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opencc-by-4.0Apr 2020View details →

Natural variation across Arabidopsis diversity panel in early responses to salt stress

The data of Arabidopsis thaliana accessions which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic.

opencc-by-4.0Apr 2020View details →

Spatially corrected dataset for natural variation across Arabidopsis diversity panel in early responses to salt stress

The spatially corrected data of Arabidopsis thaliana accessions, which were grown according to the established protocol for studying salt stress in soil experiment (described in detail here dx.doi.org/10.17504/protocols.io.4xzgxp6), in the PSI facility, Czech Republic. The spatial correction was done using the asreml package. The data was subsequently used for the Genome-Wide Association Study.

opencc-by-4.0Jan 2021View details →

Variational Inference for Learning Representations of Natural Language Edits

Performance Evaluation of Edit Representations (PEER), the dataset we use in the paper <a href="https://arxiv.org/abs/2004.09143">"Variational Inference for Learning Representations of Natural Language Edits"</a>.

opencc-zeroOct 2016View details →

Leaf growth response to mild drought: natural variation sheds light on trait architecture

Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The raw phenotyping can be found in: - cellularData.txt -> mature (23 days after stratification; DAS) leaf epidermis (third leaf) analysed for cell area, cell number, pavement cell area, pavement cell number, stomatal index and leaf area of the analysed leaf. - leaf3AreaMaturity.txt -> area of the third leaf at maturity (23DAs) in mm2. - leaf3AreaProliferation.txt -> area of the third leaf at proliferation (last day of full cell proliferation; 8-10 DAS) in mm2. - rosetteArea Maturity.txt -> projected rosette area at maturity (22DAS) The phenotyping results have been normalised for batch effects ('experiment' in raw data) - allPhenotypesNormalised.txt -> contains the normalised data for all the measured phenotypes All datafiles indicate the accession name ('Accession'), the unique identifier for each accessions ('Ecotype_ID') as used in the 1001genomes project (www.1001genomes.org) and the treatment ('C' indicate well-watered plants, 'S' the mild-drought treated plants). These results and methodological results are described in Clauw et al. (2016, The Plant Cell). Citation: Clauw, Pieter, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, et al. 2016. “Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture.” The Plant Cell, October. doi:10.1105/tpc.16.00483.

opencc-by-4.0Nov 2024View details →

Diversity of radial variations of wood properties in European beech reveals the plastic nature of juvenile wood - Dataset

The long-term (as opposed to short-term intra-ring) radial variation of wood properties in European beech (Fagus sylvatica L.) from pith to bark are largest in the young ages of the tree (internal core). This so-called juvenility reflects both cambium ageing (ontogenetic juvenility) and adaptation to the changing mechanical constraints during secondary growth (adaptive juvenility). Ring width (RW), specific gravity (SG) and specific modulus (SM) are important parameters for each new wood layer, needed for the study of mechanical stability of a standing tree. They should be sensitive to the mechanical adaptation of growth. They were measured on diametrical boards (North/South direction) issued from 86 trees from several high forest stands in European countries. Analysis of variance showed very significant influence of position within the tree (core/external), of trees within a plot and of plots, but not for North/South orientation. The share of variance was similar for SG and SM (importance of tree effect) but different for RW (importance of plot effect). The occurrence of red heartwood in the core on some trees had a significant influence, mostly on SM, but the differences between white and red wood was very small. Globally the variability was high for RW, rather small for SM and very small for SG. Accordingly, the variations of the modulus of elasticity (product of SG and SM) were much more influenced by SM than by SG for beech. The radial variations of each parameter were fitted by both a linear (2 coefficients: zero value and mean slope) and a parabolic curve (3 coefficients: zero value, initial slope and curvature). They were used to classify types or radial profile in terms of flat, up & down and straight, convex & concave. Median values of coefficients per plot (or total) were used to draw median profiles for each parameter per plot and at the global level. The median global profiles differed from the typical radial pattern (TRP) of juvenility for plantation softwoods for SG (down concave instead of up concave) and SM (convex like TRP but with a clear decrease in the mature wood). The main result was the very large variability of profiles between trees or even between plots. Even if there is a part of ontogenetic influence in the juvenile patterns for RW, SG and SM, the results suggest that the influence of mechanical constraints on tree growth (adaptive juvenility) dominates largely.  The provided file contains the data and the sheets developped to analyse them. It serves as supplementary material for the related paper submitted for recommendation to the PCI Forest and Wood Science.

