Find research datasets worth reusing

Data from: Awake responses suggest inefficient dense coding in the mouse retina

The structure and function of the vertebrate retina have been extensively studied across species with an isolated, ex vivo preparation. Retinal function in vivo, however, remains elusive, especially in awake animals. Here we performed single-unit extracellular recordings in the optic tract of head-fixed mice to compare the output of awake, anesthetized, and ex vivo retinas. While the visual response properties were overall similar across conditions, we found that awake retinal output had in general 1) faster kinetics with less variability in the response latencies; 2) a larger dynamic range; and 3) higher firing activity, by ~20 Hz on average, for both baseline and visually evoked responses. Our modeling analyses further showed that such awake response patterns convey comparable total information but less efficiently, and allow for a linear population decoder to perform significantly better than the anesthetized or ex vivo responses. These results highlight distinct retinal behavior in awake states, in particular suggesting that the retina employs dense coding in vivo, rather than sparse efficient coding as has been often assumed from ex vivo studies.

opencc-by-4.0Sep 2023View details →

Data for "Ecosystem heating experiment reveals sex-specific growth responses in fish"

Data for the paper "Ecosystem heating experiment reveals sex-specific growth responses in fish" in the Canadian Journal of Fisheries and Aquatic Sciences. One file contains the back-calculated fish length-at-age used for all analyses in the study. The other file contains the temperature data used to create Figure S2.

Response of the ozone-related health burden in Europe to changes in local anthropogenic emissions of ozone precursors (version 2.0)

This data set includes the model output of the peer-reviewed paper: Gu, Y., Henze, D. K., Nawaz, M. O., and Wagner, U. J., 2023, Response of the ozone-related health burden in Europe to changes in local anthropogenic emissions of ozone precursors, Environ. Res. Lett., doi:10.1088/1748-9326/ad0167. The data set includes: -The receptor functions, expressed as the total ozone-related premature deaths from respiratory diseases in 2005 and 2015. -The marginal benefit, expressed as the ozone-related premature deaths avoided by a 20% reduction in anthropogenic emissions of NOx, NMVOCs, and CO in 2005 and 2015, respectively -The marginal contribution (per unit), expressed as the ozone-related premature deaths caused by per unit (kg/m2/yr) anthropogenic emissions of NOx in 2005 and 2015

Prediction of the time-domain chirp response at El Castillo

WAV file of the simulated time-domain chirp response of the El Castillo pyramid to an impulsive point excitation, using a ray model and a numerically computed trapped mode dispersion curve.

Data supporting 'The Response of Midlatitude Surface Temperature Persistence to Arctic Sea-Ice Loss' by Neil T Lewis, William J M Seviour, Hannah E Roberts-Straw, and James A Screen.

Data supporting Lewis et al., 2023. The Response of Midlatitude Surface Temperature Persistence to Arctic Sea-Ice Loss. Submitted to Geophysical Research Letters.All model output is contained within the folder data/. All data is in NetCDF format.The folder data/PAMIP/ contains output from coupled AOGCMs that contributed piArcSIC and futArcSIC timeslice runs to PAMIP. The AOGCMS present are: HadGEM3-GC31-MM, IPSL-CM6A-LR, CESM2-WACCM6, and CESM-WACCM-SC. For each model + run, two data files are included. One contains the autocorrelation of surface temperature, at 5, 10, and 15 day lags. The second contains the frequency and duration of persistent extremes (as defined in Lewis et al., 2023).Additional output is included in data/PAMIP/ from extended pdSIC-ext and futArcSIC-ext experiments run using CNRM-CM6-1. For each run, a file containing the autocorrelation of surface temperature (as above) is included.The folder data/CMIP/ contains output from CMIP6 historical/SSP585 runs using three of the models listed above: HadGEM3-GC31-MM, IPSL-CM6A-LR, and CESM2-WACCM6. For each model, 'pre-industrial' and 'future' output is available. Output in these files was computed from 30-year time-periods, subsampled from the historical/SSP585 runs, selected so that the 30-year average sea-ice area matched that in the corresponding PAMIP runs above. For each model and time period, two data files are included. One contains the autocorrelation of surface temperature, at 5, 10, and 15 day lags. The second contains the frequency and duration of persistent extremes (as defined in Lewis et al., 2023).Output is also included in data/CMIP/ from CNRM-CM6-1 'present day' and 'future' time periods, selected to match the sea-ice area in the CNRM -ext PAMIP runs. For this model, output files contain the autocorrelation of surface temperaure.

