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3,121 results for “Resources”
GREEN-VARAN SV annotation resources
<p>This dataset contains a collection of BED files prepared to be used with the SV_annotation tool, part of GREEN-VARAN.</p> <p><strong>GREEN-DB regions</strong></p> <p>Regulatory regions collected in GREEN-DB (see <a href="https://github.com/edg1983/GREEN-VARAN">https://github.com/edg1983/GREEN-VARAN</a>)</p> <p><strong>Population AF annotations</strong></p> <p>These files represent SVs from gnomAD v.2.1.1, 1000G phase3, and the IMH dataset. When not directly available, the GRCh38 versions are obtained by coordinates liftover from GRCh37.</p> <p>If you use AF annotations don't forget to cite also the original papers:</p> <ul> <li>gnomAD paper as described in <a href="https://gnomad.broadinstitute.org/terms">https://gnomad.broadinstitute.org/terms</a></li> <li>1000G SV paper: <a href="https://www.nature.com/articles/nature15394">https://www.nature.com/articles/nature15394</a></li> <li>the original IMH publication <a href="https://www.nature.com/articles/s41586-020-2371-0">https://www.nature.com/articles/s41586-020-2371-0</a></li> </ul> <p><strong>Gene annotations</strong></p> <p>Genes and CDSs annotations are from GENCODE v33 basic set</p>
Data from: Climate, soil resources and microbial activity shape the distributions of mountain plants based on their functional traits
<p>While soil ecosystems undergo important modi cations due to global change, the e ect of soil properties on plant distributions is still poorly understood. Plant growth is not only controlled by soil physico-chemistry but also by microbial activities through the decomposition of organic matter and the recycling of nutrients essential for plants. A growing body of evidence also suggests that plant functional traits modulate spe- cies' response to environmental gradients. However, no study has yet contrasted the importance of soil physico-chemistry, microbial activities and climate on plant species distributions, while accounting for how plant functional traits can in uence species- speci c responses.</p> <p>Using hierarchical e ects in a multi-species distribution model, we investigate how<br> four functional traits related to resource acquisition (plant height, leaf carbon to nitro-<br> gen ratio, leaf dry matter content and speci c leaf area) modulate the response of<br> 44 plant species to climatic variables, soil physico-chemical properties and microbial 100 decomposition activity (i.e. exoenzymatic activities) in the French Alps.</p> <p>Our hierarchical trait-based model allowed to predict well 41 species according to the TSS statistic. In addition to climate, the combination of soil C/N, as a measure of organic matter quality, and exoenzymatic activity, as a measure of microbial decom- position activity, strongly improved predictions of plant distributions. Plant traits played an important role. In particular, species with conservative traits performed bet- ter under limiting nutrient conditions but were outcompeted by exploitative plants in more favorable environments.</p> <p>We demonstrate tight associations between microbial decomposition activity, plant functional traits associated to di erent resource acquisition strategies and plant dis- tributions. is highlights the importance of plant–soil linkages for mountain plant distributions. ese results are crucial for biodiversity modelling in a world where both climatic and soil systems are undergoing profound and rapid transformations.</p>
GREEN-VARAN scores resources (PhyloP100)
<p>This dataset contains processed BED files for the PhyloP100 conservation values to be used with GREEN-VARAN annotation tool.</p> <p>PhyloP100 values are available for GRCh37 and GRCh38 genome builds.</p> <p> </p>
European Language Resources Initiatives – Infrastructural and Policy Issues
<p>3<sup>rd </sup>Lecture</p>
Considering institutional type: a varieties of capitalism approach to the economic growth resource curse
<p>Defined by North (1994) as the "rules of the game", over the last few decades, many scholars have sought to understand whether quality institutions can alleviate the Resource Curse (the idea that natural resource abundance hinders rather than promotes economic growth). However, with this focus on quality, few papers have addressed the question of institutional type, and its Curse mitigating properties. This paper, via utilising the associated data, contributes towards filling this gap. Using the Varieties of Capitalism framework, we test whether certain institutional typologies possess the ability to mitigate the Resource Curse and perhaps even turn it into a blessing. Specifically, Rougier and Combarnous' cluster analysis, "The Diversity of Emerging Capitalisms in Developing Countries" (2017), whereby nations are assigned various institutional typologies is used to create our primary (dummy) independent variables of interest in this study. The remaining control variables essential for economic growth analysis are collected via the World Bank and Polity datasets.</p>
Data from: Climate-driven prediction of land water storage anomalies: An outlook for water resources monitoring across the conterminous United States
