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Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape
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Inspecting JavaScript Vulnerability Mitigation Patches with Automated Fix Generation in Mind
<p>Software security has become a primary concern for both the industry and academia in the recent years.<br> As dependency on critical services provided by software systems grows globally, a potential security threat in such systems poses higher and higher risks (e.g. economical damage, threat to human life, criminal activity).</p> <p>Finding potential security vulnerabilities at the code level automatically is a very popular approach to aid security testing.<br> However, most of the methods based on machine learning and statistical models stop at listing potentially vulnerable code parts and leave their validation and mitigation to the developers.<br> Automatic program repair could fill this gap by automatically generating vulnerability mitigation code patches.<br> Nonetheless, it is still immature, especially in targeting security relevant fixes.</p> <p>In this work we try to establish a path towards automatic vulnerability fix generation techniques in the context of JavaScript programs.<br> We inspect 361 actual vulnerability mitigation patches collected from vulnerability databases and GitHub.<br> We found that vulnerability mitigation patches are not short on average and in many cases affect not just program code but test code as well.<br> These results point towards that a general automatic repair approach targeting all the different types of vulnerabilities is not feasible.<br> The analysis of the code properties and fix patterns for different vulnerability types might help in setting up a more realistic goal in the area of automatic JavaScript vulnerability repair.</p>
Patch-level facilitation fosters high-Andean plant diversity at regional scales
<p>Survey of the alpine vegetation in seven mountains of the Patagonian Andes from January to March of 2017 and 2018. On each mountain, we established one study site at each of three elevations (1600, 1800 and 2000 m). Accordingly, we sampled a total of 21 alpine plant communities (i.e., seven mountains x three elevations) dominated by cushion plants. At each community, 50 individual cushion plants were haphazardly selected within an area of approx. 0.5 ha, pairing each cushion with an adjacent non-cushion or open area 50 cm away in a random direction. In order to sample a similar surface in the surrounding open area, a wire hoop was shaped to match the size of the sampled cushion that was then placed on the ground. The number and identity of all plant species were recorded at both cushion and open area plots. Given that cushion plants are roughly elliptical, microsites were defined as elliptical plots, and thus, the longer and shorter axes of each cushion were measured as an approximate estimation of its area. In total, we sampled 2100 plots (1050 cushion plants and 1050 open area plots).</p>
Dispersal of Drosophila melanogaster over landscapes with different food patch structures
<p>Theoretical and empirical studies often show that within populations, individuals vary in their propensity to disperse. We aspired to understand how this behavioural variation is impacted by the distribution and pattern of food patches across a landscape. In a series of experiments, we examined how inter-patch distance and the distribution of food patches influenced dispersal in wild-type strains of <em>Drosophila melanogaster</em> with natural allelic variants of the <em>foraging</em> (<em>for</em>) gene known to influence dispersal in this species. The "rover" strain was homozygous for the <em>for</em><sup>R</sup> allele (more dispersive) whereas the "sitter" strain was homozygous for <em>for</em><sup>s</sup> (less dispersive). We also assessed an outbred population of flies with an unknown dispersal propensity. Dispersal was assayed in a multi-patch lab arena (25 cells, 5 x 5 array). In the inter-patch distance trials, landscapes of two different sizes (small vs. large) were used, both with food in all 25 cells. Dispersal was reduced in the large landscape relative to the small landscape for all three fly strains. Sitter dispersal was lowest relative to both rovers and the outbred flies, whose dispersal tendencies were similar. In the patch distribution trials, flies were assayed in landscapes with varying distribution and number of cells containing food. Dispersal generally increased as the number of patches with food increased, however, rovers and sitters adopted similar dispersal strategies when food was fixed and limited. Conversely, their strategies differed when the total amount of food increased along with the number of patches. We found that both the inter-patch distance and distribution can influence dispersal. However, the effect of inter-patch distance and distribution on dispersal depends on genotype x environment interaction (G x E). Our findings highlight the importance of considering G x E when assessing how dispersal strategies and landscape dynamics influence the distribution of animal communities.</p>
Impact of Combining Syntactic and Semantic Similarities on Patch Prioritization
<p>This dataset contains 246 bugs, their fixes and corresponding buggy projects from historical bug fixes dataset (https://github.com/xuanbachle/data-bugfixes) that fulfill the following criteria:</p> <ol> <li>Unique</li> <li>Satisfy redundancy assumption at file level</li> <li>Fixed by applying replacement mutation</li> <li>Require fixing at expression level</li> <li>Having available project and dependency files</li> </ol> <p>For details, please view https://www.scitepress.org/Link.aspx?doi=10.5220/0009411301700180</p>
Figure 6 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 6 Strict consensus of two of most parsimonious trees based on morphology. Voucher specimens were chosen from those used in ongoing anchored enrichment molecular analyses. Some taxa were added for better coverage of Tetrastichinae. Unambiguous character state changes are plotted with bars.
