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Results for “parameter optimization”

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PubMed2005

Ab initio kinetics of the reaction of HCO with NO: abstraction versus association/elimination mechanism.

The kinetics and mechanism for the reaction of HCO with NO occurring by both singlet and triplet electronic state potential-energy surfaces (PESs) have been studied at the modified Gaussian-2 level of theory based on the geometric parameters optimized by the Becke-3 Lee-Yang-Parr/6-311G(d,p) method. There are two major reaction channels on both singlet and triplet PESs studied: one is direct H abstraction producing CO+HNO and the other is association forming a stable HC(O)NO (nitrosoformaldehyde) molecule. The dominant reaction is predicted to be the direct H abstraction occurring primarily by the lowest-energy path via a loose hydrogen-bonding singlet molecular complex, ON...HCO, with a 2.9-kcal/mol binding energy and a small decomposition barrier (1.9 kcal/mol). The commonly assumed HC(O)NO intermediate, predicted to lie below the reactants by 27.7 kcal/mol, has a high HNO-elimination barrier (34.5 kcal/mol). Bimolecular rate constants for the formation of the singlet products and their branching ratios have been calculated in the temperature range of 200-3000 K. The rate constant for the disproportionation process producing HNO+CO, found to be affected strongly by multiple reflections above the well of the complex at low temperature, is predicted to be k(HNO)=3.08 x 10(-12) T(0.10) exp(242T) for 200-500 K, and 1.72 x 10(-16) T(1.47) exp(888T) for 500-3000 K in units of cm(3) molecule(-1) s(-1). The high- and low-pressure rate constants for the association process forming HC(O)NO can be represented by k(infinity)=4.42 x 10(-11) T(0.25) exp(-28T) cm(3) molecule(-1) s(-1) (200-3000 K) and k(0)=7.30x10(-16) T(-5.75) exp(-719T) (200-1000 K) and 1.82 x 10(2) T(-11.92) exp(1846T) (1000-3000 K) cm(6) molecule(-2) s(-1) for N(2)-buffer gas. The absolute values of total rate constant, predicted to be weakly dependent negatively on temperature but positively on pressure, are in close agreement with most experimental data within their reported errors.

Journal Article↗

PubMed2005

Ground and excited states of the Rydberg radical H3O: electron propagator and quantum defect analysis.

Vertical excitation energies of the Rydberg radical H(3)O are inferred from ab initio electron propagator calculations on the electron affinities of H(3)O(+). The adiabatic ionization energy of H(3)O is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine oscillator strengths. Given that the experimental spectrum of H(3)O does not seem to be available, comparisons with previous calculations are discussed. A simple model Hamiltonian, suitable for the study of bound states with arbitrarily high energies is generated by these means.

Journal Article↗

PubMed2005

Density-functional calculation of CeO2 surfaces and prediction of effects of oxygen partial pressure and temperature on stabilities.

We have used density-functional theory to investigate (111), (110), (210), (211), (100), and (310) surfaces of ceria (CeO2). Compared with previous interatomic-potential-based studies, our calculations reported a slightly different relative stability ordering and significantly lower surface energies for the stoichiometric surfaces. Using a defect model, the surface stabilities were evaluated as functions of oxygen partial pressure and temperature. Our investigations were restricted to ideal surface terminations, without considering defect formation on those surfaces. We found that at 300 K, the stoichiometric (111) has the lowest free energy for a wide range of oxygen partial pressures up to 1 atm, and only at ultrahigh vacuum does the Ce-terminated (111) becomes the most stable one. The transition point for the Ce-terminated (111) surfaces moves to higher oxygen partial pressures when temperature increases. To improve the prediction of electron density of states, we used the local-density approximation plus U(J) correction method to correct the on-site Coulomb correlation and exchange interaction due to the strongly localized Ce-4f electrons. The optimal parameter combination of U = 7 eV and J = 0.7 eV was found to improve the O 2p-Ce 4f gap without much degradation of ground-state bulk properties or the O 2p-Ce 5d gap. The bulk and surface electronic structures were then analyzed based on the improved density of states.

Journal Article↗

PubMed2005

Exploring the free-energy landscape of a short peptide using an average force.

The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter xi. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a beta-turn motif and restraining xi to a region of the conformational space that extends from the alpha-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact alpha helix. Sampling of this conformation is, however, marginal when the range of xi values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized.

