Find research datasets worth reusing

opencc-by-4.0Aug 2024View details →

Spatial dynamics of CD39⁺CD8⁺ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer

Data related to the paper: "Spatial dynamics of CD39+CD8+ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer,” Nature Communications (2024) The repository data consists of two main folders: IMC_dataset and MC_normalized_dataset. IMC_dataset includes: <ol> <li> IMC_denoised_dataset: This folder contains cell mask images and noise-reduced images for each sample. </li> <li> IMC_raw_dataset: This folder contains raw, unprocessed data. </li> <li> IMC_processed_data: This folder contains standardized single-cell information and spillover-corrected FCS files, along with the compensation matrix. </li> </ol> The MC_normalized dataset includes FCS files that have been sorted by barcode. Please note that in the IMC dataset, the following mass channels are blank: <ul> <li>Tumor-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 171Yb, 174Yb, 176Yb, 190Os</li> <li>SLO-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 176Yb, 190Os</li> </ul> The names attached to the file names are IDs.

Data from: Leaf morphological traits show greater responses to changes in climate than leaf physiological traits and gas exchange variables

Adaptation to changing conditions is one of the strategies plants use to survive climate change. Here, we ask whether plants' leaf morphological and physiological traits/gas exchange variables have changed in response to recent, anthropogenic climate change. We grew seedlings from resurrected historic seeds from ex-situ seed banks and paired modern seeds in a common-garden experiment. Species pairs were collected from regions that had undergone differing levels of climate change using an emerging framework – Climate Contrast Resurrection Ecology, allowing us to hypothesise that regions with greater changes in climate (including temperature, precipitation, climate variability and climatic extremes) there would be greater trait responses in leaf morphology and physiology over time. Our found that in regions where there were greater changes in climate, there were greater changes in average leaf area, leaf margin complexity, leaf thickness and leaf intrinsic water use efficiency. Changes in leaf roundness, photosynthetic rate, stomatal density and the leaf economic strategy of our species were not correlated with changes in the climate. Our results show that leaves do have the ability to respond to changes in climate, however, there are greater inherited responses in morphological leaf traits than in physiological traits/variables, and greater responses to extreme measures of climate than gradual changes in climatic means. It is vital for accurate predictions of species' responses to impending climate change to ensure that future climate change ecology studies utilise knowledge about the difference in both leaf trait and gas exchange responses, and the climate variables that they respond to.

opencc-by-4.0Jun 2024View details →

Functional responses in habitat selection as a management tool to evaluate agri-environment schemes for farmland birds

The folder "functional_responses.zip" contains data analyzed for "Functional responses in habitat selection as a management tool to evaluate agri-environment schemes for farmland birds" The raw LPIS/IACS data are owned by the Saxon State Ministry for Energy, Climate Protection, Environment and Agriculture; they hold sensitive information and hence cannot be made publicly available. They can be requested from the agency for research purposes. Processed data are retrievable from .RDATA in "rdata_mixed_model" and "rdata_functional_responses" folders. "rscript" folder contains R functions of JAGS codes (jags_code.R), data processing (process.R), utility functions (utils.R), and figures (figure_all.R or figure_all_by_sp.R). Dg: Common whitethroat (Curruca communis) Fl: Eurasian skylark (Alauda arvensis) G: Yellowhammer (Emberiza citrinella) Ga: Corn bunting (Emberiza calandra)   If you have questions regarding data, please contact ryo.ogawa@uni-bonn.de.

Monkey V1/V2 neuronal population response to drifting gratings with varying orientation and contrast

Correlated variability in the visual cortex is modulated by stimulus properties. The stimulus dependence of correlated variability impacts stimulus coding and is indicative of circuit structure. An affine model combining a multiplicative factor and an additive offset has been proposed to explain how correlated variability in primary visual cortex (V1) depends on stimulus orientations. However, whether the affine model could be extended to explain modulations by other stimulus variables or variability shared between two brain areas is unknown. Motivated by a simple neural circuit mechanism, we modified the affine model to better explain the contrast-dependence of neural variability shared within either primary or secondary visual cortex (V1 or V2) as well as the orientation-dependence of neural variability shared between V1 and V2. Our results bridge neural circuit mechanisms and statistical models, and provide a parsimonious explanation for the stimulus-dependence of correlated variability within and between visual areas.

opencc-by-4.0Jun 2024View details →

Data set for manuscript titled "Morphological, physiological and metabolic responses of diverse barley inbreds to dry down and moderate drought stress"

The primary aim of the study was to understand the genotypic diversity on plant morphology, photosynthetic responses, metabolite shift and their relationship in diverse barley inbreds under dry down (DD) and moderate drought (MD) stress using 23 genetically diverse parental inbreds. The data were collected from over a period of 28 days after the start of stress treatment. The publised data set indcludes the emmeans of all the evaluated characters. Metabolite profiling was done in samples collected from 7 d and 12 d after the start of DD and MD stress.

