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Results for “parameter optimization”

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PubMed1996

Secondary structure determination of proteins in aqueous solution by infrared spectroscopy: a comparison of multivariate data analysis methods.

The accuracy of the secondary structure prediction from an infrared spectra data base of 39 proteins with known X-ray structure was investigated by different methods of multivariate data analysis. The best agreements with the secondary structure determined by X-ray crystallography are obtained if both the amide I and amide II bands are used for calibration. With optimized parameters the methods singular value decomposition, partial least squares, and ridge regression yield similar results. As judged by the standard error of prediction, the secondary structure elements helix and beta-sheet can be predicted with the highest accuracy. Small data sets of less than 20 protein spectra, which exhibit the variance in secondary structure content of the whole set, can pretend an increased prediction accuracy only if column cross-validation is used as reference; however, with these calibration sets the average secondary structure prediction of all 39 proteins is debased. The hydrogen-bonded turns or bridges are predicted with higher accuracy than the assigned secondary structure types helix and beta-sheet.

Multivariate Analysis↗

PubMed1997

A chemiluminescent flow sensing device for determination of choline and phospholipase D activity in biological samples.

A chemiluminescent flow-sensing device for the determination of phospholipase D (PLD) activity and/or choline (Ch) in biological samples using choline oxidase (ChO) and horseradish peroxidase (HRP) immobilized on Eupergit C (polymer beads of methacrylamide, N-methylene-bis-methacrylamide, and allyl-glycidyl-ether) was developed. The best results were obtained with immobilized ChO and HRP at a polymer beads wet weight ratio of 16:1. The optimized parameters of the developed sensing device were 56 microM luminol in working solution; sample volume, 60 microliters; flow rate, 0.3 ml/min; and sample throughput, 15/h. The detection limit (3 SD) using a luminescent enhancer was 1.2 microM for Ch, corresponding to 0.167 mIU of PLD activity per milliliter. Without enhancer the values were 3.0 microM and 0.417 mIU, respectively. The Ch recovery varied between 80.4 and 109%. The biological samples quenched the luminescent light to different extents, and this matrix effect was readily overcome by measuring the luminescent signal of added Ch standard. The flow biosensor was used for the determination of PLD in samples of different origin, including rape seeds during maturation.

Alcohol Oxidoreductases↗

PubMed1999

A standardized protocol for assessing regulators of pigmentation.

Varied effects of chemical or biological compounds on mammalian pigmentation have been reported by many groups, but to date, no standardized method has established necessary and/or optimal parameters for testing such agents. A standardized method has been developed to screen compounds with potential effects on pigmentation. The protocol comprises basic parameters to analyze melanogenic effects and allows for further characterization of candidate compounds, providing important insights into their mechanism of action. In this protocol (termed STOPR, for standardized testing of pigmentation regulators), compounds are initially screened using purified tyrosinase and are then tested on melanocytes in culture. After treatment of melanocytes with potentially bioactive compounds, cell proliferation and viability, total melanin accumulated, and melanogenic potential are measured. This protocol is an important first step in characterizing chemical regulation of effects on melanogenesis. When bioactive candidate compounds are identified, testing may proceed for pharmacological or otherwise commercial applications in coculture and/or organ culture models followed by in vivo testing. As an application of this method, results for compounds known to stimulate and/or inhibit melanogenesis (including arbutin, hydroquinone, kojic acid, melanocyte-stimulating hormone, and thymidine dimers) as well as some commercial skin whiteners are reported.

Animals↗

PubMed1994

LHRH-I release from quail hypothalamic slices measured by specific EIA.

