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PubMed2005

Iterative approach to model identification of biological networks.

BACKGROUND: Recent advances in molecular biology techniques provide an opportunity for developing detailed mathematical models of biological processes. An iterative scheme is introduced for model identification using available system knowledge and experimental measurements. RESULTS: The scheme includes a state regulator algorithm that provides estimates of all system unknowns (concentrations of the system components and the reaction rates of their inter-conversion). The full system information is used for estimation of the model parameters. An optimal experiment design using the parameter identifiability and D-optimality criteria is formulated to provide "rich" experimental data for maximizing the accuracy of the parameter estimates in subsequent iterations. The importance of model identifiability tests for optimal measurement selection is also considered. The iterative scheme is tested on a model for the caspase function in apoptosis where it is demonstrated that model accuracy improves with each iteration. Optimal experiment design was determined to be critical for model identification. CONCLUSION: The proposed algorithm has general application to modeling a wide range of cellular processes, which include gene regulation networks, signal transduction and metabolic networks.

Algorithms↗

PubMed2004

Hot air coating technique as a novel method to produce microparticles.

In this work a new technology to produce microparticles, as well as the equipment suitable for its application, is described. This technique, called hot air coating (HAC), was developed to overcome the drawbacks of the conventional spray-congealing technique and consists of a special venturimeter, deliberately designed to prevent any hindrance along the axial path through which the powder is conveyed. In HAC technology, the raw material is a solid, generally small granules, which is aspirated through the "Venturi effect" and accelerated in a flux of hot air to soften and then to melt the excipient, especially on the particle surface. The microparticles then solidify during falling in air at room temperature. Model formulations, containing acetaminophen or theophylline as drugs and glycerilmonostearate, stearic acid, or carnauba wax as coating waxes, were tested. The choice of the optimal operating parameters was found to be a function of the formulation and of the particle size of the starting material. A pressure of 3 atm and a temperature of 20-60 degrees C above the melting point of the excipient were found generally to be the optimal parameters for the coating process. The morphology, the in vitro dissolution profile, and the possible drug/excipient interactions of formulations containing different percentages (30%, 50%, and 70% w/w) of acetaminophen were evaluated. The results show that the morphology and dissolution profiles of the microparticles were quite different from those of the starting material; in particular the best coating was achieved by microparticles lower than 500 microm. Therefore, the HAC process could be a viable alternative to the conventional spray-congealing technique to produce microparticles with a high drug content.

Acetaminophen↗

PubMed2000

Optimization of a laser ablation-inductively coupled plasma "time of flight" mass spectrometry system for short transient signal acquisition.

Simultaneous ion sampling and sequential detection offered by inductively coupled plasma 'time of flight' mass spectrometry (ICP-TOFMS) provides advantages for the analysis of short transient concentration-variable signals as produced in laser ablation. In order to investigate the capabilities of ICP-TOFMS in combination with an excimer laser ablation system, ablation studies on reference materials and geological samples were carried out. Various ICP-TOFMS parameters were optimized for laser-induced aerosols. Transverse rejection ion pulse was used to extend the dynamic range in concentration. A reduced volume ablation cell was designed and used in order to increase the sample density in the ICP. Results for 63 simultaneously measured isotopes (SRM 610 from NIST) lead to limits of detection in the 1-100 microg/g range for a 80 microm crater diameter (10 Hz, 1.2 mJ pulse energy). The reproducibility of signal ratios was determined to be better than 2% RSD for transient signals using 102 ms integration time. These optimized parameters were then used for the analysis of tin-rich fluid inclusions. Preliminary results of multielement analysis and isotopic ratio determinations on individual fluid inclusions (63 isotopes, 102 ms integration time) demonstrate the capabilities of ICP-TOFMS in combination with laser ablation.

Journal Article↗

PubMed1995

Collaborative work to determine the optimal administration period and parameters to detect drug effects on male rat fertility--study on estradiol benzoate effects.

