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PubMed2001

Theoretical, thermodynamic, spectroscopic, and structural studies of the consequences of one-electron oxidation on the Fe-X bonds in 17- and 18-electron Cp*Fe(dppe)X complexes (X = F, Cl, Br, I, H, CH3).

The compounds Cp*Fe(dppe)X ([Fe]X) and the corresponding cation radicals [Fe*]X*+ are available for the series X = F, Cl, Br, I, H, CH3. This has allowed for a detailed investigation of the dependence of the nature of Fe-X bonding on the identity of X and the oxidation state (charge) of the complex. Cyclic voltammetry demonstrates that the electrode potentials for the [Fe]X0/+ couples decrease in the order I > Br > Cl > H > F > CH3. An "inverse halide order" is seen, in which the most electronegative X leads to the most easily oxidized complex. This suggests that F is the best donor among the halides. The halide trend is also reflected in NMR spectroscopic data. Mössbauer spectroscopy data also suggest that the F ligand is a strong donor (relative to H and CH3) in [Fe*]X*+. DFT calculations on CpFe(dpe)X ([Fe]X) model complexes nicely reproduce the trend in the electrode potentials for the [Fe*]X0/+ couples. Analysis of the theoretical data within the halogen series indicates that the energy of the [Fe]X HOMO does not correlate with the extent of its Fe(d(pi))-X(p(pi)) antibonding character, which varies in the order I > Br > Cl > F, but rather depends on the destabilizing electrostatic effect caused by X. This effect varies in the order F > Cl > Br > I. A thermochemical cycle that incorporates the [Fe*]X0/+ and [Fe*]0/+ electrode potentials was used to investigate the effect of the oxidation state of the complex on the homolytic bond dissociation energy (BDEhom), defined for the processes Fe-X --> Fe* + X* and Fe-X*+ --> Fe*+ + X*. For all X, it was found that a one-electron oxidation leads to a weakening of the Fe-X bond. This trend was reproduced by the DFT calculations. On the other hand, IR nu(Fe-X) spectroscopy data showed an increase in the stretching frequencies for X = H and Cl upon oxidation. X-ray crystallographic data showed a shortening of the Fe-Cl bond upon oxidation. The trends in IR and Fe-Cl bond distances were reproduced in the DFT calculations. The combined data therefore suggest that oxidation leads to weaker, but shorter, Fe-X bonds. A second thermochemical cycle was applied to investigate the effect of the one-electron oxidation on the heterolytic bond dissociation energies (BDEhet), defined for the processes Fe-X --> Fe+ + X- and Fe-X*+ --> Fe2+ + X-. In this case, the oxidation led to bond strengthening in all cases. The computed BDE values have been analyzed within Ziegler's transition state methodology and decomposed into two components, one electrostatic and one covalent, describing the interaction between the unrelaxed fragments. In all the computed BDEhom and BDEhet values of the [Fe]X models the electrostatic component is important. This helps to understand their respective variations upon oxidation.

Journal Article↗
PubMed2005

Computer-aided drug design strategies used in the discovery of fructose 1, 6-bisphosphatase inhibitors.

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-aided drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are restricted to analysis of structurally-related inhibitors. Accordingly, there is a need for methods that enable rapid assessment of a large number of structurally-unrelated molecules in a suitably accurate manner. In this review, the FEP method is compared with molecular mechanics (MM) methods to assess the advantages of each in the estimation of relative binding affinities of inhibitors to an enzyme. Qualitative predictions of relative binding free energies of fructose 1, 6-bisphosphatase inhibitors using MM methods are discussed and compared with the corresponding FEP results. The results indicate that the MM based methods and the FEP method are useful in the qualitative and quantitative assessment of relative binding affinities of enzyme inhibitors, respectively, prior to synthesis.

Computer-Aided Design↗
PubMed1998

Structure-based drug design approaches for predicting binding affinities of HIV1 protease inhibitors.

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-assisted drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are restricted to analysis of structurally-related inhibitors. Accordingly, there is a need for methods that enable rapid assessment of large number of structurally-unrelated molecules in a suitably accurate manner. In this review, the FEP method is compared with regression-based methods that employ multivariate models to assess the advantages of each in the estimation of relative binding affinities of inhibitors to an enzyme. Semiquantitative predictions of relative binding free energies of human immunodeficiency virus 1 (HIV1) protease inhibitors are also presented and compared with the corresponding FEP results. The results indicate that the regression-based methods and the FEP method are useful in the semi-quantitative and quantitative assessment of relative binding affinities of enzyme inhibitors, respectively, prior to synthesis.

