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PubMed2001

Empirical modelling of genetic algorithms.

This paper addresses the problem of reliably setting genetic algorithm parameters for consistent labelling problems. Genetic algorithm parameters are notoriously difficult to determine. This paper proposes a robust empirical framework, based on the analysis of factorial experiments. The use of a graeco-latin square permits an initial study of a wide range of parameter settings. This is followed by fully crossed factorial experiments with narrower ranges, which allow detailed analysis by logistic regression. The empirical models derived can be used to determine optimal algorithm parameters and to shed light on interactions between the parameters and their relative importance. Refined models are produced, which are shown to be robust under extrapolation to up to triple the problem size.

Algorithms↗

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↗

PubMed2007

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.

Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations, in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg(2+) and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)// B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges. Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle, and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the nonstandard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.

Catalysis↗

PubMed2006

Determination of refractory elements in atmospheric particulates using slurry sampling electrothermal vaporization inductively coupled plasma optical emission spectrometry and inductively coupled plasma mass spectrometry with polyvinylidene fluoride as chemical modifier.

Electrothermal vaporization (ETV) inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS) with polyvinylidene fluoride (PVDF) as chemical modifier are critically compared for the determination of refractory elements in coal fly ash and airborne particulates. The atmospheric particulates that collected on a PVDF filter were introduced into the graphite furnace in the form of a slurry by dissolving the filter in dimethylformamide, and the dissolved filter PVDF, along with additional added PVDF powder, was used as a chemical modifier for subsequent ETV-ICP-OES and ETV-ICP-MS determination. The vaporization behaviors of analytes (Ti, Zr, V, Mo, Cr, La) in ETV-ICP-OES/MS were studied in detail, and the optimal ETV operating parameters were obtained. Under the optimized operating conditions, the detection limits of target elements were 0.08-2.7 ng m(-3) for ETV-ICP-OES and 0.5-50 pg m(-3) for ETV-ICP-MS, respectively, with analytical precisions of 3.5-7.3% for ETV-ICP-OES and 3.9-9.6% for ETV-ICP-MS, respectively. The tolerable amounts of matrix elements for ETV-ICP-OES are higher than for ETV-ICP-MS. Both ETV-ICP-OES and ETV-ICP-MS were used to directly determine the trace refractory elements in coal fly ash and airborne particulates and the analytical results are comparable.

Journal Article↗

PubMed2002

Effects of nebulizing and drying gas flow on capillary electrophoresis/mass spectrometry.

This study was focused on examining the influence of gas flow parameters on capillary electrophoresis/mass spectrometry (CE /MS) performance using sheath-liquid CE /MS interfaces. The effects of nebulizing and drying gas velocity and drying gas temperature on CE separation and MS detection sensitivity were systematically determined. Nebulizing gas velocity was observed to be a critical parameter in the optimization of CE /MS method, since it affected both MS detection sensitivity, and also CE separation efficiency for one interface design tested. Better detection sensitivity was obtained when the nebulizing gas velocity was increased. However, high velocity of the nebulizing gas flow can cause a hydrodynamic bulk flow inside the CE capillary, thus clearly increasing the apparent mobility and decreasing the resolution obtained for the compounds studied. Increasing the drying gas velocity or temperature did not affect the apparent mobility or the separation efficiency and the temperature could be increased to achieve the optimal detection sensitivity in the CE /MS analysis. For comparison, the effects of nebulizing gas flow were studied using a different design of the coaxial sheath-liquid CE /MS interface, and in this case better detection sensitivity but no effect on CE separation efficiency was observed with increased nebulizing gas velocity. These different effects of nebulizing gas flow on the CE bulk flow were concluded to result from pressure differences at the tip of the CE capillaries for the different CE /MS interface arrangements. It is therefore recommended that the cross-sectional dimensions of the fused-silica and steel capillaries, and the gas streamlines, should be optimized when CE /MS interfaces are built. Moreover, the effect of gas flow on CE separation should be studied when optimizing the CE /MS operation parameters.

Buprenorphine↗

PubMed2005

Supercritical fluid extraction of aurentiamide acetate from Patrinia villosa Juss and subsequent isolation by silica gel and high-speed counter-current chromatography.

