Find research datasets worth reusing

Fig. 5. A–B in A new Dicranophragma (Diptera: Limoniidae) from a hypogeous environment in Catalonia (Iberian Peninsula)

Fig. 5. A–B. Female terminalia of Dicranophragma (B.) relictum Mederos sp. nov. A. Lateral view. B. Dorsal view.C–E. Comparison of the internal structures of female terminalia of threeDicranophragma species (ventral view). C. D. (B.) adjuntum (Walker, 1848). D. D. (B.) relictum Mederos sp. nov. E. D. (B.) nemorale (Meigen, 1818). Abbreviations: see Material and methods. Scale bars = 0.25 mm (images C and E after Starý & Reusch 2009).

Fig. 3 in A new Dicranophragma (Diptera: Limoniidae) from a hypogeous environment in Catalonia (Iberian Peninsula)

Fig. 3. Dicranophragma (B.) relictum Mederos sp. nov. A. Wing venation. B–H. Variations detected in some specimens such as extra cross veins (C, F–H) and the split at the end of M 3 vein creating a cell (D), as well as variations in the length and shape of cell dm and cell m1 (B, F–H). Scale bar = 1.0 mm.

Fig. 2 in A new Dicranophragma (Diptera: Limoniidae) from a hypogeous environment in Catalonia (Iberian Peninsula)

Fig. 2. Dicranophragma (B.) relictum Mederos sp. nov., holotype, ♂ (MZB 2019-0985, MNCB). Head and thorax. A. Lateral view. B. Dorsal view. Scale bars = 0.5 mm.

Fig. 1. A in A new Dicranophragma (Diptera: Limoniidae) from a hypogeous environment in Catalonia (Iberian Peninsula)

Fig. 1. A. General view of the landscape at the approach to Avenc del Daví. B. Cave topography. Indicated in red where Dicranophragma (B.) relictum Mederos sp. nov. was found. C–D. Cave entrance and view from inside. E–F. Female specimen of D. (B.) relictum Mederos sp. nov. (MZB 2019-0951, MCNB) photographed in the cave (E, dorsal view; F, lateral view).

opencc-by-4.0Dec 2020View details →

Seasonal Effects in Gastrointestinal Parasite Prevalence, Richness and Intensity in Vervet Monkeys Living in a Semi-Arid Environment

Data and R Notebook for Seasonal Effects in Gastrointestinal Parasite Prevalence, Richness and Intensity in Vervet Monkeys Living in a Semi-Arid Environment

opencc-by-4.0Sep 2020View details →

Predictive Control of Aerial Swarms in Cluttered Environments

This repository contains all data that has been used to produce the results contained in the submission to Nature Machine Intelligence titled  "Predictive Control of Aerial Swarms in Cluttered Environments". It also contains the code necessary for plotting simulation and hardware experimental data. For the code used to run simulation and hardware experiments, please visit <a href="http://doi.org/10.5281/zenodo.4379503">doi.org/10.5281/zenodo.4379503</a>.

opencc-by-4.0Jan 2021View details →

Dataset for Millimeter-wave Mobile Sensing and Environment Mapping: Models, Algorithms and Validation

Dataset of paper "Millimeter-wave Mobile Sensing and Environment Mapping: Models, Algorithms and Validation". The measurement data contains indoor mapping results using millimeter-wave 5G NR signals at 28 GHz. The measurement campaign was conducted in an indoor office environment in Hervanta Campus of Tampere University. Six different sets of measurements contain the range profiles after the proposed radar processing. The shared data contains the IQ data of both transmit and receive signals used during the measurement campaign. The file "main.m" shows how to process and plot the shared data.

opencc-zeroDec 2015View details →

Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genome-wide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví́), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví́ area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices and low geographic distance. However, fine scale structure could be detected when analyses included only this zone. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.

opencc-by-4.0Apr 2012View details →

Topology and structure of Au144(SRNH3+)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"

Positively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m.  The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided. The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a positively charged amonium terminal group. When using this structure do not forget to cite DOI: 10.1021/jp301094m.  NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRNH360_v3.itp. NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.

opencc-by-4.0Apr 2012View details →

Topology and structure of Au144(SRCOO-)60 from "Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment"