Computer Simulation↗
PubMed2002

Using a decade of data on medical student computer literacy for strategic planning.

PURPOSE: From 1991 through 2000, incoming medical students (M-Is) at the School of Medicine at Virginia Commonwealth University have been surveyed with a written questionnaire on their computer literacy. The survey's purpose is to learn the students' levels of knowledge, skill, and experience with computer technology to guide instructional services and facilities. METHODOLOGY: The questionnaire was administered during M-I orientation or mailed to students' homes after matriculation. It evolved from sixteen questions in 1991 to twenty-three questions in 2000, with fifteen questions common to all. RESULTS: The average survey response rate was 81% from an average of 177 students. Six major changes were introduced based on information collected from the surveys and advances in technology: production of CD-ROMs distributed to students containing required computer-based instructional programs, delivery of evaluation instruments to students via the Internet, modification of the lab to a mostly PC-based environment, development of an electronic curriculum Website, development of computerized examinations for medical students to prepare them for the computerized national board examinations, and initiation of a personal digital assistant (PDA) project for students to evaluate PDAs' usefulness in clinical settings. CONCLUSION: The computer literacy survey provides a snapshot of students' past and present use of technology and guidance for the development of services and facilities.

Computer Literacy↗
PubMed1993

[Neoplasms of the maxillary sinus. The clinico-radiological considerations of dental interest].

Early diagnosis of the maxillary antrum carcinoma is of considerable difficulty. There are, however, signs and a refined symptomatology that the stomatologist can recognize when the tumour is still in its intrinsic form. Although the maxillary antrum tumors are rare, they present an extremely difficult diagnosis. The patient comes to us when the tumor has already invaded all the contiguous structures pertaining to the oral cavity. For early diagnosis we can avail ourselves, besides a conventional radiographic test, also of more specific analysis, as the computed tomography and radio therapy. These last image methodologies are also employed to establish a radiation treatment plan. Actually the best therapeutic treatment seems to be the multidisciplinary one, combining therapy with surgery.

Adult↗
PubMed2001

Computational flow modeling of the left ventricle based on in vivo MRI data: initial experience.

A combined computational fluid dynamics (CFD) and magnetic resonance imaging (MRI) methodology has been developed to simulate blood flow in heart chambers, with specific application in the present study to the human left ventricle. The proposed framework employs MRI scans of a human heart to obtain geometric data, which are then used for the CFD simulations. These latter are accomplished by geometrical modeling of the ventricle using time-resolved anatomical slices of the ventricular geometry and imposition of inflow/outflow conditions at orifices notionally representing the mitral and aortic valves. The predicted flow structure evolution and physiologically relevant flow characteristics were examined and compared to existing information. The CFD model convincingly captures the three-dimensional contraction and expansion phases of endocardial motion in the left ventricle, allowing simulation of dominant flow features, such as the vortices and swirling structures. These results were qualitatively consistent with previous physiological and clinical experiments on in vivo ventricular chambers, but the accuracy of the simulated velocities was limited largely by the anatomical shortcomings in the valve region. The study also indicated areas in which the methodology requires improvement and extension.

Adult↗
PubMed1999

Relevance of accurate Monte Carlo modeling in nuclear medical imaging.

Monte Carlo techniques have become popular in different areas of medical physics with advantage of powerful computing systems. In particular, they have been extensively applied to simulate processes involving random behavior and to quantify physical parameters that are difficult or even impossible to calculate by experimental measurements. Recent nuclear medical imaging innovations such as single-photon emission computed tomography (SPECT), positron emission tomography (PET), and multiple emission tomography (MET) are ideal for Monte Carlo modeling techniques because of the stochastic nature of radiation emission, transport and detection processes. Factors which have contributed to the wider use include improved models of radiation transport processes, the practicality of application with the development of acceleration schemes and the improved speed of computers. In this paper we present a derivation and methodological basis for this approach and critically review their areas of application in nuclear imaging. An overview of existing simulation programs is provided and illustrated with examples of some useful features of such sophisticated tools in connection with common computing facilities and more powerful multiple-processor parallel processing systems. Current and future trends in the field are also discussed.