Supercritical fluid extraction (SFE) of aurentiamide acetate from Patrinia villosa Juss was performed. The optimization of parameters was carried out using an analytical-scale supercritical fluid extraction (SFE) system. Then the extraction was scaled up by 100 times using a preparative SFE system under the optimized conditions of 55 degrees C, 35 MPa and modified CO2 with 10% methanol. Then, the crude extract I obtained by SFE was chromatographed on silica gel and the solvent system composed of petroleum ether-ethyl acetate (5:1, v/v) was used to produce the crude extract II, which was further isolated and purified by high-speed counter-current chromatography (HSCCC) with a two-phase solvent system composed of n-hexane-ethyl acetate-methanol-water (1:1.2:1.2:1, v/v/v/v). One hundred fifty-five milligrams of aurentiamide acetate was obtained from 400 mg crude extract II (contained 42% target) with a purity of 99.3% determined by HPLC and 92.3% recovery in one-step elution, and identification was performed by UV, MS, 1H NMR and 13C NMR. As far as we know, this is the first report of discovering aurentiamide acetate from the plant of Patrinia genius.

Acetates↗

PubMed1999

Interpolated markov chains for eukaryotic promoter recognition.

MOTIVATION: We describe a new content-based approach for the detection of promoter regions of eukaryotic protein encoding genes. Our system is based on three interpolated Markov chains (IMCs) of different order which are trained on coding, non-coding and promoter sequences. It was recently shown that the interpolation of Markov chains leads to stable parameters and improves on the results in microbial gene finding (Salzberg et al., Nucleic Acids Res., 26, 544-548, 1998). Here, we present new methods for an automated estimation of optimal interpolation parameters and show how the IMCs can be applied to detect promoters in contiguous DNA sequences. Our interpolation approach can also be employed to obtain a reliable scoring function for human coding DNA regions, and the trained models can easily be incorporated in the general framework for gene recognition systems. RESULTS: A 5-fold cross-validation evaluation of our IMC approach on a representative sequence set yielded a mean correlation coefficient of 0.84 (promoter versus coding sequences) and 0.53 (promoter versus non-coding sequences). Applied to the task of eukaryotic promoter region identification in genomic DNA sequences, our classifier identifies 50% of the promoter regions in the sequences used in the most recent review and comparison by Fickett and Hatzigeorgiou ( Genome Res., 7, 861-878, 1997), while having a false-positive rate of 1/849 bp.

Algorithms↗

PubMedDate not supplied

An algorithm for protein secondary structure prediction based on class prediction.

An algorithm has been developed to improve the success rate in the prediction of the secondary structure of proteins by taking into account the predicted class of the proteins. This method has been called the 'double prediction method' and consists of a first prediction of the secondary structure from a new algorithm which uses parameters of the type described by Chou and Fasman, and the prediction of the class of the proteins from their amino acid composition. These two independent predictions allow one to optimize the parameters calculated over the secondary structure database to provide the final prediction of secondary structure. This method has been tested on 59 proteins in the database (i.e. 10,322 residues) and yields 72% success in class prediction, 61.3% of residues correctly predicted for three states (helix, sheet and coil) and a good agreement between observed and predicted contents in secondary structure.

Algorithms↗

PubMed1998

Identification of noise sources that influence distortion product otoacoustic emission measurements in human neonates.

OBJECTIVE: The objective of this study was to identify individual sources of noise and their contribution to the overall noise that influences valid measurement of otoacoustic emissions in neonates. The hypothesis was that careful selection of eliciting signals and signal processing parameters, unique analysis of measured results, and control of certain subject characteristics would allow isolation of these individual noise sources and determine their relative influence. DESIGN: Eliciting signal parameters were optimized and held constant to minimize equipment noise. Analysis of noise floors in relation to signal level was used to identify equipment-related noise associated with changes in signal parameters. Analysis of noise floor distributions was used to determine whether environmental noise entered the measurements via inadequate coupling of the probe to the ear. The acoustic characteristics of the middle ear were varied via subject selection to determine the influence of middle-ear characteristics on noise floor levels. RESULTS: The two sources of noise associated with the measurement equipment need not contribute to the noise floor for biologically relevant otoacoustic emissions measurements (eliciting signal levels between 30 and 75 dB SPL). Of the two pathways identified for environmental noise, the pathway resulting from an inadequate seal between the probe and the ear canal can be eliminated. One of the two sources of noise related to the subject, noise resulting from biologic activity unrelated to the ear can be minimized. However, the remaining factor, the status of the middle ear, has been shown to contribute as much as 6 dB to the overall noise floor. CONCLUSIONS: Careful selection of signal parameters and additional data analyses and procedural variables can isolate or control several sources of noise that influence distortion product otoacoustic emission measurements in neonates. Tight coupling between the probe unit and the external ear canal should be maintained for all measurements. Middle ear abnormalities can increase noise floors up to 6 dB.

