Find research datasets worth reusing

opencc-by-4.0Nov 2020View details →

Management and plant physiology data for grassland sites in Germany

Management and vegetation data for sites Fendt (DE-Fen), Rottenbuch (DE-RbW) and Graswang (DE-Gwg) in Southern Germany, observed between 2012 and 2017. Weekly resolution vegetation traits are included for 2015. The sites are part of TERENO, a network of observatories in Germany. The time period includes the ScaleX intensive observation campaigns that took place in 2015 and 2016. The data format is NetCDF4. A Jupyter notebook is available (see Related identifiers, GitLab) with technical notes and examples.

opencc-by-4.0Dec 2021View details →

Data for: Epicardial slices: an innovative 3D organotypic model to study epicardial cell physiology and activation.

Raw data set for Npj Regenerative Medicine article: Epicardial slices: an innovative 3D organotypic model to study epicardial cell physiology and activation.

opencc-by-4.0Dec 2021View details →

Data for 'Phenological shifts in a warming world affect physiology and life history in a damselfly'

In this analysis we studied, in laboratory conditions, the impact of warming and hatching dates on key life history and physiological traits in a cannibalistic damselfly, Ischnura elegans. Larvae were reared in groups from hatching to emergence through one or two growth seasons, depending on the voltinism. Larvae were equally divided by hatching dates (early and late) and temperature treatment (current and warming). Early and late hatched groups were not mixed. This data set includes: <ul> <li>survival until emergence and emergence success data</li> <li>development time (from hatching to emergence, in days)</li> <li>mass of adult insects</li> <li>growth rate (mass of adult insect/development time in days)</li> <li>protein content (μg of protein/μl of prepared homogenate)</li> <li>phenoloxidase activity (PO, value of activity curve slope)</li> <li>PO activity/protein (value of activity curve slope/(μg of protein/μl of prepared homogenate)</li> <li>insects voltinism (univoltine/semivoltine)</li> </ul>

opencc-by-4.0Sep 2021View details →

Data for "Microstructural mapping of A. islandica shells reveals environmental and physiological controls on biomineral size"

This data contains the image segmentation workflow, data processing procedure and all data generated for the publication "Microstructural mapping of A. islandica shells reveals environmental and physiological controls on biomineral size" currently under review.

opencc-by-4.0Jun 2020View details →

Close range hyperspectral camera dataset with high temporal resolution of strawberry with eco-physiological data of one leaf

This high temporal resolution dataset of a strawberry plant was captured in two experiments, each lasting 100h. On leaf was inserted into a leaf chamber of the LI-6400XT gas exchange system, capturing information on transpiration, photosynthesis and stomatal conductance. Environmental characteristics are also captured at canopy height. These experiments were conducted in a growth chamber at ILVO (Melle, Belgium) and only covered conditions that did not result in stress in the plant. As such, this dataset attempts to capture subtle dynamic variation in the plant.

opencc-by-4.0Jun 2020View details →

Data of physiology, biomechanics and hydrodynamics of a freshwater macrophyte

This data package provides post-processed data used in the manuscript “Linking plant stress and hydrodynamics: evidence from freshwater macrophytes” submitted to Water Resources Research. The data package contains data obtained from direct measurements of maximum quantum yield of photosystem II, morphological characteristics and flexural rigidity of the freshwater macrophyte Potamogeton natans. Further, data of flow velocity, drag force, plant deflected height and plant centroid height obtained from flume experiments carried out with samples of P. natans are reported.

opencc-by-4.0Apr 2017View details →

Physiological trait and genotype data for 1,038 outbred CFW mice

R data set containing physiological trait data and genotype data for 1,038 mice from the Carworth Farms White (CFW) outbred mouse stock. These data were collected as part of a large study to assess the viability of using Carworth Farms White (CFW) mice for mapping genes and genetic loci underlying complex traits relevant to the study of human disease and psychology. The data accompany the following publication: Parker CC, Gopalakrishnan G, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in commercially available outbred CFW mice. Nature Genetics 48: 919–926. To use these data for your research, please cite this Zenodo resource, as well as the paper published in Nature Genetics. After loading these data into the R environment, e.g., by running "load(cfw.RData)", you will find R objects including: "pheno"—a 1,038 x 7 matrix containing the quantitative trait, or "phenotype", data. Traits include body weight, tibia length, muscle weights (EDL and soleus), and a binary indicator for abnormal bone health. "map"—a data frame containing information for 79,748 single nucleotide polymorphisms (SNPs) on chromosomes 1–19 genotyped in the CFW mice. All genomic positions are based on Mouse Genome Assembly 38 from the NCBI database (mm10, December 2011). "geno"—a 1,038 x 79,748 matrix containing genotype data for 1,038 mice at 79,748 SNPs. For more information on these data, please refer to the Data Dryad repository: http://dx.doi.org/10.5061/dryad.2rs41 For code implementing QTL mapping of physiological, behavioral and gene expression phenotypes, and other analyses of these data, see: http://github.com/pcarbo/cfw