Data from: Ocean deoxygenation caused non-linear responses in the structure and functioning of benthic ecosystems

The O2 content of the global ocean has been declining progressively over the past decades, mainly because of human activities and global warming. Nevertheless, how long-term deoxygenation affects macrobenthic communities, sediment biogeochemistry and their mutual feedback remains poorly understood. Here, we evaluate the response of the benthic assemblages and biogeochemical functioning to decreasing O2 concentrations along the persistent bottom-water dissolved O2 gradient of the Estuary and Gulf of St. Lawrence (QC, Canada). We report several of non-linear biodiversity and functional responses to decreasing O2 concentrations, and identify an O2 threshold that occurs at approximately at 63 µM. Below this threshold, macrobenthic community assemblages change, and bioturbation rates drastically decrease to near zero. Consequently, the sequence of electron acceptors used to metabolize the sedimentary organic matter is squeezed towards the sediment surface while reduced compounds accumulate closer (as much as 0.5 to 2.5 cm depending on the compound) to the sediment-water interface. Our results illustrate the capacity of bioturbating species to compensate for the biogeochemical consequences of hypoxia and can help to predict future changes in benthic ecosystems.

Plant diversity and soil legacy independently affect the plant metabolome and induced responses following herbivory

Plant and soil biodiversity can have significant effects on herbivore resistance mediated by plant metabolites. Here, we disentangled the independent effects of plant diversity and soil legacy on constitutive and herbivore-induced plant metabolomes of three plant species in two complementary microcosm experiments. First, we grew plants in sterile soil with three different plant diversity levels. Second, single plant species were grown on soil with different plant diversity-induced soil legacies. We infested a subset of all plants with Spodoptera exigua larvae, a generalist leaf-chewing herbivore, and assessed foliar and root metabolomes. Neither plant diversity nor soil legacy had significant effects on overall foliar, root, or herbivore-induced metabolome composition. Herbivore-induced metabolomes, however, differed from those of control plants. We detected 139 significantly regulated metabolites by comparing plants grown in monocultures with conspecifics growing in plant or soil legacy mixtures. Moreover, plant-plant and plant-soil interactions regulated 141 metabolites in herbivore-induced plants. Taken together, plant diversity and soil legacy independently alter the concentration and induction of plant metabolites, thus affecting the plant's defensive capability. This is a first step towards disentangling plant and soil biodiversity effects on herbivore resistance, thereby improving our understanding of the mechanisms that govern ecosystem functioning.

Safety, effectiveness, and skin immune response in a controlled human infection model of sand fly transmitted cutaneous leishmaniasis.

Safety, effectiveness, and skin immune response in a controlled human infection model of sand fly transmitted cutaneous leishmaniasis.Vivak Parkash1, Helen Ashwin1, Shoumit Dey1, Jovana Sadlova2, Barbora Vojtkova2, Katrien Van Bocxlaer1,3, Rebecca Wiggins1, David Thompson4 Nidhi Sharma Dey1, Charles L. Jaffe5, Eli Schwartz6, Petr Volf2, Charles J. N. Lacey1, Alison M. Layton1,3 * and Paul M. Kaye1,3 *. 1 York Biomedical Research Institute, Hull York Medical School, University of York, York, UK2 Department of Parasitology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic3 Skin Research Centre, Hull York Medical School, York, UK4 York and Scarborough Teaching Hospitals NHS Foundation Trust, York, UK  5 Department of Microbiology and Molecular Genetics, Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University – Hadassah Medical School, Jerusalem, Israel6 The Center for Geographic Medicine and Tropical Diseases, Chaim Sheba Medical Center, and The School of Medicine, Tel Aviv University, Israel. *Corresponding authors: paul.kaye@york.ac.uk and alison.layton@hyms.ac.uk

Birds are better at regulating heat loss through their legs than their bills: Implications for body shape evolution in response to climate

Endotherms use their appendages – such as legs, tails, ears and bills – for thermoregulation by controlling blood flow to near-surface blood vessels, conserving heat when it is cold, and dissipating heat in hot conditions. Larger appendages allow greater heat dissipation, and appendage sizes vary latitudinally according to Allen's Rule. However, little is known about the relative importance of different appendages for thermoregulation. We investigate physiological control of heat loss via bird bills and legs using infra-red thermography of wild birds. Our results demonstrate that birds are less able to regulate heat loss via their bills than their legs. In cold conditions, birds lower their leg surface temperature to below that of their plumage surface, retaining heat at their core. In warm conditions, birds increase their leg surface temperature to above that of their plumage surface, expelling heat. In contrast, bill surface temperature remains ~2˚C warmer than the plumage surface, indicating consistent heat loss under almost all conditions. Poorer physiological control of heat loss via bird bills likely entails stronger selection for shorter bills in cold climates. This could explain why bird bills show stronger latitudinal size clines than bird legs, with implications for predicting shape-shifting responses to climate change.

