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PubMedDate not supplied

Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.

Base Sequence↗

PubMed1994

SHOWICD: a computer program to display ICD-9CM coded injury diagnoses and their corresponding injury severity scores for a particular patient.

SHOWICD is an interactive computer program designed to document severity of injury from the ICD-9CM coded injury diagnoses of a particular patient. Two severity-of-injury scores [the Abbreviated Injury Scale (AIS) and the Injury Severity Score (ISS)] are used. By employing the AIS scores, the severity of injury may be assessed per body region. The ISS provides an over-all index or summary score for severity of injury of the whole body. SHOWICD allows the user to analyze the effects of different types of injuries on the Injury Severity Score. SHOWICD may be employed either alone as a program or as a procedure in database management systems. The program is written in Turbo Pascal.

Abbreviated Injury Scale↗

PubMed1998

A computer program to compare sequence fingerprints of homologous proteins for the rapid assessment of their primary structure differences.

We have developed a computer program for the rapid assessment of the primary structure differences between a protein of unknown sequence and a homologous known protein. Both proteins are reduced, alkylated, and digested with the same hydrolytic agent. The unfractionated peptide mixtures are submitted to automatic sequence analysis. Based on the knowledge of the reference sequence, the program utilizes the analysis data to identify all the potential peptides present in the two mixtures, determining their primary structure, homology degree, and molecular weight calculated both as integer MH+ and average mass variables. These fingerprints allow the user to easily identify the structural differences between the two proteins and clarify possible doubts by a mass spectrometric analysis of the two mixtures. In order to verify the utility of the program, we provide an application example using the already reported data of two homologous proteins.

Amino Acid Sequence↗

PubMed1994

Selection of the most compatible graft recipient by computer program, used in regional tissue typing laboratory of Hellas (R.T.T.L.).

The purpose of this study was to present the new computer program that we developed in the regional tissue typing laboratory (R.T.T.L.) and use for the selection of the most suitable recipient for cadaveric allografts in a more efficient way. This new program was written and compiled in TURBO PASCAL 6.0, sorts all possible recipients to the HLA type of a donor, checks for the existence of splits and utilises them, and when requested, gives out results to more specific inquiries, i.e. all compatible recipients from 2DR2B2A to 1DR0B0A matching. It can also forecast success percentages according to different factors, i.e. combination of donor's and recipient's ages, HLA matching etc. The material used for this study were the patients who are registered in the formal cadaveric transplantation list of R.T.T.L. We have used this program since 2 January 1992 together with the old one. Since then we found that the new program is faster in sorting all the possible recipients of cadaveric renal allografts according to the criteria already mentioned. The total selection time, with all the criteria activated, averages a few seconds, whereas with the old program it took approximately 2 min just for the sorting of HLA matching, without any other criteria activated. In the printout of the final result of each inquiry are all the possible recipients in the sorted order together with relevant data (telephone number, address etc.). As a result, the laboratory personnel has been free from the tedious task of this sorting which was initially done by hand and the possibility of error has been eliminated. The program was developed exclusively by doctors and all the updates needed are done by the users. More important, however, is the fact that in many cases the time of cold ischaemia was reduced by more than 30 min with all the obvious advantages for the longevity of the graft's life.

ABO Blood-Group System↗

PubMed1984

Computer programs in nucleic acid synthesis: synthetic strategy development using solid-phase chemical techniques with data storage, retrieval and analysis capabilities.

A computer program has been designed to aid development of synthetic strategies for oligonucleotides produced by solid-phase chemical techniques. The program reduces the time required to develop a strategy and a data file from hours to minutes. The program contains inventories, provides cost analyses, and generates and stores other associated data. The program searches an inventory of sequences for that sequence to avoid duplicate synthesis. If the sequence is not in the inventory the program devises a synthetic strategy, calculates the amounts of reagents and labor costs necessary to complete the synthetic oligonucleotide. The program also deducts the reagents from inventory files. Physical data is also calculated. A file is generated in a sequence inventory for storage of the data as well as other data that will be generated during the purification processes. All variable parameters can be easily edited. The programs were designed to provide a cross-referencing feature for data analysis and can use several parameters as a constant.

Computers↗

PubMed1984

Computer programs in nucleic acid synthesis: synthetic strategy development using solid-phase chemical techniques with data storage, retrieval and analysis capabilities.

Base Sequence↗

PubMed1992

A computer program for planimetric analysis of digitized images.

