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opencc-by-4.0Jun 2024View details →

LLM4SchemaOrg: Resources

This repository contains the augmented characteristic sets dataset, used in https://github.com/GDD-Nantes/LLM4SchemaOrg.git

opencc-by-4.0Aug 2024View details →

Morphological profiling data resource enables prediction of chemical compound properties

Morphological profiling with the Cell Painting assay has emerged as a promising method in drug discovery research. The assay captures morphological changes across various cellular compartments enabling the rapid prediction of compound bioactivity. We present a comprehensive morphological profiling resource using the carefully curated and well-annotated EU-OPENSCREEN Bioactive Compounds. The data was generated across four imaging sites with high-throughput confocal microscopes using the Hep G2 as well as the U2 OS cell line. We employed an extensive assay optimization process to achieve high data quality across the different sites. An analysis of the extracted profiles validates the robustness of the generated data. We used this resource to compare the morphological features of the different cell lines. By correlating the profiles with overall activity, cellular toxicity, several specific mechanisms of action (MOAs), and protein targets, we demonstrate the dataset's potential for facilitating more extensive exploration of mechanisms of action.

opencc-by-4.0Jul 2024View details →

Supplemental information of "Food waste utilized as resources can reduce climate and resource burdens in agrifood systems"

(1) Source data (Data 1) for bootstrapping analysis to compute means and 95% CIs of carbon footprint and product metrics of food waste treatments, as well as food waste landfill emissions. The revised version incorporated the original reported carbon footprint data for different food waste managements. (2) Source data (Data 2) for food waste management schemes of US, EU, and China for emission estimation as well as emission mitigation analyses. (3) List of studies selected from a systematic literature review. (4) Script code and output report from STATA.

openapache2.0Sep 2024View details →

Salmonella In Silico Typing Resource (SISTR) commandline tool database version 1.1.3 used by SISTR release version 1.1.3 and up

<h3>Context</h3> Salmonella In Silico Typing Resource (SISTR) commandline tool enables the identification of the Salmonella serovar and cgMLST types of Salmonella from whole genome sequencing (WGS) data tby using a large database (10,000+) of Salmonella genomes and cgMLST profiles based on the 330 alleles. This database is the central part of the SISTR tool and contains both metadata on 2660 serovars and the corresponding antigenic formula, 84463 genomes to serovar mappings, sequences of the O, H1 and H2 antigens, 139729 cgMLST sequences and  38240 profiles with pairwise distances, MASH sketch of the 15465 genomes used for species and serovar identification. For more information and citation please refer to the following publication and official repository at <a href="https://github.com/phac-nml/sistr_cmd/tree/master">https://github.com/phac-nml/sistr_cmd/tree/master</a>  Note: This database was used by SISTR tool up to version 1.1.2 inclusive. From SISTR release 1.1.3 onwards the slightly modified version of this database will be used onwards with changes detailed in <a href="https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md">https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md</a> <h3>Citation</h3> The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101. <a title="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101</a>   <h3>Version changes from v2 to v3</h3> In <code>genomes-to-serovar.txt</code> following serovar changes were made to increase serovar prediction accuracy <table> <tbody> <tr> <th>genome accession</th> <th>serovar previous</th> <th>serovar current</th> </tr> <tr> <td>SRR3048937</td> <td>Ibadan</td> <td>Mississippi</td> </tr> </tbody> </table>

opencc-by-4.0Oct 2021View details →

The success of alien plants in an arid ecosystem: Structural equation modeling reveals hidden effects of soil resources

data

Resource-driven colonization by cod in a high Arctic food web

Climate change is commonly associated with many species redistributions and the influence of other factors may be marginalized, especially in the rapidly warming Arctic. The Barents Sea, a high latitude large marine ecosystem in the Northeast Atlantic has experienced above average temperatures since the mid 2000's with divergent bottom temperature trends at sub-regional scales. Concurrently, the Barents Sea stock of Atlantic cod Gadus morhua, one of the most important commercial fish stocks in the world, increased following a large reduction in fishing pressure and expanded north of 80°N. We examined the influence of food availability and temperature on cod expansion using a comprehensive data set on cod stomach fullness stratified by sub-regions characterized by divergent temperature trends. We then tested whether food availability, as indexed by cod stomach fullness, played a role in cod expansion in sub-regions that were warming, cooling or showed no trend. The greatest increase in cod occupancy occurred in three northern sub-regions with contrasting temperature trends. Cod apparently benefited from initial high food availability in these regions that previously had few large-bodied fish predators. The stomach fullness in the northern sub-regions declined rapidly after a few years of high cod abundance, suggesting that the arrival of cod caused a top down effect on the prey base. Prolonged cod residency in the northern Barents Sea is, therefore, not a certainty.

