Computer analysis of two-dimensional gels

New methods and computer programs are described which enable one to analyze autoradiograms produced by two-dimensional gel electrophoresis. These programs are completely automatic with respect to finding spots resolved by such gels and quantitating the radioactivity in them. Semiautomatic programs have also been developed to match the spot patterns of different autoradiograms, and to follow the synthesis of any individual polypeptide through a series of gels.     

Sequence data handling by computer.

The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editing and analysis of both DNA and amino acid sequences. A magnetic tape containing these programs is available on request.     

EMOTIONALLY DISTURBED CHILDREN AND ADOLESCENTS—California State Department of Mental Hygiene Programs

Through programs that are directly operated by the state and through subsidy programs using state funds and federal funds, the Department of Mental Hygiene in California provides services for children and adolescents who are emotionally disturbed. Private institutions for these purposes, in the form of residential centers and day care centers, are licensed by the Department of Mental Hygiene. Direct services provided by the Department of Mental Hygiene include residential treatment programs and outpatient clinic services.There have been increased demands for more residential treatment programs and for services for rural areas. Indications have been noted of increased need for research on questions dealing with services of this kind and increased training programs to provide adequate numbers of trained personnel.     

The current status and portability of our sequence handling software.

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.     

Evaluation of Gene Structure Prediction Programs

We evaluate a number of computer programs designed to predict the structure of protein coding genes in genomic DNA sequences. Computational gene identification is set to play an increasingly important role in the development of the genome projects, as emphasis turns from mapping to large-scale sequencing. The evaluation presented here serves both to assess the current status of the problem and to identify the most promising approaches to ensure further progress. The programs analyzed were uniformly tested on a large set of vertebrate sequences with simple gene structure, and several measures of predictive accuracy were computed at the nucleotide, exon, and protein product levels. The results indicated that the predictive accuracy of the programs analyzed was lower than originally found. The accuracy was even lower when considering only those sequences that had recently been entered and that did not show any similarity to previously entered sequences. This indicates that the programs are overly dependent on the particularities of the examples they learn from. For most of the programs, accuracy in this test set ranged from 0.60 to 0.70 as measured by the Correlation Coefficient (where 1.0 corresponds to a perfect prediction and 0.0 is the value expected for a random prediction), and the average percentage of exons exactly identified was less than 50%. Only those programs including protein sequence database searches showed substantially greater accuracy. The accuracy of the programs was severely affected by relatively high rates of sequence errors. Since the set on which the programs were tested included only relatively short sequences with simple gene structure, the accuracy of the programs is likely to be even lower when used for large uncharacterized genomic sequences with complex structure. While in such cases, programs currently available may still be of great use in pinpointing the regions likely to contain exons, they are far from being powerful enough to elucidate its genomic structure completely.     

Reduced-risk insecticides for control of grape berry moth (Lepidoptera: Tortricidae) and conservation of natural enemies

A 3-yr field study was conducted at commercial grape (Vitis spp.) farms to evaluate insect management programs for control of the grape berry moth, Paralobesia viteana Clemens (Lepidoptera: Tortricidae) and conservation of natural enemies. At each farm, one vineyard received only reduced-risk insecticides for control of second and third generation P. viteana, whereas the comparison vineyard received conventional insecticides. Both vineyards received a conventional insecticide application for control of first generation P. viteana and other insect pests. Monitoring with pheromone traps showed no differences between programs in the total number of adult male moths trapped in vineyards, and oviposition by P. viteana was similar between the two programs in all 3 yr. During weekly samples of crop infestation, both programs had a similar percentage of clusters infested by P. viteana larvae. Berries infested by P. viteana were collected from vineyard borders during the second and third P. viteana generations and held under controlled conditions. In eight of the nine berry samples, survival of larvae was significantly lower in berries collected from vineyards managed under the reduced-risk insecticide program compared with the conventional program. Parasitism of P. citeana larvae in these samples was not consistently different between the two insecticide programs over 3 yr, and similar captures of natural enemies were found on yellow sticky traps in the two programs throughout the study. Our results indicate that integrated pest management programs incorporating reduced-risk insecticides for control of P. viteana can obtain similar or greater control of P. viteana compared with programs based solely on conventional insecticides, but they may not lead to measurable long-term increases in parasitism of P. viteana.     

