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PubMed2000

Structure-based estimation of enzymatic hydrolysis rates and its application in computer-aided retrometabolic drug design.

After a brief review of the problems related to the description of enzymatic hydrolysis rates and the quantification of steric effects, a recently developed method that uses the inaccessible solid angle omega h calculated around different atoms as a novel steric parameter to estimate human blood in vitro enzymatic hydrolysis rates in noncongener ester series is summarized. Some illustrative results obtained by the integration of this method into the expert system developed for computer-aided soft drug design are also presented. Starting from a lead compound, the system can provide full libraries of possible new "soft" molecular structures, a ranking order of these candidates based on isosteric-isoelectronic analogy to the lead, and estimated hydrolytic half-lives for all structures of interest.

Animals↗
PubMed2001

[Development and applications of a computer aided complete denture design system].

OBJECTIVE: The purpose of this study was to develop a practical CAD/CAM system with knowledge databases for complete denture. METHODS: A three-dimensional coordinate measuring machine (3DCMM) was used to collect three-dimensional information of edentulous models and bite plates and the mathematics model of complete denture was established using B-Spline method. This system was established by seting eight functional models: the measuring model, the converting data model, the constructing curve-surface model, the producing base and the editing model, the arranging artificial and the editing model, the outputting income model, the imitating dynamic model and the managing model. RESULTS: (1) The soft and hard system of a computer aided complete denture design (CACDD) was established, including 3DCMM, 8 functional models and databases. (2) A CACDD system and the three-dimensional demonstration were completed. CONCLUSION: This system lay down the foundation for setting up the computer aided complete denture design/manufacturing system.

Computer-Aided Design↗
PubMed2002

A prospective study of computer users: I. Study design and incidence of musculoskeletal symptoms and disorders.

BACKGROUND: A prospective study of computer users was performed to determine the occurrence of and evaluate risk factors for neck or shoulder (N/S) and hand or arm (H/A) musculoskeletal symptoms (MSS) and disorders (MSD). METHODS: Individuals (n = 632) newly hired into jobs requiring > or = 15 hr/week of computer use were followed for up to 3 years. At study entry, workstation dimensions and worker postures were measured and medical and psychosocial risk factors were assessed. Daily diaries were used to document work practices and incident MSS. Those reporting MSS were examined for specific MSD. Incidence rates of MSS and MSD were estimated with survival analysis. Cox regression models were used to evaluate associations between participant characteristics at entry and MSS and MSD. RESULTS: The annual incidence of N/S MSS was 58 cases/100 person-years and of N/S MSD was 35 cases/100 person-years. The most common N/S MSD was somatic pain syndrome. The annual incidence of H/A MSS was 39 cases/100 person-years and of H/A MSD was 21 cases/100 person-years. The most common H/A disorder was deQuervain's tendonitis. Forty-six percent of N/S and 32% of H/A MSS occurred during the first month of follow-up. Gender, age, ethnicity, and prior history of N/S pain were associated with N/S MSS and MSD. Gender, prior history of H/A pain, prior computer use, and children at home were associated with either H/A MSS or MSD. CONCLUSIONS: H/A and N/S MSS and MSD were common among computer users. More than 50% of computer users reported MSS during the first year after starting a new job.

Adult↗
PubMedDate not supplied

Newly developed ventricular assist device with linear oscillatory actuator.

