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PubMed2004

Reverse engineering of biochemical equations from time-course data by means of genetic programming.

Increased research aimed at simulating biological systems requires sophisticated parameter estimation methods. All current approaches, including genetic algorithms, need pre-existing equations to be functional. A generalized approach to predict not only parameters but also biochemical equations from only observable time-course information must be developed and a computational method to generate arbitrary equations without knowledge of biochemical reaction mechanisms must be developed. We present a technique to predict an equation using genetic programming. Our technique can search topology and numerical parameters of mathematical expression simultaneously. To improve the search ability of numeric constants, we added numeric mutation to the conventional procedure. As case studies, we predicted two equations of enzyme-catalyzed reactions regarding adenylate kinase and phosphofructokinase. Our numerical experimental results showed that our approach could obtain correct topology and parameters that were close to the originals. The mean errors between given and simulation-predicted time-courses were 1.6 x 10(-5)% and 2.0 x 10(-3)%, respectively. Our equation prediction approach can be applied to identify metabolic reactions from observable time-courses.

Algorithms↗
PubMed2004

Prediction of retention times in linear gradient temperature and pressure programmed analysis on capillary columns.

The simultaneous temperature and inlet pressure programming (TPP) in gas chromatographic analysis decreases the retention time and the maximum value of temperature required for the elution of high boiling substances. Therefore, compounds sensitive to thermal degradation can be better analysed and column ageing is reduced. However, the empirical choice of proper analysis conditions requires many preliminary runs; this paper describes a procedure for the theoretical prediction of retention times in TPP using few preliminary runs carried out in isobaric and isothermal conditions. The used program permits the prediction of the retention times of the compounds analysed with any different TPP run carried out within the temperature and pressure ranges investigated with the preliminary runs. The influence of various analytical parameters on the accuracy of the prediction values was investigated. The proposed model also predicts the relative position in the chromatogram of closely eluting peaks and the possible coincidence of retention times or inversion of the elution order with changing temperature. It is also possible to foresee the analytical conditions, which offer a baseline separation of all of the peaks of the sample.

Chromatography, Gas↗
PubMed2006

Determination of lanthanides in international geochemical reference materials by reversed-phase high-performance liquid chromatography using error propagation theory to estimate total analysis uncertainties.

The weighted least-squares (WLS) regression method was successfully applied to establish calibration curves with variable amounts of lanthanides ranging from 0.002 to 0.430 microg. These curves were employed for the analysis of 13 lanthanides (La-Nd, Sm-Tb, and Ho-Lu) in 12 international geochemical reference materials (IGRM). The separation of the lanthanide group was achieved in approximately 15 min. Dysprosium could not be determined in IGRM because of its co-elution with Yttrium. A linear gradient program of alpha-HIBA eluent with a concentration ranging from 0.05 to 0.5 M (0.1 M OS, pH 3.8 with NH(4)OH, and a flow-rate of 1.0 ml/min) was employed. The detection was performed with a UV-vis system at 658 nm using a post-column reagent of Arsenazo III (0.5 ml/min). With this set of RP-HPLC conditions together with the use of both the ordinary least-squares (OLS) and the WLS regressions, we report the results of the measurements along with the total propagated uncertainties in individual concentration values. The uncertainties were obtained by combining standard errors in both regression parameters (slope and intercept) with those related to the chromatographic peak areas. The straight-line slopes and intercepts calculated by the WLS method provided not only considerably smaller errors than the conventional OLS method but also a much better estimation of the limits of detection. The concentrations calculated were compared with the "most probable" concentration values of these reference materials reported in the literature. Statistically significant agreement was consistently observed between the HPLC data and the literature values. The total uncertainties in estimated concentration values for the WLS were consistently smaller than the respective errors for the OLS.

Algorithms↗
PubMed2005

Simultaneous determination of nineteen hallucinogenic tryptamines/beta-calbolines and phenethylamines using gas chromatography-mass spectrometry and liquid chromatography-electrospray ionisation-mass spectrometry.

