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PubMed1991

Urodynamic assessment and quantification of prostatic obstruction before and after transurethral resection of the prostate: standardization with the aid of the computer program CLIM.

The clinical manifestations of benign prostatic hypertrophy (BPH) are ascribed entirely to the infravesical obstruction. Therefore relief of symptoms is pursued by surgical removal of obstruction, i.e. prostatectomy. On the other hand, it is generally accepted that the conventional clinical signs and symptoms do not correlate with obstruction as urodynamically defined. In the present study, objective obstruction and detrusor contractility parameters were calculated from detrusor pressure and flow rate measurements in 22 patients before and after transurethral resection of the prostate (TURP) using the computer program CLIM. The results indicate: (1) that CLIM supplies reliable obstruction and contractility parameters for preoperative assessment and follow-up in patients with BPH and (2) that greater than 25% of the patients, who underwent TURP, were objectively not obstructed. These findings form strong arguments for including CLIM parameters in the preoperative assessment to perform a TURP.

Diagnosis, Computer-Assisted↗

PubMed2006

On statistical analysis of forensic DNA: theory, methods and computer programs.

Statistics plays an important role in evaluating the evidential weight of forensic DNA. In this paper, general statistical principles for forensic DNA analysis are presented. We introduce the theory and methods for the statistical assessment in kinship determination and DNA mixture evaluation. In particular, analytical formulas for testing for biological relationship among three individuals and for assessing the DNA mixture evidence in the case of multiple subdivided ethnic groups are developed. Two user-friendly computer programs are demonstrated to exhibit their wide applicability in tackling with complex kinship/paternity and mixture problems. The EasyDNA program can solve a complicated paternity case in 1 min.

DNA↗

PubMed1981

HISTOSCAN: computer program for cytophotometry in tissue sections and its application in the evaluation of nuclear atypia.

The grading of nuclear atypia has a great and well recognized value when predicting the malignancy of neoplastic processes. Although the basic criteria for the grading are generally agreed upon, in the individual case, the final judgement is to some extent still a matter of subjectivity, which naturally impairs reproducibility. The present paper describes a method for quantification of variability of nuclear size and Feulgen-stainability. By plotting the mean optical density against the area value in a scatter-diagram, a cluster is obtained, the size of which reflects the degree of nuclear atypia. The measurements are performed in tissue sections using stage scanning cytophotometry. A computer program--HISTOSCAN--has been developed which enables measurements in highly cellular tissues. The system is also insensitive to the influence of light scattering, a factor of importance when measuring in tissue sections. The performance of the program is tested in both imprints and tissue sections.

Animals↗

PubMed2004

A computer program to estimate power and relative efficiency to assess multiplicative interactions in flexibly matched case-control studies.

Matching on one of two possibly interacting exposures can increase power and efficiency to estimate multiplicative interactions in case-control studies. We recently introduced the concept of flexible matching strategies with varying proportions of a dichotomous matching factor among controls to further increase power and efficiency. In order to facilitate the application of this concept, we developed a computer program which provides estimates of power and efficiency varying the proportion of the matching factor in controls over all possible values from 1 to 99%. The program allows one to estimate the effect of frequency matching on power and efficiency to study multiplicative interactions and to assess the optimal prevalence of the matching factor in selected controls for a given scenario which often differs from the prevalence in cases (aimed at in traditional 'fixed' frequency matching). Our program will strongly facilitate assessing the benefits of matching and flexible matching strategies in case-control studies addressing multiplicative interactions, including gene-environment interactions.

Case-Control Studies↗

PubMed1995

A computer program for the multivariate and graphical monitoring of acid-base data in an intensive care unit.

Monitoring the arterial acid-base status of ICU patients is done by measuring and calculating the acid-base variables pH, the partial pressure of carbon-dioxide (PCO2) and the bicarbonate-ion concentration ([HCO-3]). Univariate normal reference ranges exist for these values. However, it is well known that an exact linear relationship exists between pH, the logarithm of PCO2 and the logarithm of [HCO-3] values. We developed a computer program for the multivariate evaluation and graphical monitoring of these values in an intensive care setting that takes this intrinsic two-dimensionality into account. A composite index is introduced for the monitoring of all three laboratory values. Moreover, using this index, a multivariate statistical reference region based on an unselected population of ICU patients was derived.