Evolution of threat response-related polymorphisms at the SLC6A4 locus in callitrichid primates

Variation in an upstream repetitive region at the SLC6A4 locus, which encodes the serotonin transporter, is associated with anxiety-related behaviour in a few primate species, including humans and rhesus macaques, and has been suggested to be related to ecological adaptability among macaques. In this study we investigate evolution of SLC6A4 polymorphisms associated with anxiety-related behaviour in common marmosets (Callithrix jacchus). Assaying variation in the SLC6A4 repeat region across 14 species in 8 genera of callitrichid primates (marmosets and tamarins) we find large interspecific variation in the number of repeats present (24-43). The black tufted-ear marmoset (C. penicillata) has sequence polymorphisms similar to those found in the common marmoset, which is its sister species, and no other species has intraspecific variation at these sites. We conclude that, similar to humans and macaques, the functional polymorphism at SLC6A4 in common marmosets has a recent evolutionary origin, and that the anxiety-related allele is evolutionarily derived. Common/black tufted-ear marmosets and rhesus/bonnet macaques share high ecological adaptability and behavioural flexibility that we propose may be related to the maintenance of the polymorphism.

Data from: Hyperbolic discounting underpins response curves of mammalian avoidance behaviour

As humans clear natural habitat they are brought into increased conflict with wild animals. Some conflict is direct (e.g., elevated exposure of people to predators), some indirect (e.g., abandoning suitable habitat because of human activity). The magnitude of avoidance is expected to track frequency of human activity, but the type of response is an open question. We postulated that animals do not respond passively to increased disturbance, nor does response follow a power law; instead, their ability to estimate magnitude leads to 'discounting' behaviour, as in classic time-to-reward economic models in which individuals discount larger value (or risk) in more distant time. We used a ten-year camera dataset from southern California to characterise response curves of seven mammal species. Bayesian regressions of two non-discounting models (exponential and inverse polynomial) and two discounting models (hyperbolic and harmonic) revealed that the latter better fit response curves. The Arps equation, from petroleum extraction modelling, was used to estimate a discount exponent, a taxon-specific 'sensitivity' to humans, yielding a general model across species. Although discounting can mean mammal activity recovers rapidly after disturbance, increased recreational pressure on reserves limits recovery potential, highlighting a need to strike a balance between animal conservation and human use.

opencc-by-4.0Jun 2024View details →

Datasets used in Erosional response to Pleistocene climate changes in the Brazilian highlands

The data files correspond to the data tables of the ms "Erosional response to Pleistocene climate changes in the Brazilian highlands", submitted to JGR.

Response of soil fungal communities and their co-occurrence patterns to grazing exclusion in different grassland types

Overgrazing and climate change are the main causes of grassland degradation, and grazing exclusion is one of the most common measures for restoring degraded grasslands worldwide. Soil fungi can respond rapidly to environmental stresses, but the response of different grassland types to grazing control has not been uniformly determined. Three grassland types (temperate desert, temperate steppe grassland, and mountain meadow) that were closed for grazing exclusion for nine years were used to study the effects of grazing exclusion on soil nutrients as well as fungal community structure in the three grassland types. The results showed that (1) in the 0–5 cm soil layer, grazing exclusion significantly affected the soil water content of the three grassland types (P<0.05), and the pH, total phosphorous (TP) and nitrogen-to-phosphorous ratio (N/P) changed significantly in all three grassland types (P<0.05). Significant changes in soil nutrients in the 5–10 cm soil layer after grazing exclusion occurred in the mountain meadow grasslands (P<0.05), but not in the temperate desert and temperate steppe grasslands. (2) For the different grassland types, Archaeorhizomycetes was most abundant in the montane meadows, and Dothideomycetes was most abundant in the temperate desert grasslands and was significantly more abundant than in the remaining two grassland types (P<0.05). Grazing exclusion let to insignificant changes in the dominant soil fungal phyla and in α diversity but significant changes in the β diversity of soil fungi (P<0.05). (3) Grazing exclusion areas have higher mean clustering coefficients and modularity classes than grazing areas. In particular, the highest modularity class is found in temperate steppe grassland grazing exclusion areas. (4) We also found that pH is the main driving factor affecting soil fungal community structure, that plant coverage is a key environmental factor affecting soil community composition, and that grazing exclusion indirectly affects soil fungal communities by affecting soil nutrients. The above results suggest that grazing exclusion may regulate microbial ecological processes by changing the soil fungal β diversity in the three grassland types. Grazing exclusion is not conducive to the recovery of soil nutrients in areas with mountain meadow but improves the stability of soil fungi in temperate steppe grassland. Therefore, the type of degraded grassland should be considered when formulating suitable restoration programmes when grazing exclusion measures are implemented. The results of this study provide new insights into the response of soil fungal communities to grazing exclusion, providing a theoretical basis for the management of degraded grassland restoration.

