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PubMed2000

Dynamic modeling and optimal fed-batch feeding strategies for a two-phase partitioning bioreactor.

A dynamic model for the degradation of phenol in a two-phase partitioning bioreactor has been developed based on mechanistic balances around the bioreactor. The key process characteristics including substrate transfer between the organic and aqueous phases, substrate inhibition, oxygen limitation, and cell entrainment were incorporated into the model. The model predictions were validated against existing experimental data obtained for a 2-L bioreactor, and good correlation was observed for the time frames of the simulations, as well as for trends in cell and substrate concentrations. Optimal fed-batch, phenol feeding strategies were then developed based on two approaches: (1) maximization of phenol consumption in a fixed time interval and (2) consumption of a fixed amount of phenol in minimal time. The optimal feeding policies, determined using the Iterative Dynamic Programming algorithm, provided substantial improvements in the amount of phenol consumed when compared to a typical experimental heuristic approach. For example, 45.73 g of phenol was predicted to be consumed in 50 h (not including lag phase) using the optimal feeding profile compared to 10.26 g of phenol consumed in the simulated experimental approach. Oxygen limitation was predicted to be a recurring operational challenge in the partitioning bioreactor, and had a strong impact on the optimization results.

Algorithms↗

PubMed1997

One balloon approach for optimized Palmaz-Schatz stent implantation: the MUSCAT trial.

BACKGROUND: After stent deployment, larger balloons are frequently needed to optimize stent expansion according to angiographic and intravascular ultrasound (IVUS) criteria. The objective of this trial was to assess the feasibility and safety of a single-balloon approach for predilation, stent implantation, and optimization with a differential-compliant balloon allowing for focal overexpansion. We also evaluated the achieved degree of stent expansion according to IVUS criteria. METHODS AND RESULTS: Forty-seven consecutive patients with 50 lesions received single or multiple Palmaz-Schatz coronary stents. The final angiographic diameter stenosis was -2.6 +/- 12.6% (reference diameter, 2.89 +/- 0.44 mm), and the residual lumen area stenosis (IVUS) was 13.0 +/- 12.3% (reference area 10.8 +/- 3.0 mm2). This result was achieved in two steps (first angiographic, then IVUS-guided stent optimization). The balloon inflation pressure increased from 13.1 +/- 3.0 bar at step 1 to 16.1 +/- 3.0 bar at step 2, which resulted in a balloon to artery ratio of 0.97 +/- 0.12 and 1.10 +/- 0.15, respectively, at the low-compliant peripheral balloon segments. The more compliant central balloon segments showed a balloon to artery ratio of 1.09 +/- 0.17 and 1.28 +/- 0.17, respectively. The primary success rate for stent deployment was 94%. Acute complications included two type A and one type B dissection without clinical sequelae. CONCLUSIONS: The single-balloon approach for stenting is feasible and safe. The acute result is comparable to that of other studies with IVUS-guided stent optimization, the primary success rate, however, is slightly lower with the presently available catheter.

Adult↗

PubMed1991

An investigation of the optimization of search logic for the MEDLINE database.

One of the key variables in the optimization of the retrieval process is the logic imposed on a set of query terms. If the query is small, a combinatorial algorithm can be employed to identify search expressions having an optimal logical form. An experiment is described in which this was done for queries expressed against MEDLINE, for a variety of criterion variables. The method employed is useful not only for assisting in identifying optimal logical forms, as demonstrated, but also as an experimental control device to assist investigations into the effects of varying the set, and number, of search terms. The experiment also suggests several novel properties of effective searching against MEDLINE, for example that searching with four MeSH terms is likely to be more successful than searching with a lesser number of terms, provided search logic is optimal. The latter result is, surprisingly, true for both Precision and Recall, i.e., a tradeoff between the maximally attainable values of these variables fails to hold when the number of search terms varies in this range.

Algorithms↗

PubMed1997

Optimism, social support, and premenstrual dysphoria.

