An expert protein loop refinement protocol by molecular dynamics simulations with restraints

Protein structure prediction (PSP) is a long standing problem in structural biology and bioinformatics. Within the PSP problem loop refinement is a major bottleneck. In this article we report the latest version of the CReF expert predictor system for the PSP problem with emphasis on loop refinement of the approximate 3-D structure 1ZDD_P of the Z34C mini protein predicted by CReF. We designed a loop refinement protocol based on seven molecular dynamics (MD) simulations runs at different temperatures. We found that, by letting the loop residues move freely during dynamics at 325 K and restraining the internal coordinates of the correctly predicted helical structures, while allowing them to move relative to each other, the refinement protocol was very effective in predicting an accurate loop conformation in the first 100 ps of a 1000 ps MD simulation. The quality of the predictions was confirmed by the RMSD between refined and experimental structures which varied from 0.6 to 1.3 Å. In addition, stereochemical analyses showed that 100% of all residues of the refined 1ZDD_P, including those in the loop, populates the most favorable core regions of the Ramachandran plot. Our study suggests that the proposed protocol may be suitable to refine more complex mini proteins with different classes and architectures.     

Search space reduction in QoS routing

To provide real-time service or engineer constrained-based paths, networks require the underlying routing algorithm to be able to find low-cost paths that satisfy given quality-of-service constraints. However, the problem of constrained shortest (least-cost) path routing is known to be NP-hard, and some heuristics have been proposed to find a near-optimal solution. However, these heuristics either impose relationships among the link metrics to reduce the complexity of the problem which may limit the general applicability of the heuristic, or are too costly in terms of execution time to be applicable to large networks. In this paper, we focus on solving the delay-constrained minimum-cost path problem, and present a fast algorithm to find a near-optimal solution. This algorithm, called delay-cost-constrained routing (DCCR), is a variant of the k-shortest-path algorithm. DCCR uses a new adaptive path weight function together with an additional constraint imposed on the path cost, to restrict the search space. Thus, DCCR can return a near-optimal solution in a very short time. Furthermore, we use a variant of the Lagrangian relaxation method proposed by Handler and Zang [Networks 10 (1980) 293] to further reduce the search space by using a tighter bound on path cost. This makes our algorithm more accurate and even faster. We call this improved algorithm search space reduction + DCCR (SSR + DCCR). Through extensive simulations, we confirm that SSR + DCCR performs very well compared to the optimal but very expensive solution.     

New skeleton-based approaches for Bayesian structure learning of Bayesian networks

Automatically learning the graph structure of a single Bayesian network (BN) which accurately represents the underlying multivariate probability distribution of a collection of random variables is a challenging task. But obtaining a Bayesian solution to this problem based on computing the posterior probability of the presence of any edge or any directed path between two variables or any other structural feature is a much more involved problem, since it requires averaging over all the possible graph structures. For the former problem, recent advances have shown that search + score approaches find much more accurate structures if the search is constrained by a previously inferred skeleton (i.e. a relaxed structure with undirected edges which can be inferred using local search based methods). Based on similar ideas, we propose two novel skeleton-based approaches to approximate a Bayesian solution to the BN learning problem: a new stochastic search which tries to find directed acyclic graph (DAG) structures with a non-negligible score; and a new Markov chain Monte Carlo method over the DAG space. These two approaches are based on the same idea. In a first step, both employ a previously given skeleton and build a Bayesian solution constrained by this skeleton. In a second step, using the preliminary solution, they try to obtain a new Bayesian approximation but this time in an unconstrained graph space, which is the final outcome of the methods. As shown in the experimental evaluation, this new approach strongly boosts the performance of these two standard techniques proving that the idea of employing a skeleton to constrain the model space is also a successful strategy for performing Bayesian structure learning of BNs.     

A molecular dynamics and knowledge-based computational strategy to predict native-like structures of polypeptides

One of the main research problems in structural bioinformatics is the prediction of three-dimensional structures (3-D) of polypeptides or proteins. The current rate at which amino acid sequences are identified increases much faster than the 3-D protein structure determination by experimental methods, such as X-ray diffraction and NMR techniques. The determination of protein structures is both experimentally expensive and time consuming. Predicting the correct 3-D structure of a protein molecule is an intricate and arduous task. The protein structure prediction (PSP) problem is, in computational complexity theory, an NP-complete problem. In order to reduce computing time, current efforts have targeted hybridizations between ab initio and knowledge-based methods aiming at efficient prediction of the correct structure of polypeptides. In this article we present a hybrid method for the 3-D protein structure prediction problem. An artificial neural network knowledge-based method that predicts approximated 3-D protein structures is combined with an ab initio strategy. Molecular dynamics (MD) simulation is used to the refinement of the approximated 3-D protein structures. In the refinement step, global interactions between each pair of atoms in the molecule (including non-bond interactions) are evaluated. The developed MD protocol enables us to correct polypeptide torsion angles deviation from the predicted structures and improve their stereo-chemical quality. The obtained results shows that the time to predict native-like 3-D structures is considerably reduced. We test our computational strategy with four mini proteins whose sizes vary from 19 to 34 amino acid residues. The structures obtained at the end of 32.0 nanoseconds (ns) of MD simulation were comparable topologically to their correspondent experimental structures.     

