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Biomedical subjects

R Harr

Publications and source records attributed to R Harr.

31 records · Page 2Linked to original sources
PubMed1986

GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library.

We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+

Amino Acid Sequence↗
PubMed1983

Search algorithm for pattern match analysis of nucleic acid sequences.

A new type of search algorithm to find biological information inherited in nucleic acid sequences was developed. The algorithm is of pattern match type and is based on the fact that genetic information often is a function of a predictable statistical occurrence of the four bases within parts of the sequence. The search algorithm compares the known statistical pattern of bases in e.g. a promoter, with an unknown sequence and calculates the statistical significance of the match at all positions in the unknown sequence. The program was tested on 54 published prokaryotic promoters. 44 or 49 could be found with 1 or 4 false answers, respectively. The program was also used on plasmid pBR322. All promoters functioning in an in vitro transcription system were found (tet, anti-tet, p4, bla and ori) except the so called p5 promoter. A search for donor and acceptor sites was performed in a human HLA genomic sequence that contains six introns. Five of the possible six donor and acceptor sites were found.

Base Sequence↗
PubMed1982

Two-dimensional graphic analysis of DNA sequence homologies.

We describe a computer program designed to facilitate the pattern matching analysis of homologies between DNA sequences. It takes advantage of a two-dimensional plot in order to simplify the evaluation of significant structures inherited in the sequences. The program can be divided into three parts, i) algorithm for search of homologies, ii) two-dimensional graphic display of the result, iii) further graphic treatment to enhance significant structures. The power of the graphic display is presented by the following application of the program. We conducted a search for direct repeats in the mouse immunoglobulin kappa-chain genes. Both the five J DNA sequences and other shorter repeats were found. We also found a longer stretch of homology that could indicate the presence of duplicated DNA in the J4, J5 region.

Base Sequence↗
PubMedDate not supplied

Measurement of adrenal corticosteroids by high-performance liquid chromatography.

OBJECTIVE: To develop a high-performance liquid chromatography (HPLC) method for simultaneous measurement of adrenal corticosteroids important for the diagnosis of congenital adrenal hyperplasia. DESIGN: Blind comparison using convenience samples. SETTING: Research laboratory at the Department of Medical Technology, Bowling Green State University. PATIENTS: Referred samples for cortisol, 11-deoxycortisol (S), and 17-hydroxyprogesterone (OHP). Stimulation condition unknown. INTERVENTION: Venous blood collected, processed to serum, and frozen. Adrenal steroids measured by radioimmunoassay (RIA) and by HPLC. MAIN OUTCOME MEASURES: Linearity, analytic sensitivity, accuracy, and precision were evaluated using recovery, coefficient of variation (c.v.), correlation coefficient (r), Student's t test, F test, and linear regression. RESULTS: Calibration curves were linear to at least 50 mumol/L, and the low-end sensitivity was 10 nmol/L. Analytic recovery ranged from 89.8% to 103.9%. The CV was below 7.5% (n = 10) for all three steroids. Comparison to RIA yielded r values of 0.909 (n = 25), 0.932 (n = 10), and 0.983 (n = 10) for cortisol, S, and OHP, respectively. Student's t-test results were 1.13 (p = 0.27), 0.10 (p = 0.93), and 0.48 (p = 0.64) for cortisol, S, and OHP, respectively. F-test results were 1.14 (p = 0.75), 1.37 (p = 0.66), 2.39 (p = 0.21) for cortisol, S, and OHP, respectively. Results for cortisol showed a negative bias of 97.0 nmol/L (3 mug/dL). Linear regression analysis revealed proportional errors of -15.0% -7.0%, and +9.0%, for cortisol, S, and OHP, respectively. CONCLUSION: (ABSTRACT TRUNCATED AT 250 WORDS)

Adrenal Cortex Hormones↗
PubMedDate not supplied

Simultaneous measurement of VMA and HVA in 24-hour urine samples.