opencc-zeroJan 2024View details →

Data from: Physiological mortality rates of planktonic ciliates

Contrasting physiological mortality with predator-induced mortality is of tremendous importance for the population dynamics of many organisms but is difficult to assess. I performed a meta-analysis using planktonic ciliates as model organisms to estimate the maximum physiological mortality rates (δmax) across pelagic ecosystems in relation to environmental and biotic factors. Data were compiled from published numerical response (NR) experiments and experimentally determined rates of decline (ROD). Variables reported are ciliate species and order, ciliate specific growth rates (rmax), prey species, temperature, habitat (marine vs freshwater), the coefficients of the numerical response experiments, and reported or calculated ciliate mortality rates. The median δmax of planktonic ciliates was 0.62 d−1 and did not differ between marine and freshwater species. Maximum ciliate mortality rates were species-specific and affected by their rmax, cell volume, and ability to encyst. Cyst-forming species had, on average, higher δmax than species unable to encyst. Maximum mortality rates of ciliates were positively related to rmax but appeared unaffected by temperature. I conclude that (i) in the ocean, physiological mortality is more critical for controlling ciliate population size than ciliate losses imposed by microcrustacean predation, but (ii) in many lakes, the opposite holds; (iii) cyst-formation is an effective ciliate trait to cope with the high mortality of motile cells upon starvation. The lack of a temperature effect on δmax deserves further study; if correct, planktonic ciliates may take advantage of rising ocean and lake temperatures, with important implications for the pelagic food web.

opencc-by-4.0Feb 2024View details →

The AFFECT-HRI data set: physiological data for affective computing in human-robot interaction with anthropomorphic service robots

We provide a comprehensive data set AFFECT-HRI containing physiological data labeled with human affect (i.e., mood and emotion) gathered during an empirical study consisting of a complex human-robot interaction (HRI). A realistic retail scenario served as an experimental environment. In prior research, we showed the necessity to combine the expertise of the research fields of psychology, computer science, and law in the design of a responsible human-centered HRI. Therefore, we implemented five conditions (neutral, transparency, liability, moral, and immoral) covering the perspectives from these three research fields and used two different anthropomorphic service robots. Our study followed a multi-method approach, resulting in a data set containing and combining objective physiological sensor data with subjective human-affect assessments. Additionally, the data set includes insights from 146 participants regarding affect, demographics, and socio-technical questionnaire ratings, as well as robot gestures and robot speech. Our study can be split into three scenes: a consultation regarding products, a request for sensitive personal information while opening a customer account, and a successful or failing handover when buying a mold remover. Thus, this data set offers for the first time the possibility to prove established or develop new emotion recognition methods and technological capabilities for HRI. Further, our data set provides the possibility to combine affective computing with research about robot behavior (gestures, speech, and handover), liability (questionnaire), transparency (questionnaire), and psychological aspects, allowing an encompassing, human-centered view of HRI. The detailed data descriptor has been published in Nature Scientific Data. For more details on the data set, please check the paper below. Please cite the following paper if the dataset is used in a publication: Heinisch, J.S., Kirchhoff, J., Busch, P. et al. Physiological data for affective computing in HRI with anthropomorphic service robots: the AFFECT-HRI data set. Sci Data 11, 333 (2024). https://doi.org/10.1038/s41597-024-03128-z Acknowledgements This research was conducted as part of RoboTrust, a project of the Centre Responsible Digitality, supported by the Hessian Minister for Digital Strategy and Innovation. The authors would like to thank all participants for their participation in the study. We particularly want to thank Ruth Stock-Homburg for her support and for making Elenoide available. Further, we want to thank Mona Kegel, Vignesh Prasad, and all the research assistants who supported the study. We also thank the leap in time lab for serving as study location. A special thanks goes to Amer Altizini, who supported us by helping to prepare the data for publication. We want to thank Niklas Jungermann for his valuable comments on the statistical evaluation.