Alanine↗

PubMed1987

Technical frontiers for the vascular surgeon: laser anastomotic welding and angioscopy-assisted intraluminal instrumentation.

Innovations in therapy for peripheral vascular disease include laser vessel welding and angioscopy-assisted intraluminal laser instrumentation. Vascular tissue fusion by laser occurs at energy levels lower than those required to coagulate or vaporize. CO2, argon, and Nd:YAG (1.06 micron) lasers have all been reported to fuse anastomoses in microvessels, but adequate welding of larger veins and arteries (3 to 8 mm in diameter) has only been accomplished with the argon laser. Laser welds heal comparably to sutured wounds but do not have the chronic foreign body reaction and disorientation of elastin and collagen associated with sutures. Preliminary evidence suggests that argon laser-welded anastomoses have less intimal hyperplasia than sutured anastomoses. Laser welding may also be a useful adjunct for sealing intimal flaps during endarterectomy. Additional work is needed to determine the mechanism, optimal parameters, and wavelengths required for vascular tissue fusion by laser. Direct application of laser light intraluminally has thus far been associated with a high incidence of vessel perforation. Angioscopy-assisted delivery of a metal hot-tip probe shows promise for angioplasty of occluded medium-sized arteries and for valvulotomy in in situ vein bypasses.

Animals↗

PubMed1998

Reprogramming cattle somatic cells by isolated nuclear injection.

The development of a somatic cell nuclear transfer procedure for the production of blastocyst stage cattle embryos is described. Bovine fetal fibroblasts were used for fusion experiments with surgically enucleated oocytes (cytoplasts) following the establishment of optimal parameters for electrofusion from isofusion contours. Fusion rates were increased by decreasing size of the cytoplasts used but cleavage was decreased by decreasing size of the cytoplast used (quarter, half and whole cytoplasts). The use of double cytoplasts did not improve cleavage, and development to blastocysts could not be achieved. In a comparison of electrofusion of fibroblasts with cytoplasts in the subzonal perivitelline space with intracytoplasmic injection of nuclei and parthenogenetically activated oocytes, 2%, 14% and 24% developed to blastocysts respectively. In the group injected with isolated nuclei, the passage number (4 to 9) had no apparent influence on developmental competence to blastocysts. The embryos produced by nuclear injection of somatic cell nuclei showed the normal pattern of cell surface appearance of TEC-3 and TEC-4 stage-specific epitopes during development, as seen in fertilized oocytes. We conclude that the nuclear injection of somatic cell nuclei is a relatively efficient way to clone bovine embryos.

Animals↗

PubMed2005

Using fingerprint image quality to improve the identification performance of the U.S. Visitor and Immigrant Status Indicator Technology Program.

Motivated by the difficulty of biometric systems to correctly match fingerprints with poor image quality, we formulate and solve a game-theoretic formulation of the identification problem in two settings: U.S. visa applicants are checked against a list of visa holders to detect visa fraud, and visitors entering the U.S. are checked against a watchlist of criminals and suspected terrorists. For three types of biometric strategies, we solve the game in which the U.S. Government chooses the strategy's optimal parameter values to maximize the detection probability subject to a constraint on the mean biometric processing time per legal visitor, and then the terrorist chooses the image quality to minimize the detection probability. At current inspector staffing levels at ports of entry, our model predicts that a quality-dependent two-finger strategy achieves a detection probability of 0.733, compared to 0.526 under the quality-independent two-finger strategy that is currently implemented at the U.S. border. Increasing the staffing level of inspectors offers only minor increases in the detection probability for these two strategies. Using more than two fingers to match visitors with poor image quality allows a detection probability of 0.949 under current staffing levels, but may require major changes to the current U.S. biometric program. The detection probabilities during visa application are approximately 11-22% smaller than at ports of entry for all three strategies, but the same qualitative conclusions hold.

Biometry↗

PubMed2006

An auxin-driven polarized transport model for phyllotaxis.

Recent studies show that plant organ positioning may be mediated by localized concentrations of the plant hormone auxin. Auxin patterning in the shoot apical meristem is in turn brought about by the subcellular polar distribution of the putative auxin efflux mediator, PIN1. However, the question of what signals determine PIN1 polarization and how this gives rise to regular patterns of auxin concentration remains unknown. Here we address these questions by using mathematical modeling combined with confocal imaging. We propose a model that is based on the assumption that auxin influences the polarization of its own efflux within the meristem epidermis. We show that such a model is sufficient to create regular spatial patterns of auxin concentration on systems with static and dynamic cellular connectivities, the latter governed by a mechanical model. We also optimize parameter values for the PIN1 dynamics by using a detailed auxin transport model, for which parameter values are taken from experimental estimates, together with a template consisting of cell and wall compartments as well as PIN1 concentrations quantitatively extracted from confocal data. The model shows how polarized transport can drive the formation of regular patterns.