opencc-zeroAug 2019View details →

FIG. 1 in Response of bryophytes to disturbances in managed forests. A case study from a Polish forest

FIG. 1. — Number of bryophyte species in the four types of substrates considered.

Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish

The responses of marine species to environmental changes and anthropogenic pressures (e.g. fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Utilizing a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. Contemporary genomic structure showed three populations—two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects in fisheries that depend on this resource.

Shifts in the composition and distribution of Pacific Arctic larval fish assemblages in response to rapid ecosystem change

The Pacific Arctic marine ecosystem has undergone rapid changes in recent years due to ocean warming, sea ice loss, and increased northward transport of Pacific‐origin waters into the Arctic. These climate‐mediated changes have been linked to range shifts of juvenile and adult subarctic (boreal) and Arctic fish populations, though it is unclear whether distributional changes are also occurring during the early life stages. We analyzed larval fish abundance and distribution data sampled in late summer from 2010 to 2019 in two interconnected Pacific Arctic ecosystems: the northern Bering Sea and Chukchi Sea, to determine whether recent warming and loss of sea ice have restricted habitat for Arctic species and altered larval fish assemblage composition from Arctic‐ to boreal‐associated taxa. Multivariate analyses revealed the presence of three distinct multi‐species assemblages across all years: (1) a boreal assemblage dominated by yellowfin sole (Limanda aspera), capelin (Mallotus catervarius), and walleye pollock (Gadus chalcogrammus); (2) an Arctic assemblage composed of Arctic cod (Boreogadus saida) and other common Arctic species; and (3) a mixed assemblage composed of the dominant species from the other two assemblages. We found that the wind‐ and current‐driven northward advection of warmer, subarctic waters and the unprecedented low‐ice conditions observed in the northern Bering and Chukchi seas beginning in 2017 and persisting into 2018 and 2019 have precipitated community‐wide shifts, with the boreal larval fish assemblage expanding northward and offshore and the Arctic assemblage retreating poleward. We conclude that Arctic warming is most significantly driving changes in abundance at the leading and trailing edges of the Chukchi Sea larval fish community as boreal species increase in abundance and Arctic species decline. Our analyses document how quickly larval fish assemblages respond to environmental change and reveal that the impacts of Arctic borealization on fish community composition spans multiple life stages over large spatial scales.

opencc-by-4.0Nov 2023View details →

Atmospheric Response Matrices (ARMs) computed with AtRIS in: The Atmospheric Influence on Cosmic-Ray-Induced Ionization and Absorbed Dose Rates

Ionization and Dose Atmospheric Response Matrices (ARMs) computed with the Atmspheric Interaction Radiation Simulator (AtRIS) and used in the following publication:  The Atmospheric Influence on Cosmic-Ray-Induced Ionization and Absorbed Dose Rates. All files are in txt format. Files ending in '_energy_bins.txt', contain the informations about the energy binning of the primary particles used in the AtRIS simulations.  Files ending in '_ioni.txt', contain the ionization ARMs computed with the above mentioned energy binning. Files ending in '_dose.txt', contain the ICRU water sphere dose ARMs computed with the above mentioned energy binning.

opencc-by-4.0Jul 2024View details →

Beryllium Isotopes in Maar Lake Sediments Response to Rapid Climate Change Since the Last Deglaciation

