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PubMed2004

Statistical models to optimize production of probiotic characteristics.

The use of probiotic microorganisms has been widely promoted in the last 20 years. Probiotics have applied to the gastrointestinal tract as capsules or as fermented milks. The characteristics of the strains proposed as probiotics have been published or patented after elaboration of the product. The first step in designing a probiotic product is to isolate and characterize strains with beneficial properties. Our group has reported the isolation and characterization of 134 strains of lactobacilli from the vagina of women from our city. Surface properties and the production of antagonistic substances has also been published. From these studies, certain strains were selected because they shared probiotic characteristics. The second step in the design of a pharmaceutical product is to determine the optimal conditions for obtaining the highest amount of viable microorganisms, as well as the best conditions to produce antagonistic substances. To perform these types of experiments, laboratory assays can be carried out to determine the optimum conditions in which the microorganisms can be cultured. Growth parameters and optimal growth conditions can be studied by the classical methodology or by the application of alternative methodologies. Alternative methods have been widely used in the food industry, including experimental designs to test multiple conditions at the same time, complemented by the use of statistical models to evaluate and compare all the conditions tested. The object of this chapter is to describe the experimental designs used to study the technological characteristics of vaginal probiotic lactobacilli as well as the application of statistical models for evaluation of the different conditions tested for the production of biomass and antagonistic substances in these bacteria. With this objective in mind, in the present chapter, the following areas are explored: 1. Growth experiments performed to study the effect of temperature, pH, agitation, and culture media on the growth and production of antagonistic substances by vaginal lactobacilli. 2. Fractional and complete factorial experimental designs used to perform the growth experiments. 3. Statistical models applied to evaluate the growth parameters and their modifications under the conditions assayed.

Bacteriological Techniques↗

PubMed2000

Theory of the lattice boltzmann method: dispersion, dissipation, isotropy, galilean invariance, and stability

The generalized hydrodynamics (the wave vector dependence of the transport coefficients) of a generalized lattice Boltzmann equation (LBE) is studied in detail. The generalized lattice Boltzmann equation is constructed in moment space rather than in discrete velocity space. The generalized hydrodynamics of the model is obtained by solving the dispersion equation of the linearized LBE either analytically by using perturbation technique or numerically. The proposed LBE model has a maximum number of adjustable parameters for the given set of discrete velocities. Generalized hydrodynamics characterizes dispersion, dissipation (hyperviscosities), anisotropy, and lack of Galilean invariance of the model, and can be applied to select the values of the adjustable parameters that optimize the properties of the model. The proposed generalized hydrodynamic analysis also provides some insights into stability and proper initial conditions for LBE simulations. The stability properties of some two-dimensional LBE models are analyzed and compared with each other in the parameter space of the mean streaming velocity and the viscous relaxation time. The procedure described in this work can be applied to analyze other LBE models. As examples, LBE models with various interpolation schemes are analyzed. Numerical results on shear flow with an initially discontinuous velocity profile (shock) with or without a constant streaming velocity are shown to demonstrate the dispersion effects in the LBE model; the results compare favorably with our theoretical analysis. We also show that whereas linear analysis of the LBE evolution operator is equivalent to Chapman-Enskog analysis in the long-wavelength limit (wave vector k=0), it can also provide results for large values of k. Such results are important for the stability and other hydrodynamic properties of the LBE method and cannot be obtained through Chapman-Enskog analysis.

Journal Article↗

PubMed2005

A new mathematical procedure to evaluate peaks in complex chromatograms.

Automatic peak evaluation in chromatograms and subsequent quantification of compound concentrations is still a challenge in the analysis of complex samples containing hundreds or thousands of compounds. Although a number of software packages for peak evaluation exist, baseline definition and overlapping peaks of different shapes are the main reasons which prevent reliable automatic analysis of complex chromatograms. A new mathematical procedure is presented which uses peak shapes extracted from the chromatogram itself and modified by nonlinear (in fact, hyperbolic) stretching of the peak head and tail. With this approach, the peak parameters are position, height, scale of front, scale of tail, and smoothness of transition from front to tail scaling. This approach is found to give a substantially better fit than traditional analytically defined peak shapes. Together with a good peak finding heuristic and nonlinear optimization of parameters this allows a reliable automatic analysis of chromatograms with a large number of peaks, even with large groups of overlapping peaks. The analysis matches the quality of standard interactive methods, but still permits interactive refinement. This approach has been implemented and tested on a large set of data from chromatography of hydrocarbons in ambient air samples.