A competitive enzyme immunoassay (EIA) was developed for luteinizing hormone-releasing hormone (LHRH), which measures either mammalian luteinizing hormone-releasing hormone or chicken LHRH-I (cLHRH-I). There is negligible cross-reactivity with chicken LHRH-II. Assay sensitivity is 1 pg/ml and the intra- and interassay variation are 3.4 and 10.0%, respectively. The assay was validated for measuring cLHRH-I by parallelism and quantitative recovery. Using this EIA, cLHRH-I content was measured in microdissected samples of median eminence from mature quail and chickens. Mean cLHRH-I concentrations were 1.25 +/- 0.35 and 2.10 +/- 0.25 ng/mg protein in quail and chickens, respectively. In vitro release of cLHRH-I was studied by perifusion of quail medial basal hypothalamus-preoptic area (MBH-POA) slices. Challenge with increasing concentrations of K+ resulted in significant (P < 0.05) release of cLHRH-I. The release of cLHRH-I from MBH-POA slices was also measured in response to norepinephrine (NE), epinephrine (E), and isoproterenol (ISO). Chicken LHRH-I was released in a dose-dependent manner; maximal release occurred with 10(-7) M NE, 10(-8) M E, and 10(-7) M ISO. Tissue response was optimal for experimental manipulation 6-25 hr postcollection; thereafter, the response deteriorated until 60 hr postcollection. These data extend previous studies in birds by detailed characterization of responses to neurochemical challenge and description of optimal parameters for tissue response during perifusion.

Animals↗

PubMed1994

Folding the main chain of small proteins with the genetic algorithm.

Grid-free protein folding simulations were effected using the genetic algorithm, a backbone representation and standard dihedral angular conformations. The topological folding of idealized four-helix bundles was investigated in detail to differentiate among the important protein folding forces used as fitness criteria. Hydrophobic interactions were the most significant while local forces and hydrogen bonds were far less effective in promoting folding. Stable secondary structural regions were also important as nucleating centers. Using the fitness parameters optimized in idealized simulations together with standard secondary structure predictions derived from the amino acid sequence alone, the proper main-chain folding of the four-helix bundle proteins cytochrome b562, cytochrome c' and hemerythrin was achieved. In addition the backbone topology as predicted by the genetic algorithm for crambin, a mixed helix/strand protein with known structure, is presented and discussed.

Algorithms↗

PubMed1999

RNA secondary structure prediction based on free energy and phylogenetic analysis.

We describe a computational method for the prediction of RNA secondary structure that uses a combination of free energy and comparative sequence analysis strategies. Using a homology-based sequence alignment as a starting point, all favorable pairings with respect to the Turner energy function are identified. Each potentially paired region within a multiple sequence alignment is scored using a function that combines both predicted free energy and sequence covariation with optimized weightings. High scoring regions are ranked and sequentially incorporated to define a growing secondary structure. Using a single set of optimized parameters, it is possible to accurately predict the foldings of several test RNAs defined previously by extensive phylogenetic and experimental data (including tRNA, 5 S rRNA, SRP RNA, tmRNA, and 16 S rRNA). The algorithm correctly predicts approximately 80% of the secondary structure. A range of parameters have been tested to define the minimal sequence information content required to accurately predict secondary structure and to assess the importance of individual terms in the prediction scheme. This analysis indicates that prediction accuracy most strongly depends upon covariational information and only weakly on the energetic terms. However, relatively few sequences prove sufficient to provide the covariational information required for an accurate prediction. Secondary structures can be accurately defined by alignments with as few as five sequences and predictions improve only moderately with the inclusion of additional sequences.

Algorithms↗

PubMed1995

Development and optimization of three-dimensional spatial EPR imaging for biological organs and tissues.

The development and optimization procedures for obtaining high-quality three-dimensional spatial electron-paramagnetic-resonance images of large lossy samples at L band are described. Strategies for selecting optimized parameters for projection acquisition, instrumentation, and algorithms for correcting drifts in microwave frequency and inaccuracies in the static and gradient magnetic fields are described. Image reconstruction was performed using a two-stage filtered back-projection method with spectral deconvolution. With this instrumentation, correction algorithms, and image reconstruction method, spatially accurate 3D images of radical distribution were observed in complex phantoms using 0.5 mM nitroxide labels. The results indicate that high-quality images of lossy samples, including biological organs and tissues of up to 25 mm in size, could be obtained in a reasonable time with submillimeter resolution.

Algorithms↗

PubMed2001

Optimization of residual water signal removal by HLSVD on simulated short echo time proton MR spectra of the human brain.

