Relational database model for DNA mutations and a software program for implementation of the model

A relational database model for describing DNA mutations is presented. The model was developed in conjunction with the human hprt database and was succesful in representing over 1800 hprt mutations. Mutants showing aberrant mRNA splicing can be adequately described using the model, as well as mutants showing more than one mutation. The basic aspects of the relational model should be applicable to mutations in a variety of genes. A data entry program developed using Microsoft Access 2.0 is also described that implements the relational model The data entry program ensures that relational integrity is maintained between the tables and automatically generates key fields as needed. The program also has the ability to convert between the various numbering schemes that are used to decribed base pair location in the hprt gene. The program and source code are placed in the public domain so that other experimenters can adapt the program for use with other genes.     

Microcomputer information systems designed to provide documentation about patients treated with dialysis]

A program specifically designed for PC/XT/AT compatible with IBM was written. This program is intended for collecting data on the patients treated with repeated dialyses. The system collects, edits, and surveys data according certain rules. It may print required data. It may also be extended by inclusion of the additional modules and adopted to other centres of dialysis. It is used for 2 years already and proved quite useful in the center of dialysis.     

Computer-assisted identification of anaerobic bacteria.

A computer program was developed to identify anaerobic bacteria by using simultaneous pattern recognition via a Bayesian probabilistic model. The system is intended for use as a rapid, precise, and reproducible aid in the identification of unknown isolates. The program operates on a data base of 28 genera comprising 238 species of anaerobic bacteria that can be separated by the program. Input to the program consists of biochemical and gas chromatographic test results in binary format. The system is flexible and yields outputs of: (i) most probable species, (ii) significant test results conflicting with established data, and (iii) differential tests of significance for missing test results.     

Computer-assisted identification of anaerobic bacteria.

A computer program was developed to identify anaerobic bacteria by using simultaneous pattern recognition via a Bayesian probabilistic model. The system is intended for use as a rapid, precise, and reproducible aid in the identification of unknown isolates. The program operates on a data base of 28 genera comprising 238 species of anaerobic bacteria that can be separated by the program. Input to the program consists of biochemical and gas chromatographic test results in binary format. The system is flexible and yields outputs of: (i) most probable species, (ii) significant test results conflicting with established data, and (iii) differential tests of significance for missing test results.     

A mutation spectra database for bacterial and mammalian genes.

Each mutation spectrum in this database is a dataset of changes in DNA base sequence in mutations induced in a gene by a particular mutagen (including spontaneous processes) under defined conditions. There are 240 datasets with 24 500 mutants in nine bacterial genes, two phage genes, five mammalian genes and one yeast gene. The database is available on the Web at http://info.med.yale.edu/mutbase/ . The data tables can be viewed on the Web and downloaded in text form for local use. The data are also available in dBASE III, a format which can be utilized by essentially any desktop computer database program or spreadsheet, and makes feasible analyses of a large number of mutants. Researchers are invited to submit additional data. A data entry program, MUTSIN, diagrams each mutation on the computer screen as the data are entered and alerts the user to any discrepancies between the entry and the gene sequence.     

Quality of data entry using single entry, double entry and automated forms processing--an example based on a study of patient-reported outcomes

Background

The clinical and scientific usage of patient-reported outcome measures is increasing in the health services. Often paper forms are used. Manual double entry of data is defined as the definitive gold standard for transferring data to an electronic format, but the process is laborious. Automated forms processing may be an alternative, but further validation is warranted.

Methods

200 patients were randomly selected from a cohort of 5777 patients who had previously answered two different questionnaires. The questionnaires were scanned using an automated forms processing technique, as well as processed by single and double manual data entry, using the EpiData Entry data entry program. The main outcome measure was the proportion of correctly entered numbers at question, form and study level.

Results

Manual double-key data entry (error proportion per 1000 fields = 0.046 (95% CI: 0.001–0.258)) performed better than single-key data entry (error proportion per 1000 fields = 0.370 (95% CI: 0.160–0.729), (p = 0.020)). There was no statistical difference between Optical Mark Recognition (error proportion per 1000 fields = 0.046 (95% CI: 0.001–0.258)) and double-key data entry (p = 1.000). With the Intelligent Character Recognition method, there was no statistical difference compared to single-key data entry (error proportion per 1000 fields = 6.734 (95% CI: 0.817–24.113), (p = 0.656)), as well as double-key data entry (error proportion per 1000 fields = 3.367 (95% CI: 0.085–18.616)), (p = 0.319)).

