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PubMed1990

WHAT IF: a molecular modeling and drug design program.

A FORTRAN 77 computer program has been written to aid with macromolecular modeling and drug design. Called WHAT IF, it provides an intelligent and flexible environment for displaying, manipulating, and analyzing small molecules, proteins, nucleic acids, and their interactions. A relational protein structure database is incorporated to be queried. The program is suitable for most common crystallographic work. The menu-driven operation of WHAT IF, combined with the use of default values wherever user input is required, makes it very easy to use for a novice user while keeping full flexibility for more sophisticated studies. Although there are not too many unique features in WHAT IF, the fact that everything is integrated in one program makes it a unique tool for many purposes.

Computer Graphics↗
PubMed2005

A FORTRAN program for computing the exact variance of weighted kappa.

An algorithm and associated FORTRAN program are provided for the exact variance of weighted kappa. Program VARKAP provides the weighted kappa test statistic, the exact variance of weighted kappa, a Z score, one-sided lower- and upper-tail N(0,1) probability values, and the two-tail N(0,1) probability value.

Analysis of Variance↗
PubMed1996

The development of an interactive education program for heart failure patients: the Kodak Photo CD Portfolio concept.

Written information, as well as movie and video film, and computer programs have been used for information and education of patients. CD-ROM is now about to be used for the same purpose. The CD has several advantages over computer programs, such as high capacity and low production, duplication and distribution costs. It is unerasable and insensitive to electromagnetic forces. Heart failure (HF) is a common disease with poor prognosis. Due to diagnostic and treatment improvements new guidelines on evaluation and care of patients with HF have been published. Some advocate educational programs as a routine part of the care. Patients with HF (mostly elderly persons) use many drugs and need considerable education for effective self-care. To improve HF patients' knowledge of the disease and the drug treatment of the disease we have made an interactive, computer generated education program which is presented on a Kodak Photo CD Portfolio disc. The major steps and efforts in the development of the program, which uses a new principle, are explained, including some hardware and software issues. The program can be viewed on an ordinary TV set and run by the patients themselves. Unlike many educational products for health care professionals and patients, this product has now been included in a randomised patient education trial.

CD-ROM↗
PubMed1994

Comparison of a computer simulation program and a traditional laboratory practical class for teaching the principles of intestinal absorption.

Here we describe an evaluation of the effectiveness, compared with a traditional laboratory, of an interactive computer-assisted learning (CAL) program, which simulates a series of experiments performed using isolated, everted sacs of rat small intestine. The program is aimed at undergraduate students of physiology and is designed to offer an alternative student-centered learning approach to the traditional laboratory-based practical class. The evaluative study compared two groups of second-year undergraduate students studying a module on epithelial transport: one group worked independently using the CAL program and associated learning materials, and the other group followed a conventional practical class approach, working in the laboratory under supervision. Knowledge gain of each group was measured by means of a test consisting of a range of question types (e.g., short-answer factual, calculation, interpretation) given to students before and after the module. Student attitude to both approaches was assessed by questionnaire, and the resource requirements were also compared. It was found that the knowledge gain of both groups of students was the same, that students had a positive attitude toward using CAL programs of this type, and that the cost of the conventional laboratory-based approach was five times greater. The potential for integrating CAL programs into the undergraduate curriculum is discussed.

Animal Testing Alternatives↗
PubMed1982

Toward a theory of clinical expertise.

We believe that the outline of a promising approach to the study of expert clinical problem-solving is emerging. This process involves collecting as verbal transcripts the thoughts of experienced clinicians engaged in simulated clinical tasks and analyzing these transcripts to formulate theories of problem-solving tactics and strategies. In turn, these theories are embodied in a computer program that simulates the problem-solving process. The computer program's response to fresh clinical problems can be compared with physician behavior in order to revise, refute, or confirm the problem-solving theories. A scientific understanding of the expert clinician's reasoning strategies could prove exceptionally useful in improving the way we teach and practice medicine and in developing practical computer aids for medical decision-making.

