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opencc-by-4.0Mar 2022View details →

ManyTypes4TypeScript: A Comprehensive TypeScript Dataset for Sequence-Based Type Inference

In this paper, we present ManyTypes4TypeScript, a very large corpus for training and evaluating machine-learning models for sequence-based type inference in TypeScript. The dataset includes over 9 million type annotations, across 13,953 projects and 539,571 files. The dataset is approximately 10x larger than analogous type inference datasets for Python, and is the largest available for TypeScript. We also provide API access to the dataset, which can be integrated into any tokenizer and used with any state-of-the-art sequence-based model. Finally, we provide analysis and performance results for state-of-the-art code-specific models, for baselining. ManyTypes4TypeScript is available on Huggingface and Zenodo. This dataset was collected on January 22, 2022 and deduplicated with Allamanis code deduplication tool.

opencc-by-4.0Feb 2022View details →

Figures 7–12. Phyllophaga type specimens. 7 in A new species of Phyllophaga Harris (Coleoptera: Scarabaeidae: Melolonthinae) from Puerto Rico

Figures 7–12. Phyllophaga type specimens. 7) Genitalia of P. bobevelynorum, female allotype, ventral view. 8) Genitalia of P. bobevelynorum, female allotype, lateral view. 9) Sclerotized median lobe of genitalia of P. bobevelynorum, male holotype, caudal view. 10) Sclerotized median lobe of genitalia of P. adjuntas, male holotype, caudal view. 11) Posterior tarsal claw of P. bobevelynorum, male holotype. 12) P. adjuntas, holotype specimen labels.

Fig. 24 in Redescription Of The Type Species Of The Genus Argistes (Aranei, Liocranidae)

Fig. 24. Distribution records of Argistes velox. Filled circles refer to literature data and open circles refer to present data.

Figs 16–23 in Redescription Of The Type Species Of The Genus Argistes (Aranei, Liocranidae)

Figs 16–23. Somatic characters and copulatory organs of Argistes velox: 16 — innerets of male; 17–18 bulb, ventral and anterior, embolus is broken; 19 — epigyne, dorsal; 20 — right part of epigyne, antero-dorsal; 21 — tibia and cymbium of male palp, retrolateral; 22 — epiandrous region; 23 — male abdomen, ventral. Scale = 0.1 mm if not otherwise indicated. Abbreviations: Ar — accessorial receptacle, Bc — bursa copulatrix, Cd — copulatory duct, Cf — cymbial fold, Cl — colulus, Co — conductor, Ea — epiandrus, Em — embolus, Re — receptacle, Rg — gland of receptacle, Rs — round swelling, Ta — tegular apophysis.

Figs 1‒7 in Redescription Of The Type Species Of The Genus Argistes (Aranei, Liocranidae)

Figs 1‒7. Habitus and male palp of Argistes velox: 1–2 — female habitus, lateral and dorsal; 3 — male habitus, lateral; 4‒5 — male palp, retro- and prolateral; 6‒7 — prosoma frontal in female and male. Scale = 0.2 mm if not otherwise indicated.

Figs 8‒15 in Redescription Of The Type Species Of The Genus Argistes (Aranei, Liocranidae)

Figs 8‒15. Copulatory organs and abdomen of Argistes velox: 8–10 — male palp, ventral, ventro-prolateral and dorsal; 11–12 — ventral side of abdomen in female and male; 13 — intact epigyne, ventral; 14–15 — macerated epigyne, ventral and dorsal. Scale = 0.2 mm. Abbreviations: Ar — accessorial receptacle, Bc — bursa copulatrix, Cd — copulatory duct, Co conductor, Ea — epiandrus, Em — embolus, Mp — median pocket, Re — receptacle, Rg — gland of receptacle, Ta — tegular apophysis.

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Data from: Landscape diversity and local temperature, but not climate, affect arthropod predation among habitat types

Arthropod predators are relevant for top-down regulation of insect herbivores. Biotic and abiotic factors influence predator communities and their activity with consequences for the strength of top-down regulation ('arthropod predation'). Anthropogenic climate and land-use change urges a deeper understanding of the combined effects of potential drivers on arthropod predation. This study obtained arthropod predation rates on 113 plots of open herbaceous vegetation adjacent to different habitat types (forest, grassland, arable field, settlement) along climate and land-use gradients in Bavaria, Germany, using a standardized method of artificial caterpillars at ground level. Predation rates were analysed with regard to habitat characteristics (habitat type, plant species richness, local mean temperature and mean relative humidity during artificial caterpillar exposure), landscape diversity (0.5–3.0-km, six scales), climate (multi-annual mean temperature, 'MAT') and interactive effects of habitat type with other drivers. Arthropod predation rates did not substantially differ between the studied habitat types, related to plant species richness and across the Bavarian-wide climatic temperature gradient, and also no interactive effects were observed. However, arthropod predation rates were limited by low local mean temperatures, tended to decrease towards higher relative humidity and increased towards more diverse landscapes at a 2-km scale. Thus, high arthropod predation rates in open herbaceous vegetation are favoured by diverse landscapes independent of the dominant habitat in the vicinity. Diversifying landscapes may help to improve top-down control of herbivores, e.g. agricultural pests, but more research is needed to derive specific recommendations on landscape management. Little influence of MAT on predation rates suggests that moderate increases of MAT may not strongly alter this process in the near future.