Auditory Perception↗

PubMed1990

The behavior of the acoustic distortion product, 2f1-f2, from the human ear and its relation to auditory sensitivity.

The acoustic intermodulation distortion product 2f1-f2 (ADP) was measured in human subjects to investigate (1) the dependence of ADP level on stimulus parameters and (2) the relationship between ADP level and auditory sensitivity. The frequency ratio (f2/f1), at which ADP level is maximal, varies only slightly across frequency and subjects. The average optimal ratio is 1.225. Beyond the maximum, the ADP level declines with increasing f2/f1 ratio, at rates of up to 250 dB/oct. As the level of one stimulus is increased relative to the other, the ADP grows, saturates, and in most cases shows a bendover. Maximum distortion is generated when L 1 exceeds L 2. Growth rate and saturation point are dependent on which stimulus is incremented and on the level of the stationary stimulus. With optimal stimulus parameters (levels below 60 dB SPL; L 1 greater than L 2 by 15 dB; f2/f1 = 1.225), ADP levels are commonly 30 dB below L 2. Patterns of ADP level across frequency vary between subjects, but are repeatable within each subject. As the frequency of one or both of the stimuli is varied, changes in ADP level exhibit a broadly featured pattern with a fine structure superimposed upon it. This fine structure was compared with the features in the stimulus frequency emission spectrum in one subject. With appropriate stimulus parameters, half of our subjects show a statistically significant correlation across frequency, between ADP level and auditory sensitivity at the corresponding f1 frequency. Our results suggest that, with low levels of stimulation, ADP measurements could form the basis of an objective measure of cochlear function in human subjects.

Adolescent↗

PubMed2004

Using heterogeneity to predict inhibitory network model characteristics.

From modeling studies it has been known for >10 years that purely inhibitory networks can produce synchronous output given appropriate balances of intrinsic and synaptic parameters. Several experimental studies indicate that synchronous activity produced by inhibitory networks is critical to the production of population rhythms associated with various behavioral states. Heterogeneity of inputs to inhibitory networks strongly affect their ability to synchronize. In this paper, we explore how the amount of input heterogeneity to two-cell inhibitory networks affects their dynamics. Using numerical simulations and bifurcation analyses, we find that the ability of inhibitory networks to synchronize in the face of heterogeneity depends nonmonotonically on each of the synaptic time constant, synaptic conductance and external drive parameters. Because of this, an optimal set of parameters for a given cellular model with various biophysical characteristics can be determined. We suggest that this could be a helpful approach to use in determining the importance of different, underlying biophysical details. We further find that two-cell coherence properties are maintained in larger 10-cell networks. As such, we think that a strategy of "embedding" small network dynamics in larger networks is a useful way to understand the contribution of biophysically derived parameters to population dynamics in large networks.

Biological Clocks↗

PubMed2004

Effect of area x-ray beam equalization on image quality and dose in digital mammography.

In mammography, thick or dense breast regions persistently suffer from reduced contrast-to-noise ratio (CNR) because of degraded contrast from large scatter intensities and relatively high noise. Area x-ray beam equalization can improve image quality by increasing the x-ray exposure to under-penetrated regions without increasing the exposure to other breast regions. Optimal equalization parameters with respect to image quality and patient dose were determined through computer simulations and validated with experimental observations on a step phantom and an anthropomorphic breast phantom. Three parameters important in equalization digital mammography were considered: attenuator material (Z = 13-92), beam energy (22-34 kVp) and equalization level. A Mo/Mo digital mammography system was used for image acquisition. A prototype 16 x 16 piston driven equalization system was used for preparing patient-specific equalization masks. Simulation studies showed that a molybdenum attenuator and an equalization level of 20 were optimal for improving contrast, CNR and figure of merit (FOM = CNR2/dose). Experimental measurements using these parameters showed significant improvements in contrast, CNR and FOM. Moreover, equalized images of a breast phantom showed improved image quality. These results indicate that area beam equalization can improve image quality in digital mammography.

