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Front Data for Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts

Frontal Polylines for 2016 created with the network described in: https://doi.org/10.5194/wcd-3-113-2022   The work is supported by the project ``Big Data in Atmospheric Physics (BINARY)'', funded by the Carl Zeiss Foundation (grant P2018-02-003).

Data from: Three-dimensional infrared scanning: An enhanced approach for spatial registration of probes for neuroimaging

Significance: Accurate spatial registration of probes (e.g., optodes and electrodes) for measurement of brain activity is a crucial aspect in many neuroimaging modalities. It may increase measurement precision and enable the transition from channel-based calculations to volumetric representations. Aim: This technical note evaluates the efficacy of a commercially available infrared three-dimensional (3D) scanner under actual experimental (or clinical) conditions and provides guidelines for its use. Method: We registered probe positions using an infrared 3D scanner and validated them against magnetic resonance imaging (MRI) scans on five volunteer participants. Results: Our analysis showed that with standard cap fixation, the average Euclidean distance of probe position among subjects could reach up to 43 mm, with an average distance of 15.25 mm [standard deviation (SD) = 8.0]. By contrast, the average distance between the infrared 3D scanner and the MRI-acquired positions was 5.69 mm (SD = 1.73), while the average difference between consecutive infrared 3D scans was 3.43 mm (SD = 1.62). The inter-optode distance, which was fixed at 30 mm, was measured as 29.28 mm (SD = 1.12) on the MRI and 29.43 mm (SD = 1.96) on infrared 3D scans. Our results demonstrate the high accuracy and reproducibility of the proposed spatial registration method, making it suitable for both functional near-infrared spectroscopy and electroencephalogram studies. Conclusions: The 3D infrared scanning technique for spatial registration of probes provides economic efficiency, simplicity, practicality, repeatability, and high accuracy, with potential benefits for a range of neuroimaging applications. We provide practical guidance on anonymization, labeling, and post-processing of acquired scans.

Fig. 1 in Revision of the genus Eugenys Quate, 1996 (Diptera: Psychodidae), with the description of three new species

Fig. 1. Distribution map of the species of Eugenys Quate, 1996.

Rainfall threshold data for landslides in the Three Gorges reservoir area

Contains selected data on landslide susceptibility and rainfall thresholds in the Three Gorges reservoir area.

Data from: Endocranial morphology of three early-diverging ceratopsians and implications for the behavior and the evolution of the endocast in ceratopsians

Ceratopsians underwent great changes including the shift of the locomotion mode, enlarged horns and frills, and increased body size. These changes are along with the changes in endocranial morphology and ecology such as the decrease of the flocculus, the hearing range, the olfactory ratio, and the Reptile Encephalization Quotient. However, the endocranial structures and associated ecology of the earliest ceratopsians are still unknown. Here, we reconstructed the endocasts of three early-diverging ceratopsians including the Late Jurassic Yinlong, and the Early Cretaceous Liaoceratops and Psittacosaurus. These ceratopsians display prominent flocculus, large and separate olfactory bulbs, long and high anterior semicircular canal, and long endosseous cochlear duct. Unlike Liaoceratops and Psittacosaurus, Yinlong exhibits relatively stocky semicircular canals and small flocculus. In Ceratopsia, the evolutional patterns of the endocast include the merging and narrowing of the olfactory bulbs, the disappearing flocculus, the reduction of the anterior semicircular canal, the increasing of the angle between two vertical semicircular canals, and the shortening of the cochlear duct. The endocranial structures suggest early-diverging ceratopsians had a high olfactory acuity and were adapted to hearing high frequencies, unlike the condition of late-diverging ceratopsians with lower olfactory acuity and hearing frequency. Reptile Encephalization Quotient suggests that Yinlong and Psittacosaurus were more encephalized than most extant reptiles and late-diverging ceratopsians. The angle of the lateral semicircular canal suggests that heads in ceratopsians display a transition from an upward posture to a downward posture. The relatively upward head posture indicates that early-diverging ceratopsians could feed more selectively such as to eat some leaves.