The relationships between dispositional optimism, social support, and mood and performance symptoms associated with the premenstrum were examined in a sample of 101 adult women. Optimism and satisfaction with one's level of social support were positively correlated. Optimism was related inversely to mood-related symptoms, even after controlling for the effects of social support. Optimism did not correlate with premenstrual performance impairment. Social support did not correlate with any premenstrual symptoms.

Adult↗

PubMed1999

Optimal allele-sharing statistics for genetic mapping using affected relatives.

The choice of allele-sharing statistics can have a great impact on the power of robust affected relative methods. Similarly, when allele-sharing statistics from several pedigrees are combined, the weight applied to each pedigree's statistic can affect power. Here we describe the direct connection between the affected relative methods and traditional parametric linkage analysis, and we use this connection to give explicit formulae for the optimal sharing statistics and weights, applicable to all pedigree types. One surprising consequence is that under any single gene model, the value of the optimal allele-sharing statistic does not depend on whether observed sharing is between more closely or more distantly related affected relatives. This result also holds for any multigene model with loci unlinked, additivity between loci, and all loci having small effect. For specific classes of two-allele models, we give the most powerful statistics and optimal weights for arbitrary pedigrees. When the effect size is small, these also extend to multigene models with additivity between loci. We propose a useful new statistic, S(rob dom), which performs well for dominant and additive models with varying phenocopy rates and varying predisposing allele frequency. We find that the statistic S(_#alleles), performs well for recessive models with varying phenocopy rates and varying redisposing allele frequency. We also find that for models with large deviation from null sharing, the correspondence between allele-sharing statistics and the models for which they are optimal may also depend on which method is used to test for linkage.

Alleles↗

PubMed1996

Evaluation of an optimized system for random amplified polymorphic DNA (RAPD)-analysis for genotypic mapping of Candida albicans strains.

A simple, rapid, and cost-effective protocol has been developed for a PCR-based molecular typing method for Candida albicans, which includes the use of a commercially available medium (Chelex 100 Resin) for DNA extraction and a single set of two arbitrarily chosen oligonucleotide (10 nt length) primers for random amplified DNA(RAPD)-analysis. The optimized parameters for the amplification components and conditions for the selected primer combination have been determined to avoid artifactual variation (absence/presence of bands) in RAPD banding patterns in repeated assays. The optimized RAPD-assay consistently generated DNA-patterns of 33 genetically unrelated C. albicans isolates that contained ten polymorphic markers in the non-artifactual banding patterns. The intralaboratory reproducibility of RAPD patterns was efficient and consistent provided the optimized amplification conditions were rigidly controlled. Interlaboratory reproducibility was tempered by slight variations in time of cyclers of different thermocyclers. In comparison, the RAPD assay was almost equal to restriction enzyme analysis (REA) (Eco RI digested chromosomal DNA) in discrimination, and the RAPD assay was able to group isolates of C. albicans that were untypable by REA. The protocol outlined for an optimized RAPD-assay of C. albicans has the potential to be widely useful epidemiological screening tool that can be easily applied in the clinical laboratory.

Candida albicans↗

PubMed2001

Bayesian optimal designs for estimating a set of symmetrical quantiles.

We propose multiple-objective Bayesian optimal designs for the logit model. As an example, we consider the design problem for estimating several percentiles with possibly unequal interest in each of the percentiles. Characteristics of these designs are studied and illustrated for the case when the interest lies in estimating the three quartiles. We compare these optimal designs with the sequential designs generated via a generalized Pólya urn model and found the latter to be highly efficient. In addition, comparisons are made between locally optimal designs and Bayesian optimal designs.

Adult↗

PubMed2002

Design and optimization of on-chip capillary electrophoresis.

