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Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans, the causative agent of White-Nose disease in bats
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Dataset used in the article: Evaluation of goal recognition systems on unreliable data and uninspectable agents
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Supplementary material 4 from: Augustinus BA, Lommen STE, Fogliatto S, Vidotto F, Smith T, Horvath D, Bonini M, Gentili RF, Citterio S, Müller-Schärer H, Schaffner U (2020) In-season leaf damage by a biocontrol agent explains reproductive output of an invasive plant species. NeoBiota 55: 117-146. https://doi.org/10.3897/neobiota.55.46874
Figure S1. Mean plant volume ± se of A. artemisiifolia plants measured during the experiment in the four experimental sites
QSAR dataset for anti melanogenic agents - tyrosinase inhibition
<p>Kindly cite if you are using the dataset for predicting the tyrosinase inhibitory activity for your compounds.</p> <p>We generated a validated QSAR model with a dataset consisting of 69 thio-semicarbazone derivatives to elucidate the physicochemical properties of compounds essential for tyrosinase inhibition and to identify novel lead molecules with enhanced tyrosinase inhibitory activity and bioavailability.</p> <p> </p> <p>Thanks,</p> <p>Authors</p>
Dreams4Cars final Agent's abilities video
<p><em>This video shows a collection of simulations that demonstrate some of the Dreams4Cars Agent abilities. All behaviours shown here are emergent behaviours following the agent architecture described in the main video of the project.</em></p> <p><em>See paper: </em>M. Da Lio, R. Donà, G. P. Rosati Papini and K. Gurney, "Agent Architecture for Adaptive Behaviours in Autonomous Driving," IEEE Access, to be published. </p>
Resultados encuesta a usuarios de librerías proyecto: Libreros, librerías y lectores en Bogotá, Medellín y Cali. Espacios, agentes y experiencias en el presente
<p>Resultado de aplicación encuesta a usuarios de librerías del proyecto "Libreros, librerías y lectores en Bogotá, Medellín y Cali. Espacios, agentes y experiencias en el presente", realizado por el instituto Caro y Cuervo, Universidad de Antioquia y Universidad Jorge Tadeo lozano</p>
Falls Lake Agent-based Model Critical Transitions Dataset
<p>Data files are provided here. They are output from the Falls Lake ABM at <a href="https://github.com/maskarb/FallsLakeABM">https://github.com/maskarb/FallsLakeABM</a>. Four management scenarios are simulated for 16 shifting climate scenarios. Management Scenario 1 is no management. Management Scenario 2 is retrofitting. Management Scenario 3 is retrofitting with light drought restrictions. Management Scenario 4 is retrofitting with severe drought restrictions. The 16 shifting climate scenarios correspond to shifting factors equal to 0.25 - 1.0, increasing in 0.05 increments. For each of the 64 settings (16 climate settings X 4 management scenarios), 100 simulations were run to capture stochasticity.</p> <p>Files in Results-mgmt-x folders show the agent-based modeling results for each simulation. Data files (for example, res-mgmt-1-s-0.25-5.txt) describe the storage and deficit for each of the simulations in million cubic meters, reported at a monthly timestep. Columns 5-9, inflow, storage, outflow, totalWaterSupply, waterSupply, report monthly flows. </p> <p>Files in EWS-mgmt-X-window-25 shows the value of each early warning signals indicator calculated for log-transformed reservoir storage for each of 100 simulations, for management strategies 1-4 and shifting factors. Winsize is set at 25%, which means that EWS indicators are not calculated until time step 300, or 25% of 1200 time steps.</p>
Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis
<p>We provide data and code needed to re-do the analyses and figures presented in our preprint <em>Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent </em>Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ):</p> <p>- data table : <em>data_repetition01.xls</em>, with informations about each column in the file <em>data_repetition_info.pdf</em></p> <p>- data table : <em>data_individual01.xls</em>, with informations about each column in the file <em>data_indivdual_info.pdf</em></p> <p><em>- </em>The R code used to do the analyses : <em>Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R</em></p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Learning agents in black-scholes financial markets
<p>Black-Scholes (BS) is a remarkable quotation model for European option pricing in financial markets. Option prices are calculated using an analytical formula whose main inputs are strike (at which price to exercise) and volatility. The BS framework assumes that volatility remains constant across all strikes, however, in practice it varies. How do traders come to learn these parameters? We introduce natural agent-based models, in which traders update their beliefs about the true implied volatility based on the opinions of other traders. We prove exponentially fast convergence of these opinion dynamics using techniques from control theory and leader-follower models, thus providing a resolution between theory and market practices. We allow for two different models, one with feedback and one with an unknown leader.</p>
