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PubMed1977

A systematic approach to thermal conductivity detector design I. Use of computer-aided data acquisition for the evaluation of cell contributions to peak shape.

The design of thermal conductivity detectors for open tubular gas chromatography was systematically investigated with the aid of modern digital data acquisition techniques. Two important factors in such a design are sensitivity and peak broadening. The latter factor was the principle thrust of this work and contributions to peak shape from both cell design and volume were analyzed by the method of statistical moments. Peak variance (the mean square displacement along the x-axis of a chromatographic peak) was shown to correlate directly with cell volume in cells of the same design but both variance and asymmetry were found to be design dependent.

Chromatography, Gas↗
PubMed2004

Enzyme-like proteins from an unselected library of designed amino acid sequences.

Combinatorial libraries of de novo amino acid sequences can provide a rich source of diversity for the discovery of novel proteins with interesting and important activities. However, since arbitrary sequences rarely fold into well ordered protein-like structures, randomly generated libraries will yield functional proteins only very rarely. To enhance the likelihood of finding functional de novo proteins, we use binary patterning of polar and non-polar amino acids to design focused libraries of sequences that are predisposed to fold into ordered structures. Proteins isolated from binary patterned libraries have been shown previously to fold into well ordered and native-like three-dimensional structures. To probe the potential of such libraries to also yield proteins with enzyme-like activity, we measured the esterase activity of S-824, a de novo binary patterned protein whose alpha-helical three-dimensional structure was reported recently. Protein S-824 displayed a rate enhancement (k(cat)/k(uncat)) of 8700. The observed activity is similar to, or better than, that observed for several esterases designed previously using rational design or automated computational methods. Moreover, the observed activity rivals those of the first catalytic antibodies. To assess whether the activity of S-824 is representative of other proteins in binary patterned libraries, we measured the esterase activity of six additional proteins from two libraries. These libraries were 'naïve' in that they were neither designed to bind substrate, nor subjected to high throughput screens for activity. All six of the additional proteins displayed esterase activity significantly above background. These findings demonstrate that novel proteins with enzyme-like properties are surprisingly common in focused libraries designed by binary patterning. Moreover, the activity of these unselected proteins provides a reference state for the levels of activity that have been obtained by selection and/or computational design.

Amino Acid Sequence↗
PubMed1999

Wrist and forearm postures of users of conventional computer keyboards.

The aim of this study was to perform a comprehensive investigation to document wrist and forearm postures of users of conventional computer keyboards. We instrumented 90 healthy, experienced clerical workers with electromechanical goniometers to measure wrist and forearm position and range of motion for both upper extremities while typing. For an alphabetic typing task, the left wrist showed significantly greater (p < .01) mean ulnar deviation (15.0 degrees +/- 7.7 degrees) and extension (21.2 degrees +/- 8.8 degrees) than the right wrist (10.1 degrees +/- 7.2 degrees and 17.0 degrees +/- 7.4 degrees for ulnar deviation and extension, respectively). Conversely, the right forearm had greater mean pronation (65.6 degrees +/- 8.3 degrees) than the left forearm (62.2 degrees +/- 10.6 degrees). We noted minimal functional differences in the postures of the wrists and forearms between alphabetic and alphanumeric typing tasks. Ergonomists should consider the statistically significant and probable practical difference in wrist and forearm posture between the left and right hand in ergonomic interventions in the office and in the design of computer keyboards. Actual or potential applications of this research include guiding the design of new computer keyboards.

Adult↗
PubMedDate not supplied

The use of custom-designed midfacial and submalar implants in the treatment of facial wasting syndrome.

Facial wasting syndrome is part of a lipodystrophy that occurs as a complication of highly active antiretroviral therapy. The loss of subcutaneous fat in the cheeks and temples results in a hollow-eyed, bony, emaciated appearance that is characteristic of the results of treatment of human immunodeficiency virus. Cessation of therapy results in a rebound in viral load and subsequent morbidity. The appearance of facial wasting syndrome is optimally treated with custom-designed implants that are made using high-resolution computed tomography combined with surgeon input and computer-aided design and manufacturing technology. Twenty-two patients with facial wasting syndrome were treated using either submalar implants (in more moderate cases) or custom-designed implants (in more severe cases). In each patient, the appearance of volumetric soft tissue restoration was successfully achieved, returning a permanent and more healthful appearance to the face.