To investigate the trend of non-controlled drugs of abuse, simultaneous analytical methods were developed using GC-MS and LC-ESI-MS for 8 tryptamines/beta-carbolines, 6 phenethylamines of typically non-controlled substances in Japan, and, additionally, five legally controlled tryptamines and phenethylamines originally found in fungi or plants. Moreover, the proposed methods were applied to analyses of these drugs in 99 kinds of products (a total number of 123 products purchased at adult shops or via the Internet over the past 2 years in Japan), which potentially advertised psychotropic/psychoactive effects. The samples were extracted with methanol under ultrasonication. After centrifugation, the extracts were filtered prior to injections. GC-MS analysis was performed using a DB-5MS capillary column. Regarding the LC-ESI-MS analysis; the separation of the target drugs was optimized on an ODS column in acetonitrile/MeOH (7:3)-10 mM ammonium formate buffer (pH 3.5)/acetonitrile (95:5) by a linear gradient program and a quantitative analysis was carried out by the monitoring of each [M+H]+ in the positive ion mode of ESI-MS. As a result of the analyses using GC-MS and LC-ESI-MS, 5-MeO-DIPT (the synthetic substance known by the street name "Foxy") was found in 8 out of the 99 kinds of products. Additionally, AMT (from brown powder), DMT (from dried plant), harmine and harmaline (from dried plant) were also found in some of the 99 products. These analytical methods could be useful for the investigation of the distribution of the non-controlled psychotropic tryptamines/beta-carbolines and phenethylamines in the market.

Calibration↗
PubMed2006

Low-level quantitation of oxycodone and its oxidative metabolites, noroxycodone, and oxymorphone, in rat plasma by high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry.

A method was developed for quantification of oxycodone, noroxycodone, and oxymorphone in small volumes (50 microl) of rat plasma by high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry using turbo ion-spray. Deuterated (d3) opioid analogues acted as internal standards. Sample preparation involved protein precipitation with acetonitrile, centrifugal evaporation, and reconstitution in mobile phase; analyte separation was performed on a C18 (5 microm, 2.1 mm x 50 mm) column using a linear gradient program. Lower limits of quantitation (ng/ml) and their between-day accuracy and precision were-oxycodone, 0.9 (-0.2 and 7.8%); noroxycodone, 1.0 (0.6 and 6.2%); oxymorphone 1.0 (-1.8 and 9.5%).

Analgesics, Opioid↗
PubMed2006

Modelling the adsorption of Cd(II), Cu(II), Ni(II), Pb(II), and Zn(II) onto Fithian illite.

Illite samples from Fithian, IL were purified and saturated with Na(+) ions. The acid-base surface chemistry of the Na-saturated illite was studied by potentiometric titration experiments with 0.1, 0.01, and 0.001 M NaNO(3) solutions as the background electrolyte. Results showed that the titration curves obtained at different ionic strengths did not intersect in the studied pH range. The adsorption of Cd(II), Cu(II), Ni(II), Pb(II), and Zn(II) onto illite was investigated as a function of pH and ionic strength by batch adsorption experiments. Two distinct mechanisms of metal adsorption were found from the experimental results: nonspecific ion-exchange reactions at lower pH values on the basal surfaces and 'frayed edges' and specific adsorption at higher pH values on the mineral edges. Ionic strength had a greater effect on the ion-exchange reactions. The binding constants for the five heavy metals onto illite were determined using the least-square fitting computer program FITEQL. Linear free energy relationships were found between the surface binding constants and the first hydrolysis constants of the metals.

Journal Article↗
PubMed2006

Oregon Beach Monitoring Program: Bacterial exceedances in marine and freshwater creeks/outfall samples, October 2002-April 2005.

A total of 3086 samples, both marine (2916) and freshwater creeks/outfall samples (170) were collected and analyzed for enterococci during October 2002-April 2005, from 52 designated beaches in Oregon. A total of 3.2% (99/3086) of the samples at 21 beaches exceeded 158 most probable number (MPN)/100 milliliters (mL). The average enterococci levels of these 99 exceedances was 559 MPN/100 mL, with a maximum of 4352 MPN/100 mL (Otter Rock and Ona) and a minimum of 160 MPN/100 mL (Sunset Bay State Park, Bastendorff, and Mill). For marine water, 77/2916 (2.6%) exceeded 158 MPN/100 mL. For freshwater, 22/170 (12.9%) exceeded 158 MPN/100 mL, with a maximum of 587 MPN/100 mL at Sunset Bay. Sixty percent of the marine and 9% of freshwater exceedances occurred during the winter. Seventy-two percent (55/77) of the marine exceedances occurred after rainfall events (0.01-60.0 mm). At Harris and Mill Beaches, cumulative rainfall was highly correlated with bacterial densities, R = 0.7. Rainfall, at both beaches, explained about one-half the variation in log10 bacteria density (R2 = 0.5). Additional monitoring is warranted to further characterize bacterial contamination in Oregon waters.

Bathing Beaches↗
PubMed2006

The generalized quadratic knapsack problem. A neuronal network approach.

