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169 results for “morphological models”
Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Statistical and Dynamic Model of Surface Morphology Evolution during Polishing in Additive Manufacturing
<p>This repository maintains data and code associated with our accepted paper in IISE Transactions titled "Statistical and Dynamical model of Surface Morphology Evolution during Polishing in Additive Manufacturing". To briefly summarize,</p> <p><strong>1. Polishing_stagewise_data.zip</strong> - Contains height values measured at 32 different locations on the 3D printed sample using an optical profilometer prior to polishing (Stage 0) and post every stage of polishing (Stages 1 to 6). Please refer to the following paper for experimentation details and process parameters: "<em>Jin, S., A. Iquebal, S. Bukkapatnam, A. Gaynor, and Y. Ding (2019, 10). A gaussian process model-guided surface polishing process in additive manufacturing. Journal of Manufacturing Science and Engineering 142, 1–17.</em>"</p> <p><strong>2. Initial_surface_generation.m</strong> - Script containing the Initial surface generation algorithm using the random circle packing algorithm. This file generates the surface asperity distribution and their graph connectivity of a 3D printed sample prior to polishing (Figure 4(b) in paper). One such realization is stored and compared with experimental data (Refer #3).</p> <p><strong>3. Stage0_fitted_data.mat</strong> - .mat file containing data pertaining to height measures of the 3D printed sample prior to polishing and generated initial surface (simulation) which is statistically similar to the actual data.</p> <p><strong>4. Parameter_fitting_Polishing.m</strong> - Script containing the model capturing polishing dynamics with network formation, evaluated at each stage of polishing. This file generates the Bearing Area Curves of the initial surface simulated after each stage of polishing and compares with experimental data (Figures 3, 5, 6, 7 and 8 in paper). (The script makes use of other functions defined in #5).</p> <p><strong>5. surface_roughness.m, graph_evolution.m, solve_for_d.m, KLDiv.m</strong> and <strong>Gen_hurst.m</strong> - Matlab scripts containing functions that are called within the main script (Parameter_fitting_Polishing.m)</p> <p><strong>6. Simulated_Annealing.zip</strong> - Zip file containing files related to Simulated Annealing Algorithm. Please read the <strong>README_Simulated_Annealing.txt</strong> for instructions to reproduce the optimized parameter solutions.</p> <p><strong>7. pub_fig.m</strong> - Script containing the formatting options for plots and figures.</p>
Underlying data for: "Morphology as indicator of adaptive changes of model tissues in osmotically and chemically changing environments"
<p>For our publication "Morphology as indicator of adaptive changes of model tissues in osmotically and chemically changing environments" (at <a href="https://doi.org/10.1016/j.bioadv.2023.213635">DOI: 10.1016/j.bioadv.2023.213635)</a> we here provide the raw data for the included plots.</p> <p>Due to the aggregate size of the numerous microscopy images, those are provided on request.<br> Herein, we provide the data obtained by processing the microscopy images into cell nuclei positions, cell density profiles and morpological as well as topological parameters.</p>
Data and Code for: Phospholipase-catalyzed Degradation Drives Domain Morphology and Rheology Transitions in Model Lung Surfactant Monolayers
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Novel integrative modeling of molecules and morphology across evolutionary timescales
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Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.
