Image Reconstruction Using Interval Simulated Annealing in Electrical Impedance Tomography

Electrical impedance tomography (EIT) is an imaging technique that attempts to reconstruct the impedance distribution inside an object from the impedance between electrodes placed on the object surface. The EIT reconstruction problem can be approached as a nonlinear nonconvex optimization problem in which one tries to maximize the matching between a simulated impedance problem and the observed data. This nonlinear optimization problem is often ill-posed, and not very suited to methods that evaluate derivatives of the objective function. It may be approached by simulated annealing (SA), but at a large computational cost due to the expensive evaluation process of the objective function, which involves a full simulation of the impedance problem at each iteration. A variation of SA is proposed in which the objective function is evaluated only partially, while ensuring boundaries on the behavior of the modified algorithm.

Atomistic Study of Water Confined in Silica.

In this work, we have used a combined of atomistic simulation methods to explore the effects of confinement of water molecules between silica surfaces. Firstly, the mechanical properties of water severe confined (~3A) between two silica alpha-quartz was determined based on first principles calculations within the density functional theory (DFT). Simulated annealing methods were employed due to the complex potential energry surface, and the difficulties to avoid local minima. Our results suggest that much of the stiffness of the material (46%) remains, even after the insertion of a water monolayer in the silica. Secondly, in order to access typical time scales for confined systems, classical molecular dynamics was used to determine the dynamical properties of water confined in silica cylindrical pores, with diameters varying from 10 to 40A. in this case we have varied the passivation of the silica surface, from 13% to 100% of SiOH, and the other terminations being SiOH2 and SiOH3, the distribution of the different terminations was obtained with a Monte Carlo simulation. The simulations indicates a lowering of the diffusion coefficientes as the diameter decreases, due to the structuration of hydrogen bonds of water molecules; we have also obtained the density profiles of the confined water and the interfacial tension.

An algorithm for the strip packing problem using collision free region and exact fitting placement

The irregular shape packing problem is approached. The container has a fixed width and an open dimension to be minimized. The proposed algorithm constructively creates the solution using an ordered list of items and a placement heuristic. Simulated annealing is the adopted metaheuristic to solve the optimization problem. A two-level algorithm is used to minimize the open dimension of the container. To ensure feasible layouts, the concept of collision free region is used. A collision free region represents all possible translations for an item to be placed and may be degenerated. For a moving item, the proposed placement heuristic detects the presence of exact fits (when the item is fully constrained by its surroundings) and exact slides (when the item position is constrained in all but one direction). The relevance of these positions is analyzed and a new placement heuristic is proposed. Computational comparisons on benchmark problems show that the proposed algorithm generated highly competitive solutions. Moreover, our algorithm updated some best known results. (C) 2012 Elsevier Ltd. All rights reserved.

Analog circuit synthesis performing fast Pareto frontier exploration and analysis through 3D graphs

This paper presents a technique for performing analog design synthesis at circuit level providing feedback to the designer through the exploration of the Pareto frontier. A modified simulated annealing which is able to perform crossover with past anchor points when a local minimum is found which is used as the optimization algorithm on the initial synthesis procedure. After all specifications are met, the algorithm searches for the extreme points of the Pareto frontier in order to obtain a non-exhaustive exploration of the Pareto front. Finally, multi-objective particle swarm optimization is used to spread the results and to find a more accurate frontier. Piecewise linear functions are used as single-objective cost functions to produce a smooth and equal convergence of all measurements to the desired specifications during the composition of the aggregate objective function. To verify the presented technique two circuits were designed, which are: a Miller amplifier with 96 dB Voltage gain, 15.48 MHz unity gain frequency, slew rate of 19.2 V/mu s with a current supply of 385.15 mu A, and a complementary folded cascode with 104.25 dB Voltage gain, 18.15 MHz of unity gain frequency and a slew rate of 13.370 MV/mu s. These circuits were synthesized using a 0.35 mu m technology. The results show that the method provides a fast approach for good solutions using the modified SA and further good Pareto front exploration through its connection to the particle swarm optimization algorithm.