Acid-Base Equilibrium↗

PubMed1991

A system approach to pharmacodynamics. III: An algorithm and computer program, COLAPS, for pharmacodynamic modeling.

Many pharmacodynamic (PD) models may be generalized in the form E(t) = N(L[c(t)]), where E(t) is a recorded effect response, c(t) is a sampled drug level, N is a nonlinear autonomic function, and L is a linear operator that commonly is a convolution operation. The NL class of PD models includes the traditional effect compartment PD models as a subclass, but is not limited to such models. An algorithm and computer program named COLAPS, based on system analysis principles and hysteresis minimization, that enable N and L to be empirically determined for the NL class of models without addressing specific kinetic structure aspects ("model independence") are presented. The kinetic concepts of biophase conduction and transduction functions are used by COLAPS. Such an approach is more general than the effect compartment approaches because it does not assume first-order transport principles. The pitfalls of hysteresis minimization in PD modeling are discussed and the procedures taken by COLAPS to avoid these pitfalls are outlined. A transformation technique prevents improper convergence to a point. A novel reparameterization scheme is introduced that maximizes the flexibility of the kinetic functions and extends the generality of the analysis. Inequality function constraints are maintained without the need for troublesome constrained nonlinear optimization procedures. Usage of the COLAPS program is illustrated in the analysis of the PD of amobarbital. The COLAPS program resulted in an excellent minimization of the effect versus biophase level hysteresis. The biophase conduction function, the biophase drug level (normalized), and the transduction curve were determined. The transduction curve showed clear biphasic behavior.

Algorithms↗

PubMed1980

An algorithm and computer program for deconvolution in linear pharmacokinetics.

The procedure of deconvolution to evaluate the rate and the extent of input from absorption data and data from intravenous administration is the most fundamental and least assumptive method of accurately evaluating drug absorption in linear pharmacokinetics. It is shown for linear systems that if the absorption response and the response from an intravenous infusion or bolus administration are both well approximated by a polyexponential function, then the rate of absorption can be expressed as a sum of exponentials. An algorithm and computer program are presented whereby the absorption function is uniquely defined from the model-independent parameters of the polyexponential expressions fitted to the absorption data and data from intravenous administration. Fitting a sum of exponentials to data has become a routine procedure in pharmacokinetics. The method presented therefore makes the previously complex task of deconvolution a simple procedure. The deconvolution approach is discussed in relation to conventional methods of evaluating drug absorption and appears to have some distinct advantages over these methods. The method is tested using simulated data and demonstrated using pentobarbital and cimetidine data from human subjects.

Absorption↗

PubMed2003

Determination of protonation constants of some fluorinated polyamines by means of 13C NMR data processed by the new computer program HypNMR2000. Protonation sequence in polyamines.

The p K(a) values of 6-fluoro-4,8-diazadodecane-1,12-diamine (6-fluorospermine) (1), 6,6-difluoro-4,8-diazadodecane-1,12-diamine (6,6-difluorospermine) (2), 6-fluoro-4-azaoctane-1,8-diamine (6-fluorospermidine) (3) and 6,6-difluoro-4-azaoctane-1,8-diamine (6,6-difluorospermidine) (4) in D(2)O solution have been determined at 40 degrees C from (13)C NMR chemical shifts data using the new computer program HypNMR2000. The enthalpies of protonation of compounds 1-4 and the parent amines spermine (5) and spermidine (6) have been determined from microcalorimetric titration data. The values of Delta H degrees were used to derive basicity constants relative to 25 degrees C. The NMR data have been analysed by two different methods to obtain information on the protonation sequence in the polyamines 1-5. The protonation sequence for spermine is related to its biological activity.

Journal Article↗

PubMed2000

Analyzing human random time generation behavior: a methodology and a computer program.

In the present article, it is argued that in addition to the traditional random generation tasks discussed by Towse and Neil (1998), random time interval generation tasks should be considered as useful alternatives, because they allow a better empirical control of the executive task component in dual-task situations. First, a framework for discussing randomness over time is presented. Then, the article goes on to present three methods for the analysis of such tasks. A first method is based on the correlation between the intervals produced. The second method calculates the approximate entropy, and the third method converts the time sequences into binary sequences and estimates the statistical properties of the sequence on the basis of these binary data. A principal components analysis on 19 different measures based on 1,381 sequences produced in a number of single-task and dual-task experiments shows that the proposed measures form two general clusters, one related to output probability, perseveration, and alternation, and one related to sequential commonalities. The article also briefly describes a computer program that implements these methodologies.

