Find research datasets worth reusing

Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress

This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.

opencc-by-4.0Nov 2023View details →

The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes

This repository contains code to reproduce the figures in the paper titled "The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes" published in the Journal of Physical Oceanography (DOI: <a href="https://doi.org/10.1175/JPO-D-23-0165.1">https://doi.org/10.1175/JPO-D-23-0165.1</a>), as well as the barotropic vorticity budget terms for each of simulation in the paper.

Non-Perennial rivers and streams under hydrological stress – comparing the effectiveness of amplicon sequencing and digital microscopy for diatom biodiversity appraisal

ABC is project leader, data collector, contact person, etc.

Data - Krieg et al. Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)

Data used in analyses and code to produce figures.

Low-Frequency Measurements of the Effective-Stress Coefficient for Elastic Moduli of Mungaroo Sandstone

The measurements were performed on n-decane saturated sandstone using a forced-oscillation laboratory apparatus utilizing stress-strain relationship. The dynamic elastic moduli have been measured in two sets of experiments: at constant pore pressures of 0, 1 and 5 MPa and differential pressure (defined as a difference between confining and pore pressures) varied from 3 to 19 MPa; and at а constant confining pressure of 20 MPa and pore pressure varied from 1 to 17 MP. It was shown that the elastic moduli obtained in the measurements are in good agreement with the Gassmann moduli calculated for the range of differential pressures used in our experiments, which corresponds to the effective-stress coefficient equal to unity.

opencc-zeroDec 2023View details →

Fertility loss under thermal stress

Climate change models predict that the frequency and intensity of heatwaves are likely to increase, therefore understanding population responses to these extreme climatic events will be key in mitigating biodiversity loss. Here, using the male dimorphic bulb mite, Rhizoglyphus robini, we investigate and compare the impact of experimental heat stress on survival and fertility between females and male morphs that differ in the expression of a sexually selected weapon. We show that lethal limits are similar among all individuals, but find clear sex differences, although no difference between morphs, in sub-lethal temperatures causing sterility: female fertility remains high close to lethal limits, whereas both male morphs suffer fertility loss at more than 2.5°C below their lethal limits. Contrastingly, when thermal stress was lower, the sexes and morphs do not differ in their thermal sensitivity and declines in reproductive output are comparable, these declines appear to be additive as we observe the greatest declines when both sexes were exposed to thermal stress. In addition, during assays, we included an extra treatment that allowed individuals two extra days to recover and found that fertility loss was almost fully recovered when thermal stress was low, but only partially recovered under the most extreme temperatures. The impact of heat stress on fertility therefore appears to be temporary with individuals rapidly recovering: whether recovery can negate negative population level effects remains to be investigated. Our experiments reveal the impact of heat stress on survival and fertility, finding sex-specific fertility loss under the most extreme thermal conditions.

opencc-by-sa-4.0Dec 2023View details →

Illustration of stress components with Mohr's circle

Graphical illustration of the components of a plane stress tensor via Mohr's circle. Depiction of principal stresses and representation of the stresses in the respective coordinate systems.

opencc-by-sa-4.0Dec 2023View details →

Illustration of stress transformation with Mohr's circle

Graphical illustration of the components of a plane stress tensor via Mohr's circle. Depiction of stress transformation and representation of the stresses in the respective coordinate systems.

Analyse par fluorescence et par absorbance du stress acide et radiatif et influence du pH sur la structure chlorophyllienne

Ce poster récapitule les expériences réalisées pour mettre en avant la dégradation de la chlorophylle lorsqu'elle est exposée à un milieu acide ou à un milieu radiatif par suivi de l'absorbance et la fluorescence de l'échantillon lors d'un suivi de pH précis.

Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses

This repository houses a comprehensive collection of data and resources from the study "Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses." Led by Dr. Suresh Neethirajan at Mooanalytica, Department of Agriculture & Aquaculture, Faculty of Agriculture & Computer Science, Dalhousie University, this research represents a significant foray into the field of poultry ethology and welfare monitoring using advanced machine learning techniques. Key Components of the Repository <ol> <li> Experimental Audio Data <ul> <li>Control and Treatment Vocalizations: Audio recordings of laying hens under two different stress conditions – sudden umbrella opening (Treatment 1) and simulated dog barking sounds (Treatment 2), along with control groups. The processed dataset is approximately 460 MB for the control group experimental data and about 2 GB for the 2 treatment group experimental data, capturing the nuanced responses of hens to these stressors.</li> <li>Original Raw Data: The original, unprocessed audio data is around 9 GB in size. Though not included in the repository, it can be made available upon reasonable request.</li> </ul> </li> <li> Algorithm and Code Files <ul> <li>CNN Feature Extraction and Classification Algorithms Python scripts used for the extraction of features from the audio data using Convolutional Neural Networks (CNN) and subsequent classification.</li> <li>Supplementary Algorithms Additional code files that support the processing and analysis of the audio data.</li> </ul> </li> <li> MFCC Feature Dataset <ul> <li>An Excel file containing the 40 Mel Frequency Cepstral Coefficients (MFCC) features extracted from the vocalization data. This dataset provides a detailed spectral analysis of the hen's vocalizations, crucial for understanding their response to stress.</li> </ul> </li> </ol> Study Overview This study aimed to classify and analyze the vocalization patterns of laying hens subjected to different stressors. Using a CNN model, the research identified distinct vocal patterns between control and treated groups, indicating unique vocal responses to different types of stressors. This study is pivotal in understanding the impact of environmental stressors on poultry welfare and behavior. The age of the chickens and the timing of stressor application were also critical factors influencing vocalization patterns. Implications and Applications: The findings from this study have significant implications for poultry welfare monitoring and management. By providing a non-invasive method to assess the well-being of chickens, this research contributes valuable insights into enhancing poultry management practices and welfare standards. The resources in this repository are intended for researchers, academicians, and professionals in animal behavior, veterinary science, and poultry management. We encourage the use of these data and tools for further research and practical applications in the field of precision (Digital) livestock farming and animal welfare. For any queries or requests related to the raw dataset, please contact Dr. Suresh Neethirajan.

opencc-zeroDec 2023View details →

Data from: A cucumber protein, Phloem Phosphate Stress Repressed 1, rapidly degrades in response to a phosphate stress condition

Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signalling cascades. In plants, the vascular system delivers nutrients and signalling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi-stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate-Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation, within the sieve tube system, through the action of CsPPSR1 Kinase. Further, we discovered that CsPPSR1 Kinase was susceptible to Pi-starvation-induced degradation, in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.

Data from: Stress-induced loss of social resilience in honeybee colonies and its implications on fitness

Stressors may lead to a shift in the timing of life-history events of species causing a mismatch with optimal environmental conditions, potentially reducing fitness. In honeybees, the timing of brood rearing and nest emergence in late winter/early spring is critical, as colonies need to grow fast after winter to prepare for reproduction. However, the effects of stress on these life-history events in late winter/early spring and the possible consequences are not well understood. Therefore, we tested whether (1) honeybee colonies shift timing of brood rearing and nest emergence as a response to stressors, and (2) if there is a consequent loss of social resilience, reflected in colony fitness (survival, growth and reproduction). We monitored stressed (high load of the parasitic mite Varroa destructor or nutrition-restricted) colonies and presumably non-stressed colonies from the beginning of 2020 till the spring of 2021. We found that honeybee colonies do not shift the timing of brood rearing and nest emergence in spring as a coping mechanism to stressors. However, we show that there is a loss of social resilience in stressed colonies, leading to reduced growth and reproduction. Our study contributes to a better understanding of the effects of stressors on social resilience in eusocial organisms.

Data from: anterior pituitary transcriptomics following a high fat diet: impact of oxidative stress on cell metabolism

