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This study proposes an innovative method for structural health monitoring of simply supported PCI girder bridges based on dynamic strain and edge computing. Field static and dynamic load tests were conducted on a bridge consisting of a span with newly replaced PCI girders and numerous spans with old PCI girders. Both the static and dynamic test results showed that the flexural rigidity of the old PCI girders decreased significantly due to deterioration. To improve the efficiency of on-site monitoring data transmission and data analysis, this study developed a smart dynamic strain gauge node with the function of edge computing. Continuous data with a sampling frequency of 100 Hz were computed at the sensor node. Among the computed results, only the maximum dynamic strain data caused by the passage of the heaviest vehicle within 1 min were transmitted. The on-site monitoring results indicated that under routine traffic conditions, the dynamic strain response of the new PCI girder was smaller than that of the deteriorated PCI girder. When the monitored dynamic strain response has a tendency to magnify, attention should be paid to the potential prestress loss or other deterioration behaviors of the bridge.

The motivation of this investigation is to develop a single-layer Chebyshev Neural Network (ChNN) model to handle singular fractional (arbitrary)-order Lane-Emden type equations. These equations are well-known application problems of astrophysics and quantum mechanics. Fractional Lane-Emden equations are singular so it is very difficult to solve analytically. Thus, an efficient method is required to handle the above equations. Here, our main aim is to use a single-layer ChNN model for solving fractional Lane-Emden equations. ChNN model is one kind of Functional Link Neural Network (FLNN) in which the hidden layer is replaced by a functional expansion block of the input pattern using orthogonalshifted Chebyshev polynomials (SChP). Thus, the network parameters of ChNN are less than the Multi-Layer Artificial Neural Network (MLANN). We have considered factional-order singular nonlinear problems of astrophysics to show the computational effort of the proposed method. Back Propagation algorithm of the unsupervised version has been considered for minimizing the error function and updating the weights of the ChNN model. Computed results are displayed in terms of tables and graphs.

Approximate computing is an emerging design paradigm that offers trade-offs between output accuracy and computation efforts by exploiting some applications' intrinsic error resiliency. Computation of error metrics is of paramount importance in approximate circuits to measure the degree of approximation. Most of the existing techniques for evaluating error metrics apply simulations which may not be effective for evaluation of large complex designs because of an immense increase in simulation runtime and a decrease in accuracy. To address these deficiencies, we present a novel methodology that employs SAT (Boolean satisfiability) solvers for fast and accurate determination of error metrics specifically for the calculation of an average-case error and the maximum error rate in functionally approximated circuits. The proposed approach identifies the set of all errors producing assignments to gauge the quality of approximate circuits for real-life applications. Additionally, the proposed approach provides a test generation method to facilitate design choices, and acts as an important guide to debug the approximate circuits to discover and locate the errors. The effectiveness of the approach is demonstrated by evaluating the error metrics of several benchmark-approximated adders of different sizes. Experimental results on benchmark circuits show that the proposed SAT-based methodology accurately determines the maximum error rate and an average-case error within acceptable CPU execution time in one go, and further provides a log of error-generating input assignments., Competing Interests: The authors have declared that no competing interests exist.

Evolutionary multiobjective optimization for the classical vertex cover problem has been analysed in Kratsch and Neumann (2013) in the context of parameterized complexity analysis. This article extends the analysis to the weighted vertex cover problem in which integer weights are assigned to the vertices and the goal is to find a vertex cover of minimum weight. Using an alternative mutation operator introduced in Kratsch and Neumann (2013), we provide a fixed parameter evolutionary algorithm with respect to OPT , the cost of an optimal solution for the problem. Moreover, we present a multiobjective evolutionary algorithm with standard mutation operator that keeps the population size in a polynomial order by means of a proper diversity mechanism, and therefore, manages to find a 2-approximation in expected polynomial time. We also introduce a population-based evolutionary algorithm which finds a ( 1 + ɛ ) -approximation in expected time O ( n · 2 min { n , 2 ( 1 - ɛ ) O P T } + n 3 ) .

We continue recent work on the definition of multimodality in multiobjective optimization (MO) and the introduction of a test bed for multimodal MO problems. This goes beyond well-known diversity maintenance approaches but instead focuses on the landscape topology induced by the objective functions. More general multimodal MO problems are considered by allowing ellipsoid contours for single-objective subproblems. An experimental analysis compares two MO algorithms, one that explicitly relies on hypervolume gradient approximation, and one that is based on local search, both on a selection of generated example problems. We do not focus on performance but on the interaction induced by the problems and algorithms, which can be described by means of specific characteristics explicitly designed for the multimodal MO setting. Furthermore, we widen the scope of our analysis by additionally applying visualization techniques in the decision space. This strengthens and extends the foundations for Exploratory Landscape Analysis (ELA) in MO.

The hypervolume subset selection problem (HSSP) aims at approximating a set of n multidimensional points in R d with an optimal subset of a given size. The size k of the subset is a parameter of the problem, and an approximation is considered best when it maximizes the hypervolume indicator. This problem has proved popular in recent years as a procedure for multiobjective evolutionary algorithms. Efficient algorithms are known for planar points ( d = 2 ), but there are hardly any results on HSSP in larger dimensions ( d ≥ 3 ). So far, most algorithms in higher dimensions essentially enumerate all possible subsets to determine the optimal one, and most of the effort has been directed toward improving the efficiency of hypervolume computation. We propose efficient algorithms for the selection problem in dimension 3 when either k or n - k is small, and extend our techniques to arbitrary dimensions for k ≤ 3 .