Algorithms↗
PubMed2004

Traditional teaching supported by computer-assisted learning for macroscopic anatomy.

Over the years we have observed that there is a very low passing rate for the Anatomy and Neuroanatomy courses in our department, and for that reason we decided to implement the use of student-learning resources. The objective of this study was to compare the results of traditional methodology with those obtained with the support of computer-assisted learning (CAL). We performed a retrospective and joint study for Anatomy and Neuroanatomy groups during the period of September 2001 to February 2003, to establish a comparison between traditional learning and traditional learning supported by CAL. In the Anatomy group, students who used the traditional method (n1 = 365) received an average final grade of 58 (SD = 14.94), while the average final grade for students who used the traditional method supported by CAL (n2 = 283) was 68 (SD = 14.56). In the Neuroanatomy group, the students who used the traditional method (n3 = 217) had an average final grade of 61 (SD = 14.51), while the students who used the traditional method supported by CAL (n4 = 134) received an average final grade of 68 (SD = 13.52). A z-test was conducted to determine the difference in averages between the two groups (alpha = 0.05), and the results showed that the averages were significantly different (P <.001). The modified traditional method with CAL support was shown to be the best option in comparison with the traditional method.

Adult↗
PubMed2004

A methodology for extracting objective color from images.

We present a methodology for correcting color images taken in practical indoor environments, such as laboratories, factories, and studios, that explicitly models illuminant location, surface reflectance and geometry, and camera responsivity. We explicitly model surfaces by taking our color images with corresponding registered three-dimensional (3-D) range images, which provide surface orientation and location information for every point in the scene. We automatically detect regions where color correction should not be applied, such as specularities, coarse texture regions, and jump edges. This correction results in objective color measures of the imaged surfaces. This kind of integrated, comprehensive system of color correction has not existed until now. i.e., it is the first of its kind in computer vision. We demonstrate results of applying this methodology to real images for applications in photorealistic rerendering, skin lesion detection, burn scar color measurement, and general color image enhancement. We also have tested the method under different lighting configurations and with three different range scanners.

Algorithms↗
PubMed2006

Computational methods in developing quantitative structure-activity relationships (QSAR): a review.

Virtual filtering and screening of combinatorial libraries have recently gained attention as methods complementing the high-throughput screening and combinatorial chemistry. These chemoinformatic techniques rely heavily on quantitative structure-activity relationship (QSAR) analysis, a field with established methodology and successful history. In this review, we discuss the computational methods for building QSAR models. We start with outlining their usefulness in high-throughput screening and identifying the general scheme of a QSAR model. Following, we focus on the methodologies in constructing three main components of QSAR model, namely the methods for describing the molecular structure of compounds, for selection of informative descriptors and for activity prediction. We present both the well-established methods as well as techniques recently introduced into the QSAR domain.

Models, Molecular↗
PubMed2006

An empirical analysis of eating disorders and anxiety disorders publications (1980-2000)--part I: Research methods.

OBJECTIVE: The current study compared the eating disorder and anxiety disorder literature in terms of research design and methodologic features in 1980, 1990, and 2000. METHOD: Computer literature searches were conducted using PubMed and PsychInfo databases to identify relevant eating disorder and anxiety disorder articles published at each of the three time points. A total of 456 articles were randomly selected, including 228 articles from the eating disorder literature and the anxiety disorder literature. Within each specific literature, one third (76) of the articles were selected from each of the three time points (1980, 1990, 2000). Two raters, from a team of eight trained raters, were randomly assigned to independently rate each article in terms of 75 separate methodologic features. Disagreements in ratings were resolved via consensus. Ratings were tabulated separately for eating disorders and anxiety disorders across the three time points. RESULTS: Although there were some differences between anxiety disorders and eating disorders, most of the variables did not substantially differ between these two fields. There was a consistent trend for both fields to show increases in more rigorous methodologies over time. However, both the eating disorder literature and the anxiety disorder literature were characterized by a pervasive absence of many recommended methodologic procedures across the past two decades. CONCLUSION: Although the eating disorder literature and the anxiety disorder literature are increasingly characterized by improved reporting of rigorous methodologic procedures, there is still a pervasive absence of such procedures in both literatures, which limits the strength of inference in these studies.

