Microcomputer package for statistical analysis of microbial populations

We have developed a Pascal system to compare microbial populationsfrom different ecological sites using microcomputers. The valuescalculated are: the coverage value and its standard error, theminimum similarity and the geometric similarity between twobiological samples, and the Lambda test consisting of calculatingthe ratio of the mean similarity between two subsets by themean similarity within subsets. This system is written for AppleII, IBM or compatible computers, but it can work for any computerwhich can use CP/M, if the programs are recompiled for sucha system. Received on December 30, 1987; accepted on June 29, 1987     

A general purpose computer analysis system for chromatographic data

A manual integration system for the analysis of chromatographicdata is described. The analog output produced by an HPLC absorbancemonitor is passed to a non-inverting signal amplifier. Thisamplified signal is sent to an IBM PC where an analog to digitalconverter is used to digitize the data. A set of six computerprograms which collect, store and analyze these data are presented.This system was used to analyze the nucleotide content of theanaerobic organism Clostridium aceto-butylicum by strong anion-exchangeHPLC. Received on May 26, 1987; accepted on November 15, 1987     

Turbo Tree: a fast algorithm for minimal trees

A branch and bound algorithm is described for searching rapidlyfor minimal length trees from biological data. The algorithmadds characters one at a time, rather than adding taxa, as inprevious branch and bound methods. The algorithm has been programmedand is available from the authors. A worked example is givenwith 33 characters and 15 taxa. About 8 x 10¹² binary treesare possible with 15 taxa but the branch and bound program findsthe minimal tree in <5 min on an IBM PC. Received on January 15, 1987; accepted on February 23, 1987     

The mechanism of peptide-binding specificity of IAP BIR domains

We describe the peptide-binding specificity of the baculoviral IAP repeat (BIR) domains of the human inhibitor of apoptosis (IAP) proteins, X-linked IAP, cellular IAP1 and neuronal apoptosis inhibitory protein (NAIP). Synthetic peptide libraries were used to profile each domain, and we distinguish two types of binding specificity, which we refer to as type II and type III BIR domains. Both types have a dominant selectivity for Ala in the first position of the four N-terminal residues of the peptide ligands, which constitute a core recognition motif. Our analysis allows us to define the signature of type III BIRs that demonstrate a preference for Pro in the third residue of the ligand, resembling the classic IAP-binding motif (IBM). The signature of the type II BIRs was similar to type III, but with a striking absence of specificity for Pro in the third position, suggesting that the definition of an IBM must be modified depending on the type of BIR in question. These findings explain how subtle changes in the peptide-binding groove of IAP BIR domains can significantly alter the target protein selectivity. Our analysis allows for prediction of BIR domain protein-binding preferences, provides a context for understanding the mechanism of peptide selection and heightens our knowledge of the specificity of IAP antagonists that are being developed as cancer therapeutics.     

A secondary and tertiary structure editor for nucleic acids

A major difficulty in the evaluation of secondary and tertiarystructures of nucleic acids is the lack of convenient methodsfor their construction and representation. As a first step ina study of the symbolic representation of biopolymers, we reportthe development of a structure editor written in Pascal, permittingmodel construction on the screen of a personal computer. Theprogram calculates energies for helical regions, allows user-definedhelices and displays the secondary structure of a nucleic acidbased on a user-selected set of helices. Screen and printeroutputs can be in the form of a backbone or the letters of theprimary sequence. The molecule can then be displayed in a formatwhich simulates its three-dimensional structure. Using appropriateglasses, the molecule can be viewed on the screen in three dimensions.Other options include the manipulation of helices and single-strandedregions which results in changes in the spatial relationshipbetween different regions of the molecule. The editor requiresan IBM or compatible PC, 640 kbyte memory and a medium or highresolution graphics card. Received on September 19, 1987; accepted on November 15, 1987     

A fully continuous individual-based model of tumor cell evolution

The aim of this work is to develop and study a fully continuous individual-based model (IBM) for cancer tumor invasion into a spatial environment of surrounding tissue. The IBM improves previous spatially discrete models, because it is continuous in all variables (including spatial variables), and thus not constrained to lattice frameworks. The IBM includes four types of individual elements: tumor cells, extracellular macromolecules (MM), a matrix degradative enzyme (MDE), and oxygen. The algorithm underlying the IBM is based on the dynamic interaction of these four elements in the spatial environment, with special consideration of mutation phenotypes. A set of stochastic differential equations is formulated to describe the evolution of the IBM in an equivalent way. The IBM is scaled up to a system of partial differential equations (PDE) representing the limiting behavior of the IBM as the number of cells and molecules approaches infinity. Both models (IBM and PDE) are numerically simulated with two kinds of initial conditions: homogeneous MM distribution and heterogeneous MM distribution. With both kinds of initial MM distributions spatial fingering patterns appear in the tumor growth. The output of both simulations is quite similar.     