Chromatography↗

PubMed2005

Enantiomeric determination of amphetamines: exploring a novel one-step solid-phase microextraction-based approach.

The recent advances in fiber manufacturing technology, solid-phase microextraction (SPME) is now widely studied for its effectiveness for the pretreatment of various categories of samples. This study explores a novel SPME approach for enantiomeric analysis of amphetamines, in which absorption/derivatization are accomplished in one step. Specifically, (S)-(-)-N-(Trifluoroacetyl)-prolyl chloride was adopted as the chiral derivatizing reagent and added directly into the sample matrix. Analytical parameters, such as temperature, absorption/desorption duration, and the amount of derivatizing reagent, were studied to determine their effects on the yield of analytes. The derivatization products resulting from this study show excellent desorption characteristics on the polydimethylsiloxane-coated fiber adopted in this study. Optimal operational parameters (absorption: 70 degrees C for 10 min; injection: 250 degrees C for 5 min) cause minimal negative impact on the fiber, allowing repeated use of the fiber for more than 30 times. For quantitation, data were collected under selected ion monitoring (SIM) mode using m/z 237 and 251 to designate derivatized amphetamine and methamphetamine. This method was evaluated and proved to be effective in (a) quantitative determination of the enantiomeric pairs of amphetamine and methamphetamine--in terms of repeatability, linearity, and limits of detection and quantitation; and (b) generating case-specimen data comparable to those derived from a conventional Liquid-liquid extraction approach. Good linearity for the calibration curves were established in the range of 1000-50 ng/mL for both analytes. The limits of detection for these analytes were 30 ng/mL.

Amphetamines↗

PubMed2006

Combining explicitly correlated R12 and Gaussian geminal electronic structure theories.

Explicitly correlated R12 methods using a single short-range correlation factor (also known as F12 methods) have dramatically smaller basis set errors compared to the standard wave function counterparts, even when used with small basis sets. Correlations on several length scales, however, may not be described efficiently with one correlation factor. Here the authors explore a more general MP2-R12 method in which each electron pair uses a set of (contracted) Gaussian-type geminals (GTGs) with fixed exponents, whose coefficients are optimized linearly. The following features distinguish the current method from related explicitly correlated approaches published in the literature: (1) only two-electron integrals are needed, (2) the only approximations are the resolution of the identity and the generalized Brillouin condition, (3) only linear parameters are optimized, and (4) an arbitrary number of (non-)contracted GTGs can appear. The present method using only three GTGs and a double-zeta quality basis computed valence correlation energies for a set of 20 small molecules only 2.2% removed from the basis set limit. The average basis set error reduces to 1.2% using a near-complete set of seven GTGs with the double-zeta basis set. The conventional MP2 energies computed with much larger quadruple, quintuple, and sextuple basis sets all had larger average errors: 4.6%, 2.4%, and 1.5%, respectively. The new method compares well to the published MP2-R12 method using a single Slater-type geminal (STG) correlation factor. For example, the average basis set error in the absolute MP2-R12 energy obtained with the exp(-r12) correlation factor is 1.7%. Correlation contribution to atomization energies evaluated with the present method and with the STG-based method only required a double-zeta basis set to exceed the precision of the conventional sextuple-zeta result. The new method is shown to always be numerically stable if linear dependencies are removed from the two-particle basis and the zeroth-order Hamiltonian matrix is made positive definite.

Journal Article↗

PubMed2006

Transcranial magnetic stimulation for depression.

OBJECTIVE: To review the accumulated literature on the efficacy, safety and predictors of response for repetitive transcranial magnetic stimulation (rTMS) in the treatment of depression. METHODS: A descriptive review of the more than 25 published sham-controlled rTMS studies in depression was undertaken, focusing on reported meta-analyses as well as individual trial reports. Potential determinants of efficacy were examined, including the form of shams employed, stimulation parameters and clinical features. RESULTS: There is now clear evidence for the statistical superiority of left-prefrontal high frequency rTMS compared with sham therapy. However, the clinical benefits are marginal in the majority of reports. There is also still considerable uncertainty concerning the optimal stimulation parameters. Those clinical features which appear to be associated with greater response include younger age, lack of refractoriness to antidepressants and no psychotic features. CONCLUSIONS: Current studies confirm statistical efficacy, but insubstantive clinical benefit. Large multicentre studies currently underway should clarify if rTMS should be approved by regulatory agencies for widespread clinical availability. Furthermore, there is a need to clarify the preferred parameters for administering this treatment.