opencc-by-4.0Dec 2021View details →

SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure

This repository contains the source code and data used in the paper: SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure.1.

FIG. 8 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 8. — Discocyrtus cerayanus (Roewer, 1929) n. comb., MNRJ 7244†, male genitalia, distal part: A, dorsal view; B, lateral view; C, ventral view. Scale bars: A, 50 μm; B, C, 100 μm. Colored features are the genitalic macrosetae of VP: light blue, MS A; dark blue, MS B; magenta, MS C; yellow, MS D; green, MS E.

FIG. 6 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 6. — Habitus of Discocyrtus cerayanus (Roewer, 1929) n. comb., MNRJ 7244†, in alcohol, male from Caeté, Minas Gerais, Brazil: A, dorsal view; B, ventral view; C, lateral view; D, anterior view. Scale bars: 1 cm. Photos: R. Carvalho.

FIG. 1 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 1. — Previous state of knowledge of the Paradiscocyrtus Mello-Leitão, 1927 species composition between 1929-2020: A, B, Paradiscocyrtus neglectus Mello- Leitão, 1927 (male), in vivo, from Itatiaia, Rio de Janeiro, Brazil; C, Paradiscocyrtus neglectus Mello-Leitão, 1927 (female), in vivo, same locality; D, Discocyrtus cerayanus (Roewer, 1929) n. comb. [previously Paradiscocyrtus cerayanus] (male), MNRJ 7245†, in alcohol, from Caeté, Minas Gerais, Brazil; E, F, Bunopachylus orientalis (Roewer, 1913) [of which Paradiscocyrtus trochanteralis Roewer, 1929 is recognized as junior synomyn] (male), in vivo, from Águas Mornas, Santa Catarina, Brazil. Scale bar: 1 cm. Photos: A-C, A. Kury; D, R. Carvalho; E, F, M. Medrano.

FIG. 3 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 3. — Cladogram depicting proposed external and internal phylogenetic relationships of Paradiscocyrtus Mello-Leitão, 1927, with synapomorphies for each clade mapped using ACCTRAN. This is the most frequent topology (k-values = 5, 6, 10, 15 and 20) obtained by TNT. Blue squares, nonhomoplastic synapomorphies; white circles, homoplastic synapomorphies. Number of characters above and number of states below symbols.

FIG. 5 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 5. — Brazil, showing distribution of Discocyrtus cerayanus (Roewer, 1929) n. comb. and Paradiscocyrtus neglectus Mello-Leitão, 1927. In the main map: 1) shaded areas in the background represent the regionalization ("Provinces") of the Neotropics (Morrone 2014); 2) the red-checkered area shows the Brazilian state of Ceará, misinterpreted by Mello-Leitão (in Roewer 1931) as the real meaning of "Ceraya" (type locality of D. cerayanus n. comb.) recorded by Roewer (1929). Here, "Ceraya" is interpreted as "Serra do Caraça", a mountain range from the Minas Gerais state. The inset shows the areas of endemism of the Brazilian Atlantic Rain Forest used here follow the concept exposed by DaSilva et al. (2017).

FIG. 4 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 4. — Diagnostic character states of Paradiscocyrtus Mello-Leitão, 1927 (A, C, E) in contrast to Discocyrtus s. str. (B, D, F): A, B, stylus of glans (yellow); C, D, ocularium pair of spines (green); E, F, DS shape (gray), area III armature (blue), comparative shape between area IV posterior and DS posterior borders (red), Cx IV retrolateral apophysis (black); Tr IV prolateral medial apophysis (magenta, absent in Discocyrtus s. str.). Scale bars: A, B, 50 μm; C, D, E, F, 1 mm.

