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2,015 results for “context”
In the Shape of Europe Through the Islamic Lens: Circulation and Use of Turko-Mongol Textiles in Christian Context (ISETIL)
<p>5<sup>th</sup> Project Presentation</p>
Weed dataset - Crop diversity Experiment - Crop-weed relationships are context-dependent and cannot fully explain the positive effects of intercropping on yield
<p>This shows the weed mass per species and crop yield per species of each plot described in the experiment. </p>
Data from: Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure to light affects foraging expression in brood workers and foragers. Results from our field study show that the regulation of the foraging gene in harvester ants occurs at two time scales: levels of foraging mRNA are associated with ontogenetic changes over weeks in worker age, location and task, and there are significant daily oscillations in foraging expression in foragers. The temporal dissection of foraging expression reveals that gene expression changes in foragers occur across a scale of hours and the level of expression is predicted by activity rhythms: foragers have high levels of foraging mRNA during daylight hours when they are most active outside the nests. In the experimental study, we find complex interactions in foraging expression between task behaviour and light exposure. Oscillations occur in foragers following experimental exposure to 13 L : 11 D (LD) conditions, but not in brood workers under similar conditions. No significant differences were seen in foraging expression over time in either task in 24 h dark (DD) conditions. Interestingly, the expression of foraging in both undisturbed field and experimentally treated foragers is also significantly correlated with the expression of the circadian clock gene, cycle. Our results provide evidence that the regulation of this gene is context-dependent and associated with both ontogenetic and daily behavioural plasticity in field colonies of harvester ants. Our results underscore the importance of assaying temporal patterns in behavioural gene expression and suggest that gene regulation is an integral mechanism associated with behavioural plasticity in harvester ants.
Data from: Local neighbourhood and regional climatic contexts interact to explain tree performance
Tree neighbourhood modelling has significantly contributed to our understanding of the mechanisms structuring communities. Investigations into the impact of neighbouring crowding on tree performance have generally been conducted at local scales, missing important regional-scale context such as the suitability of the climate for each species. Favourable climates may enhance tree performance, but this may come at the cost of increased neighbourhood crowding and competition negatively impacting survival and growth. Through the synthesis of continental-scale forest inventory and trait datasets from the northeast USA and Puerto Rico we present an analytical approach that elucidates the important interactions between local competitive and regional climatic contexts. Our results show strong asymmetries in competitive interactions and significant niche differences that are dependent on habitat suitability. The strong interaction between local neighbourhood and regional climate highlights the need for models that consider the interaction between these two processes that have been previously ignored.
Data from: Transgenerational effects in an ecological context: conditioning of adult sea urchins to upwelling conditions alters maternal provisioning and progeny phenotype
Transgenerational plasticity occurs when the conditions experienced by the parental generation influences the phenotype of their progeny. This may in turn affect progeny performance and physiological tolerance, providing a means by which organisms cope with rapid environmental change. We conditioned adult purple sea urchins, Strongylocentrotus purpuratus, to combined pCO2 and temperature conditions reflective of in situ conditions of their natural habitat, the benthos in kelp forests of nearshore California, and then assessed the performance of their progeny raised under different pCO2 levels. Adults were conditioned during gametogenesis to treatments that reflected static non-upwelling (~650 μatm pCO2, ~17°C) and upwelling (~1300 μatm pCO2, ~13°C) conditions. Following approximately 4 months of conditioning, the adults were spawned and embryos were raised under low pCO2 (~450 μatm pCO2) or high pCO2 (~1050 μatm pCO2) treatments to determine if differential maternal conditioning impacted the progeny response to a single abiotic stressor: pCO2. We examined the size, protein content, and lipid content of eggs from both sets of conditioned female urchins. Offspring were sampled at four stages of early development: hatched blastula, gastrula, prism, and echinopluteus. This resulted in four sets of offspring: (1) progeny from non-upwelling-conditioned mothers raised under low pCO2, (2) progeny from non-upwelling-conditioned mothers raised under high pCO2, (3) progeny from upwelling-conditioned mothers raised under low pCO2, and (4) progeny from upwelling-conditioned mothers raised under high pCO2. We then assessed the effects of maternal conditioning along with the effects of developmental pCO2 levels on body size of the progeny. Our results showed that differential maternal conditioning had no impact on average egg size, although non-upwelling females produced eggs that were more variable in size. Maternal conditioning did not affect protein content but did have a modest impact on egg lipid content. Developing embryos whose mothers were conditioned to simulated upwelling conditions (~1300 μatm pCO2, ~13°C) were greater in body size, although this effect was no longer evident at the echinopluteus larval stage. Although maternal conditioning affected offspring body size, the pCO2 levels under which the embryos were raised did not. Overall, this laboratory study provides insight into how transgenerational effects may function in nature. The impacts of parental environmental history on progeny phenotype during early development have important implications regarding recruitment success and population-level effects.