Major Depressive Disorder↗

PubMed1988

Quantitative assay for binding of Bradyrhizobium japonicum to cultured soybean cells.

Incubation of Bradyrhizobium japonicum with the cultured soybean cell line SB-1 resulted in the adhesion of the bacteria to the plant cells. An antiserum was raised against B. japonicum, and the 125I-labeled immunoglobulin fraction was used to quantitate the number of bacteria bound to the soybean cells. The measurement of 125I-labeled antibody binding correlated well with parallel assays by microscopic observation. Using this quantitation, we have optimized the parameters of the assay in terms of time course, ratio of B. japonicum to SB-1 cells, and pH. We then explored the effects of saccharides, NaCl, EDTA, and culture age of the bacteria and SB-1 cells on B. japonicum binding under these optimal assay conditions. The results showed good correlation between conditions that govern B. japonicum binding to SB-1 cells in culture and those that regulate B. japonicum-induced nodulation in legume roots. Together, they suggest that this binding event may be important in controlling host specificity.

Antibodies, Bacterial↗

PubMed1984

Manipulation of mobile phase parameters for the HPLC separation of endogenous monoamines in rat brain tissue.

Multi-component mobile phases are common in ion pair reverse phase high performance liquid chromatography for the analysis of endogenous monoamines in rat brain tissue. By examining the effects of each component of a mobile phase on the separation of a number of monoamines and their metabolites, we show how optimization of parameters can achieve and/or maintain a separation both within and between different octadecyl columns. The assay itself is rapid, sensitive, demands minimal sample preparation, and results in complete resolution of the amines. More importantly, the basis for the manipulation of mobile phase components is discussed with regard to practical utilization in selective amine separation. We conclude that knowledge of mobile phase parameters, their mechanism, and manipulation is as important as the assay itself.

3,4-Dihydroxyphenylacetic Acid↗

PubMed1998

A free energy analysis by unfolding applied to 125-mers on a cubic lattice.

BACKGROUND: A common approach to the protein folding problem involves computer simulation of folding using lattice models of amino acid sequences. Key factors for good performance in such models are the correct choice of the temperature and the average interaction energy between residues. In order to push the lattice approach to its limit it is important to have a method to adjust these parameters for optimal folding that is not limited by our ability to successfully simulate folding in a reasonable time. RESULTS: In this study, we adopt a simple cubic-lattice model and present a method for calculating the free energy of a chain as a function of the number of native contacts. This does not require that we are able to fold the sequence by simulation and it provides a method of estimating the folding transition temperature. For a given set of parameters, the free energy analysis also allows an estimate of foldability. By applying the method to sequences with 27 and 125 residues, we show that optimal folding occurs near the folding transition temperature and at either zero or small negative average interaction energy. We find ourselves able to fold only 125-mers that have significant short-range native contacts. CONCLUSIONS: A free energy analysis during unfolding is a useful tool for the study of foldability and should be applicable to a variety of folding models. In this way we are able to fold some 125-mer designed sequences and our results confirm the finding that short-range contacts contribute to foldability.

Markov Chains↗

PubMed2005

Comparison of sheathless and sheath-flow electrospray interfaces for the capillary electrophoresis-electrospray ionization-mass spectrometry analysis of peptides.

Capillary electrophoresis coupled to mass spectrometry via an electrospray interface provides a powerful system for separation and characterization of a high number of biomolecules. The present paper describes a home-made sheathless interface and compares it with a commercial sheath-flow interface, using a separation method based on a peptide hormone mixture of therapeutic interest. In a previous work, we optimized the parameters involved in a sheath-flow interface and obtained good results in sensitivity and reproducibility. The sheathless interface is performed with a graphite-coated electrospray ionisation (ESI) tip attached to the separation capillary. We demonstrate that electrolyte composition is the main parameter affecting signal sensitivity and separation resolution. The effect of the nature and concentration of the organic solvent added to the separation electrolyte is carefully studied. Furthermore, a general comparison of both interfaces is made in terms of separation, reproducibility, and sensitivity obtained under the optimized conditions described. Advantages and disadvantages of both coupling setups have been evaluated.

Electrolytes↗

PubMed2005

Optimal processing method to obtain four-color confocal fluorescent images of the cytoskeleton and nucleus in three-dimensional chondrocyte cultures.