Data from: Resource predictability drives inter-annual variation in migratory behaviour in a long-lived bird

There is a growing awareness that experience may play a major role in migratory decisions, especially in long-lived species. However, empirical support remains to date scarce. Here, we use multi-year GPS-tracking data on 28 adult Lesser Black-backed Gulls (Larus fuscus), a long-lived species for which migratory strategies typically consist of a series of long stopovers, to assess how experience affects interannual variation in stopover selection. We expect that food source reliability should play a pivotal role, as it both reduces the uncertainty on food availability across years, and enables for more efficient foraging during stopovers by reducing searching efforts. We found that during stopovers gulls indeed developed high fidelity to particular foraging locations, which strongly reduced the daily distance travelled for foraging. When revisiting stopovers in consecutive years, birds used over 80% of foraging locations from the previous year. Although the average fidelity to stopovers across years was a high as 85%, stopovers where birds showed high foraging site fidelity were up to 60% more likely to be revisited compared to stopover with low foraging site fidelity. Accordingly, birds using more stopovers with reliable foraging opportunities showed significantly less interannual variation in their stopover use than birds using stopovers with less reliable foraging opportunities. Our results thus highlight the need to further deepen our understanding of the role of cognitive processes in individual variation in migratory behaviour.

Resource availability and heterogeneity shape the self‐organisation of regular spatial patterning

Explaining large-scale ordered patterns and their effects on ecosystem functioning is a fundamental and controversial challenge in ecology. Here, we coupled empirical and theoretical approaches to explore how competition and spatial heterogeneity govern the regularity of colony dispersion in fungus-farming termites. Individuals from different colonies fought fiercely, and inter-nest distances were greater when nests were large and resources scarce—as expected if competition is strong, large colonies require more resources, and foraging area scales with resource availability. Building these principles into a model of inter-colony competition showed that highly ordered patterns emerged under high resource availability and low resource heterogeneity. Analysis of this dynamical model provided novel insights into the mechanisms that modulate pattern regularity and the emergent effects of these patterns on system-wide productivity. Our results show how environmental context shapes pattern formation by social-insect ecosystem engineers, which offers one explanation for the marked variability observed across ecosystems.

Data from: Seasonal variation in resource selection by subadult golden eagles in the Great Basin Desert

Golden eagles (Aquila chrysaetos) are a long-lived and wide-ranging species believed to be stable or in slight decline across North America. Golden eagles have an extended subadult stage (4–5 years) that is critical to maintaining recruitment into the breeding population and population viability. We investigated patterns of resource selection for subadults in the Great Basin Desert of the western United States during summer and winter, 2013–2019. We monitored 46 subadults with GPS transmitters and related locations (n = 99,037) with predictors hypothesized to influence seasonal patterns of space use with mixed-effects logistic regression.

Data from: Resource exploitation collapses the home range of an apex predator

Optimizing energy acquisition and expenditure is a fundamental trade-off for consumers, strikingly reflected in how mobile organisms use space. Several studies have established that home range size decreases as resource density increases, but the balance of costs and benefits associated with exploiting a given resource density is unclear. We evaluate how the ability of consumers to exploit their resources through movement (termed "resource exploitation") interacts with resource density to influence home range size. We then contrast two hypotheses to evaluate how resource exploitation influences home range size across a vast gradient of productivity and density of human-created linear features (roads and seismic lines) that are known to facilitate animal movements. Under the Diffusion Facilitation Hypothesis, linear features are predicted to lead to more diffuse space use and larger home ranges. Under the Exploitation Efficiency Hypothesis, linear features are predicted to increase foraging efficiency, resulting in less space being required to meet energetic demands and therefore smaller home ranges. Using GPS telemetry data from 142 wolves (Canis lupus) distributed over more than 500,000 km2, we found that wolf home range size was influenced by the interaction between resource density and exploitation efficiency. Home range size decreased as linear feature density increased, supporting the Exploitation Efficiency Hypothesis. However, the effect of linear features on home range size diminished in more productive areas, suggesting that exploitation efficiency is of greater importance when resource density is low. These results suggest that smaller home ranges will occur where both linear feature density and primary productivity are higher, thereby increasing regional wolf density.

