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PubMed2004

A computer program for generating New Deal compliant SHO rosters.

In the UK, the introduction of the New Deal on junior doctors' hours has placed constraints on permissible senior house officer (SHO) rosters. This makes it difficult to construct a rota that satisfies SHOs' annual leave and study leave requirements, yet remains compliant with the New Deal. A solution is the use of a computer. A computer program is described that generates compliant, full shift, SHO rosters in accordance with annual leave requests. This has been in routine use at the Oxford Radcliffe Hospitals Trust emergency department for the past 18 months. The program lends itself to, but is not specific to A&E applications; it can be used to generate compliant full shift rosters for other specialties. A copy of the program can be downloaded free of charge from a web site.

Emergency Service, Hospital↗
PubMed1998

[EPIC-SOFT a European computer program for 24-hour dietary protocols].

Within the EPIC study (European Prospective Investigation into Cancer and Nutrition) a calibration approach is applied to compare dietary data obtained by food frequency questionnaires from 9 European countries. A software for 24-h recalls was developed as the calibration instrument by the International Agency for Research on Cancer (IARC) in collaboration with all national EPIC centers. This computer program, called EPIC-SOFT, is an interview-based dietary assessment instrument that allows one to obtain a very detailed description and quantification of foods, recipes, and supplements consumed in the course of the preceding day. Probing questions and entering consumed foods in chronological order support the respondent's memory. The standardized structure prescribes--on the food group level--possibilities of description and quantification of food items to choose from. Quantification of consumed foods is supported by the EPIC-SOFT picture book that comprises colored photographs of foods in different portion sizes. The software provides an automatic coding of food items and recipe ingredients as well as calculation of nutrient intake. EPIC-SOFT is characterized by the obtained standardization of dietary data within Europe, a large number of available foods and recipes, and a very detailed description of consumed foods. Currently, EPIC-SOFT is one of the few dietary instruments providing comparable nutritional data within Europe.

Calibration↗
PubMed1989

A resource facility for kinetic analysis: modeling using the SAAM computer programs.

Kinetic analysis and integrated system modeling have contributed significantly to understanding the physiology and pathophysiology of metabolic systems in humans and animals. Many experimental biologists are aware of the usefulness of these techniques and recognize that kinetic modeling requires special expertise. The Resource Facility for Kinetic Analysis (RFKA) provides this expertise through: (1) development and application of modeling technology for biomedical problems, and (2) development of computer-based kinetic modeling methodologies concentrating on the computer program Simulation, Analysis, and Modeling (SAAM) and its conversational version, CONversational SAAM (CONSAM). The RFKA offers consultation to the biomedical community in the use of modeling to analyze kinetic data and trains individuals in using this technology for biomedical research. Early versions of SAAM were widely applied in solving dosimetry problems; many users, however, are not familiar with recent improvements to the software. The purpose of this paper is to acquaint biomedical researchers in the dosimetry field with RFKA, which, together with the joint National Cancer Institute-National Heart, Lung and Blood Institute project, is overseeing SAAM development and applications. In addition, RFKA provides many service activities to the SAAM user community that are relevant to solving dosimetry problems.

Animals↗
PubMed1995

Quantitative forensic evaluation of bite marks with the aid of a shape analysis computer program: Part 1; The development of "SCIP" and the similarity index.

Bite marks left on human tissue and bitten material have become an important aspect of scientific evidence used for the conviction or acquittal of a suspect. Expert opinion has often been based on subjective comparisons rather than any objective metrical analysis and many experts will agree that there is a need to employ additional comparative tests to achieve unbiased objectivity in their investigation. In this study, an interactive shape analysis computer program ("SCIP"-Shape Comparison Interactive Program) has been employed in an attempt to derive experimentally a quantitative comparison, in the form of a Similarity Index (S.I.), between the "offender's" teeth and the bite marks produced on a standard flat wax form. The S.I. values obtained using "SCIP" were evaluated in a variety of experimental bite mark situations. It was found that in no case could the S.I. values produced by comparison of the bite mark with the dental casts from non-perpetrators be confused with the much lower S.I. from comparison of the bite mark with the dental cast of the perpetrator. The use of the Similarity Index derived using the "SCIP" program is recommended as a simple, accurate and objective means of comparing bite marks in suitable forensic cases.

Bites, Human↗
PubMed1995

A computer program for estimating the influence of the body bicarbonate pool during CO2 breath tests.

