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PubMed2006

Software news and updates. Carma: a molecular dynamics analysis program.

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available.

Computer Simulation↗
PubMed1989

Expert systems for human service programs.

Although computer programs called "expert systems" do not necessarily emulate the heuristics and logic used by human experts, they can consistently produce useful, better-than-average recommendations. Backward and forward reasoning chains have applicability to human service problems in social work, education, and vocational rehabilitation. There is increasing evidence that useful expert systems that do not require exotic languages and machines will soon begin inroads toward their staggering potential for "helping people" in human services make better decisions in matters of eligibility determination, casework quality control, written service plans for clients or students, job placement, service acquisition, policy interpretation, and other concerns.

Decision Making, Computer-Assisted↗
PubMed2005

Consistent indexing of a (set of) single crystal SAED pattern(s) with the ProcessDiffraction program.

A computer program called "ProcessDiffraction" helps indexing a set of single crystal selected area electron diffraction (SAED) patterns by determining which of the presumed structures can fit all the measured patterns simultaneously. Distances and angles are measured in the digitalized patterns with a graphical tool by clicking on the two shortest non-collinear vectors (spots), using user-supplied calibration data. Centers of the spots and center of the pattern are optionally refined by the program. Suggested individual indexing solutions (consistent with an assumed unit cell) are listed by the program for each pattern. Simulated patterns are also consulted to check if the shortest calculated distances coincide with measured ones. Common solutions for the set are selected by checking the angles between the suggested zone axes against the angles between the experimental goniometer settings. The indexing process is manually controlled by selecting the candidate structures (one-by-one) for indexing and by specifying the tolerances for d-values, plane angles and zone angles. Patterns of any crystal system can be indexed successfully. Although error bars are larger in electron diffraction than in X-ray diffraction (XRD), frequently, many unrelated indexings are possible for any one electron diffraction pattern (irrespective of the indexing method), a set of SAED patterns can generally be indexed unambiguously, i.e. the three-dimensional reciprocal space can be identified correctly. Two other tools also help planning tilting experiments: zones along a plane can be listed (with their angles extended from a pre-selected zone in that plane) and zones lying at a given angle (specified with a tolerance) from a zone can also be identified (as they are situated between two cones). Another tool searches the XRD database directly either for advice on possible structures for a composition or to help calibration.

Journal Article↗
PubMed1986

Peptide sequencing program.

A computer program has been devised to automate rationalization of peptide fragmentation patterns. The program systematically generates all possible linear amino acid sequences which might be attributable to a peptide with a known amino acid composition. The generated sequences are then searched to find those that most closely match the spectrum of an unknown sequence.

Algorithms↗
PubMed1990

Estimation of protein secondary structure from circular dichroism spectra: a critical examination of the CONTIN program.

The computer program CONTIN uses the Provencher and Glöckner procedure to calculate protein secondary structure from circular dichroism spectra. We have tested this program with peptides and proteins in which unfolding was either induced by denaturing treatment or was already present. Results indicate that the program does not clearly discriminate between the ordered and the unordered states of a protein.

Circular Dichroism↗
PubMed2006

Validation of a computer software program for statistical analysis of accelerated stability studies on biological standards.

Long-term stability is an essential requirement for biological measurement standards and it has been evaluated by applying the Arrhenius model to the data obtained from accelerated thermostability studies. A computer program DEGTEST suited to a mainframe computer has been used for evaluating the stability of biological standards for more than a decade. This paper describes the validation of a computer program executable in a personal computer Microsoft Windows XP environment for the analysis of accelerated thermostability study data.

Biological Products↗
PubMed1997

Medical informatics training in pathology residency programs.

