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PubMed2004

A simple computer program for calculating PSA recurrence in prostate cancer patients.

BACKGROUND: Prostate cancer is the most common tumor in men. The most commonly used diagnostic and tumor recurrence marker is Prostate Specific Antigen (PSA). After surgical removal or radiation treatment, PSA levels drop (PSA nadir) and subsequent elevated or increased PSA levels are indicative of recurrent disease (PSA recurrence). For clinical follow-up and local care PSA nadir and recurrence is often hand calculated for patients, which can result in the application of heterogeneous criteria. For large datasets of prostate cancer patients used in clinical studies PSA measurements are used as surrogate measures of disease progression. In these datasets a method to measure PSA recurrence is needed for the subsequent analysis of outcomes data and as such need to be applied in a uniform and reproducible manner. This method needs to be simple and reproducible, and based on known aspects of PSA biology. METHODS: We have created a simple Perl-based algorithm for the calculation of post-treatment PSA outcomes results based on the initial PSA and multiple PSA values obtained after treatment. The algorithm tracks the post-surgical PSA nadir and if present, subsequent PSA recurrence. Times to PSA recurrence or recurrence free intervals are supplied in months. RESULTS: Use of the algorithm is demonstrated with a sample dataset from prostate cancer patients. The results are compared with hand-annotated PSA recurrence analysis. The strengths and limitations are discussed. CONCLUSIONS: The use of this simple PSA algorithm allows for the standardized analysis of PSA recurrence in large datasets of patients who have undergone treatment for prostate cancer. The script is freely available, and easily modifiable for desired user parameters and improvements.

Algorithms↗
PubMed1990

Development and evaluation of a rapid, semi-automatic micro-method for CH50 estimation using a computer program.

Established methods for the estimation of serum complement are often unsatisfactory. Problems include complex mathematical and/or technical manipulations, lack of objectivity, and poor sensitivity. Here we present an assay that is rapid, sensitive, quantitative, simple and semi-automatic by using an 'ELISA' reader to estimate released haemoglobin. It compares very favourable with a more manual, old established method. We have used this new method to establish a normal range, investigate serum storage conditions, and demonstrate that the sensitised sheep red blood cells are suitable targets after overnight storage at 4 degrees C. Furthermore we confirm that serum from patients with systemic lupus erythematosus or Sjögren's syndrome frequently has reduced levels of CH50. Patients with rheumatoid arthritis, scleroderma, Bechet's disease or arteritis have a mean CH50 within the normal range.

Complement Hemolytic Activity Assay↗
PubMed1987

[Quality control of radioimmunoassay for TSH, LH, FSH, C-peptide, prolactin based on NIH-computer program].

As there has been no data available on the variation of RIA through a year, we assessed within kit and component of between assay variation of TSH, LH, FSH, C-peptide and PRL kit through a year (more than 12 sequential assays). The average of within kit variation was 6.9% (ranged from 4.7 to 9.8%) and that of component of between assay variation was 11.2% (ranged from 8.9 to 14.5%). These values were almost similar to those obtained for the within kit variation and component of between assay variation employing single lot of kit. These results warrant that quality of kits produced by manufacturers was homogeneous throughout the observation period.

C-Peptide↗
PubMed1999

New features and enhancements in the X-PLOR computer program.

This article describes new methods for X-ray crystallographic refinement and nuclear magnetic resonance (NMR) structure determination that are available in the recent release of the X-PLOR software, X-PLOR 98.0. The major new features of the X-PLOR 98.0 software are: (i) the introduction of maximum likelihood methods (Pannu and Read, Acta Crystallogr 1996;A52:659-668) for X-ray crystallographic refinement with structure factor amplitude, intensity and phase probability targets, (ii) the addition of the Andersen thermal coupling method for temperature control during simulated annealing refinements, (iii) a new utility function for converting reflection data in to the X-PLOR format, (iv) validated scripts and performance enhancements for structure determination from NMR distance restraints using torsion angle dynamics, (v) fast code for direct nuclear Oberhauser effect (NOE) refinement using matrix doubling and gaussian quadratures, (vi) methodologies for using ambiguous restraint information to perform automated iterative peak assignment and structure determination (Nilges et al., J Mol Biol 1997;269: 408-422). Additional developments in methodology for refining crystal structures from poor initial models include the implementation of a fast adaptive bulk solvent scattering correction and an energy minimization routine that makes use of second derivative information. Trial crystallographic refinements with an energy minimization protocol that includes these enhancements indicate significantly improved convergence. The quality of the resulting models appears comparable to models obtained from refinement protocols that incorporate torsion angle dynamics. Test applications of the new energy minimizer to NMR structure refinement with using NOE calculations also show improved convergence, leading to more optimized final models.

Crystallography, X-Ray↗