Inhibition mechanism and antibacterial activity of natural antibacterial agent citral on bamboo mold and its anti- mildew effect on bamboo
<p><span><span>Bamboo, a natural material, has been widely used in the fields of decoration, architecture and furniture. However, bamboo is easy to mildew and lose its use value. In this paper, inhibition mechanism and antibacterial activity of natural antibacterial agent citral on bamboo mold and its anti- mildew effect on bamboo were studied. The results showed that citral could change the shape of mycelium, destroy the integrity of mycelium structure, cell wall, and cell membrane structure, thereby causing leakage of nucleic acid, protein, and other substances in the cell, as well as destroy the pH balance of the inside and outside of the cell, to inhibit or kill mold. When the concentration of citral is 100mg/mL, the antibacterial rates of citral against <i>Penicillium citrinum </i>(PC), <i>Trichoderma viride</i> (TV), <i>Aspergillus niger</i> (AN) and a hybrid fungi group comprising PC, TV, and AN (Hun) were more than 100%. However, compared with the direct effect of citral on mold, the antibacterial property of bamboo treated with citral was significantly reduced, the mildew proof effect can be achieved only if the concentration of citral to treat bamboo is increased to more than 2 times of the concentration of citral directly acting on mold.</span></span></p>
FIGURES 1–6 in A new species of Bithoracochaeta Stein (Diptera: Muscidae) with comments on Mexican species of the genus and their implication as possible biocontrol agents for greenhouses pests
FIGURES 1–6. Bithoracochaeta couriae sp. nov. 1. Male, lateral view of thorax showing setae on anepisternum and katepisternum. 2. Male, sternite 5. 3-6. Male terminalia (Holotype). 3. Cercal plate, surstyli and epandrium, dorsal view. 4. Cercal plate, surstyli and epandrium, left lateral view. 5. Aedeagus, dorsal view. 6. Aedeagus, lateral view. Abbreviations: Aede= aedeagus; Anst= anepisternum; Cept= cercal plate; Epan= epandrium; Pregt= pregonite; Hypa= hypandrium; Ktst= katepisternum; Surs= surstylus.
FIGURES 7–8 in A new species of Bithoracochaeta Stein (Diptera: Muscidae) with comments on Mexican species of the genus and their implication as possible biocontrol agents for greenhouses pests
FIGURES 7–8. Bithoracochaeta couriae sp. nov. 7. Male feeding upside down. 8. Female feeding on Psychodidae.
Herbivory of a biocontrol agent on a native plant causes an indirect trait-mediated non-target effect on a native insect
<p>Identifying food web linkages between biocontrol agents of invasive plants and native species is crucial for predicting indirect non-target effects. Biocontrol insects can integrate into food webs within recipient habitats and influence native insects through apparent competition (altering shared natural enemies) or density-mediated exploitation competition (changing density of native plants). However, whether and how trait-mediated exploitation competition (modifying native plant chemical defenses and volatiles profiles) can produce indirect non-target effects remains largely overlooked, despite plant phenotypic responses to insect herbivory being common and widely documented.</p> <p>The beetle <em>Agasicles hygrophila</em> was introduced into China for management of weedy <em>Alternanthera philoxeroides</em>, but it also attacks the native congener <em>A. sessilis</em>, which may have indirect non-target effects on the native beetle <em>Cassida piperata </em>that also feeds on <em>A. sessilis</em>. Here, we examined the relationships among the abundance of <em>A. hygrophila</em> and <em>C. piperata</em>, and <em>A. sessilis</em> coverage in the field. Then, we investigated the impact of <em>A. hygrophila</em> herbivory on <em>C. piperata</em> development and oviposition, as well as<em> A. sessilis</em> primary metabolites and leaf volatiles.</p> <p><em>Cassida piperata</em> abundance was not related to <em>A. sessilis</em> coverage, but <em>C. piperata</em> was less abundant on plants with more<em> A. hygrophila</em> in the field survey and on plants with more prior<em> A. hygrophila</em> damage in the field cage experiment. <em>Cassida piperata </em>development was inhibited by prior <em>A. hygrophila </em>herbivory in bioassays in enemy-free conditions and they preferred to oviposit on <em>A. sessilis </em>plants that had experienced little or no <em>A. hygrophila</em> damage. <em>Agasicles hygrophila</em> herbivory decreased <em>A. sessilis</em> foliar glucose and protein, and substantially changed its leaf volatile blend.</p> <p>Synthesis. Our results show that <em>A. hygrophila</em> has its major indirect non-target effects on <em>C. piperata </em>through trait-mediated exploitation competition, rather than apparent competition or density-mediated exploitation competition. Our results demonstrate a new mechanism for indirect non-target effects of biocontrol agents. Furthermore, our results indicate that minor and temporary negative impacts on non-target plants might propagate to higher trophic levels and such negative impacts can strengthen with increasing intensity of the direct non-target effect.</p>
