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2,015 results for “context”
Data and R code used in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants
<p>This repository contains the data and R markdown files supporting the findings presented in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants.</p>
Mate searching context of prey influences predator-prey space race
<p>Predation risk is a strong driver of prey distribution and movement. However, fitness-influencing behaviours, such as mating, can alter risk and influence predator-prey space-use dynamics. In tree crickets, <i>Oecanthus henryi</i>, mate searching involves acoustic signalling by immobile males and phonotactic movement by females. Space-use patterns in tree crickets relative to their primary predators, green lynx spiders (<i>Peucetia viridans</i>), should therefore depend on their current mate-searching state; whether males are calling or non-calling and whether females are phonotactic or non-phonotactic. We first measured the degree of spatial anchoring of crickets to specific bushes in the field, and whether that influenced the probability of broad-scale spatial overlap with spiders. In the absence of spiders, all crickets, independent of sex or male calling status, were found to be spatially anchored to specific types of bushes and not uniformly distributed on the landscape. At the broad spatial scale, spiders were more likely to be found on bushes with female crickets, and to a lesser degree, calling male crickets. At a finer spatial scale within a bush, movement strategies of crickets not only varied depending on the presence or absence of a spider, but also on their current mate searching state. Phonotactic females showed clear predator avoidance, whereas calling and non-calling males moved towards the spider instead of away, similar to predator-inspection behaviour seen in many taxa. As the strongly-selected sex, males are more likely to undertake risky mate searching activities, which includes inspection of predator positions. Overall, we found that all crickets were predictably anchored at the landscape scale, but their sex and mate seeking behaviour influenced the degree of overlap with predators, and their antipredator movement strategies. Reproductive strategies within a prey species, therefore, can alter predator-prey space race at multiple spatial scales.</p>
Data from: Disentangling direct and indirect determinants of the duration of maternal care in brown bears: environmental context matters
<p>The duration of maternal care, an important life history trait affecting population dynamics, varies greatly within species. Yet, our understanding of its predictors is limited, mostly correlative, and subject to misinterpretations, due to difficulties to disentangle the role of maternal- and offspring-related characteristics.</p> <p>We conducted path analysis on a dataset including 217 brown bear litters captured over a 29-year period in two populations in Sweden ("North" and "South") facing contrasting environmental conditions to identify and quantify the causes of variation in the duration of maternal care (1.5 years or 5 years).</p>
SemEval-2020 Task 3: Graded Word Similarity in Context
<p>For this tasks we ask participants to build systems that try to predict the effect that context has in human perception of similarity of words.</p> <p>We have seen very interesting work that uses local context to predict <strong>discrete</strong> changes in meaning: the different senses of a polysemous word. However context also has more subtle, <strong>continuous</strong> (<strong>graded</strong>) effects on meaning, even for words not necessarily considered polysemous.</p> <p>In order to be able to look at these effects we are building several datasets where we ask annotators to score how similar a pair of words are after they have read a short paragraph (which contains the two words). Each pair is scored within two of these paragraphs, allowing us to look at changes in similarity ratings due to context.</p> <p>CodaLab was used to run this task, you can see the dedicated website and the results of the participants at: https://competitions.codalab.org/competitions/20905</p>
Context-dependent variability in the population prevalence and individual fitness effects of plant-fungal symbiosis
<p>1. Heritable symbionts, found within a diverse array of flora and fauna, are often observed at intermediate prevalence within host populations, despite expectations that positive fitness feedbacks should drive beneficial symbionts to fixation. Intermediate prevalence may reflect neutral dynamics of symbionts with weak fitness effects, transient dynamics of symbionts trending toward fixation (or elimination), or a stable intermediate outcome determined by the balance of fitness effects and failed symbiont transmission. Theory suggests these outcomes should depend on symbiont-conferred effects and vertical transmission efficiency, which may both depend on environmental context.</p> <p>2. We tested these alternatives by tracking temporal change in population-level symbiont prevalence in a three-year field experiment with grasses and vertically transmitted fungal endophytes under the context of manipulated precipitation. Precipitation can mediate endophyte effects on host grasses, and is a relevant context, as global climate models predict changes in precipitation amount and seasonal distribution.