Find research datasets worth reusing

opencc-zeroJun 2023View details →

Age specific impacts of vegetation functional traits on gastro-intestinal nematode parasite burdens in a large herbivore

<ol> <li>Gastro-intestinal nematode (GIN) parasites play an important role in the ecological dynamics of many animal populations. Recent studies suggest fine-scale spatial variation in GIN infection dynamics is important in wildlife systems, but the environmental drivers underlying this variation remain poorly understood.</li> <li>We used data from over two decades of GIN parasite egg counts, host space use, and spatial vegetation data from a long-term study of Soay sheep on St Kilda to test how spatial autocorrelation and vegetation in an individual's home range predict parasite burden across three age groups. We developed a novel approach to quantify the plant functional traits present in a home range to describe the quality of vegetation present. </li> <li>Effects of space and vegetation varied between age classes. In immature lambs, strongyle parasite faecal egg counts (FEC) were spatially structured, being highest in the north and south of our study area. Independent of host body weight and spatial autocorrelation, plant functional traits predicted parasite egg counts. Higher egg counts were associated with more digestible and preferred plant functional traits, suggesting the association could be driven by host density and habitat preference.</li> <li>In contrast, we found no evidence that parasite FEC were related to plant functional traits in the host home range in yearlings or adult sheep. Adult FEC were spatially structured, with highest burdens in the north-east of our study area, while yearling FEC showed no evidence of spatial structuring.</li> <li>Our findings support the importance of fine-scale environmental variation for wildlife disease ecology and provide new evidence that such effects may vary across demographic groups within a population. Parasite burdens in immature individuals appear more readily influenced by fine-scale spatial variation in the environment, highlighting the importance of such heterogeneity for our understanding of wildlife epidemiology and health.</li> </ol>

opencc-zeroJun 2023View details →

Data for: Cavity-breeding birds create specific microhabitats for diverse arthropod communities in boreal forests

The nests of secondary cavity-nesters located in tree cavities may form specific microhabitats of conservation importance due to their limited accessibility and availability. Species-specific nesting materials in nests of different secondary cavity-nesters may furthermore provide very different microhabitats for arthropods. The potential differences in arthropod communities inhabiting nests of different bird species in excavated cavities or nest boxes have, however, rarely been studied despite their relevance for conservation. Here we investigated the diversity and composition of arthropod communities in these different cavity types and bird species' nests in managed boreal forests. We identified morphologically and by DNA-metabarcoding arthropods in nest materials that were collected in and compared between i) woodpecker-size cavities from seven different combinations of cavity type (nest box or excavated cavity), tree species (aspen or pine) and accumulation history of nest materials (single-season cleaned or uncleaned nest boxes that accumulated nests of passerines or an owl species); and ii) nests of two different passerine species in small nest boxes. We identified 64 arthropod taxa in ten orders, from which Diptera, Coleoptera, Siphonaptera, and Lepidoptera were the most abundant. Shannon diversity index was similar among the cavity-nest-type combinations, but taxa richness was the highest in the owl nests. The arthropod communities (especially Histeridae beetles) deviated most from the other types of nests in owl and aspen cavity nests with more advanced decomposition of nest material (soil or wet environment-related taxa). The differences in arthropod communities between the different nest types point out the importance of the ecological chain "tree cavities – bird nests – arthropod communities".

opencc-by-4.0Dec 2022View details →

Data for "Analysis of Wilms' tumor protein 1 specific TCR repertoire in AML patients uncovers higher diversity in patients in remission than in relapsed"

This folder holds the data for the paper "Analysis of Wilms' tumor protein 1 specific TCR repertoire in AML patients uncovers higher diversity in patients in remission than in relapsed" (in submission) More information regarding this paper and the data is given in the GitHub repository (https://github.com/sgielis/WT1_TCR) The raw folder contains all MiXCR files for the two studied WT1 epitopes and two VZV epitopes. The VZV epitopes were not taken into account in this paper, but were used to build VZV-specific TCRex models for another paper [in submission]. Since all TCRs for the 4 epitopes were sequences together, this data was used for quality control purposes as explained in the paper. Following 4 folders are present: <ul> <li>run1: TCR data from the first run for WT1-126, WT1-37 and IE62</li> <li>run1_orf18: TCR data from the first run for ORF18</li> <li>run2: WT1-37 data filtered on high and low threshold gating.</li> <li>run 3: extra TCR data for WT1-126, WT1-37 aligned with MiXCR</li> </ul>

Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex

Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification, and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodents, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.

opencc-by-4.0Jul 2023View details →

Table 8 for the Study: "Observation of correlation between earthquake triggering of M>4.3 and specific Sun-Moon-Planets positions in the Solar System, from 1600 in Italy."

Graphs of the data distributions, with the R2 regression values of σFR and the corresponding functions. In case of display problems or missing data, the file <a href="https://zenodo.org/api/files/305630bd-70bd-4347-99eb-bfd6fb3af726/Table%208_SFR_distributions_curves.xlsx">Table 8_SFR_distributions_curves.xlsx</a> on Drive available for consultation is this one: <a href="https://docs.google.com/spreadsheets/d/17UGHZlvZ2N-g6TOzgqpIe248_IitBmka8DbGWsv-lKQ/edit?usp=sharing">https://docs.google.com/spreadsheets/d/17UGHZlvZ2N-g6TOzgqpIe248_IitBmka8DbGWsv-lKQ/edit?usp=sharing</a>  URL of the plots of the data distributions, with the R2 regression values of σFR at the time of the triggering of the 200 earthquakes analyzed in the paper "Observation of correlation between earthquake triggering of M>4.3 and specific Sun-Moon-Planets positions in the Solar System, from 1600 in Italy", paragraph 3.02.

Data for: Weak sex-specific evolution of locomotor activity of Sepsis punctum (Diptera: Sepsidae) thermal experimental evolution lines

Elevated temperatures are expected to rise beyond what the physiology of many organisms can tolerate. Behavioural responses facilitating microhabitat shifts may mitigate some of this increased thermal selection on physiology, but behaviours are themselves mediated by physiology, and any behavioural response may trade-off against other fitness-related activities. We investigated whether experimental evolution in different thermal regimes (Cold: 15°C; Hot: 31°C; Intergenerational fluctuation 15/31°C; Control: 23°C) resulted in genetic differentiation of standard locomotor activity in the dung fly Sepsis punctum. We assessed individual locomotor performance, an integral part of most behavioral repertoires, across eight warm temperatures from 24°C to 45°C using an automated device. We found no evidence for generalist-specialist trade-offs (i.e. changes in the breadth of the performance curve) for this trait. Instead, at the warmest assay temperatures, hot-selected flies showed somewhat higher maximal performance than all others, especially cold-selected flies, overall more so in males than females. Yet, the flies' temperature optimum was not higher than that of the cold-selected flies, as expected under the 'hotter-is-better' hypothesis. Maximal locomotor performance merely weakly increased with body size. These results suggest that thermal performance curves are unlikely to evolve as an entity according to theory and that locomotor activity is a trait of limited use in revealing thermal adaptation.

opencc-by-3.0-usJul 2023View details →

Temporally specific patterns of neural activity in interconnected corticolimbic structures during reward anticipation