Computers and information technology are increasingly used by pathologists, necessitating training in such technology in pathology residency programs. We surveyed 176 programs in the United States and Canada to assess informatics training in terms of instructional methods used, computer availability, and type of training offered. Eighty-four programs replied, for a response rate of 48%. Ninety percent of programs reported offering formal informatics training, but only 68% of programs required it. A rotation dedicated to teaching informatics was provided in 24% of the programs; in 44% of programs, informatics was integrated with other rotations. The most common instructional methods used were hands-on experience with microcomputers and the use of tutors. In 94% of programs, computers were available for resident use; in 60%, residents had individual computers assigned to them. Five programs offered a dedicated informatics rotation but did not provide residents with individual computers, and 22 programs required informatics training but did not provide residents with individual computers. Comparison of these data with data from 1993 shows an increase in programs offering (90% vs 84%) or requiring (68% vs 59%) informatics. Fewer programs offer a dedicated rotation (24% vs 31%) or integrate informatics training with other rotations (44% vs 69%). These data suggest that although informatics training is considered important by most training programs, inadequate resources and lack of formal, structured programs may limit training.

Canada↗
PubMed1984

Do patients like psychometric testing by computer?

Programmed a micro-computer to administer and score the Crown-Crisp Experiential Index (CCEI) (Crown & Crisp, 1979) for a study of the psychological state of 59 newly delivered mothers. This publication reports the findings of a separate paper-and-pencil questionnaire assessment of the patients' attitudes to the computer itself. The 59 patients were almost unanimous in finding the computer acceptable and easy to use; only 1 S minded using it. None found the instructions difficult to understand, and only 1 had difficulty in reading them. Only 2 would object to using the computer again.

Attitude↗
PubMed2003

Spirometry in young children: should computer-animation programs be used during testing?

Currently, computer-animation programs are frequently used to instruct and stimulate young children in performing maximal expiratory flow/volume (MEFV) curves. The reproducibility and maximal performance of MEFV manoeuvres with and without the use of two computer-animation programs (the "candles" and the "balloon" programs) were evaluated. Eighty-eight children, aged 4-8 yrs, were randomly assigned to one of the two animation programs. All children performed two series of at least three technically acceptable curves, one series with the incentive and one without, in random order. With the use of computer-animation programs, a lower proportion of children were able to fulfil international criteria for forced vital capacity (FVC) and forced expiratory volume in one second (FEV1) reproducibility. The use of incentives improved reproducibility and performance of peak expiratory flow (PEF). Performance of FVC decreased significantly in 6-8-yr-old children using the animation programs. Training with a program for a short period of time before the formal lung-function test may be valuable. According to the results, however, the use of these programs during tests under the guidance of an experienced lung-function technician cannot be routinely recommended because of possible deteriorating effects on reproducibility and performance of forced expiratory manoeuvres.

Child↗
PubMed1997

Effectiveness of an endodontic diagnosis computer simulation program.

The effectiveness of a recently developed endodontic diagnosis computer simulation program was examined. Third-year dental students (n = 90) in three successive academic classes were given a pre-test in endodontic diagnosis before any endodontic instruction, and then received ten lectures on diagnostic techniques, endodontic pathology, and radiographic interpretation. The students were subsequently divided into three equal groups not differing statistically on their pre-test results. The first group used an endodontic computer simulation program containing fifteen patient simulations for one hour. The second group had a small-group seminar aiming to cover the same material as in the computer program in the same time period. The third group (control) had no further instruction. The three groups then took a post-test to evaluate their diagnostic knowledge in endodontics. The improvement of scores from pre- to post-test in the three groups were statistically different (p = 0.018). The simulation group students improved significantly more than the seminar group (p = 0.05) and the Control Group (p = 0.0024). Difference in improvement between the seminar group and the control group was not statistically significant (p = 0.20). Students were able to cover more cases on average using the simulation program than were covered in the seminar (t-test, p < 0.0001).

Computer Simulation↗
PubMed1989

Analysis of Ter-Ter enzyme kinetic mechanisms by computer simulation of isotope exchange at chemical equilibrium: development and application of ISOTER, a personal-computer-based program.