Suppression of the residual water signal from proton magnetic resonance (MR) spectra recorded in human brain is a prerequisite to an accurate quantification of cerebral metabolites. Several postacquisition methods of residual water signal suppression have been reported but none of them provide a complete elimination of the residual water signal, thereby preventing reliable quantification of brain metabolites. In the present study, the elimination of the residual water signal by the Hankel Lanczos singular value decomposition method has been evaluated and optimized to provide fast automated processing of spectra. Model free induction decays, reproducing the proton signal acquired in human brain localized MR spectroscopy at short echo times (e.g., 20 ms), have been generated. The optimal parameters in terms of number of components and dimension of the Hankel data matrix allowing complete elimination of the residual water signal are reported.

Body Water↗

PubMed1994

Overexpression and rapid purification of rabbit fast skeletal troponin I from Escherichia coli: effect of different promoters, host strains, and culture conditions.

Rabbit fast skeletal troponin I (TnIf) cDNA was expressed using two Escherichia coli expression vectors, pRE1 containing the bacteriophage lambda pL promoter and pAED4, a T7 RNA polymerase-based vector. Although both vectors expressed TnIf, overexpression of the target protein was achieved with pAED4. The effect of several parameters such as culture condition, compatible host strain, and inhibition of protein synthesis by rifampicin on the expression of TnIf was investigated. The overexpressed target protein synthesized during a brief induction period of only 2 h was conveniently purified from inclusion bodies by a simple and rapid procedure involving extraction with urea, ultracentrifugation, DE-52 column chromatography, and gel filtration. About 50-75 mg of highly purified TnIf was obtained per liter E. coli culture by this method, which does not involve time-consuming multistep procedures such as affinity and ion exchange chromatography as previously reported in the literature. The isolated unfused protein is stable and is indistinguishable from native protein in all biological parameters examined. The parameters optimized in this report for overexpression of TnIf may also be applicable for other eukaryotic proteins.

Adenosine Triphosphatases↗

PubMed1992

Intravesical recombinant tissue plasminogen activator for the prevention of implantation-mediated bladder tumor recurrence.

The mechanism by which intravesical recombinant tissue plasminogen activator (rTPA) prevents tumor cell adherence to injured bladder surfaces, and the optimal parameters for the in vivo use of rTPA for adherence prevention, were evaluated. Intravesical rTPA decreased tumor cell adherence to sites of urothelial injury as a direct function of drug concentration in the intravesical fluid. Recombinant TPA concentrations of 1 mg/ml and 0.1 mg/ml significantly decreased tumor cell adherence relative to the control group. The efficacy of rTPA in removing adherent cells was time-dependent with maximal activity occurring at 15 min or later following intravesical administration. Intravesical rTPA effectively reduced the size of the tumor inoculum when administered either concomitant with, or subsequent to, tumor cell exposure. The relative efficacy of these two approaches was dependent upon the presence of serum in the intravesical fluid. Administration of rTPA concomitant with tumor cell exposure proved more effective in the absence of serum, while postadherence administration was more effective in the presence of 10% fetal calf serum. The addition of exogenous plasminogen to the rTPA solution did not increase anti-adherence activity relative to rTPA alone. However, blockade of endogenous plasminogen conversion with systemically administered epsilon-amino-caproic acid reversed the anti-adherence activity of exogenous rTPA. In vitro experiments evaluating cellular adherence to fibrin substrate confirmed that rTPA's anti-adherence activity was dependent on the presence of plasminogen. Exogenous rTPA administered immediately following tumor cell adherence decreased tumor cell implantation in animals receiving low to moderate tumor inoculums. These data suggest that rTPA prevents cellular adherence as a result of plasminogen activation and subsequent fibrinolysis. Intravesical rTPA administered in sufficient concentration for relatively short periods of time effectively reduces the adherent tumor inoculum and alters implantation as an inverse function of the tumor inoculum. This approach represents a novel strategy which may prove applicable for the prevention of implantation-mediated tumor recurrence at sites of surgical trauma.

Administration, Intravesical↗

PubMed1992

The orientation of transition moments of dye molecules used in fluorescence studies of muscle systems.

