Combined hardware–software multi-parallel prefiltering on the Convey HC-1 for fast homology detection

Protein databases used in research are huge and still grow at a fast pace. Many comparisons need to be done when searching similar (homologous) sequences for a given query sequence in these databases. Comparing a query sequence against all sequences of a huge database using the well-known Smith–Waterman algorithm is very time-consuming. Hidden Markov Models pose an opportunity for reducing the number of entries of a database and also enable to find distantly homologous sequences. Fewer entries are achieved by clustering similar sequences in a Hidden Markov Model. Such an approach is used by the bioinformatics tool HHblits. To further reduce the runtime, HHblits uses two-level prefiltering to reduce the number of time-consuming Viterbi comparisons. Still, prefiltering is very time-consuming. Highly parallel architectures and huge bandwidth are required for processing and transferring the massive amounts of data. In this article, we present an approach exploiting the reconfigurable, hybrid computer architecture Convey HC-1 for migrating the most time-consuming part. The Convey HC-1 with four FPGAs and high memory bandwidth of up to 76.8 GB/s serves as the platform of choice. Other bioinformatics applications have already been successfully supported by the HC-1. Limited by FPGA size only, we present a design that calculates four first-level prefiltering scores per FPGA concurrently, i.e. 16 calculations in total. This score calculation for the query profile against database sequences is done by a modified Smith–Waterman scheme that is internally parallelized 128 times in contrast to the original Streaming ‘Single Instruction Multiple Data (SIMD)’ Extensions (SSE)-supported implementation where only 16-fold parallelism can be exploited and where memory bandwidth poses the limiting factor. Preloading the query profile, we are able to transform the memory-bound implementation to a compute- and resource-bound FPGA design. We tightly integrated the FPGA-based coprocessor into the hybrid computing system by employing task-parallelism for the two-level prefiltering. Despite much lower clock rates, the FPGAs outperform SSE-based execution for the calculation of the prefiltering scores by a factor of 7.9.     

Rapid detection of viable Bacillus cereus emetic and enterotoxic strains in food by coupling propidium monoazide and multiplex PCR (PMA-mPCR)

Bacillus cereus can cause emetic and diarrheal food poisoning. It is widespread in nature and therefore, considered a major foodborne pathogen. To develop a sensitive and reliable assay for detecting enterotoxin genes (nheA, entFM, hblD, cytK) and emetic toxin (ces), specific primers each targeting one individual gene were designed. Propidium monoazide (PMA) was coupled with the developed multiplex PCR (mPCR) for the detection of viable B. cereus. The inclusivity and exclusivity of the PMA-mPCR was confirmed using a panel of 44 strains including 17 emetic and 9 enterotoxic B. cereus reference strains and 18 non-target strains. The limit of detection (LOD) without PMA treatment in pure DNA was 2 pg/reaction tube. The LOD of mPCR assay in pure heat-killed dead bacteria was 4.0 × 10² CFU/mL. Also, the LOD on the viable bacteria with or without PMA treatment was similar (3.8 × 10² CFU/mL) showing that the PMA treatment did not significantly decrease sensitivity. Finally, the newly developed PMA-mPCR successfully detected 4.8 × 10³ and 3.6 × 10³ CFU/g of viable B. cereus F4810/72 (emetic) and B. cereus ATCC 12480 (enterotoxic) reference strains, respectively, in food samples. Hence, this study combines PMA and mPCR to detect viable B. cereus with a wide range of toxin detection (5 toxins). Thus, the novel PMA-mPCR assay developed in this study is a rapid and efficient diagnostic tool for the monitoring of viable B. cereus in food samples and potentially other samples via appropriate DNA extraction.     