Artifacts↗

PubMed1998

Stepping over obstacles during locomotion: insights from multiobjective optimization on set of input parameters.

In this study we investigate possible objectives that the central nervous system (CNS) may consider in planning a strategy for stepping over an obstacle. A link segment simulation model has been developed based on Lagrangian dynamics, with which muscle force inputs can be optimized to best satisfy the postulated objectives for landing stability, obstacle clearance, and efficiency of the movement. A direct optimization approach with multiobjective criteria based on the kinematic and kinetic characteristics of the swing phase of locomotion is used in the simulation. The role of initial conditions at toe-off and biarticular muscle forces during the swing phase was also investigated. The optimization was performed for both leading limb and the trailing limb during the swing phase. The simulation results demonstrate that the use of biarticular muscles is sufficient to clear a range of obstacles with the trailing limb (obstacle encountered during early swing). Stride length or landing stability objectives need not be specified suggesting a simpler control of trailing limb trajectory by the CNS (one of stride length or landing stability objectives were not necessary). In contrast while the use of biarticular muscles can be sufficient to clear obstacles with the leading limb (obstacle encountered during mid to late swing), a stable landing and smooth toe and knee trajectories are compromised without suitable initial conditions at toe-off. The results suggest that the set of postulated objectives for the lead limb is adequate, although not complete.

Biomechanical Phenomena↗

PubMed1994

Optimizing the time course of brachytherapy and other accelerated radiotherapeutic protocols.

PURPOSE: It is likely that early-responding tissues, such as tumors, repair sublethal damage more rapidly than do late-responding tissues. This difference can be exploited to design protocols with a significantly improved therapeutic advantage for accelerated radiotherapeutic regimens, including brachytherapy. METHODS AND MATERIALS: The time course of potential protocols is computer optimized, maximizing the therapeutic difference between tumor-control probability (TCP), and normal-tissue complication probability (NTCP). These quantities are evaluated with the linear-quadratic model, using clinically derived parameters. The optimization is performed by individually adjusting doses in different parts of the treatment, maximizing the therapeutic advantage. In the main calculations, half times for damage repair were T1/2(late) = 4 h, T1/2(early) = 0.5 h. Two component (fast/slow) repair processes were also investigated. RESULTS: Protocols determined by optimization have significantly greater therapeutic advantage than continuous low-dose rate (CLDR) protocols of the same overall dose and time. The optimized protocols are either (a) acute-dose/gap/CLDR/gap/acute-dose; or (b) a series of acute doses separated by 3-4 h. As a typical example, results are given for 60 Gy/120 h CLDR brachytherapy, which is assumed to give NTCP = 0.2 and TCP = 0.8. Under our assumptions, optimized regimes, with the same overall time and dose, produce an NTCP of approximately 0.11 and TCP of approximately 0.83, a significant therapeutic gain over CLDR. CONCLUSION: Difference in repair rates between early- and late-responding tissues can be exploited to produce clinically practical protocols that are significantly superior to current regimens. Such optimized protocols produce slightly better tumor control than CLDR with the same overall dose and time, significantly less late damage, and similar early normal-tissue sequellae. Temporal optimization, thus, promises to be a powerful tool in designing better treatment protocols.

Animals↗

PubMed1997

The risk of non-melanoma skin cancer incidence in the Japanese atomic bomb survivors.

The latest Japanese atomic bomb survivor non-melanoma skin cancer incidence dataset is analysed and indicates substantial curvilinearity in the dose-response curve, consistent with a possible dose threshold of about 1 Sv, or with a dose-response in which the excess relative risk is proportional to the fourth power of dose, with a turning-over in the dose-response at high doses (> 3 Sv). The time distribution of the radiation-induced excess risk is best described by a model in which the relative excess risk is proportional to a product of powers of time since exposure and attained age. The fits of generalized relative risk models with exponential functions of time and age at exposure (and in particular of attained age) to adjust the relative risk are less satisfactory, as also are the fits of other models in which products of powers of time since exposure, age at exposure and attained age adjust the excess absolute risk. Sensitivity analyses indicate the importance of likely adjustments to the Hiroshima neutron doses for the optimal model parameters, particularly if values of the neutron relative biological effectiveness (RBE) of more than 5 are assumed. If adjustments recently proposed are made to the Hiroshima neutron doses, then using the optimal model (in which excess risk is proportional to the fourth power of dose) the best estimate of the neutron RBE is 1.3 (95% CI < 07.1). However, uncertainties in skin dose estimates for the atomic bomb survivors means that the findings with respect to the neutron RBE and the non-linearity in the dose-response curve should be treated with caution.