Accessible high-throughput virtual screening molecular docking software for students and educators

We survey low cost high-throughput virtual screening (HTVS) computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs) that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.     

EQA from an Australian perspective

Enrolment in external quality assurance programs is part of the accreditation process for medical laboratories in Australia, with the majority of Australian laboratories being enrolled in programs from RCPA Quality Assurance Programs Pty Limited, a company owned by the Royal College of Pathologists of Australasia. An important feature of these programs is that they have been developed with the involvement and contribution of the profession. For example, the Chemical Pathology programs are a joint venture between the company and the Australasian Association of Clinical Biochemists (AACB). Some of the unique features of the programs are the composition of the material, the use of target values, the structure and information in the reports and the use of the internet for data entry and data review. Over the past thirty years, the development of these programs has made a significant contribution to the quality of laboratories in Australia.     

International service learning programs: ethical issues and recommendations

Inequities in global health are increasingly of interest to health care providers in developed countries. In response, many academic healthcare programs have begun to offer international service learning programs. Participants in these programs are motivated by ethical principles, but this type of work presents significant ethical challenges, and no formalized ethical guidelines for these activities exist. In this paper the ethical issues presented by international service learning programs are described and recommendations are made for how academic healthcare programs can carry out international service learning programs in a way that minimizes ethical conflicts and maximizes benefits for all stakeholders. Issues related to project sustainability and community involvement are emphasized.     

Comparison of different approaches and computer programs for progress curve analysis of enzyme kinetics

For the analysis of enzyme kinetics, a variety of programs exists. These programs apply either algebraic or dynamic parameter estimation, requiring different approaches for data fitting. The choice of approach and computer program is usually subjective, and it is generally assumed that this choice has no influence on the obtained parameter estimates. However, this assumption has not yet been verified comprehensively. Therefore, in this study, five computer programs for progress curve analysis were compared with respect to accuracy and minimum data amount required to obtain accurate parameter estimates. While two of these five computer programs (MS‐Excel, Origin) use algebraic parameter estimation, three computer programs (Encora, ModelMaker, gPROMS) are able to perform dynamic parameter estimation. For this comparison, the industrially important enzyme penicillin amidase (EC 3.5.1.11) was studied, and both experimental and in silico data were used. It was shown that significant differences in the estimated parameter values arise by using different computer programs, especially if the number of data points is low. Therefore, deviations between parameter values reported in the literature could simply be caused by the use of different computer programs.     

International Monetary Fund programs and tuberculosis outcomes in post-communist countries

Background

Previous studies have indicated that International Monetary Fund (IMF) economic programs have influenced health-care infrastructure in recipient countries. The post-communist Eastern European and former Soviet Union countries experienced relatively similar political and economic changes over the past two decades, and participated in IMF programs of varying size and duration. We empirically examine how IMF programs related to changes in tuberculosis incidence, prevalence, and mortality rates among these countries.

Methods and Findings

We performed multivariate regression of two decades of tuberculosis incidence, prevalence, and mortality data against variables potentially influencing tuberculosis program outcomes in 21 post-communist countries for which comparative data are available. After correcting for confounding variables, as well as potential detection, selection, and ecological biases, we observed that participating in an IMF program was associated with increased tuberculosis incidence, prevalence, and mortality rates by 13.9%, 13.2%, and 16.6%, respectively. Each additional year of participation in an IMF program was associated with increased tuberculosis mortality rates by 4.1%, and each 1% increase in IMF lending was associated with increased tuberculosis mortality rates by 0.9%. On the other hand, we estimated a decrease in tuberculosis mortality rates of 30.7% (95% confidence interval, 18.3% to 49.5%) associated with exiting the IMF programs. IMF lending did not appear to be a response to worsened health outcomes; rather, it appeared to be a precipitant of such outcomes (Granger- and Sims-causality tests), even after controlling for potential political, socioeconomic, demographic, and health-related confounders. In contrast, non-IMF lending programs were connected with decreased tuberculosis mortality rates (−7.6%, 95% confidence interval, −1.0% to −14.1%). The associations observed between tuberculosis mortality and IMF programs were similar to those observed when evaluating the impact of IMF programs on tuberculosis incidence and prevalence. While IMF programs were connected with large reductions in generalized government expenditures, tuberculosis program coverage, and the number of physicians per capita, non-IMF lending programs were not significantly associated with these variables.