<p>These research data are associated with the manuscript entitled "Climate-driven prediction of land water storage anomalies: An outlook for water resources monitoring across the conterminous United States" (<a href="https://doi.org/10.1016/j.jhydrol.2020.125053" title="Persistent link using digital object identifier"><span>https://doi.org/10.1016/j.jhydrol.2020.125053</span></a>). The study focused on the conterminous United States (CONUS) which extends over a region of contrasting climates with an uneven distribution of freshwater resources. Under climate change, an exacerbation of the contrast between dry and wet regions is expected across the CONUS and could drastically affect local ecosystems, agriculture practices, and communities. Hence, efforts to better understand long-term spatial and temporal patterns of freshwater resources are needed to plan and anticipate responses. Since 2002, the Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On (GRACE-FO) satellite observations provide estimates of large-scale land water storage changes with an unprecedented accuracy. However, the limited lifetime and observation gaps of the GRACE mission have sparked research interest for GRACE-like data reconstruction. This study developed a predictive modeling approach to quantify monthly land liquid water equivalence thickness anomaly (LWE) using climate variables including total precipitation (PRE), number of wet day (WET), air temperature (TMP), and potential evapotranspiration (PET). The approach builds on the achievements of the GRACE mission by determining LWE footprints using a multivariate regression on principal components model with lag signals. The performance evaluation of the model with a lag signals consideration shows 0.5 ≤ R<sup>2</sup><span><span><span><span><span><span><span><span> ≤ 0.8 for 41.2% of the CONUS. However, the model's predictive power is unevenly distributed. The model could be useful for predicting and monitoring freshwater resources anomalies for the locations with high model performances.</span></span></span></span></span></span></span></span> The processed data used as inputs in the study are here provided including the GIS files of the different maps reported.</p>
SLURP: A Spoken Language Understanding Resource Package
<p>This resource contains supplementary audio material used in our EMNLP 2020 paper where we release SLURP, a new SLU package containing the following: (1) A new challenging dataset in English spanning 18 domains, which is substantially bigger and linguistically more diverse than existing datasets; (2) Competitive baselines based on state-of-the-art NLU and ASR systems; (3) A new transparent metric for entity labelling which enables a detailed error analysis for identifying potential areas of improvement. Textual annotations are released via the corresponding Github repository (for ease of maintenance).</p>
Spatially anonymized data for: Multistate Ornstein-Uhlenbeck approach for practical estimation of movement and resource selection around central places
<p>1. Home range dynamics and movement are central to a species' ecology and strongly mediate both intra- and interspecific interactions. Numerous methods have been introduced to describe animal home ranges, but most lack predictive ability and cannot capture effects of dynamic environmental patterns, such as the impacts of air and water flow on movement.</p> <p>2. Here, we develop a practical, multi-stage approach for statistical inference into the behavioral mechanisms underlying how habitat and dynamic energy landscapes---in this case how airflow increases or decreases the energetic efficiency of flight---shape animal home ranges based around central places. We validated the new approach using simulations, then applied it to a sample of 12 adult golden eagles (Aquila chrysaetos) tracked with satellite telemetry. </p> <p>3. The application to golden eagles revealed effects of habitat variables that align with predicted behavioral ecology. Further, we found that males and females partition their home ranges dynamically based on uplift. Specifically, changes in wind and sun angle drove differential space use between sexes, especially later in the breeding season when energetic demands of growing nestlings require both parents to forage more widely. </p> <p>4. This method is easily implemented using widely available programming languages and is based on a hierarchical multistate Ornstein-Uhlenbeck space use process that incorporates habitat and energy landscapes. The underlying mathematical properties of the model allow straightforward computation of predicted utilization distributions, permitting estimation of home range size and visualization of space use patterns under varying conditions.</p>
swash17/NCHRP-17-65: NCHRP 17-65 Resources
<p>Field data from CA, ID, MT, NC, OR</p>
An explorative Investigation into Neural Machine Translation: the Case of Low-Resource Language Pairs in Burkina Faso
<p>We explore the caveats of a promising research field, namely neural machine translation, in the context of preserving indigenous languages in Africa. We face the challenge of dealing with low-resource language pairs. Methodically, we employ some literature approaches and frameworks to learn translation models from Bible data in Moore (a major language in Burkina Faso) and French. Our experiments indeed confirm previous findings in the literature that vanilla neural machine translation models are ineffective for low resource language pairs. Surprisingly, however, we also found that we are not able to even remotely match performance recorded by the state of the art adapted methods for low-resource language pair in the literature. Nevertheless, although<br> word alignment, Byte Pair Encoding and Adam optimization did not successfully bring reasonable performance, we note that there are many remaining insightful approaches for low-resource language pairs.</p>
Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback
Many generalist species consist of specialized individuals that use different resources. This within-population niche variation can stabilize population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favor ecological diversity (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic and limnetic invertebrates, focusing on the former in small lakes, the latter in large lakes. Intermediate-sized lakes support generalist stickleback populations using an even mixture of the two prey types, due to greater among-individual variation in diet and morphology. In contrast, genomic diversity increases with lake size. Thus, phenotypic diversity and neutral genetic polymorphism are decoupled: trophic diversity being greatest in intermediate-sized lakes with high resource diversity, whereas neutral genetic diversity is greatest in the largest lakes.