Mathematical representation of physiological systems is a useful means of monitoring various parameters and factors of such systems. The use of compartmental models for the study of physiological systems has led to the introduction of several new techniques for solving problems, concerning the kinetics between the individual sites of these systems. The computer program, presented here, allows the calculation of the influence of a mammillary model, representing the bicarbonate pool, on the expiration rate of the label, administered during a breath test. It consists of two modules, one for performing non-linear least squares regression fitting of discrete measurements from a breath test (model output) and a second one for estimating the corresponding label released into the bicarbonate pool (model input), based on the measurements of expired air. Data, derived from metabolic studies using oral administration of naturally labelled 13C-glucose in man, under various metabolic conditions, was used as an input to this program.

Bicarbonates↗
PubMedDate not supplied

Determination of urine saturation with computer program EQUIL 2 as a method for estimation of the risk of urolithiasis.

To investigate the risk for the development of urolithiasis in 30 children with urolithiasis, 36 children with isolated hematuria, and 15 healthy control children, 24-h urinary excretion of calcium, sodium, oxalate, citrate, sulfate, phosphate, magnesium, urate, chloride, ammonium, and glycosaminoglycans was determined and urine saturation for calcium oxalate was calculated with the computer program EQUIL 2. Compared with controls, children with urolithiasis had significantly increased calcium excretion, oxalate excretion, and urine saturation, whereas children with isolated hematuria had significantly increased calcium excretion only. The best estimation of the relative risk of urolithiasis can be made after urine saturation, using logistic regression. The percentage of patients correctly classified after urine saturation is 85.41% in comparison with 80.95% and 73.81% when the estimation was done by calcium excretion and oxalate excretion, respectively. Using the breakpoint value of 4.29 for urine saturation, it was possible to separate children with increased risk of urolithiasis development from the group of children with isolated hematuria.

Calcium↗
PubMed2005

Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness.

Although copious qualitative information describes the members of the diverse microbial communities on Earth, statistical approaches for quantifying and comparing the numbers and compositions of lineages in communities are lacking. We present a method that addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences. We developed a computer program, DOTUR, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level. DOTUR uses the frequency at which each OTU is observed to construct rarefaction and collector's curves for various measures of richness and diversity. We analyzed 16S rRNA gene libraries derived from Scottish and Amazonian soils and the Sargasso Sea with DOTUR, which assigned sequences to OTUs rapidly and reliably based on the genetic distances between sequences and identified previous inconsistencies and errors in assigning sequences to OTUs. An analysis of the two 16S rRNA gene libraries from soil demonstrated that they do not contain enough sequences to support a claim that they contain different numbers of bacterial lineages with statistical confidence (P > 0.05), nor do they contain enough sequences to provide a robust estimate of species richness when an OTU is defined as containing sequences that are no more than 3% different from each other. In contrast, the richness of OTUs at the 3% level in the Sargasso Sea collection began to plateau after the sampling of 690 sequences. We anticipate that an equivalent extent of sampling for soil would require sampling more than 10,000 sequences, almost 100 times the size of typical sequence collections obtained from soil.

Algorithms↗
PubMed1984

A simple computer program for Scatchard plot analysis of hormone receptors including statistical analysis on a low cost desk top calculator.

A simple procedure for the estimations of standard errors in hormone binding parameters derived from Scatchard analysis is proposed by assuming an univariate linear regression statistic model. The complete set of necessary formulae is presented and a practical way for calculation is solved using the binding of human growth hormone to rat adrenal membranes, as a practical example. The comparison between the results obtained by the method proposed and by using a well proved and accepted computer program, shows unequivocally that the differences are practically undistinguishable. The complete program to calculate the Scatchard parameters and their statistical analysis is available on request.

Binding Sites↗
PubMed2006

Application of an interactive computer program to manage a problem-based dental curriculum.

