Interactive Graphics Techniques Research Articles

Expansion of Substrate Specificity of Cytochrome P450 2A6 by Random and Site-directed Mutagenesis*

The natural product indole is a substrate for cytochrome P450 2A6. Mutagenesis of P450 2A6 was done to expand its capability in the oxidization of bulky substituted indole compounds, which are not substrates for the wild-type enzyme or the double mutant L240C/N297Q, as determined in our previous work (Wu, Z.-L., Aryal, P., Lozach, O., Meijer, L., and Guengerich, F. P. (2005) Chem. Biodivers. 2, 51-65). Error-prone PCR and site-directed mutagenesis led to the identification of two critical amino acid residue changes (N297Q and I300V) that achieve the purpose. The new mutant (N297Q/I300V) was able to oxidize both 4- and 5-benzyloxy(OBzl)indoles to form colored products. Both changes were required for oxidation of these bulky substrates. The colored product derived from 5-OBzl-indole was mainly 5,5'-di-OBzl-indirubin, whereas the dominant blue dye isolated upon incubations with 4-OBzl-indole was neither an indigo nor an indirubin. Two-dimensional NMR experiments led to assignment of the structure as 4-OBzl-2-(4'-OBzl-1',7'-dihydro-7'-oxo-6'H-indol-6'-ylidene)indolin-3-one, in which a pyrrole ring and a benzene ring are connected with a double bond instead of the pyrrole-pyrrole connection of other indigoids. Monomeric oxidation products were also isolated and characterized; three phenols (4-OBzl-1H-indol-5-ol, 4-OBzl-1H-indol-6-ol, and 4-OBzl-1H-indol-7-ol) and one quinone (4-OBzl-1H-indole-6,7-dione, the postulated immediate precursor of the final blue dye) were identified. The results are interpreted in the context of a crystal structure of a P450 2A6-coumarin complex. The I300V change opens an additional pocket to accommodate the OBzl bulk. The N2297Q change is postulated to generate a hydrogen bond between Gln and the substrate oxygen. Thus, the substrate specificity of P450 2A6 was expanded, and new products were obtained in this study.

Interactive dynamic graphical techniques for the exploration of functional data

Introduction. The use of interactive dynamic graphics has become a common practice for the exploration of multidimensional data sets. The availability of powerful and inexpensive hardware and software for graphical computing makes the use of such techniques feasible for the examination of complex forms of data. This paper describes some simple techniques, which were implemented in the LISP-STAT environment, for the visualization of functional data arising from studies of optical technologies used for the detection of cervical intraepithelial neoplasia or squamous intraepithelial lesions. Materials and methods. The methods demonstrated have been implemented in software coded in LISP-STAT, a free statistical computing package available for most computer systems. The data used in this paper are drawn from a previous study in which fluorescence spectroscopy was measured from cervical sites at 337 nm, 380 nm, and 460 nm excitation in cervical screening patients. The goal of the project is to explore biographical variables to better understand the biology of fluorescence. Results. 199 measurements were taken in 55 women with normal Pap smears. The data are recorded as spectra showing the intensity of emission excitation versus emission in nanometers. Covariate variables available for analysis are current smoker vs. nonsmoker premenopausal vs. postmenopausal, tissue type (columnar, squamous, and transition zone), and age in years. Although the optical measurements show consistent changes between normal and abnormal tissue in individual patients, there is wide variation in the intensity of the measurements between patients, even for normal tissue. Patient age affects the fluorescent spectrum showing increasing intensity with increasing age. Menopausal status affects the fluorescent spectra coincidentally with age. Smoking and race do not appear to affect the spectra in this sample of patients. Conclusions. The use of interactive graphical techniques permits the data analyst to examine multidimensional data in intuitive ways. These explorations allow non-statisticians to explore the data in a perceptive manner that may lead to new approaches in algorithm development for optical technologies.

