A simple computer program for calculating, modifying and drawing circular restriction maps.

An HPL program is described which constructs and draws circular restriction maps given a set of cleavage sites, together with deletion of insertion data if required. This program is of great use in the routine interpretation of restriction patterns for the analysis of recombinant DNA molecules.     

A computer program for the analysis of dental models.

This paper presents the details and logic of a Fortran computer program which carries out routine clinical analysis of dental models resulting from impressions of the teeth and related structures, which are subsequently cast in plaster of Paris. The program is primarily intended for use by the orthodontist who is engaged in research or clinical practice, and is useful in studies related to changes in the dentition as a result of orthodontic treatment.     

Image processing software for enhanced visualization of faint or noisy autoradiographic images

A computer program for digital image processing is described which can be implemented using scanning densitometer hardware pre-existing in most biology departments plus computer video hardware which may either pre-exist in the biology department or would represent a moderate upgrade over an already planned computer purchase. The primary purpose of this computer program is to provide contrast enhancement of faint or low contrast autoradiograph images and to implement background subtraction and digital smoothing methods which permit visualization of blurry electrophoresis bands against noisy backgrounds. However, the program also has modest editing capabilities that allow its use in the routine preparation of images for publication. Finally, the program has facilities for deblurring, edge enhancement and multiple image averaging, which give it usefulness in other forms of photographic analysis.     

A computer program for the analysis of crossover designs.

We describe a program, CROSS, which we have written to obtain potency estimates and other parameters for bioassay data from assays of crossover design. The program permits testing of all assays for statistical validity and calculates the complete analysis of variance for assays of balanced design. The form of data input and the complete documentation of assay results make this program particularly useful for anyone carrying out crossover assays on a routine basis. The analysis of variance presented is also useful for more general biological or medical situations.     

Analysis of progress curves by simulations generated by numerical integration.

A highly flexible computer program written in FORTRAN is presented which fits computer-generated simulations to experimental progress-curve data by an iterative non-linear weighted least-squares procedure. This fitting procedure allows kinetic rate constants to be determined from the experimental progress curves. Although the numerical integration of the rate equations by a previously described method [Barshop, Wrenn & Frieden (1983) Anal. Biochem. 130, 134-145] is used here to generate predicted curves, any routine capable of the integration of a set of differential equations can be used. The fitting program described is designed to be widely applicable, easy to learn and convenient to use. The use, behaviour and power of the program is explored by using simulated test data.     

A dynamic,multi‐level analysis of recent immunization trends in Colombia

Abstract

During 1985–91, Latin American ministries of health carried out the ultimately successful Regional Polio Eradication Initiative. Unprecedented vaccine coverage levels were attained through a combination of mass campaigns, house‐to‐house vaccinations, and improvements in routine immunization services. Little is known, however, about the effects of these interventions on immunization demand; whether they reached so‐called high‐risk households and, if so, whether program effects were sufficient to offset the household risk factors. This paper examines the probability and timing of full immunization over this period in one case country, Colombia. Information on the immunization status of 3,609 vaccine‐eligible children born 1985–90 was extracted from Colombia's 1990 Demographic and Health Survey. Annual immunization coverage estimates from the Colombian Ministry of Health for 1985–90 for 148 sample municipios were appended to each child record, along with household‐level data. Initial non‐parametric regressions showed that five of six observed risk factors negatively influenced full immunization probability. Multivariate logit models showed that parents who had already lost a child were significantly less likely to obtain immunization cards (a proxy for exposure to the routine immunization program), despite rising cardholdership rates over the period. Among 1,376 immunization cardholders, waiting times to full immunization fell monotonically over the period. Local program coverage of 80 per cent or higher and prior use of prenatal services both increased the probability of full immunization. However, three of five maternal occupational categories decreased the probability, as did three of six observed household risk factors. The results show that demand for routine immunizations rose over the period, that only the highest‐risk households were not exposed to the routine program, and that routine program participation partially offset negative risk factor effects on the probability of full immunization. While targeted PHC interventions may increase health production by recruiting high‐risk households into the routine PHC services, further health production increases will require more intensive follow‐up of such households through routine PHC services.     