Conclusions

IMF economic reform programs are associated with significantly worsened tuberculosis incidence, prevalence, and mortality rates in post-communist Eastern European and former Soviet countries, independent of other political, socioeconomic, demographic, and health changes in these countries. Future research should attempt to examine how IMF programs may have related to other non-tuberculosis–related health outcomes.     

Trends and values of ‘Land for Wildlife’ programs for private land conservation

The Land for Wildlife program started in Victoria in 1981 as a voluntary program with the broad aim of supporting landholders in providing habitat for wildlife on their property. The program has since spread across Australia and is implemented in a range of guises, through a variety of governance approaches. This research collected qualitative and quantitative data on Land for Wildlife programs across Australia to conduct the first national review. Data were gathered on changes in program membership to assess different participation trends. In addition, phone interviews with Land for Wildlife coordinators throughout Australia were conducted to explore how the programs are positioned in delivering biodiversity outcomes in a range of different regions. Over 14,000 properties covering 2.3 million ha are currently registered under Land for Wildlife programs. with at least 500,000 ha of habitat managed for conservation. Limited resources present a large challenge faced by a number of programs, with generally low funding and staffing resulting in restricted biodiversity focus and conservation outcomes. We suggest options to enhance the programs and propose future research directions.     

Addressing consumer grievances in medicine: policies and practices of newborn screening programs in the United States

Newborn screening programs collectively administer the largest genetic testing initiative in the United States. The redress of grievances is an important mechanism for consumers to provide input into clinical and public health programs. In this study, we evaluated mechanisms for addressing consumer grievances in newborn screening programs. To do this, we surveyed all 50 state plus the District of Columbia newborn screening programs by questionnaire regarding protocols for receipt and redress of problems reported by parents of newborns and ascertained the existence and nature of complaints and how complaints were documented and addressed. Pertinent state and federal legislation and regulation were also reviewed. Six of 49 newborn screening programs reported having formal policies for handling consumer grievances. Four states reported having pertinent legislation or regulation. Thirty-eight of 49 states reported having received complaints from 1993 to 1995. Thirteen of 49 newborn screening programs reported that they actively seek feedback from consumers. Consumer grievances ranged from minor complaints to potentially life-threatening concerns. In general, complaints are managed on an ad hoc basis; formal policies are typically lacking. As newborn screening programs affect a vast number of Americans, a proactive and comprehensive approach, including solicitation of consumer feedback, could benefit both newborn screening programs and the public served by them.     

Apple Macintosh programs for nucleic and protein sequence analyses

This paper describes a package of programs for handling and analyzing nucleic acid and protein sequences using the Apple Macintosh microcomputer. There are three important features of these programs: first, because of the now classical Macintosh interface the programs can be easily used by persons with little or no computer experience. Second, it is possible to save all the data, written in an editable scrolling text window or drawn in a graphic window, as files that can be directly used either as word processing documents or as picture documents. Third, sequences can be easily exchanged with any other computer. The package is composed of thirteen programs, written in Pascal programming language.     