Managing the change from traditional to problem-based learning (PBL) curricula is complex because PBL employs problem cases as the vehicle for learning. Each problem case covers a wide range of different learning issues across many disciplines and is coordinated by different facilitators drawn from the school's multidisciplinary pool. The objective of this project was to adapt an interactive computer program to manage a problem-based dental curriculum. Through application of a commercial database software--CATs (Curriculum Analysis Tools)--an electronic database for all modules of a five-year problem-based program was developed. This involved inputting basic information on each problem case relating to competencies covered, key words (learning objectives), participating faculty, independent study, and homework assignments, as well as inputting information on contact hours. General reports were generated to provide an overview of the curriculum. In addition, competency, key word, manpower, and clock-hour reports at three levels (individual PBL course component, yearly, and the entire curriculum) were produced. Implications and uses of such reports are discussed. The adaptation of electronic technology for managing dental curricula for use in a PBL curriculum has implications for all those involved in managing new-style PBL dental curricula and those who have concerns about managing the PBL process.

Curriculum↗
PubMedDate not supplied

Data structure and computer program for fast interactive searches of clinical diagnoses.

Since 1987 the IDC codes of all diagnoses of patients treated in our hospital are stored in a patient-oriented (upright) database. In order to facilitate interactive searches for specific diagnoses and their combinations this database has been inverted into a data structure sorted by diagnoses. The report presented describes the data structure and the functionality of a computer program that allows very fast searches for complex combinations of diagnoses.

Clinical Medicine↗
PubMed2004

Determining the need for coronary revascularization by an exercise test assessment computer program (ETAP).

The rate at which coronary artery revascularization procedures are performed remains inconsistent, and their risks may be greater and long-term benefits less than imagined by the general public and open to considerable inter-individual variation. However, these risks and benefits can be explicitly estimated for an individual patient from a brief medical history and the results of a standard exercise test by a computer program that uses conventional medical decision making techniques. The program first estimates the prior and post-exercise test probability of coronary artery disease and then employs a decision analysis model to define the risks and benefits associated with different treatment options. These results are provided in a printed report that can become part of the clinical record to be reviewed with the patient. In contrast with traditional clinical intuition, the program consistently and explicitly defines the risks and benefits of coronary artery disease treatments. The program forces physicians and their patients to appraise critically the information and beliefs upon which they base their clinical decisions.

Journal Article↗
PubMed1994

A rapid algorithm and a computer program for multiple test procedures using logical structures of hypotheses.

It is demonstrated how improvements of general multiple test procedures can be obtained using information about the logical structures among the hypotheses. Based on a procedure of Bergmann and Hommel (B. Bergmann and G. Hommel, Improvements of general multiple test procedures for redundant systems of hypotheses, in Multiple Hypothesenprüfung--Multiple Hypotheses Testing, Eds. P. Bauer, G. Hommel and E. Sonnemann, pp. 100-115 (Springer-Verlag, Berlin, 1988)), a computer program was written by Bernhard (G. Bernhard, Computerunterstützte Durchführung von multiplen Testprozeduren--Algorithmen und Powervergleich, Doctoral thesis (Mainz, 1992)) using this information. It is applicable for a general class of systems of hypotheses which can be expressed in a linear way. By means of a simulation study it is shown that the proposed procedure is often substantially more powerful than other usual multiple test procedures.

Algorithms↗
PubMed1979

A computer program for simulating a distributed metabolic system. Distribution volumes in a simulated organism.

A metabolite or hormone is distributed with non-uniform concentration throughout some volume within an intact organism. Various methods involving radioactive tracers are used to estimate the total mass of the metabolite and its volume of distribution. The calculations of mass and volume are based on very simple models, and cannot usually be validated by measurements on the real animal. Hence we have developed a computer program for simulating a metabolic system with convective and diffusive transport. The tracer experiments can be simulated by solving the differential equations for convective diffusion by finite element methods. Thus the total metabolic mass and distribution volume can be both 'measured' and calculated by all the standard techniques. In this way some mathematical methods currently in general use can be seen to be patently incorrect, and others quite acceptable. The concept of a metabolic doublet was introduced, by analogy with an electrical dipole.

Biological Transport↗
PubMed1997

Development of a common 3D pharmacophore for delta-opioid recognition from peptides and non-peptides using a novel computer program.

A unified three-dimensional (3D) pharmacophore for recognition of the delta-opioid receptor by families of structurally diverse delta-opioid ligands, including peptides and non-peptides, has been determined. An additional structural feature required for delta-selectivity was also characterized using a subset of these ligands that are highly selective for the delta-opioid receptor. To obtain these pharmacophores, we have used a recently developed computer program that performs systematic and automated comparisons of molecules to determine whether any common 3D relationships exist among candidate recognition moieties in high-affinity analogs. All the low-energy conformations of each ligand are included in these comparisons. The program developed should be applicable in general to molecular superimposition problems in rational drug design and to develop both 3D recognition and activation pharmacophores for any receptor for which high- and low-affinity analogs and agonists and antagonists have been identified.