The in vitro unscheduled DNA synthesis (UDS) assay in rat primary hepatocytes: evaluation of 2-furoic acid and 7 drug candidates

The in vitro unscheduled DNA synthesis assay (UDS) is part of the routine genetic toxicology screening at The Upjohn Company. The purpose of this paper is to report results for 8 compounds which were tested in the in-house genetic toxicology program. These compounds represent diverse chemical structure and most of them entered the screening program because they are biologically active in efficacy screens. All tests were carried out under Good Laboratory Practices Regulations of the U.S. Food and Drug Administration. None of the materials reported here produced an increase in UDS and therefore the UDS results with these compounds do not suggest potential for genotoxicity.     

A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity

The computer program described in this paper facilitates resolutionof binding affinity heterogeneity by transforming binding curvedata (bound versus free) into affinity spectra (density versusaffinity). The original program, written in FORTRAN, is extendedand presented here in the language C. New applications includean ability to transform competition curves into affinity spectraand to evaluate the effects of sampling and experimental erroron spectrum analysis. We propose that this program be incorporatedin the routine evaluation of binding systems.     

The long-term impact of the Leprosy Post-Exposure Prophylaxis (LPEP) program on leprosy incidence: A modelling study

BackgroundThe Leprosy Post-Exposure Prophylaxis (LPEP) program explored the feasibility and impact of contact tracing and the provision of single dose rifampicin (SDR) to eligible contacts of newly diagnosed leprosy patients in Brazil, India, Indonesia, Myanmar, Nepal, Sri Lanka and Tanzania. As the impact of the programme is difficult to establish in the short term, we apply mathematical modelling to predict its long-term impact on the leprosy incidence.MethodologyThe individual-based model SIMCOLEP was calibrated and validated to the historic leprosy incidence data in the study areas. For each area, we assessed two scenarios: 1) continuation of existing routine activities as in 2014; and 2) routine activities combined with LPEP starting in 2015. The number of contacts per index patient screened varied from 1 to 36 between areas. Projections were made until 2040.Principal findingsIn all areas, the LPEP program increased the number of detected cases in the first year(s) of the programme as compared to the routine programme, followed by a faster reduction afterwards with increasing benefit over time. LPEP could accelerate the reduction of the leprosy incidence by up to six years as compared to the routine programme. The impact of LPEP varied by area due to differences in the number of contacts per index patient included and differences in leprosy epidemiology and routine control programme.ConclusionsThe LPEP program contributes significantly to the reduction of the leprosy incidence and could potentially accelerate the interruption of transmission. It would be advisable to include contact tracing/screening and SDR in routine leprosy programmes.     

Development of a program package for modelling biochemical systems

The development of a program for the identification of a model including up to 15 compartments is presented. The identification of the model parameters with this program package is based upon the improved Gauss Marquardt algorithm. This program, implemented on a microcomputer (Data General) Eclipse 64 K RAM), uses a calculation and automatic generation of a partial derivative routine. Thus, starting from the differential equations of the model correctly written, there is no longer any risk of error.     

A new method for automatic metaphase finding adaptable to different chromosome preparations

A FORTRAN computer program, running on a Digital PDP 11-34 minicomputer, has been developed for use in conjunction with a Cambridge Quantimet 720 image analyzer for the investigation of metaphase preparations in routine cytogenetics. During a short initiation phase the program is adapted to the type of metaphase being analyzed. The program is fast and its performance is good, even at low microscopic magnifications. It has other uses in biology for all investigations and characterizations of small distinct elements widely spread within a preparation (e.g., autoradiography, bacteriology).     