Face↗
PubMed1990

The display of three-dimensional anatomy with stereolithographic models.

Stereolithography, a new technique of prototype fabrication developed for the aerospace industry, offers a unique way to display patient anatomy. Like current computer aided design (CAD) systems, it uses digital image data from computed tomography (CT) and magnetic resonance (MR) to produce a physical model. Unlike conventional CAD it does not require a cutting tool and, therefore, CAD toolpath limitations do not exist. The stereolithography apparatus uses an ultraviolet laser to selectively polymerize and solidify a polymeric liquid plastic solution under computer control. The device was used to produce a model of cranial bony anatomy from CT image data, providing full internal detail in the constructed model, including encased sinuses, foramen, and potentially complete internal anatomy within a closed skull. The advantages and disadvantages of this technology are reviewed with an emphasis on future development.

Computer Graphics↗
PubMed1992

Design, construction and application of a fully automated equimolar peptide mixture synthesizer.

A fully automated peptide synthesizer has been constructed that is capable of the synthesis of equimolar peptide mixtures and the simultaneous synthesis of 36 individual peptides. The synthesizer was constructed from a workstation of our own design utilizing a Zymark robot arm. A Macintosh II computer coordinates the movements of the robotic arm, the switching of over 40 solenoid valves and the monitoring of sensors in the workstation. The robot hands are used to deliver solvents from pressurized spigot lines and to pipet amino acid solutions from reservoirs to an array of reaction vessels. Liquid dispensing, reagent mixing and solvent removal are controlled from a multifunction I/O board in the computer. The design features of the synthesizer are presented, as well as the characterization of multiple individual peptides, a simple mixture of 19 components, and a complex mixture of 15,625 components.

Amino Acid Sequence↗
PubMed1996

Making DNA add.

Recent studies have demonstrated the feasibility of using DNA-based experiments to compute solutions to combinatorial problems. However, a prerequisite for designing a computer useful in a wide range of applications is the ability to perform mathematical calculations. The development of a DNA-based algorithm for addition is presented. The DNA representation of two nonnegative binary numbers is presented in a form permitting a chain of primer extension reactions to carry out the addition operation. To demonstrate the feasibility of this algorithm, a simple example was executed biochemically.

Algorithms↗
PubMed1998

[Is there a place for computer-assisted Post-Academic Dental Education (PAOT)? A survey from the period 1998-2008].

OBJECTIVE: To estimate the role of computer-CPED in the Netherlands to the year 2008. DESIGN: Computer-assisted learning is currently employed in many modern undergraduate dental curricula. It could also play an important role in providing continuing professional education in dentistry (CPED) to general dental practitioners. Computer-CPED offers teacher-independent and individualized interaction by distance learning. METHODS: A simulation study was conducted. Entry data were either derived from publications or were estimated. RESULTS: The results indicate that the demand for CPED will exceed the supply by 2002. CONCLUSION: The introduction of Computer CPED may substantially contribute to the supply of CPED-courses in de first decade of the next century. By 2008 about 25% of the CPED-courses could be provided by computer education.

Computer Communication Networks↗
PubMed2006

Microarray oligonucleotide probes.

Oligonucleotide probes are increasingly the method of choice for many modern DNA microarray applications. They provide higher target specificity, probe selection gives improved experimental control of hybridization properties, and targeting of specific gene subsequences allows better discrimination of highly similar targets such as splice variants or gene families. Only recently has there been substantial progress in dealing with the complexities of probe set design and probe-specific signal interpretation. After a discussion of advantages and disadvantages of oligonucleotide probes in comparison to amplicons, this chapter focuses on recent advances and remaining key challenges in probe design and computational data analysis for spotted and in situ-synthesized oligonucleotide microarray technologies. Both experimental questions and computational aspects are addressed. Experimental issues discussed include the choice of an optimal number of probes per target and probe lengths and their influence on bias and random measurement noise, effects of different probe or substrate modifications, and laboratory protocols on signal specificity and sensitivity. Computational topics include practical considerations and a case study in probe sequence design, the exploitation of probing multiple target regions, and the modeling of probe sequence-specific signals. The current state of the art of the field is examined, and principled thermodynamic probe design criteria are proposed that are based on the free energy of the probe-target complex at the hybridization temperature rather than its melting temperature. Finally, this chapter notes and discusses an emerging trend in recent computational work toward a focus on signal interpretation rather than probe sequence design.

