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On the acceptance by code reviewers of candidate security patches suggested by Automated Program Repair tools - Dataset
<p>Dataset of the empirical experiment presented in the paper On the acceptance by code reviewers of candidate security patches suggested by Automated Program Repair tools. The dataset includes the participants' responses regarding their background, and the responses of the tasks from the experiment. </p>
DATASET Temporal shifts in algal and fish assemblages following the introduction of herbivorous species in coral reef patches (Bora Bora Island)
<p>Dataset suporting the study of fish succession in Bora Bora</p>
Figure 1 from: Al-Razi H, Maria M, Bin Muzaffar S (2019) Mortality of primates due to roads and power lines in two forest patches in Bangladesh. Zoologia 36: 1-6. https://doi.org/10.3897/zoologia.36.e33540
Figure 1 Map of two forest patches in Bangladesh, showing the locations of linear infrastructures inside the forest.
Text-fig. 4. Patelliconus primulus (BARRANDE in PERNER, 1903). Specimen MHBR 2418, revultex impression. A – apical view showing the early shell and earliest stages of teleoconch. Note patches of shell with irregular incremental structures; B – left lateral view; C – oblique left apicolateral view showing finely ribbed early shell and patches of shell in earliest stages of teleoconch, all ×....... Šárka F., Osek near Rokycany. in Patelliconus Horný, 1961 And Mytoconula Gen. N. (Mollusca, Tergomya) From The Ordovician Of Perunica
Text-fig. 4. Patelliconus primulus (BARRANDE in PERNER, 1903). Specimen MHBR 2418, revultex impression. A – apical view showing the early shell and earliest stages of teleoconch. Note patches of shell with irregular incremental structures; B – left lateral view; C – oblique left apicolateral view showing finely ribbed early shell and patches of shell in earliest stages of teleoconch, all ×....... Šárka F., Osek near Rokycany.
Text-fig. 3. Cyclurus macrocephalus REUSS. Specimen NMP Pc 2847. Ventral surface of the parasphenoid, showing its tooth patch. in Complements To The Anatomical Knowledge Of Reuss (Pisces, Actinopterygii) From The Eocene Of Kučlín, Bohemia, Czech Republic
Text-fig. 3. Cyclurus macrocephalus REUSS. Specimen NMP Pc 2847. Ventral surface of the parasphenoid, showing its tooth patch.
Data from: Habitat amount, not patch size and isolation, drives species richness of macro‐moth communities in countryside landscapes
Aim: Our aim is to test whether species richness patterns are best explained by the effect of the total amount of habitat within the landscape, or instead by a combination of patch size and patch isolation effects. To this end, we jointly contrast the habitat amount hypothesis and countryside biogeography with patch size and isolation concepts from island biogeography. Location: Three multi-habitat landscapes in Peneda-Gerês National Park, NW Portugal. Taxon: Macro-moths (Lepidoptera). Methods: Light-trapping using a semi-nested design at 84 fixed sites which were each repeatedly sampled six times. Results: Autocovariate models show that sampling sites with a higher number of forest and meadow macro-moth species (alpha diversity) were surrounded by a higher amount of forest and meadow habitat, respectively within a 160 and 320 m radius (scale of effect). These top-ranked models, containing only habitat amount as a significant variable, had lower AIC than models (only) containing patch size and/or isolation. Complementary to this, the countryside species-area relationship (SAR) model outperforms the classic SAR model, so that the effective area of habitat explains landscape species richness (gamma diversity) across spatial scales (beta diversity) better than the classic SAR. Specifically, we show that forest macro-moths have a higher spatial turnover than meadow macro-moths and that, on average, there are more species in forest than in meadow habitat. Main conclusions: The habitat amount hypothesis predicts alpha species richness in multi-habitat landscapes better than do patch size and isolation while the countryside SAR predicts beta and gamma diversity better than the classic SAR. We suggest that evidence is mounting to revise the application of the classical approaches of island biogeography and metapopulation theory to conservation biogeography.
Data from: Colour patch size and measurement error using reflectance spectrometry
1. Over the past twenty years, portable and relatively affordable spectrophotometers have greatly advanced the study of animal coloration. However, the small size of many colour patches poses methodological challenges that have not, to date, been assessed in the literature. Here, we tackle this issue for a reflectance spectrophotometry set-up widely used in ecology and evolution (the beam method). 2. We reviewed the literature on animal coloration reporting the use of reflectance spectrophotometry to explore how the minimum measurable size of a colour patch is determined. We then used coloured plastic sheets to create artificial colour patches, and quantify the relationship between colour patch size and distortions induced by resulting chimeric spectra (spectra contaminated by an adjacent colour patch). Finally, we assessed the generality of our findings using natural colour spots in the lizard Podarcis muralis, as a biologically realistic model. 3. We found a lack of consensus in the literature, frequently resulting in the rejection of valid data or the potential inclusion of unreliable data. As expected, we show that decreasing colour patch size reduces the reliability of reflectance measurements, but also that spectral distortions resulting from chimeric spectra depend on patch/background colour combinations. We found similar results using natural colour spots in P. muralis. 4. We propose a series of steps to avoid the pitfalls described above. First, we provide guidelines on how to identify chimeric spectra and estimate the minimum size of a measurable colour patch in order to avoid them. Second, we show that reducing the probe-to-surface distance allows for more accurate measurements and therefore improves the spectrophotometric assessment of small colour patches. Third, we suggest that, as a general rule of thumb, very small (< 2 mm) colour patches should be avoided when using traditional spectrophotometry methods.
Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks
A central problem in ecology is to understand how human impacts affect plant-animal interactions that lead to effective seed dispersal services for plant communities. Seed dispersal services are the outcome of plant-frugivore interactions that often form local networks of interacting species. Recent work has shown that some frugivorous bird species are more critical to network organization than others. Here, we explore how patch size and the potential local extinctions of obligate frugivorous birds affect the reorganization of seed dispersal networks. We examined the structure of 20 empirical seed dispersal networks documented across tropical avian assemblages occupying widely variable habitat patch sizes, a surrogate of the amount of remaining habitat. Networks within small forest patches consistently supported both lower plant and bird species richness. Forest patch size was positively associated with nestedness, indicating that reductions in patch size disrupted the nested organization of seed dispersal networks. Obligate frugivores, especially large-bodied species, were almost entirely absent from small forest patches. Analysis at the species level showed that obligate frugivores formed the core of interacting species, connecting species within a given seed dispersal network. Our combined results revealed that patch size reduction erodes frugivorous bird diversity, thereby affecting the integrity of seed dispersal networks. We highlight the importance of conserving large forest patches to maintain tropical forest functionality.
Data from: Frequency-dependent conspecific attraction to food patches
In many ecological situations, resources are difficult to find but become more apparent to nearby searchers after one of their numbers discovers and begins to exploit them. If the discoverer cannot monopolize the resources, then others may benefit from joining the discoverer and sharing their discovery. Existing theories for this type of conspecific attraction have often used very simple rules for how the decision to join a discovered resource patch should be influenced by the number of individuals already exploiting that patch. We use a mechanistic, spatially explicit model to demonstrate that individuals should not necessarily simply join patches more often as the number of individuals exploiting the patch increases, because those patches are likely to be exhausted soon or joining them will intensify future local competition. Furthermore, we show that this decision should be sensitive to the nature of the resource patches, with individuals being more responsive to discoveries in general and more tolerant of larger numbers of existing exploiters on a patch when patches are resource-rich and challenging to locate alone. As such, we argue that this greater focus on underlying joining mechanisms suggests that conspecific attraction is a more sophisticated and flexible tactic than currently appreciated.
Figure 27 in Descriptions of New Species of the Diverse and Endemic Land Snail Amplirhagada Iredale, 1933 from Rainforest Patches across the Kimberley, Western Australia (Pulmonata: Camaenidae)
Figure 27. Genitalia of Amplirhagada inusitata n.sp. (WAM S34728). For labelling of structures see Fig. 3. Scale bar = 10 mm.
Figure 7 in Descriptions of New Species of the Diverse and Endemic Land Snail Amplirhagada Iredale, 1933 from Rainforest Patches across the Kimberley, Western Australia (Pulmonata: Camaenidae)
Figure 7. Penial anatomy of Amplirhagada carsoniana n.sp. (WAM S34708). For labelling of structures see Fig. 4. Scale bar = 3 mm.
Figure 17. Amplirhagada vialae n in Descriptions of New Species of the Diverse and Endemic Land Snail Amplirhagada Iredale, 1933 from Rainforest Patches across the Kimberley, Western Australia (Pulmonata: Camaenidae)
Figure 17. Amplirhagada vialae n.sp. SEM of shell (AM C.472926), radula and jaw (AM C.472925). (A) Protoconch and first teleoconch whorls viewed from above. (B) Detail of first teleoconch whorls viewed from above. (C) Lateral view of shell. (D) Lateral view of last whorl. (E) Jaw. (F) Central and inner lateral teeth viewed from above. (G) Marginal teeth viewed from above. Scale bars: A, 200 µm, B–D, 1 mm; E, 100 µm, F, 20 µm; G, 10 µm.
Fig. 8 in A comparative exploration of the inquiline and prey species of Nepenthes rafflesiana pitchers in contiguous and fragmented habitat patches in Singapore
Fig. 8. First and second (a) and second and third (b) dimensions of the three-dimensional NMDS of pitcher prey assemblages. Points represent prey assemblages of individual pitchers, being coloured according to pitcher type (with green points representing lower pitchers and beige ones representing upper ones) and are filled for pitchers found within the Central Catchment Nature Reserve (CCNR) and unfilled for those outside of it. Texts denote prey taxon centroids and are sized proportionally with the frequency of occurrence of the taxa they denote. Points found close to species centroids are more likely to contain the corresponding prey taxon. Stress = 0.174.
