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4,753 results for “SHAPE”
Fig. 3 in Gladius shape variation in coleoid cephalopod Trachyteuthis from the Upper Jurassic Nusplingen and Solnhofen Plattenkalks
Fig. 3. Gladius of vampyropod coleoid Trachyteuthis hastiformis (Rüppell, 1829). A. Holotype (SMF IX1328), Lower Tithonian (Hybonoticeras hybonotum Zone), Mühlheim. A1, lower slab with gladius in dorsal aspect; A2, close−up of A1 showing the granulated area within the spindle−shaped elevation, which is flattened but easily visible in outlines; A3, original drawing of Rüppell (1829: pl. 3: 3). B. Specimen MARKM 1 (original of Meyer (1855: pl. 19: 1), Lower Tithonian (Hybonoticeras hybonotum Zone), Solnhofen area. B1, gladius in ventral aspect; B2, close−up of B1 showing the spindle−shape structure; B3, original drawing of Meyer (1855: pl. 19: 1).
Fig. 1 in Gladius shape variation in coleoid cephalopod Trachyteuthis from the Upper Jurassic Nusplingen and Solnhofen Plattenkalks
Fig. 1. Morphology, terminology and measurements of a vampyropod gladius. A. Trachyteuthis. B. Loligosepia.
Fig. 2 in Gladius shape variation in coleoid cephalopod Trachyteuthis from the Upper Jurassic Nusplingen and Solnhofen Plattenkalks
Fig. 2. Gladius shape variation in Trachyteuthis. A. Planar type. B. Nonplanar type. C. Keeled type. The granulated area is marked by a pointed line.
Fig. 6 in Gladius shape variation in coleoid cephalopod Trachyteuthis from the Upper Jurassic Nusplingen and Solnhofen Plattenkalks
Fig. 6. Gladius of vampyropod coleoid Trachyteuthis teudopsiformis sp. nov. A. Holotype (G 1306061), Lower Tithonian (Hybonoticeras hybonotum Zone), Blumenberg. A1, gladius seen in dorsal aspect; mm, mantle musculature; A2, close−up of A1 showing the granules at the anterior half of the gladius; A3, close−up of A1 showing the granules at the posterior half of the gladius. B. Paratype (MB.C.1002.4), Lower Tithonian (Hybonoticeras hybonotum Zone), Daiting. B1, gladius seen in ventral aspect; B2, close−up of B1 showing imprints of dorsal granules. C. Counterpart of the paratype (PIMUZ17826), gladius seen in dorsal aspect.
Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient
<p>The Matlab code and dataset for the manuscript "Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient". The dataset is packed in the ZIP archive 'Dataset_EjsmondTodisco_etal.zip' with variable description in the Matlab code file EjsmondTodisco_etal.m. To run the program, place the files EjsmondTodisco_etal.m and Fun_PlotResults.m in a catalog. The results are stored in two catalogs: 'ThReabsorptionAndSecretion' - modeling the rate of thiamine loss with processes of active reabsorption and secretion; and 'ThReabsorptionOnly' - modeling the rate of thiamine loss with the process of active reabsorption only. The ThReabsorptionAndSecretion catalog contains data for three life history types: iteroparity (baseline model), semelparity, and determinate growth (constant mass of somatic tissues in adults). For details see the manuscript by Ejsmond, Todisco et al.</p>
Datasets for paper "Frequent Ancient Hybridization Shape the Confounding Phylogeny of Pandanales"
<p><span>The phylogeny of Pandanales, an order of monocots comprising five distinct families (Cyclanthaceae, Pandanaceae, Stemonaceae, Triuridaceae, and Velloziaceae), has long been contentious, particularly concerning the placement of Triuridaceae. Previous phylogenetic studies have produced conflicting results, partly due to the limited scope of molecular data. In this study, we leveraged large-scale transcriptome sequencing from 17 Pandanales species and three outgroup samples, combined with whole-genome data for Acanthochlamys bracteata, to conduct a comprehensive phylogenetic analysis. Using both concatenation and coalescent-based methods, we generated a well-supported phylogeny for the group, revealing significant gene tree-species tree discordance. Our hybridization analyses revealed that ancient hybridization played a crucial role in shaping the evolutionary history of the Pandanaceae and Triuridaceae, providing a compelling explanation for the conflicting phylogenetic results in earlier studies. Additionally, whole-genome duplication (WGD) analyses identified five distinct WGD events across the order, suggesting these events played a critical role in the ecological diversification of the families. Our findings resolve key phylogenetic conflicts in Pandanales and underscore the importance of integrating hybridization detection and WGD analysis in understanding plant evolutionary history.</span></p>