Biological applications of the SAS system: an overview

The SAS system provides biologists with a flexible, easy touse software package for data analysis. Through a combinationof data management tools, a wide variety of pre-programmed proceduresfor sorting, graphing, and statistical analysis and a sophisticatedprogramming language, SAS software can perform all analyticalneeds for most problems. The recent availability of SAS softwareon mainframes other than IBM, and more recently on the microcomputer,means that most scientists can have access to the software.In this review we discuss the structure of the SAS languageand demonstrate its power in the analysis of biological problems.Although to a lesser extent now than originally, the SAS systemis statistically oriented and a working knowledge of statisticsis recommended before using its statistical capabilities. However,all biologists will find its data management and summarizationcapabilities very useful. Received on September 9, 1987; accepted on September 17, 1987     

Kinetic,isotherm and thermodynamic investigations on adsorption of trace elements and pigments from soybean oil using high voltage electric field-assisted bleaching: A comparative study

In this study, the amounts of trace elements (Fe (II) and Cu (II)) and pigments (chlorophyll and carotenoid) in soybean oil were evaluated under high voltage electric field (HVEF) bleaching method at different voltage (10 and 20 kV), temperature (35–65 °C), time (0−30 min) and clay percentage (0.5–2 %) and then were compared to the industrial bleaching method (IBM). The kinetic data of ions and pigments adsorbed on activated bentonite clay under IBM and HVEF at two voltages of 10 and 20 kV followed the mechanism of the pseudo-first-order model (PFOM). The carotenoid and chlorophyll equilibrium data followed a Freundlich isotherm type model, which demonstrated multilayer adsorption under HVEF. The thermodynamic parameters (ΔG°, ΔH°, and ΔS°) displayed that the adsorption of trace metal ions and pigments on bentonite clay under IBM and HVEF were feasible, endothermic and spontaneous between 35 and 65 °C. The results indicated that the HVEF, especially at higher voltage, has a high remarkable capability to remove metal ions and pigments from soybean oil than the IBM. The highest removal capacity for metal and pigments of soybean oil bleaching were obtained in the order of HVEF-20 kV > HVEF-10 kV > IBM.     

Programs for evaluating and characterising bacterial taxonomic data

Three programs are described for evaluating and characterisingdata collected during numerical taxonomic studies of bacteria.The program VARIANCE compares replicate cultures and evaluatesthe reproducibility of each character. Also it identifies thosecharacters that should be excluded from subsequent taxonomicanalysis because of their poor reproducibility. GPROPS summarisesthe properties of clusters of strains that have been definedfrom a cluster analysis, it can produce a probabilistic identificationmatrix and compares each strain within a cluster with the HypotheticalMean Organism (HMO) of that cluster. OVCLUST is an implementationof the program described by Sneath (1979) which calculates overlapstatistics between major clusters. These programs are designedto complement the CLUSTAN package (Wishart, 1982) which is oftenused for cluster analysis of bacterial taxonomic data. The programswere written in FORTRAN 77 and implemented on an IBM PC usingMS–DOS. Received on November 13, 1986; accepted on January 8, 1987     

Computer aided design of pellets for fixed-bed reactors performing Michaelis--Menten reactions

The problem of designing the pellet characteristics for existingfixed-bed reactors has been studied. The reactor is assumedto be a unidimensional, plug-flow, heterogeneous type. Threeparticle shapes, two intraparticle mass transfer mechanisms,two lands of film resistance to mass transfer and two poisoningpatterns have been considered. An economic balance to both productmarket price and pellet market cost was taken into account.An interactive program (HIMER) containing all these contributionswas thus developed, enabling the investigator to follow thereactor performance along the flow coordinate. Received on March 26, 1987; accepted on June 25, 1987     