Fig. 3 in Simple relationships to predict attributes of fish assemblages in patches of submerged macrophytes
Fig. 3. Relationships between macrophyte biomass and fish density (a) and species richness (b), in patches dominated by E. densa and E. najas.
Assortative mating for between-patch dispersal status in a wild bird population: Exploring the role of direct and indirect underlying mechanisms
<p><span>Previous studies have reported functional integration between dispersal and other phenotypic traits allowing individuals to alleviate dispersal costs, and such associations can affect dispersal evolution in return. In sexually reproducing species, assortative mating according to dispersal can shape the maintenance of such trait associations. Despite the potentially crucial consequences of dispersal in natural populations, assortative mating for dispersal and its underlying mechanisms remain largely unexplored. Here, we assessed assortative mating for between-patch dispersal status in a fragmented population of a small passerine bird, the collared flycatcher, and explored whether such assortative mating could result from (i) direct mate choice based on dispersal-related behavioural (aggressiveness and boldness) and morphological traits (tarsus and wing length), (ii) biased mating due to spatio-temporal heterogeneity in the distribution of dispersal phenotypes and/or (iii) post-mating adjustment of dispersal phenotype or dispersal-related traits. We found intrinsic assortative mating (i.e. positive among-pair correlation) for current dispersal status (in the year of mating) but not for natal dispersal status, even though we could not exclude it due to limited power. We also found assortative mating for boldness and age category (yearlings vs. older adults), and the probability for pair members to be assorted for current dispersal status was higher when both pair members were of similar boldness score and of the same age compared to mixed-age pairs. Mate choice based on boldness and age thus appears as a possible mechanism underlying assortative mating for dispersal status. Our analyses however remained correlative and only an experimental manipulation of these traits could allow inferring causal links. Non-random mating for dispersal-related traits may affect the evolution of dispersal syndromes in this population. More work is nevertheless needed to fully assess the evolutionary implications of age- and behaviour-based assortative mating for dispersal.</span></p>
Figure 3 from: Freitag H (2013) Hydraena (Hydraenopsis) ateneo, new species (Coleoptera, Hydraenidae) and other aquatic Polyphaga from a small habitat patch in a highly urbanized landscape of Metro Manila, Philippines. ZooKeys 329: 9-21. https://doi.org/10.3897/zookeys.329.5955
Figure 3 - Hydraena ateneo sp. n.: A, B aedeagus (holotype) in ventral (A) and lateral (B) view C spermatheca D gonocoxite E female tergite X; scale bars = 0.1 mm.
Figure 2 from: Freitag H (2013) Hydraena (Hydraenopsis) ateneo, new species (Coleoptera, Hydraenidae) and other aquatic Polyphaga from a small habitat patch in a highly urbanized landscape of Metro Manila, Philippines. ZooKeys 329: 9-21. https://doi.org/10.3897/zookeys.329.5955
Figure 2 - Digital photographs of the habitus of A Hydraena ateneo sp. n., paratype ♂ B Hydraena scabra ♀ C Hydraena palawanensis ♂ (all collected from the Ateneo de Manila University Campus); scale bar = 1.0 mm.
Figure 1 from: Freitag H (2013) Hydraena (Hydraenopsis) ateneo, new species (Coleoptera, Hydraenidae) and other aquatic Polyphaga from a small habitat patch in a highly urbanized landscape of Metro Manila, Philippines. ZooKeys 329: 9-21. https://doi.org/10.3897/zookeys.329.5955
Figure 1 - A View of Metro Manila from the well-vegetated campus of the Ateneo de Manila University with the collecting sites B Temporary pool (label code: ADM2e) where Stenelmis sp., Hydraena scabra, andHelochares lepidus were collected C Temporary headwater creek (label code: ADM3d) where all three Hydraena spp. were collected.
Figure 1 from: Hałaj R, Osiadacz B (2015) On foreign land: the conquest of Europe by Cinara curvipes (Patch, 1912). Deutsche Entomologische Zeitschrift 62(2): 261-265. https://doi.org/10.3897/dez.62.6457
Figure 1 - Distribution of Cinara curvipes in Europe – records in particular periods and predicted expansion. 1. recorded in 1999–2001; 2. recorded in 2007-2009; 3. recorded in 2013-2015; 4. 1st records in Poland; 5. probable expansion routes.
Figure 2 from: Gonçalves FMP, Goyder DJ (2016) A brief botanical survey into Kumbira forest, an isolated patch of Guineo-Congolian biome. PhytoKeys 65: 1-14. https://doi.org/10.3897/phytokeys.65.8679
Figure 2 - Turraea vogelii Hook.f. ex Benth, Cola welwitschii Exell & Mendonça ex R. Germ., Pancovia golungensis (Hiern) Exell & Mendonça, Cochlospermum angolense Welw. ex Oliv., Inga vera Willd. subsp. vera, Pavetta gossweileri Bremek, Pittosporum viridiflorum Sims, Clerodendrum poggei Gürke
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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.