scholarly journals Large-scale open-source three-dimensional growth curves for clinical facial assessment and objective description of facial dysmorphism

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Harold S. Matthews ◽  
Richard L. Palmer ◽  
Gareth S. Baynam ◽  
Oliver W. Quarrell ◽  
Ophir D. Klein ◽  
...  
Keyword(s):  
Open Source ◽  
Clinical Diagnosis ◽  
Large Scale ◽  
Three Dimensional ◽  
Growth Curves ◽  
Facial Dysmorphism ◽  
Facial Morphology ◽  
Craniofacial Dysmorphism ◽  
Facial Shape ◽  
The Rich

AbstractCraniofacial dysmorphism is associated with thousands of genetic and environmental disorders. Delineation of salient facial characteristics can guide clinicians towards a correct clinical diagnosis and understanding the pathogenesis of the disorder. Abnormal facial shape might require craniofacial surgical intervention, with the restoration of normal shape an important surgical outcome. Facial anthropometric growth curves or standards of single inter-landmark measurements have traditionally supported assessments of normal and abnormal facial shape, for both clinical and research applications. However, these fail to capture the full complexity of facial shape. With the increasing availability of 3D photographs, methods of assessment that take advantage of the rich information contained in such images are needed. In this article we derive and present open-source three-dimensional (3D) growth curves of the human face. These are sequences of age and sex-specific expected 3D facial shapes and statistical models of the variation around the expected shape, derived from 5443 3D images. We demonstrate the use of these growth curves for assessing patients and show that they identify normal and abnormal facial morphology independent from age-specific facial features. 3D growth curves can facilitate use of state-of-the-art 3D facial shape assessment by the broader clinical and biomedical research community. This advance in phenotype description will support clinical diagnosis and the understanding of disease pathogenesis including genotype–phenotype relations.

scholarly journals Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles

2020 ◽  
Vol 117 (40) ◽  
pp. 24679-24690
Author(s):  
Ishika Saha ◽  
Eric K. Dang ◽  
Dennis Svatunek ◽  
Kendall N. Houk ◽  
Patrick G. Harran
Keyword(s):  
Virtual Screening ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Three Dimensional ◽  
Pharmacological Properties ◽  
Robust Methods ◽  
Small Peptide ◽  
Multistep Reaction ◽  
Condensed Heterocycles

Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.

scholarly journals The influence of uncertain loading on topology-optimized designs

2021 ◽  
Author(s):  
Philipp Hofer ◽  
Erich Wehrle
Keyword(s):  
Topology Optimization ◽  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Applied Force ◽  
Structural Performance ◽  
Optimized Design ◽  
Applied Forces ◽  
Reducing Costs ◽  
The Relationship

The design of structures using topology optimization can improve the structural performance and save material, in turn reducing costs. Using a framework of large-scale, three-dimensional topology optimization implemented by the authors in an open-source multiphysical software, we investigate the influence of uncertain loading on the optimized design. Direct differentiation is used to reveal the relationship between displacements and applied force, giving an efficient and effective tool to postprocess optimized topologies. The developed methodology for the assessment of the sensitivity with respect to applied forces is explored using two three-dimensional examples: the classic MBB cantilever and a cableway pylon. The advantages and limitations of this method are discussed.

C haste : incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library

2009 ◽  
Vol 367 (1895) ◽  
pp. 1907-1930 ◽  
Author(s):  
Miguel O. Bernabeu ◽  
Rafel Bordas ◽  
Pras Pathmanathan ◽  
Joe Pitt-Francis ◽  
Jonathan Cooper ◽  
...  
Keyword(s):  
Open Source ◽  
Computational Efficiency ◽  
Large Scale ◽  
Three Dimensional ◽  
Testing Procedure ◽  
Two Dimensions ◽  
Multi Scale ◽  
Bidomain Equations ◽  
Cancer Modelling ◽  
Set Up

Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (C haste ) project. C haste is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into C haste . Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the C haste framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how C haste may be developed to include new physiological functionality—such as modelling a beating heart and fluid flow in the heart—and how new algorithms aimed at increasing the efficiency of the code may be incorporated.