Negatively charged monolayer-protected gold nanoparticles (AuNPs) structure and topology files for GROMACS used in DOI: 10.1021/jp301094m.  The final structure of the simulation reported in DOI: 10.1021/jp301094m for the neutral case is provided. The gold nanoparticle contain a core of 144 Au atoms and 60 functionalized alkanethiol side groups (undecanyl chain, R = C11H22), each possessing a negatively charged carboxylic terminal group. When using this structure do not forget to cite DOI: 10.1021/jp301094m.  NOTE1: Different versions for the topology files are provided of both AuNPs. All versions were used for the publication. The changes only affect the core surface and therefore had no influence in the reported properties. Still we recommentd using the latest version: AU144SRCOO60_v2.itp. NOTE2: The original simulations used GROMACS 4.0.5. The files should work, however, as well up to GROMACS 4.6.7.

opencc-by-4.0Nov 2015View details →

Supplementary Information S1 - Detailed results of the CAPRI N-LCA and S2 - Quantification of the main N budget flows in the EU25 agriculture sector of Leip, A., Billen, G., Garnier, J., Grizzetti, B., Lassaletta, L., Reis, S., Simpson, D., Sutton, M. a, de Vries, W., Weiss, F., Westhoek, H. (2015). Impacts of European livestock production: nitrogen, sulphur, phosphorus and greenhouse gas emissions, land-use, water eutrophication and biodiversity. Environ. Res. Lett. 10, 115004. doi:10.1088/1748-9326/10/11/115004

Table S1-1 Quantification of GHG and Nr flow intensities [kg CO2eq (kg product)-1 yr-1] or [g N (kg product)-1 yr-1] with the CAPRI N-LCA model for six main livestock products (BEEF: beef, PORK: pork, EGGS: eggs, POUM: poultry meat; DAIR: milk and dairy products, SGMP: meat from sheep and goats) and six main vegetable food groups (POTA: potatoes, SUGB: sugar beet before processing, OILP: oil seeds before processing; CERR: cereals, LEGU: leguminous crops) as well as other crops (OCRP) and aggregated livestock (ANIMP) and vegetable (CROPP) food. Table S2-1 Quantification of the main N budget flows in the EU25 agriculture sector

opencc-by-4.0Feb 2017View details →

Pattern formation in skyrmionic materials with anisotropic environments

Magnetic Skyrmions have attracted broad attention during recent years because they are regarded as promising candidates as bits of information in novel data storage devices. A broad range of theoretical and experimental investigations have been conducted with the consideration of axisymmetric Skyrmions in isotropic environments. However, one naturally observes a huge variety of anisotropic behavior inmany experimentally relevant materials. In the present work, we investigate the influence of anisotropic environments onto the formation and behavior of the noncollinear spin states of skyrmionic materials by means of Monte Carlo calculations. We find skyrmionic textures which are far from having an axisymmetric shape. Furthermore, we show the possibility to employ periodic modulations of the environment to create skyrmionic tracks.

opencc-by-4.0Oct 2016View details →

NeuroGentoo Presentation - Bringing the Power of Gentoo Package Management to (Neuro)Scientific Software Environments

Neuroscience, one of the most computation-reliant fields in the natural sciences, is dependent upon dozens of highly complex software suites, which scientists are often forced to manage manually. Upstream developers often ship bundled dependencies to better support this flawed workflow, and in the resulting mess documenting and reproducing analysis pipelines is neigh-impossible. We seek to correct these shortcoming of both modern software distribution as well as modern data science, by integrating high-quality ebuilds for neuroscientific software into the Gentoo Science Overlay. We also seek to publish a simple NuroGentoo world file (along with appropriate usage instructions) to allow scientists with access to OpenStack, Amazon Elastic Computing, or Docker to launch up and build a system fit for reproducing data analysis run on other NeuroGentoo systems with minimum effort.

opencc-zeroOct 2023View details →

Paternal environment effects are driven by female reproductive fluid but not sperm age in an external fertiliser

Sperm ageing after ejaculation can generate paternal environmental effects that impact offspring fitness. In many species, female reproductive fluids (FRFs), i.e. ancillary fluids released by eggs or within the female reproductive tract, may protect sperm from ageing and can additionally interact with sperm to influence offspring viability. This raises the intriguing prospect that FRFs may alleviate paternal effects associated with sperm ageing. Here, we test this novel hypothesis using the broadcast spawning mussel, Mytilus galloprovincialis. We show that incubating sperm in FRF prior to fertilisation increases offspring viability and that these effects occur independently of sperm age. Our results provide novel evidence that FRFs allow females to selectively bias fertilisation toward higher quality sperm within an ejaculate, which in turn yields more viable offspring. We consider this FRF-mediated paternal effect in the context of female physiological control over fertilisation and the transgenerational effects of female-regulated haploid selection.

opencc-zeroOct 2023View details →

Unraveling community adaption and survival strategy of soil microbiome under vanadium stress in nationwide mining environments