Temporally specific patterns of neural activity in interconnected corticolimbic structures during reward anticipation Megan E. Young, Camille Spencer-Salmon, Clayton Mosher, Sarita Tamang, Kanaka Rajan, and Peter H. Rudebeck This dataset contains peripheral physiology (heart rate) and single neuron activity data from the paper entitled “Temporally specific patterns of neural activity in interconnected corticolimbic structures during reward anticipation” by Young, Spencer-Salmon and colleagues. The study investigated how neurons in macaque subcallosal anterior cingulate cortex, basolateral amygdala, and rostromedial striatum encoded anticipated reward during Pavlovian and instrumental tasks. Heart rate data were pre-processed using methods described in the paper and were downsampled to 50 Hz for analysis. Neural activity data were pre-processed using steps as described in the paper. The dataset is saved as .MAT files. Files included: ‘Pavlovian_task_neurons.mat’ – single neuron data from the Pavlovian task. Each of the 656 rows represents a single neuron and its associated information. ‘Instrumental_task_neurons.mat’ – single neuron data from the instrumental task. Each of the 425 rows represents a single neuron and its associated information. “heart_rate.mat” – heart rate data from monkeys D and H. File structure and information: Pavlovian_task_neurons.mat Structure “Pavlovian_task_neurons” - “Pavlovian_task_neurons.unit_name” – neuron specific identifier - “Pavlovian_task_neurons.monkeynumber” – subject specific # - “Pavlovian_task_neurons.monkeyname” – subject specific name - “Pavlovian_task_neurons.date” – date on which data were recorded - “Pavlovian_task_neurons.session” – session identifier from date (a-d) - “Pavlovian_task_neurons.channel” – recording channel data recorded from - “Pavlovian_task_neurons.wavemark” – waveform number (a-e) - “Pavlovian_task_neurons.brainarea” – brain area where neuron recorded (SC = subcallosal ACC, AMY = basolateral amygdala, VS = rostromedial striatum). - “Pavlovian_task_neurons.areanum” – # brain area (subcallosal ACC = 1, BLA = 2, rostromedial striatum = 3) - “Pavlovian_task_neurons.condition” – condition # from Monkey Logic for each of the trials (1 by n trials) - “Pavlovian_task_neurons.stimspikes” – smoothed spike rate from -600 to 2500ms after stimulus onset (trials by time matrix) - “Pavlovian_task_neurons.rewardspikes” – smoothed spike rate from -600 to 2500ms after reward onset (trials by time matrix) - “Pavlovian_task_neurons.stimID” – stimulus shown on that trial (1 = neutral, 3 = CS+ juice, 4 = CS+ water, 5 = CS-) (1 by n trials). Instrumental_task_neurons.mat Structure “Instrumental_task_neurons” - “instrumental_task_neurons.unit_name” – neuron specific identifier - “instrumental_task_neurons.monkeynumber” – subject specific # - “instrumental_task_neurons.monkeyname” – subject specific name - “instrumental_task_neurons.date” – date on which data were recorded - “instrumental_task_neurons.session” – session identifier from date (a-d) - “instrumental_task_neurons.channel” – recording channel data recorded from - “instrumental_task_neurons.wavemark” – waveform number (a-e) - “instrumental_task_neurons.brainarea” – brain area where neuron recorded (SC = subcallosal ACC, AMY = basolateral amygdala, VS = rostromedial striatum). - “instrumental_task_neurons.areanum” – # brain area (subcallosal ACC = 1, BLA = 2, rostromedial striatum = 3) - “instrumental_task_neurons.condition” – condition 7-18 from Monkey Logic for each of the trials (1 by n trials). CNDs 7,8,13,14= CS+ juice vs CS+ water; CNDs 9,10,15,16= CS+ juice vs CS-; CNDs 11,12,17,18= CS+ water vs CS-. - “instrumental_task_neurons.choice” – outcome associated with chosen option (0=nothing, 1=juice, 2=water) (1 by n trials) - “instrumental_task_neurons.unchosen” - outcome associated with unchosen option (0=nothing, 1=juice, 2=water) (1 by n trials) - “instrumental_task_neurons.chosenside” – side of the screen chosen (left [0] or right [1]) (1 by n trials) - “instrumental_task_neurons.stimspikes” – smoothed spike rate from -600 to 2500ms after stimulus onset (trials by time matrix) - “instrumental_task_neurons.rewardspikes” – smoothed spike rate from -600 to 2500ms after reward onset (trials by time matrix) heart_rate.mat Structures     – “monkey_d_hr” – monkey D heart rate data         – “monkey_h_hr” – monkey H heart rate data Structure of monkey_d/h_hr - “monkey_d/h_hr.trial_type” – trial type presented (1 = neutral, 2 = unsignaled, 3 = CS+ juice, 4 = CS+ water, 5 = CS-) (1 by n trials). - “monkey_d/h_hr.trials” – number of trials in each session by trial type - “monkey_d/h_hr.session – percent change in heart rate for each trial from -200 ms to 3500ms after stimulus onset. Column 1 = session; Column 2 = trial type; Column 3 = trial number; Columns 4 – 3703 = percent change in heart rate.