</p> <p>3. We found evidence for each of the three proposed mechanisms for intermediate symbiont prevalence, but the outcome differed qualitatively across years and precipitation treatments. Specifically, within the first study year, all populations under ambient precipitation trended toward symbiont fixation, whereas elevated precipitation literally neutralized the interaction resulting in no long-run equilibrium. The second study year yielded a different result with long-run equilibria at an intermediate prevalence for both ambient and elevated precipitation treatments. We linked these population-level outcomes with individual-level symbiont effects on grasses and showed that the benefits of symbiosis were concentrated at the seedling stage, especially under drought stress during the time period coinciding with recruitment. The drought stress evident during the first year of the study was not present in the second year due to greater ambient precipitation during this time period. Together, these findings provide the first experimental evidence that population-level outcomes of host-symbiont interactions, which arise from the composite outcome of demographic vital rates and transmission, can be dynamically stable and can fluctuate in response to shifts in spatio-temporal context.</p> <p>4. Synthesis: Overall, these results indicate that intermediate prevalence of heritable microbial symbionts likely reflects a combination of neutral, transient, and stable mechanisms, and context-dependent fluctuations among them.</p>
A process proposal on how to move from data requirements to semantic data in the context of the MDA
<p>This work proposes a process for the identification of the requirements associated with the data, along with and a set of transformations in Model Driven Architecture (MDA) context, in order to obtain a semantically annotated dataset, as a result of the unification and alignment of the data in the context of its initial domain. Our proposal identifies four phases (from CIM to code), in which is describe the artifacts and transformations required to progress to the next phase: a target domain model is first obtained from the data requirements, after which the ontological schema and the ontology is generated from the previous model. A domain-specific language (DSL), also proposed in this work, is then used to obtain the semantic data model (the DSL code), which generates the final semantic dataset. We have validated the proposal by studying two cases: one with data from the public transport domain and the other with data concerning those affected by the COVID-19 pandemic.</p>
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
<p>Matlab output files and raw data used for the evaluation presented in "DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks" <a href="https://github.com/MetExplore/dexom">https://github.com/MetExplore/dexom</a></p>
Data from: Abiotic and biotic context dependency of perennial crop yield
<p>Perennial crops in agricultural systems can increase sustainability and the magnitude of ecosystem services, but yield may depend upon biotic context, including soil mutualists, pathogens and cropping diversity. These biotic factors themselves may interact with abiotic factors such as drought. We tested whether perennial crop yield depended on soil microbes, water availability and crop diversity by testing monocultures and mixtures of three perennial crop species: a novel perennial grain (intermediate wheatgrass—<i>Thinopyrum intermedium</i>-- that produces the perennial grain Kernza®), a potential perennial oilseed crop (<i>Silphium intregrifolium</i>), and alfalfa (<i>Medicago sativa</i>). Perennial crop performance depended upon both water regime and the presence of living soil, most likely the arbuscular mycorrhizal (AM) fungi in the whole soil inoculum from a long term perennial monoculture and from an undisturbed native remnant prairie. Specifically, both <i>Silphium</i> and alfalfa strongly benefit from AM fungi. The presence of native prairie AM fungi had a greater benefit to <i>Silphium </i>in dry pots and alfalfa in wet pots than AM fungi present in the perennial monoculture soil. Kernza did not benefit from AM fungi. Crop mixtures that included Kernza overyielded, but overyielding depended upon inoculation. Specifically, mixtures with Kernza overyielded most strongly in sterile soil as Kernza compensated for poor growth of <i>Silphium</i> and alfalfa. This study identifies importance of soil biota and the context dependence of benefits of native microbes and the overyielding of mixtures in perennial crops.</p>
Supplementary Material to Context-tailored Workload Model Generation for Continuous Representative Load Testing
<p>This package contains files and instructions to replicate our experiments on context-tailored workload model generation for continuous representative load testing. Please download and extract the <code>context-tailoring.tar.gz</code> file and view <code>index.html</code> (also contained in the tarball) for further instructions.</p> <p><code>cobra-db.tar.gz </code>is only required for skipping parts of the steps (see the detailed instructions).</p>
Proteomics and phosphoproteomics analysis of the tyrosine phosphatase SHP2 acquired resistance to SHP099 in the context of AML
<p>Proteomics analysis of AML cell lines (MV-4-11, MOLM-13, EOL-1 and OCI-M1) presenting acquired resistance to SHP099 and their parent sensitive cells in presence of the SHP2 allosteric inhibitor SHP099 or DMSO (control). These samples were labelled with TMT and analysed by mass spectrometry. </p> <p>The same approach was conducted to analyse the phosphoproteome of MV-4-11 cells (parent and resistant) upon SHP099 treatment.</p> <p>These data are associated with the manuscript "<strong>Tyr-62 phosphorylation of the tyrosine phosphatase SHP2 enables acquired resistance to SHP2 allosteric inhibitors</strong>"</p>