Parallel Layout Construction Algorithm for Irregular Shape Packing Problems

Cutting and packing problems arise in a variety of industries, including garment, wood and shipbuilding. Irregular shape packing is a special case which admits irregular items and is much more complex due to the geometry of items. In order to ensure that items do not overlap and no item from the layout protrudes from the container, the collision free region concept was adopted. It represents all possible translations for a new item to be inserted into a container with already placed items. To construct a feasible layout, collision free region for each item is determined through a sequence of Boolean operations over polygons. In order to improve the speed of the algorithm, a parallel version of the layout construction was proposed and it was applied to a simulated annealing algorithm used to solve bin packing problems. Tests were performed in order to determine the speed improvement of the parallel version over the serial algorithm

Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing

Background: In the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to compare structures of networks estimated from data on normal and treated cells separately. However, this approach usually fails to estimate accurate gene networks due to the limited length of time series data and measurement noise. Thus, approaches that identify changes on regulations by using time series data on both conditions in an efficient manner are demanded. Methods: We propose a new statistical approach that is based on the state space representation of the vector autoregressive model and estimates gene networks on two different conditions in order to identify changes on regulations between the conditions. In the mathematical model of our approach, hidden binary variables are newly introduced to indicate the presence of regulations on each condition. The use of the hidden binary variables enables an efficient data usage; data on both conditions are used for commonly existing regulations, while for condition specific regulations corresponding data are only applied. Also, the similarity of networks on two conditions is automatically considered from the design of the potential function for the hidden binary variables. For the estimation of the hidden binary variables, we derive a new variational annealing method that searches the configuration of the binary variables maximizing the marginal likelihood. Results: For the performance evaluation, we use time series data from two topologically similar synthetic networks, and confirm that our proposed approach estimates commonly existing regulations as well as changes on regulations with higher coverage and precision than other existing approaches in almost all the experimental settings. For a real data application, our proposed approach is applied to time series data from normal Human lung cells and Human lung cells treated by stimulating EGF-receptors and dosing an anticancer drug termed Gefitinib. In the treated lung cells, a cancer cell condition is simulated by the stimulation of EGF-receptors, but the effect would be counteracted due to the selective inhibition of EGF-receptors by Gefitinib. However, gene expression profiles are actually different between the conditions, and the genes related to the identified changes are considered as possible off-targets of Gefitinib. Conclusions: From the synthetically generated time series data, our proposed approach can identify changes on regulations more accurately than existing methods. By applying the proposed approach to the time series data on normal and treated Human lung cells, candidates of off-target genes of Gefitinib are found. According to the published clinical information, one of the genes can be related to a factor of interstitial pneumonia, which is known as a side effect of Gefitinib.

The migration of Mn2+ ions in Cd1-xMnxS nanocrystals: Thermal annealing control

This work reports evidence of the induced migration of Mn2+ ions in Cd(1-x)MnxS nanocrystals (NCs) by selecting a specific thermal treatment for each sample. The growth and characterization of these magnetic dots were investigated by atomic force microscopy (AFM), optical absorption (OA), and electronic paramagnetic resonance (EPR) techniques. The comparison of experimental and simulated EPR spectra confirms the incorporation of Mn2+ ions both in the core and at the dot surface regions. The thermal treatment of a magnetic sample, via selected annealing temperature and/or time, affects the fine and hyperfine interaction constants which modify the shape and the intensity of the EPR transition spectrum. The identification of these changes has allowed tracing the magnetic ion migration from core to surface regions of a dot as well as inferring the local density of the magnetic impurity ions. (C) 2011 Elsevier Ltd. All rights reserved.