We present a systematic, experimentally validated method of designing electrokinetic injections for on-chip capillary electrophoresis applications. This method can be used to predict point-wise and charge-coupled device (CCD)-imaged electropherograms using estimates of species mobilities, diffusivities and initial sample plug parameters. A simple Taylor dispersion model is used to characterize electrophoretic separations in terms of resolution and signal-to-noise ratio (SNR). Detection convolutions using Gaussian and Boxcar detector response functions are used to relate optimal conditions for resolution and signal as a function of relevant system parameters including electroosmotic mobility, sample injection length, detector length scale, and the length-to-detector. Analytical solutions show a tradeoff between signal-to-noise ratio and resolution with respect to dimensionless injection width and length to the detector. In contrast, there is no tradeoff with respect to the Peclet number as increases in Peclet number favor both SNR and separation solution (R). We validate our model with quantitative epifluorescence visualizations of electrophoretic separation experiments in a simple cross channel microchip. For the pure advection regime of dispersion, we use numerical simulations of the transient convective diffusion processes associated with electrokinetics together with an optimization algorithm to design a voltage control scheme which produces an injection plug that has minimal advective dispersion. We also validate this optimal injection scheme using fluorescence visualizations. These validations show that optimized voltage scheme produces injections with a standard deviation less than one-fifth of the width of the microchannel.

Diagnostic Imaging↗

PubMed2001

Process performance models in the optimization of multiproduct protein production plants.

In this work we propose a model that simultaneously optimizes the process variables and the structure of a multiproduct batch plant for the production of recombinant proteins. The complete model includes process performance models for the unit stages and a posynomial representation for the multiproduct batch plant. Although the constant time and size factor models are the most commonly used to model multiproduct batch processes, process performance models describe these time and size factors as functions of the process variables selected for optimization. These process performance models are expressed as algebraic equations obtained from the analytical integration of simplified mass balances and kinetic expressions that describe each unit operation. They are kept as simple as possible while retaining the influence of the process variables selected to optimize the plant. The resulting mixed-integer nonlinear program simultaneously calculates the plant structure (parallel units in or out of phase, and allocation of intermediate storage tanks), the batch plant decision variables (equipment sizes, batch sizes, and operating times of semicontinuous items), and the process decision variables (e.g., final concentration at selected stages, volumetric ratio of phases in the liquid-liquid extraction). A noteworthy feature of the proposed approach is that the mathematical model for the plant is the same as that used in the constant factor model. The process performance models are handled as extra constraints. A plant consisting of eight stages operating in the single product campaign mode (one fermentation, two microfiltrations, two ultrafiltrations, one homogenization, one liquid-liquid extraction, and one chromatography) for producing four different recombinant proteins by the genetically engineered yeast Saccharomyces cerevisiae was modeled and optimized. Using this example, it is shown that the presence of additional degrees of freedom introduced by the process performance models, with respect to a fixed size and time factor model, represents an important development in improving plant design.

Automation↗

PubMed2001

Application of statistically-based experimental designs for the optimization of eicosapentaenoic acid production by the diatom Nitzschia laevis.

Statistically based experimental designs were applied to the optimization of medium components and environmental factors for eicosapentaenoic acid (EPA) production by the diatom Nitzschia laevis in heterotrophic conditions. First, the Plackett-Burman design was used to evaluate the effects of variables including medium components and environmental factors on cell growth and EPA production. Among these variables, NaCl, CaCl(2), PI metal solution, pH, and temperature were identified to have the significant effects (with confidence level > 90 %). Subsequently, the concentrations of NaCl, CaCl(2), PI metal solution as well as the values of pH and temperature were optimized using central composite design. The cell growth and EPA production were found to respectively correlate to NaCl, CaCl(2), pH, and temperature that could be represented by second-order polynomial models. The optimal values of the four parameters were determined by response surface and numerical analyses as 8 g/L NaCl, 0.10 g/L CaCl(2), pH 8.5 and 19.8 degrees C for cell dry weight (DW), and 14 g/L NaCl, 0.10 g/L CaCl(2), pH 8.5 and 18 degrees C for EPA production, respectively. The subsequent verification experiments confirmed the validity of the models. This optimization strategy led to a DW of 9 g/L, an EPA yield of 280 mg/L and an EPA productivity of 28 mg/L/d, respectively, which were considerably higher than those obtained in the previous studies.