Anxiety Disorders↗
PubMed2002

Leveraging XML-based electronic medical records to extract experiential clinical knowledge. An automated approach to generate cases for medical case-based reasoning systems.

Case-based reasoning (CBR)-driven medical diagnostic systems demand a critical mass of up-to-date diagnostic-quality cases that depict the problem-solving methodology of medical experts. In practical terms, procurement of CBR-compliant cases is quite challenging, as this requires medical experts to map their experiential knowledge to an unfamiliar computational formalism. In this paper, we propose a novel medical knowledge acquisition approach that leverages routinely generated electronic medical records (EMRs) as an alternate source for CBR-compliant cases. We present a methodology to autonomously transform XML-based EMR to specialized CBR-compliant cases for CBR-driven medical diagnostic systems. Our multi-stage methodology features: (a) collection of heterogeneous EMR from Internet-accessible EMR repositories via intelligent agents, (b) automated transformation of both the structure and content of generic EMR to specialized CBR-compliant cases, and (c) inductive estimation of the weight of each case-defining attribute. The computational implementation of our methodology is presented as case acquisition and transcription info-structure (CATI).

Artificial Intelligence↗
PubMedDate not supplied

New hybrid count- and geometry-based method for quantification of left ventricular volumes and ejection fraction from ECG-gated SPECT: methodology and validation.

BACKGROUND: We have previously developed a new method for quantitative assessment of left ventricular (LV) volumes and ejection fraction (EF) from electrocardiography-gated single photon emission computed tomography (SPECT). The aims of this study were to present the methodology, to validate the gated SPECT cardiac quantification (GSCQ) method in phantoms and patients, and to determine normal values of LVEF. METHODS AND RESULTS: A simple thresholding technique was used to generate binary images from nongated SPECT images. The K-means cluster classification algorithm was used to separate the LV region from non-LV regions on the binary images. A count- and geometry-based algorithm was applied to define endocardial and epicardial boundaries for calculation of LV volumes and LVEF. Overall correlation between GSCQ-quantified volumes and actual phantom volumes was good ( r = 0.97 and standard error of estimation (SEE) = 9.99 mL for normal phantoms, r = 0.99 and SEE = 6.97 mL for phantoms with defects). In patient studies, LVEF derived by GSCQ from SPECT and from equilibrium radionuclide angiography also showed good correlation ( r = 0.90 and SEE = 6.2%). The lower limit of normal LVEF from 8-frame gated SPECT by use of GSCQ was 45%. Quantification of LVEF by the GSCQ method was highly producible and was not significantly affected by the presence of myocardial perfusion defects or intense gastrointestinal activity. CONCLUSIONS: The GSCQ method provides reliable and consistent assessments of LV volumes and EF. This methodology is less affected by intense gastrointestinal activity than other methods.

Adult↗
PubMed1997

Isoelectric focusing in immobilized pH gradients: recent analytical and preparative developments.

Isoelectric focusing in immobilized pH gradients (IPG), covering both analytical and preparative aspects, is here reviewed. An extensive introduction covers the development of the technique from its inception in 1982 to present day methodology, with particular emphasis on the development of computer programs able to calculate and optimize linear and nonlinear pH gradients, spanning as much as 9 pH units, from a mixture of as many as 10 different buffering ions and titrants. The unique resolving power of IPGs is illustrated with the resolution of fetal globin chains differing by an Ala/Gly substitution in residue 75, this bringing about a minute difference in pI value of only 0.001 pH units. IPG runs, performed under denaturing conditions, allow an excellent correlation between experimental and theoretical protein pIs, to the extent that outliers were found to be polypeptide chains which had undergone post-synthetic modifications. The IPG methodology allows easy interfacing with mass spectrometry, due to the fact that proteins eluted from an IPG gel are isoionic as well as isoelectric, and thus are not contaminated by any buffer ion. The review ends with an excursus on preparative aspects of IPGs: a novel apparatus, based on the principle of isoelectric, buffering membranes, allows pilot-scale purification of r-DNA proteins to extreme purity, with recovery in a liquid vein. Isoelectric membranes have a selectivity based on a continuous titration process, and thus act as isoelectric traps for individual protein species. This same preparative apparatus can be used as a novel immobilized enzyme reactor, with superior performance compared to conventional types of reactors.

Amino Acid Sequence↗
PubMed1992

Computer-aided decision support in hepatology.

