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172 results for “shape analysis”
Data for GLM analysis of "How thermal priming of coral gametes shapes fertilization success"
<p>Data, self-explanatory, used to conduct the GLM analysis and obtain the results presented in the article "How thermal priming of coral gametes shapes fertilization success" by Antoine Puisay, Laetitia Hédouin, Rosanne Pilon, Claire Goiran, and Benoit Pujol, published in Journal of Experimental Biology and Ecology</p>
AneuploidyML_Datasets: Machine-learning analysis of factors that shape cancer aneuploidy landscapes reveals an important role for negative selection
<p>This is raw data that were used to build the processed dataset for training and testing the machine learning</p>
Volumetric Three-dimensional Analysis of the Pediatric Upper Airway Shape Using Computed Tomography Imaging.
ClinicalTrials.gov study NCT02771171. IPD Sharing: YES. Countries: 1. Publications: 3.
Efficient Automated Localization of ECoG Electrodes in CT Images Via Shape Analysis
ClinicalTrials.gov study NCT04479410. IPD Sharing: NO. Countries: 1. Publications: 7.
Differentiating three Indian shads by applying shape analysis from digital images
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Data from: BMI and WHR are reflected in female facial shape and texture: a geometric morphometric image analysis
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Data from: Multi-locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events, and rare out-crossing
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Data associated with "Adjoint methods for stellarator shape optimization and sensitivity analysis"
<p>All data produced for this dissertation and the associated post-processing scripts have been archived. </p>
Data from: Quantitative genetic analysis of subspecific differences in body shape in the snail-feeding carabid beetle Damaster blaptoides
A dimorphic pattern of macrocephalic (wide, short) and stenocephalic (narrow, long) body shapes is observed in snail-feeding carabid beetles globally. The former exhibits high performance in crushing snail shells with powerful jaws, whereas the latter specializes in eating snails' soft body directly by inserting the head into the shell. In the snail-feeding species Damaster blaptoides, the subspecies D. b. capito has a wide short forebody, and D. b. fortunei has a narrow, long forebody. They exhibit distinct morphologies despite their geographic and phylogenetic proximity. To examine the genetic basis of the morphological differences between these two subspecies, we conducted quantitative genetic analyses by crossing these subspecies and producing F_1 and backcross hybrids. The hybrids had body shapes intermediate between the parental subspecies. The variation between wide, short and narrow, long forebodies was based on negative geneti c correlations between width and length of the head and thorax. Between one and eight genetic factors were involved in the morphological differences between subspecies. We suggest that the morphological integration of forebody parts in a small number of loci has facilitated the marked morphological diversification between subspecies of D. blaptoides.
Data from: Shape analysis of moss (Bryophyta) sporophytes: insights into land plant evolution
PREMISE OF THE STUDY: The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses—the second most diverse land-plant lineage—has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS: We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS: We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS: Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.
Data from: Shape analysis of symmetric structures: quantifying variation among individuals and asymmetry
Morphometric studies often consider parts with internal left-right symmetry, for instance, the vertebrate skull. This type of symmetry is called object symmetry and is distinguished from matching symmetry, in which two separate structures exist as mirror images of each other, one on each body side. We explain a method for partitioning the total shape variation of landmark configurations with object symmetry into components of symmetric variation among individuals and asymmetry. This method is based on the Procrustes superimposition of the original and a reflected copy of each landmark configuration and is compatible with the two-factor ANOVA model customary in studies of fluctuating asymmetry. We show a fully multivariate framework for testing the effects in the two-factor model with MANOVA statistics, which also applies to shapes with matching symmetry. We apply the new methods in a small case study of pharyngeal jaws of the Neotropical cichlid fish Amphilophus citrinellus. The analysis revealed that the symmetric component of variation in the pharyngeal jaws is dominated by the contrast between two alternative trophic morphs in this species and that there is subtle but statistically significant directional asymmetry. Finally, we provide some general recommendations for morphometric studies of symmetric shapes.