Biotin↗

PubMed2004

Optimization of rifamycin B fermentation in shake flasks via a machine-learning-based approach.

Rifamycin B is an important polyketide antibiotic used in the treatment of tuberculosis and leprosy. We present results on medium optimization for Rifamycin B production via a barbital insensitive mutant strain of Amycolatopsis mediterranei S699. Machine-learning approaches such as Genetic algorithm (GA), Neighborhood analysis (NA) and Decision Tree technique (DT) were explored for optimizing the medium composition. Genetic algorithm was applied as a global search algorithm while NA was used for a guided local search and to develop medium predictors. The fermentation medium for Rifamycin B consisted of nine components. A large number of distinct medium compositions are possible by variation of concentration of each component. This presents a large combinatorial search space. Optimization was achieved within five generations via GA as well as NA. These five generations consisted of 178 shake-flask experiments, which is a small fraction of the search space. We detected multiple optima in the form of 11 distinct medium combinations. These medium combinations provided over 600% improvement in Rifamycin B productivity. Genetic algorithm performed better in optimizing fermentation medium as compared to NA. The Decision Tree technique revealed the media-media interactions qualitatively in the form of sets of rules for medium composition that give high as well as low productivity.

Actinomycetales↗

PubMed2006

Dioxygenation of naphthalene by Pseudomonas fluorescens N3 dioxygenase: optimization of the process parameters.

The bioconversion of naphthalene to the 1,2-dihydro-1,2-dihydroxy derivative was performed in good yield using an Escherichia coli recombinant strain carrying Pseudomonas fluorescens N3 dioxygenase. However, the efficiency of such transformation is affected by many process parameters, and their optimization is essential to the scaling up of the process. The following process parameters were considered for optimization: cell concentration together with the corresponding glucose concentration (DCW/L); pH of medium; temperature; stirring speed; air flow; substrate concentration; Fe(2+) concentration; microelements concentration; reaction volume. We used a two-step multivariate experimental design to select important variables and assign them optimal values. The most significant parameters were selected by adopting a Plackett-Burman design, and were then correlated, using a full factorial design, with the experimental results. The experimental results illustrate that the optimized process of recombinant whole cell biotransformation in two-liquid phase systems enhances the naphthalene dihydrodiol yield threefold. This biotransformation opens the way to future experiments involving different substrates.

Bacterial Proteins↗

PubMed2006

Event-driven time-optimal control for a class of discontinuous bioreactors.

Discontinuous bioreactors may be further optimized for processing inhibitory substrates using a convenient fed-batch mode. To do so the filling rate must be controlled in such a way as to push the reaction rate to its maximum value, by increasing the substrate concentration just up to the point where inhibition begins. However, an exact optimal controller requires measuring several variables (e.g., substrate concentrations in the feed and in the tank) and also good model knowledge (e.g., yield and kinetic parameters), requirements rarely satisfied in real applications. An environmentally important case, that exemplifies all these handicaps, is toxicant wastewater treatment. There the lack of online practical pollutant sensors may allow unforeseen high shock loads to be fed to the bioreactor, causing biomass inhibition that slows down the treatment process and, in extreme cases, even renders the biological process useless. In this work an event-driven time-optimal control (ED-TOC) is proposed to circumvent these limitations. We show how to detect a "there is inhibition" event by using some computable function of the available measurements. This event drives the ED-TOC to stop the filling. Later, by detecting the symmetric event, "there is no inhibition," the ED-TOC may restart the filling. A fill-react cycling then maintains the process safely hovering near its maximum reaction rate, allowing a robust and practically time-optimal operation of the bioreactor. An experimental study case of a wastewater treatment process application is presented. There the dissolved oxygen concentration was used to detect the events needed to drive the controller.

Biomass↗

PubMed2007

Optimal design of non-Newtonian, micro-scale viscous pumps for biomedical devices.

