Find research datasets worth reusing

opencc-by-4.0Jan 2024View details →

Identifying Easy Instances to Improve Efficiency of ML Pipelines for Algorithm-Selection - Code and Data

This repository contains the code and data for reproducibility of the paper 'Identifying Easy Instances to Improve Efficiency of ML Pipelines for Algorithm-Selection'.  The following files are included: <ul> <li>best_algo.csv : labels for the classification and median performance of algorithms;</li> <li>ML_models.ipyb : jupyter notebook with the definition of the neural networks for both classifiers;</li> <li>pickle.zip : pickled models for the hardness classification and the algorithm selector;</li> <li>trajectories.zip : raw data files containing parts of the trajectories of each algorithm;</li> <li>Results.zip : results obtained using the approach on the stream of instances.</li> </ul>

opencc-by-4.0Sep 2023View details →

Dataset for: "Parameter identifiability and model selection for partial differential equation models of cell invasion"

This is the dataset accompanying the paper "Parameter identifiability and model selection for partial differential equation models of cell invasion" (https://arxiv.org/abs/2309.01476). It consists of a series of images taken of a barrier assay experiment to study tissue expansion of MDCK cells, along with cell density data in MATLAB format. File structure: the contents of the four zip files should be combined (they were split into four files for practical reasons regarding file size). The data corresponds to eight experiments, four with circular initial conditions, and four with triangular initial conditions, the associated data are located in 04-05-22 exp1/Circle and 04-05-22 exp1/Triangle respectively, each labeled "xy<n>", where <n> from 1 to 8 is an identifier for the experiment. The images under the xy<n>_Phase folders are the raw images taken of the experiment, those under the xy<n>_mask folder are processed images indicating the extend of the spread of the cell population. The DensityCellcyleFraction folder contain data files in MATLAB format. The most relevant is the "density" variable, which is a rank-3 tensor of size 150x150x77 such that density(i,j,k) corresponds to the cell density at location (x_i,y_j) and time t_k. The process for calculating the cell density is described in the paper. Alternatively, the density data is also provided in csv format. In the csv_data folder, xy<n>/t<k>.csv encodes a matrix representing cell density for experiment <n> at time t_k. The code for processing and analysing these data are provided in the "code" folder. It is also available at https://github.com/liuyue002/woundhealing . Abstract of the paper: When employing a mechanistic model to study biological systems, practical parameter identifiability is important for making predictions in a wide range of scenarios, as well as for understanding the mechanisms driving the system behaviour. We argue that parameter identifiability should be considered alongside goodness-of-fit and model complexity as criteria for model selection. To demonstrate, we use a profile likelihood approach to investigate parameter identifiability for four extensions of the Fisher--KPP model, given experimental data from a cell invasion assay. We show that more complicated models tend to be less identifiable, with parameter estimates being more sensitive to subtle differences in experimental procedures, and require more data to be practically identifiable. The results from identifiability analysis can inform model selection, as well as data collection and experimental design.

opencc-zeroJan 2024View details →

Application of LiDAR to assess the habitat selection of an endangered small mammal in an estuarine wetland environment

Light detection and ranging (lidar) has emerged as a valuable tool for examining the fine-scale characteristics of vegetation. However, lidar is rarely used to examine coastal wetland vegetation or the habitat selection of small mammals. Extensive anthropogenic modification has threatened the endemic species in the estuarine wetlands of the California coast, such as the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). A better understanding of SMHM habitat selection could help managers better protect this species. We assessed the ability of airborne topographic lidar imagery in measuring the vegetation structure of SMHM habitats in a coastal wetland with a narrow range of vegetation heights. We also aimed to better understand the role of vegetation structure in habitat selection at different spatial scales. Habitat selection was modeled from data compiled from 15 small mammal trapping grids collected in the highly urbanized San Francisco Estuary in California, USA. Analyses were conducted at three spatial scales: microhabitat (25 m2), mesohabitat (2,025 m2), and macrohabitat (10,000 m2). A suite of structural covariates was derived from raw lidar data to examine vegetation complexity. We found that adding structural covariates to conventional habitat selection variables significantly improved our models. At the microhabitat scale in managed wetlands, SMHM preferred areas with denser and shorter vegetation, and selected for proximity to levees and taller vegetation in tidal wetlands. At the mesohabitat scale, SMHM were associated with a lower percentage of bare ground and with pickleweed (Salicornia pacifica) presence. All covariates were insignificant at the macrohabitat scale. Our results suggest that SMHM preferentially selected microhabitats with access to tidal refugia and mesohabitats with consistent food sources. Our findings showed that lidar can contribute to improving our understanding of habitat selection of wildlife in coastal wetlands and help to guide future conservation of an endangered species.