Field-based ecological studies to assess prospective biological control agents for invasive alien plants: an example from giant rat's tail grass
<p>1. Biological control (biocontrol) of invasive alien plants is a widely utilised weed management tool. Prospective biocontrol agents are typically assessed through host-specificity testing and pre-release efficacy studies performed in quarantine. However, rearing of the potential biocontrol agents and/or test plants is often difficult or impossible under quarantine conditions. Moreover, practitioners may attain laboratory-artefacts in quarantine, which may result in the potential agent being needlessly rejected. Field-based studies in the weed's indigenous distribution could overcome these issues.</p> <p>2. Sporobolus pyramidalis and Sporobolus natalensis (giant rat's tail grass; Poaceae) are indigenous in Africa but have become problematic invasive alien plants in Australia. A previous biocontrol programme was terminated because the candidate agent could not be reared and tested in quarantine. We performed field-based host-specificity and efficacy studies for prospective biocontrol agents in South Africa (indigenous distribution). Forty-seven non-target grass species were sampled during host-specificity assessments. Candidate agent efficacy was estimated based on damage to the target weeds, for each host-specific candidate individually and in combination with other host-specific candidates.</p> <p>3. Three species of endophagous wasps were deemed host-specific. Efficacy assessments identified an undescribed stem-boring wasp (Tetramesa sp.) species as the most damaging candidate. A second Tetramesa species was much less damaging alone but had a cumulative impact on the plant in combination with the more damaging Tetramesa species. Both Tetramesa species are recommended for importation into quarantine in Australia for confirmatory host-specificity testing with a significantly reduced test plant list.</p> <p>4. Synthesis and applications: Similar field-based assessments in the indigenous distribution of weeds targeted for biocontrol could be included in future programmes. Where rearing of potential agents and/or test plants is difficult or impossible under quarantine conditions, our field-based method provides an alternative. Where quarantine-based testing is feasible, this method ensures that only candidates that have passed an ecologically realistic host-specificity and potential efficacy screening are imported into quarantine. This may reduce the number of agents that are imported and the length of time each agent is kept in quarantine. This is advantageous because quarantine space is highly valuable and is usually a limiting factor in pre-release assessments of biocontrol agents.</p>
Data from: Gape-limited predators as agents of selection on the defensive morphology of an invasive invertebrate
Invasive species have widespread and pronounced effects on ecosystems and adaptive evolution of invaders is often considered responsible for their success. Despite the potential importance of adaptation to invasion, we still have limited knowledge of the agents of natural selection on invasive species. Bythotrephes longimanus, a cladoceran zooplankton, invaded multiple Canadian Shield lakes over the past several decades. Bythotrephes have a conspicuous caudal process (tail spine) that provides a morphological defense against fish predation. We measured viability selection on the longest component of the Bythotrephes spine, the distal spine segment, through a comparison of the lengths of first and second instar Bythotrephes collected from lakes differing in the dominance of gape-limited predation (GLP) and non-gape-limited predation (NGLP) by fish. We found that natural selection varied by predator gape-limitation, with strong selection (selection intensity: 0.20-0.79) for increased distal spine length in lakes dominated by GLP, and no significant selection in lakes dominated by NGLP. Further, distal spine length was 17% longer in lakes dominated by GLP, suggesting the possibility of local adaptation. As all study lakes were invaded less than twenty years prior to our collections, our results suggest rapid divergence in defensive morphology in response to selection from fish predators.
Data from: Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution
Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.
