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PubMed2003

An exploratory study using data envelopment analysis to assess neurotrauma patients in the intensive care unit.

Patients with severe head trauma were studied retrospectively to determine if Data Envelopment Analysis (DEA) could successfully model patients early in their stay in an intensive care unit. Variables examined were cerebral perfusion pressure, body temperature, mean arterial pressure, serum osmolarity and pCO2. Unlike regression-based models that focus on mean values for the group, DEA evaluates each patient individually calculating an "efficiency" score based on a patient's ability to maximize output for a given set of physiologic inputs. Patients with high efficiency scores were found to have a better chance of making a full recovery than similarly injured patients that were inefficient. This approach needs further study but may offer physicians the opportunity to improve patient outcome subject to the manipulation of individual variables from the results of a DEA model rather than aiming for normal or average physiologic values.

Brain Injuries↗
PubMed1998

Detraining from total body exercise ergometry in individuals with spinal cord injury.

This study was designed to investigate the effects of detraining that occurred during an 8 week period of muscular inactivity following a 12 week training program of artificial computerized functional electrical stimulation cycle ergometry (CFES LE) and arm ergometry. Six spinal cord injured male individuals were followed through an 8 week detraining period that was preceded by a 12 week exercise program including CFES LE and arm ergometry. Maximal graded exercise tests were completed and measurements of peak oxygen consumption (VO2), heart rate (HR), ventilation (VE) workload, and creatine kinase were taken. Testing occurred at initial training (0T), after 12 weeks of training (12T), and after 8 weeks of detraining (DT). After the training program, peak VO2 increased significantly from 0.562 +/- 0.126 (0T) to 1.021 +/- 0.247 l/min (12T, P < 0.05). After DT, peak VO2 decreased to 0.791 +/- 0.216 l/min, which was lower than 12T (P < 0.05), yet higher than 0T (P < 0.05). After DT, peak workoad had decreased from 0.675 +/- 0.203 (12T) to 0.32 +/- 0.203 kp (P < 0.05), which was not different than 0T. Creatine kinase levels were significantly lower both at 12T and DT compared to 0T (P < 0.05). In addition, this training program induced linear increases in both VO2 and HR with workload, which were retained after DT. These increases did not reach statistical significance. however. No apparent relationship existed between these values at baseline. There were no significant differences in submaximal or peak HR of VE between the three testing periods. The results indicate that both peripheral muscular adaptations and central distribution adaptations in SCI individuals are partially maintained following 8 weeks of DT from CFES LE and arm ergometry.

Adaptation, Physiological↗
PubMed1981

Elimination and replenishment of tricarboxylic acid-cycle intermediates in myocardium.

1. The contribution of Co2 fixation to the anaplerotic mechanisms in the myocardium was investigated in isolated perfused rat hearts. 2. K+-induced arrest of the heart was used to elicit a transition in the concentrations of the intermediates of the tricarboxylic acid cycle. 3. Incorporation of 14C from [14]bicarbonate into tricarboxylic acid-cycle intermediates was measured and the rates of the reactions of the cycle were estimated by means of a linear optimization program which solves the differential equations describing a simulation model of the tricarboxylic acid cycle and related reactions. 4. The results showed that the rate of CO2 fixation is dependent on the metabolic state of the myocardium. Upon a sudden diminution of cellular ATP consumption, the pool size of the tricarboxylic acid-cycle metabolites increased and the rate of label incorporation from [14C]bicarbonate into the cycle metabolites increased simultaneously. The computer model was necessary to separate the rapid equilibration between bicarbonate and some metabolites from the potentially anaplerotic reactions. The main route of anaplerosis during metabolite accumulation was through malate + oxaloacetate. Under steady-state conditions there was a constant net outward flow from the tricarboxylic acid cycle via the malate + oxaloacetate pool, with a concomitant anaplerotic flow from metabolites forming succinyl-CoA (3-carboxypropionyl-CoA).

Animals↗
PubMed1983

Use of the F test for determining the degree of enzyme-kinetic and ligand-binding data. A Monte Carlo simulation study.