Tissue engineering of articular cartilage requires accurate imaging of the chondrocyte cytoskeleton. Past studies have applied various fixation and permeabilization protocols without optimization of parameters. In this study, we have examined procedures using glutaraldehyde and paraformaldehyde as fixatives and Triton X-100 and Octyl-POE as permeabilizing detergents. A four-color fluorescence confocal method was developed to simultaneously image actin, tubulin, vimentin, and the nucleus. We found optimal preservation and morphology of the chondrocyte cytoskeleton after simultaneous fixation and permeabilization with glutaraldehyde and Triton X-100. These images displayed less cellular shrinkage and higher-resolution filamentous structures than with paraformaldehyde or when permeabilization followed fixation.

Actins↗

PubMed1994

SOPM: a self-optimized method for protein secondary structure prediction.

A new method called the self-optimized prediction method (SOPM) has been developed to improve the success rate in the prediction of the secondary structure of proteins. This new method has been checked against an updated release of the Kabsch and Sander database, 'DATABASE.DSSP', comprising 239 protein chains. The first step of the SOPM is to build sub-databases of protein sequences and their known secondary structures drawn from 'DATABASE.DSSP' by (i) making binary comparisons of all protein sequences and (ii) taking into account the prediction of structural classes of proteins. The second step is to submit each protein of the sub-database to a secondary structure prediction using a predictive algorithm based on sequence similarity. The third step is to iteratively determine the predictive parameters that optimize the prediction quality on the whole sub-database. The last step is to apply the final parameters to the query sequence. This new method correctly predicts 69% of amino acids for a three-state description of the secondary structure (alpha helix, beta sheet and coil) in the whole database (46,011 amino acids). The correlation coefficients are C alpha = 0.54, C beta = 0.50 and Cc = 0.48. Root mean square deviations of 10% in the secondary structure content are obtained. Implications for the users are drawn so as to derive an accuracy at the amino acid level and provide the user with a guide for secondary structure prediction. The SOPM method is available by anonymous ftp to ibcp.fr.

Algorithms↗

PubMed2006

Optimization of medium and process parameters for the production of inulinase from a newly isolated Kluyveromyces marxianus YS-1.

A newly isolated strain of Kluyveromyces marxianus YS-1 was used for the production of extra cellular inulinase in a medium containing inulin, meat extract, CaCl2 and sodium dodecyl sulphate (SDS). Fermentation medium pH 6.5, cultivation temperature 30 degrees C and 5% (v/v) inoculum of 12 h-old culture were optimal for enzyme production (30.8 IU/ml) with a fermentation time of 72 h at shake flask level. Raw inulin (2%, w/v) extracted from dahlia tubers by processing at 15 kg/cm2 for 10 min was optimum for bioreactor studies. Maximum enzyme production (55.4 IU/ml) was obtained at an agitation rate of 200 rpm and aeration of 0.75 vvm in a stirred tank reactor with a fermentation time of 60 h.

Bioreactors↗

PubMedDate not supplied

Reversed-phase high-pressure liquid chromatographic tryptic peptide mapping for the comparison and study of monoclonal antibodies.

We have examined and optimized several parameters to generate efficient, high-resolution, high-information tryptic peptide maps of monoclonal antibodies and their Fab fragments, without separating the H and L chains, using reversed-phase high-pressure liquid chromatography. Use of a high protease-to-substrate ratio with optimized digestion time and HPLC gradient conditions led to a reproducible mapping of the reduced, carboxymethylated Fab fragments of two antibodies. The technique was then used to screen Fab lots for batch-to-batch consistency, and for examining the effect of 10 mM cysteine on papain cleavage of whole antibody. The technique was modified by labeling cysteine with chromophoric analogues of iodoacetamide instead of radiolabeled iodoacetamide, resulting in a three-dimensional peptide map. With multiwavelength detection, this consisted of simultaneous observation of all chromophores at 214 nm, those with aromatic residues at 280 nm, and those with cysteine at 422 nm, without collecting and counting each peak to identify cysteine-containing peptides.

Antibodies, Monoclonal↗

PubMed2006

TASSER-Lite: an automated tool for protein comparative modeling.

