A 3D visualization and simulation of the individual human jaw

A new biomechanical three-dimensional (3D) model for the human mandible based on computer-generated virtual model is proposed. Using maps obtained from the special kinds of photos of the face of the real subject, it is possible to attribute personality to the virtual character, while computer animation offers movements and characteristics within the confines of space and time of the virtual world. A simple two-dimensional model of the jaw cannot explain the biomechanics, where the muscular forces through occlusion and condylar surfaces are in the state of 3D equilibrium. In the model all forces are resolved into components according to a selected coordinate system. The muscular forces act on the jaw, along with the necessary force level for chewing as some kind of mandible balance, preventing dislocation and loading of nonarticular tissues. In the work is used new approach to computer-generated animation of virtual 3D characters (called "Body SABA"), using in one object package of minimal costs and easy for operation.     

A high-level 3D visualization API for Java and ImageJ

Background  

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.     

Celestial3D: a novel method for 3D visualization of familial data

Summary: Traditional two-dimensional (2D) software programsfor drawing pedigrees are limited when dealing with extendedpedigrees. In successive generations, the number of individualsgrows exponentially, leading to an unworkable amount of spacerequired in the horizontal direction for 2D displays. In addition,it is not always possible to place closely related individualsnear each other due to the lack of space in 2Ds. To addressthese issues we have developed three-dimensional (3D) pedigreedrawing techniques to enable clearer visualization of extendedpedigrees. Currently no other methods are available for displayingextended pedigrees in 3Ds. We have made freely available a softwaretool—‘Celestial3D’—that implements thesenovel techniques. Availability: Freely available to non-commercial users Contact: celestial3d{at}genepi.org.au Supplementary information: www.genepi.org.au/celestial3d Associate Editor: Martin Bishop ¹A more extensive list of software tools appears in the SupplementaryMaterial.     

A visualization of 3D proteome universe: Mapping of a proteome ensemble into 3D space based on the protein-structure composition

To visualize a bird’s-eye view of an ensemble of proteomes for various species, we recently developed a novel method of mapping a proteome ensemble into Three-Dimensional (3D) vector space. In this study, the “proteome” is defined as the entire set of all proteins encoded in a genome sequence, and these proteins were dealt with at the level of the SCOP Fold. First, we represented the proteome of a species s by a 1053-dimensional vector x(s), where its length ∣x(s)∣ represents the overall amount of all the SCOP Folds in the proteome, and its unit vector x(s)/∣x(s)∣ represents the relative composition of the SCOP Folds in the proteome and the size of the dimension, 1053, is the number of all possible Folds in the proteome ensemble given. Second, we mapped the vector x(s) to the 3D vector y(s), based on the two simple principles: (1) ∣y(s)∣ = ∣x(s)∣, and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). We applied to the mapping of a proteome ensemble for 456 species, which were retrieved from the Genomes TO Protein structures and functions (GTOP) database. As a result, we succeeded in the mapping in that the properties of the 1053-dimensional vectors were quantitatively conserved in the 3D vectors. Particularly, the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.95–0.96). This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner.     

VISTAL--a new 2D visualization tool of protein 3D structural alignments

We offer a tool, denoted VISTAL, for two-dimensional visualization of protein structural alignments. VISTAL describes aligned structures as a series of matched secondary structure elements, colored according to the three-dimensional distance of their Calpha atoms. AVAILABILITY: VISTAL can be downloaded from http://trantor.bioc.columbia.edu/~kolodny/software.html.     

TopoICE-R: 3D visualization modeling the topology of DNA recombination

TopoICE-R is a three-dimensional visualization and manipulation software for solving 2-string tangle equations and can be used to model the topology of DNA bound by proteins such as recombinases and topoisomerases. AVAILABILITY: This software, manual and example files are available at www.knotplot.com/download for Linux, Windows and Mac.     

FPV: fast protein visualization using Java 3D

MOTIVATION: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. RESULTS: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. AVAILABILITY: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/     

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

Background  

Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.     

Application of distance geometry to 3D visualization of sequence relationships

SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/     

3D visualization software to analyze topological outcomes of topoisomerase reactions

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases.     