A convenient, personal-computer-based program has been developed that allows simulation of isotopic exchange kinetics at chemical equilibrium catalyzed by a three reactant-three product (TerTer) enzyme system: A + B + C integral of P + Q + R. This program, ISOTER, utilizes a rapid algebraic method to calculate the exchange rate between any reactant-product pair as a function of the substrate concentration and avoids altogether the necessity of deriving an explicit (but cumbersome and impractical) equation for exchange rate. ISOTER was used to generate model saturation patterns for 16 different TerTer kinetic mechanisms, varying different combinations of reactant-product pairs in constant ratio at equilibrium: [all substrates], [A, P], [B, Q], and [C, R], while holding the nonvaried components constant. These model studies indicate that virtually every one of these mechanisms can be distinguished from the others. In addition, ISOTER has been used to fit multiple sets of experimental data for Escherichia coli glutamine synthetase, which produced a set of rate constants consistent with the previously proposed "preferred order random" kinetic mechanism.

Computer Simulation↗
PubMed1994

Evaluation of a computer-based program for teaching cardiac anatomy.

RATIONALE AND OBJECTIVES: The authors determined to what extent a computer-based program could enhance or substitute for cadaver dissection in teaching cardiac anatomy to first-year medical students. METHODS: First-year medical students (n = 175) were randomized into four groups. Group 1 (control) received no instruction, group 2 participated in cardiac dissection, group 3 viewed the computer application, and group 4 performed cardiac dissection and then viewed the computer application. Each group was tested with 10 ultrafast computed tomographic static images and 8 cardiac cadaver specimens. RESULTS: The computer program plus dissection was superior to either the computer program alone or dissection alone; however, the results varied according to the subtest used to assess the outcomes. CONCLUSIONS: Cardiac computer instruction after dissection resulted in dramatically improved image testing performance. However, computer instruction should not replace dissection for teaching cardiac anatomy.

Anatomy↗
PubMed1983

A clinical decision analysis program for the Apple computer.

A computer program written in BASIC and implemented on a 48K RAM Apple II computer was developed to assist physicians in using decision analysis to solve clinical problems. Clinicians familiar with decision analysis can easily enter, modify, store, and retrieve decision trees. Probabilities and utilities can be calculated and a sensitivity analysis can be performed and printed. An entire decision tree can be listed, and a graphic display of any node with its branches, branch probabilities, and node utilities can be viewed and printed. The program is easy to use and can be learned in a few hours. Its flexibility and power will facilitate the application of decision analysis to a wide variety of clinical problems.

Computers↗
PubMed1998

The virtual anatomy practical: a stereoscopic 3D interactive multimedia computer examination program.

Continuing advances in computer visualization and interface technologies have enabled development of "virtual reality" programs that allow users to perceive and to interact with objects in artificial three-dimensional environments. Such technologies were used to create an image database and program for administering a practical examination in human gross anatomy. Stereoscopic image pairs of prepared laboratory dissections were digitized from multiple views of the thorax, abdomen, pelvic region, and upper and lower extremities. For each view, the stereo pairs were interlaced into a single, field-sequential stereoscopic picture using an image processing program. The resulting color-corrected, interlaced image files were organized in a database stored on a large-capacity hard disk. Selected views were provided with structural identification pointers and letters (A and B). For each view, appropriate two-part examination questions were spoken by a human narrator, digitally recorded, and saved as universal audio format files on the archival hard disk. Images and digital narration were organized in an interactive multimedia program created with a high-level multimedia authoring system. At run-time, 24-bit color 3D images were displayed on a large-screen computer monitor and observed through liquid crystal shutter goggles. A 90-second interval timer and tone were provided to give student users a time limit for each question comparable to that of a conventional practical examination. Users could control the program and select regional "subexams" using a mouse and cursor to point-and-click on screen-level control words ("buttons").

Anatomy, Regional↗
PubMed1991

Nomogram for dosing warfarin at steady state.

