Validation of a computer software program for statistical analysis of accelerated stability studies on biological standards.

Long-term stability is an essential requirement for biological measurement standards and it has been evaluated by applying the Arrhenius model to the data obtained from accelerated thermostability studies. A computer program DEGTEST suited to a mainframe computer has been used for evaluating the stability of biological standards for more than a decade. This paper describes the validation of a computer program executable in a personal computer Microsoft Windows XP environment for the analysis of accelerated thermostability study data.     

Computer Program Designed to Follow Fluctuations in Microbial Populations and Its Application in a Study of Chesapeake Bay Microflora

A computer program has been developed which performs cluster analysis of microorganisms using methods of numerical taxonomy. The program is designed to group related strains, identify the groups by reference to known strains, and calculate a hypothetical median organism (HMO) for each group. The HMO serves to condense taxonomic information and provides a tag for each strain cluster. Every strain in a group is compared with the HMO established for that group. A representative strain for the group is obtained by selection of the strain showing highest similarity to the HMO. New data sets can be compared with data sets of previous analyses. Hence, the occurrence of the same taxonomic groups within separate data sets can be determined. Quantitative or qualitative differences in distribution of taxonomic groups within or between data sets can be measured. The output from the computer is a graphical display, using an on-line plotter; thus, the investigator is provided with visual comparison of data sets. Results obtained from a study applying the computer program in an analysis of taxonomic data obtained for 43 bacterial strains isolated from Chesapeake Bay indicate the usefulness of this method of taxonomic analysis in microbial ecology.     

A nonlinear regression program for small computers

A BASIC computer program for performing weighted nonlinear regression is described and a listing of the program is given. The program, which is small and simple to use, has been designed to be run by users with little knowledge of mathematics or computers. Robust methods of analysis are described which may be applied to data in which experimental errors are not normally distributed, and the program incorporates one such method. It is shown that the program is useful for the analysis of data conforming to the Michaelis-Menten equation, a single exponential, and to binding equations, and other applications are discussed.     

A risk signature-based on metastasis-associated genes to predict survival of patients with osteosarcoma

Osteosarcoma (OS) is the most common primary solid malignant bone tumor, and its metastasis is a prominent cause of high mortality in patients. In this study, a prognosis risk signature was constructed based on metastasis-associated genes. Four microarrays datasets with clinical information were downloaded from Gene Expression Omnibus, and 256 metastasis-associated genes were identified by limma package. Further, a protein-protein interaction network was constructed, and survival analysis was performed using data from the Therapeutically Applicable Research to Generate Effective Treatments data matrix, identifying 19 genes correlated with prognosis. Six genes were selected by the least absolute shrinkage and selection operator regression for multivariate cox analysis. Finally, a three-gene (MYC, CPE, and LY86) risk signature was constructed, and datasets GSE21257 and GSE16091 were used to validate the prediction efficiency of the signature. The survival times of low- and high-risk groups were significantly different in the training set and validation set. Additionally, gene set enrichment analysis revealed that the genes in the signature may affect the cell cycle, gap junctions, and interleukin-6 production. Therefore, the three-gene survival risk signature could potentially predict the prognosis of patients with OS. Further, proteins encoded by CPE and LY86 may provide novel insights into the prediction of OS prognosis and therapeutic targets.     

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.     

Computer-assisted analysis of adenosine triphosphate data.

A computer program has been written to assist in the analysis of adenosine 5'-triphosphate data. The program is designed to calculate a dilution curve and to correct sample and adenosine 5'-triphosphate standard data for background and dilution effects. In addition, basic statistical parameters and estimates of biomass carbon are also calculated for each group of samples and printed in a convenient format. The versatility of the program to analyze data from both qauatic and terrestrial samples is noted as well as its potential use with various types of instrumentation and extraction techniques.     

Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and beta-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and beta-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and beta-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the beta-tubulin region. The results indicate that third codon positions in beta-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in beta-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the beta-tubulin gene appears less useful.     

A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.     

COMAP: a comigrating analysis program for estimating the relationship of adenoviruses on the genome level.

The computer program COMAP is described that enables one to evaluate the relationship among adenovirus 6 strains by comigration analysis with regard to the genome. The required data were obtained by restriction analysis with several enzymes. The program is also important for identifying further adenovirus strains by DNA restriction analysis and to compare new restriction fragment patterns with stored data of known adenovirus strains. We believe that in this manner the DNA restriction analysis will become a valuable diagnostic procedure.     

Multilocus linkage analysis in humans: detection of linkage and estimation of recombination.

Multilocus linkage analysis is investigated from the viewpoint of the efficiency of recombination estimates under different strategies for detecting linkage and determining gene order within a linkage group. We consider the appropriateness of assuming no interference with data available in human genetic studies. Examples are given to show the significance of multilocus analysis in humans. A computer program package, LINKAGE, for multilocus linkage analysis is described.     

A computer program for characterizing root system branching patterns

A computer program is presented which measures the length, branching patterns and distribution of link length within a root system. The program skeletonizes digitized images of root systems, loads these images into a binary tree data structure and uses this data structure to characterize the root systems. Measurements of the root length and topological parameters of root systems of Senecio vulgaris made by hand and by computer program were linearly related, with r² values greater than 0.99 in all cases.     