The goal of this study was to develop a new direct electromagnetic left ventricular assist device (DEM-LVAD) with a linear oscillatory actuator (LOA). The DEM-LVAD is a pulsatile pump with a pusher plate. The pusher plate is driven directly by the mover of the LOA. The LOA provides reciprocating motion without using any movement converter such as a roller screw or a hydraulic system. It consists of a stator with a single winding excitation coil and a mover with two permanent magnets. The simple structure of the LOA is based on fewer parts to bring about high reliability and smaller size. The mover moves back and forth when forward and backward electric current is supplied to the excitation coil. The pump housings have been designed using three-dimensional computer aided design software and fabricated with the aid of computer aided manufacturing technology. Monostrut valves (Bjork-Shiley #21) were used for the prototype. The DEM-LVAD dimension is 96 mm in diameter and 50 mm thick with a mass of 0.62 kg and a volume of 280 ml. An in vitro test (afterload 100 mm Hg; preload 10 mm Hg; input power 10 W) demonstrated more than 6 L/minute maximum output and 15% maximum efficiency at 130 beats per minute (bpm). Dynamic stroke volume ranged between 40 and 60 ml. The feasibility of the DEM-LVAD was confirmed.

Biophysical Phenomena↗
PubMed2005

The role of computational models of the immune system in designing vaccination strategies.

Mathematical and computational models are designed to improve our understanding of biological phenomena, to confirm/reject hypotheses, and to find points of intervention by altering the behavior of the studied systems. Here we describe the role of mathematical/computational models of the immune system. In particular, we analyze some examples of how mathematical modeling can contribute to finding optimal vaccination strategies. Indeed, computational modeling offers an intriguing opportunity from the theoretical point of view, and it will be of interest for clinically oriented investigators who wish to find optimal therapeutic strategies and for pharmaceutical industries that want to produce effective and successful drugs.

Computational Biology↗
PubMed2003

Predicting ADME properties and side effects: the BioPrint approach.

Computational methods are increasingly used to streamline and enhance the lead discovery and optimization process. However, accurate prediction of absorption, distribution, metabolism and excretion (ADME) and adverse drug reactions (ADR) is often difficult, due to the complexity of underlying physiological mechanisms. Modeling approaches have been hampered by the lack of large, robust and standardized training datasets. In an extensive effort to build such a dataset, the BioPrint database was constructed by systematic profiling of nearly all drugs available on the market, as well as numerous reference compounds. The database is composed of several large datasets: compound structures and molecular descriptors, in vitro ADME and pharmacology profiles, and complementary clinical data including therapeutic use information, pharmacokinetics profiles and ADR profiles. These data have allowed the development of computational tools designed to integrate a program of computational chemistry into library design and lead development. Models based on chemical structure are strengthened by in vitro results that can be used as additional compound descriptors to predict complex in vivo endpoints. The BioPrint pharmacoinformatics platform represents a systematic effort to accelerate the process of drug discovery, improve quantitative structure-activity relationships and develop in vitro/in vivo associations. In this review, we will discuss the importance of training set size and diversity in model development, the implementation of linear and neighborhood modeling approaches, and the use of in silico methods to predict potential clinical liabilities.

Animals↗
PubMed2006

Application of inkjet printing to tissue engineering.

Recent advances in organ printing technology for applications relating to medical interventions and organ replacement are described. Organ printing refers to the placement of various cell types into a soft scaffold fabricated according to a computer-aided design template using a single device. Computer aided scaffold topology design has recently gained attention as a viable option to achieve function and mass transport requirements within tissue engineering scaffolds. An exciting advance pioneered in our laboratory is that of simultaneous printing of cells and biomaterials, which allows precise placement of cells and proteins within 3-D hydrogel structures. This advance raises the possibility of spatially controlling not only the scaffold structure, but also the type of tissue that can be grown within the scaffold and the thickness of the tissue as capillaries and vessels could be constructed within the scaffolds. Here we summarize recent advances in printing cells and materials using the same device.

Animals↗
PubMed1995

Integrating molecular and digital computing: an information systems design perspective.

Biological systems use a non-programmable, but evolvable and efficient mode of information processing that can be traced to its underlying macromolecular basis (Conrad, 1985, Commun. ACM 28, 464-480). Digital computers, on the other hand, are structurally programmable, but not evolvable, nor efficient. In this paper we explore ways to provide effective support of function in organizations by combining the molecular and digital modes of information processing in a synergistic manner. In particular, we look at the potential of molecular computing technology for extending the problem-solving and decision-making capabilities of humans in complex organizational systems. Synergies resulting from the integration of molecular computing (including both human and molecular computing devices) and digital computing, are analyzed from an information systems design perspective.