The predictive performance of a nomogram for dosing warfarin was compared with that of a computer program. The nomogram and the computer program were developed from the log-linear model describing warfarin pharmacodynamics at steady state. The nomogram's dose-response curves were generated by using previously reported pharmacodynamic and pharmacokinetic values for an outpatient population receiving warfarin. The series of dose-response curves were plotted by altering the pharmacodynamic values over a range of 3 standard deviations. The ability of the nomogram to predict the steady-state prothrombin time ratio (PTR) after an adjustment in the dosage of warfarin was evaluated, and the results were compared with those of a commercially available program involving Bayesian regression. Data for 65 outpatients were evaluated. The mean +/- S.D. nomogram-predicted, computer-predicted, and measured PTRs were 1.63 +/- 0.27, 1.64 +/- 0.24, and 1.66 +/- 0.23, respectively. The mean prediction errors for the nomogram and the computer program were -0.037 and -0.026, respectively, and the mean percent absolute prediction errors were 11.6% and 11.0%, respectively. Neither method was biased, and differences between the results for the two methods were not significant. The predictive performance of the warfarin dosing nomogram was comparable to that of the computer program.

Bayes Theorem↗
PubMed2005

A computer services program for residents of a continuing care retirement community: needs assessment and program design.

Preparatory to establishing a computer services program for residents, Presbyterian Homes, a multi-campus continuing care retirement community, conducted an assessment of residents' computer needs, ownership, and usage. Based on the results of the needs assessment, computer resource rooms were established at each facility, with computer hardware and software adapted for the use of seniors. We also deliver adapted computer education for residents, including small-group training in basic software skills; classes on software for computer accessibility; and workshops on themes motivating computer use. Ongoing evaluation shows that half of residents make use of computer resources, and that their computer skills have opened the door to other educational opportunities.

Aged↗
PubMed1990

ONCHOSIM: a model and computer simulation program for the transmission and control of onchocerciasis.

ONCHOSIM is a computer program for modelling the transmission and control of the tropical parasitic disease onchocerciasis, or river blindness. It is developed in collaboration with the Onchocerciasis Control Programme in West Africa (OCP), and is used as a tool in the evaluation and planning of control operations. The model comprises a detailed description of the life history of the parasite Onchocerca volvulus and of its transmission from person to person by Simulium flies. The effects of different control strategies, based on larvicide application and chemotherapy (ivermectin), on the transmission and on the disease symptoms can be evaluated and predicted. In the program two simulation techniques are mixed. Stochastic microsimulation is used to calculate the life events of individual persons and inhabitant parasites, while the dynamics of the Simulium population and the development of the parasite in the flies are simulated deterministically. Output of ONCHOSIM conforms to the format in which data collected by the OCP are reported. This enables detailed checking of model specifications against empirical data. Output can also consist of summarizing key indices for the intensity of onchocerciasis infection, which is especially useful for comparing the effectivity of control strategies.

Animals↗
PubMed1993

Computer dosing program for the initiation of vancomycin therapy.

The predictive performance of a computer dosing program used for initiating vancomycin therapy was studied. Initial serum vancomycin concentrations in 31 adult patients receiving vancomycin were estimated by using a computer program (T.D.M.S.) incorporating a two-compartment open model. Sixty-two serum vancomycin concentrations at steady state (Css) were obtained before and after one-hour infusions and compared with estimated Css values. Bias and precision were evaluated by calculating median error (ME) and median absolute error (MAE), respectively. Population-based estimates of volume of distribution (V) and clearance (CL) were compared with those obtained by fitting each patient's data set by using Bayesian analysis (BA) and non-linear least-squares regression (NLLS). Median (mean +/- S.D.) bias and precision for peak Css were 7.7 (10.2 +/- 10.8) and 7.7 (10.6 +/- 10.5) mg/L, and for trough Css were 7.4 (7.7 +/- 7.6) and 7.4 (8.8 +/- 6.2) mg/L. The medians were significantly different from zero. Estimated median (mean +/- S.D.) V, CL, and half-life were 0.72 L/kg, 0.60 (0.67 +/- 0.21) mL/min/kg, and 11.59 (12.87 +/- 3.91) hours. Median (mean +/- S.D.) CL values determined by BA and NLLS were 0.86 (0.89 +/- 0.32) and 0.85 (0.92 +/- 0.34) mL/min/kg, respectively. Both CL values were significantly greater than the population-based estimate. However, median V values determined by BA and NLLS did not differ from the population-based estimate. A revised clearance model derived from Bayesian analysis of data for the first 21 patients was tested in the 10 other patients and appeared to improve the predictive performance of the a priori model.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