The present paper addresses the numerical optimization of geometrical parameters of non-Newtonian micro-scale viscous pumps for biomedical devices. The objective is to maximize the mass flow rate per unit of shaft power consumed by the rotor when an external pressure load is applied along the channel that houses the rotor. Two geometric parameters are considered in the optimization process: (i) the height of the channel that houses the rotor (H) and (ii), the eccentricity (epsilon) of the rotor. Three different micro-scale viscous pump configurations were tested: a straight-housed pump (I-shaped housing) and two curved housed pumps (L- and U-shaped housings). The stress-strain constitutive law is modeled by a power-law relation. The results show that the geometric optimization of micro-scale viscous pumps is critical since the mass flow rate propelled by the rotor is highly dependent on epsilon and H. Numerical simulations indicate that mass flow rate is maximized when epsilon approximately 0, namely when the rotor is placed at a distance of 0.05 radii from the lower wall. The results also show that micro-scale viscous pumps with curved housing provide higher mass flow rate per unit of shaft power consumed when compared with straight-housed pumps. The results are presented in terms optimized dimensions of all three configurations (i.e., H(opt) and epsilon(opt)) and for values of the power-law index varying between 0.5 (shear thinning fluids) and 1.5 (shear-thickening fluids).

Biomedical Engineering↗

PubMed1992

Optimization of short-column gas chromatography/electron ionization mass spectrometry conditions for the determination of underivatized anabolic steroids.

A gas chromatographic/mass spectrometric method based on the use of short capillary gas chromatograph columns (3-5 m) and electron ionization mass spectrometry has been optimized and evaluated for the determination of underivatized anabolic steroids. The short-column gas chromatographic/mass spectrometric method was shown to result in short analysis times and to require minimal sample preparation, but suffered from some loss in sensitivity and chromatographic resolution compared with conventional gas chromatographic/mass spectrometric techniques for derivatized steroids. Therefore, short-column gas chromatographic conditions were optimized to maximize the sample transfer efficiency (sensitivity) from the gas chromatograph into the ion source of the mass spectrometer, while maintaining chromatographic integrity and minimizing thermal decomposition. Mass spectrometric conditions were optimized to maximize ionization efficiency with respect to the intensity of the molecular ion and degree of fragmentation such that positive identification of each steroid could be made based on the resulting mass spectra. Under optimized conditions, we have shown that underivatized anabolic steroids spiked into urine samples can be determined at low-nanogram levels using short-column chromatography/full-scan electron ionization mass spectrometry.

Anabolic Agents↗

PubMed2004

Estimation of an optimal radiotherapy utilization rate for gynecologic carcinoma: part I--malignancies of the cervix, ovary, vagina and vulva.

BACKGROUND: Radiotherapy usage rates exhibit wide variations both within and between countries. Current estimates of the proportion of cancer patients who should optimally receive radiotherapy are based either on expert opinion or on the measurement of actual usage rates rather than on the best available scientific evidence. METHODS: With the goal of developing an evidence-based benchmark for radiotherapy use in the treatment of malignancies of the cervix, vagina, vulva, and ovary (endometrial malignancies are covered in a separate article), the authors reviewed international evidence-based treatment guidelines. Optimal radiotherapy usage trees were constructed, and proportions of patients with clinical indications for radiotherapy were obtained from epidemiologic data. These ideal usage rates were compared with actual radiotherapy utilization rates recorded in Australia and elsewhere. RESULTS: According to the best available evidence, radiotherapy is indicated at least once for 58% of patients with cervical carcinoma, 4% of patients with ovarian carcinoma, 100% of patients with vaginal carcinoma, and 34% of patients with vulvar carcinoma. A review of the limited data available suggests that actual radiotherapy usage rates for patients with gynecologic malignancies are comparable to optimal usage rates. CONCLUSIONS: Actual practice appears to approximate the authors' model of optimal radiotherapy use. This finding reflects the high level of agreement among treatment guidelines as well as the existence of high-quality evidence related to the management of gynecologic malignancies, and it may also be indicative of the fact that a large proportion of patients are treated in specialist units. The management of gynecologic malignancies may serve as a good example in the development of management strategies for other types of cancer.