Arabidopsis↗

PubMed2003

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures.

The conformational space of the 10-55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 A and 4.54 A were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information.

Hydrogen Bonding↗

PubMed1997

Folding thermodynamics of a model three-helix-bundle protein.

The calculated folding thermodynamics of a simple off-lattice three-helix-bundle protein model under equilibrium conditions shows the experimentally observed protein transitions: a collapse transition, a disordered-to-ordered globule transition, a globule to native-state transition, and the transition from the active native state to a frozen inactive state. The cooperativity and physical origin of the various transitions are explored with a single "optimization" parameter and characterized with the Lindemann criterion for liquid versus solid-state dynamics. Below the folding temperature, the model has a simple free energy surface with a single basin near the native state; the surface is similar to that calculated from a simulation of the same three-helix-bundle protein with an all-atom representation [Boczko, E. M. & Brooks III, C. L. (1995) Science 269, 393-396].

Animals↗

PubMed1998

Optimization of cell surface binding enhances efficiency and specificity of molecular conjugate gene delivery.

Molecular conjugates, or polyplexes, are promising synthetic vectors for targeted, in vivo gene delivery, if their efficiency can be improved. Gaining mechanistic information on conjugate gene delivery can potentially yield significant improvements in transfer efficiency by revealing barriers to conjugate transfer from the cell surface to the nucleus. We have developed an experimental system that employs epidermal growth factor as the ligand to direct delivery of DNA encoding the green fluorescent protein to mouse fibroblasts. We report here that the initial step of delivery, binding of the conjugate to the cell surface, is a barrier to gene transfer. We examined the effects of conjugate charge, ligand cross-linker spacer length, and ligand valency on polyplex cell surface binding, internalization, and gene transfer. We find that delivery is both efficient and specific only within a relatively narrow window of conjugate charge, results that correlate with binding and internalization of radiolabeled conjugate. In addition, increasing the cross-linker length can improve binding affinity and delivery. Finally, there is a significant optimum in gene delivery as a function of ligand valency, due to saturation of receptor binding and internalization. Optimizing parameters that affect surface binding therefore improves the efficiency and specificity of molecular conjugate gene delivery.

3T3 Cells↗

PubMed2003

Axonal misdirection as contributing factor to aberrant reinnervation of muscles after facial nerve suture in cats.

Abstract Whereas basic features of post-axotomy muscle reinnervation have been extensively studied in rats, little is known about axonal regrowth and pathfinding in cats. To address the question, adult cats were subjected to facial-facial anastomosis (FFA). First group served to establish optimal parameters for labeling of the zygomatic and buccal facial branches with 1,1'dioctadecyl-3,3,3,'3'-tetramethylindo-carbocyanine perchlorate (DiI) and Fast Blue (FB) placed onto respective transected nerves. The second group of animals underwent identical bilateral labeling 3 months after transection and suture of the right facial nerve. This group served to establish the number of motoneurons, which had branched after surgery and projected into both facial branches. On control side, DiI application onto zygomatico-orbital branch labeled 3883 +/- 598 (mean +/- S.D.) perikarya were confined to the dorsal and intermediate facial subnuclei, meanwhile an application of FB onto the buccal branch labeled 1617 +/- 552 perikarya in the lateral and ventrolateral subnuclei. There were no double-labeled cells. Three months after FFA all retrogradely labeled motoneurons were scattered throughout the entire facial nucleus. To establish the proportion of perikarya, that re-grew multiple axonal branches into both nerves, double-labeled (FB + DiI) motoneurons were counted from digital images. The zygomatico-orbital nerve contained 3311 +/- 430 DiI-labeled whereas the buccal nerve 1500 +/- 442 FB-labeled motoneurons. The occurrence of 311 +/- 103 double-labeled perikarya (DiI+FB) suggested that approximately 6% of all retrogradely labeled motoneurons branched axons into both nerves. I conclude that malfunctioning axonal pathfinding rather than deviant reinnervation contributed to poor recovery of function after FFA in the cat.