Reproducible results for: pmparser and PMDB: resources for large-scale, open studies of the biomedical literature
<p>The zip file contains all code and results. See the included readme.</p>
Data from: Intraspecific variations in leaf traits, productivity, and resource use efficiencies in the dominant species of subalpine evergreen coniferous and deciduous broad-leaved forests along the altitudinal gradient
<p><span><span><span><span><span><span><span><span><span><span><span>Many studies have reported intraspecific variations in leaf functional traits, but their contribution to plant performance and ecosystem function are poorly understood. We studied altitudinal gradients of intraspecific variations in leaf traits, productivity, and resource use efficiency in the dominant species of subalpine evergreen coniferous and deciduous broad-leaved forests in Japan. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>We addressed three hypotheses, which are exclusive to each other. 1) Leaf traits vary along the leaf economics spectrum (LES). Plants that grow at lower and higher altitudes have fast- and slow-return strategies, respectively, which improve productivity or resource use efficiency in the respective habitat. 2) Leaf trait variations are not consistent with the LES, but they contribute to improving productivity or resource use efficiency in the respective habitat. 3) Leaf trait variations do not contribute to improving productivity or resource use efficiency at higher altitudes. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>On the studied mountain range, <i>Fagus crenata</i>, a deciduous broad-leaved tree, and <i>Abies</i><i> mariesii</i>, an evergreen conifer, are the dominant species at lower and higher altitudes, respectively. In <i>F. crenata</i>, leaf mass per area (LMA) and nitrogen concentrations were higher at higher altitudes. The net assimilation rate and light use efficiency during the growing season were greater at higher altitudes, which compensated for the shorter growing season in terms of annual productivity. In <i>A. mariesii</i>, the LMA was lower and the leaf life span was unchanged at higher altitudes. Productivity and resource use efficiency decreased with altitude. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>We conclude that <i>F. crenata</i> improves its productivity and resource use efficiency at higher altitudes by altering its leaf functional traits (Hypothesis 2), whereas alterations to leaf traits in <i>A. mariesii</i> are not associated with any improvement at higher altitudes (Hypothesis 3), which may result from the negative impact of environmental stress. Hence, the ecological significance of altitude to leaf trait variations depends on species and environment.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Resource limitation and responses to rivals in males of the fruit fly Drosophila melanogaster
Diet has a profound direct and indirect effect on reproductive success in both sexes. Variation in diet quality and quantity can significantly alter the capacity of females to lay eggs and of males to deliver courtship. Here, we tested the effect of dietary resource limitation on the ability of male Drosophila melanogaster to respond adaptively to rivals by extending their mating duration. Previous work carried out under ad libitum diet conditions showed that males exposed to rivals prior to mating significantly extend mating duration, transfer more ejaculate proteins and achieve higher reproductive success. Such adaptive responses are predicted to occur because male ejaculate production may be limited. Hence, ejaculate resources require allocation across different reproductive bouts, to balance current vs. future reproductive success. However, when males suffer dietary limitation, and potentially have fewer reproductive resources to apportion, we expect adaptive allocation of responses to rivals to be minimized. We tested this prediction and found that males held on agar-only diets for 5–7 days lost the ability to extend mating following exposure to rivals. Interestingly, extended mating was retained in males held on low yeast/sugar: no sugar/yeast diet treatments, but was mostly lost when males were maintained on 'imbalanced' diets in which there was high yeast: no sugar and vice versa. Overall, the results show that males exhibit adaptive responses to rivals according to the degree of dietary resource limitation and to the ratio of individual diet components.
