Find research datasets worth reusing

opencc-zeroApr 2022View details →

Data from: Experimental analysis of organ decay and pH gradients within a carcass and the implications for phosphatization of soft tissues

Replacement of soft-tissues by calcium phosphate yields spectacular fossils. Decay experiments have shown that pH is a major control on the precipitation of calcium phosphate and tissue replication: for this to occur pH must fall below the carbonic acid dissociation constant (pH 6.38). However, in the fossil record, phosphatisation is highly selective - some internal organs, such as muscles, stomachs, and intestines, appear to preferentially phosphatise while other organs seldomly phosphatise. The reasons for this are unclear but one hypothesis is that, during decay, organs create distinct chemical microenvironments and only some fall below the critical pH threshold for mineralization to occur. Here, we present a novel investigation using microelectrodes that records fluctuating dynamic spatial and temporal pH gradients inside of organs within a carcass in real time. Our experiments demonstrate that within a decaying carcass, organ-specific microenvironments are not generated. Rather, a pervasive pH environment forms within the body cavity (i.e. the coelom) which persists until integumentary failure. With no evidence to support the development of organ-specific microenvironments during decay other factors must control organ phosphatisation. We propose it is tissue histology that plays an important role in selective phosphatisation. Tissues with high phosphate content (and those rich in collagen) are most likely to phosphatise. Internal organs that have low tissue-bound phosphate, including the integuments of the stomach and intestine, only phosphatise when associated with ingested phosphate-rich organic matter. Identifying the driver behind selective phosphatisation may provide insights into other highly selective modes of soft-tissue preservation i.e. pyritization.

opencc-by-4.0Apr 2022View details →

A synaptomic analysis reveals dopamine hub synapses in the mouse striatum : Source Data

Source data for our study on dopamine hub synapses Dopamine transmission is involved in reward processing and motor control, and its impairment plays a central role in numerous neurological disorders. Despite its strong pathophysiological relevance, the molecular and structural organization of the dopaminergic synapse remains to be established. Here, we used targeted labelling and fluorescence activated sorting to purify striatal dopaminergic synaptosomes. We provide the proteome of dopaminergic synapses with 57 proteins specifically enriched. Beyond canonical markers of dopamine neurotransmission such as dopamine biosynthetic enzymes and cognate receptors, we validated 6 proteins not previously described as enriched (Cpne7, Apba1/Mint1, Cadps2, Cadm2/SynCAM 2, Stx4, Mgll). Moreover, our data reveal the adhesion of dopaminergic synapses to glutamatergic, GABAergic or cholinergic synapses in structures we named “dopamine hub synapses”. At glutamatergic synapses, pre- and postsynaptic markers are significantly increased upon association with dopamine synapses. Dopamine hub synapses may thus support local dopaminergic signalling, complementing volume transmission thought to be the major mechanism by which monoamines modulate network activity.

opencc-zeroApr 2022View details →

Maternal survival costs in an asocial mammal: Data and analysis

Abstract. Maternal characteristics, social dynamics, and environmental factors can all influence reproduction and survival as well as shape trade-offs that might arise between these components of fitness. Short-lived mammals like the golden-mantled ground squirrel (GMGS; Callospermophilus lateralis) tend to maximize effort towards current reproduction at the expense of survival but may be complicated by other aspects of the species' life history and environment.. Here, we use 25 years of data (1995-2020) collected from a population of GMGS at the Rocky Mountain Biological Research Laboratory in Gothic, Colorado, to test the effect of several maternal characteristics (e.g., age, experience, timing of litter emergence), social context (e.g., litter sex ratio, kin density), and environmental context (e.g., date of bare ground, length of vegetative growing season) on survival of reproductive female GMGS using Cox proportional hazard models. Our results indicated that social dynamics (i.e., density) and environmental conditions (i.e., standardized first day of permanent snow cover and length of growing season) explained significant variation in annual maternal survival, while maternal characteristics did not. A higher density of related breeding females and the total number of females (both related and unrelated to the focal mother) were associated with an increase in the mortality hazard. A later standardized date of the first day of permanent snow cover and a shorter growing season both reduced the maternal mortality hazard. Together, our results suggest that factors extrinsic to the squirrels affect maternal survival, and thus may also influence local population growth and dynamics in GMGS and other short-lived, territorial mammal species.

