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PubMedDate not supplied

Integration of laser surface digitizing with CAD/CAM techniques for developing facial prostheses. Part 1: Design and fabrication of prosthesis replicas.

PURPOSE: This article presents a novel manufacturing approach that integrates laser surface digitizing/scanning and computer-aided design (CAD) and manufacturing (CAM) to achieve automated fabrication of spatially and anatomically accurate extraoral facial prostheses. MATERIALS AND METHODS: Topologic data of the patient's face, including the site of deformity and the anatomy of a healthy "donor" organ, were acquired using laser surface digitizing. Two different CAD data manipulation techniques were developed to alleviate problems encountered in laser-digitized data sets. To reduce patient involvement, fitting of the prosthesis was conducted using a computer model of the patient's face. Once finalized, rapid prototyping techniques were employed to fabricate a master pattern to cast the final prosthesis. RESULTS: Three case studies involving different facial prostheses were conducted to evaluate the integrated manufacturing system. The results demonstrated the many advantages of the system for facial prosthesis production. CONCLUSION: With the new manufacturing approach, reduced patient discomfort, minimal dependence on the artistic skills of the prosthetist, and short turnaround times for prosthesis production can be expected.

Computer Simulation↗
PubMed2006

Recapitulation and design of protein binding peptide structures and sequences.

An important objective of computational protein design is the generation of high affinity peptide inhibitors of protein-peptide interactions, both as a precursor to the development of therapeutics aimed at disrupting disease causing complexes, and as a tool to aid investigators in understanding the role of specific complexes in the cell. We have developed a computational approach to increase the affinity of a protein-peptide complex by designing N or C-terminal extensions which interact with the protein outside the canonical peptide binding pocket. In a first in silico test, we show that by simultaneously optimizing the sequence and structure of three to nine residue peptide extensions starting from short (1-6 residue) peptide stubs in the binding pocket of a peptide binding protein, the approach can recover both the conformations and the sequences of known binding peptides. Comparison with phage display and other experimental data suggests that the peptide extension approach recapitulates naturally occurring peptide binding specificity better than fixed backbone design, and that it should be useful for predicting peptide binding specificities from crystal structures. We then experimentally test the approach by designing extensions for p53 and dystroglycan-based peptides predicted to bind with increased affinity to the Mdm2 oncoprotein and to dystrophin, respectively. The measured increases in affinity are modest, revealing some limitations of the method. Based on these in silico and experimental results, we discuss future applications of the approach to the prediction and design of protein-peptide interactions.

Amino Acid Sequence↗
PubMed2003

Conformational analysis by intersection: CONAN.

As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average <0.5 seconds/stereoisomer) a complete description of the low energy conformational space of a small molecule. The molecule is first decomposed into nonoverlapping nodes N (usually rings) and overlapping paths P with conformations (N and P) generated in an offline process. In a second step the node and path data are combined to form distinct conformers of the molecule. Finally, heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space.

Journal Article↗
PubMed2004

Efficiency optimization for systems and components in microwave power engineering.

The paper is concerned with one aspect of optimization of microwave thermal processing, namely, with optimization of energy coupling interpreted as a numerical characteristic of system efficiency. Since in computer-aided design coupling can be evaluated through the computed reflections, an optimization scheme is presented that is particularly suitable for minimizing the reflection coefficient in typical systems and elements of microwave power engineering. Based on response surface methodology and the sequential quadratic programming for constrained optimization, the procedure is linked with the full-wave 3-D FDTD electromagnetic simulator QuickWave-3D. Credibility and effectiveness of the method is illustrated by four examples: dimensional optimization is performed for a dry waveguide load, a waveguide T-junction with a partial-height post, a water cylinder in a cavity, and a slotted waveguide-backed radiating element.

Journal Article↗
PubMed2000

EDIBLE: experimental design and information calculations in phylogenetics.

UNLABELLED: Although evolutionary inference from molecular sequences is a statistical problem, little attention has been paid to questions of experimental design. A computer program, EDIBLE, has been developed to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics. AVAILABILITY: Source code (ANSI C), executables and documentation for EDIBLE are available from http://ng-dec1.gen.cam. ac.uk/info/index.htmland 'downstream' Web pages. CONTACT: N.Goldman@gen.cam.ac.uk

Likelihood Functions↗
PubMed1989

Mathematically directed single-cut osteotomy for correction of tibial malunion.