opencc-zeroDec 2021View details →

Visual discomfort and variations in chromaticity in art and nature

Visual discomfort is related to the statistical regularity of visual images. The contribution of luminance contrast to visual discomfort is well understood and can be framed in terms of a theory of efficient coding of natural stimuli, and linked to metabolic demand. While colour is important in our interaction with nature, the effect of colour on visual discomfort has received less attention. In this study, we build on the established association between visual discomfort and differences in chromaticity across space. We average the local differences in chromaticity in an image and show that this average is a good predictor of visual discomfort from the image. It accounts for part of the variance left unexplained by variations in luminance. We show that the local chromaticity difference in uncomfortable stimuli is high compared to that typical in natural scenes, except in particular infrequent conditions such as the arrangement of colourful fruits against foliage. Overall, our study discloses a new link between visual ecology and discomfort whereby discomfort arises when adaptive perceptual mechanisms are overstimulated by specific classes of stimuli rarely found in nature.

opencc-by-4.0Dec 2021View details →

Natural variation in Drosophila shows weak pleiotropic effects

Pleiotropy is the phenomenon that a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of power issues. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy, which integrates across many phenotypes and multiple generations to improve power. We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each with weak effects, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy were reduced by the modular architecture of gene expression, which facilitated adaptive gene expression changes with low impact on other functions.

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

opencc-by-4.0Jun 2010View details →

Figure 2: Variation of the shear stress depending on the speed rate 54-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES

The evaluation of photodegradation was carried out through the variation of photoprotective factor of the studied product kept 60 minutes under UV radiation at 65±C. The tests revealed the preservation or even a slight increase in the SPF. The use of screen substances in the formulation of photoprotective products results in undesirable sensory characteristics: visible white ¯lm on the skin surface, unpleasant sensation, dry or oily skin after application.

opencc-by-4.0Jun 2010View details →

Figure 3: Viscosity variation depending on speed rate Table-STUDIES TOWARDS OBTAINING A PHOTOPROTECTIVE DERMO-COSMETIC COMPLEX PRODUCT WITH NATURAL EXTRACTS OF INORGANIC AND ORGANIC SUBSTANCES-

Microbiological characteristics The total number of aerobic germs and fungi was determined by the decimal dilution method or the multiple tube test. For identifying pathogenic species we have used speci¯c tests (table6). The evaluation of photodegradation was carried out through the variation of photoprotective factor of the studied product kept 60 minutes under UV radiation at 65±C. The tests revealed the preservation or even a slight increase in the SPF. The use of screen substances in the formulation of photoprotective products results in undesirable sensory characteristics: visible white ¯lm on the skin surface, unpleasant sensation, dry or oily skin after application.

opencc-by-4.0Sep 2024View details →

Pre-existing natural variations of adult neurogenesis and anxiety predict hierarchical social status of inbred male mice.

CVS files and image files of all data presented in the correcponding figures.

opencc-zeroApr 2023View details →

Data for: Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster

Fertility is a major component of fitness but its genetic architecture remains poorly understood. Using a full diallel cross of 50 Drosophila melanogaster Genetic Reference Panel inbred lines with whole genome sequences, we found substantial genetic variation in fertility largely attributable to females. We mapped genes associated with variation in female fertility by genome-wide association analysis of common variants in the fly genome. Validation of candidate genes by RNAi knockdown confirmed the role of the dopamine 2-like receptor (Dop2R) in promoting egg laying. We replicated the Dop2R effect in an independently collected productivity dataset and showed that the effect of the Dop2R variant was mediated in part by regulatory gene expression variation. This study demonstrates the strong potential of genome-wide association analysis in this diverse panel of inbred strains and subsequent functional analyses for understanding the genetic architecture of fitness traits.

opencc-by-4.0Jul 2023View details →

Experimental Results for "A Unified Perspective on Natural Gradient Variational Inference with Gaussian Mixture Models"