Data from: Pest control potential of adjacent agri-environment schemes varies with crop type and is shaped by landscape context and within-field position
<ol> <li>Increasing natural pest control in agricultural fields is an important aim of ecological intensification. Combined effects of landscape context and local placement of agri-environmental schemes on natural pest control and within field distance functions of natural pest control agents have rarely been addressed but might affect the distribution of biocontrol providers. Importantly, it is currently unknown whether ecosystem services provided by adjacent agri-environmental schemes (AES) are consistent for different crop types during crop rotation.</li> <li>In this study, we assessed whether crop rotation from oilseed rape to cereals altered within-field distance functions of ground dwelling predators from adjacent agri-environmental fields along a gradient in landscape context. Additionally we recorded crop pests, predation rates, parasitoids as well as crop yields on a total of 30 study sites.</li> <li>Distance functions varied between trophic levels: Carabid richness decreased while densities of carabid beetles, staphylinid beetles as well as crop yields increased towards the field centres. Distance functions of parasitoids and pests were modulated by the amount of semi-natural habitat in the surrounding landscape, while the effects of adjacent AES were limited.</li> <li>Distance decay functions found for ground dwelling predators in oilseed rape in the previous year were not always present in cereals. Increasing distance to the field edge also increased effects of crop rotation on carabid beetle assemblages, indicating a source habitat function of field edges.</li> <li>Synthesis and applications<i>.</i> Distance functions of natural pest control are not universal and the effects of agri-environmental schemes (AES) in different adjacent crops during crop rotation vary and depends on ecological contrasts. A network of semi-natural habitats and spatially optimised AES habitats can benefit pest control in agricultural landscapes, but constraints as a result of crop type need to be addressed by annually targeted, spatially shifting AES schemes for different crops.</li> </ol> <div> </div>
Data from: Context-dependent costs and benefits of a heterospecific nesting association
The costs and benefits of interactions among species can vary spatially or temporally, making them context-dependent. For example, benefits associated with nesting near species that deter predators may give way to costs if the association increases the risk of predation during other stages of reproduction. We examined the extent to which the costs and benefits of heterospecific aggregations between a declining shorebird, the Hudsonian Godwit (Limosa haemastica), and a potential protector and predator, the Mew Gull (Larus canus), varied with breeding stage. Specifically, we assessed the spatial distribution and fate of 43 godwit and 262 gull nests in Beluga, Alaska, from 2014 – 2016. We then evaluated the effect of habitat and proximity to gulls on daily survival rates of 120 godwit nests from 2009 – 2016. We also examined the relationship between the proximity to gulls and survival of godwit chicks to five days old, the period when they are vulnerable to gull predation. Nests of godwits and gulls were significantly clustered across the landscape, a pattern that habitat heterogeneity failed to explain. Hatching success of godwit nests improved with proximity to the gull colony and increasing numbers of gull nests within 200m. In contrast, survival of godwit chicks to five days improved with increasing distance to the gull colony. The costs and benefits that godwits derived from associating with Mew Gulls were thus context-dependent, with benefits pre-hatch and costs post-hatch. Our results show how spatiotemporal variation in species interactions preclude simple generalizations about the nature of their outcomes.