Data from: Facultative bacterial endosymbionts shape parasitoid food webs in natural host populations: a correlative analysis
1.Facultative bacterial endosymbionts can protect their aphid hosts from natural enemies such as hymenopteran parasitoids. As such, they have the capability to modulate interactions between aphids, parasitoids and hyperparasitoids. However, the magnitude of these effects in natural aphid populations and their associated parasitoid communities is currently unknown. Moreover, environmental factors such as plant fertilization and landscape complexity are known to affect aphid‐parasitoid interactions but it remains unclear how such environmental factors affect the interplay between aphids, parasitoids and endosymbionts. 2.Here, we tested whether facultative endosymbionts confer protection to parasitoids in natural populations of the English grain aphid, Sitobion avenae, and if this is affected by plant fertilization and landscape complexity. Furthermore, we examined whether the effects of facultative endosymbionts can cascade up to the hyperparasitoid level and increase primary‐hyperparasitoid food web specialization. 3.Living aphids and mummies were collected in fertilized and unfertilized plots within 13 wheat fields in Central Germany. We assessed the occurrence of primary parasitoid, hyperparasitoid and endosymbiont species in aphids and mummies using a newly established molecular approach. 4.Facultative endosymbiont infection rates were high across fields (~80 %), independent of whether aphids were parasitized or un‐parasitized. Aphid mummies exhibited a significantly lower share of facultative endosymbiont infection (~38 %). These findings suggest that facultative endosymbionts do not affect parasitoid oviposition behavior, but decrease parasitoid survival in the host. Facultative endosymbiont infection rates were lower in mummies collected from fertilized compared to unfertilized plants, indicating that plant fertilization boosts the facultative endosymbiont protective effect. Furthermore, we found strong evidence for species‐specific and negative cascading effects of facultative endosymbionts on primary and hyperparasitoids, respectively. Facultative endosymbionts impacted parasitoid assemblages and increased the specialization of primary‐hyperparasitoid food webs: these effects were independent from and much stronger than other environmental factors. 5.The current findings stongly suggest that facultative endosymbionts act as a driving force in aphid‐parasitoid‐hyperparastioid networks: they shape insect community composition at different trophic levels and modulate, directly and indirectly, the interactions between aphids, parasitoids and their environment.
Fig. 3. Shape PCA for exploring female variation within Anisopteromalus calandrae and A in Morphometric analysis and taxonomic revision of Anisopteromalus Ruschka (Hymenoptera: Chalcidoidea: Pteromalidae) - an integrative approach
Fig. 3. Shape PCA for exploring female variation within Anisopteromalus calandrae and A. quinarius using all variables except gaster breadth. The analyses included three cultured laboratory strains for each OTU. (A) Scatterplot of first against second shape PC of A. calandrae: cross, strain Bamberg USA; plus signs, strain Savannah USA; open circles, strain Slough (ICSP) UK. (B) Scatterplot of first against second shape PC of A. quinarius: cross, strain Moscow (MSU) Russia; plus signs, strain Michurinsk Russia; open squares, strain Fresno USA. The variance explained by each shape PC is given in parentheses.
Leveraging Machine Learning for Size and Shape Analysis of Nanoparticles: A Shortcut to Electron Microscopy
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Comprehensive analysis of locomotion dynamics in the protochordate Ciona intestinalis reveals how neuromodulators flexibly shape its behavioral repertoire.
<p>This record contains (as of 2022-06-27) datasets corresponding to the study of behavior in swimming <em>Ciona intestinalis</em> larvae (controls and drug treated animals) that were recorded in our behavioural setups. In particular, it contains:</p> <ol> <li>multi-point tracking data of the larvae obtained using the Tierpsy Tracker (developed by Andre Brown's lab, MRC LMS).</li> <li>features like curvature, speed etc calculated from the tracking data</li> <li>results of time-series analyses (matrix-profiling, hidden markov modelling, spatio-temporal clustering) performed on the feature dataset</li> <li>Hidden Markov Models trained for inferences</li> </ol>
Fig. 1 in Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation
Fig. 1. Configuration of landmarks (red dot within yellow circles) as applied to all color pattern variation (CPV) grades of Cichla temensis. (1) the anterior point of the skull; (2) the anterior edge of the base of the first dorsal spine; (3) the center of the base of the 10 th dorsal spine; (4) the base of the first long ray of the second dorsal fin; (5) the base of the 9 th ray of the second dorsal fin; (6) the posterior point of termination of the second dorsal fin; (7) the posterior base of the anal fin; (8) the base of the 7th anal fin ray; (9) the anterior insertion of the anal fin; (10) the cloaca; (11) the ventral termination of the scale row emanating from the insertion of the 10th dorsal spine; (12) the ventral termination of the scale row emanating from the anterior point of the insertion of the pelvic fin.