Pollination dependency and deficit in three almond varieties from Morocco

The contribution of insects to pollination constitutes a globally important ecosystem service. Due to the increasing demand for entomophilous crops, the nutritional and economic importance of insect-pollinated crops and the inability of managed pollinators (Apis mellifera L) to meet the high demand for their services indicate that agriculture heavily relies on wild pollinators. Almonds are an economically valuable crop in Morocco. Therefore, it is essential to understand the fundamental pollination requirements of major almond varieties to promote their production. The main objectives of this study were to assess the dependency of three almond cultivars (Espoir, Largueta and Planeta) on insect pollination, and then to evaluate the pollination deficit resulting from the lack of these pollinators. For this purpose, we used insect-proof net bags constructed around branches of almond trees to compare fruit set and yield with open and open + hand-pollinated flowers. The results of the fruit set experiment confirmed that all three varieties require insect pollination, as fruit set and yield were significantly higher in insect-pollinated than insect-isolated trees. All three almond varieties were categorized as obligatory dependent on biotic pollinators. In addition, two out of the three studied almond varieties showed high pollination deficit resulting from the lower abundance and/or diversity of pollinating insects. Results of the current study highlights the important role of insect pollinators for almond crops and the urgent need for the implementation of sustainable strategies to preserve pollinators within agricultural ecosystems.

Data from: Nitrifier controls on soil NO and N2O emissions in three chaparral ecosystems under contrasting atmospheric N inputs

Nitrogen saturation theory predicts high rates of atmospheric N deposition can increase ecosystem N availability and stimulate ecosystem N losses via soil nitric oxide (NO; an air pollutant at high concentrations) and nitrous oxide (N2O; a strong greenhouse gas) emissions. However, it remains unclear whether theories developed in mesic ecosystems apply to drylands, where plant and soil N availability are not always coupled in dry soils. NO and N2O are often produced in soils during the oxidation of ammonia by ammonia oxidizing archaea (AOA) or ammonia oxidizing bacteria (AOB) during nitrification. AOB are thought to emit more NO and N2O during nitrification than AOA and may be favored in N-rich relative to N-limited environments, suggesting high rates of atmospheric N deposition might produce positive feedback sending more of the N to the atmosphere. To assess how high rates of atmospheric N deposition affect AOB- and AOA-derived N trace gas emissions, we selectively inhibited AOA and AOB nitrifiers and measured NO and N2O emissions from soils collected from three dryland sites exposed to relatively low (3.8 kg ha-1 = Low N) or high (11.8 kg ha-1 = High N1; 15.6 kg ha-1 = High N2) rates of atmospheric N inputs. We found that while the High N2 deposition site had the lowest AOA:AOB ratio (2.33 ± 0.57), consistent with expectations, this site did not emit the most NO and N2O. Rather, AOA emitted between 21–78% of the NO from our sites, with higher AOA-derived NO emissions from relatively coarse-textured soils in the Low N deposition site. In addition to nitrification, denitrification also contributed to NO and N2O emissions, especially in the Moderate N deposition site (where denitrification-derived NO and N2O emissions were 2.0 – 3.7 time greater than the other sites), which had finer textured soils that may favor denitrification. Interactions between soil texture and N availability, therefore, appears to be the primary mechanism determining whether atmospheric N deposition is retained in the ecosystem or reemitted to the atmosphere as NO or N2O.

FIG. 2 in Three new synonyms of Macromitrium japonicum Dozy & Molk. (Bryophyta, Orthotrichaceae) based on morphological and molecular evidence

FIG. 2. — Macromitrium japonicum Dozy & Molk. (all specimens deposited in SHTU).

Figure 11 Proterothrix papuensis n in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 11 Proterothrix papuensis n. sp., female. A – dorsal view, B – ventral view.

Figure 9 Proterothrix papuensis, male. A in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 9 Proterothrix papuensis, male. A – dorsal view, B – ventral view.

Figure 7 Figure 7. Proterothrix modestasimilis n in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 7 Figure 7. Proterothrix modestasimilis n. sp., female. A – dorsal view, B – ventral view.