Data from: Context-dependent scaling of kinematics and energetics during contests and feeding in mantis shrimp
Measurements of energy use, and its scaling with size, are critical to understanding how organisms accomplish myriad tasks. For example, energy budgets are central to game theory models of assessment during contests and underlie patterns of feeding behavior. Clear tests connecting energy to behavioral theory require measurements of the energy use of single individuals for particular behaviors. Many species of mantis shrimp (Stomatopoda: Crustacea) use elastic energy storage to power high-speed strikes that they deliver to opponents during territorial contests and to hard-shelled prey while feeding. We compared the scaling of strike kinematics and energetics between feeding and contests in the mantis shrimp Neogonodactylus bredini. We filmed strikes with high-speed video, measured strike velocity, and used a mathematical model to calculate strike energy. During contests, strike velocity did not scale with body size but strike energy scaled positively with size. Conversely, while feeding, strike velocity decreased with increasing size and strike energy did not vary according to body size. Individuals most likely achieved this strike variation through differential compression of their exoskeletal spring prior to the strike. Post-hoc analyses found that N. bredini used greater velocity and energy when striking larger opponents, yet variation in prey size was not accompanied by varying strike velocity or energetics. Our estimates of energetics inform prior tests of contest and feeding behavior in this species. More broadly, our findings elucidate the role behavioral context plays in measurements of animal performance.
Data from: Context-dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host
Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade-offs between immune and reproductive investment lead to the evolution of distinct life-history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB), an important zoonotic pathogen, in a free-ranging African buffalo (Syncerus caffer) population. We characterize these phenotypes as 'infection resistance', in which hosts delay or prevent infection, and 'proliferation resistance', in which the host limits the spread of lesions caused by the pathogen after infection has occurred. We found weak evidence that infection resistance to bTB may be heritable in this buffalo population (h2=0.10) and comes at the cost of reduced body condition and marginally reduced survival once infected, but also associates with an overall higher reproductive rate. Infection resistant animals thus appear to follow a 'fast' pace of life syndrome, in that they reproduce more quickly but die upon infection. In contrast, proliferation resistance had no apparent costs and was associated with measures of positive host health- such as having a higher body condition and reproductive rate. This study quantifies striking phenotypic variation in pathogen resistance and provides evidence for a link between life history variation and a disease resistance trait in a wild mammalian host population.
Data from: Ecosystem context illuminates conflicting roles of plant diversity in carbon storage
Plant diversity can increase biomass production in plot‐scale studies, but applying these results to ecosystem carbon (C) storage at larger spatial and temporal scales remains problematic. Other ecosystem controls interact with diversity and plant production, and may influence soil pools differently from plant pools. We integrated diversity with the state‐factor framework, which identifies key controls, or 'state factors', over ecosystem properties and services such as C storage. We used this framework to assess the effects of diversity, plant traits and state factors (climate, topography, time) on live tree, standing dead, organic horizon and total C in Québec forests. Four patterns emerged: (1) while state factors were usually the most important model predictors, models with both state and biotic factors (mean plant traits and diversity) better predicted C pools; (2) mean plant traits were better predictors than diversity; (3) diversity increased live tree C but reduced organic horizon C; (4) different C pools responded to different traits and diversity metrics. These results suggest that, where ecosystem properties result from multiple processes, no simple relationship may exist with any one organismal factor. Integrating biodiversity into ecosystem ecology and assessing both traits and diversity improves our mechanistic understanding of biotic effects on ecosystems.
Data from: Singing behaviour of Ruby-crowned Kinglets (Regulus calendula) in relation to time-of-day, time-of-year, and social context
Observational field studies provide insight on the multifunctional nature of birdsong. For example, if song production were limited to pre-fertilization, then that would suggest a mate attraction function. If it were used throughout the breeding season and in response to intruding males, then that would suggest a territorial defence function. In the present study, we determined the daily and seasonal singing patterns of male Ruby-crowned Kinglets (Regulus calendula) in Labrador, Canada, using microphone arrays in two breeding seasons. Using a playback experiment, we simulated a territorial intrusion to compare the structure of songs produced while defending a territory to the structure of songs produced during solo and contest singing. Singing peaked in the early part of the breeding season and then declined continuously for the remainder of the season, which suggests that the songs function in mate attraction. Singing peaked 2-3 h after dawn, and then declined steadily until it stopped at 2200 h. Some nocturnal singing was observed, but no dawn singing was observed. A high probability of signal overlap by heterospecific songs at dawn would hinder signal recognition and explain the observed delay in peak singing activity. Vocal responses to playback suggested a function in territory defence. However, there were no significant differences in the duty cycle, frequency modulation, and bandwidth of songs in relation to the context of song production, though songs were shorter in the intrusion context than during solo singing. Overall, the study provides the first quantitative description of the effects of time of day, time of year, and social context on singing behaviour in this understudied species.