Data from: Spatio-temporal variation of biotic and abiotic stress agents determines seedling survival in assisted oak regeneration
1. Mediterranean oak woodlands are currently undergoing considerable anthropogenic changes that globally threaten their long-term persistence. Restoration efforts via assisted regeneration depend on species traits and type of stress. However, how different sources of stress vary across space (microsites) and time (intra and inter-annual variation) for co-occurring oak species remains largely unknown. 2. We examined spatio-temporal variation of biotic (herbivory, seed predation) and abiotic (drought) stress agents to evaluate seedling survival across different regeneration microsites, and considering two climatically contrasting years. We used two co-occurring species of contrasting ecology and leaf traits in California oak woodlands: the deciduous Quercus lobata and the evergreen Q. agrifolia. 3. Most oak seedlings (98.8%) suffered from some type of stress. For both species, summer drought was the main cause of mortality, followed by rodent damage, ungulate browsing and insect damage. Rodents represented the predominant biotic stress, as all rodent-affected seedlings eventually died. Interactions among stress factors were nuanced: insect and ungulate-browsing stresses were greater during dry year, whereas rodent damage was similar in dry and average years. Intra-annually, rodent damage was the main stress agent in early spring, whereas water stress and ungulate-browsing were greater in late spring-early fall. Plant species traits were also determinant: overall, the evergreen species had greater survival probability than the deciduous one. 4. Across microsites, water stress showed higher occurrence in open grassland habitats, while rodent damage was prevalent under palatable shrubs and ungulate browsing under conspecific trees. Shrub and tree cover reduced damage attributed to water stress but increased rodent and ungulate damage, respectively. Interestingly, lower water stress but higher rodent damage was found further inside the shrub cover. 5. Synthesis and applications. Intra and inter-annual variation are critical determinants of stress type and intensity on oak recruitment. Spatial variation (microsite identity) is also informative to manipulate stress agent impact. We conclude that assisted regeneration should consider not only the predominance and lethality of each stress type and microsite, but also the interactions thereof and thus manipulate protective microsites accordingly.
Design of a near infrared fluorescent ureter imaging agent for prevention of ureter damage during abdominal surgeries - Supplemental Information
<p>Design of a near infrared fluorescent ureter imaging agent for prevention of ureter damage during abdominal surgeries - Supplemental Information</p>
Data from: Modelling mobile agent-based ecosystem services using kernel weighted predictors
1. Agriculture benefits from ecosystem services provided by mobile agents, such as biological pest control by natural enemies and pollination by bees. However, methods that can generate spatially explicit predictions and maps of these ecosystem services based on empirical data are still scarce. 2. Here we propose a generic statistical model to derive kernel functions to characterize the spatial distribution of ecosystem services provided by mobile agents. The model is similar in spirit to a generalized linear model, and uses data of landscape composition and ecosystem services assessed at target sites to estimate parameters of the kernel. The approach is tested in a simulation study and illustrated by an empirical case study on parasitism rates of the diamondback moth Plutella xylostella. 3. The simulation study shows that the scale parameter of the exponential power kernel can be estimated with limited bias, whereas estimation of the shape parameter is difficult. For the case study the model provides biologically relevant estimates for the kernel associated with parasitism of Plutella xylostella. These estimates can be used to generate ecosystem service maps for existing or planned landscapes. The case study reveals that predictions can be sensitive to the parameter values for the width and shape of the kernel, and to the link function used in the statistical model. 4. In the last two decades numerous empirical studies assessed ecosystem services at target sites and related these to the surrounding landscape. Our method can take advantage of these data by estimating underlying kernels that can be used to map the spatial distribution of ecosystem services. However, empirical data that can discriminate between alternative kernel shapes remain critical.
Data from: Density dependence, precipitation, and biological control agent herbivory influence landscape-scale dynamics of the invasive Eurasian plant Linaria dalmatica
1. Resource availability and natural enemies are among the most commonly cited mechanisms affecting competitive ability of invasive plants, but their simultaneous effects on plant dynamics are seldom evaluated in the field. Understanding how endogenous and exogenous factors affect invasive plant abundance is essential when evaluating the impact of classical weed biological control agents because misinterpretations of the mechanisms regulating plant demography may bias inference of herbivore impact. 2. In this study we report results from a citizen-science monitoring program initiated to evaluate the effects of the stem–mining weevil Mecinus janthiniformis on the Eurasian invasive weed Dalmatian toadflax Linaria dalmatica. We used a discrete model of population dynamics to evaluate the relative importance of endogenous and exogenous processes affecting changes in ramet density of L. dalmatica at 38 spatially replicated sites in Idaho, USA. 3. Analysis of per capita population growth rates based on ramet density indicated the presence of direct density dependence, which was most likely due to intraspecific competition. Changes in ramet density were not influenced by the abundance of the resident plant community. 4. Precipitation had a strong, positive effect on ramet density of L. dalmatica while the abundance of M. janthiniformis had a weaker, but significant, negative effect after accounting for the density dependence. There was no support for an interactive effect between precipitation and herbivory. 5. Synthesis and applications. Our results indicate that biological control is an important factor affecting weed population growth at the landscape scale, but they also suggest that biological control impact may vary considerably on local infestations due to site-specific variation in rainfall and density-dependent processes. We recommend that invasive plant management strategies integrate precipitation and biological control agent monitoring into their programs to estimate expected biological control efficacy. Alternative control methods should be prioritized in areas where herbivore impact is expected to be low.
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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.