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78 results for “BEAGLE”
gmap - qgis training material: Beagle Rupes (Mercury)
<p>This dataset part of the Geology and Planetary Mapping Winter School 2022 featuring Beagle Rupes as a study area.<br> Beagle Rupes is lobate scarp at Mercurys surface with a length of more than 600km cross-cutting an oval shaped crater. <br> We compiled a beginners – intermediate level training package for the area. The package includes several basemaps such as Map Projected Basemap Reduced Data Record (BDR) (Hash 2013a), High-incidence East-illumination Basemap (HIE), Map-projected High-incidence West-illumination (HIW) (Hash 2015a), Map Projected Low-Incidence Angle Basemap Reduced Data Record (LOI) (Hash 2013b), Map Projected Multispectral Reduced Data Record (MDR) Hash 2015b) and digital terrain model (DTM) (Becker et al., 2016). The data is cut to the area of interest and a training project is set up for QGIS. </p> <p>The training package is designed as a group exercise with four adjacent tiles covering the Beagle Rupes area. </p>
Fig. 4 in Psammophaga fuegia sp. nov., a New Monothalamid Foraminifera from the Beagle Channel, South America
Fig. 4. ML-tree of the genus Psammophaga, with Vellaria zucchellii as outgroup. Bootstrap values bigger than 80% are shown. Described species are highlighted in grey.
Fig. 1 in Psammophaga fuegia sp. nov., a New Monothalamid Foraminifera from the Beagle Channel, South America
Fig. 1. Map of the Beagle Channel area. The sampling sites are indicated by black dots and their correspondent numbers are shown in groups. Psammophaga fuegia was recovered by microscopy and/or environmental sequencing at fifteen sites that are highlighted by grey arrows. Specimens found in Ushuaia were sampled during a previous expedition.
Fig. 5 in Psammophaga fuegia sp. nov., a New Monothalamid Foraminifera from the Beagle Channel, South America
Fig. 5. SEM images of mineral grains found within Psammophaga fuegia specimens from sites 17 (1 and 2) and 56 (3 and 4). Images 1c, 2c, 3b, 3d, and 4b are in BSE mode highlighting density differences. All remaining images are in SE mode. Note different scales of vari- ous images and insets on images of larger scale showing the position of images in smaller scale. Mineral grains analysed for their chemical composition are marked as follows: a – amphibole, c – cordierite, h – hematite, i – ilmenite, f – ferrigehlenite, p – pyroxene, q – quartz, t – titanite, tm – titanoferous magnetite, and z – zircon.
Data and scripts for: Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI
<p>Phylogenies are central to many research areas in biology and commonly estimated using likelihood-based methods. Unfortunately, any likelihood-based method, including Bayesian inference, can be restrictively slow for large datasets–with many taxa and/or many sites in the sequence alignment–or complex substitution models. The primary limiting factor when using large datasets and/or complex models in probabilistic phylogenetic analyses is the likelihood calculation, which dominates the total computation time. To address this bottleneck, we incorporated the high-performance phylogenetic library BEAGLE into RevBayes, which enables multi-threading on multi-core CPUs and GPUs, as well as hardware-specific vectorized instructions for faster likelihood calculations. Our new implementation of RevBayes+BEAGLE retains the flexibility and dynamic nature that users expect from vanilla RevBayes. Additionally, we implemented a native parallelization within RevBayes without an external library using the message passing interface (MPI); RevBayes+MPI. We evaluated our new implementation of RevBayes+BEAGLE using multi-threading on CPUs and a powerful NVidia Titan V GPU against our native implementation of RevBayes+MPI. We found good improvements in speedup when multiple cores were used with up to 20-fold speedup when using multiple CPUs and over 90-fold speedup when using multiple GPU cores. The improvement depended on the data type used, DNA or amino acids, and the size of the alignment, but less on the size of the tree. We additionally investigated the cost of rescaling partial likelihoods to avoid numerical underflow and showed that unnecessarily frequent rescaling can increase runtimes 2.5 to 3-fold. Finally, we presented and compared a new approach to store partial likelihoods on branches instead of nodes which can speed up computations but comes at twice the memory requirements.</p> <p>Availability: The software described in the paper is available at https://github.com/revbayes/revbayes with documentation and tutorials found at https://revbayes.github.io.</p>
Figure 6 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 6. Liriopsis pygmaea. (a, b) Habitus of early subadult female; (c) ventral habitus of advanced subadult female; (d, e) dorsal and ventral habitus of adult female; (f, g) adult female, details of anterior and posterior ends of the slit. Scale bars: 5 mm (a–e); 0.5 mm (f); 1 mm (g).
Figure 5 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 5. Liriopsis pygmaea. Cryptoniscus larva. (a) Third pereopod; (b) sixth pereopod; (c) seventh pereopod, merus and carpus only; (d) first pleopod, (e) uropods. Scale bars: 0.1 mm (b and c, same scale).
Figure 3 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 3. Liriopsis pygmaea. SEM photographs of the cryptoniscus larva. (a, b) Dorsal and ventral habitus; (c) ventral view of head, arrow shows the median plate partially covering the rostral teeth of the first antenna; (d) anterior part of first and second antennular articles, arrows show the first article with a rostral tooth completely exposed and the second article with a single median tooth; (e) ventral view showing the sixth (foreground) and seventh styliform pereopods; arrow indicates seventh coxal plate. Photographs (b) and (c) belong to the same specimen, the others to different specimens. Scale bars in mm.