A simple method is described for the simultaneous measurement of vanillylmandelic acid (VMA) and homovanillic acid (HVA) in 24-hour urine samples based upon isocratic high-performance liquid chromatography with electrochemical detection (HPLC-ECD). VMA was measured using VMA-SKREEN kits (Biochemical Diagnostics), a microcolumn diazo method and HPLC-ECD test method. HVA was measured using Bio-Rad HVA HPLC reagent kits (Bio-Rad Laboratories) and the test method. No significant statistical difference was found in mean or variance when this method was compared with the micro-column diazo method for VMA and HPLC-ECD for HVA using the commercial anion-exchange kit. The linear regression equation for VMA was ŷ = 0.92 x + 0.21, and for HVA was ŷ = 1.10 x + 0.06. The Pearson correlation coefficient for VMA was r = 0.896 and for HVA was r = 0.996. This method yields results for 24-hour urinary VMA and HVA that compare well with established commercial methods.

Chromatography, High Pressure Liquid↗
PubMedDate not supplied

Characterization of spermatozoa by planar morphometry.

OBJECTIVE: To define the morphometric characteristics of normal sperm heads, and compare them to sperm head measurements used to define normal morphology using strict criteria. DESIGN: Computerized image analysis of selected normal and abnormal seminal fluid specimens collected for routine male fertility studies. SETTING: Research laboratory at the Department of Medical Technology, Bowling Green State University, Bowling Green, OH. PATIENTS: Sixty adult male patients who submitted semen samples for routine analysis. Fifty percent had normal seminal fluid analysis results. The remaining 50% demonstrated abnormal sperm morphology. CRITERION STANDARD: Microscopic evaluation of sperm head morphology. Sperm fitting the criteria of normal as defined by WHO (1987 and 1992) and Kruger (1988) were classified as normal. Sperm with a post nuclear area of less than 40% were classified as acrosomal deficient. MAIN OUTCOME MEASURES: Measurements made from stained seminal fluid smears included sperm head area, perimeter, acrosomal area, percent acrosome, Ferret's diameters, aspect ratio, shape factor, and specific length. Normal sperm heads (NL group) were compared to sperm heads demonstrating an acrosomal deficiency (AD group) for statistically significant differences using multivariate analysis of variance (MANOVA) and analysis of variance (ANOVA). Stepwise discriminant analysis was used to remove duplicating variables. Discriminant analysis was used to classify the sperm heads into NL and AD groups. Receiver-operating characteristic (ROC) curves were applied to the 2 most influential variables in order to identify a cutoff that best distinguishes normal from acrosomal deficient sperm heads. RESULTS: MANOVA and ANOVA showed all 10 variables to be statistically significant (p < .002). Discriminant analysis correctly assigned 98.7% of the normal sperm heads to the NL group and 99.0% of sperm with acrosomal deficiency to the AD group. The percent acrosome and acrosomal area were determined to be the 2 most influential variables. ROC analysis identified a cutoff of 3.6 mu2 for acrosomal area as having the highest sensitivity and specificity (99.7% and 88.0%, respectively). Similarly, a cutoff of 44% for percent acrosome gave a sensitivity of 92.3% and a specificity of 88.7%. The coefficient of variation (CV) for each of the 10 variables determined from 20 day-to-day replicates of a normal semen smear ranged from 2.6% to 8.4%. CONCLUSION: Computerized image analysis is able to define a reference range for sperm head area, percent acrosome, and acrosomal area that may be used to differentiate normal form abnormal sperm heads. Maximum and minimum Ferret's diameters measure sperm head length and width, respectively. Mean maximum Ferret's diameter, minimum Ferret's diameter, and maximum-minimum Ferret's diameter ratio correspond closely to the WHO (1987) midpoint for normal sperm head length, width, and length-width ratio. The average percent acrosome of normal sperm heads determined by morphometry closely correlate to the WHO (1992) and Kruger (1988) midpoints for percent acrosome.

Acrosome↗