Animals↗

PubMed2004

Speech recognition with a cochlear implant using triphasic charge-balanced pulses.

OBJECTIVE: Typically, symmetrical charge-balanced biphasic current pulses are used in cochlear implants to ensure biological safety. Theoretically, monophasic pulses are more effective, but potentially noxious, stimuli. In this study we charge-balanced such monophasic pulses during selected non-stimulated intervals, effectively leading to triphasic pulses with a 4:1 amplitude ratio between the cathodic and anodic phases. Apart from ensuring safety, this is also expected to reduce power consumption and channel interaction. MATERIAL AND METHODS: Seven experienced Clarion CII cochlear implant users with a multichannel (12-16 channels) monopolar continuous interleaved sampling (CIS) strategy participated in the study. Three different CIS strategies were fitted using the Clarion Research Interface (CRI-2). The reference was an implementation of each subject's own CIS program. The two strategies tested used triphasic pulses on the same channels, one with half-wave rectification (TP-HWR) and one without rectification (TP-NoR) at the input. Directly after fitting (i.e. without any training), speech perception (phoneme score on consonant-vowel-consonant words) was measured in silence (sound-only) and in speech-shaped background noise with signal:noise ratios (SNRs) of +5 and 0 dB. RESULTS: Speech perception with the reference via the CRI-2 was equal to that of the free-field condition with the subjects' own speech processor. With the TP-NoR strategy, speech perception improved significantly (from 89% to 93%) in silence and in the 0-dB SNR condition (from 43% to 49%). With a SNR of +5 dB, performance was stable at approximately 66%. With the TP-HWR strategy, performance increased significantly in the 0- and +5-dB SNR conditions, to 55% and 74%, respectively. Power consumption was reduced in both strategies, to 30% and 36% for TP-HWR and TP-NoR, respectively. CONCLUSION: The new triphasic strategies are most promising, with respect to both their improved speech perception and reduced power requirements. The optimal parameters will have to be identified following long-term use.

Adult↗

PubMed2005

Development of a system and improvement of the stimulus pattern to discriminate the acupuncture point and meridians.

The conventional acupuncture-point stimulus pattern uses direct current (DC) to discriminate acupuncture point and meridian lines, which are fundamental to diagnosis and treatment in Oriental medicine. However, DC is insufficiently reliable in discriminating these acupuncture points and lines. To overcome these problems, the authors extracted optimal parameters (e.g., squarelike waveform with a frequency of 4 kHz) with a single power alternating current (SPAC) stimulus pattern of 1.28 V. The SPAC stimulus pattern has little or no effect on cells and the body's physiological state and minimizes polarization and ionization of cells because it uses low voltage and alternating current. The authors developed a new meridian discrimination system that can be used with the SPAC.

Acupuncture Points↗

PubMed2005

An ex-vivo experimental study on optimization of bipolar radiofrequency liver ablation using perfusion-cooled electrodes.

PURPOSE: To determine optimal parameters for bipolar radiofrequency ablation (RFA) using perfusion-cooled electrodes to create a large ablation volume in ex vivo bovine liver. MATERIAL AND METHODS: Three sets of RF experiments were performed using a 200-Watt generator and two 15-gauge perfusion-cooled or internally cooled electrodes in ex vivo bovine livers. In the first set of experiments, to find the ideal inter-electrode distance for creating large coagulation necrosis, 30 ablation lesions were created by bipolar RFAs at inter-electrode spacings of 3 cm, 4 cm, and 5 cm. In the second set of experiments, to explore the ideal duration of RF application, bipolar RFAs were performed for 10 min and 20 min. In the first and second experiments, 10 lesions were made for each condition with infusion of 6% hypertonic saline (HS) at 2 ml/min. In the third set of experiments, 10 ablation lesions were created by bipolar RFAs using internally cooled electrodes without HS infusion. The mean volume of those ablation lesions was then compared to that of the lesions created by bipolar RFA using perfusion-cooled electrodes in the second experiments. Tissue impedance, dimension, and shape of the ablated areas were compared in each condition. RESULTS: In the first set of experiments, bipolar RFA created a homogeneous oval or spherical-shaped ablation area between the electrodes at 3-5 cm spacing, but showed a more spherical-shaped lesion at 3 cm inter-electrode spacing than at 4 cm and 5 cm spacing. In the second set of experiments, RF energy delivered for 20 min created a larger dimension of coagulation necrosis than energy delivered for 10 min: 107.6 +/- 34 cm3 versus 59.5 +/- 27 cm3 (P<0.05). In addition, the mean volume of ablation regions obtained with bipolar RFA using the internally cooled electrode was 47.5+/- 17 cm3, which was significantly less than that with bipolar RFA using perfusion-cooled electrodes (P <0.05). CONCLUSION: Bipolar RFA using perfusion-cooled electrodes achieves homogeneous areas of coagulation necrosis between two electrodes, preferably at 3 or 4 cm inter-electrode distance for 20 min, and is better in creating large coagulation necrosis than bipolar RFA using internally cooled electrodes.