Humans↗

PubMed1989

A computer program for incidence density sampling of controls in case-control studies nested within occupational cohort studies.

A nested case-control study is a case-control study performed with a cohort study. The nested case-control design is useful because the number of study subjects for whom risk factor information is needed is smaller than in the original cohort study. The approach is especially helpful when collection of data is expensive or time consuming, as when it is necessary to contact subjects or next of kin. Selection of controls in nested case-control studies is best performed with a method called "incidence density" sampling. An approach to incidence density sampling that yields a valid estimate of the rate ratio is sampling without replacement from noncases at the time of case occurrence. To implement this approach, a system of computer programs was written that randomly selects a user defined number of controls for each case. The case-control data produced by this program can be analyzed by conditional logistic regression.

Cohort Studies↗

PubMed2004

A computer program for automated data evaluation to support in vitro higher-throughput screening for drug metabolism and pharmacokinetics attributes.

With the advances in analytical techniques, higher-throughput screening for drug metabolism and pharmacokinetics (DMPK) attributes has become an integral part of drug discovery. However, as the number of compounds increases, the volume of data that needs to be processed and evaluated increases exponentially. As a result, a major challenge for the analytical chemist is how to quickly process the vast amount of data so as to keep up with the throughput of the screening assay. We have developed a customized computer program for automated evaluation of the liquid chromatography/tandem mass spectrometric (LC/MS/MS) data generated from the in vitro DMPK screening assays. This program performs automatic data processing and quality control. It identifies analytical anomalies, such as low internal standard intensity and poor reproducibility of replicates. All analytical anomalies for individual compounds are summarized into an 'E-Log' in a color-coded format for reviewing. With the use of this program and other supporting software, data processing and evaluation for up to 100 compounds are accomplished in several minutes.

Algorithms↗

PubMed1989

RFrAP: a computer program for analysis of complex HLA RFLPs. Assignment of restriction fragments to haplotypes by segregation analysis.

The availability of HLA class II cDNA probes has led to the development of a powerful method for the discrimination of genetic variation in this region of the major histocompatibility complex. There are problems with this approach which reduce its usefulness, including the hybridization of a probe with multiple restriction fragments (RFs) from the same locus or of two different cDNA probes with the same RF (cross-hybridizing). These problems may now be largely overcome by the relatively simple computer program presented here, which allows the entry, storage, and editing of phenotype data. It includes utilities for the automatic assignment of bands to haplotypes and also statistical functions to determine several types of correlations. The outputs are presented in a format familiar to HLA serologists and immunogeneticists. In addition, the data is stored in a manner that allows the user to easily prepare "ad hoc" figures and tables that illustrate the more complex relationships among bands and between them and other variables.

Computers↗

PubMed2006

MedDietScore: a computer program that evaluates the adherence to the Mediterranean dietary pattern and its relation to cardiovascular disease risk.

Mediterranean dietary traditions have long been associated with lower mortality rates and better health status. The Mediterranean dietary pattern has become customary to be represented in the form of a pyramid, the base of which refers to foods which are suggested to be consumed most frequently and the top of the pyramid to those foods consumed rarely. Recently, an index (diet score) that estimates the adherence level to Mediterranean diet was developed and associated with cardiovascular disease risk and biomarkers. In this work we present a computer program that can easily calculate this diet score, as well as its association with cardiovascular disease risk. The application of this software to the general public might be a useful tool for the reduction of the disease burden related with nutritional habits at population level.

Biomarkers↗

PubMed2005

The CAFE computer program for nutritional analysis of the EPIC-Norfolk food frequency questionnaire and identification of extreme nutrient values.

