabian and Leonhardt, 2010) at Laboratorio Interinstitucional de Magnetismo Natural, Instituto de Geofísica, Unidad Michoacán, UNAM, Mexico. Two kinds of files can be found: Five .txt files (M0.txt, M1.txt, M2.txt, M3.txt, M4.txt) and five .jr6 files (M0.jr6, M1.jr6, M2.jr6, M3.jr6, M4.jr6). Both types of files are in .txt format. The .txt files directly provide the measurement data generated during the multispecimen experiments. The first columns of the .jr6 files display the following information: column 1: specimen name; column 2: experimental step (explanation below); columns 3, 4 and 5: three magnetisation components M(x), M(y) and M(z); column 6: exponent of the magnetisation components to obtain the magnetisation value in A/m. In the multispecimen experiments, the specimen-name (e.g.  PRG1-3) can be divided in two parts, the first three characters indicate the sample (flow), the last character the specimen number (1 to 7). Eight different experimental steps (column 2) can be distinguished: NRM, A10, A20, A30, A40, A50, A60 and A70.  They correspond to the measurement of the NRM and of steps in which fields of 10, 20, 30, 40, 50, 60 and 70 mT where respectively applied. Files M0 (.txt and .jr6) include only NRM measurements, files M1 include measurements of specimens heated with an applied field parallel to their NRM, files M2 include measurements of specimens heated with an applied field antiparallel to their NRM, files M3 include measurements of specimens heated in zero field and cooled down in an applied field parallel to their NRM, and files M4 include again include measurements of specimens heated with an applied field parallel to their NRM. REFERENCES Biggin, A., Poidras, T., 2006. First-order symmetry of weak-field partial thermoremanence in multi-domain ferromagnetic grains. 1. Experimental evidence and physical implications. Earth Planet. Sci. Lett. 245, 438–453. doi:10.1016/j.epsl.2006.02.035 Chadima, M. and Hrouda, F., 2006. Remasoft 3.0 a user friendly paleomagnetic data browser and analyzer. Travaux Géophysiques, XXVII, 20-21. Dekkers, M.J., Böhnel, H.N., 2006. Reliable absolute palaeointensities independent of magnetic domain state. Earth Planet. Sci. Lett. 248, 507–516. doi:10.1016/j.epsl.2006.05.040 Fabian, K., Leonhardt, R., 2010. Multiple-specimen absolute paleointensity determination: An optimal protocol including pTRM normalization, domain-state correction, and alteration test. Earth Planet. Sci. Lett. 297, 84–94. doi:10.1016/j.epsl.2010.06.006 Leonhardt, R., 2006. Analyzing rock magnetic measurements; The RockMagAnalyzer 1.0 software.Computers and Geosciences, 32, 1420-1431. Leonhardt, R., Heunemann, C. and Krása, D., 2004. Analyzing absolute paleointensity determinations: Acceptance criteria and the software ThellierTool4.0. Geochem. Geophys. Geosyst., Vol. 5, no. 12, doi.: 10.1029/2004GC000807. Monster, M.W.L., de Groot, L. V., Dekkers, M.J., 2015. MSP-Tool: A VBA-Based Software Tool for the Analysis of Multispecimen Paleointensity Data. Front. Earth Sci. 3, 1–9. https://doi.org/10.3389/feart.2015.00086

opencc-by-4.0Oct 2021View details →

Data accompanying the paper titled: Evaluation of a forest parameterization to improve boundary layer flow simulations over complex terrain.

The present repository contains the namelists, output data from the Weather Research and Forecasting (WRF) numerical simulations and observations described in the article "Evaluation of a forest parameterization to improve boundary layer flow simulations over complex terrain" submitted to the Geosciences Model Development journal. The numerical simulations were developed to evaluate the influence of a forest parametrization on the simulation of the boundary layer flow over moderate complex terrain in the context of the Perdigão 2017 field campaign. The numerical simulations used WRF large eddy simulation mode (WRF-LES). The short-term high resolution (40 m horizontal grid spacing) and long-term (200 m horizontal grid spacing) WRF-LES were run for an integration time of 12 hours and 1.5 months, respectively, with and without forest parameterization. The short-term simulations focus on low-level jet events over the valley, while the long-term simulations cover the whole intensive observation period (IOP) of the field campaign. The results are validated using lidar and meteorological tower observations. The files in the repository are organized as follows: Namelists used to run the WRF model are located in the 'namelists' sub-directory. Data slices of domains d03 and d04 covering the location of the three meteorological towers and LIDAR for the whole integration time are located in the 'reduced_domain' sub-directory. Direct WRF output for selected periods (representing the low-level-jet episodes observed) for domains d03 and d04 are located in the 'files_select_time' sub-directory. The observations used to validate the model are located in the 'observations' sub-directory. The complete dataset of observations from the field campaign can be found in the official campaign data repository: re3data.org: Perdigao Field Experiment; editing status 2020-03-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMN4 last accessed: 2021-10-13. The WRF model can be downloaded from https://www2.mmm.ucar.edu/wrf/users/download/get_sources_new.php.