不同晶相结构ZrO2负载铜基催化剂用于二乙醇胺脱氢反应

通过制备不同晶相结构〔单斜相(m-ZrO_2)、四方相(t-ZrO_2)和无定型(a-ZrO_2)〕ZrO_2载体,再通过沉积沉淀法制得Cu/m-ZrO_2、Cu/t-ZrO_2和Cu/a-ZrO_2催化剂,分别用于催化二乙醇胺脱氢合成亚氨基二乙酸反应。采用XRD、氮气物理吸附脱附、XPS、H_2-TPR、CO_2-TPD对催化剂的结构进行了表征。结果表明,Cu/m-ZrO_2催化剂界面更加有利于Cu~+/Cu~0稳定存在,具有更多的碱性位点,且抗氧化性较好。在二乙醇胺脱氢反应中,Cu/m-ZrO_2催化剂性能最好,反应时间为2.5 h,亚氨基二乙酸收率为97.64%。     

Formulation of sage essential oil (Salvia officinalis,L.) monoterpenes into chitosan hydrogels and permeation study with GC-MS analysis

This study deals with the formulation of natural drugs into hydrogels. For the first time, compounds from the sage essential oil were formulated into chitosan hydrogels. A sample preparation procedure for hydrophobic volatile analytes present in a hydrophilic water matrix along with an analytical method based on the gas chromatography coupled with the mass spectrometry (GC-MS) was developed and applied for the evaluation of the identity and quantity of essential oil components in the hydrogels and saline samples. The experimental results revealed that the chitosan hydrogels are suitable for the formulation of sage essential oil. The monoterpene release can be effectively controlled by both chitosan and caffeine concentration in the hydrogels. Permeation experiment, based on a hydrogel with the optimized composition [3.5% (w/w) sage essential oil, 2.0% (w/w) caffeine, 2.5% (w/w) chitosan and 0.1% (w/w) Tween-80] in donor compartment, saline solution in acceptor compartment, and semi-permeable cellophane membrane, demonstrated the useful permeation selectivity. Here, (according to lipophilicity) an enhanced permeation of the bicyclic monoterpenes with antiflogistic and antiseptic properties (eucalyptol, camphor and borneol) and, at the same time, suppressed permeation of toxic thujone (not exceeding its permitted applicable concentration) was observed. These properties highlight the pharmaceutical importance of the developed chitosan hydrogel formulating sage essential oil in the dermal applications.     

Parallel chaos optimization algorithm with migration and merging operation

Chaos optimization algorithm (COA) utilizes the chaotic maps to generate the pseudo-random sequences mapped as the decision variables for global optimization applications. A kind of parallel chaos optimization algorithm (PCOA) has been proposed in our former studies to improve COA. The salient feature of PCOA lies in its pseudo-parallel mechanism. However, all individuals in the PCOA search independently without utilizing the fitness and diversity information of the population. In view of the limitation of PCOA, a novel PCOA with migration and merging operation (denoted as MMO-PCOA) is proposed in this paper. Specifically, parallel individuals are randomly selected to be conducted migration and merging operation with the so far parallel solutions. Both migration and merging operation exchange information within population and produce new candidate individuals, which are different from those generated by stochastic chaotic sequences. Consequently, a good balance between exploration and exploitation can be achieved in the MMO-PCOA. The impacts of different one-dimensional maps and parallel numbers on the MMO-PCOA are also discussed. Benchmark functions and parameter identification problems are used to test the performance of the MMO-PCOA. Simulation results, compared with other optimization algorithms, show the superiority of the proposed MMO-PCOA algorithm.     

Mechanical damage characterization of glass fiber-reinforced polymer laminates by ultrasonic maps

A method for simultaneous measurement of the thickness and density for Glass Fiber-Reinforced Polymer (GFRP) laminate plates with ultrasonic waves in C-Scan mode is presented in the form of maps. The method uses three different signals in immersion pulse-echo C-Scan mode. The maps obtained based on the density show the heterogeneity of the material at high resolution at the pixel level (1 × 1 mm²) and therefore they represent an efficient tool to assess and evaluate the damage of the composite structures after manufacturing and after an applied mechanical loading.     