In order to examine the optimal administration period and parameters for male fertility assessment, male rats were subcutaneously administered 0.2, 2 or 20 micrograms/kg of estradiol benzoate (E2B), a known testicular toxicant, for 4 weeks or 9 weeks before mating. After 4 weeks administration, suppression of body weight gain and food consumption, decreases in prostate and seminal vesicle weights, atrophy of Leydig cells, and mature spermatid retention at stages IX, X and XI were observed in the 2 and 20 micrograms/kg groups. In the 20, micrograms/kg group, decreases in epididymides weight and copulation index were also found but the number of sperm and sperm motility were not affected. In the 0.2 micrograms/kg group, no changes were noted in any parameters. After 9 weeks administration, decreases in testis weight and the number and motility of sperm were observed in the 20, micrograms/kg group, in addition to the changes found after 4 weeks administration. These results suggest that detailed histopathological evaluation and determination of accessory sex organ weights are sensitive for evaluating the effects of E2B on male fertility. Results with the 4-weeks treatment were comparable to those with the 9-weeks treatment in terms of these parameters.

Animals↗

PubMed2004

5-aminolevulinic acid-based photodynamic therapy in leukemia cell HL60.

A study to explore the optimal experimental parameters and the photosensitization of 5-aminolevulinic acid (ALA)-based photodynamic therapy (PDT) in promyelocytic leukemia cell HL60 has been conducted, in which HL60 cells and their control groups, peripheral blood mononuclear cell (PBMC), first are incubated with different concentrations of ALA in dark for different periods of time and then followed by irradiating with different wavebands for different fluences. Fluorescence microscope and spectrofluorometer have been used to detect the fluorescence of protoporphyrin IX (PpIX) endogenously produced by ALA. The response of the cells to ALA-PDT was evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2-5-diphenyl-2H-tetrazolium bromide (MTT) assay (interval between irradiation and the MTT assay is 24 h) and by flow cytometry (the length of time between irradiation and the flow assay is 30 min). MTT results will reflect the relative number of metabolically active mitochondria in the population. Propidium iodide uptake in flow cytometry will test for membrane damage. The results of parameter experiments were obtained: 1 x 10(5)/mL HL60 cell was first incubated with 1 mmol/L ALA in dark for 4 h and the maximum fluorescence of PpIX level appeared; then irradiated with 410 nm (4 mW/cm2) for 14.4 J/cm2 and maximum photodamage to membrane and mitochondrial function of HL60 cell resulted. With the normal granulocytes, such response was not detected. Therefore a hypothetical idea can be brought forward that ALA-based PDT can be used for inactivation of leukemia cell HL60 and these optimal parameters may be useful for clinical application.

Aminolevulinic Acid↗

PubMed2006

Impact of data quality and model complexity on prediction of pesticide leaching.

Accurate input data for leaching models are expensive and difficult to obtain which may lead to the use of "general" non-site-specific input data. This study investigated the effect of using different quality data on model outputs. Three models of varying complexity, GLEAMS, LEACHM, and HYDRUS-2D, were used to simulate pesticide leaching at a field trial near Hamilton, New Zealand, on an allophanic silt loam using input data of varying quality. Each model was run for four different pesticides (hexazinone, procymidone, picloram and triclopyr); three different sets of pesticide sorption and degradation parameters (i.e., site optimized, laboratory derived, and sourced from the USDA Pesticide Properties Database); and three different sets of soil physical data of varying quality (i.e., site specific, regional database, and particle size distribution data). We found that the selection of site-optimized pesticide sorption (Koc) and degradation parameters (half-life), compared to the use of more general database derived values, had significantly more impact than the quality of the soil input data used, but interestingly also more impact than the choice of the models. Models run with pesticide sorption and degradation parameters derived from observed solute concentrations data provided simulation outputs with goodness-of-fit values closest to optimum, followed by laboratory-derived parameters, with the USDA parameters providing the least accurate simulations. In general, when using pesticide sorption and degradation parameters optimized from site solute concentrations, the more complex models (LEACHM and HYDRUS-2D) were more accurate. However, when using USDA database derived parameters, all models performed about equally.

Adsorption↗

PubMed2006

Preparing digitized cervigrams for colposcopy research and education: determination of optimal resolution and compression parameters.