1. Initial-rate data were simulated for 13 representative enzyme mechanisms with the use of several distributions of rate constants in order to locate conditions leading to v([S]) curves in physiological ranges of substrate concentration. 2. In all, 420 sets of such v([S]) curves were generated with the use of several choices of substrate concentration range (two, three or four orders of magnitude), number of experimental points (10, 15 or 20), error on v (5-10%) and standard deviation on v (5-9%) in order to simulate experimental results in a number of possible ways. 3. Curve-fitting was carried out to rational functions of degree 1:1, 2:2, . . ., 5:5 until there was no statistically significant decrease in the sum of weighted squared residuals as judged by the F test at 95% and 99% confidence levels. 4. It was checked whether the non-linear regression program had located a good minimum in the sum of squares by also fitting the data with the correct values of parameters as starting estimates. 5. A similar procedure was adopted with 110 sets of binding data simulated for 11 models, and the F test was used to see if fractional-saturation data generated by a binding polynomial of order n could be adequately fitted by one of order m, m less than n. 6. From the 530 simulations the F test was successful in fixing the correct degree with a probability of 0.62 at the 95% confidence level, but this fell with increase in degree as follows: 1:1 (0.98), 2:2 (0.71), 3:3 (0.43) and 4:4 (0.34), the first numbers being the degree of the rate equation and those in parentheses referring to the 95% confidence level. 7. It made little difference whether the 95% or the 99% confidence level was consulted, as there were very few borderline cases. 8. The chance of detecting deviations from Michaelis-Menten kinetics, i.e. terms of at least second-order in a rate equation of degree n:n, n greater than 1, was estimated to be about 0.8. 9. The probability of the F test leading to a spurious result due to error in the data was found to be about 0.04. 10. The probability with which 4:4 mechanisms can lead to v([S]) plots with no, one, two or three turning points was computed, and it was established that there is a small but finite chance that the increase in degree that occurs in some mechanisms when ES in equilibrium EP interconversions are explicitly allowed for can be detected by the F test.

Enzymes↗
PubMed1988

Kinetic mechanism of chicken liver xanthine dehydrogenase.

The kinetic behaviour of chicken-liver xanthine dehydrogenase (xanthine/NAD+ oxidoreductase; EC 1.2.1.37) has been studied. Steady-state results, obtained from a wide range of concentrations of substrates and products, were fitted by rational functions of degree 1:1, 1:2, 2:2 and 3:3 with respect to substrates, and 0:1, 1:1, 0:2 and 1:2 with regard to products, using a non-linear regression program which guarantees the fit. The goodness of fit was improved using a computer program that combines model discrimination, parameter refinement and sequential experimental design. The AIC and F tests were also used for model discrimination. For comparative purposes, the xanthine/oxygen oxidoreductase reaction was also studied. From the functions which give the maximum improvement, the complete rate equation was deduced. The significance of the terms was stated by the above methods. It was concluded that xanthine dehydrogenase requires a minimum mechanism of degree 1:1 for xanthine, 2:2 for NAD+, 1:1 for uric acid and 1:2 for NADH in the xanthine/NAD+ oxidoreductase reaction. These are the minimum degrees required but a rate equation of higher degree is not excluded.

Animals↗
PubMed1988

Kinetic studies of chicken and turkey liver mitochondrial aspartate aminotransferase.

The kinetic behaviour of chicken liver and turkey liver aspartate aminotransferases (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) was studied. Steady-state data were obtained from a wide range of concentrations of substrates and product L-glutamate. The data were fitted by rational functions of degree 1:1, 1:2 and 2:2 with respect to substrates and 0:1, 1:1, 0:2 and 1:2 with regard to product (L-glutamate), by using a non-linear regression program that guarantees the fit. The goodness of fit was improved by the use of a computer program that combines model discrimination parameter refinement and sequential experimental design. It was concluded that aspartate aminotransferase requires a minimum velocity equation of degree 2:2 for L-aspartate, 2:2 for 2-oxoglutarate and 1:2 for L-glutamate. Finally, a plausible kinetic mechanism that justifies these experimental results is proposed.