This package contains the raw data / logs (fetched from WandB) for the experiments of the following publication: O. Arenz, P. Dahlinger, Z. Ye, M. Volpp, and G. Neumann. A unified perspective on natural gradient variational inference with gaussian mixture models. Transactions on Machine Learning Research, 2023. URL: <a href="https://openreview.net/forum?id=tLBjsX4tjs">https://openreview.net/forum?id=tLBjsX4tjs</a>.

publicApr 2023View details →

Data for: Natural genetic variation in a dopamine receptor is associated with variation in female fertility in Drosophila melanogaster

Open the record for dataset details and reuse information.

publicDec 2021View details →

Visual discomfort and variations in chromaticity in art and nature

Open the record for dataset details and reuse information.

opencc-zeroOct 2020View details →

Using ecological context to interpret spatiotemporal variation in natural selection

Spatiotemporal variation in natural selection is expected, but difficult to estimate. Pollinator-mediated selection on floral traits provides a good system for understanding and linking variation in selection to differences in ecological context. We studied pollinator-mediated selection in five populations of Dalechampia scandens (Euphorbiaceae) in Costa Rica and Mexico. Using a nonlinear path-analytical approach, we assessed several functional components of selection, and linked variation in pollinator-mediated selection across time and space to variation in pollinator assemblages. After correcting for estimation error, we detected moderate variation in net selection on two of four blossom traits. Both the opportunity for selection and the mean strength of selection decreased with increasing reliability of cross-pollination. Selection for pollinator attraction was consistently positive and stronger on advertisement than reward traits. Selection on traits affecting pollen transfer from the pollinator to the stigmas was strong only when there was a mismatch between pollinator and blossom size under unreliable cross-pollination. These results illustrate how consideration of trait function and ecological context can facilitate both the detection and the causal understanding of spatiotemporal variation in natural selection.

opencc-zeroNov 2020View details →

Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments

Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.

opencc-zeroSep 2019View details →

Data from: Corralling a black swan: natural range of variation in a forest landscape driven by rare, extreme events

The natural range of variation (NRV) is an important reference for ecosystem management, but has been scarcely quantified for forest landscapes driven by infrequent, severe disturbances. Extreme events such as large, stand-replacing wildfires at multi-century intervals are typical for these regimes; however, data on their characteristics are inherently scarce, and, for land management, these events are commonly considered too large and unpredictable to integrate into planning efforts (the proverbial 'Black Swan'). Here, we estimate the NRV of late-seral (mature/old-growth) and early-seral (post-disturbance, pre-canopy-closure) conditions in a forest landscape driven by episodic, large stand-replacing wildfires: the Western Cascade Range of Washington, USA (2.7 million ha). These two seral stages are focal points for conservation and restoration objectives in many regions. Using a state-and-transition simulation approach incorporating uncertainty, we assess the degree to which NRV estimates differ under a broad range of literature-derived inputs regarding: a) overall fire rotations, and b) how fire area is distributed through time – as relatively frequent smaller events (less episodic), or fewer but larger events (more episodic). All combinations of literature-derived fire rotations and temporal distributions (i.e. 'scenarios') indicate that the largest wildfire events (or episodes) burned up to 10^5-10^6 hectares. Under most scenarios, wildfire dynamics produced 5th-95th percentile ranges for late-seral forests of ~47-90% of the region (median 70%), with structurally complex early-seral conditions composing ~1-30% (median 6%). Fire rotation was the main determinant of NRV, but temporal distribution was also important, with more episodic (temporally clustered) fire yielding wider NRV. In smaller landscapes (20,000 ha; typical of conservation reserves and management districts), ranges were 0-100% because fires commonly exceeded the landscape size. Current conditions are outside the estimated NRV, with the majority of the region instead covered by dense mid-seral forests (i.e. a regional landscape with no historical analog). Broad consistency in NRV estimates among widely varied fire regime parameters suggests these ranges are likely relevant even under changing climatic conditions, both historical and future. These results indicate management-relevant NRV estimates can be derived for seral stages of interest in extreme-event landscapes, even when incorporating inherent uncertainties in disturbance regimes.