Atomically resolved study of the morphology change of InAs/GaAs quantum dot layers induced by rapid thermal annealing

The optoelectronic properties of InAs/GaAs quantum dots can be tuned by rapid thermal annealing. In this study, the morphology change of InAs/GaAs quantum dots layers induced by rapid thermal annealing was investigated at the atomic-scale by cross-sectional scanning tunneling microscopy. Finite elements calculations that model the outward relaxation of the cleaved surface were used to determine the indium composition profile of the wetting layer and the quantum dots prior and post rapid thermal annealing. The results show that the wetting layer is broadened upon annealing. This broadening could be modeled by assuming a random walk of indium atoms. Furthermore, we show that the stronger strain gradient at the location of the quantum dots enhances the intermixing. Photoluminescence measurements show a blueshift and narrowing of the photoluminescence peak. Temperature dependent photoluminescence measurements show a lower activation energy for the annealed sample. These results are in agreement with the observed change in morphology. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4770371]

Conformational polymorphism of the antidiabetic drug chlorpropamide

In this paper, the main features of Raman spectroscopy, one of the first choice methods in the study of polymorphism in pharmaceuticals, are presented taking chlorpropamide as a case of study. The antidiabetic drug chlorpropamide (1-[4-chlorobenzenesulphonyl]-3-propyl urea), which belongs to the sulfonylurea class, is known to exhibit, at least, six polymorphic phases. These forms are characterized not only by variations in their molecular packing but also in their molecular conformation. In this study, the polymorphism of chlorpropamide is discussed on the basis of Raman scattering measurements and quantum mechanical calculations. The main spectroscopic features that fingerprint the crystalline forms are correlated with the corresponding crystalline structures. Using a theoretical approach on the energy dependence of the conformers, simulated molecular torsion angles are plotted versus the formation energy, which provides a satisfactory agreement between the torsion angles at the energy minima and the experimental values observed in the different solid forms of chlorpropamide. Copyright (C) 2011 John Wiley & Sons, Ltd.

Monitoring internal load parameters during simulated and official basketball matches

Moreira, A, McGuigan, MR, Arruda, AFS, Freitas, CG, and Aoki, MS. Monitoring internal load parameters during simulated and official basketball matches. J Strength Cond Res 26(3): 861-866, 2012-The purpose of this study was to compare the internal load responses (session rating of perceived exertion [RPE] and salivary cortisol) between simulated and official matches (SM and OM). Ten professional basketball players participated in 2 OMs and 2 SMs during the competition season. Subjects provided saliva samples 30 minutes before the prematch warm-up (PRE) and 10 minutes after the end of the match. Session RPE (CR-10 scale) was assessed 30 minutes after each match. The results from the 2-way analysis of variance showed significant differences for post-OM salivary cortisol as compared with pre-OM values (p < 0.05). No changes were observed for cortisol during the SM. Before the OM, a significant difference in salivary cortisol was observed as compared with pre-SM values (p < 0.05). Moreover, the OM session RPE was significantly greater than that of SM. There was a significant correlation between session RPE and cortisol changes (r = 0.75). In summary, the results of this study showed a greater magnitude of cortisol and session RPE responses after OM as compared with that after SM confirming the hypothesis that a real competition generates a greater stress response than a simulated condition does. The anticipatory effect was also observed in the OM. In addition, the results indicate that session RPE seems to be a viable tool in monitoring internal loads, and the results are useful in providing a better understanding of internal loads imposed by basketball training and competitions. The precise monitoring of these responses might help the coaches to plan appropriate loads maximizing recovery and performance.