Exploitative competition for floral resources reduces sugar intake but differently impacts the foraging behaviour of two non-bee flower visitors

Identifying which behavioural strategies maximize individual fitness is a key objective in ecology. Organisms are known to adapt their foraging behaviour to their environment in response to abiotic and biotic constraints, such as the distribution of resources or the presence of competitors. For instance, bees are known to avoid recently visited flowers and thus focus their foraging on more rewarding patches. Whether other flower-visiting insects adapt their foraging behaviour in response to exploitative competition for floral resources remains unknown. Here, we asked if a predatory hoverfly (Episyrphus balteatus) and a parasitoid (Aphidius colemani) 1) are physiologically impacted by flower resource limitation following exploitation of flowers by a competitor (either the bumblebee Bombus terrestris or E. balteatus); 2) have the ability to discriminate flowers that were previously exploited by a competitor; and 3) modify their foraging behaviour accordingly. Episyrphus balteatus and A. colemani individuals foraging on previously exploited flowers were found to be less concentrated in sugar compounds, especially in fructose and glucose, suggesting that previously exploited flowers contained less available sugars. Nevertheless, individuals did not avoid previously exploited patches in the choice experiment. On the contrary, E. balteatus females preferentially landed on inflorescences that had previously been exploited by conspecifics (but not by B. terrestris), while A. colemani did not show preferences between inflorescences. However, female hoverflies spent more time feeding on unexploited patches, suggesting that exploited patches were resource limited. To our knowledge, this study provides the first evidence of the use of social cues among E. balteatus individuals in food foraging strategies. It also shows that even insects with tiny nectar requirements, such as parasitoids, can suffer from heavy exploitative competition. Such results may have applied consequences for the understanding of natural enemy conservation, in particular in agroecosystems where competition with honeybees may be important.

Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to determine the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual / interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (FST = 0.0240; P < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental drivers suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome, suggestive of selective sweeps. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with the larval dispersal modelling, which suggested a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.

opencc-zeroDec 2021View details →

Data from: Loss of fungal symbionts at the arid limit of the distribution range in a native Patagonian grass – resource ecophysiological relations

1. Crucial to our understanding of plant ecology is the consideration of the eco-physiological responses and constraints of plant-fungal symbioses throughout the native distribution range of their host. 2. We examined key eco-physiological roles of two co-occurring fungal symbionts [Epichloë endophytes and arbuscular mycorrhizal fungi (AMF)] in the endemic grass Hordeum comosum across a wide bioclimatic gradient and contrasting grazing severity. We sampled H. comosum plants along four humid-to-arid transects in Patagonia, Argentina, covering its entire distribution range and determined Epichloë presence, AMF root colonization, nitrogen and phosphorus concentration, intrinsic water use-efficiency (iWUE, the ratio of photosynthesis to stomatal conductance) and 18O-enrichment of cellulose in shoots. 3. Root colonization by AMF increased with Epichloë-presence. All plants hosted Epichloë in the humid range of the gradient, but symbioses occurrence decreased towards arid sites which also displayed severe grazing symptoms at site level. 4. Symbiosis with Epichloë correlated positively with shoot nitrogen concentration in the centre of the distribution range, and with shoot phosphorus concentration across the entire distribution range. 5. The site-level relationship of AMF colonization with 18O-enrichment and iWUE suggested that mycorrhiza boosted stomatal conductance in humid environments but curbed it in arid environments. 6. While the interpretation of interactions and potential causalities from observational studies should be done with caution, this study demonstrates distinct correlations between plant-fungal symbiont associations and key resource parameters (phosphorus, nitrogen, and iWUE vs 18O-enrichment). Such correlations may suggest particular functional roles for these symbionts in the ecology of their host plant.

opencc-zeroDec 2021View details →

Data from: Resource heterogeneity but not inbreeding affects growth and grouping behaviour in socially foraging juvenile cichlid fish