opencc-zeroMay 2022View details →

Data and scripts from: Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex

The folder contains the data and scripts used to produce the manuscript: "Long term analysis of social structure: evidence of age-based consistent associations in Alpine ibex" by Alice Brambilla, Achaz von Hardenberg, Claudia Canedoli, Francesca Brivio, Cédric Sueur and Christina R Stanley.

opencc-zeroMay 2022View details →

Data from: Dracula's ménagerie: A multispecies occupancy analysis of lynx, wildcat, and wolf in the Romanian Carpathians

The recovery of terrestrial carnivores in Europe is a conservation success story. Initiatives focused on restoring top predators, require information on how resident species may interact with the re-introduced species as their interactions have the potential to alter food webs, yet such data are scarce for Europe. In this study, we assessed patterns of occupancy and interactions between three carnivore species in the Romanian Carpathians. Romania houses one of the few intact carnivore guilds in Europe, making it an ideal system to assess intraguild interactions, and serve as a guide for reintroductions elsewhere. We used camera trap data from two seasons in Transylvanian forests to assess occupancy and co-occurrence of carnivores using multispecies occupancy models. Mean occupancy in the study area was highest for lynx ( Ywinter= 0.76 95% CI: 0.42-0.92; Yautumn= 0.71 CI: 0.38-0.84) and wolf (Ywinter= 0.60 CI: 0.34-0.78; Yautumn= 0.81 CI: 0.25-0.95) and lowest for wildcat (Ywinter= 0.40 CI: 0.19-0.63; Yautumn= 0.52 CI: 0.17-0.78) We found that marginal occupancy predictors for carnivores varied between seasons. We also found differences in predictors of co-occurrence between seasons for both lynx-wolf and wildcat-wolf co-occurrence. For both seasons, we found that conditional occupancy probabilities of all three species were higher when another species was present. Our results indicate that while there are seasonal differences in predictors of occupancy and co-occurrence of the three species, co-occurrence in our study area is high, and is dependent on the existence of continuous, relatively undisturbed forests. Terrestrial carnivore recovery efforts are ongoing worldwide. Insights into interspecific relations between carnivore species are critical when considering the depauperate communities they are introduced in. Our work showcases that apex carnivore coexistence is possible, but dependent on protection afforded to forest habitats and their prey base.

Event Data used in Seismic anisotropy along the Haida Gwaii margin from receiver function analysis

This CSV file contains metadata for earthquake events used in the study: Seismic anisotropy along the Haida Gwaii margin from receiver function analysis Event start time (UTC), latitude, longitude, depth, magnitude and the seismic station at which the event is recorded are included.

opencc-by-4.0Apr 2022View details →

Data from: Unbiased analysis of cellular plasticity in the dorsal root ganglion after peripheral nerve injury

Sectional images of rat dorsal root ganglia (DRG) 7 or 14 days after SNI or sham injury. Sections were immunostained for neurofilament (NF), glial fibrillary acidic protein (GFAP), and glutamine synthetase (GS) and imaged using large-field (tile) microscopy. Images were segmented with a deep learning method (deepflash2). Provided are:  - 2-13 images per DRG from L4 or L5, ipsilateral (IL) or contralateral (CL)  - corresponding segmentation masks for NF, GS, and GFAP  - deep learning models for oval-shaped NF-positive structures and ring-like GS/GFAP-positive structures  - annotated data that the deep learning models were trained on

opencc-zeroMay 2022View details →

Data from: Network analysis of sea turtle movements and connectivity: a tool for conservation prioritization