OBJECTIVE: Visual assessment of digitized cervigrams through the Internet needs to be optimized. The National Cancer Institute and National Library of Medicine are involved in a large effort to improve colposcopic assessment and, in preparation, are conducting methodologic research. MATERIALS AND METHODS: We selected 50 cervigrams with diagnoses ranging from normal to cervical intraepithelial neoplasia 3 or invasive cancer. Those pictures were scanned at 5 resolution levels from 1,550 to 4,000 dots per inch (dpi) and were presented to 4 expert colposcopists to assess image quality. After the ideal resolution level was determined, pictures were compressed at 7 compression ratios from 20:1 to 80:1 to determine the optimal level of compression that permitted full assessment of key visual details. RESULTS: There were no statistically significant differences between the 3,000 and 4,000 dpi pictures. At 2,000 dpi resolution, only one colposcopist found a slightly statistically significant difference (p = 0.02) compared with the gold standard. There was a clear loss of quality of the pictures at 1,660 dpi. At compression ratio 60:1, 3 of 4 evaluators found statistically significant differences when comparing against the gold standard. CONCLUSIONS: Our results suggest that 2,000 dpi is the optimal level for digitizing cervigrams, and the optimal compression ratio is 50:1 using a novel wavelet-based technology. At these parameters, pictures have no significant differences with the gold standard.

Biomedical Research↗

PubMed1999

Spatial regularization applied to factor analysis of medical image sequences (FAMIS).

Dynamic image sequences allow physiological mechanisms to be monitored after the injection of a tracer. Factor analysis of medical image sequences (FAMIS) hence creates a synthesis of the information in one image sequence. It estimates a limited number of structures (factor images) assuming that the tracer kinetics (factors) are similar at each point inside the structure. A spatial regularization method for computing factor images (REG-FAMIS) is proposed to remove irregularities due to noise in the original data while preserving discontinuities between structures. REG-FAMIS has been applied to two sets of simulations: (a) dynamic data with Gaussian noise and (b) dynamic studies in emission tomography (PET or SPECT), which respect real tomographic acquisition parameters and noise characteristics. Optimal regularization parameters are estimated in order to minimize the distance between reference images and regularized factor images. Compared with conventional factor images, the root mean square error between regularized images and reference factor images is improved by 3 for the first set of simulations, and by about 1.5 for the second set of simulations. In all cases, regularized factor images are qualitatively and quantitatively improved.

Algorithms↗

PubMed1987

Analysis of microdensitometric data in terms of probability of cleavage of DNA.

Computer-aided analysis of autoradiographic films of DNA fragments is presented. The Powell least-squares procedure is used for optimization of parameters for components of complex densitometric curves. Since each densitometric spectrum may be divided for several non-overlapped blocks of bands, there is no upper limit on the number of parameters which must be optimized. Eight shapes for the component bands are utilized: symmetric and asymmetric Gauss and Cauchy functions, direct, symmetric and asymmetric product of Gauss function and inverse of Cauchy function, and log-normal function. The probability of DNA cleavage is calculated with correction for multiple cuts. The methods presented was applied to detailed analysis of densitometric spectra of a 21-bp DNA restriction fragment and allowed for direct correlation between structural microheterogeneity of DNA and the resulting cutting pattern. This method should facilitate the analysis of densitometric data from antibiotic-induced cleavage of DNA and footprinting experiments.

Absorptiometry, Photon↗

PubMed1981

Quantitative simultaneous determination of eight common antiepileptic drugs and metabolites by liquid chromatography.