Data from: Resource stoichiometry and consumers control the biodiversity-productivity relationship in pelagic metacommunities
Recent theory suggests that biodiversity and productivity are both constrained by resource supply rates and ratios, and that resource stoichiometry is the key to understand the relationship between biodiversity and productivity. We experimentally tested this theory using pelagic metacommunities. We amended existing predictions by explicitly considering evenness as biodiversity aspect and consumer instead of competitive control of algal biomass. The metacommunities received different phosphorus (P)-supply, the three patches within each metacommunity differed in nitrogen (N)-supply to create different N:P ratios (2, 16, 128). All patches were inoculated with a phytoplankton assemblage consisting of 5 species, half of the metacommunities received 2 ciliate species as consumers. At the level of the entire metacommunity, algal biomass increased whereas species richness and evenness decreased with increasing P-supply. Without consumers, resource use efficiency (RUE, realized biomass per unit P) increased with increasing richness and evenness. Consumer presence reduced overall biomass and richness and precluded a correlation between RUE and biodiversity. At the patch level, local evenness correlated to higher RUE at both imbalanced N:P ratios (2 or 128) but not at balanced N:P. In conclusion, overall P-supply constrained realized biomass and altered diversity, whereas resource stoichiometry shaped the relationship between biodiversity and RUE.
Data from: Evolution of resource use along a gradient of stress leads to increased facilitation
The stress-gradient hypothesis (SGH) posits that the relative importance of facilitative interactions versus negative interactions increases as levels of abiotic stress increase. Originally formulated in empirical studies of plant populations, in recent years the SGH has been found to describe how interactions change in response to stress in a wide range of species including algae, mussels and moths. However, there has been little theory attempting to predict patterns from first principles in relation to different types of interactions. Here, we use mathematical models of microbial populations to investigate whether patterns consistent with the SGH arise when species interact through resource use and allelopathy. Evolution alters the degree to which competition for resource use versus facilitation (cross-feeding) occurs. Our results are consistent with the SGH; species interactions evolve to be more facilitative as average stress intensifies. This occurs because at greater stress the species evolve to become specialists on either of the two resources thereby decreasing overlap in resource use and increasing facilitation through cross-feeding. In addition, the production of toxic allelopathic compounds decreases as stress intensifies due to density-dependent effects. Our results suggest that the SGH could arise through fundamental interactions that are common to many organisms and therefore that the SGH could be a more widespread phenomenon than previously recognised.
Data from: How does environment influence fighting? The effects of tidal flow on resource value and fighting costs in sea anemones
An animal's decision to enter into a fight depends on the interaction between perceived resource value (V) and fighting costs (C). Both could be altered by predictable environmental fluctuations. For intertidal marine animals, such as the sea anemone Actinia equina, exposure to high flow during the tidal cycle may increase V by bringing more food. It may also increase C via energy expenditure needed to attach to the substrate. We asked whether simulated tidal cycles would alter decisions in fighting A. equina. We exposed some individuals to still water and others to simulated tidal cycles. To gain insights into V, we measured their startle responses before and after exposure to the treatments, before staging dyadic fights. Individuals exposed to flow present shorter startle responses, suggesting that flowing water indicates high V compared with still water. A higher probability of winning against no-flow individuals and longer contests between flow individuals suggests that increased V increases persistence. However, encounters between flow individuals were less likely to escalate, suggesting that C is not directly related to V. Therefore, predictable environmental cycles alter V and C, but in complex ways.