opencc-by-4.0Dec 2022View details →

Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance

Processed datasets for publication at BMC Genomics. We exposed human primary monocytes from healthy donors (n=6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2hr LPS; LPS2) and two models of endotoxin tolerance: repeated stimulations (6+6hr; LPS6:6) and prolonged exposure to endotoxin (24hr LPS; LPS24). Another subset of monocytes was left untreated (naïve; UT). We performed total RNA-seq and ATAC-seq for monocytes across these treatment conditions. The following processed datasets include the raw and normalised count data for each gene or ATAC peak, and the bedGraph and bigWig format for genome-wide signal data. [ bigWig files for RNA-seq (monocytes_*_mean.bw); bigWig files for ATAC-seq (Monocyte_ATAC_*_mean_normalised.by.1/size.factor.bw); bedgraph files for eRNA visualization (*RPKM_FR.bedgraph.gz); raw and normalised count files for ATAC-seq and RNA-seq data (Monocyte.featureCounts_RNAseq.txt.gz; Monocyte_filtered_log2.normalized_RNAseq_counts.txt.gz; Meta.file.txt.gz; Monocyte_raw.counts_ATACseq.txt.gz.).] Data curator: Ping Zhang

Data for: The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling

Mutations in the tyrosine phosphatase SHP2 are associated with various human diseases. Most of these mutations increase the basal catalytic activity of SHP2 by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, several other disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, molecular dynamics simulations, and cellular assays. We show that, while several of these mutants alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also alters ligand-binding specificity. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

opencc-by-4.0Mar 2023View details →

Table 4 for the Study: "Observation of correlation between earthquake triggering of M>4.3 and specific Sun-Moon-Planets positions in the Solar System, from 1600 in Italy."

Video explaining the determination of the Resulting Gravitational Force sigma for the 2009 L'Aquila earthquake. For subtitles in English: <a href="https://youtu.be/-OVk2r8U8QA?t=563">https://youtu.be/-OVk2r8U8QA?t=563</a> --> URL of the video explaining the determination of the Resulting Gravitational Force sigma for the 2009 L'Aquila earthquake, for the article "Correlation observation between the triggering of M>4.3 earthquakes and specific Sun-Moon-Planet positions in the Solar System since 1600 in Italy" , SUBTITLES IN EN, paragraph 2.16.

Data from: The costs of living on the coast: reduction in body size and size-specific reproductive output in coastal populations of a widespread amphibian

<ol> <li>Body size is a critical component of organismal biology. Body size is known to be influenced by a plethora of environmental conditions, among which exposure to large-scale variations of salinity has been comparatively overlooked. Yet, exposure to salinity is known to affect energetic allocation toward growth and reproduction.</li> <li>In this study, we investigated the morphological differences between inland and coastal individuals of spined toads (Bufo spinosus) in Western France. </li> <li>We measured adult morphology both outside and during the reproductive season on 190 individuals, and assessed reproduction in pairs originating from inland (N=20) and coastal (N=30) environments.</li> <li>Overall, we found that adult coastal toads were smaller and lighter than inland individuals. Reproductive correlates of these differences included lower fecundity and smaller egg size (but higher egg density) in coastal females. Interestingly, these differences were not allometric correlates of body size, as coastal females invested proportionally less in all components of reproduction (fecundity, egg size and egg protection).</li> <li>These results suggest altered resource allocation to growth and reproduction in coastal amphibians, which may be related to the marked spatial gradient of salinity (measured in reproductive ponds) and the associated costs of osmoregulation (higher osmolality in coastal individuals), for which local adaptation and higher tolerance to salinity remains to be tested.</li> </ol>

Mitigating bycatch in trammel net fisheries using species-specific gear modifications