Animals↗
PubMed1982

[Dynamics of egg maturation in the parasitoid Lixophaga diatraeae (Diptera, Tachinidae) raised in a substitute host, Galleria mellonella (Lepidoptera, Pyralidae)].

The content of the uterus and ovaries of L. diatraeae (an ovolarviparous tachinid fly) was studied by dissecting 121 females 0 to 25 days old. Several size classes of flies (p: small; m: medium; g: big) were used, weighing 10 to 12.5 mg, 12.5 to 13.5 mg, and 13.5 to 16 mg, respectively. The mean number of ovarioles per ovary, correlated to female size, was 12.1 for p as against 12.9 for m + g females. The total mean number of eggs and oocytes changed with female age and weight. For 0, 5, 10 and 15-day old females, this number was 56, 149, 158 and 202, respectively in g flies and 51, 128, 141 and 139, respectively, in p ones. To study egg maturation dynamics, we counted the total number of eggs + oocytes per p female (Y1), the eggs in the uterus (Y2), partially embryonated eggs (Y3), and entirely embryonated eggs (Y4). The experimental results were fitted to various age functions using a non-linear adjustment program. The models fitting each datum best were asymptotic functions of the form, Y = A [1-e-K(x-D)], where A is the asymptotic value, K a speed constant of the studied phenomenon and D age at the beginning of the phenomenon. At emergence time, each female contained a mean of 50 oocytes which passed into the uterus immediately after mating. Egg production continued for at least 10 days after emergence. The rate of embryogenesis seemed to be influenced by the number of eggs in the uterus and/or the age of the fly; it was high for the first eggs then decreased progressively. In our conditions, the first eggs with a planidium ready to hatch appeared at 10 days post-emergence. To obtain a maximum number of larvae in good health, it is better to dissect 12 to 18-day old females. The egg volume increases slightly during embryogenesis.

Animals↗
PubMed2003

Equations of substrate-inhibition kinetics applied to pig kidney diamine oxidase (DAO, E.C. 1.4.3.6).

Pig kidney diamine oxidase (DAO) and other semicarbazide-sensitive amine oxidases (SSAO) show clear substrate-inhibition kinetics and a reaction-scheme mechanism based on two substrate binding sites. We evaluated several reaction scheme mechanisms with a non-linear regression program (NCSS), estimating R2, the constants of the equations and their standard errors and we determined the deviation of experimental data from theoretical equations. The best fit was obtained with a "dead end" mechanism with two binding sites. Based on this scheme, other schemes for a two-substrate reaction and for mechanisms of inhibition were constructed. These reaction schemes, even at low substrate concentration, fitted experimental data better than Michaelis-Menten kinetics, and provided information on the mechanisms of action of inhibitors. The presence of two substrate-binding sites on pig kidney DAO was confirmed by all experimental data.

Amine Oxidase (Copper-Containing)↗
PubMed2004

Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model.

Multitiered quantitative analysis of biological systems is rapidly becoming the desired approach to study hierarchical functional interactions between proteins and metabolites. We describe here a novel systematic approach to analyze organisms with complex metabolic regulatory networks. By using precise analytical methods to measure biochemical constituents and their relative abundance in whole plasma of transgenic ApoE*3-Leiden mice and an isogenic wild-type control group, simultaneous snapshots of metabolic and protein states were obtained. Novel data processing and multivariate analysis tools such as Impurity Resolution Software (IMPRESS) and Windows-based linear fit program (WINLIN) were used to compare protein and metabolic profiles in parallel. Canonical correlations of the resulting data show quantitative relationships between heterogeneous components in the TG animals. These results, obtained solely from whole plasma analysis allowed us, in a rapid manner, to corroborate previous findings as well as find new events pertaining to dominant and peripheral events in lipoprotein metabolism of a genetically modified mammalian organism in relation to ApoE3, a key mediator of lipoprotein metabolism.

Animals↗
PubMed2005

A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes.