The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested to correctly reproduce solvation free energy in DMSO, ion solvation in DMSO, and DMSO coordination prediction. Our findings establish a united atom (UA) type parameterization as the best model of DMSO for use in 3D-RISM-KH theory based calculations.

Pooling is an attractive strategy in screening infected specimens, especially for rare diseases. An essential step of performing the pooled test is to determine the group size. Sometimes, equal group size is not appropriate due to population heterogeneity. In this case, varying group sizes are preferred and could be determined while individual information is available. In this study, we propose a sequential procedure to determine varying group sizes through fully utilizing available information. This procedure is data driven. Simulations show that it has good performance in estimating parameters.

Background: The T wave represents ECG repolarization, whose detection is required during myocardial ischemia, and the first significant change in the ECG signal is being observed in the ST segment followed by changes in other waves like P wave and QRS complex. To offer guidance in clinical diagnosis, decision-making, and daily mobile ECG monitoring, the T wave needs to be detected firstly. Recently, the sliding area-based method has received an increasing amount of attention due to its robustness and low computational burden. However, the parameter setting of the search window's boundaries in this method is not adaptive. Therefore, in this study, we proposed an improved sliding window area method with more adaptive parameter setting for T wave detection., Methods: Firstly, k -means clustering was used in the annotated MIT QT database to generate three piecewise functions for delineating the relationship between the RR interval and the interval from the R peak to the T wave onset and that between the RR interval and the interval from the R peak to the T wave offset. Then, the grid search technique combined with 5-fold cross validation was used to select the suitable parameters' combination for the sliding window area method., Results: With respect to onset detection in the QT database, F 1 improved from 54.70% to 70.46% and 54.05% to 72.94% for the first and second electrocardiogram (ECG) channels, respectively. For offset detection, F 1 also improved in both channels as it did in the European ST-T database., Conclusions: F 1 results from the improved algorithm version were higher than those from the traditional method, indicating a potentially useful application for the proposed method in ECG monitoring.

Background: With progress on both the theoretical and the computational fronts the use of spline modelling has become an established tool in statistical regression analysis. An important issue in spline modelling is the availability of user friendly, well documented software packages. Following the idea of the STRengthening Analytical Thinking for Observational Studies initiative to provide users with guidance documents on the application of statistical methods in observational research, the aim of this article is to provide an overview of the most widely used spline-based techniques and their implementation in R., Methods: In this work, we focus on the R Language for Statistical Computing which has become a hugely popular statistics software. We identified a set of packages that include functions for spline modelling within a regression framework. Using simulated and real data we provide an introduction to spline modelling and an overview of the most popular spline functions., Results: We present a series of simple scenarios of univariate data, where different basis functions are used to identify the correct functional form of an independent variable. Even in simple data, using routines from different packages would lead to different results., Conclusions: This work illustrate challenges that an analyst faces when working with data. Most differences can be attributed to the choice of hyper-parameters rather than the basis used. In fact an experienced user will know how to obtain a reasonable outcome, regardless of the type of spline used. However, many analysts do not have sufficient knowledge to use these powerful tools adequately and will need more guidance.

Bacterial computing is a known candidate in natural computing, the aim being to construct "bacterial computers" for solving complex problems. In this paper, a new kind of bacterial computing system, named the bacteria and plasmid computing system (BP system), is proposed. We investigate the computational power of BP systems with finite numbers of bacteria and plasmids. Specifically, it is obtained in a constructive way that a BP system with 2 bacteria and 34 plasmids is Turing universal. The results provide a theoretical cornerstone to construct powerful bacterial computers and demonstrate a concept of paradigms using a "reasonable" number of bacteria and plasmids for such devices.

Background: Pneumonia is the leading cause of mortality for children below 5 years of age. The majority of these occur in poor countries with limited access to diagnosis. The World Health Organization (WHO) criterion for pneumonia is the de facto method for diagnosis. It is designed targeting a high sensitivity and uses easy to measure parameters. The WHO criterion has poor specificity., Methods: We propose a method using common measurements (including the WHO parameters) to diagnose pneumonia at high sensitivity and specificity. Seventeen clinical features obtained from 134 subjects were used to create a series of logistic regression models. We started with one feature at a time, and continued building models with increasing number of features until we exhausted all possible combinations. We used a k-fold cross validation method to measure the performance of the models., Results: The sensitivity of our method was comparable to that of the WHO criterion but the specificity was 84%-655% higher. In the 2-11 month age group, the WHO criteria had a sensitivity and specificity of 92.0%±11.6% and 38.1%±18.5%, respectively. Our best model (using the existence of a runny nose, the number of days with runny nose, breathing rate and temperature) performed at a sensitivity of 91.3%±13.0% and specificity of 70.2%±22.80%. In the 12-60 month age group, the WHO algorithm gave a sensitivity of 95.7%±7.6% at a specificity of 9.8%±13.1%, while our corresponding sensitivity and specificity were 94.0%±12.1% and 74.0%±23.3%, respectively (using fever, number of days with cough, heart rate and chest in-drawing)., Conclusions: The WHO algorithm can be improved through mathematical analysis of clinical observations and measurements routinely made in the field. The method is simple and easy to implement on a mobile phone. Our method allows the freedom to pick the best model in any arbitrary field scenario (e.g., when an oximeter is not available).

