MOTIVATION: MIB2 (metal ion-binding) attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types. RESULTS: MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more MIB residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://bioinfo.cmu.edu.tw/MIB2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors. RESULTS: Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy. CONCLUSIONS: The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/ .

Applying quantum processors to model a high-dimensional function approximator is a typical method in quantum machine learning with potential advantage. It is conjectured that the unitarity of quantum circuits provides possible regularization to avoid overfitting. However, it is not clear how the regularization interplays with the expressibility under the limitation of current Noisy-Intermediate Scale Quantum devices. In this article, we perform simulations and theoretical analysis of the quantum circuit learning problem with hardware-efficient ansatz. Thorough numerical simulations show that the expressibility and generalization error scaling of the ansatz saturate when the circuit depth increases, implying the automatic regularization to avoid the overfitting issue in the quantum circuit learning scenario. This observation is supported by the theory on PAC learnability, which proves that VC dimension is upper bounded due to the locality and unitarity of the hardware-efficient ansatz. Our study provides supporting evidence for automatic regularization by unitarity to suppress overfitting and guidelines for possible performance improvement under hardware constraints.

Controlling the gripping force on fragile objects has been a challenging task for industrial grippers. The solution often requires an electric gripper with embedded force sensors and control feedback. This approach is costly and leads to extra gripper complexity. To avoid damage while handling fragile objects, this paper presents a novel force regulation mechanism (FRM) to be installed on pneumatic grippers. Without using additional sensors and control, the FRM can passively produce an adjustable contact force between the gripper jaws and objects of various sizes. Together with pneumatic grippers that have a higher gripping speed, lower cost, and simpler structure, this approach offers a more attractive solution than the use of electric grippers. In this paper, the design and analysis of the FRM are presented. A prototype of the FRM is illustrated to demonstrate the effectiveness and accuracy of force regulation. This novel mechanism is expected to serve as a reliable alternative for fragile object manipulation. Note to Practitioners-Pneumatic grippers are popular due to their low cost and simple structure. However, it is difficult to control the gripping force to handle fragile objects without damage. The FRM has a small size and can be easily installed on pneumatic grippers to provide fast force regulation. The gripping force depends on axial preload of the FRM rather than air pressure of the gripper. Axial preload is passively regulated using a screw or spacer. No additional source of power or sensor is required. The FRM has a large force adjustment range and can grip objects of various sizes using the same force. Applications include the automation in electronics, food, agricultural, and medical industries.

Without STP and LLDP, we propose a new approach to find faster paths between the source and the destination and fully utilize the links between switches under the Software Defined Network paradigm. To find round-trip path with lighter load, we design a mechanism to compose special ARP packets for exploring the routing path and avoid broadcast storm by dropping late or duplicate packets. Meanwhile, the controller can carefully regulate other packets without affecting the behavior of the special packets. The evaluation results with the Clos-like network topology show that our approach can be used to improve the performance of transmission throughput. We believe our method is very suitable, especially, for a dynamic network environment, where links are up and down frequently. Our implementation can be seen as an instance showing the flexibility of SDN.

A new soft switching resonant converter is presented in this paper to reduce the switching losses on power MOSFETs and overcome the reverse recovery losses on rectifier diodes. Two half-bridge legs connected in series and two split capacitors are adopted to limit the voltage stress of each MOSFET at half input voltage and to reduce the current rating of transformer windings and passive components at output side. A flying capacitor is connected between two half-bridge legs in order to automatically balance two input capacitor voltages. Therefore, MOSFETs with low voltage stress can be used at high input voltage applications. The resonant converter is adopted in each half-bridge circuit to reduce the switching losses of active devices. Finally, experiments based on a laboratory prototype are provided to verify the circuit performance.

In this paper, the problem of estimating the asymptotic stability region (ASR) of uncertain nonlinear systems is considered. Our approach is based on Takagi-Sugeno (T-S) fuzzy model and variable structure control (VSC) technique. To simplify the problem, we use a state transformation to reduce the system order of the T-S fuzzy systems. Then we design the sliding surface for the transformed system. By the Lyaponov stability theorem, the ASR can be estimated. A simulation example is presented to verify the effectiveness of the proposed scheme.