Interactive visualization applied to multivariate geochemical data: A case study

Geochemical survey data have commonly been analysed combining methods from several disciplines - statistics, geostatistics, geographic information technology, visualization. In initial stages of analysis, tables are often used to describe the data and present statistical measures. Far too often the original data are manipulated in one or another way, for example, using mathematical transformations, or interpolation of points to a surface. It is the author's opinion that raw geochemical data should be used in initial stages of data description, thus preserving the original details. This is not a simple task, as geochemical data are commonly complex, multivariate, and collected on irregular grid. Data contain outliers, element contents vary within thousands of ppm (parts per million), and different chemical elements may be correlated. In the present study a graphical approach has been used to study distribution of 5 heavy metals in glacial till. Using interactive visualization and multiple linked views of the data, the following issues were addressed: multi-element outliers, spatial trends, multi-element correlations and patterns. Interactive graphical techniques proved to be especially suitable for studying outliers and identifying and locating samples that are redundant and may be removed from data without loss of information. Visualization using linked views gave valuable insights about metal correlations and spatial trends. As the development of appropriate tools for analysing multivariate spatial data are still in its early stages, visualization freeware seems to be a good alternative providing powerful, easy to use and intuitive techniques for exploratory data analysis.

A putative three-dimensional arrangement of the human serotonin transporter transmembrane helices: a tool to aid experimental studies

The human serotonin transporter is the molecular target for selective serotonin reuptake inhibitor drugs which are being used for treatment of depression. A three-dimensional model of the membrane spanning parts of the transporter was constructed. The transporter was assumed to consist of 12 transmembrane α-helices. The model was based on published experimental data of cocaine binding to mutant transporters, amino acid sequence analysis, and interactive molecular graphics. The model suggests that a high affinity cocaine binding site is situated in a region of the model where Asp98 acts like an anchor, while a putative low affinity site is situated in another region with Glu508 as the anchoring amino acid. A series of docking experiments with various reuptake inhibitors were conducted, using interactive molecular graphics techniques combined with energy calculations and analysis of the transporter-ligand complexes. Experiments involving molecular mapping of ligand binding areas may benefit from using the current model in experimental design. From the current model, several amino acids were proposed as prime candidates for mutagenesis and subsequent ligand binding studies. Also for evaluation of results from site directed mutagenesis experiments with SERT and similar transporters we assume the model will be helpful.

A comparison of the Maslov integral seismogram and the finite-difference method

The Maslov asymptotic method addresses some of the problems with standard ray theory, such as caustics and shadows. However, it has been applied relatively little, perhaps because its accuracy remains untested. In this study we examine Maslov integral (MI) seismograms by comparing them with finite-difference (FD) seismograms for several cases of interest, such as (1) velocity gradients generating traveltime triplications and shadows, (2) wave-front bending, kinking and folding in a low-velocity waveguide, and (3) wavefield propagation perturbed by a high-velocity slab. The results show that many features of high- and intermediate-frequency waveforms are reliably predicted by Maslov's technique, but also that it is far less reliable and even fails for low frequencies. The terms ‘high’ and ‘low’ are model-dependent, but we mean the range over which it is sensible to discuss signals associated with identifiable wave fronts and local (if complicated) effects that potentially can be unravelled in interpretation. Of the high- and intermediate-frequency wave components, those wave- front anomalies due to wave-front bending, kinking, folding or rapid ray divergence can be accurately given by MI. True diffractions due to secondary wave-front sections are theoretically not included in Maslov theory (as they require true diffracted rays), but in practice they can often be satisfactorily predicted. This occurs roughly within a wavelength of the truncated geometrical wave front, where such diffractions are most important since their amplitudes may still be as large as half that on the geometrical wave front itself. Outside this region MI is inaccurate (although then the diffractions are usually small). Thus waveforms of high and intermediate frequencies are essentially controlled by classical wave-front geometry. Our results also show that the accuracy of MI can be improved by rotating the Maslov integration axis so that the nearest wave-front anomaly is adequately ‘sampled’. This rotation can be performed after ray tracing and it can serve to avoid pseudo-caustics by using it in conjunction with the phase-partitioning approach. The effort needed in phase partitioning has been reduced by using an interactive graphics technique. It is difficult to formulate a general rule prescribing the limitations of MI accuracy because of model dependency. However, our experiences indicate that two space- and two timescales need to be considered. These are the pulse width in space, the length scale over which the instantaneous wave-front curvature changes, and the timescales of pulse width and significant features in the ray traveltime curve. It seems, from our examples, that when these scales are comparable, the Maslov method gives very acceptable results.