In 1986 and 1987, four patients with tibial malunion involving both angular and torsional misalignment underwent surgical correction by a single-cut technique based on a mathematical model of long bone deformity. The technique involved a single surgical cut, followed by rotation of the two fragments along the osteotomy plane. The orientation of the osteotomy is based on a computer-assisted design. The deformity is measured on radiographs, computed tomography, and clinical exam and is then plotted on graphs to find the osteotomy orientation. The deformity involved varus and extension in four cases, internal rotation in 2, and external rotation in two. The deformities ranged from 9 to 26 degrees. The cutting angle of the osteotomy ranged from 50 to 66 degrees as measured from the transverse plane. Actual lengthening of 1 cm and functional lengthening over 1.5 cm was obtained without the use of bone graft. As no wedge of bone was removed, all corrected bones were easily suited to rigid internal fixation across the cut surface. In all cases, the desired correction was obtained within measurable error, and union was obtained with minimal immobilization. There were no soft tissue or joint contractures, and no neurovascular complications. In one patient, who had had four prior surgical procedures on the involved limb, an infection developed 6 weeks postoperatively that required debridement and delayed primary closure. As the technique involves only one cut, no wedge of bone is removed, no shortening occurs, and the osteotomy is highly suitable for rigid internal fixation. The described technique is the first to integrate in a precise way the correction of torsion with the correction of angular deformity.(ABSTRACT TRUNCATED AT 250 WORDS)

Biomechanical Phenomena↗
PubMed2002

Informatics training in pathology residency programs.

Information management is crucial in pathology, and previous reports have stressed the needfor improved informatics training in pathology residency programs. We surveyed 150 US programs to assess informatics training with respect to types of training, proficiency expectations, and computing infrastructure. Seventy-two programs (48.0%) responded. Of the respondents, 67 (93%) reported offering informatics training; of these, 52 (78%) required it. Most programs integrated informatics into another rotation, usually management. In 37 programs (55%), the amount of informatics training has increased during the last 3 to 5 years. The most common instructional methods were hands-on training and self-study; 61 programs (91%) used multiple methods. In all but 2 programs, computers were designated for residents; 9 programs offered individual computers to residents. All programs provided productivity software. These data suggest progress in informatics training but that considerable room for improvement exists. Our data also document for the first time detailed computing resources available to residents.

Internet↗
PubMed1989

Computers in a human perspective: an alternative way of teaching informatics to health professionals.

An alternative way of teaching informatics, especially health informatics, to health professionals of different categories has been developed and practiced. The essentials of human competence and skill in handling and processing information are presented parallel with the essentials of computer-assisted methodologies and technologies of formal language-based informatics. Requirements on how eventually useful computer-based tools will have to be designed in order to be well adapted to genuine human skill and competence in handling tools in various work contexts are established. On the basis of such a balanced knowledge methods for work analysis are introduced. These include how the existing problems at a workplace can be identified and analyzed in relation to the goals to be achieved. Special emphasis is given to new ways of information analysis, i.e. methods which even allow the comprehension and documentation of those parts of the actually practiced 'human' information handling and processing which are normally overlooked, as e.g. non-verbal communication processes and so-called 'tacit knowledge' based information handling and processing activities. Different ways of problem solving are discussed involving in an integrated human perspective--alternative staffing, enhancement of the competence of the staff, optimal planning of premises as well as organizational and technical means. The main result of this alternative way of education has been a considerably improved user competence which in turn has led to very different designs of computer assistance and man-computer interfaces. It is the purpose of this paper to give a brief outline of the teaching material and a short presentation of the above mentioned results.(ABSTRACT TRUNCATED AT 250 WORDS)

Attitude to Computers↗
PubMed2001

Combinatorial and computational challenges for biocatalyst design.

