Lossless filter for multiple repetitions with Hamming distance

Similarity search in texts, notably in biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been created in order to speed up the solution of the problem. However, previous filters were made for speeding up pattern matching, or for finding repetitions between two strings or occurring twice in the same string. In this paper, we present an algorithm called Nimbus for filtering strings prior to finding repetitions occurring twice or more in a string, or in two or more strings. Nimbus uses gapped seeds that are indexed with a new data structure, called a bi-factor array, that is also presented in this paper. Experimental results show that the filter can be very efficient: preprocessing with Nimbus a data set where one wants to find functional elements using a multiple local alignment tool such as Glam, the overall execution time can be reduced from 7.5 hours to 2 minutes.     

Characterization and identification of saikosaponins in crude extracts from three Bupleurum species using LC-ESI-MS

A LC-diode array detection (DAD)-ESI-MS/MS method was established for the online characterization and identification of saikosaponins (SSs) from extracts of roots of Bupleurum scorzonerifolium Willd, B. marginatum var. stenophyllum and B. komarovianum. In ESI-MS/MS spectra of SSs, [M-H](- )ions were subjected to the cleavage of glycosidic bonds and produced Y type ions, which can be used to elucidate the structures of saccharide chains and aglycones. Fragmentation of aglycones provided mass information about their major substitutions. For three structural types of SSs, type III can be easily identified by their fragmentation behaviors; while type I and II often occur as isomers and they can be discriminated by their typical UV absorption data. The only sugar ring-cross cleavage corresponding to 76 Da took place at a furanose sugar moiety. As a result, more than 75 SSs, including eight novel compounds, were identified or tentatively characterized based on their UV and mass spectra and retention times. The approach established here allows a comprehensive analysis of the SSs in the genus of Bupleurum and will be helpful for quality control of the crude materials and their related preparations.     

Analysis of the recent antipsychotic aripiprazole in human plasma by capillary electrophoresis and high-performance liquid chromatography with diode array detection

Two methods, based on the use of capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC), respectively, were developed for the analysis of the atypical antipsychotic aripiprazole in plasma of schizophrenic patients for therapeutic drug monitoring purposes. Good analytical performances were obtained with the CE method, using uncoated fused silica capillaries and a background electrolyte composed of 50 mM phosphate buffer at pH 2.5. With 20 kV voltage, aripiprazole was detectable at 214 nm within 5 min. The second analytical method, based on HPLC with diode array detection, employed a C8 reversed-phase column and a mixture of a 12.5 mM phosphate buffer, pH 3.5, containing triethylamine and acetonitrile as the mobile phase. Aripiprazole was detected at 254 nm and a complete chromatographic run lasted about 10 min. For both analytical methods loxapine was used as the internal standard and the same plasma sample pre-treatment by means of solid-phase extraction on cyano cartridges was carried out, with extraction yield values always higher than 91.3%. Linear responses for aripiprazole were obtained between 70 and 700 ng mL⁻¹ and precision assays (expressed as relative standard deviation values) were lower than 7.0%. After validation, both methods were successfully applied to human plasma samples drawn from schizophrenic patients undergoing therapy with Abilify^® tablets. Accuracy was satisfactory, with recovery value higher than 91.0%.     

Current approaches for global post-translational modification discovery and mass spectrometric analysis

More and more attention is being focused on the analysis of post-translational modifications (PTMs) on proteins as researchers are continually learning how essential they are for proper cellular function. As there are hundreds of different types of known PTMs, traditional methods of modification analysis are incapable of comprehensively monitoring for post-translational modifications, a task which is a necessity for truly understanding a cell's biology. This review highlights recent developments in novel multiplexed methods of PTM analysis including: fluorescent stain and immuno-based methods, hardware-based mass spectrometric methods and computational-based mass spectrometric methods. Many of these techniques show great promise and will likely be a valuable resource for the biological community.     

Screening of anti-HIV-1 inophyllums by HPLC-DAD of Calophyllum inophyllum leaf extracts from French Polynesia Islands

Various pyranocoumarins, calophyllolide, inophyllums B, C, G₁, G₂ and P, from Calophyllum inophyllum (Clusiaceae) leaves of French Polynesia (Austral, Marquesas, Society and Tuamotu archipelagos) have been determined in 136 leaf extracts using a high pressure liquid chromatography-UV-diode array detection (HPLC-UV-DAD) technique. Results show a wide range in chemical composition within trees growing on eighteen islands. The use of multivariate statistical analyses (PCA) shows geographical distribution of inophyllums and indicate those rich in HIV-1 active (+)-inophyllums. Inophyllum B and P contents (0.0-39.0 and 0.0-21.8 mg kg⁻¹, respectively) confirm the chemodiversity of this species within the large area of French Polynesia. The study suggests the presence of interesting chemotypes which could be used as plant source for anti-HIV-1 drugs.     