Differences among patients in opioid self-administration during bone marrow transplantation

The distinctive features of individual patients, here termed individual differences, are inescapable aspects of day-to-day patient pain management, but classically designed research studies ignore such differences. This paper introduces statistical pattern visualization methodology for the study of complex individual differences in clinical settings. We demonstrate the application of such methods in patients undergoing bone marrow transplantation (BMT) and suffering severe oral mucositis as a consequence of the aggressive BMT preparative regimen. Oral mucositis produces severe pain and patients often require parenteral opioid medication for several weeks. Unfortunately, the opioid can cause side-effects that limit drug use for pain control. Patients differ in severity and duration of oral mucositis, analgesic response to opioids, and side-effects. We identified and classified individual differences in patterns of drug use, pain control and side-effects in 33 BMT patients who received opioid drug via patient-controlled analgesia (PCA) systems for 7 days or more. These systems allowed bolus dosing and also provided a basic level of analgesic protection through continuous drug infusion. Continuous infusion levels increased or decreased in response to patient bolus self-administration. We employed statistical smoothing (moving average) techniques to remove random variation from the individual data sets and created three-way (trivariate) plots of change over time in drug use, pain and an opioid side-effect (impairment of concentration). The patterns apparent in these plots indicated that 24.2% of patients used PCA optimally (increases in drug use associated with reductions in pain and little or no side-effect), an additional 30.3% manifested a potentially optimal pattern limited by side-effect that worsened with dosing, and 36.4% used PCA suboptimally (modest pain control plus side-effects). In addition, for each subject we created a summary measure for the simultaneous change in three variables: the distance of each day's trivariate score from the origin of a three dimensional plot. This summary measure correlated significantly with the changing severity of patients' oral mucositis over time ( r=0.502). This study demonstrates how interactive graphic techniques can provide a basis for examining changes over time among multiple, correlated variables associated with a single individual. It illustrates the application of such techniques and demonstrates that individual subject data sets merit examination in cases where clinical data reflect human performance.

Use of T cell receptor/HLA-DRB1*04 molecular modeling to predict site-specific interactions for the DR shared epitope associated with rheumatoid arthritis.

To use molecular modeling tools to analyze the potential structural basis for the genetic association of rheumatoid arthritis (RA) with the major histocompatibility complex (MHC) "shared epitope," a set of conserved amino acid residues in the third hypervariable region of the DRbeta chain. Homology model building techniques were used to construct molecular models of the arthritis-associated DRB1*0404 molecule and a T cell receptor (TCR) from T cell clone EM025, which is specific for DR4 molecules containing the shared epitope sequence. Interactive graphics techniques were used to orient the TCR on the DR molecule, guided by surface complementarity analysis. The predicted TCR-MHC-peptide complex involved multiple interactions and specificity for the shared epitope. TCR residues CDR1beta D30, CDR2beta N51, and CDR3beta Q97 were positioned to potentially participate in hydrogen bond interactions with the shared epitope DRbeta residues Q70 and R71. These results suggest a structural mechanism in which specific TCR recognition and possibly Vbeta selection are directly influenced by the disease-associated MHC polymorphisms.

VISTAnet deployment and system integration experiences

VISTAnet is a three-year research effort that involves the deployment of prototype broadband switching systems interconnecting specialized supercomputers. The project partners include BellSouth, GTE, MCNC, North Carolina State University (NCSU), and the University of North Carolina at Chapel Hill (UNC-CH). In addition to the deployment and evaluation of experimental network facilities, the project supports research activities in several areas: gigabit communications, metacomputing, advanced visualization techniques, and medical treatment planning techniques, specifically dynamic radiation therapy planning. VISTAnet is organized as a testbed. It is an environment that has been established to experiment with and evaluate techniques associated with gigabit networking. These experiments include methods for moving data into and out of host computers from the application to the network at gigabit rates, demonstrations and evaluations of an application that requires gigabit networking, and interactive three-dimensional graphics techniques. The overall goal of the testbed is to advance the state-of-the-art in gigabit networking and its application. VISTAnet is one of five gigabit test beds coordinated by the Corporation for National Research Initiatives in cooperation with DARPA and NSF.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Two effective schemes of automatic mesh generation for 2D-nonlinear BEM

This paper presents two effective automatic mesh generation schemes for the 2D-nonlinear boundary element method (BEM), using a transfinite method and the Poisson equation. A new modified Laplacian-Poisson method is proposed, which is particularly applicable for a circular region. Transfinite mappings with boundary information represented in continuous form are also found to possess distinct advantages for BEM mesh generation. Interactive computer graphics techniques are used to facilitate data preparation and display. Numerical examples are computed by using the two methods. Comparison of results between the two methods shows them to be effective and useful for the 2D-nonlinear BEM.