opencc-zeroOct 2021View details →

Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs

Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require collecting data from many species, a challenge when data collection is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework—the Ornstein-Uhlenbeck process—that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold-temperature tolerance and characterized thermal performance curves in jumping for twelve species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our paper shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.

opencc-zeroApr 2022View details →

Data from: Divergent physiological acclimation responses to warming between two co-occurring salamander species and implications for terrestrial survival

Small differences in physiological responses are known to influence demographic rates such as survival. We tested for differences in the physiological acclimation responses of two closely-related salamander species that often co-occur, Ambystoma maculatum and A. opacum. Specifically, we measured changes in critical thermal maxima (CTmax), standard metabolic rates (SMRs), and respiratory surface area water loss (RSAWL) following exposure to three temperature treatments under laboratory conditions. While the magnitude of RSAWL and CTmax acclimation responses to warming did not differ between the study species, SMR was maintained across acclimation temperatures among A. maculatum, but declined among A. opacum acclimated to warmer temperatures. Metabolic compensation may facilitate maintained A. maculatum activity levels during warm periods following the relatively cool spring breeding season. In contrast, metabolic suppression may allow A. opacum to conserve energy when exposed to surface conditions during fall breeding and nest guarding. We simulated how these different SMR responses would likely alter post-metamorphic survival in our study species using previously collected data representing six weeks under relatively warm seminatural conditions. Our simulation indicated that, following warming and under identical study conditions, metabolic compensation may allow juvenile A. maculatum to maintain survival likelihoods, whereas metabolic depression may cause juvenile A. opacum to experience increased survivorship. These findings underscore that comparable physiological responses among ecologically similar, sympatric species cannot be assumed. Further, results of this study suggest that metabolic responses may play an important role in amphibian species persistence as temperatures increase due to habitat modification and climate change.

opencc-zeroJul 2022View details →

Data from: Non-native grazers affect physiological and demographic responses of Greater Sage-grouse

1. Non-native ungulate grazing has negatively impacted native species across the globe, leading to massive loss of biodiversity and ecosystem services. Despite their pervasiveness, interactions between non-native grazers and native species are not fully understood. We often observe declines in demography or survival of these native species, but lack understanding about the mechanisms underlying these declines. Physiological stress represents one mechanism of (mal)adaptation but data are sparse. 2. We investigated glucocorticoid levels in a native avian herbivore exposed to different intensities of non-native grazing in the cold desert Great Basin ecosystem, USA. We measured corticosterone, a glucocorticoid in feathers for a large sample (n = 280) of female Greater Sage-grouse (Centrocercus urophasianus) from three study areas in Northern Nevada and Southern Oregon with different grazing regimes of livestock and feral horses. 3. We found greater feral horse density was associated with higher corticosterone levels, and this effect was exacerbated by drought conditions. Livestock grazing produced similar results; however there was more model uncertainty about the livestock effect. Subsequent nesting success was lower with increased feather corticosterone, but corticosterone levels were not predictive of other vital rates. 4. Our results indicate a physiological response by sage-grouse to grazing pressure from non-native grazers. We found substantial among-individual variation in the strength of the response. These adverse effects were intensified during unfavorable weather events, highlighting the need to reevaluate management strategies in the face of climate change.

opencc-zeroSep 2022View details →

Data associated with: Emergence of the physiological effects of elevated CO2 on land-atmosphere exchange of carbon and water