Scenario database of the SHAPE project
<p>The scenario data from the SHAPE project are available for interactive visualisation and download in the SHAPE Scenario Explorer: <a href="https://shape.apps.ece.iiasa.ac.at/">https://shape.apps.ece.iiasa.ac.at/</a> . Please refer to the Explorer webpage for documentation, license and suggested references when using the data.</p> <p>This data release accompanies the following publication: </p> <p>B. Soergel, S. Rauner, V. Daioglou, et al., Multiple pathways towards sustainable development goals and climate targets, Environmental Research Letters, 2024, <a href="https://doi.org/10.1088/1748-9326/ad80af">https://doi.org/10.1088/1748-9326/ad80af</a></p> <p>The SHAPE project investigated interactions between options to mitigate climate change and the broader agenda of the United Nations' Sustainable Development Goals (SDGs). It modelled and analysed Sustainable Development Pathways that make as much progress towards the SDGs as possible by 2030, and maintain sustainable development thereafter, while meeting the climate targets set out in the Paris agreement. The project was funded by the <a href="https://jpi-climate.eu/programme/axis/">ERA-NET AXIS Call</a> initiated by the JPI Climate, and funded by FORMAS (SE), FFG/BMBWF (AT), DLR/BMBF (DE), NWO (NL) and RCN (NO) with co-funding by the European Union.</p>
Dataset and code for article "Explicit description of viral capsid subunit shapes by unfolding dihedrons"
<p>This repository contains data and codes used in a paper "Explicit description of viral capsid subunit shapes by expanding dihedrons" by Toyooka et al.</p> <p>- [grasshopper/] contains a GH file used in the 3D CAD Rhinoceros/Grasshopper.<br>- [docking_axes_viper/] contains notebooks for aligning the subunit coordinates with the VIPER coordinate system (Z-axis is the 2-fold axis, 3-fold axis is on the X-axis, and 5-fold axis is on the Y-axis)</p> <p>- [docking_pairwise/] contains input scipts and analysis notebooks for pairwise docking simulations for subunits<br> - [1stm_zdock_iter/df.jld2] data containing top docking scores and poses, and screw motion parameters<br> - [1stm_zdock_iter/rmsd.jld2] RMSD data of docking poses with regard to the experimental structure - [1stm_zdock_iter/run.sh] is a batch script for conducting docking simulations with ZDOCK<br> - [1stm_zdock_iter/run_each.sh] is a script for a single docking simulation with a specified random seed. Called from `run.sh`<br> - [1stm_zdock_iter/skrew_parameters.ipynb] analyzes the result of docking simulations. Sort the results accoring to docking scores and find the skrew axis of each docking pose<br> - [1stm_zdock_iter/visualize.ipynb] plots the docking score and the screw axis parameters, and also calculates and plots RMSDs from the reference structure (whole-shell structure)<br> - [1stm_zdock_iter/ref.pdb] is a sympolic link to a refrence structure (whole-shell structure)<br> - [4v4m_zdock_iter/] PDB ID: 4V4M<br> - [6s44_zdock_iter/] PDB ID: 6S44<br> - [7odw_zdock_iter/] PDB ID: 7ODW<br> - [3r0r_zdock_iter/] PDB ID: 3R0R<br> - [5zju_zdock_iter/] PDB ID: 5ZJU<br> - [1vb4_zdock_iter/] PDB ID: 1VB4<br> - [1m1c_zdock_iter/] PDB ID: 1M1C<br> - [6r7m_zdock_iter/] PDB ID: 6R7M<br> - [2m99_zdock_iter/] PDB ID: 2M99</p>
Figure 7 in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 7. Results of sliding semilandmark process from 3D data, and specimens warped along Principal Component 1 (PC1). A. Thin plate spline deformation grid showing transformation of Echmatemys callopyge mean type along PC1. B. 3D image of Echmatemys callopyge showing the positions of landmarks along the curve indicated in A, specimen no.UNMN.VP.27621. C. 3D image of Echmatemys uintensis showing the positions of landmarks along the curve indicated in D, UMNH.VP.27429. D. Thin plate spline deformation grid showing transformation of E. uintensis mean type along PC1.