Modeling the three-dimensional structure of RNA.

The limited number of RNA structures determined by X-ray crystallography and NMR spectroscopy compels the use of experimental and theoretical methods that are less precise to obtain information on RNA conformation. RNA flexibility, a consequence of rotational freedom about seven intra- and internucleotide bonds, is unfortunately of such magnitude that these alternate techniques fall short of providing sufficient information to build robust tertiary structures. Various RNA modeling methods, described herein, permit the organization of this structural data to the form of three-dimensional structures. Interactive computer graphics techniques, for example, have generated several useful models. Also, conventional computer algorithms involving the minimization of empirical energy functions, previously limited to small molecules, are giving way to methods able to handle much larger molecules. Modified distance geometry and molecular mechanics algorithms, using simplified "pseudoatom" representations, can generate structures consistent with input data. A constraint satisfaction algorithm combined with discrete representations of nucleotide conformations systematically explores poorly defined regions of a molecule yielding all-atom representations, but requires enough structural constraints to avoid a computational explosion.

Jeepers

Jeepers is a software tool for conducting empirical studies of user perception of graphical interface features. It was developed in the context of a research program on dynamic interactive graphical techniques for data visualization and exploration. The tool was effectively applied in researching the problem of discerning point cloud highlighting patterns such as those that would be displayed in interactive data "painting". Other potential research uses for the software are discussed.

Visual Fits in the Teaching of Regression Concepts

Abstract This article describes the pedagogical benefits of a classroom exercise that involves interactive graphical techniques on the personal computer. In the exercise, a microcomputer-based software routine termed LINEFIT is used in a statistics course to enhance student understanding of regression concepts. LINEFIT allows the student to visually fit a simple linear regression model to a screen display of points plotted on an (x—y) coordinate system. The comparison of these visual fits to the fits produced by standard statistical procedures such as ordinary least squares or minimum absolute deviation provides the basis for a discussion of the problem of fitting a straight line to a set of points.

A computer system for the interactive planning and prediction of maxillofacial surgery

A computer system has been developed for the simulation of facial surgery with interactive three-dimensional graphic techniques and data derived from computed tomographic scans and a purpose-built laser scanning system. The simulation includes the surgery on the hard tissues, and modeling of the soft tissue for prediction of the postoperative facial appearance. The facilities available are described and an example of their use is given.

Evolutionary and functional relationships between the basic and acidic β-crystallins

beta-Crystallins are complex oligomers composed of many related subunits. In order to understand their interactions we have built molecular models of several bovine beta-crystallins, based on their sequence similarity to the well-defined gamma-II crystallin structure, using interactive computer graphics techniques. Their common origin with gamma-crystallin is displayed in both the retention of four-fold sequence repeats of critical residues involved with stabilizing a folded beta-hairpin and the conservation of core-filling hydrophobic side-chains. The beta-crystallins have been built as bilobal molecules with each domain composed of two 'Greek key' motifs which associate about an approximate two-fold axis to form beta-sheets. The beta-crystallin sequences have previously been shown to comprise two families, the basic and acidic subunits, which have extensions of sequence. The three-dimensional models show how the two families appear to stabilize the folded beta-hairpin in the N- and C-terminal domains in ways which suggest that they have diverged from a common ancestor in different ways. Acidic beta-crystallins, like gamma-crystallins, have a regular array of charges on their N-terminal domain which has been interrupted in basic beta-crystallins by hydrophobic residues which may be related to the presence of a C-terminal extension. beta-Crystallins are more highly charged than gamma-crystallins although their charge density is higher in certain regions of the N-terminal domain, particularly in beta B1-crystallin. beta-crystallins also differ from gamma-crystallins in the virtual absence of core-filling sulphydryl groups whereas they have numerous sulphur-containing side-chains together with tryptophan and histidine rings protruding from the globular domains, particularly in the acidic subunits. The burial of these residues in subunit contacts is consistent with their spectroscopic and electrostatic properties. Protein subunit aggregation commonly occurs through hydrophobic interaction or beta-sheet extension. Analysis of the subunit surfaces has identified an N-terminal hydrophobic region common to beta B1 and beta B2 whereas a C-terminal hydrophobic loop region is common to beta B1 and beta A1 and may be correlated with their association properties. It is suggested that the polar C-terminal domain of beta B2 contributes towards the solubility of higher aggregates by interactions involving beta-sheet structure.

