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.     

An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis

Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produce reliable and reproducible microarray expression data. Here we compare the use of RNA isolated from human archival tissues fixed in ethanol and formalin to frozen tissue in cDNA microarray experiments. Since an additional factor that can limit the utility of archival tissue is the often small quantities available, we also evaluate the use of the tyramide signal amplification method (TSA), which allows the use of small amounts of RNA. Detailed analysis indicates that TSA provides a consistent and reproducible signal amplification method for cDNA microarray analysis, across both arrays and the genes tested. Analysis of this method also highlights the importance of performing non-linear channel normalization and dye switching. Furthermore, archived, fixed specimens can perform well, but not surprisingly, produce more variable results than frozen tissues. Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling.     

Applications of a signal averager for neurophysiological investigations in clinical function laboratories using a general signal-processing unit

A general 'coherent signal averager' software package which can be run on a small laboratory computer is presented as an application of a new approach to medical instrumentation. The combination of the minicomputer, preprocessing hardware and the above-mentioned software yields a flexible multipurpose averaging system for electrophysiological signals. The possibilities of the system are discussed with reference to visual evoked potential measurements in a clinical function laboratory.     

A hypertext-like approach to navigating through the GCG sequence analysis package

Programs of the recently released Unix version of the GeneticsComputing Group (GCG) sequence analysis package can now be accessedvia a user-friendly hypertext-like navigation system, HYGCG.The resultant system organizes the diverse suite of programsinto logical groups, and provides a guide and explanation ofcommands. In addition, for users unfamiliar with the Unix operatingsystem, the program also provides a similar interface to commonlyused Unix commands. Options for personal customization and expansionto accommodate GCG extensions and other software are also provided.This system should be useful especially to the inexperiencedor infrequent user as context-sensitive on-line help is providedwithin this simple and consistent approach. Written in the Clanguage and using the curses and termcap libraries, the systemis easily portable to most Unix environments and has been madefreely available via anonymous file transfer protocol (FTP)through the Internet global computer network. No modificationof the GCG package is needed.     

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.     

Une methode de tri de fichiers pour des mini-et des micro-ordinateurs

The authors describe a new sorting method of files which belongs to the class of direct-addressing sorting methods. It makes use of a variant of the classical technique of ‘virtual memory’. It is particularly well suited to mini- and micro-computers which have a small core memory (32 K words, for example) and are fitted with a direct-access peripheral device, such as a disc unit. When the file to be sorted is medium-sized (some thousand records), the running of the program essentially occurs inside the core memory and consequently, the method becomes very fast. This is very important because most medical files handled in our laboratory are in this category. However, the method is also suitable for big computers and large files; its implementation is easy. It does not require any magnetic tape unit, and it seems to us to be one of the fastest methods available.     

Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization

This study describes novel algorithms for searching for most parsimonious trees. These algorithms are implemented as a parsimony computer program, PARSIGAL, which performs well even with difficult data sets. For high level search, PARSIGAL uses an evolutionary optimization algorithm, which feeds good tree candidates to a branch-swapping local search procedure. This study also describes an extremely fast method of recomputing state sets for binary characters (additive or nonadditive characters with two states), based on packing 32 characters into a single memory word and recomputing the tree simultaneously for all 32 characters using fast bitwise logical operations. The operational principles of PARSIGAL are quite different from those previously published for other parsimony computer programs. Hence it is conceivable that PARSIGAL may be able to locate islands of trees that are different from those that are easily located with existing parsimony computer programs.     

A computer program for Wiener filtering of evoked potential data.

We have developed a computer program for Wiener filtering of evoked potential data. The basic algorithm involves computation of the difference berween the power spectrum of the sweep sum and the sum of power spectra of individual sweeps. Power spectra are computed by means of the discrete Fourier transform. The program is now being run on a LSI-11 computer in a neurophysiology research laboratory to analyze somatic evoked potential data from monkeys.     

A gravimetric method for the measurement of total spontaneous activity in rats.