The Grid scheduler, schedules user jobs on the best available resource in terms of resource characteristics by optimizing job execution time. Resource failure in Grid is no longer an exception but a regular occurring event as resources are increasingly being used by the scientific community to solve computationally intensive problems which typically run for days or even months. It is therefore absolutely essential that these long-running applications are able to tolerate failures and avoid re-computations from scratch after resource failure has occurred, to satisfy the user's Quality of Service (QoS) requirement. Job Scheduling with Fault Tolerance in Grid Computing using Ant Colony Optimization is proposed to ensure that jobs are executed successfully even when resource failure has occurred. The technique employed in this paper, is the use of resource failure rate, as well as checkpoint-based roll back recovery strategy. Check-pointing aims at reducing the amount of work that is lost upon failure of the system by immediately saving the state of the system. A comparison of the proposed approach with an existing Ant Colony Optimization (ACO) algorithm is discussed. The experimental results of the implemented Fault Tolerance scheduling algorithm show that there is an improvement in the user's QoS requirement over the existing ACO algorithm, which has no fault tolerance integrated in it. The performance evaluation of the two algorithms was measured in terms of the three main scheduling performance metrics: makespan, throughput and average turnaround time.

Background: Machine-learning models may aid cardiac phenotypic recognition by using features of cardiac tissue deformation., Objectives: This study investigated the diagnostic value of a machine-learning framework that incorporates speckle-tracking echocardiographic data for automated discrimination of hypertrophic cardiomyopathy (HCM) from physiological hypertrophy seen in athletes (ATH)., Methods: Expert-annotated speckle-tracking echocardiographic datasets obtained from 77 ATH and 62 HCM patients were used for developing an automated system. An ensemble machine-learning model with 3 different machine-learning algorithms (support vector machines, random forests, and artificial neural networks) was developed and a majority voting method was used for conclusive predictions with further K-fold cross-validation., Results: Feature selection using an information gain (IG) algorithm revealed that volume was the best predictor for differentiating between HCM ands. ATH (IG = 0.24) followed by mid-left ventricular segmental (IG = 0.134) and average longitudinal strain (IG = 0.131). The ensemble machine-learning model showed increased sensitivity and specificity compared with early-to-late diastolic transmitral velocity ratio (p < 0.01), average early diastolic tissue velocity (e') (p < 0.01), and strain (p = 0.04). Because ATH were younger, adjusted analysis was undertaken in younger HCM patients and compared with ATH with left ventricular wall thickness >13 mm. In this subgroup analysis, the automated model continued to show equal sensitivity, but increased specificity relative to early-to-late diastolic transmitral velocity ratio, e', and strain., Conclusions: Our results suggested that machine-learning algorithms can assist in the discrimination of physiological versus pathological patterns of hypertrophic remodeling. This effort represents a step toward the development of a real-time, machine-learning-based system for automated interpretation of echocardiographic images, which may help novice readers with limited experience., (Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.)

Many domains of empirical research produce or analyze spatial paths as a measure of behavior. Previously, approaches for measuring the similarity or deviation between two paths have either required timing information or have used ad hoc or manual coding schemes. In this paper, we describe an optimization approach for robustly measuring the area-based deviation between two paths we call ALCAMP (Algorithm for finding the Least-Cost Areal Mapping between Paths). ALCAMP measures the deviation between two paths and produces a mapping between corresponding points on the two paths. The method is robust to a number of aspects in real path data, such as crossovers, self-intersections, differences in path segmentation, and partial or incomplete paths. Unlike similar algorithms that produce distance metrics between trajectories (i.e., paths that include timing information), this algorithm uses only the order of observed path segments to determine the mapping. We describe the algorithm and show its results on a number of sample problems and data sets, and demonstrate its effectiveness for assessing human memory for paths. We also describe available software code written in the R statistical computing language that implements the algorithm to enable data analysis.

The mechanisms of enzymatic reactions are studied via a host of computational techniques. While previous methods have been used successfully, many fail to incorporate the full dynamical properties of enzymatic systems. This can lead to misleading results in cases where enzyme motion plays a significant role in the reaction coordinate, which is especially relevant in particle transfer reactions where nuclear tunneling may occur. In this chapter, we outline previous methods, as well as discuss newly developed dynamical methods to interrogate mechanisms of enzymatic particle transfer reactions. These new methods allow for the calculation of free energy barriers and kinetic isotope effects (KIEs) with the incorporation of quantum effects through centroid molecular dynamics (CMD) and the full complement of enzyme dynamics through transition path sampling (TPS). Recent work, summarized in this chapter, applied the method for calculation of free energy barriers to reaction in lactate dehydrogenase (LDH) and yeast alcohol dehydrogenase (YADH). We found that tunneling plays an insignificant role in YADH but plays a more significant role in LDH, though not dominant over classical transfer. Additionally, we summarize the application of a TPS algorithm for the calculation of reaction rates in tandem with CMD to calculate the primary H/D KIE of YADH from first principles. We found that the computationally obtained KIE is within the margin of error of experimentally determined KIEs and corresponds to the KIE of particle transfer in the enzyme. These methods provide new ways to investigate enzyme mechanism with the inclusion of protein and quantum dynamics., (© 2016 Elsevier Inc. All rights reserved.)