Small-scale fisheries (SSF) use static gears like hanging nets, which are thought to interact with marine ecosystems more benignly than towed gears. Despite this, trammel nets, one of the most regularly used fishing gears in the Mediterranean SSF, generate large amounts of discards, which can account for 25% or more of the captured biomass. Discarded organisms may include endangered or threatened species such as elasmobranchs, as well as non-commercial invertebrates that damage fishing gear or cause disentanglement delays. We tested various trammel-net gear modifications, including (a) the use of a guarding net attached to the footrope, (b) increasing the size of the rigging twine between the footrope and the netting panel, and (c) decreasing the mesh size of the outer panels. The last two modifications were successful in lowering captures of the marbled electric ray Torpedo marmorata, which is commonly discarded in the study area. Both sorts of modifications are relatively simple and inexpensive to implement. The current study shows that prior evaluation of the discards profile of distinct métiers is essential to accomplish species-specific gear modifications and underlines the importance of collaboration among scientists, fishers and gear manufacturers.

Data for: Cooperative assembly confers regulatory specificity and long-term genetic circuit stability

A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly-interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc finger-based TFs. We show that circuits 'wired' using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-termcontinuous culture. Our naturally-inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.

openmit-licenseJul 2023View details →

PANDA cell-type-specific networks for S858R and WT mouse cerebral cortex

The below files are from the data/results directory of this associated project and include the following: <ul> <li>PANDA networks : cell-type-specific TF-gene regulatory networks constructed using multi-omic inputs (snRNA-seq, TF-motif, and PPI) for all cell types in S858R and WT mouse cerebral cortex tissues (n = 16). All the files included for PANDA networks indicate the condition (heterozygous or control), tissue (cerebral cortex) followed by _PANDA.Rdata. (example: astrocytes_heterozygouscortexexpression_PANDA.Rdata)</li> </ul>

openmit-licenseJul 2023View details →

PANDA cell-type-specific networks for S858R and WT mouse kidney

The below files are from the data/results directory of this associated project and include the following: <ul> <li>PANDA networks : cell-type-specific TF-gene regulatory networks constructed using multi-omic inputs (snRNA-seq, TF-motif, and PPI) for all cell types in S858R and WT kidney tissues (n = 34). All the files included for PANDA networks indicate the condition (heterozygous or control), tissue (kidney) followed by _PANDA.Rdata. (example: pericytes_heterozygouskidneyexpression_PANDA.Rdata)</li> </ul>

A reference dataset of global gridded average-state specific yield

The uploaded data is related with our manuscript "A reference dataset of global gridded average-state specific yield".

Data and results for "Germline-encoded specificities and the predictability of the B cell response"

Data and results for Vieira et al., <a href="https://www.biorxiv.org/content/10.1101/2022.09.16.508315v4">Germline-encoded specificities and the predictability of the B cell response</a> Code for the analyses is available at <a href="https://github.com/cobeylab/v_gene_selection/">https://github.com/cobeylab/v_gene_selection/</a>

Stage-specific genotype-by-environment interactions determine yield components in wheat

The tables (climate_data.csv, and Yield_data.csv) include the recorded climatic and measured yield components data from multi-environment field trails (2014-2017). The table (soil_water_data.csv) presents the simulated water content for the experiments. The tables (Coefficients_data.csv, and multiple_regression_coefficients_data.csv) present the log p-values of comparing models M1, M2, and M3 and their coefficients. All the necessary information to read these datasets is provided in the table (read_me.csv).

Data from "Tissue and toxin-specific divergent evolution in plant defense"

Files and code necessary to replicate the results from the manuscript are described as follows: Syrfampop.sas --> SAS code to conduct the analyses. HPLC_asyr.csv --> contains the cardenolide data of root, leaf and seed tissue from each individual plant belonging to multiple families of each of the two populations (main analysis in SAS code). chemmantelcorr.csv --> contains the correlation matrices between cardenolides within a given tissue (permutation test in SAS code) SS.csv --> contains the sums of squares matrices of cardenolide concentrations at the population and family levels for each tissue and whole plant after the MANOVA in the SAS code (used for the R code in Martin et al. (2008)). ehdbp.vcf --> Description of SNP data used for this study. ehdbp.arp --> SNP data in Arlequin format ready for FST analysis.