Base Sequence↗
PubMed1996

A computer program for comprehensive ST-segment depression/heart rate analysis of the exercise ECG test.

The ST-segment depression/heart rate (ST/HR) analysis has been found to improve the diagnostic accuracy of the exercise ECG test in detecting myocardial ischemia. Recently, three different continuous diagnostic variables based on the ST/HR analysis have been introduced; the ST/HR slope, the ST/HR index and the ST/HR hysteresis. The latter utilises both the exercise and recovery phases of the exercise ECG test, whereas the two former are based on the exercise phase only. This present article presents a computer program which not only calculates the above three diagnostic variables but also plots the full diagrams of ST-segment depression against heart rate during both exercise and recovery phases for each ECG lead from given ST/HR data. The program can be used in the exercise ECG diagnosis of daily clinical practice provided that the ST/HR data from the ECG measurement system can be linked to the program. At present, the main purpose of the program is to provide clinical and medical researchers with a practical tool for comprehensive clinical evaluation and development of the ST/HR analysis.

Exercise Test↗
PubMed1985

A BASIC computer program for evaluating the effect of sample distribution on the least-squares regression slope estimate.

Least-squares regression analysis is widely used in analytical method comparison studies even though model assumptions are typically violated. The advantages favoring the use of the least-squares technique, when applicable, are that its theoretical characteristics are thoroughly developed and the calculations are straightforward and universally known. In order to aid an investigator in determining whether or not the least-squares technique can be acceptably applied in a given method comparison situation, a BASIC computer program is developed that evaluates the bias of the least-squares slope estimate as a function of the precision characteristics of the analytical methods and the proposed sampling distribution for the method comparison experiment.

Clinical Laboratory Techniques↗
PubMed1990

A computer program to assist in the choice of restriction endonucleases for use in DNA analyses.

Type II restriction endonucleases cleave double stranded DNA molecules at sites characterized by one or more sets of nucleotide pairs sequences. These digestions are essential in such procedures as DNA cloning, DNA sequencing and restriction fragment length polymorphism (RFLP) analyses. A large number of enzymes with different sequence specificities are available. To date, most choices of restriction endonucleases have been made by trial and error. A computer program, REDI, has been developed that predicts the ability of a particular restriction enzyme to detect mutations. Characteristics of both the restriction endonuclease used and the DNA being cut are incorporated as variables in the program. The program was tested using mouse mitochondrial DNA (mtDNA) and bacteriophage lambda DNA because these have been sequenced and are well characterized. REDI was strongly correlated (rs = +0.862, n = 11, P less than 0.001) with mouse mtDNA RFLP detected by Ferris et al. [1] (Genetics, 105 (1983) 681-721). Even though predictions may be altered by a non-random association of nucleotides, which varies among DNA molecules, the predictions increase the probability of selecting the most efficient enzymes for use in the analysis of a particular DNA molecule.

Animals↗
PubMed1995

A computer program linking physiologically based pharmacokinetic model with cancer risk assessment for breast-fed infants.

The risk assessment process predicts the chances of adverse health effects that the toxicant possibly can do to the target organism under expected conditions of exposure. Regulators chose among several mathematical approaches to estimate the risk, but in each case it is necessary to link the dosemetrics of the toxicant with its predicted health effect. In this paper, a computer program is described that allowed us to link a physiologically based pharmacokinetic (PBPK) model for tetrachloroethylene (PCE) in the lactating mother with the estimate of extra cancer risk for breast-fed infants, according to the U.S. Environmental Protection Agency (EPA) methodology. When inhaled by a lactating woman, PCE may partition into breast milk and may be transferred to the breast-fed infant. We have developed and validated experimentally a PBPK model for lactational transfer of PCE in rats, including a quantitative description of a milk compartment and the nursing pup. Subsequently, the model has been scaled to describe human physiology, and was validated with literature data for human cases of PCE exposure. Finally, we linked the dosage predictions of the PBPK model with equations used by EPA to estimate the cancer risk from PCE. The model predictions are in good agreement with both the measured values and those reported in the literature for exposure to PCE. This comparison confirms the usefulness of PBPK modeling in risk assessments.

Air Pollutants↗