Existing sensitivity analysis approaches are not able to handle efficiently stochastic reaction networks with a large number of parameters and species, which are typical in the modeling and simulation of complex biochemical phenomena. In this paper, a two-step strategy for parametric sensitivity analysis for such systems is proposed, exploiting advantages and synergies between two recently proposed sensitivity analysis methodologies for stochastic dynamics. The first method performs sensitivity analysis of the stochastic dynamics by means of the Fisher Information Matrix on the underlying distribution of the trajectories; the second method is a reduced-variance, finite-difference, gradient-type sensitivity approach relying on stochastic coupling techniques for variance reduction. Here we demonstrate that these two methods can be combined and deployed together by means of a new sensitivity bound which incorporates the variance of the quantity of interest as well as the Fisher Information Matrix estimated from the first method. The first step of the proposed strategy labels sensitivities using the bound and screens out the insensitive parameters in a controlled manner. In the second step of the proposed strategy, a finite-difference method is applied only for the sensitivity estimation of the (potentially) sensitive parameters that have not been screened out in the first step. Results on an epidermal growth factor network with fifty parameters and on a protein homeostasis with eighty parameters demonstrate that the proposed strategy is able to quickly discover and discard the insensitive parameters and in the remaining potentially sensitive parameters it accurately estimates the sensitivities. The new sensitivity strategy can be several times faster than current state-of-the-art approaches that test all parameters, especially in "sloppy" systems. In particular, the computational acceleration is quantified by the ratio between the total number of parameters over the number of the sensitive parameters.

Background: Recent recommendations for lung protective mechanical ventilation include a tidal volume target of 6 mL/kg predicted body weight (PBW). Different PBW equations might introduce important differences in tidal volumes delivered to research subjects and patients., Methods: PBW equations use height, age, and sex as input variables. We compared National Institutes of Health (NIH) ARDS Network (ARDSNet), actuarial table (ACTUARIAL), and Stewart (STEWART) PBW equations used in clinical trials, across physiologic ranges for age and height. We used three-dimensional and two-dimensional surface analysis to compare these PBW equations. We then used age and height from actual clinical trial subjects to quantify PBW equation differences., Results: Significant potential differences existed between these PBW predictions. The ACTUARIAL and ARDSNet surfaces for women were the only surfaces that intersected and produced both positive and negative differences. Mathematical differences between PBW equations at limits of height and age exceeded 30% in women and 24% in men for ACTUARIAL vs ARDSNet and about 25% for women and 15% for men for STEWART vs ARDSNet. The largest mathematical differences were present in older, shorter subjects, especially women. Actual differences for clinical trial subjects were as high as 15% for men and 24% for women., Conclusions: Significant differences between PBW equations for both men and women could be important sources of interstudy variation. Studies should adopt a standard PBW equation. We recommend using the NIH National Heart, Lung, and Blood Institute ARDS Network PBW equation because it is associated with the clinical trial that identified 6 mL/kg PBW as an appropriate target.

Flux balance analysis (FBA) is one of the most often applied methods on genome-scale metabolic networks. Although FBA uniquely determines the optimal yield, the pathway that achieves this is usually not unique. The analysis of the optimal-yield flux space has been an open challenge. Flux variability analysis is only capturing some properties of the flux space, while elementary mode analysis is intractable due to the enormous number of elementary modes. However, it has been found by Kelk et al. (2012) that the space of optimal-yield fluxes decomposes into flux modules. These decompositions allow a much easier but still comprehensive analysis of the optimal-yield flux space. Using the mathematical definition of module introduced by Müller and Bockmayr (2013b), we discovered useful connections to matroid theory, through which efficient algorithms enable us to compute the decomposition into modules in a few seconds for genome-scale networks. Using that every module can be represented by one reaction that represents its function, in this article, we also present a method that uses this decomposition to visualize the interplay of modules. We expect the new method to replace flux variability analysis in the pipelines for metabolic networks.

Genetic regulatory networks are the key to understanding biochemical systems. One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network. The attractors of these Boolean networks will help biologists to identify determinant and stable factors. Existing methods identify attractors based on a random initial state or the entire state simultaneously. They cannot identify the fixed length attractors directly. The complexity of including time increases exponentially with respect to the attractor number and length of attractors. This study used the bounded model checking to quickly locate fixed length attractors. Based on the SAT solver, we propose a new algorithm for efficiently computing the fixed length attractors, which is more suitable for large Boolean networks and numerous attractors' networks. After comparison using the tool BooleNet, empirical experiments involving biochemical systems demonstrated the feasibility and efficiency of our approach.

Background: Estimated effects vary across studies, partly because of random sampling error and partly because of heterogeneity. In meta-analysis, the fraction of variance that is due to heterogeneity is estimated by the statistic I(2). We calculate the bias of I(2), focusing on the situation where the number of studies in the meta-analysis is small. Small meta-analyses are common; in the Cochrane Library, the median number of studies per meta-analysis is 7 or fewer., Methods: We use Mathematica software to calculate the expectation and bias of I(2)., Results: I(2) has a substantial bias when the number of studies is small. The bias is positive when the true fraction of heterogeneity is small, but the bias is typically negative when the true fraction of heterogeneity is large. For example, with 7 studies and no true heterogeneity, I(2) will overestimate heterogeneity by an average of 12 percentage points, but with 7 studies and 80 percent true heterogeneity, I(2) can underestimate heterogeneity by an average of 28 percentage points. Biases of 12-28 percentage points are not trivial when one considers that, in the Cochrane Library, the median I(2) estimate is 21 percent., Conclusions: The point estimate I(2) should be interpreted cautiously when a meta-analysis has few studies. In small meta-analyses, confidence intervals should supplement or replace the biased point estimate I(2).