Dose-Response Relationship, Radiation↗

PubMed2002

A dual-energy subtraction technique for microcalcification imaging in digital mammography--a signal-to-noise analysis.

Breast cancer may manifest as microcalcifications (microCs) in x-ray mammography. However, the detection and visualization of microCs are often obscured by the overlapping tissue structures. The dual-energy subtraction imaging technique offers an alternative approach for imaging and visualizing microCs. With this technique, separate high- and low-energy images are acquired and their differences are used to "cancel" out the background tissue structures. However, the subtraction process could increase the statistical noise level relative to the calcification contrast. Therefore, a key issue with the dual-energy subtraction imaging technique is to weigh the benefit of removing the cluttered background tissue structure over the drawback of reduced signal-to-noise ratio in the subtracted microC images. In this report, a theoretical framework for calculating the (quantum) noise in the subtraction images is developed and the numerical computations are described. We estimate the noise levels in the dual-energy subtraction signals under various imaging conditions, including the x-ray spectra, microC size, tissue composition, and breast thickness. The selection of imaging parameters is optimized to evaluate the feasibility of using a dual-energy subtraction technique for the improved detection and visualization of microCs. We present the results and discuss its dependence on imaging parameters.

Breast↗

PubMed1997

Technical considerations for acquiring and processing indium-111 capromab pendetide images.

A diagnostic quality 111In capromab pendetide study depends on parameters such as the quality control of the camera, thorough patient preparation, adequate imaging time and accurate computer processing. Comparisons of different patient preparation methods, imaging times, and camera and processing parameters were evaluated to provide high-quality 111In capromab pendetide images and to develop acquisition and processing parameters for 111In capromab pendetide imaging. SPECT images provide the best views of metastatic pelvic nodal involvement. Volume rendered three-dimensional registration best differentiates between normal vasculature and metastatic disease. Optimal acquisition parameters for delayed imaging included 128 x 128 matrix and 65 sec/step. The LFOV dual-head SPECT camera required only one SPECT acquisition that encompassed both the pelvis and abdomen. Planar and SPECT positioning was critical in evaluating questionable lymph nodes. In processing these images, the most diagnostic results were obtained with a three-dimensional low-pass post filter. The most effective patient preparation consisted of an oral cathartic, enema and catheterization when needed.

Antibodies, Monoclonal↗

PubMed1985

MR imaging parameters in the study of lung water. A preliminary study.

The use of magnetic resonance (MR) to evaluate lung water is made difficult by several factors: paucity of proton signal from normal lung, respiratory and cardiac motion, and long relaxation times of lung fluids. To optimize scanning parameters for this use, and to test MR's ability to detect and quantitate regional and temporal variations in signal intensity in hydrostatic pulmonary edema, in vivo experiments were performed with a 0.5 tesla whole body MR imaging device. Human volunteers were studied in prone and supine positions using spin echo technique (TE = 30 msec) with varying TR, and with respiratory and cardiac gating. In addition, sedated, intubated, chronically prepared sheep were paralyzed to control extraneous motion and allow the use of a high frequency ventilator, thereby eliminating respiratory gating. Elevated pulmonary hydrostatic pressure was induced in these sheep by inflation of a left atrial balloon. Relative signal intensity from the lung rises with lengthening TR. Cardiac gating diminishes motion artifact, but masks extravascular water by enhancing signal from slowly flowing blood by an average of 44%. A gravity-dependent gradient of signal intensity predictably shifts in supine and prone positions. The use of longer TRs, respiratory gating, and cardiac gating all proportionally prolong data acquisition times to an objectionable degree. Without the use of gating, a gradual rise in relative signal intensity is seen in the sheep lung following the establishment of elevated hydrostatic pressure in the pulmonary circuit, and is most pronounced in the dependent portion of the lung.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