1. Spatial food distribution determines resource profitability, defensibility and encounter rate of foragers. Clumped food distribution can promote aggressiveness and resource monopolisation, in turn increasing within-group variation in food intake and growth. However, the effects of food distribution may depend on foraging strategies. Little is known about the impact of spatial food heterogeneity on growth and grouping behaviour in social foragers in the absence of monopolisation. 2. Social foraging is present in many fishes, particularly at early juvenile life stages when fish are especially sensitive to environmental variation. Here, a heterogeneous food distribution may impair foraging success and growth and juveniles may increase sociability to attain social information about food resources. 3. We examined the impact of the spatial distribution of food as well as inbreeding on growth and social behaviour in juveniles of the cichlid fish Pelvicachromis pulcher. Inbred individuals often show poorer performance than outbred individuals (inbreeding depression), but inbreeding effects can be environment-dependent. In the experiment, in- and outbred fish were reared in a split-clutch design either under homogeneously distributed or spatially clumped food conditions for eight weeks starting one week after juveniles could actively feed. We documented growth and performed a shoaling assay and a sociality test (choice between a large vs. a small shoal) after six weeks. 4. Spatial food distribution did not affect within-group body length variation, but individuals reared under clumped food conditions were smaller. Shoals of the different feeding conditions differed in social behaviour. Shoals of the clumped treatment group showed higher variation in inter-individual distances compared to shoals of the homogeneous treatment group. Furthermore, focal fish of the clumped treatment adjusted their association preference to the position of the groups' largest individual. We did not find significant inbreeding or environment-dependent inbreeding effects regarding growth or social behaviour. 5. Our study suggests that a clumped food distribution can impede localisation of food resources and thus growth in juvenile social foragers. Accordingly, in heterogeneous environments, the use of social information may be highly relevant to increase individuals' foraging success potentially explaining orientation on successful foragers, i.e. large individuals. Inter-individual variation in juvenile social behaviour may precede variation in food monopolisation capability and in growth emerging at later life stages.

opencc-zeroDec 2021View details →

Predator community and resource use jointly modulate the inducible defense response in body height of crucian carp

Phenotypic plasticity can be expressed as changes in body shape in response to environmental variability. Crucian carp (Carassius carassius), a widespread cyprinid, displays remarkable plasticity in body morphology and increases body depth when exposed to cues from predators, suggesting the triggering of an anti-predator defense mechanism. However, these morphological changes could also be related to resource use and foraging behavior, as an indirect effect of predator presence. In order to determine whether phenotypic plasticity in crucian carp is driven by a direct or indirect response to predation threat, we compared twelve fish communities inhabiting small lakes in southeast Norway grouped by four categories of predation regimes: no predator fish, or brown trout (Salmo trutta), perch (Perca fluviatilis) or pike (Esox lucius) as main piscivores. We predicted the body shape of crucian carp to be associated with the species composition of predator communities, and that the presence of efficient piscivores results in a deeper body shape. We use stable isotope analyses to test if this variation in body shape was related to a shift in individual resource use – i.e., littoral rather than pelagic resource use would favor the development of a specific body shape - or other environmental characteristics. The results showed that increasingly efficient predator communities induced progressively deeper body shape, larger body size and lower population densities. Predator maximum gape size and individual trophic position were the best variables explaining crucian carp variation in body depth among predation categories, while littoral resource use did not have a clear effect. The gradient in predation pressure also corresponded to a shift in lake productivity. These results indicate that crucian carp have a fine-tuned morphological defense mechanism against predation risk, triggered by the combined effect of predator presence and resource availability.

opencc-by-4.0Jan 2022View details →

Data from: Intersexual flower differences in an andromonoecious species: small pollen‐rich staminate flowers under resource limitation

Data archived here were used for analyses in Murakami et al. "Intersexual flower differences in an andromonoecious species: small pollen‐rich staminate flowers under resource limitation." Data is in three worksheets.

opencc-zeroJan 2022View details →

Data from: Floral resource diversification promotes solitary bee reproduction and may offset insecticide effects – evidence from a semi-field experiment