In this paper, a computational photography system is utilized to sample 4D light fields. The system is implemented using a normal DSLR camera with a mask printed using Kodak LVT technique. We reconfigure the camera by inserting a pinhole array mask in front of the sensors. The mask blocks part of light and samples the rest that passes through the pinholes. With these 4D light field data, the refocused images are obtained by rearranging the captured sub-images. The range of refocusing is also studied to avoid diffraction blurring effect in the refocused images.

In this paper, depth estimation of light field data obtained from the pinhole-masked camera system is proposed. In the first approach, the sharpness of objects in the refocused images is evaluated using the FFT method, from which an empirical formula can be obtained to estimate the depth of objects. The second method uses the raw data in sub-images to calculate an index, Average Absolute Difference (AAD), for depth estimation purposes. The advantages and disadvantages of two proposed approaches are discussed and compared.

BACKGROUND: Template selection and target-template alignment are critical steps for template-based modeling (TBM) methods. To identify the template for the twilight zone of 15~25% sequence similarity between targets and templates is still difficulty for template-based protein structure prediction. This study presents the (PS)2-v2 server, based on our original server with numerous enhancements and modifications, to improve reliability and applicability. RESULTS: To detect homologous proteins with remote similarity, the (PS)2-v2 server utilizes the S2A2 matrix, which is a 60 x 60 substitution matrix using the secondary structure propensities of 20 amino acids, and the position-specific sequence profile (PSSM) generated by PSI-BLAST. In addition, our server uses multiple templates and multiple models to build and assess models. Our method was evaluated on the Lindahl benchmark for fold recognition and ProSup benchmark for sequence alignment. Evaluation results indicated that our method outperforms sequence-profile approaches, and had comparable performance to that of structure-based methods on these benchmarks. Finally, we tested our method using the 154 TBM targets of the CASP8 (Critical Assessment of Techniques for Protein Structure Prediction) dataset. Experimental results show that (PS)2-v2 is ranked 6th among 72 severs and is faster than the top-rank five serves, which utilize ab initio methods. CONCLUSION: Experimental results demonstrate that (PS)2-v2 with the S2A2 matrix is useful for template selections and target-template alignments by blending the amino acid and structural propensities. The multiple-template and multiple-model strategies are able to significantly improve the accuracies for target-template alignments in the twilight zone. We believe that this server is useful in structure prediction and modeling, especially in detecting homologous templates with sequence similarity in the twilight zone.

This paper presents a unified systolic architecture for inter and intra predictions in H.264/AVC decoder. To increase hardware utilization and minimize cost, we combine inter and intra predictions by a reprogrammable FIR filter, which is further implemented using systolic array. For intra prediction, the boundary pixels are reshuffled before feeding into the systolic array. For inter prediction, the 2-D interpolation is conducted through separable 1-D filtering. As compared with the state-of-the-art approaches, our architecture provides higher performance while maintaining relatively lower cost and input bandwidth. Specifically, up to 4x throughput improvement has been achieved. Moreover, the input bandwidth is significantly reduced. Further, combining inter and intra predictions saves the cost by 22~88%.

The paper describes a biomimetic autonomous underwater vehicle (BAUV) that mimics the shape and behavior of fish. The swimming motion of the BAUV is achieved using an oscillating body. The body spline is specified by a set of parameters, which are utilized using genetic algorithm (Gas) by evaluating a fitness function of the optimization which is defined as the ratio of the forward velocity to the required driving power of the joint motors. The resulting body spline is found to be better than all other body splines at all tail-beating frequencies. Each body spline has an optimal tail-beating frequency.

The authors present a novel and efficient maximum-likelihood soft-decision decoding algorithm for linear block codes. The approach used here converts the decoding problem into a search problem through a graph that is a trellis for an equivalent code of the transmitted code. A generalized Dijkstra's algorithm, which uses a priority-first search strategy, is employed to search through this graph. This search is guided by an evaluation function f defined to take advantage of the information provided by the received vector and the inherent properties of the transmitted code. This function f is used to reduce drastically the search space and to make the decoding efforts of this decoding algorithm adaptable to the noise level. For example, for most real channels of the 35 000 samples tried, simulation results for the (128,64) binary extended BCH code show that the proposed decoding algorithm is fifteen orders of magnitude more efficient in time and in space than that proposed by Wolf (1978). Simulation results for the (104, 52) binary extended quadratic residue code are also given.>