The dataset of the paper titled "Context-Aware Code Change Embedding for Better Patch Correctness Assessment"
<p>The dataset of the paper titled "Context-Aware Code Change Embedding for Better Patch Correctness Assessment".</p> <p>This is the online repository of the paper "Context-Aware Code Change Embedding for Better Patch Correctness Assessment" under review by ASE2021. We release the source code of Cache, the patches used in our evaluation, as well as the experiment results.</p> <ul> <li> <p>Patches: Two patch benchmarks included in our study.</p> <ul> <li>Small: The 1,183 deduplicated patches from Tian's <a href="https://conf.researchr.org/details/ase-2020/ase-2020-papers/3/Evaluating-Representation-Learning-of-Code-Changes-for-Predicting-Patch-Correctness-i">ASE20</a> paper and Wang's <a href="https://conf.researchr.org/details/ase-2020/ase-2020-papers/54/Automated-Patch-Correctness-Assessment-How-Far-are-We-">ASE20</a> paper.</li> <li>Large: The patches collected by ourselves, which is consist of totally 49,694 patches from <a href="https://dl.acm.org/doi/10.1145/3338906.3338911">RepairThemAll</a> and <a href="https://dl.acm.org/doi/10.1145/3379597.3387491">ManySStuBs</a>.</li> </ul> </li> <li> <p>Results</p> <ul> <li> <p>RQ1: The detailed result files in RQ1, which are named by the format of <em><code>[model]_[classifier].csv</code></em>. For example, the file named <em><code>BERT_DT.csv</code></em> in the folder <em><code>Small</code></em> means that this file is the result of patches from <strong>Small</strong> dataset embedded by <strong>BERT</strong> and classified by <strong>Decision Tree</strong>.</p> <ul> <li>Small: The detailed result files on Small dataset.</li> <li>Large: The detailed result files on Large dataset.</li> <li> <p>Cross: The detailed result files of representation learning techniques when training on Large dataset and testing on Small dataset.</p> </li> </ul> </li> <li> <p>RQ2: The detailed result files in RQ2.</p> <ul> <li>Wang_Cache.csv: The detailed result of Cache on the dataset from Wang's <a href="https://conf.researchr.org/details/ase-2020/ase-2020-papers/54/Automated-Patch-Correctness-Assessment-How-Far-are-We-">ASE20</a> paper.</li> <li> <p>ODS_Cache.csv: The datailed result of Cache on the dataset from Xiong's <a href="https://dl.acm.org/doi/10.1145/3180155.3180182">ICSE18</a> paper. We directly compare against the results reported by the authors of ODS on 139 patches from Xiong's paper since the data and source code of ODS is unavailable.</p> </li> <li> <p>Table_5_Effectiveness_APCA.xlsx: The detailed version of <strong>Table 5</strong> in the paper.</p> </li> <li> <p>Table_6_Effectiveness_ODS.xlsx: The detailed version of <strong>Table 6</strong> in the paper.</p> </li> </ul> </li> </ul> </li> <li>Source: The source code and lib for running Cache. Guidance for replicating our study is available at <em><code>source/Readme.md</code></em>. We will build a homepage for Cache on GitHub upon acceptance.</li> </ul>
Investigating Transformers as Context-aware Word Search Engines - Data and Code
<p>This is the review version, please use the published record: </p> <p> https://zenodo.org/record/6425595</p> <p> </p> <p>Data and code for the paper 'Investigating Transformers as Context-aware Word Search Engines' as submitted for review at ACL21. </p> <p> </p>
Data from: Inbreeding alters context‐dependent reproductive effort and immunity in male crickets
Infection can cause hosts to drastically alter their investment in key life‐history traits of reproduction and defence. Infected individuals are expected to increase investment in defence (e.g., by increasing immune function) and, due to trade‐offs, investment in other traits (e.g., current reproduction) should decrease. However, the terminal investment hypothesis postulates that decreased lifespan due to infection and the associated reduction in the expectation for future offspring will favour increased investment towards current reproduction. Variation in intrinsic condition will likely influence shifts in reproductive investment post‐infection, but this is often not considered in such assessments. For example, the extent of inbreeding can significantly impact an individual's lifetime fitness and may influence its reproductive behaviour following a threat of infection. Here, we investigated the effects of inbreeding status on an individual's reproductive investment upon infection, including the propensity to terminally invest. Male crickets (Gryllodes sigillatus) from four genetically distinct inbred lines and one outbred line were subjected to a treatment from an increasing spectrum of simulated infection cue intensities, using heat‐killed bacteria. We then measured reproductive effort (calling effort), survival and immune function (antibacterial activity, circulating haemocytes and haemocyte microaggregations). Inbred and outbred males diverged in how they responded to a low‐dose infection cue: relative to unmanipulated males, outbred males decreased calling effort, whereas inbred males increased calling effort. Moreover, we found that inbred males exhibited higher antibacterial activity and numbers of circulating haemocytes compared with outbred males. These results suggest that an individual's inbreeding status may have consequences for context‐dependent shifts in reproductive strategies, such as those triggered by infection.
