Screening for the prevention of cervical cancer in the era of human papillomavirus vaccination: an Australian perspective

Australia has a unique and highly successful screening program for cervical cancer which is based on the conventional Pap smear. Since its introduction in 1991 there has been a decline in both the incidence of and mortality from this disease. Part of the success of this program has been the introduction of Pap test registers and strict quality assurance measures for cervical cytology, including compulsory key performance indicators for laboratories. Using these measures, nationwide calculations give cervical cytology in Australia a sensitivity of 78% for high-grade lesions and a positive predictive value (PPV) of 78%. Australia was the first country to introduce a widespread government-funded human papillomavirus (HPV) vaccination program in 2007. Because of the high accuracy of Australian cytology, HPV testing alone, given its low PPV and high cost, is unlikely to be a viable alternative to cytology for primary screening in this country. Australia therefore faces unique issues and choices in integrating its extensive vaccination program with a successful cervical screening program.     

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.     

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given.     

Picking lowest-cost measurements for identifying unknowns

One way to identify an unknown item is to measure its traits and compare the measurements with those of items the unknown might be. This paper outlines a way to pick what to measure from given known traits to (1) minimize measurement cost and (2) ensure that measuring the picked traits is as good as measuring all the given traits for purposes of identifying unknowns. The paper also relates a computer program which has been written to do this, and the program's use with the Protein Atlas in minimizing the number of amino acids to measure in an experiment involving polypeptide identification.     

Time course equations of the amount of substance in a linear compartmental system and their computerized derivation

In this contribution, we present the symbolic time course equations corresponding to a general model of a linear compartmental system, closed or open, with or without traps and with zero input. The steady state equations are obtained easily from the transient phase equations by setting the time --> infinity. Special attention has been given to the open systems, for which an exhaustive kinetic analysis has been developed to obtain important properties. Besides, the results have been particularized to open systems without traps and an alternative expression for the distribution function of exit times has been provided. We have implemented a versatile computer program, that is easy to use and with a user-friendly format of the input of data and the output of results. This computer program allows the user to obtain all the information necessary to derive the symbolic time course equations for closed or open systems as well as for the derivation of the distribution function of exit times.     

EFFORTS TO CONTROL ANTIBIOTIC RESISTANT INFECTIONS—A Coordinated Community Effort

Since June 1958 the medical society, the medical institutions and the medical professions in Orange County have conducted an intensive program to control and prevent the spread of antibiotic resistant infections.In this community-wide effort, rules designed to protect the hospital population against infectious dangers have been developed and enforced, courses in food-handling and housekeeping sanitation have been given to hospital employees, and a program to solve some of the laboratory aspects of antibiotic resistant infections has been developed.     

A program which automatically quantitates gel electrophoretic autoradiograms

The use of a computer-coupled film scanner to measure and analyze autoradiograms of gel electropherograms is described. A program has been written which fits Gaussian curves to the complex band pattern that constitutes a density profile without the need for estimated parameters in the input. The great majority of the fits are satisfactory. This program, which is written in FORTRAN, runs on a small, inexpensive computer. Another program which approximates a Gaussian least squares fit has been run for comparison; this procedure can also be used to refine occasional unsatisfactory fits. Finally, a program has been written which sums the density profile within specified limits, so that the integrated intensities of bands due to isolated protein components may be found.     

G-PRIMER: greedy algorithm for selecting minimal primer set

G-PRIMER, a web-based primer design program, has been developed to compute a minimal primer set specifically annealed to all the open reading frames in a given microbial genome. This program has been successfully used in the microarray experiment for analyzing the expression of genes in the Xanthomonas campestris genome. AVAILABILITY: It is available at http://mammoth.bii.a-star.edu.sg/gprimer/. Its source code is available upon request.     

PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length

A computer program written in C++ has been developed which can detect all potential H-type RNA pseudoknots within any given RNA sequence. There is no limit on the length of the input sequence. A validation run of the program using the full-length (8173 nt) genomic mRNA of simian retrovirus type-1 (SRV-1) identifies the established -1 frameshift stimulating pseudokont at the gagpro junction as the most stable pseudoknot within the genomic mRNA.     

Community Rehabilitation Program

A broad outline of a community program has been given, with particular stress on in-sanatorium facilities.It is reasonable to conclude that rehabilitation is feasible, desirable and economically sound.The object of the program is complete rehabilitation in all categories of the greatest possible number of persons incapacitated by tuberculosis.     

An efficient algorithm for minimal primer set selection

SUMMARY: We have developed U-PRIMER, a primer design program, to compute a minimal primer set (MPS) for any given set of DNA sequences. The U-PRIMER algorithm, which uses automatic variable fixing and automatic redundant constraint elimination to tackle the binary integer programming problem associated with the MPS selection problem. The program has been tested successfully with 32 adipocyte development-related genes and 9 TB-specific genes to obtain their respective MPSs. AVAILABILITY: A free copy of U-PRIMER implemented in C++ programming language is available from http://www.u-vision-biotech.com     

A concept of a general computer program for the iterative calculation of maximum likelihood estimators with application to qualitative dose response analyses

In this article we describe the construction of a general computer program for the iterative calculation of maximum likelihood estimators. The program is general in the sense that it allows the maximization of any given likelihood function. The user only has to write a subroutine LKLHD, in which the special likelihood function and their first and second derivatives will be calculated. This subroutine is an input parameter of the optimization program. This enables the user to employ one main program for the maximization of various likelihood functions. This advantage will be shown for the evaluation of qualitative dose response relationships (quantal assays: probit-, logit-analysis).     