The solution of an optimization problem through the continuous Hopfield network (CHN) is based on some energy or Lyapunov function, which decreases as the system evolves until a local minimum value is attained. A new energy function is proposed in this paper so that any 0-1 linear constrains programming with quadratic objective function can be solved. This problem, denoted as the generalized quadratic knapsack problem (GQKP), includes as particular cases well-known problems such as the traveling salesman problem (TSP) and the quadratic assignment problem (QAP). This new energy function generalizes those proposed by other authors. Through this energy function, any GQKP can be solved with an appropriate parameter setting procedure, which is detailed in this paper. As a particular case, and in order to test this generalized energy function, some computational experiments solving the traveling salesman problem are also included.

Algorithms↗
PubMed1999

High-speed gas chromatography: an overview of various concepts.

An overview is given of existing methods to minimise the analysis time in gas chromatography (GC) being the subject of many publications in the scientific literature. Packed and (multi-) capillary columns are compared with respect to their deployment in fast GC. It is assumed that the contribution of the stationary phase to peak broadening can be neglected (low liquid phase loading and thin film columns, respectively). The treatment is based on the minimisation of the analysis time required on both column types for the resolution of a critical pair of solutes (resolution normalised conditions). Theoretical relationships are given, describing analysis time and the related pressure drop. The equations are expressed in reduced parameters, making a comparison of column types considerably simpler than with the conventional equations. Reduction of the characteristic diameter, being the inside column diameter for open tubular columns and the particle size for packed columns, is the best approach to increase the separation speed in gas chromatography. Extremely fast analysis is only possible when the required number of plates to separate a critical pair of solutes is relatively low. Reducing the analysis time by reduction of the characteristic diameter is accompanied by a proportionally higher required inlet pressure. Due to the high resistance of flow of packed columns this seriously limits the use of packed columns for fast GC. For fast GC hydrogen has to be used as carrier gas and in some situations vacuum-outlet operation of capillary columns allows a further minimisation of the analysis time. For fast GC the columns should be operated near the conditions for minimum plate height. Linear temperature programmed fast GC requires high column temperature programming rates. Reduction of the characteristic diameter affects the sample capacity of the "fast columns". This effect is very pronounced for narrow-bore columns and in principle non-existing in packed columns. Multi-capillary columns (a parallel configuration of some 900 narrow-bore capillaries) take an intermediate position.

Chromatography, Gas↗
PubMed2002

Clinical implementation of intensity-modulated arc therapy.

PURPOSE: Intensity-modulated arc therapy (IMAT) is a method for delivering intensity-modulated radiation therapy (IMRT) using rotational beams. During delivery, the field shape, formed by a multileaf collimator (MLC), changes constantly. The objectives of this study were to (1) clinically implement the IMAT technique, and (2) evaluate the dosimetry in comparison with conventional three-dimensional (3D) conformal techniques. METHODS AND MATERIALS: Forward planning with a commercial system (RenderPlan 3D, Precision Therapy International, Inc., Norcross, GA) was used for IMAT planning. Arcs were approximated as multiple shaped fields spaced every 5-10 degrees around the patient. The number and ranges of the arcs were chosen manually. Multiple coplanar, superimposing arcs or noncoplanar arcs with or without a wedge were allowed. For comparison, conventional 3D conformal treatment plans were generated with the same commercial forward planning system as for IMAT. Intensity-modulated treatment plans were also created with a commercial inverse planning system (CORVUS, Nomos Corporation). A leaf-sequencing program was developed to generate the dynamic MLC prescriptions. IMAT treatment delivery was accomplished by programming the linear accelerator (linac) to deliver an arc and the MLC to step through a sequence of fields. Both gantry rotation and leaf motion were enslaved to the delivered MUs. Dosimetric accuracy of the entire process was verified with phantoms before IMAT was used clinically. For each IMAT treatment, a dry run was performed to assess the geometric and dosimetric accuracy. Both the central axis dose and dose distributions were measured and compared with predictions by the planning system. RESULTS: By the end of May 2001, 50 patients had completed their treatments with the IMAT technique. Two to five arcs were needed to achieve highly conformal dose distributions. The IMAT plans provided better dose uniformity in the target and lower doses to normal structures than 3D conformal plans. The results varied when the comparison was made with fixed gantry IMRT. In general, IMAT plans provided more uniform dose distributions in the target, whereas the inverse-planned fixed gantry treatments had greater flexibility in controlling dose to the critical structures. Because the field sizes and shapes used in the IMAT were similar to those used in conventional treatments, the dosimetric uncertainty was very small. Of the first 32 patients treated, the average difference between the measured and predicted doses was -0.54 +/- 1.72% at isocenter. The 80%-95% isodose contours measured with film dosimetry matched those predicted by the planning system to within 2 mm. The planning time for IMAT was slightly longer than for generating conventional 3D conformal plans. However, because of the need to create phantom plans for the dry run, the overall planning time was doubled. The average time a patient spent on the table for IMAT treatment was similar to conventional treatments. CONCLUSION: Initial results demonstrated the feasibility and accuracy of IMAT for achieving highly conformal dose distributions for different sites. If treatment plans can be optimized for IMAT cone beam delivery, we expect IMAT to achieve dose distributions that rival both slice-based and fixed-field IMRT techniques. The efficient delivery with existing linac and MLC makes IMAT a practical choice.