Fluorescence and phosphorescence depolarization techniques can provide information on orientational order and rotational motion of crossbridges in muscle fibres. However the depolarization experiment monitors the orientation and motion of the crossbridges indirectly. The changes in depolarization arise from a change in the orientation of the transition dipoles of the dye attached to the crossbridge. In order to extract the physiologically relevant orientations from the data it is therefore necessary to characterize the orientation of the dye molecule relative to the crossbridge and the orientation of the transition moments in the frame of the dyes. The dyes 1,5-I-AEDANS and eosin-5-maleimide are commonly used for labelling the crossbridge in muscle fibres. The orientations of the absorption and fluorescence emission dipoles of these two dyes in the molecular frame were determined. Angle resolved fluorescence depolarization experiments on the dyes, macroscopically aligned in a stretched polymer matrix of poly vinyl alcohol, were carried out. The data were analyzed in terms of an orientational distribution of the dye molecules in the film and the orientations of the absorption and emission dipoles in the frame of the dye molecule. Experimental data, obtained from a given sample at different excitation wavelengths, were analyzed simultaneously in a global target approach. This leads to a reduction in the number of independent parameters optimized by the non-linear least squares procedure.

Animals↗

PubMed1980

Facilitation and inhibition of jaw reflexes evoked by electrical stimulation of the cat's cerebral cortex.

The effects of electrical stimulation of the cerebral cortex on the monosynaptic jaw closing and the disynaptic jaw opening reflexes were studied in cats anaesthetized with chloralose. The time course of the reflex effects was recorded. Similar rhythmic sequences of facilitation and inhibition were observed in both reflexes (Fig. 3). The sequence could start with facilitation or inhibition. The latency of the initial effects was short (2.5 ms) indicating a minimum of two synapses in the descending path. The period of the rhythmic sequence was approximately 10 ms. Optimal parameters for the conditioning cortisol stimuli were found to be: trains of 3-5 surface anodal pulses, 0.5 ms, 400 Hz. The threshold of the cortical effects on the reflexes was 0.3 mA. A single pulse evoked effects. The cortical origin of the effects was located and related to the somatosensory projections, and to the cytoarchitecture. The effects of largest amplitude and most complex time course were evoked from the oral and perioral projections to areas 3a and 3b. Effects evoked from areas 4 gamma, 5a, and 6a beta were less complex and of lower amplitude. It is suggested that a trigemino-cortico-trigeminal loop via 3a may function in reflex modulation of the jaw movements. In addition area 3a may contribute to cortico-cortical motor elaborations via U-fiber connections to area 4 gamma.

Animals↗

PubMed1994

Analysis, classification, and coding of multielectrode spike trains with hidden Markov models.

It is shown that hidden Markov models (HMMs) are a powerful tool in the analysis of multielectrode data. This is demonstrated for a 30-electrode measurement of neuronal spike activity in the monkey's visual cortex during the application of different visual stimuli. HMMs with optimized parameters code the information contained in the spatiotemporal discharge patterns as a probabilistic function of a Markov process and thus provide abstract dynamical models of the pattern-generating process. We compare HMMs obtained from vector-quantized data with models in which parametrized output processes such as multivariate Poisson or binomial distributions are assumed. In the latter cases the visual stimuli are recognized at rates of more than 90% from the neuronal spike patterns. An analysis of the models obtained reveals important aspects of the coding of information in the brain. For example, we identify relevant time scales and characterize the degree and nature of the spatiotemporal variations on these scales.

Animals↗

PubMed1995

Chromaffin cell xenografts in the rat neocortex can produce antidepressive activity in the forced swimming test.

Adrenal medullary allografts, as well as other monoaminergic tissues, have been demonstrated in our laboratory to increase antidepressive activity when transplanted into the frontal neocortex of rats. Refinement in the optimal parameters for xenograft viability has indicated that isolated bovine chromaffin cells may be an improved source of graft donor tissue. The aim of the present study was to determine whether isolated bovine chromaffin cell grafts to the rat frontal neocortex could provide an alternative source of catecholamines for antidepressant activity. Isolated bovine chromaffin cells, isolated bovine fibroblasts, or an equal volume of vehicle were unilaterally implanted into the right or left frontal cortex or right visual cortex. All rats were assessed before and 6 weeks after transplantation using the forced swimming test, a popular measure of antidepressant activity. Bovine chromaffin cell grafts in either the right or left frontal cortex produced significant increases in antidepressant activity compared to grafts of bovine fibroblasts and sham-operated or nontransplanted rats. In contrast, bovine chromaffin cells transplanted to the visual cortex did not affect antidepressant activity. Bovine fibroblast grafts in the frontal cortex also induced slight increases in antidepressant activity, although significantly less than chromaffin cell grafts. Morphological analysis revealed robust survival of tyrosine hydroxylase-positive chromaffin cells that retained their in situ ultrastructure and occasionally formed synaptic connections with the host parenchyma. These results suggest that xenografted isolated bovine chromaffin cells can provide a viable source of catecholamines for antidepressive activity.