Currently available methods for the measurement of spontaneous activity of laboratory animals require expensive, specialized equipment and may not be suitable for use in low light conditions with nocturnal species. We developed a gravimetric method that uses common laboratory equipment to quantify the total spontaneous activity of rats and is suitable for use in the dark. The rat in its home cage is placed on a top-loading electronic balance interfaced to a computer. Movements are recorded by the balance as changes in weight and transmitted to the computer at 10 Hz. Data are analyzed on-line to derive the absolute value of the difference in weight between consecutive samples, and the one-second average of the absolute values is calculated. The averages are written to file for off-line analysis and summed over the desired observation period to provide a measure of total spontaneous activity. The results of in vitro experiments demonstrated that: 1) recorded weight changes were not influenced by position of the weight on the bottom of the cage, 2) values recorded from a series of weight changes were not significantly different from the calculated values, 3) the constantly decreasing force exerted by a swinging pendulum placed on the balance was accurately recorded, 4) the measurement of activity was not influenced by the evaporation of a fluid such as urine, and 5) the method can detect differences in the activity of sleeping and waking rats over a 10-min period, as well as during 4-hr intervals recorded during active (night-time) and inactive (daytime) periods. These results demonstrate that this method provides an inexpensive, accurate, and noninvasive method to quantitate the spontaneous activity of small animals.     

On-line analysis of neuromuscular bioelectric potentials

A computer system is presented which provides for on-line data capture and analysis of evoked end-plate potentials and action potentials, and on-line data capture with off-line analysis of spontaneously occurring miniature end-plate potentials at the end-plate region of the neuromuscular junction. Sampling of evoked waveforms begins after an adjustable delay following the stimulus. Spontaneously occurring waveforms are captured by 'freezing' the contents of a circular buffer. The software provides MENU selectable support functions including storage and retrieval of data and calculated parameters, analog and digital display of waveforms, data calibration and gain modification, data editing, file management, and hardcopy output. Calculated parameters of the waveform are optionally placed in a data base file by the analysis programs. The data base may be used for editing, arithmetic operations, and subsetting of variables as well as statistical analysis and plotting of any selected variables.     

Transient state kinetics tutorial using the kinetics simulation program, KINSIM.

This article provides an introduction to a computer tutorial on transient state kinetics. The tutorial uses our Macintosh version of the computer program, KINSIM, that calculates the time course of reactions. KINSIM is also available for other popular computers. This program allows even those investigators not mathematically inclined to evaluate the rate constants for the transitions between the intermediates in any reaction mechanism. These rate constants are one of the insights that are essential for understanding how biochemical processes work at the molecular level. The approach is applicable not only to enzyme reactions but also to any other type of process of interest to biophysicists, cell biologists, and molecular biologists in which concentrations change with time. In principle, the same methods could be used to characterize time-dependent, large-scale processes in ecology and evolution. Completion of the tutorial takes students 6-10 h. This investment is rewarded by a deep understanding of the principles of chemical kinetics and familiarity with the tools of kinetics simulation as an approach to solve everyday problems in the laboratory.     

Dendroscope: An interactive viewer for large phylogenetic trees

Background  

Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.     

The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations

Summary Restriction endonucleases and agarose gel electrophoresis have been used to demonstrate extensive nucleotide sequence diversity in mitochondrial DNA (mtDNA) within and between conspecific populations of rodents and other mammals. Cleavage of mtDNA samples with a relatively small number of endonucleases provides information concerning the phylogenetic relatedness of individual organisms which cannot now be readily obtained by any other type of molecular analysis. This information is qualitatively different from that available from the study of nuclear genes or gene products because the mitochondrial genome is inherited intact from the female parent and is not altered by recombination or meiotic segregation.The requirements for large tissue samples and laborious DNA purification procedures have imposed severe limitations on the kinds of population surveys in which this technique could be utilized. Here, we show that these difficulties can be overcome by using DNA-DNA hybridization to detect minute amounts of mtDNA in crude tissue fractions which can be more easily and rapidly prepared from very small amounts of tissue without the use of expensive and immobile laboratory equipment. The techniques are described in detail in an effort to make restriction analysis of mtDNA available to biologists who may be unfamiliar with current DNA technology.     

PC-based system for an objective quantification of manual movement disability for clinical and scientific purposes

In clinical management and research of movement disorders exact knowledge about the extent of motor impairment is essential. This paper presents a computer program which allows for an objective measurement of manual movement disability. The program was developed for standard hardware and can easily be used in a variety of clinical and research environments. The program runs on MS-DOS computers and uses a Microsoft computer mouse as the only input device. The temporal resolution is 100 Hz, the spatial resolution 400 dots per inch. The user may choose between standard test sets or he may design sets according to his individual needs from a pool of available protocols which includes tracking tasks, ballistic tasks, complex sequential tasks, and finger tapping. All tasks are implemented in a similar way in order to keep the test environment as consistent as possible for the patient. The patient must usually carry out movements which correspond to the movements of a target symbol on the computer screen. This entails the manipulation of a follower symbol, also visible on the computer screen, via the computer mouse. The program itself and the theoretical background of the protocols are described in the paper. Additionally, preliminary results from pilot experiments are presented.     