DSM: Deep Sequential Model for Complete Neuronal Morphology Representation and Feature Extraction
<p>This is an open-source repository for hosting codes and data files from research, "DSM: Deep Sequential Model for Complete Neuronal Morphology Representation and Feature Extraction". We also provided a web service based on our methods, please go to http://114.117.165.134:8501/.</p><p>(1)raw_dataset.zip: </p><ol><li>1,282 neuron reconstructions from SEU-Allen dataset;</li><li>1,002 neuron reconstructions from Janelia dataset;</li><li>1,100 neuron reconstructions from ION dataset.</li></ol><p>(2)Supplementary.zip: Supplementary information, including tables and figures;</p><p>(3)DSM-tools.zip: A python package for converting neuron morphology into sequences and implementing DSM models.</p><ol><li>NeuronSequenceDataset class: to transform SWC files to sequence dataframes by binary tree traversals, and prepare for the input of DSM networks.</li><li>DSMDataConverter class: a helper to convert the sequence dataframes for classification and clustering.</li><li>DSMHierarchicalAttentionNetwork class: classification model, giving a pre-trained DSM-HAN model by default.</li><li>DSMAutoencoder class: clustering model, giving a pre-trained DSM-AE model by default.</li></ol><p>(4)neuron2seq_for_developer.zip: A repository for further development of the models, including source codes and all data files.</p>
GLobAl building MOrphology dataset for URban climate modelling
<p>GLobAl building MOrphology dataset for URban climate modelling (GLAMOUR) offers the building footprint and height files at the resolution of 100 m in global urban centers.</p> <ul> <li>the `BH_100m` contains the building height files where each file is named as `BH_{lon_start}_{lon_end}_{lat_start}_{lat_end}.tif`.</li> <li>the `BF_100m` contains the building footprint files where each file is named as `BF_{lon_start}_{lon_end}_{lat_start}_{lat_end}.tif`.</li> </ul> <p>Here `lon_start`, `lon_end`, `lat_start`, `lat_end` denote the starting and ending positions of the longitude and latitude of target mapping areas.</p> <p>To avoid possible confusion, it should be clarified that the 'building footprint' in GLAMOUR represents the 'building surface fraction', i.e., the ratio of building plan area to total plan area.</p> <p> </p> <p>We also offer the snapshot of source code used for the generation of the GLAMOUR dataset including:</p> <ul> <li>`GC_ROI_def.py` defines regions of interest (ROI) used in the mapping of the GLAMOUR dataset.</li> <li>`GC_user_download.py` retrieves satellite images including Sentinel-1/2, NASADEM and Copernicus DEM from Google Earth Engine and exports them into Google Cloud Storage.</li> <li>`GC_master_pred.py` downloads exported data records from Google Cloud Storage and then performs the estimation of building footprint and height using Tensorflow-based models.</li> <li>`GC_postprocess.py` performs postprocessing on initial estimations by pixel masking with the World Settlement Footprint layer for 2019 (WSF2019).</li> <li>`GC_postprocess_agg.py` aggregates masked patches into larger tiles contained in the GLAMOUR dataset.</li> </ul>
Stanza Models for Morphologically enhanced Universal Dependencies for Korean (morphUD)
<p>Stanza (<a href="https://stanfordnlp.github.io/stanza/">Stanford NLP Group</a>) models for Morphologically enhanced Universal Dependencies for Korean (morphUD) including ko.vectors.xz files for morphUD and wordUD. </p> <p> </p> <p>Embedding files are generated with https://doi.org/10.5281/zenodo.5869738</p> <p> </p> <p>All files are listed in file.txt </p> <p> </p>
Data and model output for "Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation"
<p>Data, model output, and scripts supporting the manuscript:</p> <p>Litwin, D. G., & Harman, C. J. (2024) Evidence of subsurface control on the coevolution of hillslope morphology and runoff generation. <em>Water Resources Research</em>, 60, e2024WR037301. https://doi.org/10.1029/2024WR037301</p>
SPH modelling of companion-perturbed AGB outflows including a new morphology classification scheme
<p><strong>ABSTRACT</strong></p> <p><em>Context.</em> Asymptotic giant branch (AGB) stars are known to lose a significant amount of mass by a stellar wind, which controls the remainder of their stellar lifetime. High angular-resolution observations show that the winds of these cool stars typically exhibit mid- to small-scale density perturbations such as spirals and arcs, believed to be caused by the gravitational interaction with a (sub-)stellar companion.<br> <em>Aims.</em> We aim to explore the effects of the wind-companion interaction on the 3D density and velocity distribution of the wind, as a function of three key parameters: wind velocity, binary separation and companion mass. For the first time, we compare the impact on the outflow of a planetary companion to that of a stellar companion. We intend to devise a morphology classification scheme based on a singular parameter.<br> <em>Methods.</em> We ran a small grid of high-resolution polytropic models with the smoothed particle hydrodynamics (SPH) numerical code Phantom to examine the 3D density structure of the AGB outflow in the orbital and meridional plane and around the poles. By constructing a basic toy model of the gravitational acceleration due to the companion, we analysed the terminal velocity reached by the outflow in the simulations.<br> <em>Results.</em> We find that models with a stellar companion, large binary separation and high wind speed obtain a wind morphology in the orbital plane consisting of a single spiral structure, of which the two edges diverge due to a velocity dispersion caused by the gravitational slingshot mechanism. In the meridional plane the spiral manifests itself as concentric arcs, reaching all latitudes. When lowering the wind velocity and/or the binary separation, the morphology becomes more complex: in the orbital plane a double spiral arises, which is irregular for the closest systems, and the wind material gets focussed towards the orbital plane, with the formation of an equatorial density enhancement (EDE) as a consequence. Lowering the companion mass from a stellar to a planetary mass, reduces<br> the formation of density perturbations significantly.<br> <em>Conclusions.</em> With this grid of models we cover the prominent morphology changes in a companion-perturbed AGB outflow: slow winds with a close, massive binary companion show a more complex morphology. Additionally, we prove that massive planets are able to significantly impact the density structure of an AGB wind. We find that the interaction with a companion affects the terminal velocity of the wind, which can be explained by the gravitational slingshot mechanism. We distinguish between two types of wind focussing to the orbital plane resulting from distinct mechanisms: global flattening of the outflow as a result of the AGB star’s orbital motion and the formation of an EDE as a consequence of the companion’s gravitational pull. We investigate different morphology classification schemes and uncover that the ratio of the gravitational potential energy density of the companion to the kinetic energy density of the AGB outflow yields a robust classification parameter for the models presented in this paper.</p>
Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
<p>Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression, and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.</p>
Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation
<p>The group Anguimorpha represents one of the most unified squamate clades in terms of body plan, ecomorphology, ecophysiology and evolution. On the other hand, the anguimorphs vary between different habitats and ecological niches. Therefore, we focused on the group Anguimorpha to test a possible correlation between heart morphology and ecological niche with respect to phylogenetic position in Squamata with <em>Sphenodon</em>, <em>Salvator</em>, and <em>Pogona</em> as the outgroups. The chosen lepidosaurian species were investigated by microCT. Generally, all lepidosaurs had two well-developed atria with complete interatrial septum and one ventricle divided by ventricular septa to three different areas. The ventricles of all lepidosaurians had a compact layer and abundant trabeculae. The compact layer and trabeculae were developed in accordance with the particular ecological niche of the species; the trabeculae in nocturnal animals with low metabolism, such as <em>Sphenodon, Heloderma</em> or <em>Lanthanotus</em>, were more massive. On the other hand, athletic animals, such as varanids or <em>Salvator</em>, had ventricle compartmentalization divided by three incomplete septa. A difference between varanids and <em>Salvator</em> was found in compact layer thickness: thicker in monitor lizards and possibly linked to their mammalian-like high blood pressure, and the level of ventricular septation. In summary: heart morphology varied among clades in connection with the ecological niche of particular species and it reflects the phylogenetic position in the model clade Anguimorpha. In the absence of fossil evidence, this is the closest approach to understanding heart evolution and septation in clades with different cardiac compartmentalization levels. </p>
Quantitative variables related to color, territory, behavior, and morphology for male lesser prairie-chickens used in discrete choice models in mate choice study
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Assessing the adequacy of morphological models using Posterior Predictive Simulations
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Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation
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Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
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Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
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Data from: A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian saber-tooth
<p>Morphological convergence can be assessed through a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here we introduce a new method to chart patterns of convergence on three-dimensional models, deployed with the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well-known case study, the saber-tooth morphotype which has evolved independently among distinct mammalian clades, from placentals to metatherians. Although previous authors have concluded that saber-tooths kill using a stabbing 'bite' to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the saber-tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among saber-tooths than for any other taxa. We found that the morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence implies similarity in function among these phylogenetically distant species. In our view this function is most likely the killing of relatively large prey by a stabbing bite.</p>
Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
Accurate modeling of the complexity of morphological evolution is crucial for morphological phylogenetics and for performing tests on a wide variety of evolutionary scenarios. In this context, morphological integration and the problem of correlated categorical characters represent a major challenge. In particular, the magnitude and implications of correlations among serially homologous structures such as teeth have been much debated but were never tested statistically within a broad phylogenetic context. Here, we present a large-scale empirical study analyzing the serial variation of cingular crests on successive molars (M1, M2 and M3) of 274 placental species in a phylogenetic context. Both likelihood analyses and analysis of phylogenetic co-distributions demonstrated highly correlated evolution in the entire sample and thus the non-independence of these serial features at a macroevolutionary scale. Likelihood analyses show that their serial variation should be better scored within a single composite character model with constrained paths for transitions enabling simultaneous changes on all three molars, which suggests a strong developmental or genetic integration. These results are congruent with current molecular and developmental knowledge related to dental morphological variation and call into question the frequent use of separate characters scored on serially homologous structures of the dentition in phylogenetic analyses. Overall, they provide long-overdue and clear empirical evidence that in-depth studies of patterns of integration constitute an essential step towards more realistic character construction and modeling. This approach is critical for more accurate morphological phylogenetics and, more generally, for testing macroevolutionary scenarios on groups of correlated characters.
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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.