MOTIVATION: It is known that steady-state flux distributions in metabolic networks can be expressed as non-negative combinations of elementary modes. However, little understanding has been achieved so far in how individual elementary modes contribute to the reconstruction of actual physiological flux distributions. RESULTS: We introduce an approach for decomposing steady-state flux distributions onto elementary modes based on quadratic programming. The decomposition is performed so as to favour modes that are closest to the actual state of the system, i.e. most relevant for biological interpretation. As an illustration, an application of this approach to a model of yeast glycolysis is presented. AVAILABILITY: Software is available upon request from the authors.

Algorithms↗
PubMed2005

Predicting a set of minimal free energy RNA secondary structures common to two sequences.

MOTIVATION: Function derives from structure, therefore, there is need for methods to predict functional RNA structures. RESULTS: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low-energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20% of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence. AVAILABILITY: Dynalign can be downloaded at http://rna.urmc.rochester.edu

Algorithms↗
PubMed1986

Disposition of propofol in patients undergoing surgery. A comparison in men and women.

The disposition kinetics of propofol have been determined in 12 patients (six female) receiving propofol 2.5 mg kg-1 for induction of anaesthesia, which was maintained with 67% nitrous oxide in oxygen and 1-1.5% halothane. Peripheral blood samples were collected at selected times up to 8 h after the injection of the drug, and whole blood propofol concentrations determined by HPLC with fluorescence detection. Drug concentration-time data were analysed by the non-linear regression program ELSFIT. This showed the data to be describable by a tri-exponential equation, corresponding to a three-compartment model. There were no differences in the derived kinetic indices for the male and female patients, with the exception of a greater Vdss:V gamma ratio in the males. The terminal half-life in the male patients was 262 min (SEM 44), and in the female patients 309 min (60). Vdss was 329 litre (67) and 313 litre (69) in male and female patients, respectively. The clearance in both groups was 1.8 litre min-1. Seven out of 12 patients showed significant secondary peaks in blood propofol concentration associated with recovery from anaesthesia.

Adult↗
PubMed2000

Measurement of gas-liquid partition coefficient and headspace concentration profiles of perfume materials by solid-phase microextraction and capillary gas chromatography-mass spectrometry

An empirical model describing the relationship between the partition coefficients (K) of perfume materials in the solid-phase microextraction (SPME) fiber stationary phase and the Linearly Temperature Programmed Retention Index (LTPRI) is obtained. This is established using a mixture of eleven selected fragrance materials spiked in mineral oil at different concentration levels to simulate liquid laundry detergent matrices. Headspace concentrations of the materials are measured using both static headspace and SPME-gas chromatography analysis. The empirical model is tested by measuring the K values for fourteen perfume materials experimentally. Three of the calculated K values are within 2-19% of the measured K value, and the other eleven calculated K values are within 22-59%. This range of deviation is understandable because a diverse mixture was used to cover most chemical functionalities in order to make the model generally applicable. Better prediction accuracy is expected when a model is established using a specific category of compounds, such as hydrocarbons or aromatics. The use of this method to estimate distribution constants of fragrance materials in liquid matrices is demonstrated. The headspace SPME using the established relationship between the gas-liquid partition coefficient and the LTPRI is applied to measure the headspace concentration of fragrances. It is demonstrated that this approach can be used to monitor the headspace perfume profiles over consumer laundry and cleaning products. This method can provide high sample throughput, reproducibility, simplicity, and accuracy for many applications for screening major fragrance materials over consumer products. The approach demonstrated here can be used to translate headspace SPME results into true static headspace concentration profiles. This translation is critical for obtaining the gas-phase composition by correcting for the inherent differential partitioning of analytes into the fiber stationary phase.

Journal Article↗
PubMed2001

The efficiency of the delivery of neonatal care in the UK.