Specific antiepileptic drug (AED) concentrations in serum are believed to cause therapeutic effects in individual patients. Communication between the clinician and the laboratory performing the drug level determinations is therefore essential for safe and effective medication. The now common practice of multiple drug therapy preferably requires simultaneous separation and quantitation of the various drugs and their metabolites. The advantages and disadvantages of current AED analysis methods are discussed. Liquid chromatography (LC) was found to be the most versatile technique for routine and research analysis and can be applied to the determination of common, less common and new AED and metabolites. Carbamazepine and its metabolite, carbamazepine-10,11-epoxide, were determined with high accuracy. The sample preparation procedures, the internal standards, and mode of LC separation used for the analysis are given. The chromatographic parameters for optimized resolution and analysis are given. The chromatographic parameters for optimized resolution and analysis time of eight AEDs and metabolites were devised with special consideration for the influence of the oven temperature on resolution. About 300 patient serum samples were analyzed by automatic unattended operation. By this method some 50 samples per day can be extracted and analysed. Quantitative results achieved by LC and gas liquid chromatography (GLC) on the same patient samples are reported and chromatograms discussed. Peak scanning was used to demonstrate the presence of compounds which could eventually interfere with the detection of phenylethylmalonamide. The overall accuracy of the employed LC method, the repeatability of retention times on three different columns, and the measured ranges of AED concentrations are reported.

Anticonvulsants↗

PubMedDate not supplied

Delineating a recharge area for a spring using numerical modeling, Monte Carlo techniques, and geochemical investigation.

Recharge areas of spring systems can be hard to identify, but they can be critically important for protection of a spring resource. A recharge area for a spring complex in southern Wisconsin was delineated using a variety of complementary techniques. A telescopic mesh refinement (TMR) model was constructed from an existing regional-scale ground water flow model. This TMR model was formally optimized using parameter estimation techniques; the optimized "best fit" to measured heads and fluxes was obtained by using a horizontal hydraulic conductivity 200% larger than the original regional model for the upper bedrock aquifer and 80% smaller for the lower bedrock aquifer. The uncertainty in hydraulic conductivity was formally considered using a stochastic Monte Carlo approach. Two-hundred model runs used uniformly distributed, randomly sampled, horizontal hydraulic conductivity values within the range given by the TMR optimized values and the previously constructed regional model. A probability distribution of particles captured by the spring, or a "probabilistic capture zone," was calculated from the realistic Monte Carlo results (136 runs of 200). In addition to portions of the local surface watershed, the capture zone encompassed areas outside of the watershed--demonstrating that the ground watershed and surface watershed do not coincide. Analysis of water collected from the site identified relatively large contrasts in chemistry, even for springs within 15 m of one another. The differences showed a distinct gradation from Ordovician-carbonate-dominated water in western spring vents to Cambrian-sandstone-influenced water in eastern spring vents. The difference in chemistry was attributed to distinctive bedrock geology as demonstrated by overlaying the capture zone derived from numerical modeling over a bedrock geology map for the area. This finding gives additional confidence to the capture zone calculated by modeling.

Geological Phenomena↗

PubMed2006

Design of adjustable superresolving filters based on birefringent crystals.

A two-mode adjustable superresolving filter based on a birefringent filter is proposed. This kind of filter has superresolution in two modes of adjustment. One is rotation of the binary pupil filter on the optical axis of the system and the other is the tilt of the filter away from the pupil plane on axis parallel or perpendicular to the optical axis of the crystal. The filters act as complex amplitude filters in the former mode, and as pure phase filters in the latter. By analyzing two superresolving parameters, we obtain the optimal design parameters that ensure a large field of view, a large superresolving range, and a high setting accuracy. This kind of filter can provide more flexibility in practical applications.

Journal Article↗

PubMed2001

High-throughput identification, database storage and analysis of SNPs in EST sequences.

Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation and disease-causing mutations in many genes. Due to their abundance and slow mutation rate within generations, they are thought to be the next generation of genetic markers that can be used in a myriad of important biological, genetic, pharmacological, and medical applications. There are several strategies both experimental, and in-silico for SNP discovery and mapping. Experimental SNP discovery consists of a number of labourious steps that make this process complex and expensive. In-silico discovery has been proposed as an alternative discovery method that makes use and takes advantage of large data sets with potential SNP information that have been generated with other purposes and have not been used as a SNP information source yet. However, in order to successfully apply the in-silico method to large data sets, the following challenges need to be addressed: First it is necessary to build an integrated SNP pipeline that handles data processing steps smoothly from the beginning (collecting sequence information) to end (SNPs in the database). Also, SNP detection tool parameters have to be optimized to satisfy specific goals of the project. Finally, SNP data could not be fully used until the in-silico method is validated experimentally. In this paper we present a design and implementation of an in-silico SNP detection software pipeline that exploits the existence of large EST (expressed sequence tag) data sets and effectively addresses the above challenges. First, the pipeline allows for smooth data transition between its different components by implementing data interfaces that translate the data formats of the different tools in the different stages. Second, we optimized PolyBayes parameters for SNP detection in maize EST. Finally, we implemented a user interface that along with the database structure created allows the scientist to perform preliminary analysis of the data and to perform basic statistics on the SNP data prior to experimental validation. The pipeline works with two different types of sequence assemblers (PHRAP (http://www.phrap.org/) and CAT from DoubleTwist (http://www.doubletwist.com/). It uses a Bayesian engine for SNP detection (PolyBayes), selects relevant polymorphism information which is then uploaded into a database. We detected 2439 SNPs and 822 insertion deletions (INDELs) with a PolyBayes probability higher than 0.99 on the public set of 68,000 maize ESTs. The user interface allowed us analyzing the polymorphism information right after discovery in several ways that allowed us to gain insight into the distribution and significance of the newly acquired data.

Animals↗

PubMed2006

[Real-time fluorescent quantitative PCR for detection of peripheral blood T-cell receptor excision circles].

OBJECTIVE: To develop and optimize real-time fluorescence quantitative PCR (FQ-PCR) with the housekeeping gene RAG2 as cell number control to quantify T-cell receptor excision circle (TREC) in the peripheral blood. METHODS: The real-time PCR system for amplifying TREC and RAG2 genes was established on the basis of ABI 7000 apparatus using Golden Taq system, designed primers, TaqMan-MGB probes and optimized buffer. PCR conditions were optimized with standard samples of TREC plasmid. RESULTS: The amplification with the primer pair T(3) and T(4) was more efficient than that with T(1) and T(2). More specific and efficient amplification in FQ-PCR was achieved using TaqMan-MGB probes as compared with general Taq-Man probes. Golden Taq was more effective than general Taq in improving the specificity and decreasing the artifact, and 95 degrees C; for 10 min, 95 degrees C; for 5 s, and 53 degrees C; for 30 s for a total of 40 cycles using ABI7000 was found as the optimized thermal parameter setting. CONCLUSION: An optimized real-time PCR protocol for detecting TREC in peripheral blood mononuclear cells is established.

Adolescent↗

PubMed1995

Collaborative assessment of optimal administration period and parameters to detect effects on male fertility in the rat: effects of cyclophosphamide on the male reproductive system.

As part of a collaborative project to determine optimal administration period and parameters to detect compound effects on male fertility in the rat, adult male rats were administered cyclophosphamide daily at 5, 10, 20 and 40 mg/kg for 2 weeks, or at 2.5, 5 and 10 mg/kg for 4 or 9 weeks. After the pre-pairing administration period, each male was paired with an untreated female. After mating, testes and epididymides were removed and examined for organ weights, sperm head counts, sperm morphology and histopathology. Mated females were caesarean-sectioned on Day 13 of gestation. Although atrophy of epithelia in the cauda epididymides and decreases of spermatogenic cells in the testes were observed in the higher dose groups in the 2w study, no other effects on the male reproductive system were noted in any of the studies. There were clear effects on pregnancy outcome; implantation efficiency was decreased in the highest dosage groups and postimplantation losses increased in all the dosage groups in all studies. These results suggest that a fertility study with females is needed particularly in the case of mutagenic agents, together with a detailed histopathological evaluation for reliable detection of toxicity on the male reproductive system.

Animals↗

PubMed1998

[Spiral CT in arytenoid cartilage dislocation: the optimization of the study parameters with a cadaver phantom and its clinical evaluation].