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.     

A minicomputer program for rapid graphical and statistical analysis of laboratory data

The utility of a FORTRAN program package, which enables the scientific investigator to make a rapid assessment of laboratory data is described. Data are submitted from the keyboard or specified disk files in the form of coordinate pairs. The program includes routines for plotting values as a series of X-Y pairs on the computer video monitor or for comparing the X and Y arrays via paired differences and Student's t-test. A least squares linear regression of plotted data may also be called. Data modification, curve fitting, and I/O are easily handled in either single pair or column format. Examples of both statistical and graphical data analysis are presented.     

Computer-assisted method for multi-exponential curve fitting for determining cerebral blood flow.

A computer program has been developed for use in determining cerebral blood flow using an inert radioactive gas. The basic algorithm involves the determination of multiple exponential coefficients from the complex concentration-time function. The exponential coefficients are determined by 'peeling' away slower exponentials complex function one at a time. The procedure involves the use of a small laboratory computer in the interactive graphics mode. The method is currently in use analyzing data in a cerebral vascular research laboratory.     

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

A wide range of methods are currently available for determining the dissociation constant between a protein and interacting small molecules. However, most of these require access to specialist equipment, and often require a degree of expertise to effectively establish reliable experiments and analyze data. Differential scanning fluorimetry (DSF) is being increasingly used as a robust method for initial screening of proteins for interacting small molecules, either for identifying physiological partners or for hit discovery. This technique has the advantage that it requires only a PCR machine suitable for quantitative PCR, and so suitable instrumentation is available in most institutions; an excellent range of protocols are already available; and there are strong precedents in the literature for multiple uses of the method. Past work has proposed several means of calculating dissociation constants from DSF data, but these are mathematically demanding. Here, we demonstrate a method for estimating dissociation constants from a moderate amount of DSF experimental data. These data can typically be collected and analyzed within a single day. We demonstrate how different models can be used to fit data collected from simple binding events, and where cooperative binding or independent binding sites are present. Finally, we present an example of data analysis in a case where standard models do not apply. These methods are illustrated with data collected on commercially available control proteins, and two proteins from our research program. Overall, our method provides a straightforward way for researchers to rapidly gain further insight into protein-ligand interactions using DSF.     

Evaluation of the effect of aqueous extract of Croton urucurana Baillon (Euphorbiaceae) on the hemorrhagic activity induced by the venom of Bothrops jararaca, using new techniques to quantify hemorrhagic activity in rat skin

Aqueous extracts of Croton urucurana (Sangra D'agua), a plant popularly considered a cicatrizant, were analyzed for anti-Bothrops jararaca venom activity. The plant extracts antagonized the hemorrhagic activity of the venom and proanthocyanidins were involved in this activity. Two new methods for the quantification of hemorrhagic activity evoked by bothropic venoms were employed. The first consists of graphic computer analysis of the hemorrhagic halo evoked in rats by dorsal intradermic administration of venom. The second method involves quantification of the hemoglobin present in the hemorrhagic halo. Based on the results, we suggest that these methods, easily implemented in the laboratory routine, allow for quantification of venom-induced hemorrhagic activity. In addition, this study demonstrates that the rich extracts of proanthocyanidins are powerful inhibitors of bothropic venom metalloproteinases.     

Membrane probability profile construction based on amino acids sequences multiple alignment

Prediction of membrane segments in sequences of membrane proteins is well known and important problem. Accuracy of the solution of this problem by methods that don't use homology search in additional data bank can be improved. There is a lack of testing data in this area because of small amount of real structures of membrane proteins. In this work, we create a testing set of structural alignments of membrane proteins, in which positioning of the membrane segments reflects agreement of known 3D-structures of proteins in the alignment. We propose a method for predicting position of membrane segments in multiple alignment based on forward-backward algorithm from HMM theory. This method not only allows to predict positions of membrane segments but also forms probability membrane profile, which can be used in multiple alignment methods that take into account secondary structure information about sequences. Method is implemented in computer program available on the World-Wide Web site http://bioinf.fbb.msu.ru/fwdbck/. Proposed method provides results better than MEMSAT method, which is nearly only tool for prediction of membrane segments in multiple alignments without additional homology search.