The vanadium (V) smelters soil harbor wide ranges of microorganisms, whose survival relies on their metabolic activities under stress. Nonetheless, the characteristics and functions of soil microbiome in V mining environments have not been recognized at a continental scale. This study investigates microbial diversity, community assembly and metabolic traits of soil microbiome across 90 V smelters in China. A decrease in alpha diversity is observed, along with community variation, which is also jointly explained by other environmental, climatic and geographic factors. Null model shows that V promotes homogeneous selection. V also mediates co-occurrence patterns, with increased positive interspecific associations under higher V concentrations (>559.6 mg/kg), e.g., f_Gemmatimonadaceae, Nocardioides, Micromonospora, Rubrobacter. In addition, 67 metagenome assembled genomes are retrieved via metagenomic analysis. The metabolic pathways of keystone taxa are disentangled to reveal their putative involvement in the V(V) reduction process. Nitrate and nitrite reductase (nirK, narG), and mtrABC are found to be taxonomically affiliated with Micromonospora. sp, FEN-1250. sp, Nocardioides. sp, etc. Additionally, reverse citric acid cycle (rTCA) serves the main carbon fixation pathway, synthetizing alternative energy for putative V reducers, highlighting a synergistic relationship between autotrophic and heterotrophic processes to support the microbial survival. Our findings comprehensively reveal the driving forces for soil community variation under V stress, suggesting the robust strategies adopted by indigenous microorganisms to alleviate V impact, which can be exploited for bioremediation application.

opencc-by-4.0Nov 2023View details →

STREAM - Sub-THz Radar sensing of the Environment for future Autonomous Marine platforms: RLG Dataset Coniston A

This dataset contains the files corresponding to which results have been included in the journal paper. The full descirption of conducted trials and data structure is mentioned in the attached pdf document.STREAM trials were conducted by the University of Birmingham (UoB) and the University of St. Andrews from 29/08/2022 - 02/09/2022 at Coniston Lake in the UK. The primary aim was to gather propagation data across lakes and measure the returns from the lake surface. The data will be used to develop algorithms to extract the information needed for pilotage.The experiments were performed with radars operating in the 79, 150, and 300 GHz bands to investigate the Doppler and imaging capabilities of these radars.This report describes the measurement scenarios and data structure of INRAS Radarlog (76 GHz – 81 GHz) used for data collection campaign.Contact: a.a.a.pirkani@bham.ac.uk or m.s.gashinova@bham.ac.uk

opencc-by-4.0Nov 2023View details →

Micro-CT image of cell-populated collagen scaffold in the aqueous environment (contrasted with PTA)

A dataset of the collagen scaffold populated with the 3T3 cells scanned in the aqueous environment using Bruker Skyscan 1276 machine (Bruker, Belgium). Scaffold productionThe processes of obtaining and working with collagen scaffolds were conducted in an isolated environment under sterile conditions. The collagen sponge matrix was manufactured at the Center for Collagen Innovation within the Institute of Regenerative Medicine at Sechenov University and provided to us for experimental purposes. In order to obtain the collagen, the authors utilized animal-derived materials sourced from the tendons of large horned cattle. To do this, the tendons were cleaned of excess tissues, cut into pieces with a thickness of 0.5-1 cm, and sequentially treated for 12 hours in a 0.5 M NaCl solution. Subsequently, the mass was homogenized in a 0.83 M acetic acid solution. The resulting suspension was hydrolyzed with 0.24% pepsin for 2 days, after which 1 M NaOH was added to adjust the pH to 7.5, halting the hydrolysis process. The suspension was precipitated with a 12% NaCl solution, the resulting precipitate was redissolved in 0.02 M acetic acid, and then dialyzed. To obtain collagen porous matrices (sponges), the obtained solution was neutralized using 0.1 M NaOH until a pH of 7-7.5 was reached, and the resulting suspension was lyophilized at -40°C for 2 days.Subsequently, the collagen matrix was cut into cubes with sides measuring 0.5 cm. These cubes were placed in 15 ml test tubes filled with 70% ethyl alcohol for sterilization. The test tubes were then placed on a shaker and left in the refrigerator at +4°C for 24 hours. Afterward, the collagen matrices were removed from the alcohol and rinsed five times with 0.9% NaCl.Following the alcohol rinse to confirm the absence of toxicity, an elution test, adapted following the ISO 10993 protocol, was conducted. To obtain collagen cube extracts, they were incubated in a cell culture medium at a volume of 1 ml per sample for 24 hours at 37°C. The 3T3 cell culture was passaged, with 5000 cells seeded in each well of a 96-well plate. After 24 hours, the cells were treated with extract at a volume of 200 µl per well and left in the incubator at 37°C for 24 hours. The following day, extracts were collected, and AlamarBlue reagent (Invitrogen, Waltham, MA, USA) was added according to the manufacturer's instructions to assess the metabolic activity of the cells. Serial dilutions of sodium dodecyl sulfate (SDS) were used as the positive control. Fluorescence intensity was measured using a Victor Nivo spectrofluorimeter (PerkinElmer, Waltham, Massachusetts, USA) at an excitation wavelength of 530 nm and an emission wavelength of 590 nm.Cell seedingAfter confirming the absence of cytotoxic effects, collagen sponges were seeded with the NIH 3T3 cell line at a density of 50,000 cells per sample (cubes of collagen sponge measuring 0.5 cm per side). Staining techniqueFixed specimens in 10% formalin with PBS were washed after 24 hours with distilled water and after that placed in 3% phosphotungstic acid dissolved in distilled water for 24 hours and kept on the rotary shaker at room temperature. After staining, samples were washed and stored in distilled water at 5 °C. Image acquisition and reconstructionA plastic tube filled with distilled water containing the contrasted sample was placed on the sample holder in a SkyScan 1276 micro-CT (Bruker, Kontich, Belgium) and were scanned at 3 μm voxel resolution with 70 kV voltage and 200 uA source power and an aluminum filter with 1 mm of thickness. The rotation was set to 360° around the vertical axis of the sample, with two middle frames for each 0.2° angle step.After scanning, the data were reconstructed using Bruker's NRecon software. During reconstruction, the ring artifact reduction value was set to 20% and the beam hardening correction value to 30%. After that, samples were exported as a series of 16-bit TIFF images which could be opened in the specialized software.