Clinical Competence↗
PubMed2002

[User friendly analysis of MR investigations of the cerebral perfusion: Windows(R)-based image processing].

PURPOSE: Quick and user-friendly analysis of perfusion and diffusion weighted MRI by means of interactive computer software. METHOD: A Windows(R)-based software was developed for analysis of perfusion (PWI) and diffusion (DWI) MR imaging. The computer program was developed in the programming language C++ using optimized algorithms, so that a high computing speed on Win95/98/NT systems is achieved. The established SVD algorithms of Østergaard et al. for quantitative perfusion analysis were implemented. RESULTS: Perfusion parameter maps of the cerebral blood flow (rCBF), the mean transit time (MTT) and the cerebral blood volume (rCBV) in consideration of the arterial input function (AIF) can be calculated and visualized using color tables. Additionally, the calculation of "time-to-peak" maps (TTP) and of maps of the percentage change in signal intensity (PC) is possible. The analysis of n = 10 normal persons shows perfusion values that agree with those found in the literature. DISCUSSION: With the computer program developed here color-coded perfusion parameter maps can be calculated easily. Because of the high computing speed it is possible to get information about tissue perfusion on the basis of the large MR data sets even in acute investigations.

Algorithms↗
PubMed2001

Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape.

The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (MAKEPIXB), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program (HYDROPIX) which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.

Biopolymers↗
PubMed1995

A new three-dimensional treatment algorithm for complex surfaces: applications in surgery.

PURPOSE: Recent advances in computer technology enable automatic reconstruction of surface models using digitized contour lines and three-dimensional (3D) representation on a graphic terminal. This work was aimed at obtaining 3D reconstructions of facial bones to help guide oral surgery and complex dental implantology procedures. MATERIAL AND METHODS: The starting point was a computed tomographic examination. The limits of the cortical bone were automatically outlined and then digitized using a special computer program. The resulting data were then compiled for computer-aided design (CAD) purposes, and a virtual 3D model of the bone was mathematically computed. This model was next transferred to a computer program that piloted a CAD/computer-aided manufacture (CAM) machine that guided a laser stereolithography process. RESULTS: The early results of the use of 3D images, as well as solid models, for clinical and surgical purposes, indicate a high degree of reliability in morphologic diagnosis, determining the surgical procedure, and establishing the subsequent prognosis.

Algorithms↗
PubMed2004

How predictable is orthognathic surgery?

There are a number of increasingly sophisticated techniques available for orthognathic treatment planning. All are based on the determination of the skeletal pattern and the position of the dentition. However, they all suffer from difficulties associated with predicting the soft tissue profile. The aim of this retrospective cephalometric investigation was, therefore, to compare the ability to predict accurately the outcome of orthognathic treatment using the 'hand planning' technique and the orthognathic planning and analysis (OPAL) computer program, with an emphasis on the soft tissue profile. Seventy adult subjects were divided into two groups not specific for gender or age: the Class III patients had undergone bimaxillary surgery and the Class II patients sagittal split mandibular advancement. In each group, the pre-treatment and post-debond lateral cephalograms were utilized to calculate the actual orthodontic and surgical movements. These values were then used to produce a prediction using both the hand planning technique and the OPAL program. The resultant predictions were digitized using a customized computer program and compared with the actual outcome. The results show that there was marked individual variation when planning by hand and using the OPAL program. In the mandibular surgery group, hand planning and OPAL were of similar accuracy and few points differed significantly between prediction and outcome. However, for the bimaxillary group, a number of points showed bias and the hand planning technique appeared to be more accurate than the OPAL program, particularly in the region of the lips. Although the usefulness of predictions is acknowledged, these results suggest that they should be used with a certain amount of caution.

Adult↗
PubMed1998

SeqHelp: a program to analyze molecular sequences utilizing common computational resources.

Here we describe a tool to analyze molecular sequences utilizing the internet and existing computational resources for molecular biology. The computer program SeqHelp organizes information from database searches, gene structure prediction, and other information to generate multiply aligned, hypertext-linked reports to allow for fast analysis of molecular sequences. The efficient and economical strategy in this program can be employed to study molecular sequences for gene cloning, mutation analysis, and identical sequence search projects.

