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opencc-zeroFeb 2022View details →

Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism

The mutualism between the thioautotrophic bacterial ectosymbiont Candidatus Thiobius zoothamnicola and the giant ciliate Zoothamnium niveum thrives in a variety of shallow-water marine environments with highly fluctuating sulfide emissions. To persist over time, both partners must reproduce and ensure the transmission of symbionts before the sulfide stops, which enables carbon fixation of the symbiont and nourishment of the host. We experimentally investigated the response of this mutualism to depletion of sulfide. We found that colonies released some initially present but also newly produced macrozooids until death, but in fewer numbers than when exposed to sulfide. The symbionts on the colonies proliferated less without sulfide, and became larger and more rod-shaped than symbionts from freshly collected colonies that were exposed to sulfide and oxygen. The symbiotic monolayer was severely disturbed by growth of other microbes and loss of symbionts. We conclude that the response of both partners to the termination of sulfide emission was remarkably quick. The development and the release of swarmers continued until host died and thus this behavior contributed to the continuation of the association.

opencc-by-4.0Feb 2022View details →

Tumor-Immune Microenvironment Revealed by Imaging Mass Cytometry in a Metastatic Sarcomatoid Urothelial Carcinoma with a Prolonged Response to Pembrolizumab - IMC data

<blockquote> Sarcomatoid urothelial carcinoma (SUC) is a rare subtype of urothelial carcinoma (UC), that typically presents at an advanced stage compared to more common variants of UC. Locally advanced and metastatic UC have a poor long-term survival following progression on first-line platinum-based chemotherapy. Antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1) are now approved to be used in these scenarios. The need for reliable biomarkers for treatment stratification is still under research. Here we present a novel case report of the first Image Mass Cytometry (IMC) analysis done in SUC to investigate the immune cell repertoire and PD-L1 expression in a patient who presented with metastatic SUC and experienced a prolonged response to the anti-PD1 immune checkpoint inhibitor pembrolizumab after progression on first line chemotherapy. This case report provides an important platform for translating these findings to a larger cohort of UC and UC variants. </blockquote> We make available TIFF files containing imaging mass cytometry data for 4 regions of interest of a sample of metastatic sarcomatoid urothelial carcinoma. The order of the axis in the image stacks is "CYX". The CSV files indicate the identity of the channels.

opencc-by-4.0Dec 2021View details →

Sustainable Smart Tags with Two-Step Verification for Anticounterfeiting Triggered by the Photothermal Response of Upconverting Nanoparticles

Dataset accompanying figures published in the publication DOI: https://doi.org/10.5281/zenodo.6245930

opencc-by-4.0Feb 2022View details →

Data and code from: Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia

Data and code accompanying:  Hegg, Radersma & Uller. 2022. Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia. Freshwater Biology, accepted. Abstract <ol> <li>Many populations of water fleas (Daphnia) are exposed to algal blooms dominated by microcystin-producing cyanobacteria. However, the severity of these effects on Daphnia fitness remain poorly understood in natural populations. </li> <li>We investigated seasonal changes in body size, reproduction and survival of Daphnia longispina individuals from five eutrophic lakes in southern Sweden. We tested whether individuals collected before, during or following algal blooms differed in their reproduction and survival when experimentally exposed to microcystin-producing cyanobacteria. </li> <li>The concentration of microcystin in the lakes was significantly higher during summer and autumn compared to spring, but there were substantial differences between lakes. The reproductive output of individuals declined consistently over the season, and this decline was stronger for Daphnia collected during periods of, or lakes from, high microcystin concentration. There was little evidence that individuals adapted to the toxin over the season. </li> <li>The strong seasonal changes in body size, reproduction and survival in these Daphnia longispina appears to be partly caused by variation in the abundance of toxin-producing cyanobacteria. Populations were unable to adapt sufficiently quickly during summer and autumn to recover from the negative effects of microcystin. We therefore suggest that seasonal increases in tolerance to microcystin-producing cyanobacteria have limited effects on the eco-evolutionary dynamics between Daphnia and phytoplankton.</li> </ol>

