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837
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837 results for “associational effects”
Effects of cold or warm ischemia and ex-vivo lung perfusion on the release of damage associated molecular patterns and inflammatory cytokines in experimental lung transplantation
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Data from: Effects of landscape complexity on pollinators are moderated by pollinators’ association with mass-flowering crops
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Data from: Female Salix viminalis are more severely infected by Melampsora spp. but neither sex experiences associational effects
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Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)
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Data from: The balance of canopy and soil effects determines intraspecific differences in foundation species’ effects on associated plants
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Data from: Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta)
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Data for: Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition
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Data from: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation
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Data for: Wild bees and landcover: bee species’ body size does not predict the scale of effect, but bee phenology predicts association with landcover type
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Cost-effectiveness of preventative care for perinatal anxiety and associated disorders: A rapid review
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Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding
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Some neighbors are better than others: variation in associational effects among plants in an old field community
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Data associated with: Minor genetic consequences of a major mass mortality: Short-term effects in Pisaster ochraceus
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Dataset associated with the manuscript titled "Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans"
<p>The dataset is a part of the supporting information of the <a href="https://chayast.github.io/frag-manuscript/#fragmentation-schemes-can-be-assessed-by-their-ability-to-preserve-the-chemical-environment-while-minimizing-fragment-size">fragmenter manuscript</a>, which also describes how this dataset was generated in more detail.</p> <p>This dataset includes all fragments generated from 730 FDA approved molecule without fragmenting rings.</p> <p>Scripts used to generate this set live <a href="https://github.com/choderalab/fragmenter_data/tree/master/combinatorial_fragmentation">here</a>.</p> <p>1. Filter DrugBank with the following criteria:<br> 1. FDA approved<br> 2. Largest ring size has less than 14 heavy atoms<br> 3. Smallest ring size has at least 3 heavy atoms<br> 4. Molecule has less than 10 rotatable bonds<br> 5. Molecule must have at least one aromatic ring<br> 6. Molecule has only one connected component<br> 2. Enumerate tautomers at physiological pH (this step generated 1243 molecules)<br> 3. Exhaustive fragmentation without fragmenting rings (~300,000 fragments)<br> 4. Generate conformations for each fragment using Omega<br> 5. Calculate AM1 WBO for each conformation </p>
Data from: Canalisation in the wild: effects of developmental conditions on physiological traits are inversely linked to their association with fitness
Ecological conditions affect fitness, but mechanisms causing such effects are not well known, while evolved responses to environmental variation may depend on the underlying mechanisms. Consequences of environmental conditions vary strongly between traits, but a framework to interpret such variation is lacking. We propose that variation in trait response may be explained by differential canalisation, with traits with larger fitness effects showing weaker responses to environmental perturbations due to preferential resource allocation to such traits. We tested the canalisation hypothesis using brood size manipulation in wild jackdaw nestlings in which we measured eight physiological traits (mainly oxidative stress markers), and two feather traits. For each trait, we estimated manipulation response and association with fitness (over-winter survival). As predicted, a strong negative correlation emerged between manipulation response and association with fitness (r=-0.76). We discuss the consequences of differential trait canalization for the study of mechanisms mediating environmental effects on fitness.
Data from: Effects of parasitic sex-ratio distorters on host genetic structure in the Armadillidium vulgare-Wolbachia association
In the pill bug Armadillidium vulgare (Crustacea, Oniscidea) Wolbachia facilitates its spread through vertical transmission via the eggs by inducing feminization of genetic males. The spread of feminizing Wolbachia within and across populations is therefore expected to influence mtDNA genetic structure by hitchhiking. To test this hypothesis, we analysed nuclear and mtDNA genetic structure, and Wolbachia prevalence in 13 populations of the pill bug host. Wolbachia prevalence (ranging from 0 to 100% of sampled females) was highly variable among populations. All three Wolbachia strains previously observed in A. vulgare were present (wVulC, wVulM and wVulP) with wVulC being the most prevalent (9 out of 13 populations). The host showed a genetic structure on five microsatellite loci that is compatible with isolation by distance. The strong genetic structure observed on host mtDNA was correlated to Wolbachia prevalence: three mitotypes were in strong linkage disequilibrium with the three strains of Wolbachia. Neutrality tests showed that the mtDNA polymorphism is not neutral and we thus suggest that this unusual pattern of mtDNA polymorphism found in A. vulgare was due to Wolbachia.
Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses
Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotype. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, but also 83,290 markers for marker-by-ecotype interactions and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected based on marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for carbon content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected based on pairwise marker correlations. Furthermore, one marker-by-ecotype interaction and one pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits in switchgrass. Moreover, they exemplified the importance of interactive effects for the depiction of genetic bases, and illustrated the usefulness of preselection of marker pairs for identifying pairwise marker interactions in association testing.
Data from: Mating affects resource selection and modulates associational effects between neighbouring resources
Associational effects occur when the attack rate on a resource depends on neighbouring resources in the environment. These effects are predicted to result from mismatches experienced by the consumer organism in resource selection along hierarchical search levels. As resource selection depends on sensory information used during search behaviour, we expected that different physiological states of an insect might modulate the outcome of associational effects due to differences in resource selection. We used Drosophila melanogaster, as a model organism for olfactory-guided behaviour in insects, to study the effects of mating induced behavioural changes on associational effects between two alternative resources. We found that mating has no effect on the ability of D. melanogaster to locate resource patches, but rather affects the perception of the resources within the patch. Consequently, we only found associational effects in the experiments with unmated females and not in the experiments with mated females. Our results suggest that the lack of associational effects for mated females resulted from changes in the use of short-range olfactory cues, leading to random selection among the resources. In conclusion, our results suggest that the physiological state of an insect modulates associational effects by affecting resource selection rates within the patch.
Data from: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expression
Many species exhibit transgenerational plasticity by which environmental cues experienced by either parent can be transmitted to their offspring, resulting in phenotypic variants in offspring to match ancestral environments. However, the manner by which paternal experiences affect offspring plasticity through epigenetic inheritance in animals generally remains unclear. In this study, we examined the transgenerational effects of population density on phase-related traits in the migratory locust Locusta migratoria. Using an experimental design that explicitly controls genetic background, we found that the effects of crowd or isolation rearing on phase plasticity could be inherited to the offspring. The isolation of gregarious locusts resulted in reduced weight in offspring eggs and altered morphometric traits in hatchlings, whereas crowding of solitarious locusts exhibited opposite effects. The consequences of density changes were transmitted by both maternal and paternal inheritance, although the expression of paternal effects was not as pronounced as that of maternal effects. Prominent expression of heat-shock proteins (Hsps), such as Hsp90, Hsp70, and Hsp20.6, could be triggered by density changes. Hsps were significantly upregulated upon crowding but downregulated upon isolation. The variation in parental Hsp expression was also transmitted to the offspring, in which the pattern of inheritance was consistent with that of phase characteristics. These results revealed a paternal effect on phase polyphenism and Hsp expression induced by population density, and defined a model system that could be used to study the paternal epigenetic inheritance of environmental changes.
Data from: Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.