Data from: Social context alters spatial memory performance in free-living male prairie voles
<p>Spatial memory is crucial for mating success because it enables males to locate potential mates and potential competitors in space. Intraspecific competition and its varying intensity under certain conditions are potentially important for shaping spatial memory. For example, spatial memory could enable males to know where competitors are (contest competition), it could help males find mating partners (scramble competition), or both. We manipulated the intensity of intraspecific competition in two distinct contexts by altering the operational sex ratio of prairie voles (<i>Microtus ochrogaster</i>) living in outdoor enclosures by creating male- and female-biased sex ratios. After living freely under these contexts for four weeks, we compared males' performance in a laboratory spatial memory test. Males in the male-biased context demonstrated better spatial memory performance than males in the female-biased context. Notably, these data show that in spite of experiencing equally complex<i>spatial</i>contexts (i.e., natural outdoor enclosures), it was the <i>social </i>context that influenced spatial cognition, and it did so in a manner consistent with the hypothesis that spatial memory is particularly relevant for male-male interactions. Attached are the supporting data for this project.</p>
Data from: Social context affects thermoregulation but not activity level during avian immune response
Determining how an animal's social context alters its immune responses will help us understand how pathogens impact individual health and spread within groups. Several studies have shown that group-housed animals can suppress components of the acute phase immune response, specifically sickness behaviors like lethargy. However, we do not know whether individuals alter sickness behaviors or other components of the acute phase response, including thermoregulation, in response to the infection status of other group members. We used automated radio telemetry on captive house sparrows (Passer domesticus) to test whether sickness behaviors and thermoregulation differed during immune challenge under 2 social contexts: 1) all of the flock inoculated with lipopolysaccharide (LPS), a non-replicating component of gram-negative bacterial cell walls, or 2) half of the flock inoculated. We predicted that with half of the flock inoculated, LPS-treated birds would be under more pressure to maintain competitive behaviors, so would suppress components of the acute phase response. As we predicted, LPS-inoculated birds showed less pronounced heterothermia (fever) when housed with a mixture of inoculated and healthy flockmates. In contrast, LPS-inoculated birds exhibited similar degrees of lethargy regardless of the infection status of their flockmates. Our results show that the infection status of an individual's social group did exert an effect on the acute phase response but surprisingly did not impact the expression of lethargy, a canonical sickness behavior. Determining the mechanisms underlying these responses will require testing additional social contexts with different ratios of infected to uninfected birds.
Data from: Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim
Pathogens entering the marine environment as pollutants exhibit a spatial signature driven by their transport mechanisms. The sea otter (Enhydra lutris), a marine animal that lives much of its life within sight of land, presents a unique opportunity to understand land-sea pathogen transmission. Using a dataset on Toxoplasma gondii prevalence across sea otter range from Alaska to California, we found that the dominant drivers of infection risk vary depending upon the spatial scale of analysis. At the population level, regions with high T. gondii prevalence had higher human population density and a greater proportion of human-dominated land uses suggesting a strong role for population density of the felid definitive host of this parasite. This relationship persisted when a subset of data were analysed at the individual level: large-scale patterns in sea otter T. gondii infection prevalence were largely explained by individual exposure to areas of high human housing unit density, and other landscape features associated with anthropogenic land use, such as impervious surfaces and cropping land. These results contrast with the small-scale, within-region analysis, in which age, sex and prey choice accounted for most of the variation in infection risk, and terrestrial environmental features provided little variation to help in explaining observed patterns. These results underscore the importance of spatial scale in study design when quantifying both individual-level risk factors and landscape-scale variation in infection risk.