PURPOSE: To evaluate an optimal scan protocol in a cadaver phantom and its clinical assessment in 40 patients. MATERIALS AND METHODS: In a cadaver larynx phantom helical CT (HiSpeed Advantage; GE, Milwaukee, Wis) was performed with increasing collimation (1-10 mm) and pitch (1.0-3.0). 40 patients with an immobile vocal cord were randomly assigned to undergo CT with a certain protocol. RESULTS: Best resolution was obtained with a collimation of 1 mm and pitch 1. The pitch could be increased up to 2 without losing information. With a collimation of 3 mm and higher, anatomical details were missed. In the patient studies a combination of 1 mm collimation with a pitch of 2.0 showed less motion artifacts than a pitch of 1.0. CONCLUSION: The quality of CT imaging of the arytenoid cartilage depends greatly on the scanning parameters, the compliance of the patients and the mineralisation of the cartilage. For clinical assessment a collimation of 1 mm with a pitch of 2 is recommended. The increase pitch has the advantage of shorter acquisition times and decreased radiation exposure.

Artifacts↗

PubMed1997

Optimizing the metal binding parameters of an EF-hand-like calcium chelation loop: coordinating side chains play a more important tuning role than chelation loop flexibility.

In calcium signaling pathways regulated by the EF-hand Ca2+ binding motif, proper regulation requires that the equilibrium and kinetics of Ca2+ binding to the EF-hand chelation loop be precisely optimized for each physiological application. Studies of small-molecule organic chelators have shown that metal binding parameters can be tuned both by the nature of the coordinating ligands and by the structural framework to which these ligands are attached. By analogy, the present study tests the relative importance of (i) coordinating side chains and (ii) backbone torsion angle constraints to the tuning of an EF-hand-like Ca2+ chelation loop. A series of engineered chelation loops are generated by modifying Ca2+ binding site of the Escherichia coli galactose binding protein. The resulting loops, each containing an altered coordinating side chain or a Gly substitution, are compared with respect to their metal binding affinities, specificities, and dissociation kinetics. The Gly variants examined include substitutions which eliminate or introduce a Gly at each of the nine chelation loop positions. The results reveal that Gly is not tolerated at loop positions 1, 3, 5, or 8 or at the external coordinating position, where the removal of a key coordinating or hydrophobic side chain destabilizes the protein. In contrast, Gly residues at loop positions 2, 4, 6, and 7, none of which is required for side chain coordination, have little effect on Ca2+ affinity and the ability to discriminate between cations of different size and charge. Kinetic measurements show that some of these Gly residues measurably alter the rates of metal ion association and dissociation, but in each case the two rates are changed by approximately the same factor so that the effects on equilibrium are minor. Overall, Gly residues yield surprisingly small effects at loop positions 2, 4, 6, and 7, especially when compared to the larger equilibrium and kinetic effects observed for coordinating side chain substitutions. It follows that the conserved Gly at position 6 is not required for Ca2+ binding and that constraints on the backbone torsion angles at the non-coordinating side chain positions 2, 4, 6, and 7 play a relatively minor role in tuning metal binding parameters. Instead, specific coordinating side chains optimize the metal binding parameters of the GBP chelation loop for its protein context and biological application.

Calcium↗

PubMed2000

The Prognosis of Survival in Patients with Some Solid Tumors Based on Optimal Partitions of Immunological Parameter Ranges.

New logical and statistical methods were used for the analysis of relationships between survival rate of solid tumor patients and immunological variables. These methods are based on the search of the regularities (syndromes) in the multidimensional space. The syndromes are the elements of partitions of allowable areas of variables. To estimate the statistical validity of found regularities the new technique based on Monte-Carlo computer simulation was used. The broad panel of monoclonal antibodies for lymphocyte differentiation antigens was used for subpopulation analysis. The two tasks are described. The purpose of the first task was the evaluation of significance of immunological parameters for prediction of one-year metastasis-free survival in non-metastatic osteosarcoma of extremities. The second task was the construction of the predicting algorithm for prognosis of two-year survival of patients with stomach cancer. The optimal sets of parameters for prediction of survival were found for both tasks. We found out the high predictive value of HLA DR(+) cells percentage in the 1st task, and the percentage of adhesion cells (CD50(+) lymphocytes) is the most significant parameter in the 2nd task. The predictive algorithms were developed.

Journal Article↗