opencc-zeroFeb 2024View details →

Data from: Digging deeper: habitat selection within the home ranges of a threatened marsupial

While resource selection varies according to the scale and context of study, gathering data representative of multiple scales and contexts can be challenging especially when a species is small, elusive, and threatened. We explore resource selection in a small, nocturnal, threatened species—the greater bilby (Macrotis lagotis)—to test (a) which resources best predict bilby occupancy, and (b) whether responses are sex-specific and/or vary over time. We tracked a total of 20 bilbies and examined within home range resource selection over multiple seasons in a large (110ha) fenced sanctuary in temperate Australia. We tested a set of plausible models for bilby resource selection, showing that food biomass (terrestrial and subterranean invertebrates, and subterranean plants) and soil textures (% sand, clay and silt) best predicted bilby resource selection for all sampling periods. Selection was also sex-specific; female resource use, relative to males, was more closely linked to the location of high-quality resources (sandier soils, and terrestrial invertebrate biomass). Bilby selection for roads was independent of season but varied over time with females selecting for areas closer to roads when plants increased in density off roads. Our findings demonstrate the importance of considering resource selection over multiple contexts and highlight a method to collect such data on a difficult to study, threatened species. Collecting such data is critical to understanding the habitat required by species.

opencc-zeroFeb 2024View details →

Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection

Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on phylogenetic inference and introgression detection.

opencc-by-4.0Mar 2024View details →

Selective recovery of boron, cobalt, gallium and germanium from seawater solar saltworks brines using N-methylglucamine sorbents: Column operation performance

The European Union (EU) identified a list of Critical Raw Materials (CRMs) crucial for its economy, aiming to find alternative sources. Seawater is a promising option as it contains almost all elements, although most at low concentrations. However, to the present, the CRMs' recovery from seawater is technically and economically unfeasible. Other alternatives to implement sea mining might be preferred, such as reverse osmosis brines or saltworks bitterns (after sodium chloride crystallisation). The CRMs' extraction in a selective way can be achieved using highly selective recovery processes, such as chelating sorbents. This study focuses on extracting Trace Elements (TEs) from solar saltworks brines, including boron, cobalt, gallium and germanium, using commercial N-methylglucamine sorbents (S108, CRB03, CRB05). The application of these sorbents has shown potential for boron recovery, but their selectivity for cobalt, gallium, and germanium requires further investigation. This research aims to assess these sorbents' kinetics and column mode performance for TEs recovery from synthetic bitterns. Boron and germanium were rapidly sorbed, reaching equilibrium (>90 %) within 1 h, except for S108, which took 2 h. In column mode, 20–25 pore volumes of bittern were treated to remove boron and germanium, but competition from other elements reduced treatment capacity. An acidic elution (1 M hydrochloric acid) allowed to elute them (>90 %), reaching concentration factors for germanium and boron of 35 and 11, respectively, while cobalt and gallium had less affinity for the sorbents. In addition, the experiments performed were fitted by a mass transfer model to determine the equilibrium constants and selectivities. Therefore, bittern mining has been proven as a secondary/alternative source to obtain CRMs, which can lead the EU to a position in which its dependence on other countries to obtain these raw materials would be decreased.

opencc-zeroMar 2024View details →

The effect of experimental pollinator decline on pollinator-mediated selection on floral traits