Animals↗
PubMed2000

Applications of computer-aided learning in biomedical sciences: considerations in design and evaluation.

Multimedia computer-aided learning (CAL) is an area that has become increasingly prevalent in biomedical science. Here we describe the advances that have taken place in the computing industry that have led to this trend. We also outline areas within the subject of biomedical science that can most benefit from using multimedia CAL as a teaching aid. Furthermore, issues concerning the design of CAL (i.e. iterative design, structure, development tools) are discussed. As the evaluation of CAL is an essential part of the iterative design process, we look at new approaches to evaluation that have emerged in response to the superficial focus on usability that many evaluations take.

Computer-Assisted Instruction↗
PubMed1998

Interactive computer-assisted position acquisition procedure designed for the analysis of organelle movement in pollen tubes.

An interactive computer-assisted video microscopy method has been developed for the acquisition of extensive data on the sequential positions of pollen tube organelles, which cannot be automatically tracked using geometric or motion patterns. The method consists of video microscopy, analog and digital contrast enhancement, digital time-lapsing of the images, and interactive selection of positions in a coordinate system corresponding to the cell shape and real size. Data on 15,000 positions acquired with this method have been used to make quantitative analyses of the movement patterns of the organelles. From these analyses and the reconstruction of 900 trajectories, it appears that movements are random in the tip of the pollen tube but become more directed in distal regions of the cell, indicating an increase in axial arrangement of the actin filaments. (All custom-made software is available from the authors on request.)

Cell Movement↗
PubMedDate not supplied

Bio-inspired computing tissues: towards machines that evolve, grow, and learn.

Biological inspiration in the design of computing machines could allow the creation of new machines with promising characteristics such as fault-tolerance, self-replication or cloning, reproduction, evolution, adaptation and learning, and growth. The aim of this paper is to introduce bio-inspired computing tissues that might constitute a key concept for the implementation of 'living' machines. We first present a general overview of bio-inspired systems and the POE model that classifies bio-inspired machines along three axes. The Embryonics project--inspired by some of the basic processes of molecular biology--is described by means of the BioWatch application, a fault-tolerant and self-repairable watch. The main characteristics of the Embryonics project are the multicellular organization, the cellular differentiation, and the self-repair capabilities. The BioWall is intended as a reconfigurable computing tissue, capable of interacting with its environment by means of a large number of touch-sensitive elements coupled with a color display. For illustrative purposes, a large-scale implementation of the BioWatch on the BioWall's computational tissue is presented. We conclude the paper with a description of bio-inspired computing tissues and POEtic machines.

Cell Differentiation↗
PubMed1999

Branch-and-terminate: a combinatorial optimization algorithm for protein design.

BACKGROUND: Several deterministic and stochastic combinatorial optimization algorithms have been applied to computational protein design and homology modeling. As structural targets increase in size, however, it has become necessary to find more powerful methods to address the increased combinatorial complexity. RESULTS: We present a new deterministic combinatorial search algorithm called 'Branch-and-Terminate' (B&T), which is derived from the Branch-and-Bound search method. The B&T approach is based on the construction of an efficient but very restrictive bounding expression, which is used for the search of a combinatorial tree representing the protein system. The bounding expression is used both to determine the optimal organization of the tree and to perform a highly effective pruning procedure named 'termination'. For some calculations, the B&T method rivals the current deterministic standard, dead-end elimination (DEE), sometimes finding the solution up to 21 times faster. A more significant feature of the B&T algorithm is that it can provide an efficient way to complete the optimization of problems that have been partially reduced by a DEE algorithm. CONCLUSIONS: The B&T algorithm is an effective optimization algorithm when used alone. Moreover, it can increase the problem size limit of amino acid sidechain placement calculations, such as protein design, by completing DEE optimizations that reach a point at which the DEE criteria become inefficient. Together the two algorithms make it possible to find solutions to problems that are intractable by either algorithm alone.

Algorithms↗
PubMed1990

A computer program for selection of oligonucleotide primers for polymerase chain reactions.

