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PubMed2005

Nonaqueous capillary electrophoresis in coated capillaries: an interesting alternative for proteomic applications.

This work brings together some contributions for the use of nonaqueous media for proteomic analysis, for both capillary electrophoresis (CE) separation and the preparation of tryptic digests. First, a ternary nonaqueous buffer consisting of 60/30/10 v/v methanol/acetonitrile/acetic acid with 12.5 mmol/L ammonium acetate was optimized for CE separation of the tryptic digest of lysozyme. Lysozyme was chosen as a model system for the protein digestion, which has also been prepared in an organic-rich medium with methanol/50 mmol/L NH(4)HCO(3), pH 8.0 (60/40 v/v). The separation results were compared to in silico (PeptideCutter program) digestion conditions, and high-efficiency peak separation (18 peaks) was obtained in 20 min with an electric field of 350 V/cm. In addition, we have evaluated the stability of a coated capillary with poly-N,N-dimethylacrylamide (60/30 cm total/effective length and 75 microm ID) for over 100 runs of tryptic digest with the nonaqueous background electrolyte solvent system. The migration times for ten selected peptide peaks presented 3-7% relative standard deviation.

Buffers↗
PubMed2002

Maximum feasibility guideline in the design and analysis of protein folding potentials.

Protein folding potentials are expected to have the lowest energy for the native shape. The Linear Programming (LP) approach achieves exactly that goal for a training set, or indicates that this goal is impossible to obtain. If a solution cannot be found (i.e., the problem is infeasible) two possible routes are possible: (a) choosing a new functional form for the potential, (b) finding the best potential with a feasible subset of the data, and (or) detecting inconsistent subset of the data in the training set. Here, we explore option (b). A simple heuristic for finding an approximate solution to an infeasible set of linear inequalities is outlined. An approximately feasible solution is obtained iteratively, starting from a certain initial guess, by computing a series of analytic centers of the polyhedra defined by all the inequalities satisfied at the subsequent iterations. Standard interior point algorithms for Linear Programming can be used to compute efficiently the analytic center of a polyhedron. We demonstrate how this procedure can be used for the design of folding potentials that are linear in their parameters. The procedure shows an improvement in the quality of the potentials and sometimes points to flaws in the original data.

Algorithms↗
PubMed2006

A new parallel algorithm of MP2 energy calculations.

A new parallel algorithm has been developed for second-order Møller-Plesset perturbation theory (MP2) energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2-16) show that the program has high CPU and parallel efficiency. Timings are presented for two relatively large molecules, taxol (C(47)H(51)NO(14)) and luciferin (C(11)H(8)N(2)O(3)S(2)), the former with the 6-31G* and 6-311G** basis sets (1,032 and 1,484 basis functions, 164 correlated orbitals), and the latter with the aug-cc-pVDZ and aug-cc-pVTZ basis sets (530 and 1,198 basis functions, 46 correlated orbitals). An MP2 energy calculation on C(130)H(10) (1,970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.

Algorithms↗
PubMed1994

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site.

A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular "skeletons" from a database into the protein binding region by making bonds between sites ("hooks") on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 10(5) or more skeletons for binding to 10(2) or more functional group minima are outlined.

Algorithms↗
PubMed1986

An incentive management plan for hospital-based physicians.

Arthur D. Little, Inc., has developed an incentive management program for salaried, hospital-based physicians. The program is based on the tracking of physician productivity through the assignment of work units for both routine inpatient care and all medically performed tests and outpatient procedures. A monetary pool based on increases in the hospital's profitability over a base year is divided among physicians on the basis of their relative productivity throughout the year. Administratively assigned work units can be used to give physicians credit for activities which benefit the institution but which are not revenue producing. The system puts incentives in place for physicians to increase revenues while holding down costs. The main feature of the incentive system is a bonus pool, the size of which is based on hospital net income. A reporting application was developed that downloads data from the hospital's service bureau data-processing vendor, preprocesses the data through a C program, and produces reports through an extremely user-friendly, menu-driven, spreadsheet-based program.

Efficiency↗
PubMed1990

Measuring technical efficiency in health care organizations.

The rising cost of health care has created great interest in developing methods to increase the efficiency of health care organizations. Despite this interest most analyses of prospective payment and other programs designed to control expenditures have examined costs and not efficiency. This article examines a new technique--data envelopment analysis (DEA)--that facilitates the conduct of efficiency studies. The utility of DEA is analyzed by comparing this technique with other methods used to measure efficiency, by discussing the application of DEA in the health care industry and by assessing the validity of results from DEA studies. The article concludes with an assessment of the strengths and weaknesses of DEA and suggestions for refining this technique.