Figure 5 in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 5. Principal components plots from geometric morphometric analyses of 2D epiplastral shape data. A. Dorsal epiplastral shape: PC1 (49.3% variance) versus PC2 (16.7% variance). B. Ventral epiplastral shape: PC 1 (47.7% variance) versus PC2 (20.8%) variance.
Figure 4 in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 4. Plot of Tooth-Midline versus Tooth-Lip (TM/TL) values for each specimen. The correlation between these two variables is significant (R2=0.403). Correlation coefficients do not differ significantly between any pair of taxa.
Figure 1 in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 1. Morphological differences in dorsal epiplastral shape between Uintan Echmatemys species. A. Echmatemys callopyge (UMNH.VP.27220). B. Echmatemys uintensis (UMNH.VP.26558). The gular scale is indicated in grey.
Figure 2. A in Epiplastral and geographic variation in Echmatemys, a geoemydid turtle from the Eocene of North America: A multi-tiered analysis of epiplastral shape complexity
Figure 2. A. Standard linear measurements for quantifying the dimensions of the gular scale on the epiplastron of Echmatemys species depicted on UMNH.VP.27220. TM=tooth-midline: Distance between the epiplastral tooth and the anatomical midline. TL=tooth-lip: Distance between the epiplastral tooth and the caudal lip of the gular-humeral sulcus. B. Two-dimensional epiplastral landmarks and semilandmarks used in 2D geometric morphometric comparisons of this study: Ventral surface. Data points were digitized from digital photographs. C. Three-dimensional epiplastral landmarks and semilandmarks used in 3D geometric morphometric analyses in this study. All data points were obtained from 3D NextEngine laser scans. Scale bar=2 cm.
Dataset from: "Which search are you on? Adapting to color while searching for shape"
<p>Dataset for Bergmann, N., Tünnermann, J., & Schubö, A. (2020). Which search are you on? Adapting to color while searching for shape. <em>Attention, Perception, & Psychophysics, 82</em>, 457–477. https://doi.org/10.3758/s13414-019-01858-6</p>
PLATE IVA. Metioche Stal, 1877. (A–J), Metioche japonica (Ichikawa, 2001): A, Male; B, Inner margin of eyes more brightlyrimmed; C, Male sub-genital plate; D, Fore tibiae without tympanum on both sides; E, Shape of last segment of maxillary palpi-securiform; F, Male genitalia; G, Female; H, Tegmina convex; I, Female ovipositor upturned, shaped; apex sharp with teeth on; J, subgenital plate triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IVA. Metioche Stal, 1877. (A–J), Metioche japonica (Ichikawa, 2001): A, Male; B, Inner margin of eyes more brightlyrimmed; C, Male sub-genital plate; D, Fore tibiae without tympanum on both sides; E, Shape of last segment of maxillary palpi-securiform; F, Male genitalia; G, Female; H, Tegmina convex; I, Female ovipositor upturned, shaped; apex sharp with teeth on; J, subgenital plate triangular.