Human-mediated environmental change, by reducing mean fitness, is hypothesized to strengthen selection on traits that mediate interactions among species. For example, human-mediated declines in pollinator populations are hypothesized to reduce mean seed production by increasing the magnitude of pollen limitation and thus strengthen pollinator-mediated selection on floral traits that increase pollinator attraction or pollen transfer efficiency. To test this hypothesis, we measured two female fitness components and six floral traits of Lobelia siphilitica plants exposed to supplemental hand-pollination, ambient open-pollination, or reduced open-pollination treatments. The reduced treatment simulated pollinator decline, while the supplemental treatment was used to estimate pollen limitation and pollinator-mediated selection. We found that plants in the reduced pollination treatment were significantly pollen-limited, resulting in pollinator-mediated selection for taller inflorescences and more vibrant petals, both traits that could increase pollinator attraction. This contrasts with plants in the ambient pollination treatment, where reproduction was not pollen-limited and there was no significant pollinator-mediated selection on any floral trait. Our results support the hypothesis that human-mediated environmental change can strengthen the selection on traits of interacting species and suggest that these traits have the potential to evolve in response to changing environments.

opencc-zeroMar 2024View details →

Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, non-sister sea urchin species: Strongylocentrotus pallidus and S. droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% - 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the non-introgressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.

opencc-by-4.0Mar 2024View details →

ERA5-Land selected indicators daily aggregates for the Latin America region, 2023

This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 2023. Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates. For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation. Those files were created using the <a href="https://github.com/ErikKusch/KrigR">KrigR</a> package.

opencc-zeroMar 2024View details →

Data from: Early-life variation in migration is subject to strong fluctuating survival selection in a partially migratory bird

Population dynamic and eco-evolutionary responses to environmental variation and change fundamentally depend on combinations of within- and among-cohort variation in phenotypic expression of key life-history traits, and on corresponding variation in selection on those traits. Specifically, in partially migratory populations, spatio-seasonal dynamics depend on the degree of adaptive phenotypic expression of seasonal migration versus residence, where more individuals migrate when selection favours migration. Opportunity for adaptive (or, conversely, maladaptive) expression could be particularly substantial in early life, through initial development of migration versus residence. However, within- and among-cohort dynamics of early-life migration, and of associated survival selection, have not been quantified in any system, preventing any inference on adaptive early-life expression. Such analyses have been precluded because data on seasonal movements and survival of sufficient young individuals, across multiple cohorts, have not been collected. We undertook extensive year-round field resightings of 9,359 colour-ringed juvenile European Shags (Gulosus aristotelis) from 11 successive cohorts in a partially-migratory population. We fitted advanced Bayesian multi-state capture-mark-recapture models to quantify early-life variation in migration versus residence and associated survival across short temporal occasions through each cohort's first year from fledging, thereby quantifying the degree of adaptive phenotypic expression of migration within and across years. All cohorts were highly partially migratory, but the degree and timing of migration varied considerably within and among cohorts. Episodes of strong survival selection on migration versus residence occurred both on short timeframes within years, and cumulatively across whole years, generating instances of instantaneous and cumulative net selection that would be obscured at coarser temporal resolutions. Further, the magnitude and direction of selection varied among years, generating strong fluctuating survival selection on early-life migration across cohorts, as rarely evidenced in nature. Yet, the degree of migration did not strongly covary with the direction of selection, indicating limited early-life adaptive phenotypic expression. These results reveal how dynamic early-life expression and selection on a key life-history trait, seasonal migration, can emerge across seasonal, annual, and multi-year timeframes, yet be substantially decoupled. This restricts the potential for adaptive phenotypic, micro-evolutionary, and population dynamic responses to changing seasonal environments.

Data for 'Graphene oxide aerogels for gas phase adsorption and selective separation of aromatic hydrocarbons and cycloalkanes'

### Selected experimental data for the 'Graphene oxide aerogels for gas phase adsorption and selective separation of aromatic hydrocarbons and cycloalkanes ### Authors of the manuscript related to the uploaded data: 1. Maksymilian Plata-Gryl, Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdansk University of Technologym, email: maksymilian.plata-gryl@pg.edu.pl 2. Roberto Castro-Muñoz, Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, email: food.biotechnology88@gmail.com 3. Emilia Gontarek-Castro, Department of Environmental Technology, Faculty of Chemistry, University of Gdansk 4. Alan Miralrio, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey 5. Grzegorz Boczkaj, Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, email: grzegorz.boczkaj@pg.edu.pl Package contains following data: 1. Fourier-transform infrared spectra of rGOA, GO, and graphite samples, format: .csv, number of files: 5 2. Raman spectra of rGOA samples, format: .csv, number of files: 3 3. Low temperature nitrogen adsorption-desorption isotherms, format: .txt, number of files: 4 4. Raw chromatograms of test probes for rGOA samples, format .txt, number of files: 234 in 12 subfolders For more information about experimental conditions or data please see the manuscript/publication or contact author/s.