Figure 3 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 3 A–F. AKressleinius celans gen. et sp. nov. holotype female, mesosoma, lateral, tps = transepimeral sulcus BAprostocetus hibus, mesosoma, lateral, syn = syntergum CCirrospilus cinctithorax, mesosoma lateral DPnigalio coloni, mesosoma, lateral EAprostocetus hibus, mesosoma dorsal smg = submarginal grooves FNesolynx sp., mesosoma, dorsal.
Figure 2 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 2 A–E. AKressleinius celans gen. et sp. nov., holotype female, fore wing venation, pmv = postmarginal vein, ams = admarginal setae, sms = submarginal vein setae B, CPeckelachertus sp.: B fore wing C habitus DNesolynx sp. habitus EQuadrastichodella sp., habitus.
Figure 1 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 1 A–F.Kressleinius celans gen. et sp. nov., holotype female (SMNS BB-2847) A habitus B habitus, dorsal view, not = notaulus C body, ventral view, pl1 = propleuron D antenna, ocs = ocellar triangle sulcus E mesosoma, lateral, pre = prepectus, tps = transepimeral sulcus F mesosoma, oblique lateral, axl = axillula, pcs = propodeal callus setae, pet = petiole.
Figure 5 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 5 A–D. ASympiesis cf. conica, head, tfs = transfacial sulcus, scs = scrobal sulcus BCrataepus marbis, head, oos = occellar ocular sulcus, ocs = occellar triangle sulcus, uos = upper ocular sulcus CZagrammosoma americanum, mesosoma lateral, pcs = propodeal callus setae DFoersterella erdoesi, mesosoma, lateral.
Figure 4 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 4 A–F. AQuadrastichodella sp., head. F1 = first funicular segment C1 = first clavomere BSympiesis cf. conica, head CBurkseus vittatus, head DNaumanniola sp. head EAprostocetus hibus, mesosoma lateral pcs = propodeal callus setae FDicladocerus westwoodii, mesosoma lateral.
Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity
<p>Ecological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (<i>Zostera marina</i> L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution modelling to understand the contribution of environmental conditions, spatial distance between meadows, and species co-occurrences to epifaunal invertebrate abundance and distribution across the region. We found that patterns of taxonomic compositional similarity among meadows were inconsistent with dispersal limitation, and meadows in the same region were often no more similar to each other than meadows over 1000 km away. Abiotic environmental conditions (temperature, dissolved oxygen) explained a small fraction of variation in taxonomic abundances patterns across the region. We found novel co-occurrence patterns among taxa that could not be explained by shared responses to environmental gradients, suggesting the possibility that interspecific interactions influence seagrass invertebrate abundance and distribution. Our results suggest that biodiversity and ecosystem functions provided by seagrass meadows reflect ecological processes occurring both within meadows and across seascapes, and that management of eelgrass habitat for biodiversity may be most effective when both local and regional processes are considered.</p>
Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED
<p>Here we share the necessary files and scripts to run Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered protein studied in the preprint uploaded to bioRxiv (doi: https://doi.org/10.1101/2020.06.16.155374). It requires software GROMACS patched with PLUMED.</p>
Data from: Boundary strength analysis: combining colour pattern geometry and coloured patch visual properties for use in predicting behaviour and fitness