We have designed a computer program which rapidly scans nucleic acid sequences to select all possible pairs of oligonucleotides suitable for use as primers to direct efficient DNA amplification by the polymerase chain reaction. This program is based on a set of rules which define in generic terms both the sequence composition of the primers and the amplified region of DNA. These rules (1) enhance primer-to-target sequence hybridization avidity at critical 3'-end extension initiation sites, (2) facilitate attainment of full length extension during the 72 degrees C phase, by minimizing generation of incomplete or nonspecific product and (3) limit primer losses occurring from primer-self or primer-primer homologies. Three examples of primer sets chosen by the program that correctly amplified the target regions starting from RNA are shown. This program should facilitate the rapid selection of effective and specific primers from long gene sequences while providing a flexible choice of various primers to focus study on particular regions of interest.

Algorithms↗
PubMed2000

Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.

Six helix surface positions of protein G (Gbeta1) were redesigned using a computational protein design algorithm, resulting in the five fold mutant Gbeta1m2. Gbeta1m2 is well folded with a circular dichroism spectrum nearly identical to that of Gbeta1, and a melting temperature of 91 degrees C, approximately 6 degrees C higher than that of Gbeta1. The crystal structure of Gbeta1m2 was solved to 2.0 A resolution by molecular replacement. The absence of hydrogen bond or salt bridge interactions between the designed residues in Gbeta1m2 suggests that the increased stability of Gbeta1m2 is due to increased helix propensity and more favorable helix dipole interactions.

Algorithms↗
PubMed1986

Design and use of a computer-assisted postmortem identification system.

The organization and rationale for the design of a computer-assisted postmortem identification system are discussed along with results of the use of this system in extensive simulation trials on a database of 578 records. The selectivity of dental characteristics is so great that any individual with 4 or more characteristics (either fillings or missing teeth), can be separated from a group of 578 people for final verification of the identity match. The effects of errors in the database are discussed and the actual effects of different error rates on identification are shown. Error rates of up to 30% have only small effects on the ability of the system to pick out correct identity matches. The system is presently implemented on a portable microcomputer, a representative desktop computer, and a large minicomputer. The present efforts include statistical analysis of an enlarged database and testing of a data acquisition system to allow the building of a large identification database (25 000 records) in a quick and economical manner.

Computers↗
PubMedDate not supplied

Dental lab technology in the digital age.

The "Information Age" is starting to have an impact on dental technology. Procera, Cerac and several other digital systems are commonly used by many technicians. Other systems are being developed and marketed. Computer Aided Design (CAD) can be used by dental technicians to create precise dental restorations. Solid modeling techniques can provide unique dental applications.

Computer Simulation↗
PubMed2006

Algorithmically designed peptides ameliorate behavioral defects in animal model of ADHD by an allosteric mechanism.

This study exemplifies the use of three ADHD-relevant methodological innovations. (1) The use of novel, patented, computational peptide design techniques to generate peptides targeting the extra-cellular and para-transmembrane amino acid loops of the putatively ADHD-involved, D(2) dopamine receptor, D(2)DAR; (2) experimental evidence that these peptides in L-amino acid/ortho ordered or D-amino acid/reverse ordered (retro-inverso), D(2)DAR, hydrophobic eigenmode matched forms, evoked positive allosteric and indirect agonist influences on in vitro stably receptor transfected CHO and LtK cells and on in vivo, brain mediated activity; (3) a representative 15 residue all-D-amino acid, D(2) mode matched peptide, given parenterally, was found to "repair" a key aberrant ADHD behavioral characteristic in a standard animal model of ADHD, the Spontaneously Hypertensive Rat, SHR, relative to its progenitor species control, the Wistar-Kyoto rat, WKY. The representative, retro-inverso peptide, all-D-LLYKNKPRYPKRNRE, reversed SHR's relative deficiency in sensory motor gating (pre-pulse inhibition, PPI) while leaving SHR's nonselective attention (rearings), impulsive behavior (time in center), and activity level (timed total motor behavior) unchanged. Amphetamine also reversed SHRs sensory gating defect, but with significant increases in nonselective attention, impulsivity and hyperactivity. These preliminary results suggest the possibility of a new, "softer" pharmacological approach to ADHD: hydrophobic mode matched peptide allosteric augmentation of the activity of indigenous dopamine with respect to D(2)DAR mediated function, in place of stimulant drug-induced presynaptic dopamine release or impairment of dopamine uptake.

Acoustic Stimulation↗