The Routine Fitting of Kinetic Data to Models: A Mathematical Formalism for Digital Computers

A mathematical formalism is presented for use with digital computers to permit the routine fitting of data to physical and mathematical models. Given a set of data, the mathematical equations describing a model, initial conditions for an experiment, and initial estimates for the values of model parameters, the computer program automatically proceeds to obtain a least squares fit of the data by an iterative adjustment of the values of the parameters. When the experimental measures are linear combinations of functions, the linear coefficients for a least squares fit may also be calculated. The values of both the parameters of the model and the coefficients for the sum of functions may be unknown independent variables, unknown dependent variables, or known constants. In the case of dependence, only linear dependencies are provided for in routine use. The computer program includes a number of subroutines, each one of which performs a special task. This permits flexibility in choosing various types of solutions and procedures. One subroutine, for example, handles linear differential equations, another, special non-linear functions, etc. The use of analytic or numerical solutions of equations is possible.     

Segmentation of the epileptic EEG by means of a finite state automation

The aims and merits of the syntactical decomposition of the epileptic EEG are discussed in some detail. General assumptions in the design of segmenting algorithm - an essential part of the reduction of data program - are considered and a working example of segmenting routine os presented. This routine is designed as a finite state automaton, equivalent to a formal regular grammar. The performance of the routine on two sets of experimental data is presented and its intrinsic stability is shown in terms of cluster analysis of the segments produced. Means of extension of the proposed scheme to other cases of potential interest as well as possible applications in the higher level syntactical analysis are pointed out.     

Sweet Substitute: a software tool for in silico fragmentation of peptide-linked N-glycans

A software tool, Sweet Substitute, is described, which assists tandem mass spectrometry (MS/MS)-based glycosylation characterization from within a tryptic digest. The algorithm creates a virtual nanoelectrospray-quadrupole time-of-flight style-MS/MS spectrum of any user-defined N-linked glycan structure. An empirical peak height modeling routine is implemented in the program. By comparing the theoretical MS/MS data with the deconvoluted and deisotoped experimental MS/MS data, the user is able to quickly assess whether a proposed candidate oligosaccharide structure is a plausible one.     

Quantitative infrared spectroscopy of lipids in solution: III. Automated data collection and computer aided calculations of lipid analysis.

In the third part of this series, a data acquisition system is described which digitizes the analog signal from a commercial infrared spectrometer and records the data on paper tape. The paper tape is then processed off-line with a microcomputer and an infrared spectrum is printed. The correction routine for absorbance due to the O-H stretching band is discussed as well as the integration limits for calculation of integrated intensities of the C-H stretching band. The computer program is briefly described and statistical data on correlation between integrated intensity and lipid concentration given.     

Estuary ecosystem restoration: implementing and institutionalizing adaptive management

We implemented and institutionalized an adaptive management (AM) process for the Columbia Estuary Ecosystem Restoration Program, which is a large‐scale restoration program focused on improving ecosystem conditions in the 234‐km lower Columbia River and estuary. For our purpose, “institutionalized” means the AM process and restoration programs are embedded in the work flow of the implementing agencies and affected parties. While plans outlining frameworks, processes, or approaches to AM of ecosystem restoration programs are commonplace, their establishment for the long‐term is not. This article presents the basic AM process and explains how AM was implemented and institutionalized. Starting with a common goal, we pursued a well‐understood governance and decision‐making structure, routine coordination and communication activities, data and information sharing, commitment from partners and upper agency management to the AM process, and meaningful cooperation among program managers and partners. The overall approach and steps to implement and institutionalize AM for ecosystem restoration explained here are applicable to situations in which it has been incomplete or, as in our case, the restoration program is just getting started.     

THE ORGANIZATION AND OPERATION OF A STUDY OF DIARRHEAL DISEASE IN FRESNO COUNTY

The procedures used in the organization and operation of a special study on diarrheal diseases involving federal, state, and local agencies are outlined. The integration of such a project into a local routine program is discussed and the possible benefits derived by the various agencies are briefly evaluated.     

Conversion of linear histogram flow cytometry data to a logarithmic display

A routine is described that readily allows the rescaling of linear histographic data to a corresponding logarithmic histogram. This procedure significantly improves data display, particularly where a wide range in the measured parameter is encountered. The logarithmic scale displays peaks with band widths more proportional to their respective coefficients of variation than is the case in a linear display. Rescaling several linear histograms to a common logarithmic scale allows the combination of these linear data even though the linear ranges are different. This routine is presented as a program written in BASIC for execution on a microcomputer.