1.Colour patterns are used by many species to make decisions that ultimately affect their Darwinian fitness. Colour patterns consist of a mosaic of patches that differ in geometry and visual properties. Although traditionally pattern geometry and colour patch visual properties are analysed separately, these components are likely to work together as a functional unit. Despite this, the combined effect of patch visual properties, patch geometry, and the effects of the patch boundaries on animal visual systems, behaviour and fitness are relatively unexplored. 2.Here we describe Boundary Strength Analysis (BSA), a novel way to combine the geometry of the edges (boundaries among the patch classes) with the receptor noise estimate (ΔS) of the intensity of the edges. The method is based upon known properties of vertebrate and invertebrate retinas. The mean and SD of ΔS (mΔS, sΔS) of a colour pattern can be obtained by weighting each edge class ΔS by its length, separately for chromatic and achromatic ΔS. This assumes those colour patterns, or parts of the patterns used in signalling, with larger mΔS and sΔS are more stimulating and hence more salient to the viewers. BSA can be used to examine both colour patterns and visual backgrounds. 3.BSA was successful in assessing the estimated conspicuousness of colour pattern variants in two species, guppies (Poecilia reticulata) and Gouldian finches (Erythrura gouldiae), both polymorphic for patch colour, luminance and geometry. 3D representations of the ΔS of patch edges (Fort Diagrams) of both species show that there is little or negative geometric correspondence between the chromatic and achromatic edges. All individuals have mΔS > 1.5 for both chromatic and achromatic measures, indicating the high within‐pattern contrast expected for display signals. In contrast from what one would expect from sexual selection, all guppies have mΔS less than expected from random contacts between all pairs of patch colour/luminance classes. The correlation between chromatic and luminance ΔS is negative in both species but zero when correlating all possible kinds of edges between the colours of each species and morph indicating non‐random colour geometry. 4.The pattern difference between chromatic and achromatic edges in both species reveals the possibility that chromatic and achromatic edges could function differently. The smaller than random expected mΔS values in guppies suggests an anti‐predator function because guppies are never found without predators. Moreover, mΔS could vary with predation intensity within and among species. BSA can be applied to any colour pattern used in intraspecific and interspecific behaviour. Seven predictions and four questions about colour patterns are presented. 5.In species which are very convex, both chromatic and luminance mΔS change with viewing angle; geometry of signalling is as important as signal geometry.
Data from: Taking movement data to new depths: Inferring prey availability and patch profitability from seabird foraging behavior
Detailed information acquired using tracking technology has the potential to provide accurate pictures of the types of movements and behaviors performed by animals. To date, such data have not been widely exploited to provide inferred information about the foraging habitat. We collected data using multiple sensors (GPS, time depth recorders, and accelerometers) from two species of diving seabirds, razorbills (Alca torda, N = 5, from Fair Isle, UK) and common guillemots (Uria aalge, N = 2 from Fair Isle and N = 2 from Colonsay, UK). We used a clustering algorithm to identify pursuit and catching events and the time spent pursuing and catching underwater, which we then used as indicators for inferring prey encounters throughout the water column and responses to changes in prey availability of the areas visited at two levels: individual dives and groups of dives. For each individual dive (N = 661 for guillemots, 6214 for razorbills), we modeled the number of pursuit and catching events, in relation to dive depth, duration, and type of dive performed (benthic vs. pelagic). For groups of dives (N = 58 for guillemots, 156 for razorbills), we modeled the total time spent pursuing and catching in relation to time spent underwater. Razorbills performed only pelagic dives, most likely exploiting prey available at shallow depths as indicated by the vertical distribution of pursuit and catching events. In contrast, guillemots were more flexible in their behavior, switching between benthic and pelagic dives. Capture attempt rates indicated that they were exploiting deep prey aggregations. The study highlights how novel analysis of movement data can give new insights into how animals exploit food patches, offering a unique opportunity to comprehend the behavioral ecology behind different movement patterns and understand how animals might respond to changes in prey distributions.