Anterior pituitary cells are highly active with regards to protein synthesis and secretion, processes which depend heavily on mitochondrial ATP production and functional endoplasmic reticula. It is well known that obesity adds an allostatic overload to tissues, requiring them to adapt to inflammation and oxidative stress. Therefore, we hypothesized that the pituitary is highly vulnerable to the stress of high fat diet-induced weight gain. In this study, we utilized a 10-15 week high fat diet (HFD, 60%) plus a thermoneutral housing paradigm, testing both male and female FVB.129P mice. We quantified serum hormones and cytokines, characterized the metabolic phenotype, and defined changes in the pituitary transcriptome using single-cell RNA-seq. Weight gain was significant by 3 weeks in HFD mice, and by 10 weeks all HFD groups had gained 20 g. HFD females (15 weeks) had increased energy expenditure and decreased activity. All HFD groups showed increases in serum leptin, Il-6, resistin, MCP-1, and TNFα. HFD males had increased insulin; both HFD males and females had increased TSH, and HFD females had decreased serum prolactin and growth hormone (GH) pulse amplitude. Pituitary scRNA-seq revealed modest or no changes in pituitary cell gene expression in the different cell types from HFD males after 10 or 15 weeks or HFD females after 10 weeks. However, females exposed to a HFD for 15 weeks showed significant numbers of differentially expressed genes in lactotropes and stem cells. Pathway analyses identified a reduction in pathways that supported protein translation, ribosome biogenesis, and oxidative phosphorylation, indicating mitochondrial dysfunction. Collectively, these studies reveal that pituitary cells from males are more resilient to the oxidative stress of obesity than females and identify the most vulnerable pituitary cell populations in females.

Data from: Seeking temporal refugia to heat stress: Increasing nocturnal activity despite predation risk

Flexibility in activity timing may enable organisms to quickly adapt to environmental changes. Under global warming, diurnally adapted endotherms may achieve a better energy balance by shifting their activity towards cooler nocturnal hours. However, this shift may expose animals to new or increased environmental challenges (e.g., increased predation risk, reduced foraging efficiency). We analysed a large dataset of activity data from 47 ibex (Capra ibex) in two protected areas, characterized by varying levels of predation risk (presence vs absence of the wolf – Canis lupus). We found that ibex increased nocturnal activity following warmer days and during brighter nights. Despite the considerable sexual dimorphism typical of this species and the consequent different predation-risk perception, males and females demonstrated consistent responses to heat in both predator-present and predator-absent areas. This supports the hypothesis that shifting activity towards nighttime may be a common strategy adopted by diurnal endotherms in response to global warming. As nowadays different pressures are pushing mammals towards nocturnality, our findings emphasize the urgent need to integrate knowledge of temporal behavioural modifications into management and conservation planning.

QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat

The mapping population comprises of 180 RILs developed from a cross between GW322 and KAUZ. Phenotypic data Phenotypic evaluation was conducted across two consecutive crop seasons (2021-22 and 2022-23) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at ICAR-IARI, New Delhi. Various physiological and agronomic traits of importance were measured. The component traits of yield including days to heading (DH), normalized difference vegetation index (NDVI), SPAD chlorophyll content (SPAD), plant height (PH), spike length (SL), thousand-grain weight (TGW), grain weight per spike (GWPS), biomass (BM) and grain yield per plot (PY) were measured under heat and combined stress conditions. Genotypic data DNA was isolated from 21-day-old seedlings using the CTAB method (Murray and Thompson, 1980). DNA quality check was done using 0.8% agarose gel electrophoresis. The Axiom Breeders' array containing 35K Single Nucleotide Polymorphism (SNP) was employed for the genotyping of RILs and parents.

opencc-by-4.0Feb 2024View details →

Glacially induced stresses and strains in Canada

Dataset of finite element (FE) model input files for software Abaqus and rebound stress and strain tensor results in 2.5 km depth. FE_models.zip contains Abaqus input files for 7 different FE models of glacial isostatic adjustment (GIA) in Canada. The GIA models use ice model f0050rn001_2022 with 147 time steps, which is a special version of the well known ICE-6G_C GIA-based reconstruction (Argus et al., 2014; Peltier et al., 2015). It combines University of Toronto Glacial Systems Model simulations of the second generation (2.0) with updated ice physics and simulation of surface hydrology (lakes and rivers) (Stuhne & Peltier, 2016, 2017). The loading files also contain load changes from sea level variations corresponding to global ice load changes on the selected Earth model. There are 7 Earth models with different rheologic structure. Details can be found in the corresponding manuscript (Steffen & Steffen, 2024). results.tar.gz contains the rebound stress and strain tensors in 2.5 km depth in Canada for each time step of a GIA model, resulting in 1029 (147*7) files named "{earth_model_name}_stress_strain_{time_in_1000_years_before_present}.dat". The files contain both the internal coordinates of the model and their corresponding longitude and latitude. Note that the grid is partly irregular as there are model parts which have a finer mesh. The format of the files is: x-coordinate of model in km, y-coordinate of model in km, longitude in degree E, latitude in degree N, GIA stress tensor (S11, S22, S33, S12, S13, S23) in MPa and strain tensor (E11, E22, E33, E12, E13, E23) in strain.

