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opencc-by-4.0May 2017View details →

An Empirical Study of Activity, Popularity, Size, Testing, and Stability in Continuous Integration

A good understanding of the practices followed by software development projects can positively impact their success --- particularly for attracting talent and on-boarding new members. In this paper, we perform a cluster analysis to classify software projects that follow continuous integration in terms of their activity, popularity, size, testing, and stability. Based on this analysis, we identify and discuss four different groups of repositories that have distinct characteristics that separates them from the other groups. With this new understanding, we encourage open source projects to acknowledge and advertise their preferences according to these defining characteristics, so that they can recruit developers who share similar values.

opencc-by-4.0Jun 2024View details →

Train and Evaluation Code, Road Classification Models and Test set of the paper "Insights into the Effects of Image Overlap and Image Size on Semantic Segmentation Models Trained for Road Surface Area Extraction from Aerial Orthophotography"

This repository contains the Python scripts built for training and evaluation of the implementation, together with the test data and the resulting road segmentation models corresponding to the paper "Insights into the Effects of Image Overlap and Image Size on Semantic Segmentation Models Trained for Road Surface Area Extraction from Aerial Orthophotography". The scripts make use of the Tensorflow with Keras framework and their additional required dependencies. The training and validation set is based on the binary SROADEX dataset (<a href="../records/6482346">https://zenodo.org/records/6482346</a>) that was re-split into tiles that feature the image resolutions (256 x 256, 512 x 512, and 1024 x 1024 pixels) and image overlaps (0% and 12.5%) considered in this study. The data have been generated using scripts developed in Python using Open Source libraries (GDAL/OGR and MapScript) for rasterization of vector cartography that represents the axes of the different types of roads (urban, interurban and rural). This binary road data contains information from 16 full orthoimages (28.5 km * 18.5 km) with spatial resolution of 0.5 m/pixel from the insular and peninsular Spanish territory. Due to the size on disk of approximately 492 gigabytes, this training and validation data is only available upon request from the corresponding author. The test set has been generated from a novel area from Palencia (Spain) and features 18 million pixels labelled with the positive "Road" class. The test sets are provided in the repository for each resolution (with no overlap), so that additional DL models can be evaluated on the same data and compared with the results achieved in this study. The structure of the information shared in this repository is as follows: The scripts have been grouped by tile resolution (256, 512 and 1024). First, the test set and the evaluation script can be found. For each tile resolution, there are two subfolders (corresponding to the "no overlap" and "12.5% overlap"). In each case, the Python scripts for training the models in the three repetitions are shared, and the trained models (H5 format) are shared in compressed form. Finally, for each resolution we also share the testing dataset which consists of two folders. The material is distributed under a CC-BY 4.0 license.

Fig. 2 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 2. Index map (A) and release points of transplanted substrates in southwest Kochi Prefecture (B). a and b: this study, c and d: Nagamune (1918), and Kuno (1922). respectively. Table 1. Release and collection dates of transplanted substrates

Fig. 4 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 4. Examples of the coral fragments showing substantial growth. Coenenchyme and branch growth, cross-section repair, and polyp increase were confirmed. Left side with capital letters: Before the release. Right side with small letters: After the collection. A and a: 215 days (Jul. 26, 2016, to Feb. 26, 2017), B and b: 328 days (Feb. 26, 2017, to Jan. 20, 2018), C and c: 340 days (Jul. 26, 2016, to Jul. 1, 2017), D and d: 363 days (Jun. 9, 2017, to Jun. 7, 2018), E and e: 461 days (Feb. 26, 2017, to Jun. 2, 2018), F and f: 936 days (Jul. 1, 2017, to Jan. 22, 2020). Scale bars = 10 mm. A–B is based on Koido and Toshino (2022).

Fig. 3 in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 3. An example of living broken and dead fragments. A: Coenenchyme had spread over the mount with the formation of many tiny polyps. Blue arrow: cross section was covered with coenenchyme, and a polyp had formed. Green arrow: Newly growing branch. B: Comparison of the dead specimen. Left: Before the release (Jun. 9, 2017). Right: After the collection (Jun. 7, 2018). Scale bars = 10 mm.

Fig. 1. Precious coral colonies used for transplantation. A in Fig. 4 in Transplantation Tests of Precious Coral Fragments Using Small-sized Artificial Substratum.