Computer simulation modelling and visualization of 3D architecture of biological tissues

Recent technical improvements, such as 3D microscopy imaging, have shown the necessity of studying 3D biological tissue architecture during carcinogenesis. In the present paper a computer simulation model is developed allowing the visualization of the microscopic biological tissue architecture during the development of metaplastic and dysplastic lesions.The static part of the model allows the simulation of the normal, metaplastic and dysplastic architecture of an external epithelium. This model is associated to a knowledge base which contains only data on the nasal epithelium. The latter has been well studied by numerous authors and its lesional states are well known. An inference engine allows the initialization of the static model parameters. A statistical comparison between simulated epithelia and real epithelia is achieved by adjusting the parameter values during the simulation.The dynamic part of the model allows the simulation of a growth process on a 3D representation based on the static model. The main hypothesis is that nasal epithelium is submitted to a continuous transformation from normal to cancer through metaplasia and dysplasia. The evolution of each cell (represented by its nucleus) depends on its local environment and also on its heritage from its mother-cell.Simulation of tissue renewal of the nasal pseudostratified epithelium has been achieved. The evolution from normal to hyperplasia has been simulated. After modification of the cell cycle modelling, the simulation of the development of metaplastic foci has been obtained.     

A density functional theory approach toward substituent effect in Meerwein-Eschenmoser-Claisen rearrangement

B3LYP/6-31 G(d) level of theory has been used for the examination of substituent effect in the concerted step of the Meerwein-Eschenmoser-Claisen rearrangement. In this regard, the effect of NO₂ and NH₂ groups in different positions has been investigated. The obtained results show that substituent effect is very sensitive to its position and configuration. Electron withdrawing and electron donating groups in different positions and various configurations show different and sometimes opposite results.     

A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns

The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT.     

The effect of the methyl substituent on the bioconversion of cyclohexene derivatives

Summary The absence of the methyl substituent at the 2position of the cyclohexene ring of TCHP enhances the conversion rate as well as the yields of the 3-hydroxy product obtained byStreptomyces natalensis and the 3-keto product obtained byMycobacterium smegmatis.Abbreviations TCHP 1-(2-thienyl)-3-(1-cyclohexen-1-yl)-1-propanone - TCHP-OH 1-(2-thienyl)-3-(3-hydroxyl-1-cyclohexen-1-yl)-1-propanone - TCHP-ketone 1-(2-thienyl)-3-(1-cyclohexen-1-yl-3-one)-1-propane - TMCHP 1-(2-thienyl)-3-(2-methyl-1-cyclohexen-1-yl)-propanone     

3D parallel coordinate systems--a new data visualization method in the context of microscopy-based multicolor tissue cytometry.

BACKGROUND: Presentation of multiple interactions is of vital importance in the new field of cytomics. Quantitative analysis of multi- and polychromatic stained cells in tissue will serve as a basis for medical diagnosis and prediction of disease in forthcoming years. A major problem associated with huge interdependent data sets is visualization. Therefore, alternative and easy-to-handle strategies for data visualization as well as data meta-evaluation (population analysis, cross-correlation, co-expression analysis) were developed. METHODS: To facilitate human comprehension of complex data, 3D parallel coordinate systems have been developed and used in automated microscopy-based multicolor tissue cytometry (MMTC). Frozen sections of human skin were stained using the combination anti-CD45-PE, anti-CD14-APC, and SytoxGreen as well as the appropriate single and double negative controls. Stained sections were analyzed using automated confocal laser microscopy and semiquantitative MMTC-analysis with TissueQuest 2.0. The 3D parallel coordinate plots are generated from semiquantitative immunofluorescent data of single cells. The 2D and 3D parallel coordinate plots were produced by further processing using the Matlab environment (Mathworks, USA). RESULTS: Current techniques in data visualization primarily utilize scattergrams, where two parameters are plotted against each other on linear or logarithmic scales. However, data evaluation on cartesian x/y-scattergrams is, in general, only of limited value in multiparameter analysis. Dot plots suffer from serious problems, and in particular, do not meet the requirements of polychromatic high-context tissue cytometry of millions of cells. The 3D parallel coordinate plot replaces the vast amount of scattergrams that are usually needed for the cross-correlation analysis. As a result, the scientist is able to perform the data meta-evaluation by using one single plot. On the basis of 2D parallel coordinate systems, a density isosurface is created for representing the event population in an intuitive way. CONCLUSIONS: The proposed method opens new possibilities to represent and explore multidimensional data in the perspective of cytomics and other life sciences, e.g., DNA chip array technology. Current protocols in immunofluorescence permit simultaneous staining of up to 17 markers. Showing the cross-correlation between these markers requires 136 scattergrams, which is a prohibitively high number. The improved data visualization method allows the observation of such complex patterns in only one 3D plot and could take advantage of the latest developments in 3D imaging.     