Photophysiological response of autumn phytoplankton in the Antarctic Sea-Ice Zone

The datasets in this repository are part of the manuscript entitled "Photophysiological response of autumn phytoplankton in the Antarctic Sea-Ice Zone".

opencc-by-4.0Oct 2021View details →

Supporting data for ``Summer-Winter Contrast in the Response of Precipitation Extremes to Climate Change over Northern Hemisphere Land'"

Here we have the processed data used in the preprint ``'Summer-Winter Contrast in the Response of Precipitation Extremes to Climate Change over Northern Hemisphere Land'' The README.md file includes explanations about the data in the repository.

openmit-licenseDec 2016View details →

Strong piezoelectric response in stable TiZnN2, ZrZnN2, and HfZnN2 found by ab initio high-throughput approach

The phase diagrams of the Ti-Zn-N, Zr-Zn-N, and Hf-Zn-N systems are determined using large-scale high-throughput density functional calculations. In total 12,815 relaxed structures are shared alongside their energy calculated using the VASP DFT code. The High-Throughput Toolkit was used to manage the calculations. A README file is included that describes how to load the data and the contents of the DataFrame.

opencc-zeroAug 2022View details →

Data for: Growing faster, longer or both? Modelling plastic response of Juniperus communis growth phenology to climate change

Aim: Plant growth and phenology plastically respond to changing climatic conditions both in space and time. Species-specific levels of growth plasticity determine biogeographical patterns and the adaptive capacity of species to climate change. However, a direct assessment of spatial and temporal variability in radial-growth dynamics is complicated, as long records of cambial phenology do not exist. Location: 16 sites across European distribution margins of Juniperus communis L. (the Mediterranean, the Arctic, the Alps and the Urals). Time period: 1940-2016 Major taxa studied: Juniperus communis Methods: We applied the Vaganov-Shashkin process-based model of wood formation to estimate trends in growing season duration and growth kinetics since 1940. We assumed that J. communis would exhibit spatially and temporally variable growth patterns reflecting local climatic conditions. Results: Our simulations indicate regional differences in growth dynamics and plastic responses to climate warming. Mean growing season duration is the longest at Mediterranean sites and, recently, there is a significant trend towards its extension of up to 0.44 days per year. However, this stimulating effect of longer growing season is counteracted by declining summer growth rates caused by amplified drought stress. Consequently, overall trends in simulated ring-widths are marginal in the Mediterranean. By contrast, durations of growing seasons in the Arctic show lower and mostly non-significant trends. However, spring and summer growth rates follow increasing temperatures, leading to a growth increase of up to 0.32 % per year. Main conclusions: This study highlights the plasticity in growth phenology of widely distributed shrubs to climate warming–an earlier onset of cambial activity that offsets the negative effects of summer droughts in the Mediterranean and, conversely, an intensification of growth rates during the short growing seasons in the Arctic. Such plastic growth responsiveness allows woody plants to adapt to the local pace of climate change.

Linear rheology of liquid foam - data from "Delayed elastic contributions to the viscoelastic response of foams"

Linear rheological data of Gillette shaving cream "normal skin" made by Gillette UK LTD, acquired at the Department of Physics, University of Fribourg, Switzerland, between 2019 and 2022. Dataset contains elastic modulus, creep-recovery, stress relaxation, and frequency sweep experimental data, together with model data, as described in "Delayed elastic contributions to the viscoelastic response of foams", The Journal of Chemical Physics, 2022, published in the special issue Slow Dynamics [DOI: 10.1063/5.0085773].

Data for manuscript: Ecological lags govern the pace and outcome of plant community responses to 21st century climate change

These data were used in the analyses reported in Block et al. "Ecological lags govern the pace and outcome of plant community responses to 21st century climate change".