Synthesis and analysis of flow about airfoils with interactive graphics

This paper describes the development of an interactive computer graphics technique for visualization and analysis of flow about Joukowski airfoils. The method employs conformal mapping techniques for establishing the flow about a lifting-airfoil profile, determining velocity distribution on the profile contour and pressure distribution around the profile, and evaluating profile geometric and aerodynamic characteristics. These have been implemented in a stand-alone computer featuring graphics, an interactive operation and a menu-driven environment with graphical facilities, to be exploited as an aid for simulating flow fields about airfoils. These features with the variety of flows that can be studied point out the method versatility and broader usefulness over other flow visualization techniques.

Robocell: A computer-aided robots modelling and workstation layout system

The use of computer simulation to assist in robot selection and programming and to evaluate robotic workcell layout provides the user with an effective tool for planning new robot installations or modifying existing ones. It enables the system planner to examine robot reach and geometry features, calculate cycle time and plan, develop and debug task programs prior to installation. This paper discusses the robot modelling and interactive graphics techniques used in the robot/cell simulation package ROBOCELL. Three industrial robots are used in examples to illustrate the kinematic and geometric modelling, cycle time computation and program features of ROBOCELL. A detailed model of a cylindrical robot is outlined. The application of the simulator for designing a flexible final motor assembly workcell and a packaging/palletising workstation is described.

Three-dimensional PTx phase diagrams through interactive computer graphics

Interactive computer graphic techniques have been developed for the display of binary mixture phase diagrams. The diagrams are defined in temperature-pressure-composition space, and are portrayed as wireframe objects with depth perception in order to provide a three-dimensional effect. The displays used were vectro refresh workstations whose transformation hardware allows real-time rotation, rescaling, and translation of the diagrams, while software allows the extraction of constant property Px, Tx, PT and x - y plots. The equilibrium surfaces and the critical lines were calculated using the Redlich-Kwong equation of state and its Soave modification.

Inagal - Interactive Allocation of Hydroelectric Units

The paper describes a conceptually new way of solving the traditional unit commitment problem in hydro power dominated systems. The main intention behind the system is to create a complete operations schedule covering the next 36 hours with unit settings and times for starts and stops indicated. The operations are limited by planned bounds for exchange with neighbouring network or power pool in addition to technical/juridical constraints and bounds induced by higher planning levels. Strong operator involvement combined with interactive graphic techniques, substitutes traditional LP or DP optimizing algorithms.

Interactive Graphics for the Analysis of Tires

Abstract The finite element method, which is a numerical discretization technique for obtaining approximate solutions to complex physical problems, is accepted in many industries as the primary tool for structural analysis. Computer graphics is an essential ingredient of the finite element analysis process. The use of interactive graphics techniques for analysis of tires is discussed in this presentation. The features and capabilities of the program used for pre- and post-processing for finite element analysis at GenCorp are included.

Computer graphics in CAM applications

Correct structuring and representation of production management-information will make the decision process more efficient in a factory. Graphic representation of survey data and comparisons are often very useful, although one loses some accuracy, compared with tables. The use of colours in this context makes the charts easier to understand, and more information may be shown without making the chart unclear. These facts have made the interactive graphic techniques useful for planning and resource allocation purposes. The result has been installed in industry. The study also presents a new method for automatic quality supervision. A detailed analysis of workpieces and products from mechanical industry is carried out. The method is a substitute for visual inspection as well as manual measurements: Missing holes, broken corners, and undesired material are detected. Important details are measured. There are individual tolerances on all measures. Parts that do not meet the requirements are rejected. The supervision program is easily changed, and the method is therefore suitable for small series production. The picture from a special TV camera is the basis for the quality supervision, which is of the noncontact type.