Algorithms↗
PubMed1982

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.

Base Sequence↗
PubMed1986

Phase plane modeling of leg motion.

Phase plane analysis of dynamical systems, in which variables are plotted against their time derivatives, has been recently emphasized as a general method for reconstructing system dynamics from data. The purpose of this experiment was to develop a model of leg movement in a stepping task using the phase plane approach. In this model, the leg is represented as a three-body linkage and the motion of the leg is assumed to be planar with four degrees of freedom. Experimental data was collected on one subject stepping six times, using a two dimensional videomotion analysis system with reflective markers placed on the lower limb joints. A computer program able to solve the equations of motion and compute the state of the system for a given task was implemented. This computer program was written to generate the motion of the leg for a given task using inverse kinematics and a preplanned foot path. Foot trajectories with cycloidal, constant acceleration/deceleration and sinusoidal velocity profiles were studied. From the results, an attempt was made to identify the variables which are measured and to determine the motion characteristics during stepping. The preliminary results support the concept of a hierarchical control structure with open-loop control during normal operation. During routine activity there is no direct intervention of the Central Nervous System (CNS). The results support the existence of preprogramming and provide a starting point for the study of the development of control in multiarticulate movements.

Foot↗
PubMed2001

Estimation of body fat from skinfold thickness.

The fat content of the human body has physiological and medical importance. It may influence morbidity and mortality, it may affect the ability to withstand exposure to cold and starvation, and it may alter the effectiveness of drugs and anaesthetics. It may also be the cause of reduced insulin sensitivity in some population groups. Thus, the measurement of the total body fat provides useful information. A computer program, written in quick basic language, was developed, to compute the equivalent fat content, as a percentage of body-weight, for a range of values for the sum of the four skinfolds, of Egyptian males and females of different ages. This is based on a table developed by Durnin and Womersley. The computer program was run using skinfolds of Egyptian males and females of different ages. Satisfactory results were obtained. This program can be used to calculate the total body fat with relative ease and reasonable accuracy. This should make it of common use in many fields of medicine, physiology, nutrition and anthropology, particularly in population studies comprising a large number of subjects.

Adipose Tissue↗
PubMed1977

[Cell image analysis on the PDP-12 computer: a software system for processing the image information from a scanning microscope photometer (author's transl)].

A system of computer programs is introduced which allows image analyzing of cytological or histological preparations. The software system was especially developed for a microprocessor (PDP-12, Digital Equipment Corporation) which is often implied in connection with microscope photometers (SMP 05, Carl Zeiss). Users need not to know anything about computer programming because the computer gives the necessary orders via CRT-display or printer. The different descriptors as they are available after different cytochemical or histochemical staining procedures are combined to a pattern vector which is to be a numerical equivalent of cell morphology. A novel method in numerically describing the fine structure of cell nuclei is emphasized. Different cell populations are compared by means of a simplified multivariate discrimiatory analysis. All programs are written in assembler language and they are stored on LINC tapes (Digital Equipment Corporation). Copies of system tapes respectively tapes with the source programs are available from the authors on sending of blank magnetic tapes (2,000 blocks marked). Description and print out of individual programs are published in the dissertation cited in References. Changes and additions of the system which have been done mean-while will be summarized, and lateron such summaries are available on request.

Cell Nucleus↗
PubMed1975

Analytical approach for depth dose calculations (60Co beams with fixed source-target distance).

A method is described to calculate depth dose distribution to a principal plane using analytical formulas for 60Co teletherapy units and constant source-to-target distance. The formulas were derived from experimental measurements taking into consideration the obliquity of the beam. For the purposes of dose calculation the beam was divided into primary and scattered components. A computer program incorporating the formulas was developed for an IBM 360/67 computer. Dose distributions computed and obtained from experimental measurements were in good agreement. The computer program is now in use for treatment planning, including rotational techniques.

Cobalt Radioisotopes↗

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