ESMARConf2022 evaluation responses and interaction statistics

Responses to the ESMARConf2022 post-event evaluation for participants and presenters, statistics for the ESMARConf website (https://esmarconf.github.io), and YouTube channel viewing data for ESMARConf2021.

opencc-zeroMar 2022View details →

Stability of rocky intertidal communities in response to species removal varies across spatial scales

Improving our understanding of stability across spatial scales is crucial in the current scenario of biodiversity loss. Still, most empirical studies of stability target small scales. Here we experimentally removed the local space-dominant species (macroalgae, barnacles, or mussels) at eight sites spanning more than 1000 km of coastline in north- and south-central Chile, and quantified the relationship between area (the number of aggregated sites) and stability in aggregate community variables (total cover) and taxonomic composition. Resistance, recovery, and invariability increased nonlinearly with area in both functional and compositional domains. Yet, the functioning of larger areas achieved a better, albeit still incomplete, recovery than composition. Compared with controls, smaller disturbed areas tended to overcompensate in terms of total cover. These effects were related to enhanced available space for recruitment (resulting from the removal of the dominant species), and to increasing beta diversity and decaying community-level spatial synchrony (resulting from increasing area). This study provides experimental evidence for the pivotal role of spatial scale in the ability of ecosystems to resist and recover from chronic disturbances. This knowledge can inform further ecosystem restoration and conservation policies.

opencc-by-4.0Feb 2021View details →

Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response

We performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant Ny‐1-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. This dataset s a deposit of all the raw microscopy images of the study, plus the relevant metadata in ISA-tab compliant folder structure.  After receiving reviews, we have made an additional experiment using a ROS inhibitor. The raw and processed data for this is in a separate file: _S_chlROS_inhibitor.zip   Additional information about the microscopy images in this data deposit <ol> <li>Images of which name ends with ch00/ch01/ch02 are maximum projections from Z-stacks for each ROI for each of three channels: chlorophyll fluorescence (ch00), GFP fluorescence after excitation with 405 nm laser line (ch01) and GFP fluorescence after excitation with 488 laser line (ch02), exported from Leica LAS X software.</li> <li>Only mesophyll cells are included in z-stack, except for the experiments with GFP-tagged PVY where additional z-stacks including  both mesophyll and epidermal cells were produced ( »_2« added in the image name, see images with the comment »epidermal cells included in z-stack« in S_PhenodataRedox).</li> <li>Images of which name ends with ch00.tif and ch00.tif_ratio are analysed images, obtained using in-house Matlab script. These images were obtained by the analysis of ch00/ch01/ch02 images with the following steps: conversion to grayscale, filtering out pixels of low intensity, conversion to binary format using spatial adaptive thresholding, a round or erosion and dilation to remove single pixel noise around the chloroplasts, followed by size-based segmentation of individual chloroplasts. The ratios of fluorescence intensities 405/488 were then calculated for each pixel belonging to the chloroplast masks obtained in the previous step. Results were calculated per image (normalized to the fraction of pixels belonging to chloroplasts) and per individual chloroplast in each image.</li> <li>In the experiments with GFP-tagged PVY, due to high background signal in the cell death zone as a result of virus derived GFP fluorescence, signal in the 488 channel and 405/488 ratio (images named »scaled 488« and »405/488 in chloroplasts« in ch00.tif_ratio) in the cell death zone are not accurate.</li> <li>Figures of which name ends with ch00.tif_spatial_ROI1/ROI2 show the 405/488 ratios in ROI1 or ROI2, determined for each pixel inside chloroplast masks for each Bin. See Image analysis in Methods for details.</li> <li>Experiment names and image names correspond to the names in S_PhenodataRedox. Details regarding experimental set-up and transgenic lines used are specified in S_PhenodataRedox.</li> </ol> The Zenodo_reanalysis.zip file contains processed microscopic images in a new red/blue colormap.