Motivation: Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects., Results: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods., Availability and Implementation: http://kiharalab.org/patchsurfer2.0/ CONTACT: dkihara@purdue.edu, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

This paper is concerned with the passivity analysis for switched neural networks subject to stochastic disturbances and time-varying delays. First, using the multiple Lyapunov functions method, a state-dependent switching law is designed to present a stochastic passivity condition. Second, a hysteresis switching law involving both the current state and the previous value of the switching signal are presented to avoid chattering resulted from the state-dependent switching. Third, based on the average dwell-time approach, a class of switching signals is determined to guarantee the switched neural network stochastically passive. Finally, three numerical examples are provided to illustrate the characteristics of three proposed switching laws.

Multi-objective optimisation yields an estimated Pareto front of mutually non- dominating solutions, but with more than three objectives, understanding the relationships between solutions is challenging. Natural solutions to use as landmarks are those lying near to the edges of the mutually non-dominating set. We propose four definitions of edge points for many-objective mutually non-dominating sets and examine the relations between them. The first defines edge points to be those that extend the range of the attainment surface. This is shown to be equivalent to finding points which are not dominated on projection onto subsets of the objectives. If the objectives are to be minimised, a further definition considers points which are not dominated under maximisation when projected onto objective subsets. A final definition looks for edges via alternative projections of the set. We examine the relations between these definitions and their efficacy in many dimensions for synthetic concave- and convex-shaped sets, and on solutions to a prototypical many-objective optimisation problem, showing how they can reveal information about the structure of the estimated Pareto front. We show that the "controlling dominance area of solutions" modification of the dominance relation can be effectively used to locate edges and interior points of high-dimensional mutually non-dominating sets.

We study the behaviour of a [Formula: see text]-ES that handles constraints by resampling infeasible candidate solutions for linear optimization problems with a conically constrained feasible region. The analysis generalizes prior work in that no particular orientation of the cone relative to the gradient of the objective function is assumed. Expressions that describe the strategy's single-step behaviour are derived. Assuming that the mutation strength is adapted in a scale-invariant manner, a simple zeroth-order model is used to determine the speed of convergence of the strategy. We then derive expressions that approximately characterize the average step size and convergence rate attained when using cumulative step size adaptation and compare the values with optimal ones.

Traditionally, identification of epileptogenic zones primarily relied on visual inspection of intracranial electroencephalography (iEEG) recordings by experienced epileptologists; however, removal of epileptogenic zones identified by iEEG does not always guarantee favorable surgical outcomes. To confirm visual inspection results, and assist in making decisions about surgical resection areas, computational iEEG analysis methods have recently been used for the localization of epileptogenic zones. In this study, we have proposed a new approach for the localization of epileptogenic zones in Lennox-Gastaut syndrome (LGS), and have investigated whether the proposed approach could confirm surgical resection areas and predict seizure outcome before surgery. The proposed approach simultaneously used results of 2 iEEG analysis methods, directed transfer function (DTF) and time delay estimation, to enhance localization accuracy. This new combined method was applied to patients who became seizure-free after resective epilepsy surgery, as well as those who had unsuccessful surgery. A quantitative metric was also introduced that can measure how well the localized epileptogenic zones coincided with the surgical resection areas, with the aim of verifying whether the approach could confirm surgical resection areas determined by epileptologists. The estimated epileptogenic zones more strongly coincided with surgical resection areas in patients with successful, compared to those with unsuccessful surgical outcomes. Both qualitative and quantitative analyses showed that the combined use of 2 iEEG analyses resulted in a more accurate estimate of epileptogenic zones in LGS than the use of a single method. A combination of multiple iEEG analyses could not only enhance overall accuracy of localizing epileptogenic zones in LGS, but also has the potential to predict outcomes before resective surgery.

Given a set of points on the plane and an assignment of values to them, an optimal linear partition is a division of the set into two subsets which are separated by a straight line and maximally contrast with each other in the values assigned to their points. We present a method for inspecting and rating all linear partitions of a finite set, and a package of three functions in the R language for executing the computations. One function is for finding the optimal linear partitions and corresponding separating lines, another for graphically representing the results, and a third for testing how well the data comply with the linear separability condition. We illustrate the method on possible data from a psychophysical experiment (concerning the size-weight illusion) and compare its performance with that of linear discriminant analysis and multiple logistic regression, adapted to dividing linearly a set of points on the plane., (© 2013 The British Psychological Society.)

The computational complexity of one-dimensional time fractional reaction-diffusion equation is O(N²M) compared with O(NM) for classical integer reaction-diffusion equation. Parallel computing is used to overcome this challenge. Domain decomposition method (DDM) embodies large potential for parallelization of the numerical solution for fractional equations and serves as a basis for distributed, parallel computations. A domain decomposition algorithm for time fractional reaction-diffusion equation with implicit finite difference method is proposed. The domain decomposition algorithm keeps the same parallelism but needs much fewer iterations, compared with Jacobi iteration in each time step. Numerical experiments are used to verify the efficiency of the obtained algorithm.

We study the use of nonparametric multicompare statistical tests on the performance of simulated annealing (SA), genetic algorithm (GA), particle swarm optimization (PSO), and differential evolution (DE), when used for electroencephalographic (EEG) source localization. Such task can be posed as an optimization problem for which the referred metaheuristic methods are well suited. Hence, we evaluate the localization's performance in terms of metaheuristics' operational parameters and for a fixed number of evaluations of the objective function. In this way, we are able to link the efficiency of the metaheuristics with a common measure of computational cost. Our results did not show significant differences in the metaheuristics' performance for the case of single source localization. In case of localizing two correlated sources, we found that PSO (ring and tree topologies) and DE performed the worst, then they should not be considered in large-scale EEG source localization problems. Overall, the multicompare tests allowed to demonstrate the little effect that the selection of a particular metaheuristic and the variations in their operational parameters have in this optimization problem.