Hummingbird torpor in context: duration, more than temperature, is the key to nighttime energy savings
Torpor is an important energy saving strategy in some small birds, but it has rarely been studied in natural field conditions. We compared torpor use across 43 wild-caught individuals of eight hummingbird species across sites with different natural temperature regimes. Most laboratory studies focus on the relationship between metabolic rate and temperature, but our aim was to evaluate what environmental factors most influence hummingbird nighttime energy management under natural conditions. We found that the probability of an individual entering torpor was weakly correlated with mass but unrelated to nighttime temperature and that hummingbirds at both warm, tropical and cooler, temperate sites used torpor. Energy savings in torpor were maximized as ambient temperatures approached a species' minimum body temperature, consistent with laboratory studies; energy savings ranged between 65-92% of energy per hour in torpor compared to normothermy. However, regardless of the degree of energy savings in torpor, variation in total nighttime energy expenditure was most significantly influenced by torpor bout duration. Lab studies largely assess the effect of temperature on torpor use, but our findings indicate that other environmental conditions are more important in determining hummingbirds' total nighttime energy expenditure under natural temperature cycles. Our results show that a small endotherm's nighttime energy management in its natural habitat is more affected by torpor bout duration, which is linked to photoperiod, than by temperature. This result suggests that in their natural environments hummingbirds are able to save energy in torpor across a range of nighttime temperatures, indicating that they may have sufficient physiological flexibility to tolerate climatic variation.
Data from: Context-dependent defences in turtle ants: resource defensibility and threat level induce dynamic shifts in soldier deployment
1. Induced defences involve the dynamic deployment of limited and specialized defensive resources across multiple locations, to maximize organismal defensive function and fitness. They have been studied intensively in plants and solitary animals, but the induced defences of complex animal societies are poorly understood by comparison, despite the coordinated defensive actions of these taxa. 2. Here, we ask whether the level of environmental danger induces shifts in the deployment of limited and morphologically specialized soldiers across multiple nests in colonies of the turtle ant Cephalotes rohweri. Specifically, we test whether less defensible nests induce greater soldier deployment, and whether elevated enemy threat induced further increases in deployment, or reduced deployment consistent with a risk-limiting strategy. 3. We used colony-collection data to provide natural ecological context to our experiments, a field experiment to address how nest-entrance defensibility and soldier number impact defensive performance, and laboratory experiments to test whether differences in nest defensibility and threat level induce dynamic shifts in soldier deployment to new nests. 4. Less defensible nests were lost rapidly in our field experiment, irrespective of soldier number, but soldier deployment significantly increased survivorship of more defensible nests. Concordantly, less defensible nests induced the deployment of more soldiers per nest under low threat in laboratory experiments. Nevertheless, high-threat conditions revealed a risk-limiting soldier deployment strategy: with more danger, the number of soldiers per nest was significantly reduced in less defensible nests, as was the overall number of new soldier-defended nests. Total deployment to new nests was also consistently lower under high threat, dropping from 40% to 30% across colonies. 5. Induced soldier-based defences in turtle ants are therefore context-dependent, and dynamically scaled back at multiple levels when the environment is more dangerous. This dynamic, risk-limiting strategy is in strong contrast to stable patterns of soldier production in ants, and to typical task-allocation dynamics in members of the worker caste. Moreover, these findings establish that the evolution of specialized defensive agents can be coupled with sophisticated and inducible deployment strategies in complex social taxa, as we see for organisms at other levels of biological complexity.