共享交通的时空轨迹检索与群体发现

为解决共享交通下的共乘用户群体发现效率低、准确率不高问题，依据R-树原理建立GeoOD-Tree索引，并在此基础上提出以最大化共乘率为目标的群体发现策略。首先，对原始时空轨迹数据进行特征提取与标定处理，挖掘有效出行起讫点（OD）轨迹；其次，针对用户起讫点轨迹的特征，建立GeoOD-Tree索引进行有效的存储管理；最后，给出以最大化共乘行程为目标的群体发现模型，并运用K最近邻（KNN）查询对搜索空间剪枝压缩，提高群体发现效率。采用西安市近12000辆出租车营运轨迹数据，选取动态时间规整（DTW）等典型算法与所提算法在查询效率与准确率上进行性能对比分析。与DTW算法相比，所提算法的准确率提高了10.12%，查询效率提高了约15倍。实验结果表明提出的群体发现策略能有效提高共乘用户群体发现的准确率和效率，可有效提升共乘出行方式的出行率。     

An adaptive image steganographic scheme based on Noise Visibility Function and an optimal chaotic based encryption method

Steganography is the science of hiding secret message in an appropriate digital multimedia in such a way that the existence of the embedded message should be invisible to anyone apart from the sender or the intended recipient. This paper presents an irreversible scheme for hiding a secret image in the cover image that is able to improve both the visual quality and the security of the stego-image while still providing a large embedding capacity. This is achieved by a hybrid steganography scheme incorporates Noise Visibility Function (NVF) and an optimal chaotic based encryption scheme. In the embedding process, first to reduce the image distortion and to increase the embedding capacity, the payload of each region of the cover image is determined dynamically according to NVF. NVF analyzes the local image properties to identify the complex areas where more secret bits should be embedded. This ensures to maintain a high visual quality of the stego-image as well as a large embedding capacity. Second, the security of the secret image is brought about by an optimal chaotic based encryption scheme to transform the secret image into an encrypted image. Third, the optimal chaotic based encryption scheme is achieved by using a hybrid optimization of Particle Swarm Optimization (PSO) and Genetic Algorithm (GA) which is allowing us to find an optimal secret key. The optimal secret key is able to encrypt the secret image so as the rate of changes after embedding process be decreased which results in increasing the quality of the stego-image. In the extracting process, the secret image can be extracted from the stego-image losslessly without referring to the original cover image. The experimental results confirm that the proposed scheme not only has the ability to achieve a good trade-off between the payload and the stego-image quality, but also can resist against the statistics and image processing attacks.     

Multiobjective PSO based adaption of neural network topology for pixel classification in satellite imagery

The proposed work involves the multiobjective PSO based adaption of optimal neural network topology for the classification of multispectral satellite images. It is per pixel supervised classification using spectral bands (original feature space). This paper also presents a thorough experimental analysis to investigate the behavior of neural network classifier for given problem. Based on 1050 number of experiments, we conclude that following two critical issues needs to be addressed: (1) selection of most discriminative spectral bands and (2) determination of optimal number of nodes in hidden layer. We propose new methodology based on multiobjective particle swarm optimization (MOPSO) technique to determine discriminative spectral bands and the number of hidden layer node simultaneously. The accuracy with neural network structure thus obtained is compared with that of traditional classifiers like MLC and Euclidean classifier. The performance of proposed classifier is evaluated quantitatively using Xie-Beni and β indexes. The result shows the superiority of the proposed method to the conventional one.     

Iterative equalization combining algorithm in intersymbol interference channel

To realize joint optimization of spatial diversity and equalization combining in the intersymbol interference (ISI) channel, an iterative equalization combining algorithm is proposed. The proposed algorithm uses the coefficients of Turbo equalization to calculate the combination weights without estimating the signal to noise ratio in each diversity branch. The equalized symbols from different diversity branches are combined, and the extrinsic information output from the decoder is fed back to the equalizers, so as to exchange soft information between the equalizers and the decoder. The performance of the proposed algorithm is analyzed using the extrinsic information transfer (EXIT) chart and verified by simulations. Results show that our approach fully exploits time domain information from the multipath channel and spatial domain information from multi receiving antennas, which efficiently improve the performance of the receiver in the severe ISI channel.