Aim: Understanding the spatial ecology of animal movements is a critical element in conserving long-lived, highly mobile marine species. Analysing networks developed from movements of six sea turtle species reveals marine connectivity and can help prioritize conservation efforts. Location: Global. Methods: We collated telemetry data from 1,235 individuals and reviewed the literature to determine our dataset's representativeness. We used the telemetry data to develop spatial networks at different scales to examine areas, connections, and their geographic arrangement. We used graph theory metrics to compare networks across regions and species and to identify the role of important areas and connections. Results: Relevant literature and citations for data used in this study had very little overlap. Network analysis showed that sampling effort influenced network structure and the arrangement of areas and connections for most networks was complex. However, important areas and connections identified by graph theory metrics can be different than areas of high data density. For the global network, marine regions in the Mediterranean had high closeness while links with high betweenness among marine regions in the South Atlantic were critical for maintaining connectivity. Comparisons among species-specific networks showed that functional connectivity was related to movement ecology, resulting in networks composed of different areas and links. Main conclusions: Network analysis identified the structure and functional connectivity of the sea turtles in our sample at multiple scales. These network characteristics could help guide the coordination of management strategies for wide-ranging animals throughout their geographic extent. Most networks had complex structures that can contribute to greater robustness, but may be more difficult to manage changes when compared to simpler forms. Area-based conservation measures would benefit sea turtle populations when directed towards areas with high closeness dominating network function. Promoting seascape connectivity of links with high betweenness would decrease network vulnerability.

Research data: "Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe"

This data set belongs to the paper Effects of Network Structures on the Production Planning in Closed-loop Supply Chains – A Case Study based Analysis for Lithium-ion Batteries in Europe in the International Journal of Production Economics (DOI). The BatPac model, as well as, the model for the economic assessment of the recycling route are not included. The needed data can be found in the file (name). Further, the BatPaC model can be gather from the website of Argonne National Laboratory and the assessment tool for the recycling routes via this DOI: 10.5281/zenodo.6500946.   This work is part of the research project Recycling 4.0 (EFRE | ZW 6-85018080), which is funded by the European Regional Development Fund and managed by the development bank for the German federal state of Lower Saxony (NBank).

Input files and data for sensitivity analysis of ParFlow-CLM

This zip file includes all the input files and forcing data for the sensitivity analysis of ParFlow-CLM. The file of "Stettbach_SA" includes all the information for the sensitivity analysis of Stettbach catchment. The file of "high_slope_SA" includes all the information for the sensitivity analysis of high slope effect in section 2.5.1 Topography effects. The file of "low_slope_SA" includes all the information for the sensitivity analysis of low slope effect in section 2.5.1 Topography effects. The file of "Barcelona_SA" includes all the information for the sensitivity analysis of Barcelona in section 2.5.2 Climate effects. The file of "LK_SA" includes all the information for the sensitivity analysis of Lemmenjoke national park in Finland in section 2.5.2 Climate effects. The file of "Stettbach_2020_2021" includes all the information for the runoff comparison between simulation and observation in 2020 and 2021 in section 3.1 (Model performance in Stettbach catchment). The file of "results_process_code" includes all the scripts used for the analysis of this study.

Data and Analysis Script for Cluster2022 Submission pap254: "Painless Transposition of Reproducible Distributed Environments with NixOS Compose"

Data and Analysis Script for Cluster2022 Submission pap254: "Painless Transposition of Reproducible Distributed Environments with NixOS Compose" The experiments repository is available at: <a href="https://gitlab.inria.fr/nixos-compose/articles/cluster2022">https://gitlab.inria.fr/nixos-compose/articles/cluster2022</a>

Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank

The results of BIGKnock analyses of manuscript ''Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank''

Data, scripts and supplementary information for analysis of the functioning of a three-species microcosm under cadmium pressure

Data files of different experiments conducted with a three-species microcosm + Rscript for infering paremeters from a mechanistic EDO based model describing the functioning of the microcosm and the effect of cadmium + JAGS script of the model + supplementary information

Mass spectrometric investigation of pharmaceuticals in environmental matrices - homogenate analysis: Thesis Data 2

RT Thesis - Mass spectrometric investigation of pharmaceuticals in environmental matrices - homogenate analysis_data set 4 contains Mass Lynx data sets part 2   RT Thesis - Mass spectrometric investigation of pharmaceuticals in environmental matrices - homogenate analysis_data set 5 contains Mass Lynx data sets part 3

opencc-zeroJun 2022View details →

Molecular data and analysis specifications for a study on Atriophallophorus parasites from New Zealand