Wind farm power prediction based on wavelet decomposition and chaotic time series

In this paper, a prediction model is proposed for wind farm power forecasting by combining the wavelet transform, chaotic time series and GM(1, 1) method. The wavelet transform is used to decompose wind farm power into several detail parts associated with high frequencies and an approximate part associated with low frequencies. The characteristic of each high frequencies signal is identified, if it is chaotic time series then use weighted one-rank local-region method to predict it. If not, use GM(1, 1) model to predict it. And the GM(1, 1) model is also used to predict the approximate part of the low frequencies. In the end, the final forecasted result for wind farm power is obtained by summing the predicted results of all extracted high frequencies and the approximate part. According to the predicted results, the proposed method can improve the prediction accuracy of the wind farm power.     

Energy-efficient bi-objective single-machine scheduling with power-down mechanism

This paper considers a single-machine scheduling problem with power-down mechanism to minimize both total energy consumption and maximum tardiness. The aim is to find an optimal processing sequence of jobs and determine if the machine should be executed a power-down operation between two consecutive jobs. To formulate the problem, a mixed-integer linear programming (MILP) model is developed. Then a basic ε − constraint method is proposed to obtain the complete Pareto front of the problem. Considering the particularity of the problem, we also develop local search, preprocessing technique and valid inequalities to strengthen the basic ε − constraint method. Finally, to obtain approximate Pareto fronts for large-size problems, we utilize the method of cluster analysis to divide the jobs into several sorted clusters according to their release times and due dates. Any job in a preceding cluster must be processed before all jobs in a subsequent cluster. Thus, the solution space is reduced significantly. Computational experiments on benchmark and randomly generated instances demonstrate the effectiveness of the proposed exact and approximation approaches.     

A neural network-based local rainfall prediction system using meteorological data on the Internet: A case study using data from the Japan Meteorological Agency

In this study, we develop and test a local rainfall (precipitation) prediction system based on artificial neural networks (ANNs). Our system can automatically obtain meteorological data used for rainfall prediction from the Internet. Meteorological data from equipment installed at a local point is also shared among users in our system. The final goal of the study was the practical use of “big data” on the Internet as well as the sharing of data among users for accurate rainfall prediction. We predicted local rainfall in regions of Japan using data from the Japan Meteorological Agency (JMA). As neural network (NN) models for the system, we used a multi-layer perceptron (MLP) with a hybrid algorithm composed of back-propagation (BP) and random optimization (RO) methods, and radial basis function network (RBFN) with a least squares method (LSM), and compared the prediction performance of the two models. Precipitation (total amount of rainfall above 0.5 mm between 12:00 and 24:00 JST (Japan standard time)) at Matsuyama, Sapporo, and Naha in 2012 was predicted by NNs using meteorological data for each city from 2011. The volume of precipitation was also predicted (total amount above 1.0 mm between 17:00 and 24:00 JST) at 16 points in Japan and compared with predictions by the JMA in order to verify the universality of the proposed system. The experimental results showed that precipitation in Japan can be predicted by the proposed method, and that the prediction performance of the MLP model was superior to that of the RBFN model for the rainfall prediction problem. However, the results were not better than those generated by the JMA. Finally, heavy rainfall (above 10 mm/h) in summer (Jun.–Sep.) afternoons (12:00–24:00 JST) in Tokyo in 2011 and 2012 was predicted using data for Tokyo between 2000 and 2010. The results showed that the volume of precipitation could be accurately predicted and the caching rate of heavy rainfall was high. This suggests that the proposed system can predict unexpected local heavy rainfalls as “guerrilla rainstorms.”     