Virtual Demonstration Tests of Large-Scale and Complex Artifacts Using an Open Source Parallel CAE System, ADVENTURE

2006 ◽  
Vol 110 ◽  
pp. 133-142 ◽  
Author(s):  
Shinobu Yoshimura
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Element Model ◽  
General Purpose ◽  
Full Scale ◽  
Grid Environments ◽  
Dimensional Finite Element ◽  
Three Dimensional Finite Element ◽  
Cae System

The ADVENTURE project started as one of the research projects in the "Computational Science & Engineering" field selected for the "Research for the Future" Program sponsored by the Japan Society for the Promotion of Science during 1997-2002. Since March 2002, the project has continued as an independent project. In the project we have been developing an advanced general-purpose computational mechanics system, named ADVENTURE, running in various kinds of parallel and ditributed environments. The system is designed to be able to analyze a three-dimensional finite element model of arbitrary shape with 10-100 million DOFs mesh, and additionally to enable parametric and non-parametric shape optimization. The first version of the system has been released from the project website as open source software since March, 2002. 2,049 registered users in academia and industries have downloaded 12,827 modules and been using them, while one company has developed and released its commercial version named ADVENTUREcluster. The ADVENTURE system has been successfully implemented in various types of parallel and distributed environments including PC clusters, massively parallel processers such as Hitachi SR8000/MPP and the Earth Simulator, and Grid environments such as ITBL (IT-based Laboratory). The system has been successfully applied to solve various real world problems such as response of a full scale nuclear pressure vessel model and thermoelastic deformation of full scale electric mounting board of a mobile PC.

scholarly journals Wnt Signaling Drives Correlated Changes in Facial Morphology and Brain Shape

2021 ◽  
Vol 9 ◽  
Author(s):  
Marta Marchini ◽  
Diane Hu ◽  
Lucas Lo Vercio ◽  
Nathan M. Young ◽  
Nils D. Forkert ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Three Dimensional ◽  
Facial Morphology ◽  
Ontogenetic Changes ◽  
Expression Domain ◽  
Head Development ◽  
Facial Shape ◽  
Close Relationship ◽  
The Face ◽  
Canonical Wnt

Canonical Wnt signaling plays multiple roles critical to normal craniofacial development while its dysregulation is known to be involved in structural birth defects of the face. However, when and how Wnt signaling influences phenotypic variation, including those associated with disease, remains unclear. One potential mechanism is via Wnt signaling’s role in the patterning of an early facial signaling center, the frontonasal ectodermal zone (FEZ), and its subsequent regulation of early facial morphogenesis. For example, Wnt signaling may directly alter the shape and/or magnitude of expression of the sonic hedgehog (SHH) domain in the FEZ. To test this idea, we used a replication-competent avian sarcoma retrovirus (RCAS) encoding Wnt3a to modulate its expression in the facial mesenchyme. We then quantified and compared ontogenetic changes in treated to untreated embryos in the three-dimensional (3D) shape of both the SHH expression domain of the FEZ, and the morphology of the facial primordia and brain using iodine-contrast microcomputed tomography imaging and 3D geometric morphometrics (3DGM). We found that increased Wnt3a expression in early stages of head development produces correlated variation in shape between both structural and signaling levels of analysis. In addition, altered Wnt3a activation disrupted the integration between the forebrain and other neural tube derivatives. These results show that activation of Wnt signaling influences facial shape through its impact on the forebrain and SHH expression in the FEZ, and highlights the close relationship between morphogenesis of the forebrain and midface.

scholarly journals Solar3D: An Open-Source Tool for Estimating Solar Radiation in Urban Environments

2020 ◽  
Vol 9 (9) ◽  
pp. 524
Author(s):  
Jianming Liang ◽  
Jianhua Gong ◽  
Xiuping Xie ◽  
Jun Sun
Keyword(s):  
Solar Radiation ◽  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Solar Irradiation ◽  
Slope Aspect ◽  
Atmospheric Conditions ◽  
3D City Models ◽  
Grass Gis ◽  
City Models