Biotechnology↗
PubMedDate not supplied

On the computer-aided and optimal design of keratorefractive surgery.

BACKGROUND: Several recent papers have discussed the use of engineering-based computer methods for the analysis of keratorefractive surgical procedures. What has been lacking is a broader view of the role of engineering analysis in keratorefractive surgery. This article demonstrates how these various analysis methods can be coupled to provide a comprehensive methodology for the design of refractive surgical procedures. METHODS: A structural model of the eye, based on a linearly elastic, transversely isotropic finite element formulation is coupled to a full-eye optical model. The optical errors due to refractive keratotomy are estimated by ray tracing through the optical model and measuring the position of the resulting focal plane relative to the retina. Computer-based optimization methods are employed to determine the surgical parameters necessary to correct myopia for a given set of surgical design goals. RESULTS: Results based on a hypothetical eye demonstrate agreement with clinical trends. Radial keratotomies are designed that eliminate refractive error while minimizing invasiveness in one case and maximizing the optical zone size in another. It is also shown that there is significant potential to customize this process on a patient-by-patient basis using clinically measured data. CONCLUSIONS: We present an overview of the research necessary to bring this approach to fruition. While only a first step, the methodology presented in this article has the potential to increase the predictability of keratorefractive surgery by substantially increasing both the quality and the quantity of the information available to the refractive surgeon preoperatively.

Biomechanical Phenomena↗
PubMed2004

A technique for fabricating patterns for removable partial denture frameworks using digitized casts and electronic surveying.

Although computer-aided design and manufacture techniques have shown some promising applications in the fabrication of crowns, inlays, and maxillofacial and oral surgery, the field of removable prosthodontics has not embraced these technologies so far. This article describes the development and investigation of computer-aided techniques that may eventually enable prosthodontic procedures such as surveying and the production of sacrificial patterns to be performed digitally. A 3-dimensional computer model of a conventional cast from a patient was obtained using an optical surface capture device (a scanner). The shape of a number of components of a removable partial denture framework was modeled on the 3-dimensional scan electronically, using computer-aided design software. A physical plastic shape of the components was produced using a Rapid Prototyping machine and used as a sacrificial pattern. Techniques to allow digital cast surveying before the production of sacrificial patterns were also developed. The results show that digital dental surveying and machine-produced sacrificial patterns can be accomplished. This article forms a basis for further developments leading to a fully integrated approach to the computer-aided design and fabrication of removable partial denture frameworks.

Computer Simulation↗
PubMed1999

Automated constraint-based nucleotide sequence selection for DNA computation.

We present techniques for automating the design of computational systems built using DNA, given a set of high-level constraints on the desired behavior and performance of the system. We have developed a program called SCAN that exploits a previously implemented computational melting temperature primitive to search a 'nucleotide space' for sequences satisfying a pre-specified set of constraints, including hybridization discrimination, primer 5' end and 3' end stability, secondary structure reduction, and prevention of oligonucleotide dimer formation. The first version of SCAN utilized 24 h of computer time to search a space of over 7.5 billion unary counter designs and found only nine designs satisfying all of the pre-specified constraints. One of SCAN's designs has been implemented in the laboratory and has shown a marked improvement in performance over the products of previous attempts at manual design. We conclude with some novel ideas for improving the overall speed of the program that offer the promise of an efficient method for selecting optimal nucleotide sequences in an automated fashion.

Animals↗
PubMed2006

Ultra-fast evaluation of protein energies directly from sequence.

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling.

Algorithms↗
PubMed1995

Accuracy of pedicle screw placement in lumbar fusions by plain radiographs and computed tomography.