A novel adaptive cuckoo search algorithm for intrinsic discriminant analysis based face recognition

This paper presents a novel adaptive cuckoo search (ACS) algorithm for optimization. The step size is made adaptive from the knowledge of its fitness function value and its current position in the search space. The other important feature of the ACS algorithm is its speed, which is faster than the CS algorithm. Here, an attempt is made to make the cuckoo search (CS) algorithm parameter free, without a Levy step. The proposed algorithm is validated using twenty three standard benchmark test functions. The second part of the paper proposes an efficient face recognition algorithm using ACS, principal component analysis (PCA) and intrinsic discriminant analysis (IDA). The proposed algorithms are named as PCA + IDA and ACS–IDA. Interestingly, PCA + IDA offers us a perturbation free algorithm for dimension reduction while ACS + IDA is used to find the optimal feature vectors for classification of the face images based on the IDA. For the performance analysis, we use three standard face databases—YALE, ORL, and FERET. A comparison of the proposed method with the state-of-the-art methods reveals the effectiveness of our algorithm.     

A combined neural network and genetic algorithm based approach for optimally designed femoral implant having improved primary stability

Excessive implant-bone relative micromotion is detrimental to both primary as well as long-term stability of a hip stem in cementless total hip arthroplasty (THA). The shape and geometry of the implant are known to influence the resulting post-operative micromotion. Finite element (FE)-based design evaluations are manually intensive and computationally expensive, especially when a large number of designs need to be evaluated for an optimum outcome. This study presents a predictive mathematical model based on back-propagation neural network (BPNN) to relate femoral stem design parameters to the post-operative implant-bone micromotion, with no recourse to tedious nonlinear FE analysis. The characterization of the design parameters were based on our earlier study on shape optimization of femoral implant. The BPNN led to faster prediction of the implant-bone relative micromotion as compared to the FE analysis. Using the BPNN-predicted output as the objective function, a genetic algorithm (GA) based search was performed in order to minimize post-operative micromotion, under simulated physiological loading conditions. The micromotion predicted by the neural network was found to have a significant correlation with FE calculated results (correlation coefficient R² = 0.80 for training; R² = 0.82 for test). The optimal stems, evolved from the GA search of over 12,500 designs, were found to offer improved primary stability, as compared to the initial TriLock (DePuy) design. Our predicted results favour lateral-flared designs having rectangular proximal transverse sections with greater stem-sizes.     

Experimental blood glucose interval identification of patients with type 1 diabetes

Many problems are confronted when characterizing a type 1 diabetic patient such as model mismatches, noisy inputs, measurement errors and huge variability in the glucose profiles. In this work we introduce a new identification method based on interval analysis where variability and model imprecisions are represented by an interval model as parametric uncertainty.The minimization of a composite cost index comprising: (1) the glucose envelope width predicted by the interval model, and (2) a Hausdorff-distance-based prediction error with respect to the envelope, is proposed. The method is evaluated with clinical data consisting in insulin and blood glucose reference measurements from 12 patients for four different lunchtime postprandial periods each.Following a “leave-one-day-out” cross-validation study, model prediction capabilities for validation days were encouraging (medians of: relative error = 5.45%, samples predicted = 57%, prediction width = 79.1 mg/dL). The consideration of the days with maximum patient variability represented as identification days, resulted in improved prediction capabilities for the identified model (medians of: relative error = 0.03%, samples predicted = 96.8%, prediction width = 101.3 mg/dL). Feasibility of interval models identification in the context of type 1 diabetes was demonstrated.     

GPU-based parallel vertex substitution algorithm for the p-median problem

We introduce a GPU-based parallel vertex substitution (pVS) algorithm for the p-median problem using the CUDA architecture by NVIDIA. pVS is developed based on the best profit search algorithm, an implementation of vertex substitution (VS), that is shown to produce reliable solutions for p-median problems. In our approach, each candidate solution in the entire search space is allocated to a separate thread, rather than dividing the search space into parallel subsets. This strategy maximizes the usage of GPU parallel architecture and results in a significant speedup and robust solution quality. Computationally, pVS reduces the worst case complexity from sequential VS’s O(p · n²) to O(p · (n ? p)) on each thread by parallelizing computational tasks on GPU implementation. We tested the performance of pVS on two sets of numerous test cases (including 40 network instances from OR-lib) and compared the results against a CPU-based sequential VS implementation. Our results show that pVS achieved a speed gain ranging from 10 to 57 times over the traditional VS in all test network instances.     