opencc-zeroFeb 2024View details →

Data from: Natural thermal stress-hardening of corals through cold temperature pulses in the Thai Andaman Sea

Stress-hardening by environmental priming could increase the odds for corals to resist ocean warming. Natural environmental fluctuations, such as those observed on offshore reefs in the Andaman Sea, provide an ideal natural environment to study these effects. Here, internal waves (IW) generate short cold-water pulses that peak from January to June and are absent from August to November. Additionally, only western shores of islands are exposed to this stress-hardening stimulus of IWs, while eastern shores remain sheltered. Therefore, this study examined (1) whether exposed corals were more heat stress resistant than their sheltered conspecifics and (2) whether this trait would persist during the season of stimulus absence. We exemplify that thermal regimes featuring cold-temperature pulses successfully induced thermal stress-hardening in corals. Corals from the IW-sheltered shore responded strongly to heat stress irrespective of the season, while stress responses of IW-exposed corals were either undetectable (during stimulus presence) or very weak (during stimulus absence). However, this demonstrates the relevance of stimulus re-occurrence in maintaining heat resistance. Furthermore, priming stimuli do not need to exceed certain upper thermal thresholds to be effective and we argue that cooling pulses represent a safer stress-hardening regimen potentially implemented in conservation strategies since it avoids warming-stress accumulation.

opencc-by-4.0Oct 2023View details →

Data/code from: Long-term data reveal that grazer density mediates climatic stress in salt marshes

Understanding how climate and local stressors interact is paramount for predicting future ecosystem structure. The effects of stressors are often examined in small-scale and short-term field experiments, limiting understanding of the spatial and temporal generality of the findings. Using a 22-year observational dataset of plant and grazer abundance in a Southeastern US salt marsh, we analyzed how changes in drought and snail density combined to affect plant biomass. We found: (1) increased drought severity and higher snail density both correlated with lower plant biomass; (2) drought and snail effects interacted additively; and, (3) snail effects had a threshold, with additive top-down effects only occurring when snails were present at high densities. These results suggest that the emergence of multiple stressor effects can be density-dependent, and they validate short-term experimental evidence that consumers can exacerbate environmental stress. These findings have important implications for predicting future ecosystem structure and managing natural ecosystems.The data and code included here can be used to replicate all analyses and figures in our manuscript.

opencc-zeroFeb 2024View details →

Vertical structural complexity of plant communities represents the combined effects of resource acquisition and environmental stress on the Tibetan Plateau

Knowledge of vertical structural complexity (VSC) is important, because the resulting spatial partitioning is closely linked to resource utilization and environmental adaptation. However, the spatial pattern of VSC on large scales and its underlying mechanisms are poorly understood. Here, we systematically investigated 2,013 plant communities through grid sampling on the Tibetan Plateau (TP). VSC was quantified as the maximum plant height within a plot (Height-max), coefficient of variation of plant height (Height-var), and Shannon evenness of plant height (Height-even). Precipitation dominated the spatial variation in VSC in forests and shrublands, supporting the classic physiological tolerance hypothesis (PTH). In contrast, for alpine meadows, steppes, and desert grasslands in extreme environments, non-resource limiting factors (e.g., wide diurnal temperature ranges and strong winds) dominate VSC variation. Generally, with the shifting of climate from favorable to extreme, the effect of resource availability gradually decreases, but the effect of non-resource limiting factors gradually increases, and that the PTH only applicable in "favorable conditions". With the help of machine learning models, maps of VSC at 1-km resolution were produced for the TP for the first time. Our new findings and maps of VSC provide new insights into macroecological studies, especially for adaptation mechanisms and model optimization.