BACKGROUND: A recent paper in Journal of Public Health Medicine (O'Neill et al., 2000; 22(1): 108-115) used regression modelling to determine the average costs of neonatal care services for a sample of 49 units in the United Kingdom in 1990-1991, and concluded that economies of scale were present in the sample as a whole. Although this form of modelling is useful, analysis of the efficiency of production for individual units is also important. METHODS: Data envelopment analysis (DEA) was used to analyse the data set published by O'Neil et al., to determine technical efficiency of neonatal units, measuring efficiency compared with a benchmark efficient frontier, and estimating economies of scale for each unit. Potential cost savings if units were to operate efficiently are estimated. RESULTS: There is evidence of substantial levels of technical inefficiency. Economies of scale varied between units, with increasing returns in the 36 inefficient units, and mainly constant returns in the 13 efficient units. This suggests that the presence of technical inefficiency was as important as scale inefficiencies. Total cost savings, if all units were operating efficiently, are estimated at ł10.4 million, equivalent to 10 extra units producing 57,000 additional days of care. CONCLUSIONS: DEA is a technique of great potential value in analysing the efficiency of health care production. As well as inefficiencies in the production of neonatal care in the United Kingdom due to differences in the scale of production, there appears to have been considerable technical inefficiency, which was not due to differences in case mix. The potential cost savings from efficiency gains are large.

Data Interpretation, Statistical↗
PubMed2002

Operating room managers' use of integer programming for assigning block time to surgical groups: a case study.

UNLABELLED: A common problem at hospitals with fixed amounts of available operating room (OR) time (i.e., "block time") is determining an equitable method of distributing time to surgical groups. Typically, facilities determine a surgical group's share of available block time using formulas based on OR utilization, contribution margin, or some other performance metric. Once each group's share of time has been calculated, a method must be found for fitting each group's allocated OR time into the surgical master schedule. This involves assigning specific ORs on specific days of the week to specific surgical groups, usually with the objective of ensuring that the time assigned to each group is close to its target share. Unfortunately, the target allocated to a group is rarely expressible as a multiple of whole blocks. In this paper, we describe a hospital's experience using the mathematical technique of integer programming to solve the problem of developing a consistent schedule that minimizes the shortfall between each group's target and actual assignment of OR time. Schedule accuracy, the sum over all surgical groups of shortfalls divided by the total time available on the schedule, was 99.7% (SD 0.1%, n = 11). Simulations show the algorithm's accuracy can exceed 97% with > or =4 ORs. The method is a systematic and successful way to assign OR blocks to surgeons. IMPLICATIONS: At hospitals with a fixed budget of operating room (OR) time, integer programming can be used by OR managers to decide which surgical group is to be allocated which OR on which day(s) of the week. In this case study, we describe the successful application of integer programming to this task, and discuss the applicability of the results to other hospitals.

Elective Surgical Procedures↗
PubMed1998

Beneficial and harmful effects of augmented feedback on physicians' clinical-teaching performances.

PURPOSE: To evaluate whether clinical-teaching skills could be improved by providing teachers with augmented student feedback. METHOD: A randomized, controlled trial in 1994 included 42 attending physicians and 39 residents from the Department of Medicine at the Indiana University School of Medicine who taught 110 students on medicine ward rotations for one-month periods. Before teaching rotations, intervention group teachers received norm-referenced, graphic summaries of their teaching performances as rated by students. At mid-month, intervention group teachers received students' ratings augmented by individualized teaching-effectiveness guidelines based on the Stanford Faculty Development Program framework. Linear models were used to analyze the students' mean ratings of teaching behaviors at mid-month and end-of-month. Independent variables included performance ratings, intervention status, teacher status, teaching experience, and interactions with baseline ratings. RESULTS: Complex interactions with baseline performance were found for most teaching categories at mid-month and end-of-month. The intervention-group teachers who had high baseline performance scores had higher student ratings than did the control group teachers with similar baseline scores; the intervention group teachers who had low baseline performance scores were rated lower than were the control group teachers with comparable baseline scores. The residents who had medium or high baseline scores were rated higher than were the attending physicians with comparable baseline scores; the performance of the residents who had low baseline scores was similar to that of the attending physicians with comparable baseline scores. CONCLUSION: Baseline performance is important for targeting those teachers most likely to benefit from augmented student feedback. Potential deterioration in teaching performance warrants a reconsideration of distributing students' ratings to teachers with low baseline performance scores.

Clinical Clerkship↗