Fig. 1. Precious coral colonies used for transplantation. A: Before cutting. The broken yellow line shows the separation line. B: After cutting. C: Precious coral fragments were transplanted on the concrete part of substrate (Kaiso-kun). D: Pre-release substrate. Blue arrows show fragments detached along with epoxy mount. E: Recovered substrate. C–E is based on Koido and Toshino (2022).

opencc-by-4.0May 2018View details →

Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata

Here we provide an extensive image library of Globoconella puncticulata, with accompanying 2D and 3D coordinate data and morphometric measurements.  This data was generated using high-throughput imaging methods (AutoMorph) developed in P.M. Hull's lab at Yale University. This dataset accompanies the manuscript: Brombacher, J.A., Elder, L.E., Hull, P.M., Wilson, P.A. and Ezard, T.H.(In Press) Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata. Journal of Foraminiferal Research. The manuscript describes important details related to data collection and usage and should be consulted before using the data provided here.  Samples were obtained from three sites in the Atlantic Ocean: equatorial Ocean Drilling Program (ODP) Site 925, subtropical ODP Site 659, and mid-latitude Integrated Ocean Drilling Program (IODP) Site U1313. 1233 individual foraminifera of the species Globoconella puncticulata were picked from these samples to be imaged. Nine slides of microfossils were imaged at multiple focal heights (z-planes; 31.1um step distance) using a light microscope with an automated stage and processed with the image processing models of AutoMorph. AutoMorph software and tutorials can be accessed here: https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nelson, Kaylea, Elder, Leanne E., Liu, Yusu, & Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557. Slides were named with the IODP or ODP site number. Each slide was imaged with the foraminifera arranged in 2-3 orientations (i.e., umbilical, spiral, and/or edge). One of the nine slide was imaged with both light and computed tomography in order to compare the volumetric data obtained from the two approaches. This slide had 6 individual foraminifera. All individuals imaged with this combination of approaches have ‘CTscan’ included in the file name. This AutoMorph/CT scanned slide was imaged from three orientations (umbilical, spiral, and edge) and with two z-step distances (distance between imaged focal planes on the z-axis) of 11.2 um and 31.31 um. Images and morphometric data are provided in 9 datasets detailed below. Do note: our slide scanning technique often identifies background light scatter and/or other slide debris (glue, shell fragments, etc.) as ‘objects’, and these objects are numbered in sequence. We have excluded all non-foraminiferal objects from the datasets below, so the object numbers of the foraminifera will often be discontinuous (i.e.: 2,3,4,10,11,16). 1) 2d_coordinates.tar provides the 2D coordinates of each successfully extracted orientation from the 1233 individual Globoconella puncticulata (2811 total successfully extracted orientations) in a single csv (all2dcoordinates.csv). 2d_coordinates.tar also provides a csv for each slide scan at a particular orientation (26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample)). 2) 2dmorph_data_all.tar contains all Globoconella puncticulata with 2D measurements extracted by the AutoMorph routine run2morph (2811 total successfully extracted orientations), and a text file listing all objects with failed 2D extractions and non-forminiferal objects. 3) 2d_outline_check.tar provides an overlay of the extracted 2D outline on the Globoconella puncticulata EDF for quality control purposes for all extracted Globoconella puncticulata (2811 total successfully extracted orientations). 5) 3d_obj_files.tar provides directories for each slide scan with the 3D mesh coordinates as obj files for each extracted Globoconella puncticulata (2270 total successfully extracted orientations). Note: more 3D extractions failed than 2D extractions, accounting for the difference in the number of 2D extractions (2811) and 3D extractions (2270). 6) 3d_pdfs.tar provides directories of each slide scan with the 3D pdfs of each Globoconella puncticulata extracted (2270 total successfully extracted orientations) for quality control purposes. 3D pdfs, meshes and shape measurements were generated by the AutoMorph module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly.  4) 3dmorph_data.tar contains a csv file for each slide scan with the 3d measurements generated for each Globoconella puncticulata by the AutoMorph module run3dmorph (2270 total successfully extracted objects in 26 directories representing each slide scan at a particular orientation). 7) object_ edf_images.tar contains the extended depth of focus (EDF)images in 26-directories for each slide scan at a particular orientation. The EDFs are 2D image composites created from the z-stacked photographic images by the AutoMorph focus module. Together, the 26-directories contain 2811 total images representing the successfully extracted 2D orientations. 8) sampleID.csv is a csv of all sample information. This includes the Slide name for the physical slide each sample is on, the Object number on that slide scan for each foraminifera used in the study, and the Ocean Drilling Program information for each object. Ocean Drilling Program details consist of the Leg: the Leg number for the drilling cruise, Site: the Ocean Drilling Program collection site number, the Hole:  the drilling hole ID, the Core: the Core number from that drilling site, the core Type: the type of drilling equipment used (H for all these samples which is an advanced hydraulic piston core), the Section: the section number on the core, and the Top and Bottom: the sample top and bottom interval in cm from the top of the section.  9) slide_images_boxed.tar contains one image for each slide view at a particular orientation 26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample). A red box delineates each object extracted using the AutoMorph segment module. Slides are named according to their ocean drilling sample identification (see dataset #10). 10) z-stacks.tar.gz contains the original z-stack images of each Globoconella puncticulata (2811 total representing the successfully extracted 2D orientations) in 26 directories representing each slide scan at a particular orientation).