Elevated atmospheric CO2 (eCO2) influences the carbon assimilation rate and stomatal conductance of plants and thereby can affect the global cycles of carbon and water. Yet, the detection of these physiological effects of eCO2 in observational data remains challenging, because natural variations and confounding factors (e.g., warming) can overshadow the eCO2 effects in observational data of real-world ecosystems. In this study, we aim at developing a method to detect the emergence of the physiological CO2 effects on various variables related to carbon and water fluxes. We mimic the observational setting in ecosystems using a comprehensive process-based land surface model QUINCY to simulate the leaf-level effects of increasing atmospheric CO2 concentrations and their century-long propagation through the terrestrial carbon and water cycles across different climate regimes and biomes. We then develop a statistical method based on the signal-to-noise ratio to detect the emergence of the eCO2 effects. The signal in gross primary production (GPP) emerges at relatively low CO2 increase (Δ[CO2] ~ 20 ppm) where the leaf area index is relatively high. Compared to GPP, the eCO2 effect causing reduced transpiration water flux (normalized to leaf area) emerges only at relatively high CO2 increase (Δ[CO2] >> 40 ppm), due to the high sensitivity to climate variability and thus lower signal-to-noise ratio. In general, the response to eCO2 is detectable earlier for variables of the carbon cycle than the water cycle, when plant productivity is not limited by climatic constraints, and stronger in forest-dominated rather than in grass-dominated ecosystems. Our results provide a step toward when and where we expect to detect physiological CO2 effects in in-situ flux measurements, how to detect them and encourage future efforts to improve the understanding and quantification of these effects in observations of terrestrial carbon and water dynamics.

opencc-by-sa-4.0May 2024View details →

A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments: Supporting Data

Experimental data including Excel analysis and microscopy supporting the publication 'A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments' <a href="https://doi.org/10.1063/1.4821498" target="_blank" rel="noopener">https://doi.org/10.1063/1.4821498</a>

opencc-zeroJun 2024View details →

Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment

Proarrhythmic cardiotoxicity remains a substantial barrier to drug development as well as a major global health challenge. In vitro human pluripotent stem cell-based new approach methodologies have been increasingly proposed and employed as alternatives to existing in vitro and in vivo models that do not accurately recapitulate human cardiac electrophysiology or cardiotoxicity risk. In this study, we expanded the capacity of our previously established three-dimensional human cardiac microtissue model to perform quantitative risk assessment by combining it with a physiologically based pharmacokinetic model, allowing a direct comparison of potentially harmful concentrations predicted in vitro to in vivo therapeutic levels. This approach enabled the measurement of concentration responses and margins of exposure for two physiologically relevant metrics of proarrhythmic risk (i.e., action potential duration and triangulation assessed by optical mapping) across concentrations spanning three orders of magnitude. The combination of both metrics enabled accurate proarrhythmic risk assessment of four compounds with a range of known proarrhythmic risk profiles (i.e., quinidine, cisapride, ranolazine, and verapamil) and demonstrated close agreement with their known clinical effects. Action potential triangulation was found to be a more sensitive metric for predicting proarrhythmic risk associated with the primary mechanism of concern for pharmaceutical-induced fatal ventricular arrhythmias, delayed cardiac repolarization due to inhibition of the rapid delayed rectifier potassium channel, or hERG channel. This study advances human induced pluripotent stem cell-based three-dimensional cardiac tissue models as new approach methodologies that enable in vitro proarrhythmic risk assessment with high precision of quantitative metrics for understanding clinically relevant cardiotoxicity.

opencc-zeroJul 2024View details →

Data from: A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation

<div> Understanding how plant phenotypes are shaped by their environments is crucial for addressing questions about crop adaptation to new environments. This study investigated the interplay between developmental responses to temperature fluctuations and photoperiod perception in maize that contribute to genotype-by-environment variation in flowering time. We present a physiological reaction norm for flowering time plasticity (PRN-FTP) for studying large collections of genotypes tested in multi-environment trial (MET) networks. Using a new variable for computational envirotyping of sensed photoperiod, it was found that, at high latitudes, different genotypes in the same environment can experience hours-long differences in photoperiod. This emphasizes the importance of considering genotype-specific differences in the experienced environment when investigating plasticity. A statistical framework is introduced for modeling the PRN-FTP as a non-linear response function, with parameters putatively linked to different regulatory modules for flowering time. Applying the PRN-FTP to a sample of global breeding material for maize showed that tropical and temperate maize occupy distinct territories of the trait space for PRN-FTP parameters, supporting that the geographical spread and adaptation of maize was differentially mediated by exogenous and endogenous pathways for flowering time regulation. Our results have implications for understanding crop adaptation and for future crop improvement efforts. </div>

opencc-by-4.0Jun 2018View details →

Slow motion in films and video clips: Music influences perceived duration and emotion, autonomic physiological activation and pupillary responses [data set]

Data set for a study to be published by PLOS ONE.