IEF simulation is an effective tool to investigate the transport phenomena and separation performance as well as to design IEF microchip. However, multidimensional IEF simulations are computationally intensive as one has to solve a large number of mass conservation equations for ampholytes to simulate a realistic case. In this study, a parallel scheme for a 2D IEF simulation is developed to reduce the computational time. The calculation time for each equation is analyzed to identify which procedure is suitable for parallelization. As expected, simultaneous solution of mass conservation equations of ampholytes is identified as the computational hot spot, and the computational time can be significantly reduced by parallelizing the solution procedure for that. Moreover, to optimize the computing time, electric potential behavior during transient state is investigated. It is found that for a straight channel the transient variation of electric potential along the channel is negligible in a narrow pH range (5∼8) IEF. Thus the charge conservation equation is solved for the first time step only, and the electric potential obtain from that is used for subsequent calculations. IEF simulations are carried out using this algorithm for separation of cardiac troponin I from serum albumin in a pH range of 5-8 using 192 biprotic ampholytes. Significant reduction in simulation time is achieved using the parallel algorithm. We also study the effect of number of ampholytes to form the pH gradient and its effect in the focusing and separation behavior of cardiac troponin I and albumin. Our results show that, at the completion of separation phase, the pH profile is stepwise for lower number of ampholytes, but becomes smooth as the number of ampholytes increases. Numerical results also show that higher protein concentration can be obtained using higher number of ampholytes., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Background: Boosting algorithms to simultaneously estimate and select predictor effects in statistical models have gained substantial interest during the last decade., Objectives: This review highlights recent methodological developments regarding boosting algorithms for statistical modelling especially focusing on topics relevant for biomedical research., Methods: We suggest a unified framework for gradient boosting and likelihood-based boosting (statistical boosting) which have been addressed separately in the literature up to now., Results: The methodological developments on statistical boosting during the last ten years can be grouped into three different lines of research: i) efforts to ensure variable selection leading to sparser models, ii) developments regarding different types of predictor effects and how to choose them, iii) approaches to extend the statistical boosting framework to new regression settings., Conclusions: Statistical boosting algorithms have been adapted to carry out unbiased variable selection and automated model choice during the fitting process and can nowadays be applied in almost any regression setting in combination with a large amount of different types of predictor effects.

Based on the falling shadow theory, the concept of falling fuzzy (implicative) ideals as a generalization of that of a T ∧-fuzzy (implicative) ideal is proposed in MV-algebras. The relationships between falling fuzzy (implicative) ideals and T-fuzzy (implicative) ideals are discussed, and conditions for a falling fuzzy (implicative) ideal to be a T ∧-fuzzy (implicative) ideal are provided. Some characterizations of falling fuzzy (implicative) ideals are presented by studying proprieties of them. The product ⊛ and the up product ⊚ operations on falling shadows and the upset of a falling shadow are established, by which T-fuzzy ideals are investigated based on probability spaces.

We study a special property of free cumulants. We prove that coefficients of a reciprocal generating function correspond to "free cumulants with the first two elements in the same block."

Based on He's variational iteration method idea, we modified the fractional variational iteration method and applied it to construct some approximate solutions of the generalized time-space fractional Schrödinger equation (GFNLS). The fractional derivatives are described in the sense of Caputo. With the help of symbolic computation, some approximate solutions and their iterative structure of the GFNLS are investigated. Furthermore, the approximate iterative series and numerical results show that the modified fractional variational iteration method is powerful, reliable, and effective when compared with some classic traditional methods such as homotopy analysis method, homotopy perturbation method, adomian decomposition method, and variational iteration method in searching for approximate solutions of the Schrödinger equations.

Background and Objectives: In clinical trials involving multiple tests it is often difficult to obtain informative simultaneous confidence intervals (SCIs). In particular in hierarchical testing, no quantification of effects is possible for the first tested (and most important) hypothesis after its rejection. Our goal is a construction of SCIs that are always informative., Methods: We present an approach where the level is split after rejection of each hypothesis to obtain an informative confidence bound. The splitting weights are continuous functions of the parameters. Our method is realizable by a simple algorithm and is illustrated by an intuitive graphical representation., Results: We show theoretically and by an example that the new SCIs always provide information when a hypothesis is rejected. The power to reject the first hypothesis is not smaller than for the classical fixed-sequence procedure. The price for the extra information is a small power loss in the hypotheses proceeding the most important one., Conclusions: Given the substantial gain in information, a small loss of power for the non-primary hypotheses seems often acceptable. Especially in the context of non-inferiority trials, this method is a useful alternative. The flexibility in the choice of the weight functions makes the procedure attractive for applications.

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

The concept of soft translations of soft subalgebras and soft ideals over BCI/BCK-algebras is introduced and some related properties are studied. Notions of Soft extensions of soft subalgebras and soft ideals over BCI/BCK-algebras are also initiated. Relationships between soft translations and soft extensions are explored.