Brain Neoplasms↗
PubMed1999

Binding of centchroman with human serum as determined by charcoal adsorption method.

Protein binding of drugs is an important factor influencing both pharmacokinetic and pharmacodynamic parameters. Thus, knowing the extent of protein binding of drugs is crucial. Centchroman is a non-steroidal once a week oral contraceptive. It has been reported to be useful for the treatment of breast cancer and osteoporosis. Ample data has been generated on pharmacokinetics of centchroman in animals and humans. The extent of protein binding of centchroman has not been established so far. Non-specific adsorption of the drug limits the use of conventional methods like ultrafiltration and equilibrium dialysis. A method of charcoal adsorption as reported by Yuan et al. (method I) was used after modification (method II) to determine its binding to human serum. The extent of protein binding (%) is estimated from decline of percent drug remaining in the supernatant after adding the charcoal. Study was carried out at 1- and 10-microg/ml concentrations in drug free human serum samples and an HPLC assay was used to determine concentration-time data. The percentage of centchroman remaining in serum versus time data was analysed using non-linear fitting programs on WinNonlin software. Method II was found to give higher estimates of protein binding than the former method by preventing the dilution effect. Using this method, the extent of protein binding of centchroman was found to be 101.83+/-1.28 and 94.87+/-3.59% at 1 and 10 microg/ml, respectively. However, it was approximately 90% in the individual serum samples showing intersubject variability in protein binding of centchroman.

Adsorption↗
PubMed2002

Optimization of urease immobilization onto non-porous HEMA incorporated poly(EGDMA) microbeads and estimation of kinetic parameters.

Jack bean urease (urea aminohydrolase, EC 3.5.1.5) was immobilized onto modified non-porous poly(ethylene glycol dimethacrylate/2-hydroxy ethylene methacrylate), (poly(EGDMA/HEMA)), microbeads prepared by suspension copolymerization for the potential use in hemoperfusion columns, not previously reported. The conditions of immobilization; enzyme concentration, medium pH, substrate and ethylene diamine tetra acetic acid (EDTA) presence in the immobilization medium in different concentrations, enzyme loading ratio, processing time and immobilization temperature were investigated for highest apparent activity. Immobilized enzyme retained 73% of its original activity for 75 days of repeated use with a deactivation constant kd = 3.72 x 10(-3) day(-1). A canned non-linear regression program was used to estimate the intrinsic kinetic parameters of immobilized enzyme with a low value of observable Thiele modulus (phi < 0.3) and these parameters were compared with those of free urease. The best-fit kinetic parameters of a Michaelis-Menten model were estimated as Vm = 3.318 x 10(-4) micromol/s mg bound enzyme protein, Km = 15.94 mM for immobilized, and Vm = 1.074 micromol NH3/s mg enzyme protein, Km = 14.49 mM for free urease. The drastic decrease in Vm value was attributed to steric effects, conformational changes in enzyme structure or denaturation of the enzyme during immobilization. Nevertheless, the change in Km value was insignificant for the unchanged affinity of the substrate with immobilization. For higher immobilized urease activity, smaller particle size and concentrated urease with higher specific activity could be used in the immobilization process.

Enzymes, Immobilized↗
PubMed2005

Progressive thermal desorption of vapor mixtures from a preconcentrator with a porous metal foam internal architecture and variable thermal ramp rates.

A vapor preconcentrator has been designed with the porous polymer (Tenax) packed into a highly porous metal foam to facilitate thermal conductivity and temperature uniformity throughout the bed of the preconcentrator during heating. Vapors were desorbed using linear temperature programming from room temperature to a maximum temperature of 170 or 200 degrees C; the programmed duration of the thermal ramp was varied from 10 to 180 s. The partial separation of vapor mixtures that are thermally desorbed from the preconcentrator has been examined in terms of a metric for resolution, using methyl ethyl ketone, toluene, and dimethyl methylphosphonate as a test mixture. Vapors desorbed as a sequence of partially separated overlapping peaks, as observed with a polymer-coated flexural plate wave sensor. It was shown that vapor mixture resolution improved as the total time of the thermal ramp was extended from 30 to 120 s. In this way, the preconcentrator serves to act as a preseparator in addition to its usual functions for sampling, signal modulation, and improving sensitivity. Overlapping peaks were modeled, and peak areas were extracted using an exponentially modified Gaussian model. Peak areas were independent of the thermal ramp rate. Uses of such preconcentrators with multivariate detectors, such as sensor arrays, are discussed.