Data Interpretation, Statistical↗
PubMed2000

A new bicortical tibial fixation technique in anterior cruciate ligament reconstruction with quadruple hamstring graft.

We report a prospective series of 101 patients receiving a four-strand semitendinosus-gracilis autograft for anterior cruciate ligament reconstruction using a new bicortical tibial fixation technique with bioabsorbable interference screws. Patients (average age 32 years) were operated on between November 1997 and Mai 1998, and follow-up was at least 12 months postoperatively. The evaluation consisted of history, clinical examination, IKDC score, Cincinnati Knee Score, KT-1000 testing, standardized radiography and magnetic resonance imaging. One hundred patients were available for follow-up. There were two traumatic reruptures 6 and 11 months postoperatively. By IKDC score 87 patients were in groups A and B, 12 in group C, and 2 with a rerupture in group D. Mean Cincinnati Knee Score was 82 (range 46-100), KT-1000 manual maximum at follow-up showed an average difference of 1.7 mm between the sides. Full extension was rapidly achieved in all cases, and flexion averaged 135 degrees . Considering the enlargement caused by the bioabsorbable interference screws, the incidence of tunnel widening was 6.6% on the femoral side and 1.7% on the tibial side. Tunnel widening did not affect the clinical results. Three patients experienced an effusion after more than 6 months postoperatively. There was one infection, which settled without functional impairment after early arthroscopic lavage and intravenous antibiotics. Otherwise no complications occurred. The described technique for anterior cruciate ligament reconstruction combines the advantage of anatomical graft position with sufficient graft fixation. A short intra-articular graft construct with a strong tendon to bone interface was created. Clinically, 87% of patients had a normal or nearly normal IKDC score at follow-up. Magnetic resonance imaging revealed a considerable increase in tunnel area caused by the insertion of the interference screws. On the other hand, the development of a "fibrous interzone" between the graft and the bone tunnel was prevented in most cases. At short-term follow-up the bicortical tibial fixation proved to be efficient even with an aggressive rehabilitation program.

Absorbable Implants↗
PubMed2000

An integrated web interface for large-scale characterization of sequence data.

Large-scale genome projects require the analysis of large amounts of raw data. This analysis often involves the application of a chain of biology-based programs. Many of these programs are difficult to operate because they are non-integrated, command-line driven, and platform-dependent. The problem is compounded when the number of data files involved is large, making navigation and status-tracking difficult. To demonstrate how this problem can be addressed, we have created a platform-independent Web front end that integrates a set of programs used in a genomic project analyzing gene function by transposon mutagenesis in Saccharomyces cerevisiae. In particular, these programs help define a large number of transposon insertion events within the yeast genome, identifying both the precise site of transposon insertion as well as potential open reading frames disrupted by this insertion event. Our Web interface facilitates this analysis by performing the following tasks. Firstly, it allows each of the analysis programs to be launched against multiple directories of data files. Secondly, it allows the user to view, download, and upload files generated by the programs. Thirdly, it indicates which sets of data directories have been processed by each program. Although designed specifically to aid in this project, our interface exemplifies a general approach by which independent software programs may be integrated into an efficient protocol for large-scale genomic data processing.

Clinical Laboratory Information Systems↗
PubMed1991

Occupational exposure to HIV: frequency and rates of underreporting of percutaneous and mucocutaneous exposures by medical housestaff.

PURPOSE: To study the frequency of work-related exposures to human immunodeficiency virus (HIV)-infected blood and reporting of exposures among medical housestaff. SETTINGS: Three teaching hospitals where HIV infection is prevalent among patients. SUBJECTS: Internal medicine interns and residents in training in 1988-1989. METHODS: In a cross-sectional survey, house officers were asked to complete anonymously a questionnaire reviewing their past percutaneous and mucocutaneous exposure to blood products. RESULTS: Nineteen percent of the respondents (16 of 86) recalled accidental exposure to HIV-infected blood, and 36% (31 of 86) recalled exposure to blood from patients at high risk for having HIV infection. Of the exposures recalled in the 12 months prior to the survey, 81% (47 of 58) of all needlestick injuries and all (nine of nine) needlestick injuries from HIV-infected blood occurred in postgraduate year 1 or 2 trainees. Only 30% (31 of 103) of the needlestick injuries recalled by subjects were reported. The principal reasons for not reporting were time constraints, perception that the percutaneous injury did not represent a significant exposure, lack of knowledge about the reporting mechanism, and concern about confidentiality and professional discrimination. CONCLUSIONS: Medical housestaff are at substantial risk for occupational infection with HIV. A large proportion of internal medicine housestaff recall accidental exposure to blood during medical school and residency, and the majority of exposures were not reported. Hospitals may be able to increase rates of reporting of percutaneous exposures to HIV by developing programs that are easy to access, efficient, and strictly confidential.