Application of microcomputers to the interpretation of high-resolution nuclear magnetic resonance spectra of asparagine-linked oligosaccharides: evaluation of high-mannose structures

A microcomputer program for determining primary oligosaccharide structures by high-resolution nuclear magnetic resonance is reported. The program uses the data base obtained from spectra of model compounds reported in the literature. A number of high-mannose-type asparagine-linked glycopeptide spectra containing tabulated chemical shifts measured at room temperature were tested to determine the ability of the computer to correctly assign carbohydrate units into a complete structure. High-mannose structures ranging from five to nine oligomannosyl units were completely and unambiguously analyzed to give complete structural assignments. The computer program will also resolve glycopeptide mixtures. The method provides investigators with a useful tool for accurately evaluating nuclear magnetic resonance spectra and should greatly facilitate the complicated and time-consuming evaluation of microheterogeneity in samples commonly isolated from biological systems.     

Computer management of oligonucleotide synthesis on cellulose filters.

A computer program, OLIGO, is described which was designed to manage projects involving the synthesis of large numbers of oligonucleotide fragments using cellulose discs as immobilizing support. The program performs the functions of data entry, verification, analysis and modification; the sorting of filters before each step and project status updating after each reaction step; output of the project status at any point and storage of the finalized project data in a permanent reference file.     

Programming for the DNA analysis of FCM data on an IBM microcomputer

The analysis of data generated on a flow cytometer (FCM) is often performed on a computer obtained especially for dedicated use with the flow cytometer. This computer component can be expensive and also presents the FCM user with the added burden of mastering specialized programming language or of accepting the secret analytical processes of protected proprietary program routines. We believe that the evolution of more accurate and efficient FCM analyses that have the power to consider complex signal distributions can be assisted by the availability of analysis programs written in languages common to many users. DNA analysis routines written for a relatively inexpensive microcomputer (IBM PC/XT) in Basic and Pascal are described here. The routines can automatically process multiple FCM data files and can provide high-resolution graphic hardcopy. A foreground/background utilization is also described that allows the computer to be available for other uses in the laboratory.     

DIODA: delineation and feature extraction of microscopical objects.

A computer program is described for delineation and measurement of microscopical objects, such as cells and chromosomes, which may have been scanned using absorbance, fluorescence or reflectance microscopy. The quality of the object delineation is optimized through the controur ratio, which is simply computed from the object contour. Geometrical features, like the perimeter and area are computed. A new definition is introduced for the background region, especially suited for the analysis of closely packed objects. This definition is based upon a comparison between total staining material content values resulting from a variety of methods and circumstances. The program is principally intended for use in the on-line real-time environment of a small laboratory computer, but may be used off-line as well. It has facilities for displaying the results and the process by which they are produced. A program module is described for displaying scan data on a bilevel display using an adaptation of the sigma-delta method.     

The revised edition of a computerized plankton counter for plankton,periphyton and sediment diatom analyses

A revised computer counting program is presented with faster processing and more efficient features to enhance counting precision. The program is now capable of counting epilithic communities and sediment samples for diatom analysis. This version (2.3) is available for APPLE, IBM, TANDY-RADIO SHACK, and HYPERION systems using standard Basic commands. New improvements include, density and biovolume calculations, a Chi square transect test for randomness, D'Agostino's test for a normal taxa distribution and a three file output with raw and processed data.     

Identification of psychrotrophic pseudomonads from goats' milk by computer-assisted analysis of carbon source assimilation data

The results of carbon source assimilation tests on a group of psychrotrophic pseudomonas were compared with published data for established Pseudomonas taxa, using computer-assisted numerical taxonomic analysis and a modified diagnostic computer program. Several phenons were not grouped at the biovar level by numerical taxonomic analysis. Identification of strains by the diagnostic program revealed heterogeneity among those in the unassigned phenons, and supported a continuum concept among the fluorescent pseudomonads.     

Identification of psychrotrophic pseudomonads from goats'milk by computer-assisted analysis of carbon source assimilation data

The results of carbon source assimilation tests on a group of psychrotrophic pseudomonas were compared with published data for established Pseudomonas taxa, using computer-assisted numerical taxonomic analysis and a modified diagnostic computer program. Several phenons were not grouped at the biovar level by numerical taxonomic analysis. Identification of strains by the diagnostic program revealed heterogeneity among those in the unassigned phenons, and supported a continuum concept among the fluorescent pseudomonads.     

An application of multivariate ratio methods for the analysis of a longitudinal clinical trial with missing data.

This paper presents an analysis of a longitudinal multi-center clinical trial with missing data. It illustrates the application, the appropriateness, and the limitations of a straightforward ratio estimation procedure for dealing with multivariate situations in which missing data occur at random and with small probability. The parameter estimates are computed via matrix operators such as those used for the generalized least squares analysis of catetorical data. Thus, the estimates may be conveniently analyzed by asymptotic regression methods within the same computer program which computes the estimates, provided that the sample size is sufficiently computer program which computes the estimates, provided that the sample size is sufficiently large.