A computer program allows the separation of a wide range of chromosome sizes by pulsed field gel electrophoresis

The introduction of Pulsed Field Gel Electrophoresis techniques, which allow the separation of DNA molecules of molecular weights as high as chromosomes of lower eukaryotes, has given a powerful tool to geneticists. The resolution expected from these techniques is dependent on numerous parameters, among them pulse time and field strength. A given set of these parameters allows only a limited range of molecular weights to be resolved. To allow the separation of a broader molecular weight range on a single gel, we designed a computer program, driving a simple switching device, to take care of switching electrodes and power supplies in OFAGE migrations. This program has been designed to be used with any technique calling for periodic switching or inversion of the electric field, and/or variation of the electric field applied during electrophoresis. As an example, we show the results obtained with yeast genera in which chromosome sizes range from 260 to 9,000 kilobase pairs.     

Application of bromodeoxyuridine incorporation measurements to the determination of cell distribution within the S phase of the cell cycle

Flow cytofluorimetric measurement of incorporated bromodeoxyuridine, using a double-stained cell population, allows the determination of the distribution of cells along the cell cycle. We have developed a simple computer program for the direct treatment of 64 x 64 channel histograms. This analysis appears to provide interesting data about the distribution of cells in the various phases of the cell cycle, namely the S phase. Two examples have been chosen to illustrate possible fields for the application of such a program. Comparison of two cell lines such as friend murine erythroleukemia cells (MELC) and fibroblasts FR3T3 cells has shown that this analysis can be used for cell-cycle characterization of a given cell line. The program also allows the differential analysis of cell distribution along the cell cycle as a function of a given parameter. This possibility has been applied to study the variation of cell-cycle parameters as a function of the time of induced differentiation of MELC and reveals changes in the distribution of the cells along the various phases of the cell cycle, namely in the S phase.     

Aeration of concentrated activated sludge

A multiphase project has been planned to develop a new biological process capable of economically treating high BOD wastes. Herein is presented the results of the first phase of the program, in which the feasibility of growing concentrated microbial cultures was investigated and the oxygen and power requirements for maintaining such cultures were determined. An example is given of the scale-up of power requirements for oxygen transfer in a prototype system.     

Experience of an interactive program in undergraduate investigative practicals

A microcomputer program is described which has been used by first-year undergraduates throughout an investigation in microbiology, totalling five hours of practical work. The computer is used by students to check their suggestions of possible lines of investigation, the results of practical procedures, and the decisions made on the basis of this experimental evidence. The program offers advice when entries which are inadvisable or incorrect are entered thus providing guidance without usurping student control of the investigation. Evidence for the effectiveness of this program is presented and the potential for this type of consultative program in other areas is indicated. Based on this experience, advice is offered on the general design of this type of program.     

SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data

High-density genetic linkage maps can be used for purposes such as fine-scale targeted gene cloning and anchoring of physical maps. However, their construction is significantly complicated by even relatively small amounts of scoring errors. Currently available software is not able to solve the ordering ambiguities in marker clusters, which inhibits the application of high-density maps. A statistical method named SMOOTH was developed to remove genotyping errors from genetic linkage data during the mapping process. The program SMOOTH calculates the difference between the observed and predicted values of data points based on data points of neighbouring loci in a given marker order. Highly improbable data points are removed by the program in an iterative process with a mapping algorithm that recalculates the map after cleaning. SMOOTH has been tested with simulated data and experimental mapping data from potato. The simulations prove that this method is able to detect a high amount of scoring errors and demonstrates that the program enables mapping software to successfully construct a very accurate high-density map. In potato the application of the program resulted in a reliable placement of nearly 1,000 markers in one linkage group.     

Structure‐based barcoding of proteins

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha‐numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/ .     

The breeding of captive wild species by artificial methods

The growing interest in many zoos, wildlife parks and game ranches in the captive breeding of wild species has brought about much interest and research in developing and testing artificial methods of breeding. Much of this work has been concentrated in endangered species. The author outlines the relevance and utilization of such techniques and reviews successful attempts in this area and elaborates on future potential ones. A brief review is given of successful artificial methods of breeding domestic species and how this may be applied to non-domestic ones. Areas that are covered are semen collection, semen freezing, induction of estrus, artificial insemination, embryo transfer including interspecies transfer and embryo surgery. It is acknowledged that it is highly unlikely that an artificial program could save a species from extinction but such methods could greatly assist a comprehensive natural breeding program.