Protein sequence redundancy reduction: comparison of various method

Non-redundant protein datasets are of utmost importance in bioinformatics. Constructing such datasets means removing protein sequences that overreach certain similarity thresholds. Several programs such as 'Decrease redundancy', 'cd-hit', 'Pisces', 'BlastClust' and 'SkipRedundant' are available. The issue that we focus on here is to what extent the non-redundant datasets produced by different programs are similar to each other. A systematic comparison of the features and of the outputs of these programs, by using subsets of the UniProt database, was performed and is described here. The results show high level of overlap between non-redundant datasets obtained with the same program fed with the same initial dataset but different percentage of identity threshold, and moderate levels of similarity between results obtained with different programs fed with the same initial dataset and the same percentage of identity threshold. We must be aware that some differences may arise and the use of more than one computer application is advisable.     

Estimated number of snake species that can be managed by Species Survival Plans in North America

A survey designed to estimate the number of snake enclosures available for Species Survival Plan (SSP) programs was distributed to all North American zoos containing 100 or more reptile and amphibian specimens. Of the 52 zoos surveyed, 44 (84.6%) responded, indicating that 790 (26.3%) of the 3,012 snake enclosures were available for SSP programs. Available enclosures were classified by size and existing themes to help define limitations of the potential SSP space. This spatial information was then used in conjunction with existing population genetics models to estimate that up to 16 snake species can be accommodated by SSP programs in these zoos collectively. Values used in the models were estimates of those for an average snake species with a generation time of 15 years, lambda of 1.15, with 26 effective founders, and an n_e/n ratio of 0.3. It was further assumed that 90% of the genetic variation would be maintained in each species for a period of 100 years. Tactics to increase the number of species that SSP programs can accommodate include: increase reserve space, devote more space for SSP snakes, lengthen generation time, promote gene exchange with wild populations, goal SSP programs for less than 200 years, invest in short-term programs, involve the private sector, build new enclosures, increase the number of snakes per enclosure, and encourage participation of non-North American institutions. To maximize biological diversity in relation to captive carrying capacity, it is recommended that SSP programs represent both infraorders of living snakes and as many families within those infraorders as possible. Although not all 16 families of snakes are likely to be represented due to exhibit value, obtainability, and husbandry success, it may be possible to represent as many as nine families in 16 SSP programs. © 1993 Wiley-Liss, Inc.     

Methods in sustainable monitoring: plot sampling versus interviews

Biodiversity monitoring in developing countries has long been haunted by problems with sustaining monitoring programs, especially after funding stops. Current programs are developed to fulfill strict scientific demands, which often results in high priced programs, with little local participation and attention. Thus, to enhance sustainability of the biodiversity programs, there is a great need to reconcile scientific rigor with local involvement. In this paper, we analyze the cost-effectiveness and usefulness of a standard and a participatory monitoring method, in their ability to monitor biodiversity, while rising local participation. As a standard method we used a forest characteristic with tree basal area and Shannon index as proxy for biodiversity. Interviews were used as a participatory approach, with hunters’ catch-effort as proxy. The analysis showed that the interviews reached a better precision with fewer work hours spent and at the same time involved local populations and stake holders. As a tradeoff, the interviews lacked the scientific rigor from forest characteristic. In order to sustain monitoring programs, we conclude that conservation biologists needs to compromise between scientific rigor and public participation.     

Quality assurance activities of the College of American Pathologists

Since its inception, the College of American Pathologists (CAP) has played a fundamental and pivotal role in the development and execution of quality assurance programs for laboratories. Within the realm of anatomic pathology, operational programs include those in surgical pathology, immunohistochemistry and cytopathology. The emphasis of prior cytopathology programs on cervical cytology has now been expanded to include body fluids and fine needle aspiration material. CAP's role in the expansion of quality assurance programs in cytology may be enhanced in the future by intersociety cooperation with established cytology organizations and will also be influenced by and closely linked to the expansion of its quality assurance programs in surgical pathology. As for the Papanicolaou smear, it can no longer be regarded as the "Cinderella of cytology"; it is in fact the present-day cynosure in the laboratory. In recognition of this, CAP has undertaken efforts to help heighten public awareness about the value of Papanicolaou smear testing and is encouraging women to become more informed about the process involved in the examination of their smears.