Detecting binocular 3D motion in static 3D noise: no effect of viewing distance

Relative binocular disparity cannot tell us the absolute 3D shape of an object, nor the 3D trajectory of its motion, unless the visual system has independent access to how far away the object is at any moment. Indeed, as the viewing distance is changed, the same disparate retinal motions will correspond to very different real 3D trajectories. In this paper we were interested in whether binocular 3D motion detection is affected by viewing distance. A visual search task was used, in which the observer is asked to detect a target dot, moving in 3D, amidst 3D stationary distractor dots. We found that distance does not affect detection performance. Motion-in-depth is consistently harder to detect than the equivalent lateral motion, for all viewing distances. For a constant retinal motion with both lateral and motion-in-depth components, detection performance is constant despite variations in viewing distance that produce large changes in the direction of the 3D trajectory. We conclude that binocular 3D motion detection relies on retinal, not absolute, visual signals.     

24,25(OH)2D3 enhances the calcemic effect of 1,25(OH)2D3

The effect of 24,25(OH)2D3 on 1,25(OH)2D3-induced hypercalcemia was studied in normal rats. Serum (S) levels and urinary excretion of Ca2+ (UCaV) were measured in (a) control rats, (b) rats receiving a daily sc injection of 54 ng 1,25(OH)2D3, (c) rats receiving 24,25(OH)2D3 in the same dose and same manner, and (d) rats receiving 1,25(OH)2D3 + 24,25(OH)2D3. The animals were housed in metabolic cages and 24-hr urine specimens were collected. After 24 hr SCa2+ increased similarly with 1,25(OH)2D3 and with 1,25(OH)2D3 + 24,25(OH)2D3, while 24,25(OH)2D3 alone did not change SCa2+. UCaV after 24 hr increased significantly less (P less than 0.025) with 1,25(OH)2D3 + 24,25(OH)2D3 than with 1,25(OH)2D3 alone. After 5 days of 1,25(OH)2D3, SCa2+ rose from 5.1 +/- 0.15 to 6.29 +/- 0.08 whereas 1,25(OH)2D3 + 24,25(OH)2D3 effected a greater increase in SCa2+ up to 6.63 +/- 0.09 (P less than 0.01). 24,25(OH)2D3 alone did not change SCa2+. UCaV after 5 days of treatment rose similarly with 1,25(OH)2D3 and with 1,25(OH)2D3 + 24,25(OH)2D3. After 10 days of 1,25(OH)2D3 SCa2+ was 6.17 +/- 0.15 meq/liter while with the combination SCa2+ rose to 6.74 +/- 0.2 (P less than 0.025). 24,25(OH)2D3 alone did not change SCa2+. These results show that (a) 24,25(OH)2D3 alone does not alter SCa2+ in normal rats, (b) combined administration of 1,25(OH)2D3 + 24,25(OH)2D3 enhances the hypercalcemic response to 1,25(OH)2D3 without a parallel increase in UCaV, and (c) it is suggested that the effect of 24,25(OH)2D3 on serum Ca2+ level, at least partly, may result from its hypocalciuric effect.     

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules. A new version of BRAGI has been developed that is supported on Windows, Linux and SGI. The user interface has been rewritten to give the standard 'look and feel' of the chosen operating system and to provide a more intuitive, easier usage. A large number of new features have been added. Information from public databases such as SWISS-PROT, InterPro, DALI and OMIM can be displayed in the 3D viewer. Structures can be searched for homologous sequences using the NCBI BLAST server.     

A theory on the determination of 3D motion and 3D structure from features

The present paper proposes a mathematical theory and a method of recognition of both the 3D structure and the motion of a moving object from its monocular image. Initially, characteristic features are extracted from the 2D perspective image of the object. Because motion of the object induces a change in its 2D perspective image, it also induces a change in the features which depends on the 3D structure and the velocity of the object. This suggests the possibility of detecting the 3D structure and the motion directly from the features and their changing rate, without the need for calculating optical flows. An analysis is made of the relation between the 3D rigid motion of a surface element and the change in local linear features. From this relation, a method is proposed for calculating the velocity of and the normal to the surface element without considering any correspondence of points. An optical flow can also be calculated by this method. Two simple computer simulations are provided.