opencc-by-4.0Jun 2023View details →

Pregnancy-Responsive Pools of Adult Neural Stem Cells For Transient Neurogenesis in Mothers

These are the RDS objects of the resulting files from our analyses, converted to Spatial Experiment object. These files can be loaded into spatialLIBD directly to allow interactive exploration of the data locally. In the new version of the dataset, we included the high resolution .tiff images of all of the samples. Furthermore, we included the low resolution (lowres) output from the spaceranger for the researchers who want to use these files. Higher resolution images (hires) were previously shared in the GEO submission alongside the raw sequencing data.

opencc-by-4.0Jun 2024View details →

Reproductive aging weakens offspring survival and constrains the telomerase response to herpesvirus in Pacific oysters

These datasets and codes report the impacts of aging on oyster parents and their offspring. We compared proteomic profiles (“parent_proteomic_rawdata.tsv”) of reproductive oysters (12 males and 12 females) of three age classes (young, middle age and old) (“parent_proteomic_design.txt”). We crossbred these adult oysters as described in the paper (DOI: 10.1126/sciadv.adq2311) to examine the impacts of parental aging on their offspring phenotypes. We explored the effects of reproductive aging on offspring growth (“offspring_growth_dataset.csv”) and survival rate at larval life stage from 0 to 40 days old(“larval_survival.csv”). We also measured spat resistance to OsHV1 in laboratory (“spat_mortality_OsHV1.csv”) and in the field (“spat_mortality_OsHV1_field.csv”), and offspring survival once they attained adulthood (“adult_survival.csv”). In parallel, we assayed intra- and inter-familial telomere length dynamics (“Telomere_dataset.csv”) and telomerase (“Telomerase_dataset.csv”) as described in the manuscript. We also uploaded the R codes used to analyse proteomic data on parents (“ADupoue - Analyses code-Parent proteomic.R”) and the impacts of parental aging on their offspring traits (“ADupoue - Analyses code-Offspring.R”). Finally, we provided the output of Markov Chain Monte Carlo models used to estimate narrow sense heritability in offspring traits (“growth_larvae.rds”, “growth_spat.rds”, “survival_larvae.rds”, “survival_OsHV1_lab.rds”, “survival_adult.rds”, “Telomere_preInf.rds”, “Telomere_postInf.rds”, “Telomerase_preInf.rds”, “Telomerase_postInf.rds”).

controlledIPD-YESFeb 2026View details →

Single-arm Trial to Evaluate the Role of the Immune Response to Talimogene Laherparepvec in Unresected Melanoma

ClinicalTrials.gov study NCT02366195. IPD Sharing: YES. Countries: 13. Publications: 1.

Effect of Paroxetine on Smokers' Cardiovascular Response to Stress - 1

ClinicalTrials.gov study NCT00218439. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Modulation of the Inflammatory Response in Bariatric Surgery

ClinicalTrials.gov study NCT06915558. IPD Sharing: NO. Countries: 1. Publications: 13.

A Study to Evaluate the Dose Response Based on the Efficacy, Safety and Tolerability of Bimekizumab in Subjects With Active Psoriatic Arthritis Which is a Type of Inflammatory Arthritis

ClinicalTrials.gov study NCT02969525. IPD Sharing: Not stated. Countries: 6. Publications: 3.

closedIPD-NOFeb 2026View details →

Genomic Predictors of Decitabine Response in Patients With Acute Myeloid Leukemia or Myelodysplastic Syndromes

ClinicalTrials.gov study NCT01687400. IPD Sharing: NO. Countries: 1. Publications: 1.

Response to Kuvan® in Subjects With Phenylketonuria (PKU) in a 4 Weeks Testing Period

ClinicalTrials.gov study NCT01082328. IPD Sharing: Not stated. Countries: 1. Publications: 22.

Safety of and Immune Response to Dolutegravir in HIV-1 Infected Infants, Children, and Adolescents

ClinicalTrials.gov study NCT01302847. IPD Sharing: Not stated. Countries: 8. Publications: 6.

A Study of Ocrelizumab in Participants With Relapsing Remitting Multiple Sclerosis (RRMS) Who Have Had a Suboptimal Response to an Adequate Course of Disease-Modifying Treatment (DMT)

ClinicalTrials.gov study NCT02861014. IPD Sharing: Not stated. Countries: 17. Publications: 1.

Effects of Body Mass Index on the Hyperemic Response to Regadenoson

ClinicalTrials.gov study NCT00859833. IPD Sharing: Not stated. Countries: 1. Publications: 1.