Nature provides a fantastic array of catalysts extremely well suited to supporting life, but usually not so well suited for technology. Whether biocatalysis will have a significant technological impact depends on our finding robust routes for tailoring nature's catalysts or redesigning them anew. Laboratory evolution methods are now used widely to fine-tune the selectivity and activity of enzymes. The current rapid development of these combinatorial methods promises solutions to more complex problems, including the creation of new biosynthetic pathways. Computational methods are also developing quickly. The marriage of these approaches will allow us to generate the efficient, effective catalysts needed by the pharmaceutical, food and chemicals industries and should open up new opportunities for producing energy and chemicals from renewable resources.

Biotechnology↗
PubMedDate not supplied

Use of CAD/CAM system to fabricate dental prostheses. Part 1: CAD for a clinical crown restoration.

The development of a computer-aided design system for a clinical crown restoration is reported. Initially, the shape of the standard crown was deformed and adapted on the die depending on the shape of the margin. Then, the measured occlusal record data were taken in the computer graphics, and the adapted crown was adjusted with these data to obtain the centric occlusion. The occlusal data were replaced with data obtained using a functionally generated path record and the occlusal interferences eliminated. The ends of the adapted crown were connected with the margin. Thus, the entire crown was efficiently designed using the computer program developed.

Computer-Aided Design↗
PubMed2004

NMR quantum computing: applying theoretical methods to designing enhanced systems.

Density functional theory results for chemical shifts and spin-spin coupling constants are presented for compounds currently used in NMR quantum computing experiments. Specific design criteria were examined and numerical guidelines were assessed. Using a field strength of 7.0 T, protons require a coupling constant of 4 Hz with a chemical shift separation of 0.3 ppm, whereas carbon needs a coupling constant of 25 Hz for a chemical shift difference of 10 ppm, based on the minimal coupling approximation. Using these guidelines, it was determined that 2,3-dibromothiophene is limited to only two qubits; the three qubit system bromotrifluoroethene could be expanded to five qubits and the three qubit system 2,3-dibromopropanoic acid could also be used as a six qubit system. An examination of substituent effects showed that judiciously choosing specific groups could increase the number of available qubits by removing rotational degeneracies in addition to introducing specific conformational preferences that could increase (or decrease) the magnitude of the couplings. The introduction of one site of unsaturation can lead to a marked improvement in spectroscopic properties, even increasing the number of active nuclei.

Journal Article↗
PubMed1987

Computer-aided dosage form design. I. Methods for defining a long-acting first-order delivery system of maximum formulating flexibility.

The method provides an a priori assessment of the maximum allowable flexibility in the rate of release from a prolonged-release formulation. The clinical pharmacokinetic parameters describing the drug candidate are employed to calculate the ranges of rate constants and doses required for the formulation to provide a selected therapeutic duration. For a given patient, there may be an infinite number of combinations of release rate constants and dose sizes which will maintain steady-state plasma drug concentrations within a desired range when the formulation is administered at the selected dosing interval. Computer simulations of steady-state plasma concentrations are employed to establish the ranges for all of the acceptable rate constants and doses for each member of a group. The entire group is then examined to define the range of release rate constants and doses which would provide a useful formulation for every member in the group. Literature values for theophylline clinical pharmacokinetics in children and adults have been employed to illustrate the application of this method. The method is unique in that it provides an entire range of release rates on which to gauge the feasibility for success.

Administration, Oral↗
PubMed2003

Design of focused and restrained subsets from extremely large virtual libraries.

With the current and ever-growing offering of reagents along with the vast palette of organic reactions, virtual libraries accessible to combinatorial chemists can reach sizes of billions of compounds or more. Extracting practical size subsets for experimentation has remained an essential step in the design of combinatorial libraries. A typical approach to computational library design involves enumeration of structures and properties for the entire virtual library, which may be unpractical for such large libraries. This study describes a new approach termed as on the fly optimization (OTFO) where descriptors are computed as needed within the subset optimization cycle and without intermediate enumeration of structures. Results reported herein highlight the advantages of coupling an ultra-fast descriptor calculation engine to subset optimization capabilities. We also show that enumeration of properties for the entire virtual library may not only be unpractical but also wasteful. Successful design of focused and restrained subsets can be achieved while sampling only a small fraction of the virtual library. We also investigate the stability of the method and compare results obtained from simulated annealing (SA) and genetic algorithms (GA).