Guided local search as a network planning algorithm that incorporates uncertain traffic demands

A search based heuristic for the optimisation of communication networks where traffic forecasts are uncertain and the problem is NP-complete is presented. While algorithms such as genetic algorithms (GA) and simulated annealing (SA) are often used for this class of problem, this work applies a combination of newer optimisation techniques specifically: fast local search (FLS) as an improved hill climbing method and guided local search (GLS) to allow escape from local minima. The GLS + FLS combination is compared with an optimised GA and SA approaches. It is found that in terms of implementation, the parameterisation of the GLS + FLS technique is significantly simpler than that for a GA and SA. Also, the self-regularisation feature of the GLS + FLS approach provides a distinctive advantage over the other techniques which require manual parameterisation. To compare numerical performance, the three techniques were tested over a number of network sets varying in size, number of switch circuit demands (network bandwidth demands) and levels of uncertainties on the switch circuit demands. The results show that the GLS + FLS outperforms the GA and SA techniques in terms of both solution quality and optimisation speed but even more importantly GLS + FLS has significantly reduced parameterisation time.     

Analysis of the structure and morphology of fenoxycarb crystals

In this paper, we have explored the relationship between surface structure and crystal growth and morphology of fenoxycarb (FC). Experimental vs. predicted morphologies/face indices of fenoxycarb crystals are presented. Atomic-scale surface structures of the crystalline particles, derived from experimentally indexed single crystals, are also modelled. Single crystals of fenoxycarb exhibit a platelet-like morphology which closely matches predicted morphologies. The solvent choice does not significantly influence either morphology or crystal habit. The crystal morphology is dominated by the {0 0 1} faces, featuring weakly interacting aliphatic or aromatic groups at their surfaces. Two distinct modes of interaction of a FC molecule in the crystal can be observed, which appear to be principal factors governing the microscopic shape of the crystal: the relatively strong collateral and the much weaker perpendicular bonding. Both forcefield-based and quantum-chemical calculations predict that the aromatic and aliphatic terminated {0 0 1} faces have comparably high stability as a consequence of weak intermolecular bonding. Thus we predict that the most developed {0 0 1} surfaces of fenoxycarb crystals should be terminated randomly, favouring neither aliphatic nor aromatic termination.     

Design of high speed gate driver employing IZO TFTs

This paper presents a new bi-side gate driver integrated by indium-zinc-oxide thin film transistors (IZO TFTs). Our optimized operate method can achieve high speed performance by employing a lower duty ratio (25%) CK2 with its pulse located in the middle of the pulse of CK2L to fully use the bootstrapped high voltage of node Q. In addition, the size of devices is optimized by calculation and simulation, and the function of the proposed gate driver is predicted by the circuit simulation. Furthermore, the proposed gate driver with 20 stages is fabricated by the IZO TFTs process. It is shown that a 2.6 μs width pulse with good noise-suppressed characteristic can be successfully output at the condition of R_load = 6 kΩ and C_load = 150 pF. The power consumption of the proposed gate driver with 20 stages is measured as 1 mW. Hence, the proposed gate driver may be applied to the display of 4K resolution (4096 × 2160) at a frame rate of 120 Hz. Moreover, there is a good stability for the proposed gate driver under 48 h operation.     

A new discrete circuit for readout of resistive sensor arrays

In this paper, we present a method that simplifies the interconnect complexity of N × M resistive sensor arrays from N × M to N + M. In this method, we propose to use two sets of interconnection lines in row–column fashion with all the sensor elements having one of their ends connected to a row line and other end to a column line. This interconnection overloading results in crosstalk among all the elements. This crosstalk causes the spreading of information over the whole array. The proposed circuit in this method takes care of this effect by minimizing the crosstalk. The circuit makes use of the concept of virtual same potential at the inputs of an operational amplifier in negative feedback to obtain a sufficient isolation among various elements. We theoretically present the suitability of the method for small/moderate sized sensor arrays and experimentally verify the predicted behavior by lock-in-amplifier based measurements on a light dependent resistor (LDR) in a 4 × 4 resistor array. Finally, we present a successful implementation of this method on a 16 × 16 imaging array of LDR.     

An interval space reducing method for constrained problems with particle swarm optimization

In this paper, we propose a method for solving constrained optimization problems using interval analysis combined with particle swarm optimization. A set inverter via interval analysis algorithm is used to handle constraints in order to reduce constrained optimization to quasi unconstrained one. The algorithm is useful in the detection of empty search spaces, preventing useless executions of the optimization process. To improve computational efficiency, a space cleaning algorithm is used to remove solutions that are certainly not optimal. As a result, the search space becomes smaller at each step of the optimization procedure. After completing pre-processing, a modified particle swarm optimization algorithm is applied to the reduced search space to find the global optimum. The efficiency of the proposed approach is demonstrated through comprehensive experimentation involving 100 000 runs on a set of well-known benchmark constrained engineering design problems. The computational efficiency of the new method is quantified by comparing its results with other PSO variants found in the literature.     