Data from: Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean
Porites white patch syndrome (PWPS) is a coral disease recently described in the western Indian Ocean. This study aimed to isolate and identify potential pathogens associated with PWPS utilising both culture and non-culture screening techniques and inoculation trials. A total of 14 bacterial strains (those dominant in disease lesions, absent or rare in healthy tissues and considered potential pathogens in a previous study) were cultured and used to experimentally inoculate otherwise healthy individuals in an attempt to fulfil Henle-Koch's postulates. However, only one (P180R), identified as closely related (99-100% sequence identity based on 1.4 kb 16S RNA sequence) to Vibrio tubiashii, elicited signs of disease in tank experiments. Following experimental infection (which resulted in a 90% infection rate), the pathogen was also successfully re-isolated from the diseased tissues and re-inoculated in healthy corals colonies, therefore fulfilling the final stages of Henle-Koch's postulates. Finally we report that PWPS appears to be a temperature-dependent disease, with significantly higher tissue loss (ANOVA: df= 2, F=39.77, P<0.01) occurring at 30°C (1.45 ± 0.85 cm2 day−1 (mean ± SE)) compared to ambient temperatures of 28°C and 26°C (0.73 ± 0.80 cm2 day−1 (mean ± SE) and 0.51 ± 0.50 cm2 day−1 (mean ± SE), respectively).
Data from: Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina
Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the center of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea / Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea / Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these Southern Iberia populations compared to more central populations is possibly the effect of drift due to small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea / Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographic history and as marginal diversity hotspots have very high conservation value.
Data from: Face patch resting state networks link face processing to social cognition
Faces transmit a wealth of social information. How this information is exchanged between face-processing centers and brain areas supporting social cognition remains largely unclear. Here we identify these routes using resting state functional magnetic resonance imaging in macaque monkeys. We find that face areas functionally connect to specific regions within frontal, temporal, and parietal cortices, as well as subcortical structures supporting emotive, mnemonic, and cognitive functions. This establishes the existence of an extended face-recognition system in the macaque. Furthermore, the face patch resting state networks and the default mode network in monkeys show a pattern of overlap akin to that between the social brain and the default mode network in humans: this overlap specifically includes the posterior superior temporal sulcus, medial parietal, and dorsomedial prefrontal cortex, areas supporting high-level social cognition in humans. Together, these results reveal the embedding of face areas into larger brain networks and suggest that the resting state networks of the face patch system offer a new, easily accessible venue into the functional organization of the social brain and into the evolution of possibly uniquely human social skills.
Data from: The spatial distribution of foragers and food patches can influence antipredator vigilance
Antipredator vigilance is a major component of defenses against predators for many prey species. For group foragers, such vigilance is predicted by models to decrease with group size reflecting better predator detection ability and risk dilution in larger groups. Influential vigilance models for group foragers have made simplifying and often quite restrictive assumptions. Prey species, for instance, are expected to search for resources in groups of fixed sizes although frequent changes in group sizes often occur while foraging. Groups of prey in the same area are also assumed to be attacked independently, but predators could sequentially target several local groups after a failed attempt. I propose a framework in which prey animals can form groups by joining feeding neighbors and also adjust their vigilance in these groups of varying sizes. Predators can attack one of the many groups that occur in the same area and can also target groups of specific sizes. I used a genetic algorithm approach to simultaneously tackle joining and vigilance choices by prey individuals. I show that joining tendencies and the effect of group size on vigilance can vary with forager population size, the spatial distribution of resources, and predator attack tactics. The modeling framework adopted here generates several novel predictions about vigilance and joining tendencies for group foragers, and highlights the importance of considering the availability and vulnerability of prey groups in the same habitat when predicting antipredator vigilance.
Data from: Optimal management strategy of insecticide resistance under various insect life histories: heterogeneous timing of selection and inter-patch dispersal
Although theoretical studies have shown that the mixture strategy, which uses multiple toxins simultaneously, can effectively delay the evolution of insecticide resistance, whether it is the optimal management under different insect life histories and insecticide types remains unknown. To test the robustness of the management strategy over the life histories, we developed a series of simulation models which cover almost all the diploid insect types and have the same basic structure describing pest population dynamics and resistance evolution with discrete time-steps. For each of two insecticidal toxins, one-locus two-allele autosomal inheritance of resistance was assumed. The simulations demonstrated the optimality of the mixture strategy either when insecticide efficacy was incomplete or when some part of the population disperses between patches before mating. The rotation strategy, which uses one insecticide on one pest generation and a different one on the next, did not differ from sequential usage in the time to resistance, except when dominance was low. It was the optimal strategy when insecticide efficacy was high and pre-mating selection and dispersal occur.
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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.