Figure 5 Figure 5. Proterothrix modestasimilis n in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 5 Figure 5. Proterothrix modestasimilis n. sp., male. A – dorsal view, B – ventral view.

Figure 3 Figure 3. Proterothrix maior n in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 3 Figure 3. Proterothrix maior n. sp., female. A – dorsal view, B – ventral view.

Figure 1 Proterothrix maior n in Three new feather mite species of the genusProterothrix Gaud, 1968 (Analgoidea: Proctophyllodidae: Pterodectinae) from birds of paradise (Passeriformes: Paradisaeidae)

Figure 1 Proterothrix maior n. sp., male. A – dorsal view, B – ventral view.

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Repository of camera trap data recorded during three pilot studies of the Amsterdamse Waterleidingduinen

Three camera trap data packages (https://camtrap-dp.tdwg.org/) of data collected as part of pilot studies carried out in the  Amsterdamse Waterleidingduinen. The pilots were aimed at determining how different types of camera deployment (e.g. regular vs. wide lens, various heights, inside/outside exclosures) might influence species detections, and how to deploy autonomous wildlife monitoring networks. Two pilots were conducted in herbivore exclosures and mainly detected European rabbits (Oryctolagus cuniculus) and red fox (Vulpes vulpes). The third pilot was conducted outside exclosures, with the European fallow deer (Dama dama) being most prevalent. Across all three pilots, a total of 47,597 images were annotated using the Agouti platform. All annotations were verified and quality-checked by a human expert. A total of 2,779 observations of 20 different species (including humans) were observed using 11 wildlife cameras during 2021–2023. The raw image files (excluding humans), image metadata, deployment metadata and observations from each pilot are shared using the Camtrap DP open standard and the extended data publishing capabilities of GBIF to increase the findability, accessibility, interoperability, and reusability of this data. The data are freely available and can be used for developing artificial intelligence (AI) algorithms that automatically detect and identify species from wildlife camera images. <a name="_Hlk161305518"></a>The repository contains a data package in <a href="https://camtrap-dp.tdwg.org/">Camtrap DP format </a> for each of the three pilots. Camtrap DP is an open standard for the exchange and archiving of camera trap data using a standardized data structure. Each data package consists of the following resources: ·        datapackage.json: Contains metadata about the data package and camera trap project from which the data originates. Describes taxonomic, temporal, and spatial extent. ·        deployments.csv: Table of individual camera trap deployments, detailing exact location and times active of each camera deployment. ·        media.csv: Table detailing every image in the data package. Lists the filenames and paths of images within the data package. ·        observations.csv: Table of observations of species (or lack thereof) derived from the images. ·        events.csv: Table linking observation events to media. ·        media folder: Folder containing a subfolder for each deployment, which contains the raw images from that deployment. Some additional notes, specific to these datasets: ·        The deployment table contains “deployment tags”, which specify extra information about the deployment, formatted as key:value pairs, separated by pipes (‘|’). Of particular interest for these datasets are the tags that state lens angle, specify habitat type and identify paired cameras (e.g. to assess differences in species detections between cameras with regular and wide lens, respectively). ·        In all three pilots, most observations are linked to sequences of images recorded within 120 seconds of each other. Hence, observations in these datasets are generally linked to an “event” (i.e. a sequence of images) rather than to an individual media file. We have added an events table to more easily link observation events and the media items that make up that event. This is an extension of the camera trap DP standard. ·        All annotations were verified and checked by a human expert, even in cases where an observation is listed as being made by an AI algorithm. ·        Whether or not an image is included in the data package is indicated by the ‘filePublic’ column in the media table. All raw images are included except for those where humans were detected. Images in which humans were detected have a ‘filePublic’ value of FALSE. Although the current location of these files within the Agouti platform (<a href="https://www.agouti.eu/">https://www.agouti.eu/</a>) is recorded in the ‘filePath’ column, these files cannot be accessed. The ‘fileName’ of these filles is the original filename they possessed when uploaded to Agouti. ·        Where ‘filePublic’ is TRUE, the `filePath` given is relative to the root of the data package (e.g. ‘media/<deployment>’) and the `fileName` of the file is the current name of the file within the data package (‘<mediaID>.JPG’).  More details about individual metadata fields in the Camtrap DP format can be found on <a href="https://camtrap-dp.tdwg.org/">https://camtrap-dp.tdwg.org/</a>.