Data from: Resource specialists lead local insect community turnover associated with temperature – analysis of an 18-year full-seasonal record of moths and beetles
Insect responses to recent climate change are well documented, but the role of resource specialization in determining species vulnerability remains poorly understood. Uncovering local ecological effects of temperature change with high-quality, standardized data provides an important first opportunity for predictions about responses of resource specialists, and long-term time series are essential in revealing these responses. Here, we investigate temperature-related changes in local insect communities, using a sampling site with more than a quarter-million records from two decades (1992–2009) of full-season, quantitative light trapping of 1543 species of moths and beetles. We investigated annual as well as long-term changes in fauna composition, abundance and phenology in a climate-related context using species temperature affinities and local temperature data. Finally, we explored these local changes in the context of dietary specialization. Across both moths and beetles, temperature affinity of specialists increased through net gain of hot-dwelling species and net loss of cold-dwelling species. The climate-related composition of generalists remained constant over time. We observed an increase in species richness of both groups. Furthermore, we observed divergent phenological responses between cold- and hot-dwelling species, advancing and delaying their relative abundance, respectively. Phenological advances were particularly pronounced in cold-adapted specialists. Our results suggest an important role of resource specialization in explaining the compositional and phenological responses of insect communities to local temperature increases. We propose that resource specialists in particular are affected by local temperature increase, leading to the distinct temperature-mediated turnover seen for this group. We suggest that the observed increase in species number could have been facilitated by dissimilar utilization of an expanded growing season by cold- and hot-adapted species, as indicated by their oppositely directed phenological responses. An especially pronounced advancement of cold-adapted specialists suggests that such phenological advances might help minimize further temperature-induced loss of resource specialists. Although limited to a single study site, our results suggest several local changes in the insect fauna in concordance with expected change of larger-scale temperature increases.
Data from: Resource availability and sexual size dimorphism: differential effects of prey abundance on the growth rates of tropical snakes
1. Broad phylogenetic patterns in sexual size dimorphism (SSD) are shaped by sex differences in net selection pressures (e.g., sexual selection, fecundity selection, survival selection), but environmental and ecological factors can also affect the expression of SSD. 2. Discussions of proximate ecological influences on SSD have focused on niche divergence; for example, increase in a prey type used by only one sex can elevate growth rates of that sex but not the other. Food limitation also can generate spatial and temporal variation in SSD. Under restricted prey abundance, curtailed growth may mask SSD even if the optimal size is greater for one sex than the other. Because an increase in food availability then elicits increased feeding and growth by the sex that benefits more from increased body size, variation in prey abundance can generate variation in SSD. 3. We used mark-recapture methods to study growth rates relative to prey (frog) abundance in two species of sexually dimorphic colubrid snake species in tropical Australia. 4. In Slatey-grey snakes (Stegonotus cucullatus), a species in which larger body size enhances reproductive output in both sexes (because larger males win combat bouts, and larger females produce more / heavier eggs), increased abundance of frogs caused equivalent increases in growth rates in both sexes, and hence did not affect SSD. In Keelbacks (Tropidonophis mairii), a species in which larger size enhances reproductive output in females more than males (reflecting a lack of male-male combat), increased abundance of frogs elicited higher growth rates of females only. Thus, SSD in Keelbacks was modified by prey abundance. 5. Our results show that the magnitude of sex differences in adult body size can be influenced by proximate environmental factors, and support the hypothesis of sex-specific targets for maximum feeding rates.
Data from: Poor resource quality lowers transmission potential by changing foraging behaviour
Resource quality can have conflicting effects on the spread of disease. High quality resources could hinder disease spread by promoting host immune function. Alternatively, high quality food might enhance the spread of disease through other traits of hosts or parasites. Thus, to assess how resource quality shapes epidemics, we need to delineate mechanisms by which food quality affects key epidemiological traits. Here, we disentangle effects of food quality on 'transmission potential' – a key component of parasite fitness that combines transmission rate and parasite production – using a zooplankton host and fungal parasite. We estimated the components of transmission potential (i.e., parasite encounter rate, susceptibility, and yield of parasite propagules) for hosts fed a high quality green alga and a low quality cyanobacterium. A focal experiment was designed to disentangle food quality effects on various components of transmission potential. The low quality resource decreased transmission potential by stunting host growth and altering foraging behaviour. Hosts reared on low quality food were smaller and had lower size-corrected feeding rates. Due to their slower grazing, they encountered fewer parasite spores in the water. Smaller hosts also had lower risk of an ingested spore causing infection (i.e., lower susceptibility), and yielded fewer parasite propagules. Hosts switched from high to low quality food during spore exposure also had low transmission potential – despite their large size – because the poor quality resource strongly depressed foraging. A follow-up experiment investigated traits of the low quality resource that might have driven those results. Cyanobacterial compounds that can inhibit digestive proteases of a related grazer likely did not cause the observed reductions in transmission potential. Our study highlights the value of using mechanistic models to pinpoint how resource quality can change transmission potential. Overall, our results show that low quality resources could inhibit the spread of disease through effects on multiple components of transmission potential. They also provide insight into how disease outbreaks in wildlife may respond to shifts in resource quality caused by eutrophication or climate change.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.