Fig. 2 in Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation
Fig. 2. Thin-plate-spline deformation grids depicting (a) overall body shape differences between extremes of CPV grades (magnified 3x); (b) the increase in area at the bases of the second dorsal and anal fins between extremes of CPV grades (magnified 3x).
Fig. 4 in Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation
Fig. 4. Height to length ratio of color pattern variants of Cichla temensis. The average height/SL ratio increased with CPV grade from a low of 0.2694 for CPV Grade 1 (paca), 0.2725 for CPV Grade 2, 0.2771 for CPV Grade 3 and 0.2822 for CPV Grade 4 (açu).
Fig. 4 in Does size matter for horny beetles? A geometric morphometric analysis of interspecific and intersexual size and shape variation in Colophon haughtoni Barnard, 1929, and C. kawaii Mizukami, 1997 (Coleoptera: Lucanidae)
Fig. 4 Box plots and deformation grids showing size variations and shape deformations in Colophon beetles: female Colophon, male C. haughtoni and male C. kawaii. Size was measured as natural log transformed centroid size (LnCS). Deformation grids show the shape changes related to size from the smallest to the largest individuals. Values in parentheses are the magnification applied to improve visualisation of shape deformations
Synthetic Data for Neutrophil Analysis: Sets one large neutrophil shape and Poisson noise
<p><strong>Synthetic Datasets with one large irregular shape and Poisson noise.</strong></p> <p><strong>Part of the PhagoSight neutrophil tracking and analysis package (Henry, et al., PLOS ONE, 2013):</strong></p> <p> </p> <p>https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636</p> <p>http://www.phagosight.org</p> <p>https://github.com/phagosight/phagosight</p> <p> </p> <p>A series of synthetic data sets that reproduce different behaviour characteristics of migrating neutrophils were generated in MATLAB. The data sets consisted of one artificial neutrophil that travelled along a path that presented different conditions of tortuosity, times to activation during 98 time frames.</p> <p>Numerous data sets of neutrophils in zebrafish were carefully observed before setting the characteristics. One trajectory was manually determined by setting the row, column positions of the centroid at every time point for 98 time frames. The trajectory was designed so that it would represent different neutrophil behaviours: some moments were very oriented and had movements with uniform distance between time frames, whilst others were less uniform and would move at different velocities, some were tortuous whilst others were straight.</p> <p>Each time frame consisted of 11 slices of z-stack each with 275 x 275 pixels, where the neutrophil was formed by Gaussian distributions of higher intensities than the background and <strong>Poisson noise </strong>(check the corresponding sets with <strong>smaller </strong>regular shapes with Gaussian noise and irregular shapes with Poisson noise).</p> <p> </p> <p>Files corresponding to the sets with irregular shapes and Poisson noise (noise increases from 1 to 5):</p> <ul> <li><strong> Ground Truth syntheticData_L_mat_La </strong></li> <li><strong> First data set syntheticData_L1_mat_Re</strong></li> <li><strong> Second data set syntheticData_L2_mat_Re</strong></li> <li><strong> Third data set syntheticData_L3_mat_Re</strong></li> <li><strong> Fourth data set syntheticData_L4_mat_Re</strong></li> <li><strong> Fifth data set syntheticData_L5_mat_Re</strong></li> </ul> <p> </p> <p>Corresponding GIF files are also included as illustrations of the cells in motion.</p> <p> </p> <p>Main Reference:</p> <p><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636"><strong><em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model</strong> </a><br> Henry KM, Pase L, Ramos-Lopez CF, Lieschke GJ, Renshaw SA, Reyes-Aldasoro CC. (2013) <em>PhagoSight</em>: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model. PLOS ONE 8(8): e72636. <a href="https://doi.org/10.1371/journal.pone.0072636">https://doi.org/10.1371/journal.pone.0072636</a></p>
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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.