FIG. 7 in Review of Paradiscocyrtus Mello-Leitão, 1927 (Gonyleptidae, Opiliones), with the transfer of Paradiscocyrtus cerayanus Roewer, 1929 to Discocyrtus Holmberg, 1878 and a new interpretation of its type locality

FIG. 7. — Discocyrtus cerayanus (Roewer, 1929) n. comb., (SMF RII 996/53), male holotype, from "Ceraya" [Serra do Caraça, Minas Gerais], Brazil: A, habitus, dorsal view; B, same, lateral view; C, ocularium, anterior view; D, Cx IV, ventral view; E, right Tr-Fe IV, dorsal view; F, same, prolateral view; G, same, ventral view; H, same, retrolateral view; I, right Pa-Ti IV, prolateral view; J, same, ventral view. Scale bars: 1 cm.

opencc-zeroMay 2022View details →

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Data from: eDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection

Fauna monitoring often relies on visual monitoring techniques such as camera trappings, which have biases leading to underestimates of vertebrate species diversity. Environmental DNA (eDNA) has emerged as a new source of biodiversity data that may improve biomonitoring; however, eDNA based assessments of species richness remain relatively untested in terrestrial environments. We investigated the suitability of fallen log hollow sediment as a source of vertebrate eDNA, across two sites in south-western Australia - one with a Mediterranean climate and the other semi-arid. We compared two different approaches (camera trapping and eDNA metabarcoding) for monitoring of vertebrate species, and investigated the effect of other factors (frequency of species, timing of visits, frequency of sampling, body size) on vertebrate species detectability. Metabarcoding of hollow sediments resulted in the detection of higher species richness in comparison Hollow sediment detected higher species richness (29 taxa: six birds, three reptiles and 20 mammals) to metabarcoding of soil at the entrance of the hollow (13 taxa: three birds, two reptiles and eight mammals). We detected 31 taxa in total with eDNA metabarcoding and 47 with camera traps, with 14 taxa detected by both (12 mammals and two birds). By comparing camera trap data with eDNA read abundance, we were able to detect vertebrates through eDNA metabarcoding that had visited the area up to two months prior to sample collection. Larger animals were more likely to be detected, and so were vertebrates that were identified multiple times in the camera traps. These findings demonstrate the importance of substrate selection, frequency of sampling, and animal size, on eDNA based monitoring. Future eDNA experimental design should consider all these factors as they affect detection of target taxa.

opencc-by-4.0Feb 2022View details →

Rather Multifaceted than Disruptors: Exploring Gamification User Types of Crowdworkers

Dataset employed for the statistical analysis presented in the paper "Rather Multifaceted than Disruptors: Exploring Gamification User Types of Crowdworkers."  The dataset corresponds to the demographic data, HEXAD user type scores, and performance score (mean_score) for 481 crowdworkers who participated in a user study conducted via Microworkers and Amazon MTurk. The dataset is presented in a CSV file. The dataset only includes the data of crowdworkers who pass all the reliability checks described in the paper. The paper can be cited as: E.Gamboa, M. Bauer, M. Reham Khawaja, and M. Hirth, “Rather Multifaceted than Disruptors: Exploring Gamification User Types of Crowdworkers,” Human Factors in Virtual Environments and Game Design. AHFE International, 2022. DOI: 10.54941/ahfe1002069.

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Camera trap data suggest uneven predation risk across vegetation types in a mixed farmland landscape

Ground-nesting farmland birds such as the grey partridge (Perdix perdix) have been rapidly declining due to a combination of habitat loss, food shortage and predation. Predator activity is the least understood factor, especially its modulation by landscape composition and complexity. An important question is whether agri-environment schemes such as flower strips are potentially useful for reducing predation risk, e.g., from red fox (Vulpes vulpes). We employed 120 camera traps for two summers in an agricultural landscape in Central Germany to record predator activity (i.e., the number of predator captures) as a proxy for predation risk and used generalized linear mixed models (GLMMs) to investigate how the surrounding landscape affects predator activity in different vegetation types (flower strips, hedges, field margins, winter cereal and rapeseed fields). Additionally, we used 48 cameras to study the distribution of predator captures within flower strips. Vegetation type was the most important factor determining the number of predator captures and captures rates in flower strips were lower than in hedges or field margins. Red fox capture rates were the highest of all predators in every vegetation type, confirming their importance as a predator for ground-nesting birds. The number of fox captures increased with woodland area and decreased with structural richness and distance to settlements. In flower strips, capture rates in the centre were approximately 9 times lower than at the edge. We conclude that the optimal landscape for ground-nesting farmland birds seems to be open farmland with broad extensive vegetation elements and a high structural richness. Broad flower blocks provide valuable, comparatively safe nesting habitats and the predation risk can further be minimized by placing them away from woods and settlements. Our results suggest that adequate landscape management may reduce predation pressure.

opencc-zeroMay 2022View details →

opencc-zeroJun 2022View details →

FIG. 31 in The type specimens of extant asteroids (Echinodermata) in the Muséum national d'Histoire naturelle of Paris

FIG. 31. — Diplasterias turqueti Koehler, 1905: A, abactinal; B, actinal surfaces of a syntype; MNHN-IE-2014-615. Scale bar: 20 mm.