Pollinator declines in agricultural landscapes are driven by multiple stressors, but potential interactions of these remain poorly studied. Using a highly replicated semi-field study with 56 mesocosms of varying wild plant diversity (2-16 species) and oilseed rape treated with a neonicotinoid, we tested the interacting effects of resource diversity and insecticides on reproduction of a solitary wild bee. Compared to mesocosms with oilseed rape monocultures, availability of resources from wild plants complementing oilseed rape doubled brood cell production. In addition, bee reproduction increased due to plant diversity and identity effects. Exposure to neonicotinoid-treated oilseed rape reduced bee larval to adult development by 69%, but only in mesocosms with oilseed rape monocultures. Availability of complementary flower resources can thus offset negative effects of neonicotinoid-treated oilseed rape on wild bee reproduction. Policy should encourage the implementation of diverse floral resources mitigating negative effects of crop monocultures and insecticides, thereby sustaining solitary bee populations in agricultural landscapes.

opencc-zeroJan 2022View details →

Impact of water resources development on connectivity and primary productivity across a tropical river floodplain

1. Floodplain wetlands provide an important subsidy for riverine food webs as sites of high algal production. However, this subsidy depends on the degree of landscape connectivity during flood pulses, which provides the opportunity for movement of higher order consumers between rivers and floodplains to access these productive habitats. Changes in floodplain inundation extent and duration, due to variable wet season flows or water resources development (WRD), can impact landscape connectivity and ultimately the magnitude of the food web subsidy. 2. We explored landscape connectivity using graph theory and derived four new metrics to measure how different flow scenarios can affect connectivity and algal production. We considered a historic scenario with the present level of water resource development in our study area, the Mitchell River, and a WRD scenario with the inclusion of three new dams in the catchment. We generated 240 unique daily spatial graphs, using surface water inundation maps across 40-day flood events to compare a dry year (2006), an average flow year (2001), and a wet year (2009) with and without a WRD scenario. 3. Drier years and WRD scenario resulted in floodplain fragmentation, potentially constraining the movement of higher order consumers. Changes in connectivity due to WRD resulted in predicted reductions of up to 26% of algal production on the floodplain that was otherwise connected to the main river channels. 4. Synthesis and applications. The approach developed in this study provides new metrics to identify how changes in floodplain surface water extent due to water resource development and climatic variation may impact ecosystem function such as connectivity that facilitates access of higher order consumers to primary production in floodplain wetlands. With a direct link to river flow alteration, these metrics can inform catchment planning and management to ensure that the conservation of floodplain ecosystem functions is adequately considered in water resource management decisions.

opencc-zeroJan 2022View details →

Influence of habitat quality and resource density on breeding-season female monarch butterfly (Danaus plexippus) movement and space use in north-central USA agroecosystem landscapes

<ol> <li> The eastern North American monarch butterfly is at risk of quasi-extinction due, in part, to the loss of breeding habitat in agricultural landscapes of the USA Midwest. Because adult females are not patch residents, egg abundance and distribution across the landscape are a function of their perceptual range, flight directionality, and flight step lengths. Conservation actions that account for habitat use in agricultural landscapes can enhance functional connectivity.</li> <li>Field-captured females (n=114) were released in a 64-ha area containing restored prairies, grass-dominated fields, and crop fields in Floyd County, Iowa, USA, and two 1,000 m linear north-south sections of grass-dominated roadside along secondary roads (~ 35 ha) with different proximity to prairie habitat in rural Story County, Iowa. Radio-tagged or untagged monarchs were released in areas with high-density, low-density, and zero density of forage and oviposition resources, as well as on habitat edges between high and zero-density habitats. Monarchs were observed for one hour. Radio-tagged individuals that flew beyond visual detection were relocated using handheld radio telemetry.</li> <li>Monarchs moved within and between habitat classes and typically performed up-wind search behavior. Monarchs successfully located resources, with some flying over 500 m to find high-density areas, providing evidence that the monarch's perceptual distance is > 100 m. Regardless of habitat class or field site, most step lengths were < 50 m, and turn angles were directional. Large steps (≥ 50 m) crossing habitat boundaries occurred with approximately half of the monarchs, which may indicate initiation of long-range searches for suitable habitat, consistent with their vagile behavior. Establishing habitat patches 50 m apart in agricultural landscapes would facilitate efficient movement.</li> <li>This study provides an extensive dataset of directly observed breeding-season monarch butterflies to assess the utilization of agricultural landscapes. Documentation of step lengths > 50 m in complex, agricultural landscapes would not have been possible without the aid of radio telemetry. Results provide improved estimates of perceptual range and flight patterns within and between habitat patches that support models that simulate natural population dynamics to enable conservation planning at a landscape scale.</li> </ol>