Benchmarking↗

PubMed2005

Estimating the optimal external-beam radiotherapy utilization rate for genitourinary malignancies.

BACKGROUND: Benchmark radiotherapy utilization rates for genitourinary malignancies are largely unknown, despite the finding that genitourinary cancers comprise approximately 19% of all registered malignancies in Australia. METHODS: To develop an evidence-based benchmark of the optimal proportion of patients with genitourinary malignancies who should receive at least one course of radiotherapy at some time during their illness, the authors studied treatment guidelines and treatment reviews regarding genitourinary malignancies. Optimal radiotherapy utilization trees were constructed to show the clinical attributes that indicated possible benefit from radiotherapy based on evidence. Epidemiologic incidence data for each of these clinical attributes were obtained to calculate the optimal proportion of all patients with genitourinary cancer for whom radiotherapy was considered appropriate. RESULTS: The proportion of patients with genitourinary malignancies for whom radiotherapy was indicated at some point in their illness, according to the best available evidence, was estimated to be 27% of patients with renal cancer, 58% of patients with bladder cancer, 60% of patients with prostate cancer, and 49% of patients with testicular cancer. The occurrence of ureteric and penile cancers among patients was too rare, and, therefore, these patients were not included in the current study. CONCLUSIONS: There was a large discrepancy between actual radiotherapy utilization and the evidence-based optimal rate. The authors recommended strategies to implement the evidence-based guidelines. Evidence-based benchmarks for radiotherapy utilization rates such as the ones described in the current study were important in the evaluation of the appropriate use of radiotherapy.

Australia↗

PubMed2002

Optimality in the developing vascular system: branching remodeling by means of intussusception as an efficient adaptation mechanism.

The theory of bifurcating vascular systems predicts vessel diameters that are related to optimality criteria like minimization of pumping energy or of building material. However, mechanisms for producing the postulated optimality have not been described so far, and quantitative data on bifurcation diameters during development are scarce. We used an embryonic vascular bed that rapidly grows and adapts to changing hemodynamic conditions, the chicken chorioallantoic membrane (CAM), and correlated vascular cast and tissue section morphology with in vivo time-lapse video monitoring. The bifurcation exponent delta and associated parameters were quantitatively assessed in arterial and venous microvessels ranging in diameter from 30 to 100 microm. We observed emergence of optimality by means of intussusception, i.e., formation of transvascular tissue pillars. In addition to intussusceptive microvascular growth (IMG = expansion of capillary networks) and intussusceptive arborization (IAR = formation of feeding vessels from capillaries) the observed intussusception at bifurcations represents a third variant of nonsprouting angiogenesis. We call it intussusceptive branching remodeling (IBR). IBR occurred in vessels of considerable diameter by means of two alternative mechanisms: either through pillars arising close to a bifurcation, which increased in girth until they merged with the connective tissue in the bifurcation angle; or through pillars arising at some distance from the bifurcation point, which then expanded by formation of ingrowing tissue folds until they became connected to the tissue of the bifurcation angle. Morphologic evidence suggests that IBR is a wide-spread phenomenon, taking place also in lung, intestinal, kidney, eye, etc., vasculature. Irrespective of the mode followed, IBR led to a branching pattern close to the predicted optimum, delta = 3.0. Significant differences were observed between delta at arterial bifurcations (2.70 to 2.90) and delta at venous bifurcations (2.93 to 3.75). IBR, by means of eccentric pillar formation and fusion, was also involved in vascular pruning. Experimental changes in CAM hemodynamics (by locally increasing blood flow) induced onset of IBR within less than 1 hr. Our study provides morphologic and quantitative evidence that a similar cellular machinery is used for all three variants of vascular intussusception, IMG, IAR, and IBR. It thus provides a mechanism of efficiently generating complex blood transport systems from limited genetic information. Differential quantitative outcome of IBR in arteries and veins, and the experimental induction of IBR strongly suggest that hemodynamic factors can instruct embryonic vascular remodeling toward optimality.

Allantois↗