Planimetrical measurements are made to calculate the area of an entity. By digitizing the entity the planimetrical measurements may be done by computer. This computer program was developed in conjunction with a research project involving measurement of the pneumatized cell system of the temporal bones as seen on X-rays. By placing the X-rays on a digitizer tablet and tracing the outline of the cell system, the area was calculated by the program. The calculated data and traced images could be stored and printed. The program is written in BASIC; necessary hardware is an IBM-compatible personal computer, a digitizer tablet and a printer.

Anthropometry↗

PubMedDate not supplied

A computer program for the analysis of dental arch form using the catenary curve.

This paper presents the logic and details of a FORTRAN computer program which fits a two parameter catenary curve, using the method of least squares, to a set of data points arising from an exact size photograph of a dental model. Error is assessed by evaluating the difference between the observed and fitted y values. Finally, the length of the arc is measured. The program is useful in studies related to dental arch form as a part of orthodontic treatment. The measurement of the arc length provides as assessment of space available in the dental arch, which is an important part of treatment planning for the orthodontic patient.

Computers↗

PubMed1985

An interactive computer program for the determination of the binding constants of monoclonal antibodies by non-linear regression analysis of radioimmunoassay data.

A computer program is presented for non-linear regression analysis of radioimmunoassay data, which allows the determination of the binding parameters of monoclonal antibodies, i.e., affinity constant and number of available binding sites. The program is based on the median method and gives the values of the binding constants and their 95% confidence limits, without the necessity for their preliminary, approximate evaluation. The program may also be used to determine the binding constants for the interaction of receptors with labelled ligands.

Antibodies, Monoclonal↗

PubMed1997

A computer program for correlating dental plaque pH values, cH+, plaque titration, critical pH, resting pH and the solubility of enamel apatite.

A computer program was written in Visual Basic (Microsoft) to calculate (a) the area between a plaque pH curve (as seen after a sucrose rinse) and either a resting pH (around pH 7) or a critical pH value (around 5.5) above at least parts of the pH curve; (b) the solubility of apatite at the pH values in plaque; (c) the area between the plaque pH solubility curve and the apatite solubility at the resting pH/critical pH; (d) the area between plaque cH+ curve and the cH+ value at resting pH/ critical pH; and (e) the area between a plaque pH curve and a cut-off pH value below the curve, e.g. pH 3. It was found that because both the cH+ and the solubility of apatite increased logarithmically with a pH drop, the two latter area functions (d, e) were basically different from those based directly on pH curves. Thus, pH changes around the resting pH value had little effect on areas calculated from concentrations of H+ and solubility. In contrast, a small pH change around pH 4 had a strong impact on both demineralization potential and areas based on cH+. Also, because of the logarithmic nature, demineralization potentials were generally large in comparison to remineralization potentials, a point that has hitherto received little attention.

Apatites↗

PubMed1991

Breeding and management of BB rats by the aid of the computer program BB RADABA.

In the process of breeding laboratory animals for experimental research a host of data will be produced. Our computer program BB RADABA permits the management of breeding and experimental data as well as planning of experiments and evaluation of experimental results. More than one year of practical work with this program has shown that BB RADABA provides a better survey over the data, moreover it is able to supply objective recommendations of suitable breeding pairs and had the advantage of graphic and statistic data presentation.

Animal Husbandry↗

PubMed1976

Computer programs suitable for processing behavioral data characterized by alternation of two states.

A program system is described which is suitable for processing behavioral and psychophysiological data characterized by alternation of two states (the transition between which is instantaneous). It is adapted for a LINC D.E.C. computer and is composed of a control program and several system programs computing different statistics and performing necessary input and output operations with the data.

Behavior↗

PubMed2002

Usability testing and outcomes of an interactive computer program to promote smoking cessation in low income women.

The purpose of this study was to develop and test an interactive computer-mediated smoking cessation program for inner-city women. A non-probability sample of 100 women who receive care at an inner-city community health center in Indianapolis participated in the usability study. Women completed the computer program in the clinic following baseline data collection. Next, participants completed a brief satisfaction instrument. Data on cognitive and behavioral outcomes of the program were obtained by telephone interview one week later. Satisfaction with the program was high (mean satisfaction score was 60.2 with 70 indicating highest possible satisfaction). Average time for completing the computer program was 13.6 minutes. Overall, 79% of the participants reported at least one behavioral change related to smoking. The results indicate that interactive computer technology may be useful for promoting smoking cessation in low-income women.

Adolescent↗

PubMed1994

Computer program for the analysis of mutational spectra: application to p53 mutations.