Restriction map construction using a 'complete sentences compatibility' algorithm

We have developed a new algorithm ‘Complete sentencescompatibility’ (CSC) which uses single and double digestionfragments to rapidly determine restriction maps of circularDNA. From possible combinations of fragments of each simpledigestion, which we call ‘sentences of decomposition’,we construct a restriction map which combines the sentenceswhile taking into account compatibility rules. The algorithmcan also deal with experimental errors of fragment weight andcan suggest solutions that account for non-readable bands (fragmentsof zero length or multiple bands) on the gel. Because experimentsusing pairs of restrictive enzymes often result in multiplesolutions, a complementary algorithm tries to reduce the numberof proposed solutions by establishing consensus maps. The restrictionmap construction algorithm was tested on real cases, some containingmore than fifteen fragments. Execution times range from 1 –10 s on an IBM PC compatible microcomputer. Received on July 21, 1987; accepted on December 31, 1987     

Scheduling parallel machines with major and minor setup times

This article discusses the problem of scheduling a large set of parts on an FMS so as to minimize the total completion time. Here, the FMS consists of a set of parallel identical machines. Setup time is incurred whenever a machine switches from one type of part to another. The setup time may be large or small depending on whether or not the two part types belong to the same family. This article describes a fast heuristic for this scheduling problem and derives a lower bound on the optimal solution. In computational tests using random data and data from an IBM card test line, the heuristic archieves nearly optimal schedules.     

Detection and quantification of microorganisms in a heterogeneous foodstuff by image analysis

A relatively inexpensive image analysis system has been developedto semi-automate the detection and quantification of microbialgrowth in sections of food. A system based on an IBM PC compatible,with a frame store card, was programmed to scan Gram-stainedsections using a motorized stage. Each field of view was thresholdedafter subtraction of a background image and the area betweentwo thresholds measured. In the food studied it was found that,by using a size limit, it was possible to reduce the numberof fields that needed to be examined by a microscopist to 3%of those scanned. Visual examination was still required to distinguishbacterial cells from other stained objects which occasionallyoccur. Received on September 8, 1987; accepted on January 2, 1988     

将一株原红霉素链霉菌转入拟无枝菌酸菌属的分类学研究

对保藏的红霉素链霉菌AS4.894、AS4.198的化学分类研究表明,它们的胞壁类型为IV/A型,不属于胞壁为Ⅱ型的链霉菌属。菌株AS4.198与已由Labeda(1987)转入糖多孢菌属(Saccharopolyspora),定名为Saccharopolyspora erythreus的菌株相似;菌株AS4.894虽然胞壁型与糖多孢菌相似,但磷酸类脂为PⅡ型,应转入拟无枝菌酸菌属(Amycolatopsis Lechevalier,1986)。通过与红霉素糖多孢菌(Saccharopolyspora erythreus)和白色拟无枝菌酸菌(Amycolatopsis alba,A83850~T)进行比较,菌株AS4.894的生长Ph范围广泛,耐盐和耐50℃高温,DNA G+C mol％高,区别于拟无枝菌酸菌属中的任何已知种,而建议命名为新种——红霉素拟无枝菌酸菌(Amycolatopsis erythreus comb.nov.)。     

A software system to record and analyze digitized cell images

This paper describes basic software for digitization and processing of microscopic cell images used at the Department of Clinical Cytology at Uppsala University Hospital. A family of programs running on a PDP-8 minicomputer which is connected to a Leitz Orthoplan microscope with two image scanners, one diode-array scanner and a moving-stage photometer, is used for data collection. The digitized image data is converted by converted by conversion program to IBM compatible format. The data structures for image processing and statistical evaluation on the IBM system are also described. Finally, some experiences from the use of the software in cytology automation are discussed.     