opencc-by-4.0Jun 2023View details →

Low-cost test rig for characterization of photocatalytic two dimensional materials using photonically sized UV-A LED light sources

In the presented studies, a system for the characterization of two-dimensional photocatalysts was developed and tested. In the system, reference substances can be studied online with regard to their degradability and adsorption on photocatalytic materials. In order to perform accurate calculations of the quantum and photon efficiency of the catalysts, the LED arrays used were adjusted in their spacing by simulations so that a homogeneous light field is imaged on the catalysts. The system was tested with respect to measurement accuracy and reproducibility and the photocatalytic degradation of methylene blue, methyl orange and rhodamine B was investigated. Exemplarily, the reaction kinetics, photolysis and adsorption on the tested photocatalysts were determined for these compounds and the calculation was presented in detail. The exact construction plans and circuits as well as the sensors and their programming are presented in detail and should encourage other scientists to replicate the experimental setup, since especially in the field of photocatalysis research, often the results of publications cannot be compared with each other.

dryad40/100

Data used in: Heritability and variance components of seed size in wild species: influences of breeding design and the number of genotypes tested

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publicJan 2023View details →

opencc-zeroNov 2019View details →

Extreme variation in testes size in an insect is linked to recent mating activity

Ample sperm production is essential for successful male reproduction in many species. The amount of sperm a male can produce is typically constrained by the size of his testes, which can be energetically expensive to grow and maintain. Whilst the economics of ejaculate allocation has been the focus of much theoretical and empirical literature, relatively little attention has been paid to individual adult variation and plasticity at the source of sperm production, the testes themselves. We experimentally address this issue using the insect Narnia femorata Stål (Hemiptera: Coreidae). We established the metabolic cost of testicular tissue, then quantified variation in individual testes mass in response to multiple mate quality and quantity treatments. We uncovered extreme variation across individuals and considerable short-term effects of mating activity on testes dry mass. Importantly, the observed variation in testes mass was associated with notable fitness consequences; females paired with males with larger testes had greater hatching success. Overall, pairing with a female resulted in a 11% reduction in dry testes mass. Despite this apparent considerable mating investment, we found no evidence of strategic allocation to higher quality females or longer-term changes in testes mass. The dynamic nature of testes mass and its metabolic cost is vital to consider in the context of re-mating rates, polyandry benefits and general mating system dynamics both in this species and more broadly.

opencc-zeroJan 2024View details →

Supporting information for: Discrimination ability of central visual field testing using stimulus size I, II, and III and relationship with macular ganglion cell thickness in chiasmal compression

Purpose: To compare the relationship between macular ganglion cell layer (mGCL) thickness and 10-2 visual field (VF) sensitivity using different stimulus sizes in patients with temporal hemianopia from chiasmal compression. Methods: A cross-sectional study was conducted involving 30 eyes from 25 patients with temporal VF loss on 24-2 SITA standard automated perimetry due to previous chiasmal compression and 30 healthy eyes (23 controls). Optical coherence tomography (OCT) of the macular area and 10-2 VF testing using Goldmann stimulus size I (GI), II (GII), and III (GIII) were performed in the Octopus 900 perimeter. For the sake of analysis, mGCL thickness and VF data were segregated into four quadrants (two temporal and two nasal) and two halves (temporal and nasal) centered on the fovea, and the groups were compared using generalized estimated equations. The discrimination ability of GI, GII, and GIII was evaluated, as was the correlation between mGCL and 10-2 VF sensitivity using GI, GII, and GIII. Results: All mGCL parameters were significantly reduced in patients compared to controls. 10-2 VF test sensitivity using GI, GII, and GIII was significantly lower in patients than in controls (p≤0.008) for all parameters, except the three nasal divisions when using GI (p=0.41, 0.07 and 0.18) Significant correlations were found between temporal VF sectors (all stimulus sizes) and the corresponding nasal mGCL measurements, with similar discrimination ability. Significant correlations were also observed between all three nasal VF divisions and the corresponding temporal mGCL thickness when using stimulus sizes I and II, but not stimulus size III. Conclusions: On 10-2 VF testing, GII outperformed GI and GIII with regard to discrimination ability and structure-function correlation with mGCL thickness in chiasmal compression. Our findings suggest that the use of GII can enhance the diagnostic power of 10-2 VF testing, although further studies are necessary to support this conclusion.