Raw diffraction images of the crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody

The diffraction datasets was collected at X10SA, SLS. The dataset was collected from one crystal using a rotation scheme for 222º oscillation with the following experimental parameters; Wavelength: 0.9998 Å, Detector: EIGER2 Si 16M (DECTRIS Co. Ltd.). The crystal belonged to space group C 1 2 1 with unit cell parameters a=207.66, b=39.51, c=177.98 Å, and beta=117.12°.PDB ID: 8TBQ

opencc-zeroApr 2024View details →

Data from: Corals that survive repeated thermal stress show signs of selection and acclimatization

Climate change is transforming coral reefs by increasing the frequency and intensity of marine heatwaves, often leading to coral bleaching and mortality. Coral communities have demonstrated modest increases in thermal tolerance following repeated exposure to moderate heat stress, but it is unclear whether these shifts represent acclimatization of individual colonies or mortality of thermally susceptible individuals. For corals that survive repeated bleaching events, it is important to understand how past bleaching responses impact future growth potential. Here, we track the bleaching responses of 1,832 corals in leeward Maui through multiple marine heatwaves and document patterns of coral growth and survivorship over a seven-year period. While we find limited evidence of acclimatization at population scales, we document reduced bleaching over time in specific individuals, primarily in the stress-tolerant taxa Porites lobata, indicative of acclimatization. For corals that survived both bleaching events, we find no relationship between bleaching response and coral growth in three of four taxa studied. This decoupling between bleaching and growth suggests that coral survivorship is a better indicator of future growth than is a coral's bleaching history. Based on these results, we recommend restoration practitioners in Hawaiʻi obtain outplants from Porites and Montipora colonies with a proven track-record of growth and survivorship, rather than devote resources toward identifying and cultivating bleaching-resistant phenotypes. Survivorship followed a latitudinal thermal stress gradient, but because this gradient was small, it is likely that local environmental factors also drove differences in coral performance between sites. Efforts to reduce human impacts at low performing sites would likely improve coral survivorship in the future.

Porous Organic Polymers with Heterocyclic Crown Ethers for Selective Lithium-Ion Capture

Abstract of the publication: Lithium is a key resource of the 21st century. Despite that, Li is traditionally mined rather than obtained from maritime brines or secondary sources such as spent energy-storage devices owing to the difficulties in Li recovery. Herein, we present a porous organic polymer capable of capturing Li ions from aqueous solutions through highly pre-organized heterocyclic crown ether-like pores in the polymer backbone. These features enable Li+ uptake capacities over 120 mg g-1 and selectivity versus highly competitive ions such as Na+, Ca2+, and Mg2+.

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Zn(II)-methionine) at 200 keV

This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: "CompoundName_AcceleratingVoltage_Temperature.zip" Diffraction datasets within each folder are named according to the format: CompoundName_static_diffraction_AcceleratingVoltage_Temperature_series#.mrc

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (biotin, Cu(II)-serine, Zn(II)-histidine) at 200 keV

Deciphering anthropogenic and biogenic contributions to selected NMVOC emissions in an urban area

This netcdf data file is related to a study published in ACP by Peron et al., 2024. Selected concentration, fluxes of NMVOC as well as meteorological data are reported for the urban area of Innsbruck, Austria. For a complete site description we also refer to Ward et al., 2022: https://doi.org/10.5194/acp-22-6559-2022 and Karl et al., 2020: https://doi.org/10.1175/BAMS-D-19-0270.1

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Co(II) meso-tetraphenyl porphyrine at high fluence, ~100 electrons per square Angstrom) at 200 keV

BIR-MicroED: selected area electron diffraction datasets from static microcrystals (Co(II) meso-tetraphenyl porphyrin) at 200 keV

BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Co(II) meso-tetraphenyl porphyrin) at 200 keV

<div> This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: "CompoundName_multipass_RotationSpeed_FrameRate_SpotSize_tiltseries_Temperature.zip" Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux Diffraction datasets within each folder are named according to the format: "CompoundName_tiltseries_AcceleratingVoltage_Temperature_IncidentFlux_crystal#sweep#.mrc" Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively. </div>