Conclusions

Automated forms processing is a valid alternative to double manual data entry for highly structured forms containing only check boxes, numerical codes and no dates. Automated forms processing can be superior to single manual data entry through a data entry program, depending on the method chosen.     

TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species

An earlier program, TetraploidMap, enabled linkage analysis to be performed for autotetraploid species, with a text-based input and output. The current program, TetraploidMap for Windows, is considerably enhanced, and now goes beyond linkage analysis to perform quantitative trait locus (QTL) interval mapping, with a range of models and thresholds assessed by permutation tests. A Windows-based interface facilitates data entry and exploration. TetraploidMap for Windows is freely available from the Web site of Bioinformatics and Statistics Scotland at http://www.bioss.ac.uk/ (user-friendly software).     

WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data.

SUMMARY: WebBLAST is a suite of programs intended to assist in organizing sequencing data and to provide first-pass sequence analysis in an automated fashion. Data processing is fully automated, with end-users being presented both graphical and tabular summaries of data that can be viewed using any Web browser. AVAILABILITY: The program is free and available at http://genome.nhgri.nih. gov/webblast.     

Biopotentials of marine sponges from China oceans: past and future

An extensive literature survey of over 17 Journals was carried out on Chinese sponges and their natural products in the period from 1980 to 2001. This review is thus intended to provide the first thorough overview of research on marine sponges from China Ocean territories. Information is provided about the rather-limited taxonomic study of Chinese marine sponges, with an analysis on their distribution and diversity. Research findings on the natural products and their bioactivity screening from Chinese sponges are summarized. The weaknesses, gaps and problems in the past R&D program of Chinese sponges are identified, which point to the future opportunities in exploiting these huge untapped sponge resources. The report is expected to serve as an entry point for understanding Chinese sponges and for furthering R&D on their bioactive compounds for new drug development.     

Two computer programs for rapid entry of DNA sequence data

Two computer programs for the IBM personal computer are describedfor rapid and accurate entry of DNA sequence data. The DNA sequencefiles produced can be used directly by the DNA sequence manipulationprograms by R. Staden (the DataBase system), the Universityof Wisconsin Genetics Computer Group, DNASTAR, or D. Mount.The first program, DIGISEQ, utilizes a sonic digitizer for semi-automationof sequence entry. To enter the DNA sequence each band of agel reading is touched by the stylus of the sonic digitizer.DIGISEQ corrects for both changes in lane width and lane curvature.The algorithm is extremely efficient and rarely requires re-entenngthe centers of the lanes. The second program, TYPESEQ, usesonly the keyboard for input. The keyboard is reconfigured toplace nucleotides and ambiguity codes under the fingers of onehand, corresponding to the order of the nucleotides on the geldefined by the user Both programs produce individual tones foreach nucleotide, and certain ambiguity codes. This verifiesinput of the correct nucleotide or ambiguity code, and thuseliminates the need to visually check the screen display duringsequence entry. Received on November 16, 1986; accepted on June 16, 1987     

Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico

The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.     

GELENT: a sequence gel entry program for keyboard and sonic digitizer input

A program is described for sequence data entry which allowsflexible program control by responding to both the keyboardand a sonic digitizer concurrently. Simplification of the initializationstage of each gel reading has been achieved, in comparison withother programs. Received on July 7, 1988; accepted on January 10, 1989     

Comprehensive Approach to Improving Maternal Health and Achieving MDG 5: Report from the Mountains of Lesotho

Background

Although it is now widely recognized that reductions in maternal mortality and improvements in women''s health cannot be achieved through simple, vertical strategies, few programs have provided successful models for how to integrate services into a comprehensive program for maternal health. We report our experience in rural Lesotho, where Partners In Health (PIH) in partnership with the Ministry of Health and Social Welfare implemented a program that provides comprehensive care of pregnant women from the community to the clinic level.

Methods

Between May and July 2009, PIH trained 100 women, many of whom were former traditional birth attendants, to serve as clinic-affiliated maternal health workers. They received performance-based incentives for accompanying pregnant women during antenatal care (ANC) visits and facility-based delivery. A nurse-midwife provided ANC and delivery care and supervised the maternal health workers. To overcome geographic barriers to delivering at the clinic, women who lived far from the clinic stayed at a maternal lying-in house prior to their expected delivery dates. We analyzed data routinely collected from delivery and ANC registers to compare service utilization before and after implementation of the program.