Journal Article↗
PubMed2006

Generating multiple independent retention index data in dual-secondary column comprehensive two-dimensional gas chromatography.

A method producing simultaneously three retention indexes for compounds has been developed for comprehensive two-dimensional gas chromatography by using a dual secondary column approach (GC x 2GC). For this purpose, the primary flow of the first dimension column was equally diverted into two secondary microbore columns of identical geometry by means of a three-way flow splitter positioned after the longitudinally modulated cryogenic system. This configuration produced a pair of comprehensive two-dimensional chromatograms and generated retention data on three different stationary phases in a single run. First dimension retention indexes were determined on a polar SolGel-Wax column under linear programmed-temperature conditions according to the van den Dool approach using primary alcohol homologues as the reference scale. Calculation of pseudoisothermal retention indexes in both second dimensions was performed on low-polarity 5% phenyl equivalent polysilphenylene/siloxane (BPX5) and 14% cyanopropylphenyl/86% dimethylpolysiloxane (BP10) columns. To construct a retention correlation map in the second dimension separation space upon which KovAts indexes can be derived, two methods exploiting "isovolatility" relationships of alkanes were developed. The first involved 15 sequential headspace samplings of selected n-alkanes by solid-phase microextraction (SPME), with each sampling followed by their injection into the GC at predetermined times during the chromatographic run. The second method extended the second dimension retention map and consisted of repetitive introduction of SPME-sampled alkane mixtures at various isothermal conditions incremented over the temperature program range. Calculated second dimension retention indexes were compared with experimental values obtained in conventional one-dimensional GC. A case study mixture including 24 suspected allergens (i.e., fragrance ingredients) was used to demonstrate the feasibility and potential of retention index information in comprehensive 2D-GC.

Journal Article↗
PubMed2001

Measuring efficiency of long-term care units in Finland.

Data Envelopment Analysis (DEA) was used to measure the nursing care efficiency of 64 long-term care units in Finland. New approaches introduced for evaluating efficiency were unit/ward level analysis, and the case-mix classification Resource Utilization Groups (RUG-III). Efficiency determinations were based on four DEA measures: cost, technical, allocative, and scale efficiency. The results indicated considerable variation in efficiency between units, suggesting that efficiency could be improved through better management and allocation of resources. Larger units seemingly operated more efficiently than smaller units. Allocative inefficiency resulted from using too many registered nurses and aides, and too few licensed practical nurses.

Cost-Benefit Analysis↗
PubMed2000

Data envelopment analysis to determine efficiencies of health maintenance organizations.

We use Data Envelopment Analysis (DEA) to measure the relative technical efficiencies of 164 HMOs licensed to practice in the United States in 1995 with data collected from the American Association of Health Plans. Health care output measures used in the analysis are the number of commercial, Medicare and Medicaid lives covered in each plan. Inputs to the model are health care utilization measures such as the number of medical and surgical inpatient days, number of maternity and newborn stays in days, number of outpatient and emergency room visits and the number of non-invasive and invasive procedures performed on patients in an ambulatory setting. Mean efficiency of health plans was 40% (of the most efficient). We use multivariate analysis to try and explain variations in efficiency. Enrollment influences efficiency, with larger HMOs being more efficient than those with fewer enrollees. Plans with a more even distribution of Commercial, Medicare and Medicaid patients were more efficient on average than plans with heterogeneous mixes in enrollment. HMOs with Medicare patients are significantly less efficient, with efficiency decreasing with increasing Medicare participation in plan membership. Health plans in operation for longer periods of time had greater outputs with the same inputs. Health plans that had a majority of their enrollees in network or IPA type arrangements were more efficient as were for-profit plans compared to not-for-profits. Policy implications are discussed.

Chi-Square Distribution↗
PubMed2002

Operations research methods applied to workflow in a medical records department.

Transcribing medical documents accurately into pre-defined formats and within certain time frames is vital for administrative and medical purposes in any hospital. This paper describes quantitative models incorporating available data to represent transcription activities of a medical records department. We forecasted the workload of the department, determined the optimal worker schedule and designed a simulation model to represent the workflow of the transcription function of a medical record department. The findings provided insight into the workflow, staffing and performance of the department.

Computer Simulation↗