PLATE IVB. Metioche Stal, 1877. (A–G), Metioche japonica (Ichikawa, 2001): A, Eyes rounded, large and widely separated; B,Antennae: Scape and pedicel dark black, flagellum light in colour; C, Shape of last segment of maxillary palpi-securiform; D, Female sub-genital plate triangular; E, Male sub-genital plate; F, Male genitalia; G, Female ovipositor upturned, sabre shaped; apexsharp with teeth on ventre. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IVB. Metioche Stal, 1877. (A–G), Metioche japonica (Ichikawa, 2001): A, Eyes rounded, large and widely separated; B,Antennae: Scape and pedicel dark black, flagellum light in colour; C, Shape of last segment of maxillary palpi-securiform; D, Female sub-genital plate triangular; E, Male sub-genital plate; F, Male genitalia; G, Female ovipositor upturned, sabre shaped; apexsharp with teeth on ventre.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular.
Environment and phenology shape local adaptation in thermal performance
Populations within species often exhibit variation in traits that reflect local adaptation and further shape existing adaptive potential for species to respond to climate change. However, our mechanistic understanding of how the environment shapes trait variation remains poor. Here, we used common garden experiments to quantify thermal performance in eight populations of the marine snail <i>Urosalpinx cinerea </i>across thermal gradients on the Atlantic and the Pacific coasts of North America. We then evaluated the relationship between thermal performance and environmental metrics derived from time-series data. Our results reveal a novel pattern of "mixed" trait performance adaptation, where thermal optima was positively correlated with spawning temperature (cogradient variation), while maximum trait performance was negatively correlated with season length (countergradient variation). This counterintuitive pattern likely arises because of phenological shifts in the spawning season, whereby "cold" populations delay spawning until later in the year when temperatures are warmer compared to "warm" populations that spawn earlier in the year when temperatures are cooler. Our results show that variation in thermal performance can be shaped by multiple facets of the environment and are linked to organismal phenology and natural history. Understanding the impacts of climate change on organisms therefore requires the knowledge of how climate change will alter different aspects of the thermal environment.
Linking micro and macroevolution of head shape in an island radiation
<p>Phenotypic traits have been shown to evolve in response to variation in the environment. However, the evolutionary processes underlying the emergence of phenotypic diversity can typically only be understood at the population level. Consequently, how subtle phenotypic differences at the intraspecific level can give rise to larger-scale changes in performance and ecology remains poorly understood. We here tested for the covariation between ecology, bite force, jaw muscle architecture, and the three-dimensional shape of the cranium and mandible in 16 insular populations of the lizards <i>Podarcis melisellensis</i> and <i>P. sicula</i>. We then compared the patterns observed at the among-population level with those observed at the interspecific level. We found that three-dimensional head shape as well as jaw musculature evolve similarly under similar ecological circumstances. Depending on the type of food consumed or on the level of sexual competition, different muscle groups were more developed and appeared to underlie changes in cranium and mandible shape. Our findings show that the local selective regimes are primary drivers of phenotypic variation resulting in predictable patterns of form and function. Moreover, intraspecific patterns of variation were generally consistent with those at the interspecific level, suggesting that microevolutionary variation may translate into macroevolutionary patterns of ecomorphological diversity.</p>
Fig. 20 in A New Subfamily of Spiders with Grate-shaped Tapeta from Australia and Papua New Guinea (Araneae: Stiphidiidae: Borralinae)
Fig. 20. Asmea capella. (a,b), male palp (SAM NN19576): a, ventral; b, retrolateral. (c–f), epigynum (holotype): c, ventral; d, lateral; e, posterior; f, dorsal—internal genitalia. Scale lines 0.5 mm: upper, a,b; lower, c–f.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.