This study involves the development of a rapid comparative modeling tool for homologous sequences by extension of the TASSER methodology, developed for tertiary structure prediction. This comparative modeling procedure was validated on a representative benchmark set of proteins in the Protein Data Bank composed of 901 single domain proteins (41-200 residues) having sequence identities between 35-90% with respect to the template. Using a Monte Carlo search scheme with the length of runs optimized for weakly/nonhomologous proteins, TASSER often provides appreciable improvement in structure quality over the initial template. However, on average, this requires approximately 29 h of CPU time per sequence. Since homologous proteins are unlikely to require the extent of conformational search as weakly/nonhomologous proteins, TASSER's parameters were optimized to reduce the required CPU time to approximately 17 min, while retaining TASSER's ability to improve structure quality. Using this optimized TASSER (TASSER-Lite), we find an average improvement in the aligned region of approximately 10% in root mean-square deviation from native over the initial template. Comparison of TASSER-Lite with the widely used comparative modeling tool MODELLER showed that TASSER-Lite yields final models that are closer to the native. TASSER-Lite is provided on the web at (http://cssb.biology.gatech.edu/skolnick/webservice/tasserlite/index.html).

Automation↗

PubMed1999

Magnetic resonance navigator echo diaphragm monitoring in patients with suspected diaphragm paralysis.

Real-time magnetic resonance (MR) navigator echo (NE) monitoring of the diaphragm is now possible. Using this technique, temporal changes in diaphragm position can be analyzed in a non-invasive fashion, without x-ray exposure. In this preliminary study, we have optimized three NE parameters (the NE column area, the NE repeat time, and the location of the NE on the diaphragm surface), and demonstrated the clinical application of MR NE diaphragm monitoring in patients with suspected diaphragm paralysis. The NE parameters were defined in 10 healthy volunteers, and diaphragm traces were scored for variance in NE diaphragm position registration. Using the optimal NE column parameters, we investigated four patients with diaphragm paralysis, one of whom required positive pressure ventilation while in the MR scanner, to show the utility of this technique. The NE diaphragm position registration was significantly affected by the area of the NE column, with poor position registration for the smallest column area (2.25 cm2 vs. 4 cm2 vs. 6.25 cm2, variance 6.3 vs. 0.6 vs. 0.3, P = 0.006). Diaphragm position registration was also significantly affected by the NE repeat time, with misregistration for the shortest repeat time (250 msec vs. 500 msec vs. 1000 msec, variance 11.9 vs. 0.6 vs. 1.0, P = 0.02), and data clipping, with loss of end-expiratory and end-inspiratory position registration, for the longest repeat time. Finally, if the NE was positioned too anteriorly, the diaphragm traces were of poor quality (anterior vs. dome vs. posterior, variance 11.8vs. 0.6vs. 3.2, P < 0.001). Application of the technique confirmed diaphragm paralysis in all four patients. The technique can be applied during positive pressure ventilation if necessary. The optimal NE parameters for diaphragm monitoring at 0.5 T were: column area, 400 mm2; NE repeat time; 500 msec; NE column positioned on the diaphragm dome. MR NE diaphragm monitoring provides a safe, non-invasive method of assessing diaphragm motion in patients with suspected diaphragm paralysis and may prove useful for long-term follow-up and monitoring of therapeutic interventions in these subjects.

Adult↗

PubMed2005

Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.

Alkanes↗

PubMedDate not supplied

Simplified methods for estimation of 99mTc-pentetate and 131I-orthoiodohippurate plasma clearance in dogs and cats.

The purpose of this study was to evaluate simplified methods for estimation of Technetium Tc 99m (99mTc)-pentetate and orthoiodohippurate I 131 (131I-OIH) plasma clearance in dogs and cats with 1 and 2 blood samples. Plasma clearances were calculated after a bolus injection of 1.85-11.1 MBq of 99mTc-pentetate and 131I-OIH with a 2-compartment model based on a 12-point curve as a reference method in 21 dogs and 18 cats. Three 2-sample and 3 single-sample methods were investigated. The method yielding the smallest standard deviation of the difference between the reference method and the simplified method was selected as the optimal one. Linear regression analysis was performed between the reference method and the simplified method and coefficient of determination (R2) was calculated. For 99mTc-pentetate plasma clearance, the optimal 2-sample method was the one with a mono-compartment model with samples taken at specific times. For 131I-OIH plasma clearance, the estimation was improved slightly by raising the clearance calculated with a mono-compartment model to the power of an empirically determined parameter. The optimal single-sample method was the one with a linear quadratic regression between the volume of distribution of the tracer at a specific time and the clearance calculated with 12 samples. Two-sample methods performed significantly better than did single-sample methods. The conclusion is made that 99mTc-pentetate and 131I-OIH plasma clearances can be estimated in dogs and cats with 1 or 2 blood samples with a reasonable margin of error compared to plasma clearances calculated with a 2-compartment model and 12 blood samples.

Animals↗