opencc-zeroDec 2023View details →

Environmental effects on genetic variance are likely to constrain adaptation in novel environments

Adaptive plasticity allows populations to cope with environmental variation but is expected to fail as conditions become unfamiliar. In novel conditions, populations may instead rely on rapid adaptation to increase fitness and avoid extinction. Adaptation should be fastest when both plasticity and selection occur in directions of the multivariate phenotype that contain abundant genetic variation. However, tests of this prediction from field experiments are rare. Here, we quantify how additive genetic variance in a multivariate phenotype changes across an elevational gradient, and test whether plasticity and selection align with genetic variation. We do so using two closely related, but ecologically distinct, sister species of Sicilian daisy (Senecio, Asteraceae) adapted to high and low elevations on Mount Etna. Using a paternal half-sibling breeding design, we generated and then reciprocally planted c.19,000 seeds of both species, across an elevational gradient spanning each species' native elevation, and then quantified mortality and five leaf traits of emergent seedlings. We found that genetic variance in leaf traits changed more across elevations than between species. The high-elevation species at novel lower elevations showed changes in the distribution of genetic variance among the leaf traits, which reduced the amount of genetic variance in the directions of selection and the native phenotype. By contrast, the low-elevation species mainly showed changes in the amount of genetic variance at the novel high elevation, and genetic variance was concentrated in the direction of the native phenotype. For both species, leaf trait plasticity across elevations was in a direction of the multivariate phenotype that contained a moderate amount of genetic variance. Together, these data suggest that where plasticity is adaptive, selection on genetic variance for an initially plastic response could promote adaptation. However, large environmental effects on genetic variance are likely to reduce adaptive potential in novel environments.

opencc-zeroDec 2023View details →

Experimental evolution under varying sex ratio and behavioral plasticity in response to perceived competitive environment independently affect calling effort in male crickets

The operational sex ratio (OSR) is a key component influencing the magnitude of sexual selection driving the evolution of male sexual traits, but males often also retain the ability to plastically modulate trait expression depending on the current environment. Here we employed an experimental evolution approach to determine whether the OSR affects the evolution of male calling effort in decorated crickets, a costly sexual trait, and whether plasticity in calling effort is altered by the OSR under which males have evolved. Calling effort of males from two selection regimes maintained at different OSRs over 18–20 generations (male- versus female-biased) was recorded at two different levels of perceived competition, in the absence of rivals or in the presence of an experimentally muted competitor. The effect of the OSR on the evolution of male calling effort was modest and in the opposite direction predicted by theory. Instead, the immediate competitive environment strongly influenced male calling effort as males called more in the presence of a rival, revealing considerable plasticity in this trait. This increased calling effort came at a cost, however, as males confined with a muted rival experienced significantly higher mortality.