Cofactors, such as NAD(H) and NADP(H), play important roles in energy transfer within the cells by providing the necessary redox carriers for a myriad of metabolic reactions, both anabolic and catabolic. Thus, it is crucial to establish the overall cellular redox balance for achieving the desired cellular physiology. Of several methods to manipulate the intracellular cofactor regeneration rates, altering the cofactor specificity of a particular enzyme is a promising one. However, the identification of relevant enzyme targets for such cofactor specificity engineering (CSE) is often very difficult and labor intensive. Therefore, it is necessary to develop more systematic approaches to find the cofactor engineering targets for strain improvement. Presented herein is a novel mathematical framework, cofactor modification analysis (CMA), developed based on the well-established constraints-based flux analysis, for the systematic identification of suitable CSE targets while exploring the global metabolic effects. The CMA algorithm was applied to E. coli using its genome-scale metabolic model, iJO1366, thereby identifying the growth-coupled cofactor engineering targets for overproducing four of its native products: acetate, formate, ethanol, and lactate, and three non-native products: 1-butanol, 1,4-butanediol, and 1,3-propanediol. Notably, among several target candidates for cofactor engineering, glyceraldehyde-3-phosphate dehydrogenase (GAPD) is the most promising enzyme; its cofactor modification enhanced both the desired product and biomass yields significantly. Finally, given the identified target, we further discussed potential mutational strategies for modifying cofactor specificity of GAPD in E. coli as suggested by in silico protein docking experiments.

Purpose: The purpose of this study is to determine the optimal scoring method and parameter settings of actigraphy by comparison to simultaneous polysomnography (PSG)., Methods: Fifteen studies of simultaneous PSG and actigraphy were completed in adolescents (mean age = 16.3 years) and analyzed. Scoring actigraphy by the human eye was compared to a commercial computerized algorithm using various parameters. The PSG was considered the reference standard., Results: There was a better correlation between actigraphy and PSG sleep start/end, total sleep time, wake after sleep onset, and sleep efficiency when the rest period was determined by the human (mean r = 0.640) rather than auto-set by the software (r = 0.406). The best results came when the rest intervals were set based on the PSG (r = 0.694). Scoring the printed actogram by the human eye was superior to the auto analyses as well (r = 0.575). Higher correlations and lower biases were obtained from lower wake threshold settings (low and medium) and higher immobility times (10 and 15 min)., Conclusions: Visual scoring by simple inspection of the actigraphy tracing had a reasonable correlation with the gold standard PSG. Accurate determination of the rest interval is important in scoring actigraphy. Scoring actigraphy by the human eye is superior to this computer algorithm when auto-setting major rest periods. A low wake threshold and 10-15 min of immobility for sleep onset and sleep end yield the most accurate computerized results. Auto-setting major rest intervals should be avoided to set start/end of rest intervals; adjustments for artifacts and/or a sleep diary for comparison are helpful.

In the present article, we demonstrates the use of SAS PROC CALIS to fit various types of Level-1 error covariance structures of latent growth models (LGM). Advantages of the SEM approach, on which PROC CALIS is based, include the capabilities of modeling the change over time for latent constructs, measured by multiple indicators; embedding LGM into a larger latent variable model; incorporating measurement models for latent predictors; and better assessing model fit and the flexibility in specifying error covariance structures. The strength of PROC CALIS is always accompanied with technical coding work, which needs to be specifically addressed. We provide a tutorial on the SAS syntax for modeling the growth of a manifest variable and the growth of a latent construct, focusing the documentation on the specification of Level-1 error covariance structures. Illustrations are conducted with the data generated from two given latent growth models. The coding provided is helpful when the growth model has been well determined and the Level-1 error covariance structure is to be identified.

Background: Parameter estimation in biological models is a common yet challenging problem. In this work we explore the problem for gene regulatory networks modeled by differential equations with unknown parameters, such as decay rates, reaction rates, Michaelis-Menten constants, and Hill coefficients. We explore the question to what extent parameters can be efficiently estimated by appropriate experimental selection., Results: A minimization formulation is used to find the parameter values that best fit the experiment data. When the data is insufficient, the minimization problem often has many local minima that fit the data reasonably well. We show that selecting a new experiment based on the local Fisher Information of one local minimum generates additional data that allows one to successfully discriminate among the many local minima. The parameters can be estimated to high accuracy by iteratively performing minimization and experiment selection. We show that the experiment choices are roughly independent of which local minima is used to calculate the local Fisher Information., Conclusions: We show that by an appropriate choice of experiments, one can, in principle, efficiently and accurately estimate all the parameters of gene regulatory network. In addition, we demonstrate that appropriate experiment selection can also allow one to restrict model predictions without constraining the parameters using many fewer experiments. We suggest that predicting model behaviors and inferring parameters represent two different approaches to model calibration with different requirements on data and experimental cost.

This study examined the effects of different sample sizes and different levels of bias (systematic error) between replicated measurements on the accuracy of estimates of random error calculated using two common formulae: Dahlberg's and the 'method of moments' estimator (MME). Computer-based numerical simulations were used to generate clinically realistic measurements involving random errors with a known distribution. For each simulation, two sets of 'measured values' were generated to provide the replicated data necessary for the estimation of the random error. Dahlberg's and the MME formula were applied to these paired data sets and the resulting estimates of error compared with the 'true' error. Nine different sample sizes (n = 2, 5, 10, 15, 20, 25, 30, 50, and 100) and two different types of bias (additive and multiplicative) were examined for their effect on the estimated error. In each case, the estimates of the random error were based on the distribution of 5000 separate simulations. The results indicate that with a sample of less than 25-30 replicated measurements, the resulting estimates of error are potentially unreliable and may under or overestimate the true error, irrespective of the formula used in the calculation. Where, however, a bias exists between the replicate measurements, Dahlberg's formula can be expected to overestimate the true value of the random error even where the biases are small and difficult to detect by standard statistical tests. No such distorting effect was found for the MME formula, which provided estimates of error that were not meaningfully different from the true value even where relatively large biases existed between the replicates. These results suggest the following: 1. A sample of at least 25-30 cases should be replicated to provide an estimate of the random error. 2. Where the original study contains fewer than 20 cases, the estimate of error will be unreliable. In these circumstances, it would be helpful if a confidence interval for the true error was also quoted. 3. Unless one can be absolutely sure that no bias exists between the replicate measurements, Dahlberg's formula should be avoided and the MME formula used instead.