Context-dependent effects of relative temperature extremes on bill morphology in a songbird
<p><span>Species increasingly face environmental extremes. While responses of morphological traits to changes in average environmental conditions are well-documented, responses to environmental extremes remain poorly understood. Bird bills contribute to thermoregulation, with considerable heat loss possible through the bill surface, and with bill morphology shaped by long-term thermal conditions. We used museum specimens to investigate the relationship of bill surface area (SA) in dark-eyed juncos <i>Junco hyemalis</i> to traditional measures of climate (temperature and precipitation) and to a novel measure of short-term relative temperature extremity, which quantifies the degree to which temperature maxima or minima have diverged from the recent five-year norm. We found that bill SA exhibits different patterns of association with relative extremity depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger bill SA at higher relative temperature extremities, we found this to be the case only when the measure of temperature extremity existed in an environmental context that opposed it: relative minimum temperature in a warm climate, or relative maximum temperature in a cool climate. When, instead, environmental context amplified the relative temperature extremity, we found a negative relationship between bill SA and relative temperature extremity. We also found that the strength of associations between bill SA and relative temperature extremity increased as precipitation increased. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments should be of particular concern. Extreme-on-extreme environmental change may produce responses that cannot be predicted from observations in less extreme contexts, which should make it a priority for research on species' responses to climate change as well as trait evolution generally.Species increasingly face environmental extremes. Morphological responses to changes in average environmental conditions are well-documented, but responses to environmental extremes remain poorly understood. We used museum specimens to investigate relationships between a thermoregulatory morphological trait, bird bill surface area (SA), and a measure of short-term relative temperature extremity (RTE), which quantifies the degree that temperature maxima or minima diverge from the five-year norm. Using a widespread, generalist species, <i>Junco hyemalis</i>, we found that SA exhibited different patterns of association with RTE depending on the overall temperature regime and on precipitation. While thermoregulatory function predicts larger SA at higher RTE, we found this only when the RTE existed in an environmental context that opposed it: atypically cold minimum temperature in a warm climate, or atypically warm maximum temperature in a cool climate. When environmental context amplified the RTE, we found a negative relationship between SA and RTE. We also found that the strength of associations between SA and RTE increased with precipitation. Our results suggest that trait responses to environmental variation may qualitatively differ depending on the overall environmental context, and that environmental change that extremifies already-extreme environments may produce responses that cannot be predicted from observations in less extreme contexts.</span></p>
Data from: Correlational selection on personality and social plasticity: morphology and social context determine behavioural effects on mating success
Despite a central line of research aimed at quantifying relationships between mating success and sexually dimorphic traits (e.g., ornaments), individual variation in sexually selected traits often explains only a modest portion of the variation in mating success. Another line of research suggests that a significant portion of the variation in mating success observed in animal populations could be explained by correlational selection, where the fitness advantage of a given trait depends on other components of an individual's phenotype and/or its environment. We tested the hypothesis that interactions between multiple traits within an individual (phenotype dependence) or between an individual's phenotype and its social environment (context dependence) can select for individual differences in behaviour (i.e., personality) and social plasticity. To quantify the importance of phenotype- and context-dependent selection on mating success, we repeatedly measured the behaviour, social environment and mating success of about 300 male stream water striders, Aquarius remigis. Rather than explaining individual differences in long-term mating success, we instead quantified how the combination of a male's phenotype interacted with the immediate social context to explain variation in hour-by-hour mating decisions. We suggest that this analysis captures more of the mechanisms leading to differences in mating success. Males differed consistently in activity, aggressiveness and social plasticity. The mating advantage of these behavioural traits depended on male morphology and varied with the number of rival males in the pool, suggesting mechanisms selecting for consistent differences in behaviour and social plasticity. Accounting for phenotype and context dependence improved the amount of variation in male mating success we explained statistically by 30–274%. Our analysis of the determinants of male mating success provides important insights into the evolutionary forces that shape phenotypic variation. In particular, our results suggest that sexual selection is likely to favour individual differences in behaviour, social plasticity (i.e., individuals adjusting their behaviour), niche preference (i.e., individuals dispersing to particular social conditions) or social niche construction (i.e., individuals modifying the social environment). The true effect of sexual traits can only be understood in interaction with the individual's phenotype and environment.
Data from: Connecting the dots: Stopover strategies of an intercontinental migratory songbird in the context of the annual cycle
The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black-and-white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time-schedule, which has previously been linked to habitat conditions experienced in the preceding phase of the annual cycle. Birds in close proximity to their breeding destination accumulate additional energy reserves prior to arrival on the breeding grounds, as reflected by higher migratory condition upon arrival, higher refueling rates measured via blood plasma metabolites, and longer stopover durations compared to birds migrating to breeding destinations farther from the stopover site. However, late birds near their breeding destination were more likely to depart on the day of arrival (i.e., transients), and among birds that stopped over at the site, the average duration of stopover was almost half the time of early conspecifics, suggesting late birds are trying to catch-up with the overall time-schedule of migration for optimal arrival time on the breeding grounds. In contrast, birds with long distances remaining to breeding destinations were more likely to depart on the day of arrival and primarily used stopover to rest before quickly resuming migration, adopting similar strategies regardless of a bird's time-schedule. Our study demonstrates that migrants adjust their en route strategies in relation to their time-schedule and distance remaining to their breeding destination, highlighting that strategies of migration should be examined in the context of other phases of the annual cycle.