The aim of this study was to describe and to evaluate the publications of the last 30 years devoted to computer-aided decision support in clinical hepatology. The search used Medlars and references of articles. Computer-aided decision support (CADS) was classified in two categories: statistical systems and knowledge-based systems. Two specific questionnaires were used for methodologic evaluation, one for statistical systems and one for knowledge-based systems. They were filled out independently by two observers. A total of 31 papers were selected among 55 identified between 1960 and 1991. The maximum possible for the two scores was 24. The methodologic quality ranged from 4 to 22 (median, 12) for statistical systems and from 8 to 12 (median, 9) for knowledge-based systems. The poor level of methodology could explain in part the lack of utilization of computer-aided decision support in the daily clinical practice of hepatologists.

Bayes Theorem↗
PubMedDate not supplied

Spatial normalization of 3D brain images using deformable models.

PURPOSE: The spatial normalization and registration of tomographic images from different subjects is a major problem in several medical imaging areas, including functional image analysis, morphometrics, and computer-aided neurosurgery. The focus of this article is the development of a computerized methodology for the spatial normalization of 3D images. METHOD: We propose a technique that is based on geometric deformable models. In particular, we first describe a deformable surface algorithm that finds a mathematical representation of the outer cortical surface. Based on this representation, a procedure for obtaining a map between corresponding regions of the outer cortex in two different images is established. This map is subsequently used to derive a 3D elastic warping transformation, which brings two images into register. RESULTS: The performance of our algorithm is demonstrated on several datasets. In particular, we first test our deformable surface algorithm on MR images. We then register MR images to atlas images. In our third experiment, we apply a procedure for matching distinct cortical features identified through the curvature map of the outer cortex. Finally, we apply our technique to images from elderly individuals with substantial ventricular enlargement, and we show a good registration in the ventricular area and the surrounding brain structures. CONCLUSION: We present a highly automated methodology for spatial normalization of images, using deformable models. Applications of our methodology include stereotactic normalization of functional and structural images, morphological analysis of the brain, and computer-aided neurosurgery.

Algorithms↗
PubMed1997

Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT.

MOTIVATION: When routinely analysing protein sequences, detailed analysis of database search results made with BLAST and FASTA becomes exceedingly time consuming and tedious work, as the resultant file may contain a list of hundreds of potential homologies. The interpretation of these results is usually carried out with a text editor which is not a convenient tool for this analysis. In addition, the format of data within BLAST and FASTA output files makes them difficult to read. RESULTS: To facilitate and accelerate this analysis, we present for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition. Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.

Amino Acid Sequence↗
PubMed1995

A computer-controlled conformal radiotherapy system. III: Graphical simulation and monitoring of treatment delivery.

PURPOSE: Safe and efficient delivery of radiotherapy using computer-controlled machines requires new procedures to design and verify the actual delivery of these treatments. Graphical simulation and monitoring techniques for treatment delivery have been developed for this purpose. METHODS AND MATERIALS: A graphics-based simulator of the treatment machine and a set of procedures for creating and manipulating treatment delivery scripts are used to simulate machine motions, detect collisions, and monitor machine positions during treatment. The treatment delivery simulator is composed of four components: a three-dimensional dynamic model of the treatment machine; a motion simulation and collision detection algorithm, user-interface widgets that mimic the treatment machine's control and readout devices; and an icon-based interface for creating and manipulating treatment delivery scripts. These components are used in a stand-alone fashion for interactive treatment delivery planning and integrated with a machine control system for treatment implementation and monitoring. RESULTS: A graphics-based treatment delivery simulator and a set of procedures for planning and monitoring computer-controlled treatment delivery have been developed and implemented as part of a comprehensive computer-controlled conformal radiotherapy system. To date, these techniques have been used to design and help monitor computer-controlled treatments on a radiotherapy machine for more than 200 patients. Examples using these techniques for treatment delivery planning and on-line monitoring of machine motions during therapy are described. CONCLUSION: A system that provides interactive graphics-based tools for defining the sequence of machine motions, simulating treatment delivery including collision detection, and presenting the therapists with continual visual feedback from the treatment machine has been successfully implemented for routine clinical use as part of an overall system for computer-controlled conformal radiotherapy treatment, and is considered a necessary part of the routine treatment methodology.

Computer Graphics↗