Monthly production and open-circuit string voltage measurements after 10-year operation of three photovoltaic plants in Southern Spain affected by severe potential-induced degradation

Data are formated in a spreadsheet file.  Data are presented from three photovoltaic plants in Southern Spain (Córdoba province - Northern Andalucía) designed and installed by the same person, with the same photovoltaic module and the same model of inverter, deployed at the same time (end 2009). The plants are severely affected by potential-induced degradation (PID), so that secondary effects produce some by-pass diodes to activate, producing three families of open-circuit voltage (Voc) in the modules (~40V), (~26V) and (~12V) of a total of nominal Voc of 42,6V.  Monthly production is shown along 11 years (2010-2021), and the measurements of the open-circuit voltage of the strings after 10 years of operation along with the voltage range of the modules of each string. Sheet 1: configuration of the architecture of the three photovoltaic plants and the features of the photovoltaic module installed. Sheet 2: energy production for 11 years of opetation. In the last years some recovery is shown in plant 1 and 2 because a repowering project. Sheet 3: partial climate data of the towns were the plants are located. Sheet 4: open-circuit voltages of the strings and number of modules in each string with open-circuit voltage in the ranges (~40V) and (<=26V) in plant 1, july-2018. Sheet 5: open-circuit voltages of the strings and number of modules in each string with open-circuit voltage in the ranges (~40V), (~26V) and (~12V) in plant 2, july-2020.

OBSERVATION ON THREE FLOWER CRAB SPIDERS (ARANEAE: THOMISIDAE: THOMISUS) FROM SOUTH AFRICA

The general behaviour of three crab spider species Thomisus citrinellus Simon, 1875, T. daradioides Simon, 1890 and T. stenningi Pocock, 1900 are discussed. They are common flower dwellers found in gardens. With their strong front legs, prey are grabbed, and overpowered by their strong venom enabling them to kill prey that are frequently 2-4 times their size. They prey on seven insect orders and flies were the most commonly caught prey followed by bees. Most of the prey (79%) are caught in the neck region. They can change colour but only 53% of the spider were found on flowers of the same colour.

All-sky three-dimensional dust density and extinction Maps of the Milky Way out to 2.8 kpc

Three-dimensional dust density maps are crucial for understanding the structure of the interstellar medium of the Milky Way and the processes that shape it. However, constructing these maps requires large datasets and the methods used to analyse them are computationally expensive and difficult to scale up. As a result it is has only recently become possible to map kiloparsec-scale regions of our Galaxy at parsec-scale grid sampling. We present all-sky three-dimensional dust density and extinction maps of the Milky Way out to 2.8~kpc in distance from the Sun using the fast and scalable Gaussian Process algorithm Dustribution. The sampling of the three-dimensional map is $l,b,d = 1^{\circ} \times1^{\circ} \times 1.7$~pc. The input extinction and distance catalogue contains 120 million stars with photometry and astrometry from Gaia DR2, 2MASS and AllWISE. This combines the strengths of optical and infrared data to probe deeper into the dusty regions of the Milky Way. We compare our maps with other published 3D dust maps. All maps quantitatively agree at the $0.001$~mag~pc$^{-1}$ scale with many qualitatively similar features, although each map also has its own features. We recover Galactic features previously identified in the literature. Moreover, we also see a large under-density that may correspond to an inter-arm or -spur gap towards the Galactic Centre.   Here we provide the full dataset generated from Dustribution covering the full sky out to 2.8 kpc. We provide the 3D dust extinction and density files as well the l,b,d coordinate grid that the data is presented in.    The data in each file is as follows: <ul> <li>lbdGrid_l_bounds.pkl.npy: The boundaries of the grid cells of the merged map in l (degrees). Numpy array of size 881.</li> <li>lbdGrid_b_bounds.pkl.npy: The boundaries of the grid cells of the merged map in b (degrees). Numpy array of size 273.</li> <li>lbdGrid_d_bounds.pkl.npy: The boundaries of the grid cells of the merged map in d (pc). Numpy array of size 1644.</li> <li>Density_Median_lbd.pkl.npy: The median of 100 density samples of the merged map (mag pc^-1). Treat this as the estimate of the density. Numpy array of size (880, 272, 1644)</li> <li>Density_16P_lbd.pkl.npy: The 16th percentile of the density of the merged map (mag pc^-1). Treat median-16p as the estimate of the lower uncertainty on the density. Numpy array of size (880, 272, 1644)</li> <li>Density_84P_lbd.pkl.npy: The 84th percentile of the density of the merged map (mag pc^-1). Treat 84p-median as the estimate of the upper uncertainty on the density. Numpy array of size (880, 272, 1644) </li> <li>Ext_Median_lbd.pkl.npy: The median of the integral of 100 sample maps at each cell in the merged map (mag). Treat this as the estimate of the extinction in each cell. Numpy array of size (880, 272, 1644). </li> <li>Ext_16P_lbd.pkl.npy: The 16th percentile of the integral of 100 sample maps at each cell in the merged map (mag). Treat median-16p as the estimate of the lower uncertainty on the extinction in each cell. Numpy array of size (880, 272, 1644)</li> <li>Ext_84P_lbd.pkl.npy: The 84th percentile of the integral of 100 sample maps at each cell in the merged map (mag). Treat 84p-median as the estimate of the upper uncertainty on the extinction in each cell. Numpy array of size (880, 272, 1644)</li> <li>read_and_plot.ipynb: a short jupyter notebook demonstrating how to read in the data files, with some quick examples of plotting them.</li> </ul>