Algorithms↗
PubMed2004

Synthesis of ribozyme against vascular endothelial growth factor165 and its biological activity in vitro.

AIM: To investigate the designation, synthesis and biological activity of against vascular endothelial growth factor165 (VEGF165) ribozyme. METHODS: The ribozyme against VEGF165 was designed with computer. The transcriptional vector was constructed which included the anti-VEGF165 ribozyme and 5', 3' self-splicing ribozymes. The hammerhead ribozyme and substrate VEGF165 mRNA were synthesized through transcription in vitro. The cleavage activity of the ribozyme on target RNA was observed in a cell-free system. RESULTS: The anti-VEGF165 ribozyme was released properly from the transcription of pGEMRz212 cleaved by 5' and 3' self-splicing ribozymes which retained its catalytic activity, and the cleavage efficiency of ribozyme reached 90.7%. CONCLUSION: The anti-VEGF165 ribozyme designed with computer can cleave VEGF165 mRNA effectively.

Computer Simulation↗
PubMed2004

Computer-aided tissue engineering: overview, scope and challenges.

Advances in computer-aided technology and its application with biology, engineering and information science to tissue engineering have evolved a new field of computer-aided tissue engineering (CATE). This emerging field encompasses computer-aided design (CAD), image processing, manufacturing and solid free-form fabrication (SFF) for modelling, designing, simulation and manufacturing of biological tissue and organ substitutes. The present Review describes some salient advances in this field, particularly in computer-aided tissue modeling, computer-aided tissue informatics and computer-aided tissue scaffold design and fabrication. Methodologies of development of CATE modelling from high-resolution non-invasive imaging and image-based three-dimensional reconstruction, and various reconstructive techniques for CAD-based tissue modelling generation will be described. The latest development in SFF to tissue engineering and a framework of bio-blueprint modelling for three-dimensional cell and organ printing will also be introduced.

Animals↗
PubMed2005

A control study to evaluate a computer-based microarray experiment design recommendation system for gene-regulation pathways discovery.

The main topic of this paper is evaluating a system that uses the expected value of experimentation for discovering causal pathways in gene expression data. By experimentation we mean both interventions (e.g., a gene knock-out experiment) and observations (e.g., passively observing the expression level of a "wild-type" gene). We introduce a system called GEEVE (causal discovery in Gene Expression data using Expected Value of Experimentation), which implements expected value of experimentation in discovering causal pathways using gene expression data. GEEVE provides the following assistance, which is intended to help biologists in their quest to discover gene-regulation pathways: Recommending which experiments to perform (with a focus on "knock-out" experiments) using an expected value of experimentation (EVE) method. Recommending the number of measurements (observational and experimental) to include in the experimental design, again using an EVE method. Providing a Bayesian analysis that combines prior knowledge with the results of recent microarray experimental results to derive posterior probabilities of gene regulation relationships. In recommending which experiments to perform (and how many times to repeat them) the EVE approach considers the biologist's preferences for which genes to focus the discovery process. Also, since exact EVE calculations are exponential in time, GEEVE incorporates approximation methods. GEEVE is able to combine data from knock-out experiments with data from wild-type experiments to suggest additional experiments to perform and then to analyze the results of those microarray experimental results. It models the possibility that unmeasured (latent) variables may be responsible for some of the statistical associations among the expression levels of the genes under study. To evaluate the GEEVE system, we used a gene expression simulator to generate data from specified models of gene regulation. Using the simulator, we evaluated the GEEVE system using a randomized control study that involved 10 biologists, some of whom used GEEVE and some of whom did not. The results show that biologists who used GEEVE reached correct causal assessments about gene regulation more often than did those biologists who did not use GEEVE. The GEEVE users also reached their assessments in a more cost-effective manner.

Animals↗
PubMed1990

The use of computer simulation in the design and analysis of cell proliferation experiments.

The simulation language CELLSIM is used to model a population of cells undergoing proliferation, death and migration. It is shown that standard analytical methods can successfully describe the system in its unperturbed state, but may be considerably in error if the system has recently been subjected to cytotoxic insult. It is suggested that laboratory experiments should be performed on perturbed systems only if simulations have shown that the methods of data analysis will be satisfactorily powerful and accurate.

Animals↗