Results

After the establishment of the program, the average number first ANC visits increased from 20 to 31 per month. The clinic recorded 178 deliveries in the first year of the program and 216 in the second year, compared to 46 in the year preceding the program. During the first two years of the program, 49 women with complications were successfully transported to the district hospital, and no maternal deaths occurred among the women served by the program.

Conclusions

Our results demonstrate that it is possible to achieve dramatic improvements in the utilization of maternal health services and facility-based delivery by strengthening human resource capacity, implementing active follow-up in the community, and de-incentivizing home births.     

Development and Evaluation of Patient‐Centered Software for a Weight‐Management Clinic

Objective: To describe a weight‐management clinic software system and to report on its preliminary evaluation. Research Methods and Procedures: The software system standardizes the collection of relevant patient information from an initial medical assessment, weekly clinic visits, and laboratory testing protocol of a medically supervised proprietary meal‐replacement program in a university‐based referral clinic. It then generates monthly patient feedback reports with graphs of clinical and laboratory parameters to support a patient‐centered approach to weight management. After patients and clinic physicians review the data to ensure accuracy, the database is used for subsequent patient feedback reports, reports to referring physicians, quality assurance, and research. Clinic physicians and referring physicians were asked to rate their acceptance of the system. In addition, in a retrospective analysis of data generated by the system, outcomes for patients who received system‐generated feedback (n = 620) were compared with those who participated in the program before the introduction of feedback (n = 130). Results: Clinic and referring physicians reported that they had high overall satisfaction with the software and that the system saved them time, and the latter group reported that it decreased laboratory use. Regarding patients, the feedback group had lower dropout rates in the latter half of the program, better rates of attendance, completion of laboratory tests, and weight loss after 8 weeks. Discussion: The software seems to facilitate the effectiveness of the treatment protocol for obesity and generates a high‐quality database for patient care, clinic administration, quality assurance, and research purposes.     

An access interface for the MS-DOS diskette format of GenBank(R), a gene sequence database

An interface program has been developed for users of MS-DOScomputers and the GenBank(R) gene sequence files in their disketteformat. With the program a user is able to produce keyword,author and entry name listings of GenBank items or to selectGenBank sequences for viewing, printing or decoding. The decodeoption uncompresses sequence data and yields a character filewhich has the format used on GenBank magnetic tapes. Programoptions are chosen by selecting items from command menus. Whilethe program is designed primarily for hard disk operation, italso allows users of diskette-based computers to work with GenBankfiles. Received on July 15, 1987; accepted on July 15, 1987     

A proportional hazards model for multivariate interval-censored failure time data

This paper focuses on the methodology developed for analyzing a multivariate interval-censored data set from an AIDS observational study. A purpose of the study was to determine the natural history of the opportunistic infection cytomeglovirus (CMV) in an HIV-infected individual. For this observational study, laboratory tests were performed at scheduled clinic visits to test for the presence of the CMV virus in the blood and in the urine (called CMV shedding in the blood and urine). The study investigators were interested in determining whether the stage of HIV disease at study entry was predictive of an increased risk for CMV shedding in either the blood or the urine. If all patients had made each clinic visit, the data would be multivariate grouped failure time data and published methods could be used. However, many patients missed several visits, and when they returned, their lab tests indicated a change in their blood and/or urine CMV shedding status, resulting in interval-censored failure time data. This paper outlines a method for applying the proportional hazards model to the analysis of multivariate interval-censored failure time data from a study of CMV in HIV-infected patients.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiringthe use of computer programs offering high-resolution analysisand comparison of nucleotide sequence data. The strategy involvesthe development of a pair of computer programs, called SEQANALand SEQTALK, designed to operate in tandem. SEQANAL is a largeand complex program intended to be used to discover regionsof internal repeats and dyad symmetries within one sequence,or regions of homology, complementarity or optimal alignmentbetween two sequences. Three algorithms are supported: thoseof Staden (1977, 1978); of Korn et al. (1977); Queen and Korn(1980); and the newly-described exhaustive tree-searching algorithmof Burnett et al. (1985, 1986). The SEQTALK program is a small,portable, interactive, frontend program with which the usercan specify the instructions to control the SEQANAL program.Together, the SEQANAL and SEQTALK programs permit analyses tobe performed at a remote facility on a mainframe computer underthe complete control of a distant user equipped with minimalcomputing facilities, and without needing networking facilities. Received on May 23, 1985; accepted on August 13, 1985