Adrenal Medulla↗

PubMed1988

Auto-association by multilayer perceptrons and singular value decomposition.

The multilayer perceptron, when working in auto-association mode, is sometimes considered as an interesting candidate to perform data compression or dimensionality reduction of the feature space in information processing applications. The present paper shows that, for auto-association, the nonlinearities of the hidden units are useless and that the optimal parameter values can be derived directly by purely linear techniques relying on singular value decomposition and low rank matrix approximation, similar in spirit to the well-known Karhunen-Loève transform. This approach appears thus as an efficient alternative to the general error back-propagation algorithm commonly used for training multilayer perceptrons. Moreover, it also gives a clear interpretation of the rôle of the different parameters.

Mathematics↗

PubMed1984

Time series modeling of neuromuscular system.

The dynamic response of the human ankle joint to a bandlimited random torque perturbation superimposed on a constant bias torque is observed in normal human subjects. The applied torque input, the joint angular rotation output, and the electromyographic activity using surface electrodes from the extensor and the flexor muscles of the ankle joint were recorded. Transfer function models using time series techniques were developed for the torque - angular rotation input-output pair and for the angular rotation - electromyographic activity input-output pair. A parameter constraining technique was applied to develop more reliable models. It is shown that the asymptotic behavior of the system must be taken into account during parameter optimization to develop better predictive models.

Ankle Joint↗

PubMed1979

[First experiences with an instrument for TV display of digitally encoded text information for the visually handicapped (author's transl)].

An instrument was developed which allows the display, in enlarged form--especially for visually handicapped persons--of text information as used in modern data-acquisition systems such as writing automats, screen editing devices, and television text display (in England, Ceefax). With the aid of electronic character generators, the text is displayed continually, moving from right to left in one line on the screen of a commercial TV set. Rate of movement, size, brightness, and color of the characters (and/or the background) can be selected arbitrarily. We performed a preliminary reading test with visually handicapped subjects from a rehabilitation center for blind persons. The resulting optimal parameters for text display and the achieved reading speed with the system are discussed.

Adult↗

PubMed1986

Modeling of microbial substrate conversion, growth and product formation in a recycling fermentor.

Paracoccus denitrificans and Bacillus licheniformis were grown in a carbon- and energy source-limited recycling fermentor with 100% biomass feedback. Experimental data for biomass accumulation and product formation as well as rates of carbon dioxide evolution and oxygen consumption were used in a parameter optimization procedure. This procedure was applied on a model which describes biomass growth as a linear function of the substrate consumption rate and the rate of product formation as a linear function of the biomass growth rate. The fitting procedure yielded two growth domains for P. denitrificans. In the first domain the values for the maximal growth yield and the maintenance coefficient were identical to those found in a series of chemostat experiments. The second domain could be described best with linear biomass increase, which is equal to a constant growth yield. Experimental data of a protease producing B. licheniformis also yielded two growth domains via the fitting procedure. Again, in the first domain, maximal growth yield and maintenance requirements were not significantly different from those derived from a series of chemostat experiments. Domain 2 behaviour was different from that observed with P. denitrificans. Product formation halts and more glucose becomes available for biomass formation, and consequently the specific growth rate increases in the shift from domain 1 to 2. It is concluded that for many industrial production processes, it is important to select organisms on the basis of a low maintenance coefficient and a high basic production of the desired product. It seems less important that the maximal production becomes optimized, which is the basis of most selection procedures.

Bacillus↗