opencc-by-4.0Apr 2022View details →

Dataset for pupil response measurements for trustworthiness

Data file name: trustpupil.csv  Data labels photo_num =stimulus number 1–81 age (participants’ age) deception: 0–24 (deception score) Flanders: -10–10 (handedness score) Side: l or r (posing direction) trust_iris: iris diameter of trustworthy face in pixel trust_pupil: pupil diameter of trustworthy face in pixel neutral_iris: iris diameter of neutral face in pixel neutral_pupil: pupil diameter of neutral face in pixel    "-" stands for "unmeasured" reason: reason for unmeasurement

Prosociality as response to slow- and fast-onset climate hazards

This repository contains the information videos used in the treatments, as well as the data and code that replicates tables and figures for the following paper: Title: Prosociality as response to slow- and fast-onset climate hazards Authors: Ivo Steimanis1 & Björn Vollan1,* Affiliations: 1 Department of Economics, Philipps University Marburg, 35032 Marburg, Germany *Correspondence to: Björn Vollan <a href="mailto:bjoern.vollan@wiwi.uni-marburg.de">bjoern.vollan@wiwi.uni-marburg.de</a> ORCID: Steimanis: 0000-0002-8550-4675; Vollan: 0000-0002-5592-4185 Classification: Social Sciences, Economic Sciences Keywords: climate hazards, prosociality, in-group favoritism, antisociality

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-zeroApr 2022View details →

Differences in dogs' event related potentials in response to human and dog vocal stimuli: A non-invasive study

Recent advances in the field of canine neuro-cognition allow for the non-invasive research of brain mechanisms in family dogs. Considering the striking similarities between dog's and human (infant)'s socio-cognition at the behavioural level, both similarities and differences in neural background can be of particular relevance. The current study investigates brain responses of N=17 family dogs to human and conspecific emotional vocalisations using a fully non-invasive ERP paradigm. We found that similarly to humans, dogs show a differential ERP response depending on the species of the caller demonstrated by a more positive ERP response to human vocalisations compared to dog vocalisations in a time-window between 250-650 ms after stimulus onset. A later time-window between 800-900 ms also revealed a valence sensitive ERP response in interaction with the species of the caller. Our results are the first ERP evidence to show the species sensitivity of vocal neural processing in dogs along with indications of valence sensitive processes in later post-stimulus time-periods.

opencc-by-4.0Nov 2019View details →

Fig. 5. The marginal response curve for the explanatory variable Bio14 in Modelling The Bioclimatic Niche And Distribution Of The Steppe Mouse, Mus Spicilegus (Rodentia, Muridae), In Ukraine

Fig. 5. The marginal response curve for the explanatory variable Bio14 (Precipitation of driest week). (HS — habitat suitability).

opencc-by-4.0Nov 2019View details →

Fig. 4. The marginal response curve for the explanatory variable Bio09 in Modelling The Bioclimatic Niche And Distribution Of The Steppe Mouse, Mus Spicilegus (Rodentia, Muridae), In Ukraine

Fig. 4. The marginal response curve for the explanatory variable Bio09 (Mean temperature of driest quarter). (HS — habitat suitability).

MR Gradient System Long-Term Stability Investigation and Protocol Optimization for Quality Control using Gradient Impulse Response Function (GIRF)

The dataset of the abstract "MR Gradient System Long-Term Stability Investigation and Protocol Optimization for Quality Control using Gradient Impulse Response Function (GIRF)" for ISMRM 2022, London, UK. The data processing code with instructions could be found <a href="https://github.com/BRAIN-TO/girfISMRM2022">here</a>.   Meas1.zip and Meas2.zip contain the first and the second measurements of the raw T2* decay signal acquired with the phantom-based method. Note that the coil dimension has been averaged to save data volume for demonstration purposes. This will lead to a lower SNR of the calculated output gradient and GIRF.   CalculatedGIRF.zip provides the author's pre-calculated GIRFs using the data without coil averaging. This data is used for all the postprocessing (e.g. SNR and stability analysis, etc.) in the published abstract with the source code provided in the same Github repository.