STUDY DESIGN: Postoperative radiographs and computed tomography scans were used to evaluate 74 pedicle screws in 16 consecutive patients who underwent lumbar spine fusion with pedicle screw fixation. OBJECTIVE: To evaluate pedicle screw placement using plain radiographs versus computed tomographic scans. SUMMARY OF BACKGROUND DATA: Plain radiographs are the primary means of assessing pedicle screw placement. Comparison of plain radiographs and computed tomography has not been done. METHODS: Screws were graded as IN, OUT, or QUESTIONABLE; the direction of misplacement was noted. All evaluations were performed independently by three observers. RESULTS: Fewer screws were clearly within the pedicle on computed tomography when compared with plain radiographs. Computed tomography showed 10 times as many screws violating the medial cortex as did radiographs. Interobserver differences were not statistically significant. Intraobserver differences approached statistical significance when the two tests were compared. No recognized neurologic complications resulted from pedicle screw placement. CONCLUSIONS: Plain radiographs alone may not accurately reveal pedicle screw placement. Plain radiographs and thin section computed tomographic scans should be used to evaluate postoperative neurologic deficits in patients undergoing instrumented lumbar spine fusion with pedicle screws.

Bone Screws↗
PubMedDate not supplied

Porcelain-veneered computer-generated partial crowns.

OBJECTIVE: It would be advantageous to be able to use computer-aided design and manufacturing to fabricate a restoration that can be layered with a conventional porcelain veneer in the occlusal region, thus optimizing esthetics, function, and strength. This case study reports the laboratory technique and the clinical performance of 38 partial crowns fabricated with computer technology and veneered with porcelain. METHOD AND MATERIALS: Twenty-one mandibular and 17 maxillary molars in 27 patients were prepared for partial crowns. The occlusal surfaces were lowered (1.5 to 2.0 mm), deep shoulders (1.5 mm) were prepared around the functional cusps, and 1.0-mm-deep shoulders were prepared in the proximal gingival regions. The nonfunctional cusps were prepared with an occlusal shoulder at approximately a right angle with the axial surfaces of the seat. In the computer-aided design procedure, the occlusal table was reduced to 1.4 mm above the preparation surface. The marginal ridge points, the marginal ridge line, the equator line, and the fissure line heights were adjusted accordingly. RESULTS: The lowest occlusal table thickness was 1.1 mm in six partial crowns, 1.2 mm in 26 partial crowns, and 1.3 mm in six partial crowns. The lowest occlusal table thickness of the porcelain veneers varied between 0.4 and 0.6 mm. The total occlusal table thickness thus was 1.5 mm or more. Clinically, no fractures occurred during an observation period varying between 1 and 4 years after placement. CONCLUSION: Computer-aided design and manufacturing technology is also convenient for partial crown preparation design with shoulder finish lines.

Cementation↗
PubMed1998

Heuristic lipophilicity potential for computer-aided rational drug design: optimizations of screening functions and parameters.

In this research we test and compare three possible atom-based screening functions used in the heuristic molecular lipophilicity potential (HMLP). Screening function 1 is a power distance-dependent function, bi/[formula: see text] Ri-r [formula: see text] gamma, screening function 2 is an exponential distance-dependent function, bi exp(-[formula: see text] Ri-r [formula: see text]/d0), and screening function 3 is a weighted distance-dependent function, sign(bi) exp[-xi [formula: see text] Ri-r [formula: see text]/magnitude of bi)]. For every screening function, the parameters (gamma, d0, and xi) are optimized using 41 common organic molecules of 4 types of compounds: aliphatic alcohols, aliphatic carboxylic acids, aliphatic amines, and aliphatic alkanes. The results of calculations show that screening function 3 cannot give chemically reasonable results, however, both the power screening function and the exponential screening function give chemically satisfactory results. There are two notable differences between screening functions 1 and 2. First, the exponential screening function has larger values in the short distance than the power screening function, therefore more influence from the nearest neighbors is involved using screening function 2 than screening function 1. Second, the power screening function has larger values in the long distance than the exponential screening function, therefore screening function 1 is effected by atoms at long distance more than screening function 2. For screening function 1, the suitable range of parameter gamma is 1.0 < gamma < 3.0, gamma = 2.3 is recommended, and gamma = 2.0 is the nearest integral value. For screening function 2, the suitable range of parameter d0 is 1.5 < d0 < 3.0, and d0 = 2.0 is recommended. HMLP developed in this research provides a potential tool for computer-aided three-dimensional drug design.