Solar3D is an open-source software application designed to interactively calculate solar irradiation on three-dimensional (3D) surfaces in a virtual environment constructed with combinations of 3D-city models, digital elevation models (DEMs), digital surface models (DSMs) and feature layers. The GRASS GIS r.sun solar radiation model computes solar irradiation based on two-dimensional (2D) raster maps for a given day, latitude, surface and atmospheric conditions. With the increasing availability of 3D-city models and demand for solar energy, there is an urgent need for better tools to computes solar radiation directly with 3D-city models. Solar3D extends the GRASS GIS r.sun model from 2D to 3D by feeding the model with input, including surface slope, aspect and time-resolved shading, which is derived directly from the 3D scene using computer graphics techniques. To summarize, Solar3D offers several new features that—as a whole—distinguish this novel approach from existing 3D solar irradiation tools in the following ways. (1) Solar3D can consume massive heterogeneous 3D-city models, including massive 3D-city models such as oblique airborne photogrammetry-based 3D-city models (OAP3Ds or integrated meshes); (2) Solar3D can perform near real-time pointwise calculation for duration from daily to annual; (3) Solar3D can integrate and interactively explore large-scale heterogeneous geospatial data; (4) Solar3D can calculate solar irradiation at arbitrary surface positions including on rooftops, facades and the ground.

Verification and Validation of High-Fidelity Open-Source Simulation Tools for Supersonic Aircraft Aerodynamic Analysis

2021 ◽  
Author(s):  
Henry Stoldt ◽  
Artem Korobenko ◽  
Paul Ziade ◽  
Craig Johansen
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Delta Wing ◽  
Three Dimensional ◽  
Aircraft Design ◽  
Verification And Validation ◽  
Small Scale ◽  
High Fidelity ◽  
Supersonic Aircraft ◽  
Academic Settings

Abstract Small supersonic vehicle concepts used as research platforms to test new aerospace technologies, such as advanced propulsion systems or large sensor payloads, require major modifications to conventional, large-scale, manned, supersonic airframe design. High-fidelity numerical simulation of these concepts in academic settings often requires the use of in-house or available open-source tools instead of expensive commercial software or those with export-control restrictions. A verification and validation analysis of two widely-used open-source compressible-flow solvers, rhoCentralFoam (rCF) and SU2, is performed for several flow problems relevant to the supersonic aerodynamics of small-scale, autonomous aircraft concepts. The one-dimensional shock tube problem, two-dimensional supersonic turbulent boundary layer, and three-dimensional delta wing are simulated with both solvers. The effects of flux scheme, flux limiters, and Courant-Friedrichs-Lewy (CFL) number on solution accuracy, stability, and solver speed are assessed. The solvers' limitations and their usefulness as supersonic aircraft design tools in a holistic sense are discussed.

Study on erythrocytes by SEM photogrammetry (SEMP) technique

1990 ◽  
Vol 48 (3) ◽  
pp. 724-725
Author(s):  
Tong Wensheng ◽  
Lu Lianhuang ◽  
Zhang Zhijun
Keyword(s):  
Quantitative Analysis ◽  
Cell Membrane ◽  
Clinical Diagnosis ◽  
Human Body ◽  
Blood Cells ◽  
Three Dimensional ◽  
Normal Person ◽  
Blood Disease ◽  
Computation Technique ◽  
Important Basis

This is a combined study of two diffirent branches, photogrammetry and morphology of blood cells. The three dimensional quantitative analysis of erythrocytes using SEMP technique, electron computation technique and photogrammetry theory has made it possible to push the study of mophology of blood cells from LM, TEM, SEM to a higher stage, that of SEM P. A new path has been broken for deeply study of morphology of blood cells.In medical view, the abnormality of the quality and quantity of erythrocytes is one of the important changes of blood disease. It shows the abnormal blood—making function of the human body. Therefore, the study of the change of shape on erythrocytes is the indispensable and important basis of reference in the clinical diagnosis and research of blood disease.The erythrocytes of one normal person, three PNH Patients and one AA patient were used in this experiment. This research determines the following items: Height;Length of two axes (long and short), ratio; Crevice in depth and width of cell membrane; Circumference of erythrocytes; Isoline map of erythrocytes; Section map of erythrocytes.

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