BACKGROUND: Food frequency questionnaires (FFQs) are widely used in nutritional epidemiology but no papers detail the development of the supporting programs and nutritional databases. The principles involved in data collection, processing and treatment of the European Prospective Investigation into Cancer Study (EPIC)-Norfolk Study FFQ and development of the structure and content of the Compositional Analyses from Frequency Estimates (CAFE) program for calculating nutrient intakes are described. Extreme nutrient values and derivation of cut-points for data exclusion are also discussed. METHODS: The FFQ was sent to 25,637 participants. To exclude extreme (nonphysiological) outliers of nutrient intakes, the extreme top and bottom 0.5% of the ratio of energy intake to estimated basal metabolic rate was used. RESULTS: The CAFE computer program modifies nutrient intake according to specific fats used in food preparation and the amount of visible fat on meat. It incorporates different breakfast cereals and distinguishes between text for brands and types. After exclusion of outliers of nutrient intake some extreme values remained for energy, carbohydrate, protein, fat and alcohol, because of high reported frequencies of certain foods. CONCLUSIONS: The features of CAFE include flexible, updateable, databases and a novel method for matching text. The effect of extreme nutrient values on the accuracy of the FFQ in estimating diet in nutritional epidemiology should be investigated further.

Adult↗

PubMed1994

An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics.

A program running on personal computers (either Apple Macintosh or PC, using Excel worksheets) for the prediction of some protein structural characteristics is reported. The program runs according to the Chou and Fasman algorithm, with some modifications, for secondary structure prediction. The program also incorporates several complementary analyses for secondary structure prediction to help the user in the decision-making process: rules for amino acid preferences in the N-cap and C-cap of alpha-helices; prediction of the protein structural class and search of sequential motifs related to secondary structure. Additional algorithms performed by the program are: prediction of domain boundaries, prediction of loops, prediction of the state of cysteines (reduced or in disulfide bridge), hydropathy profiles according to Kyte and Doolittle, Hoop and Woods, and flexibility plot according to Karplus and Schulz.

Algorithms↗

PubMed1994

An algorithm and computer program for calculating the mean transit time and distribution rate parameters of generated metabolites undergoing linear tissue distribution and linear or non-linear central elimination.

A method is described for calculating the mean transit time and distribution rate parameters of a generated primary metabolite undergoing linear distribution and linear or non-linear central elimination, and of catenary metabolites with any precursor order. It is also applicable to a drug and its interconversion metabolite and does not require separate administration of the metabolite. The method allows steady-state volume of distribution and distribution clearance of a metabolite to be calculated, provided that the central volume of distribution of the metabolite is known. An algorithm and computer program to implement the proposed method are presented. The calculations require the plasma concentration versus time curves of the metabolite and its precursor. The method is applied to both published and simulated data.

Algorithms↗

PubMedDate not supplied

Computer program to calculate vectorial change of refraction induced by refractive surgery.

BACKGROUND: After refractive surgery, there may be changes in the spherical and the cylindrical components of the ametropia. In astigmatism, there may be variations in both the power and the axis. The best way to describe change in astigmatism caused by surgery is by vectorial analysis, which indicates the changes in power and the axis. However, in clinical practice, this procedure is limited by the tedious calculations required to establish the oblique cylinder combinations. METHODS: We propose a computer program for the calculation, by vectorial analysis, of the refractive changes induced by surgery. The program allows for reference to refractive data or keratometric readings. When the refractive data are considered, it is also possible to obtain the transposition of the correction values from the spectacle plane to that of the cornea. Finally, the program enables the user to calculate the coupling ratio. RESULTS: Some selected surgical cases are discussed by way of example. CONCLUSIONS: We think that this program will be a simple and accurate means of evaluating the results of refractive and corneal surgery.

Algorithms↗

PubMed2000

ECG variable cine: computer program for presentation of temporal changes in ECG variables over different number of ECG leads.

The analysis of exercise electrocardiogram (ECG) is based on the alteration of the measured variables in the detection of coronary artery disease (CAD). In its existing form the analysis of the exercise ECG is laborious and requires much time. The temporal analysis of the ECG variable and the comparison between different phases of the exercise test is difficult and time consuming, especially the simultaneous examination of the variables over several leads. In this article we present a computer program, ECG Variable Cine, for the visualization of the temporal changes of values of exercise ECG variables over the selected ECG lead system. The program includes the stationary 3-D presentation for the variables' alteration simultaneously in all selected leads over the time of exercise test. In addition, the program determines two parameters; the average value of the variable over the selected leads at every sample moment, and the chronotropic index, a parameter that indicates heart rate response to exercise. According to the results the average value of ST-segment deviation at the end of the exercise over the leads and chronotropic index are clinically more competent than the maximum value of ST-segment depression in the detection of CAD.

Electrocardiography↗