Effects of RegCM3 parameterizations on simulated rainy season over South America

The impacts of change in the Grell convective scheme and biosphere-atmosphere transfer scheme (BATS) in RegCM3 are described. Three numerical experiments (RegZhang, RegClaris and RegArain) are conducted to reduce the RegCM3-Grell rainfall underestimation over tropical South America. The simulation referred to as RegZhang follows modifications made by Zhang et al. (2008) in the BATS. The RegClaris combines the RegZhang BATS parameters with a reduction of water drainage at the bottom of the subsoil layer in the regions covered by the tropical rain forest and a shorter convective time period for the Grell scheme. The RegArain considers this same modification in the Grell scheme, but uses a deeper total soil column and a deeper root system in the BATS. After the first year of simulation, the soil water content in RegZhang is progressively drained out of the soil column resulting in a deficit of rainfall in the Amazon. The RegClaris and RegArain, on the other hand, simulate a similar rainfall annual cycle in the Amazon, showing substantial improvement not only in phase but also in intensity. This improvement is partially related to an increase in evapotranspiration due to a larger availability of water in the soil column. A remote effect is also noted over the La Plata Basin region, where the larger summer rainfall rate may be related to the increase in moisture transport from the Amazon. Wind- and rainfall-based indices are applied to identify South American monsoon (SAM) timing. The RegClaris rainfall rates are adequate to identify the onset and the demise of SAM according to the observed data, whereas the rainfall deficit in RegZhang is associated with a delay in the onset and an early demise of the SAM.

The Effects of High Pressure on the Point of No Return in Simulated Penalty Kicks

We investigated the effects of high pressure on the point of no return or the minimum time required for a kicker to respond to the goalkeeper's dive in a simulated penalty kick task. The goalkeeper moved to one side with different times available for the participants to direct the ball to the opposite side in low-pressure (acoustically isolated laboratory) and high-pressure situations (with a participative audience). One group of participants showed a significant lengthening of the point of no return under high pressure. With less time available, performance was at chance level. Unexpectedly, in a second group of participants, high pressure caused a qualitative change in which for short times available participants were inclined to aim in the direction of the goalkeeper's move. The distinct effects of high pressure are discussed within attentional control theory to reflect a decreasing efficiency of the goal-driven attentional system, slowing down performance, and a decreasing effectiveness in inhibiting stimulus-driven behavior.

The influence of mouthrinses and simulated toothbrushing on the surface roughness of a nanofilled composite resin

The aim of this study was to determine the influence of mouthrinses on the surface roughness of a nanofilled composite resin after toothbrushing. One hundred nanofilled composite resin specimens were prepared and randomly distributed into two groups-brushed and non-brushed-and then assigned to five subgroups, according to the mouthrinse solutions (n = 10): Colgate Plax Fresh Mint, Oral B, Cepacol, Colgate Plax, and artificial saliva. Each sample was immersed in 20 mL of the mouthrinses for 1 minute, 5 days per week, twice a day, for a 3-week period. The control group used in the study was one in which the specimens were not subjected to brushing and remained only in artificial saliva. Toothbrushing was performed once a week for 1 minute, for 3 weeks. Surface roughness measurements (Ra) were performed after the immersion period and toothbrushing, by means of a profilometer. Data were analyzed by two-way ANOVA and Tukey's test. Analysis revealed that the association between toothbrushing and Colgate Plax Fresh Mint produced the lowest surface roughness (p < 0.05). All other groups tested (Oral B, Cepacol, Colgate Plax, artificial saliva) exhibited no statistically significant differences between surfaces, whether subjected to toothbrushing or not (p < 0.05). It was concluded that the surface roughness of the nanofilled composite resin tested can be influenced by the mouthrinse associated with toothbrushing.

New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.

Detection of simulated incipient furcation involvement by CBCT: an in vitro study using pig mandibles

The aim of the present study was to test the reproducibility, sensitivity, and specificity of cone-beam computed tomography (CBCT) in detecting incipient furcation involvement. Fifteen macerated pig mandibles, with intact second molar teeth and preserved adjacent cortical areas, were used. Simulated lesions were created in the furcation region of these teeth by applying 70% perchloric acid in up to four possible buccal/lingual sites in the right/left sides of each mandible. The mandibles were then submitted to a CBCT scan. Two blinded and calibrated experienced oral and maxillofacial radiologists interpreted the exams. Furcation involvement was also assessed in the regions without simulated lesions. CBCT showed high levels of accuracy, ranging from 78% to 88%. The variations in Kappa values for intra- and inter-observer agreement (0.41-0.59) were considered moderate. CBCT can be considered a reliable and accurate method for detecting incipient furcation involvement.