Adult↗
PubMed1988

Software systems to control sensitivity studies of Monte Carlo simulation models.

Studies of the sensitivity of Monte Carlo models to changes in the values of their features involve repetitive simulations. Subsequent displays and analyses express variation in simulated outcomes as a function of change in location in multidimensional feature space and provide feedback via inputs for future simulations. A software system has been designed to control execution of the interacting programs required, reducing the need for human intervention. Assumptions about the goals and operation of the system as a whole are isolated within a program which executes component packages using interprogram control and communication mechanisms. The latter allow component programs to operate independently of the sources of data or the execution environment: they may be used separately, or in software systems, such as for sensitivity analysis of a Monte Carlo epidemic model. The methodology contributes to modularity at the level of executable programs and to the plausibility and efficiency of sensitivity studies.

Computer Simulation↗
PubMed1989

The use of the ventilatory anaerobic threshold for the development of exercise guidelines.

The general interest in the application of exercise testing to evaluate the work capacity or change in the functional ability of individuals has resulted in the development of a variety of noninvasive tests and test parameters such as the anaerobic threshold. This paper presents a computer program written in BASIC that determines the anaerobic threshold from expired respiratory gases collected from an incremental exercise test. Results are summarized in tabular as well as graphical format. The use of the incremental exercise test in conjunction with this computer program will provide another means of efficiently determining the exercise capability of the patient.

Anaerobic Threshold↗
PubMed1977

Semiautomatic processing of neurophysiological data: part II--a computer program for data reduction.

This paper describes a program for the processing of trains of nerve or muscle impulses (spikes). The program is designed to allow the efficient use of semiautomatic or manual measuring devices. It will handle up to six different sets of spikes and one cyclic,non-spike event (e.g., changing light intensity or limb position, etc.) Output may include computed interspike intervals and instantaneous frequencies, phase relationships between sets of spikes and between spikes and the non-spike event, and parameters of bursts found in the spike trains. Output is presented numerically and in the form of line-printer graphs,

Action Potentials↗
PubMed1992

Mutant prohead RNAs in the in vitro packaging of bacteriophage phi 29 DNA-gp3.

The 174-base prohead RNA encoded by bacteriophage phi 29 of Bacillus subtilis, essential for packaging of the DNA-gp3 (DNA-gene product 3) complex, was expressed efficiently from the cloned gene. Computer programs for RNA structure analysis were used to fold hypothetical RNA mutants and thus to target mutagenesis of the RNA for studies of structure and function. Five mutants of the RNA were then produced by oligonucleotide-directed mutagenesis that were altered in the primary sequence at selected sites; two of these mutants were predicted to be altered in secondary structure from a model established previously by a phylogenetic analysis. The binding of the 32P end-labeled mutant RNAs to RNA-free proheads was comparable with that of the wild-type RNA. However, the capability of the mutant RNAs to reconstitute RNA-free proheads for DNA-gp3 packaging in the defined in vitro system and for assembly of phage in RNA-free extracts was variable, depending upon the alteration. Changes of highly conserved bases that retained the predicted secondary structure of the RNA model were tolerated to a much greater extent than changes predicted to alter the RNA secondary structure.

Bacteriophages↗
PubMed1995

The educational implications of reproductive problems identified during investigations at Michigan dairy farms.

This study constitutes the review of 44 dairy herd investigations that were initiated because of complaints relating to decreased reproductive efficiency. Each investigation was conducted at the request of the veterinary practitioner who provided the routine reproductive examinations and consultations at the farm. Thus the types of problems identified were those not resolved by routine veterinary care and management practices. A total of 4.5, 27.3 and 31.8% of the farms, respectively, failed to keep reproductive records, failed to maintain accurate records on events such as breeding dates, or failed to evaluate available summary reports with the local veterinary practitioner. Of the 44 farms, 50.0, 38.6, 54.5 and 11.4%, respectively, reported problems related to estrus detection rate, number of days to first service (for reasons other than estrus detection), conception rate and early embryonic death. Within each of these reproductive parameters specific problems were defined and discussed. Reproductive inefficiency was found to be most commonly associated with ineffective estrus detection and decreased conception rate. Most importantly, farm managers and employees frequently misunderstood the relationship between the accuracy of estrus detection and the conception rate (61.4% of the farms). We therefore identified factors which have an impact on dairy herd reproductive efficiency to suggest topics for training programs for producers and practicing veterinarians as well as for elective courses for veterinary students in the area of theriogenology.

Journal Article↗
PubMed1986

A cost/effectiveness evaluation of lay therapy treatment for child abusing and high risk parents.