An innovative method of three-dimensional bone reconstruction of the anterior mandible with preserved dentition using an allogeneic bone block- 6-month follow-up- supplementary materials

Table S1. The Shapiro-Wilk’s normality test (N=32 for each variable and each tooth) for the differences between before and after the treatment. W – test values, p – statistical significance. Table S2. Descriptive statistics of the studied bone growth parameters. Table S3 . Relative Treatment Effects for the studied teeth and the statistical significance of the differences between before and after treatment. Table S4. Spearman’s correlations of the bone growth parameters (averaged data for all teeth). N – sample size, R – correlation coefficient, t(N-2) – test value, p – statistical significance. Table S5. The differences in bone growth parameters (averaged data for all teeth) between sexes. N – sample size, U – test value, p – statistical significance. Table S6. The differences in bone growth parameters (averaged data for all teeth) between patients who underwent orthodontic treatment with a passive wire (Wire) and patients without ongoing treatment (Without wire). N – sample size, U – test value, p – statistical significance. Table S7. The differences in bone growth parameters (averaged data for all teeth) between patients with recessions (Yes) and patients without recession (No). N – sample size, U – test value, p – statistical significance. Table S8. The differences in bone growth parameters (averaged data for all teeth) between patients with thin biotype (Thin) and patients with thick biotype (Thick). N – sample size, U – test value, p – statistical significance. Table S9. The differences in bone growth parameters (averaged data for all teeth) between patients with excessive mentalis muscle tension (Yes) and patients without such the feature (No). N – sample size, U – test value, p – statistical significance.

Characterizing multidimensional cellular physiological states with quantitative three-dimensional shape descriptors for cell membranes

<h3>Supplementary dataset and code for the article "Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes"</h3> CShaper Dataset.zip: The 3D cell regions reused from the previously published article <a href="https://doi.org/10.1038/s41467-020-19863-x">https://doi.org/10.1038/s41467-020-19863-x</a>. Cell Shape Descriptors - Code & Data.zip: The code (exemplifed by embryo Sample04) and data (including embryo Sample04-Sample20) of 12 3D shape descriptors for all 3D cell regions in the CShaper dataset. GUI.zip: The user-friendly software Shape Descriptor Tool is a Graphical User Interface based on Matlab for calculating 12 shape descriptors for a 3D cell region (exemplified by embryo Sample20, time point 14, ABpl cell in the CShaper dataset). The instruction guidebook is included in the Supplementary Material of the article.