Mutations in the p53 oncogene are extremely common in human cancers, and environmental exposure to mutagenic agents may play a role in the frequency and nature of the mutations. Differences in the patterns of p53 mutations have been observed for different tumor types. It is not trivial to determine if the differences observed in two mutational spectra are statistically significant. To this end, we present a computer program for comparison of two mutational spectra. The program runs on IBM-compatible personal computers and is freely available. The input for the program is a text file containing the number and nature of mutations observed in the two spectra. The output of the program is a P value, which indicates the probability that the two spectra are drawn from the same population. To demonstrate the program, the mutational spectra of single base substitutions in the p53 gene are compared in (i) bladder cancers from smokers and non-smokers, (ii) small-cell lung cancers, non-small-cell lung cancers and colon cancers and (iii) hepatocellular carcinomas from high- and low-aflatoxin exposure groups. p53 mutations differ in several important aspects from a typical mutational spectra experiment, where a homogeneous population of cells is treated with a specific mutagen and mutations at a specific locus are recovered by phenotypic selection. The means by which p53 mutations are recognized is by the appearance of a cancer, and this phenotype is very complex and varied.

Base Composition↗

PubMed1998

Teaching the microscopic examination of urine sediment to second year medical students using the Urinalysis-Tutor computer program.

The microscopic examination of urine sediment is a common diagnostic tool taught to medical students, medical technologists, and others. The urine microscopic exam is difficult to teach because supervised instruction and textbook-based teaching suffer from numerous drawbacks. Here, we describe Urinalysis-Tutor, a computer program that uses digitized microscope images and computer-based teaching techniques to systematically teach the urine microscopic exam. In addition, we report the results of a 2-year study that evaluated the effectiveness of the program in 314 second year medical students who were required to use the program. The program contained two, 20-question exams. In the first year of the study (1996), one of the exams was chosen as the pretest and the other as the posttest; the pretest had to be completed before the students viewed the contents of the program, and the posttest was taken after finishing the tutorial. In 1997, the order of the two exams was reversed. In 1996, 159 students completed the study. The mean pretest score was 34% (SD, 14%), the mean posttest score was 71% (SD, 13%), and the improvement was significant (P <0.001, paired t-test). In 1997, 155 students participated. The mean pretest score was 41% (SD, 11%), the mean posttest score was 71% (SD, 13%), and the improvement was significant (P <0.001, paired t-test). The study shows that Urinalysis-Tutor helps medical students learn to interpret the microscopic appearance of urine sediment and that it is feasible to implement this tutorial in a medical school class.

Computer-Assisted Instruction↗

PubMed1989

Duplicates or singletons? An analysis of the need for replication in immunoassay and a computer program to calculate the distribution of outliers, error rate and the precision profile from assay duplicates.

The nature, frequency, statistics and methods of detection of both Gaussian and catastrophic errors in immunoassay are described. The method of sequential analysis is applied to the rates of catastrophic errors and is used to calculate the number of results which must be examined in order to achieve a stated confidence that the error rate is acceptable so that a rational decision on use of duplicate or singleton assay can be made. A simple computer program is described, which allows computation of the precision profile and an analysis of errors using accumulated data from duplicate assays. These methods have been applied to an enzyme amplification immunometric assay for thyroid-stimulating hormone (TSH) and an analysis is made of the errors detected in a sample of 1419 patient results.

Chemistry, Clinical↗

PubMed1995

Identification of the coding region of Saccharomyces cerevisiae chromosome VI using the computer program GenMark.

We searched the nucleotide sequence of budding yeast Saccharomyces cerevisiae chromosome VI (270 kb) for candidate coding regions, using the computer program GenMark. One hundred and twenty-nine putative genes were identified, which is almost the same as the number of ORFs on this chromosome. Nineteen new putative genes were identified through the GenMark analysis. Most large ORFs were also correctly identified (87% of the predicted putative genes identified by the GenMark (110 of 127) matched the reported ORFs). The new coding regions were mostly small but they were distinguished from the more than 2000 ORFs identified by Genetyx. GenMark did not predict 17 ORFs that were over 300 bp long. As these ORFs include known genes, their sequence context may differ somewhat from that of typical yeast genes. These analyses revealed the high potential of GenMark to identify putative genes from numerous short ORFs and will produce information on the likelihood of their being actual genes.

Base Sequence↗

PubMed1989

[A computer program for the drug dosage of patients with chronic kidney failure].

On the basis of the formula Mt = Mo.e-(Cl/Vd).t, a computer program was developed for estimating the maintenance drug dose in patients with chronic renal failure, depending on the creatinine clearance levels and the body mass. The hypothesis of the intact nephron and the presumption that in chronic renal failure the extrarenal clearance of the drugs does not change is considered a precondition. Any drug whose distribution volume and extrarenal clearance are known may be implicated in the program. The program may also help to determine the additional dose after hemodialysis, depending on the duration of the dialysis and the dialysis clearance of the drug.

Combined Modality Therapy↗