基于动态载波AM算法参量阵的DSP设计与实现

为了解决普通AM参量阵产生的解调信号质量差、效率低等问题,设计了一个动态载波AM算法。以此算法为基础设计了一个DSP处理平台,并在此平台上实现了参量阵系统。经过系统硬件和软件两方面的优化设计,保证了算法运行的实时性和稳定性。最后,使用500Hz、800Hz和1100Hz的合成波作为测试信号,测试了系统输出的波形和参量阵前方5米处的频谱。对比测得的波形和理论波形,验证了此系统能够可靠地运行。对比普通AM和动态载波AM参量阵输出信号的频谱图,验证了动态载波AM参量阵能输出更好信噪比和能量更高的解调信号。     

Interference synthesis of cross beams from sparse array北大核心CSCD

Based on principle of power synthesis of sparse array, mathematical model of spatial power combining is established. Relation between cross angle of beams and synthesis efficiency on aimed point from two antenna nodes is derived. Furthermore, the setting principle of sampling interval is analyzed for simulation experiment. Energy distributions of the useful points under different cross angles were simulated. Simulation shows that if distance between the antenna nodes and aimed point are equal, and frequency, polarization and an- tenna type are the same, synthesis efficiency relies on the cross angles of beams, shape and density on the useful points accumulation area also rely on the cross angles of beams.     

交汇测量系统线阵相机标定方法

为了提高大靶面交汇测量系统的测量准确度,分析了交汇测量原理,推导出脱靶量坐标公式.根据脱靶量公式分析其各项参量,利用几何关系建立像元坐标与偏移角度之间的映射模型.根据映射模型,利用光栅尺设计了一种针对线阵相机的标定方法,该方法不考虑相机参量,将整个光学系统看作一个整体,基于整体参量直接对像元坐标和它所对应的偏移角进行标定.实验结果表明,标定后的交汇测量系统在1.4m处的平均测量误差为0.4mm,最大测量误差优于0.6mm.该方法简单高效,可提高系统标定的速度,且标定误差满足系统交汇测量准确度的要求.     

Vortex identification in the wake of a model wind turbine array

Vortex identification techniques are used to analyse the wake of a 4 × 3 array of model wind turbines. The Q-criterion, Δ-criterion, and λ₂-criterion are applied to particle image velocimetry data gathered fore and aft of the last row centerline turbine. The Q-criterion and λ₂-criterion provide a clear indication of regions where vortical activity exists, while the Δ-criterion is not successful. Galilean decomposition, Reynolds decomposition, vorticity, and swirling strength are used to further understand the location and behaviour of the vortices. The techniques identify and display the high-magnitude vortices in high-shear zones resulting from the blade tips. Using Galilean and Reynolds decomposition, swirling motions are shown encapsuling vortex regions in agreement with the identification criteria. The Galilean decompositions selected are 20% and 50% of a convective velocity of 7 m/s. As the vortices convect downstream, the strength of the vortices decreases in magnitude, particularly in the far wake of the array, to approximately 25% of those present in the near wake. A high level of vortex activity is visualised as a result of the top tip of the wind turbine blade -- the location where the highest vertical entrainment is present. Analysing the full frame set, the Q-criterion, λ₂-criterion, and swirling strength prove comparable, while the Δ-criterion under-performs in regions of high turbulence activity, namely in the back of the turbine. Entraining flow into the turbine canopy interacting with the turbine generates high-magnitude vortices concentrated at the blade tips. The count of vortices decreases when moving from the top tip down to the wall, as well as their strength for each Galilean technique when a non-zero threshold is applied. Vortex sizes in the near wake are found comparable to turbine blade, hub, and mast dimensions. In the far wake, the resulting size of the vortices is approximately 30% of those in the near wake. These vortices increase in velocity as they convect downstream, following the mean velocity behaviour. The lowest magnitude vortices reside at the hub height in the near-wake region, where they convect at nearly half the speed of those at the blade tips.     

圆环形聚焦声场的构建与调控

提出了一种由径向振动模式的圆环形压电换能器晶片组成的圆柱形阵列换能器结构, 依据阵元激励信号的相位调控机理, 推导了圆环形聚焦声场的调控公式, 在三维空间中构建了圆环形聚焦声场, 实现了对其聚焦区域大小、聚焦圆环半径以及轴向位置移动的调控. 理论分析和仿真研究表明, 所提出的圆柱形阵列换能器实现了对圆环形聚焦声场的调控. 为检测超声、功率超声、医学超声等应用领域提供了一种可实现的新型圆环形可调控聚焦声场.