Computer-Aided Design↗
PubMed2006

Design of a computer-controlled multileaf collimator for advanced electron radiotherapy.

A multileaf collimator for electrons (eMLC) has been designed that fulfils the technical requirements for providing advanced irradiation techniques with electrons. In the present work, the basic design parameters of leaf material, leaf height, leaf width and number of leaves as well as leaf overtravel and leaf shape were determined such that an eMLC with motorized leaves can be manufactured by a company specialized in MLC technology. For this purpose, a manually driven eMLC with variable source-to-collimator distance (SCD) was used to evaluate the chosen leaf specification and investigate the impact of the SCD on the off-axis dose distribution. In order to select the final SCD of the eMLC, a compromise had to be found between maximum field size, minimum beam penumbra and necessary distance between eMLC and isocentre to eliminate patient realignments during gantry rotation. As a result, the eMLC is placed according to the target position at 72 and 84 cm SCD, respectively. This feature will be achieved by interchangeable distance holders. At these SCDs, the corresponding maximum field sizes at 100 cm source-to-isocentre distance are 20 x 20 cm and 17 x 17 cm, respectively. Finally, the off-axis dose distribution at the maximum opening of the eMLC was improved by fine-tuning the settings of the accelerator jaws and introducing trimmer bars above the eMLC. Following this optimization, a prototype eMLC consisting of 2 x 24 computer-controlled brass leaves is manufactured by 3D Line Medical Systems.

Biophysical Phenomena↗
PubMed1975

[Attempt at classification and orientation of prescriptions using an index of psychotropic drugs in computers].

We designed a method of rational classification of psychotropic drugs belonging to neuroleptic class. Standard profiles were determined along BELSON'S Method (partially modified). Neuroleptic population is analysed according to two leading variables : desinhibiting action and powerful sedative action. The remaining variables are graded depending upon their binding with leading variable, we called them explanatory variables. Profile of drug is found along these explanatory variables. Results are set out with : list of decomposition with clauses, list of variables selected by method, dichotomic graphic, identification of drugs. Our purpose is to find objective tests, for classification of these therapeutic drugs. It must enable a best evaluation of indications and contra-indications, practice in every day.

Computers↗
PubMed1996

Impact of working environments upon human-machine dialogues: a formal logic for the integrated specification of physical and cognitive ergonomic constraints on user interface design.

A range of techniques have been developed to improve the integration of computer systems into complex working environments. For instance, computer aided design tools can be used to simulate operators' posture at a particular workstation. Fitting studies can then be used to validate potential layouts. Unfortunately, few of these techniques can also be used to support the development of interactive dialogues. This is a critical problem for systems where designers must distribute application data amongst a number of different presentation devices. The position of these displays can be used to reflect the salience and priority of information. This paper presents techniques that support both user interface development and workstation layout. First order logic can be used to represent and reason about constraints on the design of human computer dialogues. The same formalism can also be used to identify appropriate locations for presentation devices within their working context; control rooms and offices. The findings of ergonomic studies can then be applied to analyze the mental and physical demands imposed by the interactive dialogues that are supported by particular devices. Unfortunately, formal specifications provide little impression of what it would be like to interact with a system within a particular environment. We have developed simulation tools to address this problem. Prototype displays can be presented within three dimensional models of their working context. The resulting simulations are directly derived from formal specifications and can be shown to members of concurrent design teams. They also provide a medium for communication with potential operators.

Computer Systems↗