Bayesian state-space modeling of metapopulation dynamics in the Glanville fritillary butterfly

The complexity of mathematical models of ecological dynamics varies greatly, and it is often difficult to judge what would be the optimal level of complexity in a particular case. Here we compare the parameter estimates, model fits, and predictive abilities of two models of metapopulation dynamics: a detailed individual-based model (IBM) and a population-based stochastic patch occupancy model (SPOM) derived from the IBM. The two models were fitted to a 17-year time series of data for the Glanville fritillary butterfly (Melitaea cinxia) inhabiting a network of 72 small meadows. The data consisted of biannual counts of larval groups (IBM) and the annual presence or absence of local populations (SPOM). The models were fitted using a Bayesian state-space approach with a hierarchical random effect structure to account for observational, demographic, and environmental stochasticities. The detection probability of larval groups (IBM) and the probability of false zeros of local populations (SPOM) in the observation models were simultaneously estimated from the time-series data and independent control data. Prior distributions for dispersal parameters were obtained from a separate analysis of mark–recapture data. Both models fitted the data about equally, but the results were more precise for the IBM than for the SPOM. The two models yielded similar estimates for a random effect parameter describing habitat quality in each patch, which were correlated with independent empirical measures of habitat quality. The modeling results showed that variation in habitat quality influenced patch occupancy more through the effects on movement behavior at patch edges than on carrying capacity, whereas the latter influenced the mean population size in occupied patches. The IBM and the SPOM explained 63% and 45%, respectively, of the observed variation in the fraction of occupied habitat area among 75 independent patch networks not used in parameter estimation. We conclude that, while carefully constructed, detailed models can have better predictive ability than simple models, this advantage comes with the cost of greatly increased data requirements and computational challenges. Our results illustrate how complex models can be helpful in facilitating the construction of effective simpler models.     

The STRESS program: A computer program for the analysis of stresses in long bones

A computer program was developed to compute torsional and bending stresses in long bones. The input format for the program is designed to be as convenient to the user as possible, allowing him to transmit to the program only as many points as he feels are required to describe the cross-sectional geometry. The program permits the user to specify by which method torsional stresses are to be computed, what type of stresses are to be computed, and to what accuracy the results are desired. Computation times are of the order of 5 sec or less (on an IBM 360), making use of the program more economical than manual computations.     

Sequence similarity (‘Homology’) searching for molecular biologists

Major types of sequence similarity searching (often, and incorrectly, called ‘homology’ searching) are reviewed and examples of each are presented. The features and limitations of each type of program, and individual implementations of each type are discussed. Two pairs of sequences are used as examples to show how implementations of each type differ in their results and their presentation. Both local and global alignment programs are examined, and the programs reviewed run on many different types of computer architectures, from laboratory computers such as the IBM PC, minicomputers such as the VAX, to large mainframe computers such as DEC-10/20 series.     

Modeling dengue outbreaks

We introduce a dengue model (SEIR) where the human individuals are treated on an individual basis (IBM) while the mosquito population, produced by an independent model, is treated by compartments (SEI). We study the spread of epidemics by the sole action of the mosquito. Exponential, deterministic and experimental distributions for the (human) exposed period are considered in two weather scenarios, one corresponding to temperate climate and the other to tropical climate. Virus circulation, final epidemic size and duration of outbreaks are considered showing that the results present little sensitivity to the statistics followed by the exposed period provided the median of the distributions are in coincidence. Only the time between an introduced (imported) case and the appearance of the first symptomatic secondary case is sensitive to this distribution. We finally show that the IBM model introduced is precisely a realization of a compartmental model, and that at least in this case, the choice between compartmental models or IBM is only a matter of convenience.     

Inclusion Body Myositis: A View from the <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> Muscle

Inclusion body myositis (IBM) is the most common myopathy in people over 50 years of age. It involves an inflammatory process that, paradoxically, does not respond to anti-inflammatory drugs. A key feature of IBM is the presence of amyloid-β-peptide aggregates called amyloid deposits, which are also characteristic of Alzheimer’s disease. The use of animals that mimic at least some characteristics of a disease has become very important in the quest to elucidate the molecular mechanisms underlying this and other pathogeneses. Although there are some transgenic mouse strains that recreate some aspects of IBM, in this review, we hypothesize that the great degree of similarity between nematode and human genes known to be involved in IBM as well as the considerable conservation of biological mechanisms across species is an important feature that must be taken into consideration when deciding on the use of this nematode as a model. Straightforward laboratory techniques (culture, transformation, gene knockdown, genetic screenings, etc.) as well as anatomical, physiological, and behavioral characteristics add to the value of this model. In the present work, we review evidence that supports the use of Caenorhabditis elegans as a biological model for IBM.