This dataset accompanies the manuscript "Phylogeography and Cryptic Species Structure of a Locally Adapted Parasite in New Zealand". In our study we have shown that multiple species of the trematode parasite from the Atriophallophorus genus co-exist within the same lakes. When focusing on the most common of these species, Atriophallophorus winterbourni, we found that the Southern Alps and Pleistocene glaciation are a likely explanation for its phylogeographic patterns. This dataset consists of three parts: (I) An Excel file containing SNP data, all sample information and the output of phylogeographic analysis with MASCOT1, (II) all sequence alignments, including NADH5, 28S, ITS2 and COI, as they are used for the manuscript and (III) input files for the various analyses as they were prepared for the analysis. 1MASCOT: marginal approximation of the structured coalescent as implemented in BEAST2

opencc-by-4.0Jun 2022View details →

Applying an Inconsistency Repair Mechanism for clone-and-own Code Smell Analysis: the Apo-games Case Study (Evaluation Data)

This is a repository containing the artifacts and the results of the evaluation of the solution paper "Applying an Inconsistency Repair Mechanism for clone-and-own Code Smell Analysis: the Apo-games Case Study"

opencc-by-4.0Jun 2022View details →

Data set from "Absolute Treatment Effects for the Primary Outcome and All-cause Mortality in the Cardiovascular Outcome Trials of New Antidiabetic Drugs – A Meta-Analysis of Digitalized Individual Patient Data"

This data set contains the complete digitalized individual patient data that are used in the manuscript "Absolute Treatment Effects for the Primary Outcome and All-cause Mortality in the Cardiovascular Outcome Trials of New Antidiabetic Drugs – A Meta-Analysis of Digitalized Individual Patient Data", which is accepted from "Acta Diabetologica". The data file is in CSV format and contains the five variables "OutcomeType" (with values "AllcauseMortality" or "PrimaryOutcome"), "Study" (denoting the respective cardiovascular outcome trial), "Treatment" (denoting the respective study treatment or placebo), "Event" (denoting if the respective has been observed (Event=1) or not (Event=0)), and "SurvivalTimeMonths" (denoting the respective time to the event or censoring in months).

opencc-zeroJun 2022View details →

DNA metabarcoding sequence data for diet analysis of caribou

Woodland caribou (Rangifer tarandus caribou) are threatened in Canada due to the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew based on relative read abundance (Taxus spp.; 83.68%) with dogwood (Cornus spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.

opencc-zeroJun 2022View details →

Data from: Girth increment changes in response to soil water availability in lowland dipterocarp forest in Borneo: an individualistic time-series analysis

Time-series data offer a way of investigating the causes driving ecological processes as phenomena. To test for possible differences in water relations between species of different forest structural guilds at Danum (Sabah, NE Borneo), daily stem girth increments (gthi), of 18 trees across six species were regressed individually on soil moisture potential (SMP) and temperature (TEMP), accounting for temporal autocorrelation (in GLS-arima models), and compared between a wet and a dry period. The best-fitting significant variables were SMP the day before and TEMP the same day. The first resulted in a mix of positive and negative coefficients, the second largely positive ones. An adjustment for dry-period showers was applied. Interactions were stronger in dry than wet period. Negative relationships for overstorey trees can be interpreted in a reversed causal sense: fast transporting stems depleted soil water and lowered SMP. Positive relationships for understorey trees meant they took up most water at high SMP. The unexpected negative relationships for these small trees may have been due to their roots accessing deeper water supplies (if SMP was inversely related to that of the surface layer), and this was influenced by competition with larger neighbour trees. A tree-soil flux dynamics manifold may have been operating. Patterns of mean diurnal girth variation were more consistent among species, and time-series coefficients were negatively related to their maxima. Expected differences in response to SMP in the wet and dry periods did not clearly support a previous hypothesis differentiating drought and non-drought tolerant understorey guilds. Trees within species showed highly individual responses when tree size was standardized. Data on individual root systems and SMP at several depths are needed to get closer to the mechanisms that underlie the tree-soil water phenomena in these tropical forests. Neighborhood stochasticity importantly creates varying local environments experienced by individual trees.