Figure 1 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 1. Liriopsis pygmaea. SEM photographs of the epicaridium larva. (a) Ventral habitus; (b) ventral view of abdomen; (c) detail of anal tube. All photographs belong to the same specimen.
Figure 2 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 2. Liriopsis pygmaea. Epicaridium larva. (a) Second antenna; (b) sixth pereopod; (c) fourth pleopod; (d) uropods. Scale bars: 0.05 mm.
Figure 4 in First record of the hyperparasite Liriopsis pygmaea (Cryptoniscidae, Isopoda) from a rhizocephalan parasite of the false king crab Paralomis granulosa from the Beagle Channel (Argentina), with a redescription
Figure 4. Liriopsis pygmaea. Cryptoniscus larva. (a) Dorsal habitus; (b) first antenna; (c) second antenna; (d) first pereopod, with detail of distal process of propodus. Scale bars: 0.5 mm (a); 0.1 mm (b–d).
FIG. 4 in Populations of a new morphotype of corrugate Lessonia Bory in the Beagle Channel, sub-Antarctic Magellanic ecoregion: a possible case of on-going speciation
FIG. 4. — Phylogenetic tree based on concatenated ITS1 and atp8-trnS partial sequences (418 bp). Note that corrugated Lessonia Bory specimens are grouped with Lessonia flavicans Bory specimens which have smooth blade surface. First number on the branches refers to the bootstrap value determined from the ML phylogeny and the second is the posterior probability from the BI analysis. Scale bar: 0.05 substitution per site.
FIG. 5 in Populations of a new morphotype of corrugate Lessonia Bory in the Beagle Channel, sub-Antarctic Magellanic ecoregion: a possible case of on-going speciation
FIG. 5. — Phylogenetic tree based on concatenated cox1 and cox3 partial sequences (1176 bp). Note that corrugated Lessonia Bory specimens are grouped with Lessonia flavicans Bory specimens which have smooth blade surface. First number on the branches refers to the bootstrap value determined from the ML phylogeny and the second is the posterior probability from the BI analysis. Scale bar: 0.01 substitution per site.
FIG. 3 in Populations of a new morphotype of corrugate Lessonia Bory in the Beagle Channel, sub-Antarctic Magellanic ecoregion: a possible case of on-going speciation
FIG. 3. — Internal morphology of the corrugate Lessonia Bory: A, small angular meristodermal cells on the surface of blade; B, transverse section through a sterile portion of the blade; C, detail of meristoderm and cortex showing cells with full (right arrow) and reduced (left arrow) protoplast and golden bodies in outer cortex and mid cortex; and rounded light refracting bodies (arrowheads); D, detail of medulla showing cylindrical cells (arrow) and some elongated filaments (arrowhead) immersed in a dense intercellular matrix; E, surface view of a sorus; F, transverse section through a sorus; G, detail of sorus. Abbreviations: mer, meristoderm; oc, outer cortex; mc, mid cortex; ic, inner cortex; m, medulla; p, paraphyses; l, part of the lacuna; s, sporangia. Scale bars: A, 15 µm; B, 50 µm; C, G, 20 µm; D, E, 40 µm; F, 30 µm.
FIG. 1 in Populations of a new morphotype of corrugate Lessonia Bory in the Beagle Channel, sub-Antarctic Magellanic ecoregion: a possible case of on-going speciation
FIG. 1. — Map of the sub-Antarctic ecoregion of Magellan showing the collection sites of the corrugate morphotype of Lessonia Bory, Lessonia flavicans Bory, and Lessonia searlesiana Asensi & Reviers. Strait of Magellan-Cockburn channel: a, Fuerte Bulnes; b, Carlos III Island. Beagle channel-Orange Bay: c, London Island; d, Puerto Aguirre; e, London Island; f, Cormoran Bay; g, Paula Cove; h, Puerto Toro; i, Tekenika Bay; j, Orange Bay. Cape Horn-Diego Ramirez Island: k, Diego Ramirez Island.
FIG. 2. — A in Populations of a new morphotype of corrugate Lessonia Bory in the Beagle Channel, sub-Antarctic Magellanic ecoregion: a possible case of on-going speciation
FIG. 2. — A, External morphology of the corrugate Lessonia Bory showing the brownish terete stipe; B, corrugated blades; C, that arise from the base of the blade and from dichotomously divided branches; D, the holdfast is rhizoidal in shape and composed mainly of fused haptera. Scale bars: holotype, 30 cm; A, C, 2 cm; B, 5 cm; D, 8 cm.
Data and scripts for: Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI
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Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study
<p>Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both the magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of <em>Leptospira</em> bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to <em>Leptospira</em> antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between the overall heritability of vaccine-induced immune response to <em>Leptospira</em> antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.</p>
Fig. 2 in Psammophaga fuegia sp. nov., a New Monothalamid Foraminifera from the Beagle Channel, South America
Fig. 2. Holotype of Psammophaga fuegia from Bahia Romanche. Scale bar: 500 µm.
Salinity, temperature and PAR collected at Outer Bahía Brown, Beagle Channel, Argentina
<p>This is a series of environmental data collected at fixed moorings in Brown Bay in the Begale Channel, Tierra del Fuego, Argentina. The moorings were placed in 2021 and left in place for two years. Continuous data, collected at 3 or 4 depths (sub-surface, 6, 11 and 16 meters).</p>
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