Hospital readmissions depend on numerous factors. Automated risk calculation using electronic health record (EHR) data could allow targeting care to prevent them. EHRs usually are incomplete with respect to data relevant to readmissions prediction. Lack of standard data representations in EHRs restricts generalizability of predictive models. We propose developing such models by first generating derived variables that characterize clinical phenotype. This reduces the number of variables, reduces noise, introduces clinical knowledge into model building, and abstracts away the underlying data representation, thus facilitating use of standard data mining algorithms. We combined this pre-processing step with a random forest algorithm to compute risk for readmission within 30 days for patients in ten disease categories. Results were promising for encounters that our algorithm assigned very high or very low risk. Assigning patients to either of these two risk groups could be of value to patient care teams aiming to prevent readmissions.

This paper introduces a novel concept for creating an ensemble of classifiers. The concept is based on generating an ensemble of classifiers through clustering of data at multiple layers. The ensemble classifier model generates a set of alternative clustering of a dataset at different layers by randomly initializing the clustering parameters and trains a set of base classifiers on the patterns at different clusters in different layers. A test pattern is classified by first finding the appropriate cluster at each layer and then using the corresponding base classifier. The decisions obtained at different layers are fused into a final verdict using majority voting. As the base classifiers are trained on overlapping patterns at different layers, the proposed approach achieves diversity among the individual classifiers. Identification of difficult-to-classify patterns through clustering as well as achievement of diversity through layering leads to better classification results as evidenced from the experimental results.

This paper describes an artificial neuron structure and an efficient learning procedure in the complex domain. This artificial neuron aims at incorporating an improved aggregation operation on the complex-valued signals. The aggregation operation is based on the idea underlying the weighted root-power mean of input signals. This aggregation operation allows modeling the degree of compensation in a natural manner and includes various aggregation operations as its special cases. The complex resilient propagation algorithm ([Formula: see text]-RPROP) with error-dependent weight backtracking step accelerates the training speed significantly and provides better approximation accuracy. Finally, performance evaluation of the proposed complex root-power mean neuron with the [Formula: see text]-RPROP learning algorithm on various typical examples is given to understand the motivation.

This paper proposes a hybrid multilogistic methodology, named logistic regression using initial and radial basis function (RBF) covariates. The process for obtaining the coefficients is carried out in three steps. First, an evolutionary programming (EP) algorithm is applied, in order to produce an RBF neural network (RBFNN) with a reduced number of RBF transformations and the simplest structure possible. Then, the initial attribute space (or, as commonly known as in logistic regression literature, the covariate space) is transformed by adding the nonlinear transformations of the input variables given by the RBFs of the best individual in the final generation. Finally, a maximum likelihood optimization method determines the coefficients associated with a multilogistic regression model built in this augmented covariate space. In this final step, two different multilogistic regression algorithms are applied: one considers all initial and RBF covariates (multilogistic initial-RBF regression) and the other one incrementally constructs the model and applies cross validation, resulting in an automatic covariate selection [simplelogistic initial-RBF regression (SLIRBF)]. Both methods include a regularization parameter, which has been also optimized. The methodology proposed is tested using 18 benchmark classification problems from well-known machine learning problems and two real agronomical problems. The results are compared with the corresponding multilogistic regression methods applied to the initial covariate space, to the RBFNNs obtained by the EP algorithm, and to other probabilistic classifiers, including different RBFNN design methods [e.g., relaxed variable kernel density estimation, support vector machines, a sparse classifier (sparse multinomial logistic regression)] and a procedure similar to SLIRBF but using product unit basis functions. The SLIRBF models are found to be competitive when compared with the corresponding multilogistic regression methods and the RBFEP method. A measure of statistical significance is used, which indicates that SLIRBF reaches the state of the art.

Computational and biological systems are often distributed so that processors (cells) jointly solve a task, without any of them receiving all inputs or observing all outputs. Maximal independent set (MIS) selection is a fundamental distributed computing procedure that seeks to elect a set of local leaders in a network. A variant of this problem is solved during the development of the fly's nervous system, when sensory organ precursor (SOP) cells are chosen. By studying SOP selection, we derived a fast algorithm for MIS selection that combines two attractive features. First, processors do not need to know their degree; second, it has an optimal message complexity while only using one-bit messages. Our findings suggest that simple and efficient algorithms can be developed on the basis of biologically derived insights.

In this paper, we propose an extension of a self-organizing map called self-organizing multilayer perceptron (SOMLP) whose purpose is to achieve quantization of spaces of functions. Based on the use of multilayer perceptron networks, SOMLP comprises the unsupervised as well as supervised learning algorithms. We demonstrate that it is possible to use the commonly used vector quantization algorithms (LVQ algorithms) to build new algorithms called functional quantization algorithms (LFQ algorithms). The SOMLP can be used to model nonlinear and/or nonstationary complex dynamic processes, such as speech signals. While most of the functional data analysis (FDA) research is based on B-spline or similar univariate functions, the SOMLP algorithm allows quantization of function with high dimensional input space. As a consequence, classical FDA methods can be outperformed by increasing the dimensionality of the input space of the functions under analysis. Experiments on artificial and real world examples are presented which illustrate the potential of this approach.