Artificial neural network-based model for predicting VO2max from a submaximal exercise test

The goal of this study is to develop an accurate artificial neural network (ANN)-based model to predict maximal oxygen uptake (VO₂max) of fit adults from a single stage submaximal treadmill jogging test. Participants (81 males and 45 females), aged from 17 to 40 years, successfully completed a maximal graded exercise test (GXT) to determine VO₂max. The variables; gender, age, body mass, steady-state heart rate and jogging speed are used to build the ANN prediction model. Using 10-fold cross validation on the dataset, the average values of standard error of estimate (SEE), Pearson’s correlation coefficient (r) and multiple correlation coefficient (R) of the model are calculated as 1.80 ml kg^?1 min^?1, 0.95 and 0.93, respectively. Compared with the results of the other prediction models in literature that were developed using Multiple Linear Regression Analysis, the reported values of SEE, r and R in this study are considerably more accurate.     

Fast binary and multiway prefix searches for packet forwarding

Backbone routers with tens-of-gigabits-per-second links are indispensable communication devices to deploy on the Internet. The IP lookup operation is the most critical task that must be improved in routers. In this paper, we first present a systematic method to compare prefixes of different lengths. The list of prefixes can then be sorted and stored in a sequential array, which is contrary to the linked lists used in most of trie-based structures. Next, fast binary and multiway prefix searches assisted by auxiliary prefixes are proposed. We also developed a 32-bit representation to encode the prefixes of different lengths. For the large routing tables currently available on the Internet, the proposed multiway prefix search can achieve the worst-case number of memory accesses of three and four if the sizes of the CPU cache lines are 64 bytes and 32 bytes, respectively. The IPv4 simulation results show that the proposed prefix searches outperform the existing IP lookup schemes in terms of lookup times and memory consumption. The simulations using IPv6 routing tables also show the performance advantages of the proposed binary prefix searches. We also analyze the performance of the existing lookup schemes by concurrently considering the lookup speed, the update speed, and the memory consumption. Although the update speed of the proposed prefix search is worse than the dynamic routing table schemes with log(N) complexity for a table of N prefixes, our analysis shows that the overall performance of the proposed binary prefix search outperforms all the existing schemes.     

Precipitation forecasting by using wavelet-support vector machine conjunction model

A new wavelet-support vector machine conjunction model for daily precipitation forecast is proposed in this study. The conjunction method combining two methods, discrete wavelet transform and support vector machine, is compared with the single support vector machine for one-day-ahead precipitation forecasting. Daily precipitation data from Izmir and Afyon stations in Turkey are used in the study. The root mean square errors (RMSE), mean absolute errors (MAE), and correlation coefficient (R) statistics are used for the comparing criteria. The comparison results indicate that the conjunction method could increase the forecast accuracy and perform better than the single support vector machine. For the Izmir and Afyon stations, it is found that the conjunction models with RMSE=46.5 mm, MAE=13.6 mm, R=0.782 and RMSE=21.4 mm, MAE=9.0 mm, R=0.815 in test period is superior in forecasting daily precipitations than the best accurate support vector regression models with RMSE=71.6 mm, MAE=19.6 mm, R=0.276 and RMSE=38.7 mm, MAE=14.2 mm, R=0.103, respectively. The ANN method was also employed for the same data set and found that there is a slight difference between ANN and SVR methods.     

Exploitation of aeroelastic effects for drift reduction,in an all-polymer air flow sensor

This paper presents a vibration amplitude measurement method that greatly reduces the effects of baseline resistance drift in an all-polymer piezoresistive flow sensor or microtuft. The sensor fabrication is based on flexible printed circuit board (flex-PCB) technology to enable the potential for low-cost and scalable manufacture. Drift reduction is accomplished by discriminating the flow-induced vibration (‘flutter’) amplitude of the microtuft-based sensor as a function of flow velocity. Flutter peak-to-peak amplitude is measured using a microcontroller-based custom readout circuit. The fabricated sensor with the readout circuitry demonstrated a drift error of 2.8 mV/h, which corresponds to a flow-referenced drift error of 0.2 m/s of wind velocity per hour. The sensor has a sensitivity of 14.5 mV/(m/s) with less than 1% non-linearity over the velocity range of 5–16 m/s. The proposed vibration amplitude measurement method is also applied to a sensor array with a modified structure and a reduced dimension, which demonstrated a sensitivity of 13.2 mV/(m/s) with a flow-referenced drift error of 0.03 m/s of wind velocity per hour.