Data from: Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure
Once hunted to the brink of extinction, humpback whales (Megaptera novaeangliae) in the North Atlantic have recently been increasing in numbers. However, uncertain information on past abundance makes it difficult to assess the extent of the recovery in this species. While estimates of pre-exploitation abundance based upon catch data suggest the population might be approaching pre-whaling numbers, estimates based on mtDNA genetic diversity suggest they are still only a fraction of their past abundance levels. The difference between the two estimates could be accounted for by inaccuracies in the catch record, by uncertainties surrounding the genetic estimate, or by differences in the timescale to which the two estimates apply. Here we report an estimate of long-term population size based on nuclear gene diversity. We increase the reliability of our genetic estimate by increasing the number of loci, incorporating uncertainty in each parameter and increasing sampling across the geographic range. We report an estimate of long-term population size in the North Atlantic humpback of ~112,000 individuals (95% CI: 45,000 – 235,000). This value is 2-3 fold higher than estimates based upon catch data. This persistent difference between estimates parallels difficulties encountered by population models in explaining the historical crash of North Atlantic humpback whales. The remaining discrepancy between genetic and catch-record values, and the failure of population models, highlights a need for continued evaluation of whale population growth and shifts over time, and continued caution about changing the conservation status of this population.
Data from: Breeding success but not mate choice is phenotype- and context-dependent in a color polymorphic raptor
Morph-specific mate choice has been proposed as one of the evolutionary mechanisms that contribute to the maintenance of variation in color polymorphic systems. Coloration usually covaries with other phenotypic traits affecting life history and thus is often used as a criterion for mate choice. Here, we assess whether mating patterns, natal dispersal, and breeding output are phenotype-dependent in the color polymorphic Eleonora's falcon. We used a long-term dataset of 946 individually ringed adult falcons that included 109 individuals monitored from birth up to recruitment into the breeding population. Overall, patterns of mate choice with regard to coloration were neither assortative nor disassortative. Natal dispersal distance was greater in females but was not associated with coloration. Breeding success was both morph-dependent and context-dependent. Although clutch size was similar in differently colored pairs, differences arose in the number of chicks that fledge. In some years, dark males raised more offspring, regardless of female color morph. Differences in the breeding tactics between male morphs could be associated with intraspecific predation and may thus contribute to the observed differences in breeding output, especially when food availability is low. This suggests that mating patterns may interact with other factors and give rise to the observed higher breeding output of dark males only under certain environmental conditions.
Data from: Context-dependency of top-down, bottom-up, and density-dependent influences on cheetah demography
1. Research on drivers of demographic rates has mostly focused on top predators and their prey, and comparatively less research has considered the drivers of mesopredator demography. Of those limited studies, most focused on top-down effects of apex predators on mesopredator population dynamics, whereas studies investigating alternative mechanisms are less common. 2. In this study, we tested hypotheses related to top-down, bottom-up, and density-dependent regulation of demographic rates in an imperiled mesopredator, the cheetah (Acinonyx jubatus). 3. We used a 25-year dataset of lion density, cheetah density, and prey density from the Mun-Ya-Wana Conservancy in South Africa and assessed the effects of top-down, bottom-up, and density-dependent drivers on cheetah survival and reproduction. 4. In contrast to the top-down and bottom-up predications, both adult and juvenile cheetahs experienced the lowest survival during months with high prey densities and low lion densities. We only observed support for a density-dependent response in juvenile cheetahs, where they had a higher probability of reaching independence during times with low cheetah density, and low prey density. We did not identify any strong drivers of litter size. 5. Collectively, our results indicate that high apex predator abundance might not always have negative effects on mesopredator populations, and suggest that context dependency in top-down, bottom-up, and density-dependent factors may regulate demographic rates of cheetahs and other mesopredators. Our results highlight the complexities of population-level drivers of cheetah demographic rates and the importance of considering multiple hypotheses of mesopredator population regulation.
Data from: Negative effects of pesticides on wild bee communities can be buffered by landscape context
Wild bee communities provide underappreciated but critical agricultural pollination services. Given predicted global shortages in pollination services, managing agroecosystems to support thriving wild bee communities is, therefore, central to ensuring sustainable food production. Benefits of natural (including semi-natural) habitat for wild bee abundance and diversity on farms are well documented. By contrast, few studies have examined toxicity of pesticides on wild bees, let alone effects of farm-level pesticide exposure on entire bee communities. Whether beneficial natural areas could mediate effects of harmful pesticides on wild bees is also unknown. Here, we assess the effect of conventional pesticide use on the wild bee community visiting apple (Malus domestica) within a gradient of percentage natural area in the landscape. Wild bee community abundance and species richness decreased linearly with increasing pesticide use in orchards one year after application; however, pesticide effects on wild bees were buffered by increasing proportion of natural habitat in the surrounding landscape. A significant contribution of fungicides to observed pesticide effects suggests deleterious properties of a class of pesticides that was, until recently, considered benign to bees. Our results demonstrate extended benefits of natural areas for wild pollinators and highlight the importance of considering the landscape context when weighing up the costs of pest management on crop pollination services.
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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.