This longitudinal investigation tested the effectiveness and cost-efficiency of a lay therapy treatment program in comparison with a standard social work treatment approach. A pretest-extended posttest research design was used to follow a group of child abusing and high risk mothers who received lay therapy (N = 27) and a randomized control group of similar clients (N = 28) over a 12-month period. Outcome data were obtained through interview and direct observation of the parents and children at six-month intervals. A variety of standardized instruments were used including Cattell's 16 Personality Factor Test, Coopersmith's Self-Opinion Form, and the Nurturance and Parent Observation Scales, adapted from Baumrind. Treatment success was defined as progression toward the mean scores of a matched comparison group (N = 21) obtained from the general population of the community during the pretest. The results indicated a trend toward improvement on the outcome measures for both treatment groups. The group receiving lay therapy treatment improved only slightly more than the group receiving standard treatment; however, there was also significantly less attrition with the lay therapy group. Analysis of time budget study data indicated that the lay therapists spent an average of 17.46 hours per month with each of their clients thus permitting the social workers to spend considerably less time with lay therapy clients. Analysis of the direct costs of the programs, based on time budget information, indicated that the lay therapy treatment involved more direct client contact than the standard treatment approach and was also substantially more costly. The high cost of the program was attributed to low caseloads and redundancy in supervision. This study presents several practical program and research recommendations.

Child↗
PubMed1983

Relationship of service satisfaction to life satisfaction and perceived well-being.

Two procedures for gaining patients' evaluations of health services were compared: (a) the Client Satisfaction Questionnaire (CSQ-18B), a direct approach assessing the setting and services actually encountered, and (b) the Patient Satisfaction Questionnaire (PSQ), an approach that indirectly assesses satisfaction with service by inquiring about general health care attitudes. Results from 148 public health patients indicated that the PSQ produced the most acceptability problems and was tapping aspects of life satisfaction other than service satisfaction. However, the PSQ produced significantly lower reports of satisfaction. Additional comparison and interpretation of typical responses generated from the two approaches suggested, on the whole, that the CSQ-18B data provided clearer, more efficient, and more useful information for program planning and evaluation. In this study, service satisfaction measured by the CSQ-18B did not have any significant relationship to global or multidimensional (LDQ-30) measures of life satisfaction and well-being. In contrast, over a third of the variance in PSQ scores was accounted for by measures of life satisfaction. It appears that the PSQ elicits attitudes toward the more generalized health care delivery system as well as aspects of life satisfaction rather than reactions to specific services actually received.

Analysis of Variance↗
PubMed2005

[Neuromuscular effects of superimposed and combined transcutaneous electrical stimulation with voluntary activity: a review].

With voluntary muscular contraction (VOL), small motor units (MUs) are recruited before large MUs are (a submaximal muscular contraction recruits only small MUs), whereas electrical stimulation (ES) tends to reverse the recruitment order. On the basis of this observation, some authors have tested the physiological effects of ES superimposed simultaneously with VOL (superimposed technique [ST]) or separately (combined technique [CT]). With healthy subjects, ST does not recruit more MUs than VOL, except with eccentric contractions. After health subjects undergo training programs, ST appears to be as efficient as VOL in enhancing subjects' neuromuscular qualities. Nevertheless, the use of CT seems more effective than VOL. In postsurgical rehabilitation, both ST and CT are more effective than VOL. Actually, following knee surgery, ST and CT compensate for volume and muscle strength deficits with more efficiency than does VOL.

Combined Modality Therapy↗
PubMed2004

Analysis of approach to therapy for chronic liver disease in an HCV hyperendemic area of Japan.

In 1990, we conducted an epidemiological study of 509 residents in a hepatitis C virus (HCV) hyperendemic area in Japan. The purpose of the present study was to examine the approach to therapy for liver diseases accompanied by HCV and hepatitis B virus (HBV) infections among the surviving residents in the town after 12 years. Fifty-three with HCV or HBV infections among 385 people who resided in the town were clearly analyzed in 2002. The number of persons diagnosed with the liver diseases was as follows: HCV-related asymptomatic healthy carrier (1), past history of HCV infection (15), chronic hepatitis C (22), HCV-related liver cirrhosis (6), HCV-related hepatocellular carcinoma (HCC) (5), and HBV-related asymptomatic healthy carrier (4). HCC was detected in residents who did not have periodic regular hospital checkups. Only 19% of the 53 inhabitants consulted liver medical specialists, and 75% (3/4) who received interferon therapy received treatment from a liver medical specialist. It is necessary to provide continuous medical treatment to HCV carriers, minimizing difference in treatment quality in different medical institution. An efficient HCV medical checkup and a program of subsequence health management are important problems to be solved for improved health care.

Journal Article↗