opencc-zeroJun 2022View details →

A test of Bergmann's rule in the Early Triassic: Latitude, body size, and sampling in Lystrosaurus

The ecogeographical rule known as Bergmann's rule suggests that there is a positive relationship between body size and latitude when comparing closely related taxa. The underlying mechanism, or mechanisms, to explain this pattern vary as widely as the taxa that seem to follow it, which has led to skepticism over whether Bergmann's rule should be considered a rule at all. Despite this, Bergmann's rule is widespread among modern birds, mammals, beetles, and some amphibians, but far fewer extinct taxa have been subjected to tests of Bergmann's rule. To test whether Bergmann's rule is detected in extinct taxa, we compared body size proxies in Lystrosaurus recovered from Early Triassic-aged strata in Antarctica, South Africa, India, and China. Our results reveal that average body size is largest at mid-northern paleolatitudes (~45°N) instead of the highest southern paleolatitudes (~70°S). Additionally, maximum body size is consistent across northern and southern hemispheres, indicating that Bergmann's rule did not apply for Lystrosaurus during the Early Triassic. To test potential sample size biases in our results, we used rarefaction and subsampling to show that only the Karoo Basin is well sampled, and that large individuals are exceedingly rare except in the Turpan-Junggar Basin of Xinjiang, China. Taken together, our results suggest that Lystrosaurus had the potential to reach large body sizes in each of the latitudinally widespread tectonic basins studied here, but that local conditions may have allowed individuals at mid-northern paleolatitudes a greater chance of reaching large size compared to southern congeners that suffered increased mortality at young/small sizes.

zenodo36/100

All body size data (EOL v3 test): body size

All records for Body size, run Aug. 7 Query in EOL beta platform: https://beta.eol.org/terms/search_results?term_query%5Bclade_id%5D=&term_query%5Bfilters_attributes%5D%5B0%5D%5Bop%5D=is_any&term_query%5Bfilters_attributes%5D%5B0%5D%5Bpred_uri%5D=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0100005&term_query%5Bresult_type%5D=record

opennotspecifiedAug 2024View details →

zenodo36/100

Mammal body size (EOL v3 test): mammal body size

A sample of data downloaded from the new EOL search interface. All available data for mammals for any measure of body size, with full metadata. https://beta.eol.org/terms/search_results?term_query%5Bclade_id%5D=1642&term_query%5Bfilters_attributes%5D%5B0%5D%5Bop%5D=is_any&term_query%5Bfilters_attributes%5D%5B0%5D%5Bpred_uri%5D=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0100005&term_query%5Bresult_type%5D=record

opennotspecifiedAug 2024View details →

opencc-zeroJun 2023View details →

Data for: Guppies in large groups cooperate more frequently in an experimental test of the group size paradox

The volunteer's dilemma, in which a single individual is required to produce a public good, predicts that individuals in larger groups will cooperate less frequently. Mechanistically, this could result from trade-offs between costs associated with volunteering and costs incurred if the public good is not produced (nobody volunteers). During predator inspection, one major contributor to the cost of volunteering is likely increased probability of predation; however, a predator also poses a risk to all individuals if nobody inspects. We tested the prediction that guppies in larger groups will inspect a predator less than those in smaller groups. We also predicted that individuals in larger groups would perceive less threat from the predator stimulus because of the protective benefits of larger groups (e.g. dilution). Contrary to prediction, we found that individuals in large groups inspected more frequently than those in smaller groups but (as predicted) spent less time in refuges. There was evidence that individuals in intermediate-sized groups made the fewest inspections and spent the most time in refuges, suggesting that any link between group size, risk and cooperation is not driven by simple dilution. Extensions of theoretical models that capture these dynamics will likely be broadly applicable to risky cooperative behaviour.

publicFeb 2025View details →

Data from: Guppies in large groups cooperate more frequently in an experimental test of the group size paradox

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publicAug 2022View details →

A test of Bergmann’s rule in the Early Triassic: Latitude, body size, and sampling in Lystrosaurus

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publicFeb 2021View details →

Variation in body size and sexual size dimorphism in the most widely-ranging lizard: testing the effects of reproductive mode and climate

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publicJun 2025View details →

Dominance rank, facial morphology, and testes size in male white-faced capuchins: evidence for pre- and post-mating competition

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