Data for "Beryllium Isotopes in Maar Lake Sediments Response to Rapid Climate Change Since the Last Deglaciation"

opencc-by-4.0Jul 2024View details →

"Towards Responsible Publishing" - Structured organisational feedback responses

<a href="https://www.research-consulting.com/" target="_blank" rel="noopener">Research Consulting</a> and the <a href="https://www.cwts.nl/" target="_blank" rel="noopener">Centre for Science and Technology Studies (CWTS)</a> were commissioned to determine to what extent the vision, mission and objectives set out in the TRP proposal serve the needs of the global research community. Through a consultative approach, we sought to assess whether there is appetite for the type of change proposed by cOAlition S in the TRP proposal. In addition, we aimed to understand how the ‘Towards Responsible Publishing’ proposal may be modified or refined to ensure it resonates with the research community and sees broad adoption; identify any showstoppers or unintended consequences and propose proactive measures to mitigate them, ensuring successful implementation; and ascertain whether the existing scholaly communication infrastructure can support this proposal and if not, identify where research funders can strengthen the infrastructure.  As part of our consultation, we gathered structured organisational feedback from underrepresented groups and organisations in the scholarly communication ecosystem. We received responses from a total of 10 organisations, of which 9 were willing to be named publicly in the document enclosed below and 1 opted to remain anonymous. We would like to thank our contributors, which include (in alphabetical order) Abel Laerte Packer (sciELO), Arianna Becerril García (Redalyc), Consejo Directivo LA Referencia, Red Latinoamericana y de España para la Ciencia Abierta (LA Referencia), Dominique Babini (CLASCO), Iryna Kuchma (EIFL), Kazuhiro Hayashi (NISTEP), Laura Rovelli (CLASCO), Milica &Scaron;evku&scaron;ić (EIFL), Moumita Koley (IISc), Susan Veldesman (ASSAf) and Takayuki Hayashi (GRIPS).

opencc-zeroJul 2024View details →

"Towards Responsible Publishing" - Online researcher survey questionnaire

<a href="https://www.research-consulting.com/" target="_blank" rel="noopener">Research Consulting</a> and the <a href="https://www.cwts.nl/" target="_blank" rel="noopener">Centre for Science and Technology Studies (CWTS)</a> were commissioned to determine to what extent the vision, mission and objectives set out in the TRP proposal serve the needs of the global research community. Through a consultative approach, we sought to assess whether there is appetite for the type of change proposed by cOAlition S in the TRP proposal. In addition, we aimed to understand how the ‘Towards Responsible Publishing’ proposal may be modified or refined to ensure it resonates with the research community and sees broad adoption; identify any showstoppers or unintended consequences and propose proactive measures to mitigate them, ensuring successful implementation; and ascertain whether the existing scholaly communication infrastructure can support this proposal and if not, identify where research funders can strengthen the infrastructure. As part of the consultation, the Centre for Science and Technology Studies and Research Consulting developed a researcher survey to gather researcher feedback on aspects of the scholarly communication system. This deposit provides our online survey questionnaire.

opencc-by-4.0Jul 2024View details →

Cholinergic input to mouse visual cortex signals a movement state and acutely enhances layer 5 responsiveness

<div>All raw data and Matlab code necessary to produce the figures of <a href="https://elifesciences.org/reviewed-preprints/89986">https://elifesciences.org/reviewed-preprints/89986</a></div> <div> <div> </div> </div>

opencc-zeroJul 2024View details →

One of these things is not like the other: mixed predator cues result in lopsided phenotypic responses in a Neotropical tadpole

Many organisms have evolved to produce different phenotypes in response to environmental variation. Dendropsophus ebraccatus tadpoles develop opposing shifts in morphology and coloration when they are exposed to invertebrate vs vertebrate predators. Each of these alternate phenotypes is adaptive, conferring a survival advantage against the predator with which tadpoles were reared but imposing a survival cost with the mismatched predator. Here, we measured the phenotypic response of tadpoles to graded cues and mixed cues of both fish and dragonfly nymphs. Prey species like D. ebraccatus commonly co-occur with both of these types of predators, amongst many others as well. In our first experiment, tadpoles increased investment in defensive phenotypes in response to increasing concentrations of predator cues. Whereas morphology only differed in the strongest cue predator, tail spot coloration differed even at the lowest cue concentration. In our second experiment, tadpoles reared with cues from both predators developed an intermediate yet skewed phenotype that was most similar to the fish-induced phenotype. Fish are more lethal than dragonfly larvae and thus tadpoles responded most strongly to the more dangerous predator, even though cues of each predator were evenly mixed. We demonstrate that not only do tadpoles assess predation risk via the concentration of predation cues in the water, but they also produce a stronger response to a more lethal predator even when the strength of cues is identical.

opencc-by-4.0Mar 2013View details →

Fig. 7 in Ecophysiological responses to the effect of annual management on an endemic viviparous fish in central plateau of México

Fig. 7. Bimonthly energy expenditure during cycles of mexcalpique nictemeral in San Martin.