Analysis of Variance↗

PubMedDate not supplied

A technique for sequential segmental neuromuscular stimulation with closed loop feedback control.

In dynamic myoplasty, dysfunctional muscle is assisted or replaced with skeletal muscle from a donor site. Electrical stimulation is commonly used to train and animate the skeletal muscle to perform its new task. Due to simultaneous tetanic contractions of the entire myoplasty, muscles are deprived of perfusion and fatigue rapidly, causing long-term problems such as excessive scarring and muscle ischemia. Sequential stimulation contracts part of the muscle while other parts rest, thus significantly improving blood perfusion. However, the muscle still fatigues. In this article, we report a test of the feasibility of using closed-loop control to economize the contractions of the sequentially stimulated myoplasty. A simple stimulation algorithm was developed and tested on a sequentially stimulated neo-sphincter designed from a canine gracilis muscle. Pressure generated in the lumen of the myoplasty neo-sphincter was used as feedback to regulate the stimulation signal via three control parameters, thereby optimizing the performance of the myoplasty. Additionally, we investigated and compared the efficiency of amplitude and frequency modulation techniques. Closed-loop feedback enabled us to maintain target pressures within 10% deviation using amplitude modulation and optimized control parameters (correction frequency = 4 Hz, correction threshold = 4%, and transition time = 0.3 s). The large-scale stimulation/feedback setup was unfit for chronic experimentation, but can be used as a blueprint for a small-scale version to unveil the theoretical benefits of closed-loop control in chronic experimentation.

Algorithms↗

PubMed2002

Removal of sulfacid brilliant pink from an aqueous stream by adsorption onto surfactant-modified Ti-pillared montmorillonite.

A modified hydrophobic and organophilic pillared clay (CTAC-TiH-montm) was prepared by exchanging some Ti polymeric cations into the interlamellar space of one Algerian montmorillonite (montm) and then by co-adsorption of some surfactant molecules such as cetyltrimethylammonium chloride (CTAC). These new materials were used in adsorption of an anionic textile dye: Sulfacid brilliant pink (SAP). According to adsorption isotherms, the organic modification of Ti-montmorillonite clay by CTAC surfactant increases the amount of textile dye fixed to more than 1000 mg g(-1). The adsorption experiments showed that a ratio of 3 mmol of CTAC per g of clay and an acidic medium (pH = 4) were the optimal parameters necessary to obtain good adsorption uptake and colourless treated solutions. A comparative study proved the high adsorption capacity of the synthesised adsorbents; they can thus be considered as powerful competitors to activated carbon in the treatment of aqueous textile plants and industry effluents.

Adsorption↗

PubMed2002

Feature-based, automated segmentation of cerebral infarct patterns using T2- and diffusion-weighted imaging.

Diffusion-weighted imaging enables the diagnosis of cerebral ischemias very early, thus supporting therapies such as thrombolysis. However, morphology and tissue-characterizing parameters (e.g. relaxation times or water diffusion) may vary strongly in ischemic regions, indicating different underlying pathologic processes. As the determination of the parameters by a supervised segmentation is very time consuming, we evaluated whether different infarct patterns may be segmented by an automated, multidimensional feature-based method using a unified segmentation procedure. Ischemias were classified into 5 characteristic patterns. For each class, a 3D histogram based on T(2)- and diffusion-weighted images as well as calculated apparent diffusion coefficients (ADC) was generated from a representative data set. Healthy and pathologic tissue classes were segmented in the histogram as separate, local density maxima with freely shaped borders. Segmentation control parameters were optimized in a 3-step procedure. The method was evaluated using synthetic images as well as results of a supervised segmentation. For the analysis of cerebral ischemias, the optimal control parameter set led to sensitivities and specificities between 1.0 and 0.9.

Algorithms↗