Treatment of temporal aliasing effects in the context of next generation satellite gravimetry missions
<p><strong>Simulated gravity field solutions</strong> published in:<br> Daras, I. and Pail, R. (2017), <em>Treatment of temporal aliasing effects in the context of next generation satellite gravimetry missions</em>, Journal of Geophysical Research: Solid Earth (in revision)</p> <p>Results relate to the solutions used for generating the Figures of the publication.</p> <p>All gravity field solutions are in <strong>icgem </strong>format. The solutions include the effect of static gravity field model GOCO03s.</p> <p><strong>Filename description </strong>for Figures 3, 4, 6, 8, 10 and 11 (fields appear only if applicable):<br> Retrieval content<br> - AOHIS : Atmosphere, Hydrology, Ocean, Ice and Solid Earth <br> - HIS : Hydrology, Ice and Solid Earth<br> - A : Atmosphere<br> - O : Ocean<br> - H : Hydrology<br> - OTerr : OT error retrieval</p> <p>Strategies for HIS retrieval<br> - str1 : strategy 1<br> - str2 : strategy 2</p> <p>Constellation<br> - asc : alternative constellation</p> <p>Retrieval period<br> - hd : half-daily<br> - 1d : daily<br> - 3d : 3-daily<br> - 11d : 11- daily</p> <p>Noise case<br> - fn : full noise case<br> - un : undersampling noise case<br> - ind : individual parameter noise case (see text)</p> <p>Parameterization method<br> - d120 : nominal 11-day solution up to d/o 120<br> - CoPa.1d10.d120 : CoPa 1/10-11/120<br> - CoPa.1d20.3d30.1d120 : CoPa 1/20-3/30-11/120 (sequential parameterization)</p> <p>Time indexing (for Co-estimated short-term solutions)<br> - 01 : Co-estimated solution refering to epoch 01</p> <p><strong>Filename description</strong> for Figure 7:<br> - icgem : format of gravity field solution<br> - yymmdd : starting epoch of the long-term solution for which the daily solutions were co-estimated <br> (e.g. 960112 : refers to the 11-day solution of the time period 1996/01/12 - 1996/01/22)<br> - dual : 2-pair Bender-type solution (standard for all simulations of the paper)<br> - 20.1.11 : 1-day solutions with d/o 20 spatial resolution resulting from a daily co-parameterization of an 11-day long-term solution<br> - wiese : dummy, refers to the paper of D. Wiese <br> - dd : day of the 11-day period</p>
On the Effect of Semantically Enriched Context Models on Software Modularization
<p>The dataset used for evaluating the approaches outlined in this paper, comprising of 10 open source Java projects. The algorithms employed can be found at https://github.com/amirms/GeLaToLab, </p>
Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences
<p>The dataset and code used for the publication of "<a href="https://www.biorxiv.org/content/10.1101/2024.11.12.623335v1" target="_blank" rel="noopener"><strong>Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences</strong></a>".</p> <div> <div><strong>Data path</strong></div> <div> <ol> <li>derivatives (./data/derivatives/): preprocessed data. <ul> <li>meg_quat-tsss-withEOG_100hz_0d3-40: meg data preprocessed at 100 Hz filtered between 0.3 and 40 Hz.</li> <li>FreeSurfer: anatomy data preprocessed</li> </ul> </li> <li>behavior_data (./behavior_data/)</li> <li>stimuli (./exp_procedure/material/): exp stimuli and procedure</li> <li>features (./data/features/): calculated phonological and linguistic features.</li> </ol> </div> <strong>Code path</strong></div> <div><br> <div>Preprocessing<strong>:</strong></div> <div> <ol> <li>[preprocessing.py]: preprocessing of behavior and MEG data.</li> <li>[recon.py]: reconstruction of T1 .niift data into surface data in FreeSurfer.</li> <li>[analysis_stimuli.ipynb]: preprocessing and feature extraction of stimuli.</li> </ol> </div> Analysis</div> <div> <ul> <li>[analysis_meg.ipynb]: spectral, time course, and RSA analysis.</li> </ul> </div>
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
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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.