Interoperability of GADU in using heterogeneous grid resources for bioinformatics applications.

Bioinformatics tools used for efficient and computationally intensive analysis of genetic sequences require large-scale computational resources to accommodate the growing data. Grid computational resources such as the Open Science Grid and TeraGrid have proved useful for scientific discovery. The genome analysis and database update system (GADU) is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications. This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids. The paper describes the resource-independent configuration of GADU using the Pegasus-based virtual data system that makes high-throughput computational tools interoperable on heterogeneous Grid resources. The paper also highlights the features implemented to make GADU a gateway to computationally intensive bioinformatics applications on the Grid. The paper will not go into the details of problems involved or the lessons learned in using individual Grid resources as it has already been published in our paper on genome analysis research environment (GNARE) and will focus primarily on the architecture that makes GADU resource independent and interoperable across heterogeneous Grid resources.     

BacMam recombinant baculoviruses in G protein-coupled receptor drug discovery

With completion of the sequencing of the human and mouse genomes, the primary sequences of close to 400 non-olfactory G protein-coupled receptors (GPCRs) have been determined. There are intensive efforts within the pharmaceutical industry to discover and develop new therapeutic agents acting via GPCRs. In addition, there is a concerted effort to identify potential new drug targets from the remaining 150+orphan GPCRs through the identification of their ligands. Access to functionally expressed recombinant receptors underpins both of these key drug discovery activities. Typically, GPCR drug discovery screening activities are carried out using mammalian cell lines stably expressing the target of interest. The influx of new receptor sequences originating from genomic sequencing efforts has caused a shift toward wider applications of transient rather than stable expression systems, especially in support of assays for orphan receptor ligand screening. Recombinant baculoviruses in which the polyhedrin promoter has been replaced with a mammalian promoter, termed BacMam viruses, were originally designed as potential new gene therapy delivery vehicles. This same technology offers numerous advantages as a transient expression system in the assay of membrane-expressed drug targets, including GPCRs. Data presented show that BacMam can be used rapidly to generate robust and pharmacologically authentic GPCR assays in several formats, with the potential to transform drug discovery screening processes for this gene family.     

Real-time motion compensation, image formation and image enhancement of moving targets in ISAR and SAR using S-methodbased approach

The commonly used technique for inverse synthetic aperture radar (ISAR)/synthetic aperture radar signal analysis is a two-dimensional Fourier transform (FT), which results in an image of the target's reflectivity mapped onto a range and cross-range plane. However, in cases where the line-of-sight projections of the target's point velocities change or there is uncompensated movement within the coherent integration time, the FT produces blurred images. For target recognition applications, mainly those in military surveillance and reconnaissance operations, a blurred ISAR image has to be refocused quickly so that it can be used for real-time target identification. Two standard techniques used for improvement of blurred ISAR images are motion compensation and the use of quadratic time-frequency representations. Both are computationally intensive. The authors present an effective quadratic time-frequency representation, the S-method. This approach performs better than the Fourier transform method by drastically improving images of fast manoeuvring targets and by increasing the SNR in both low and high noise environments. These advantages are a result of the S-method's ability to automatically compensate for quadratic and all even higher-order phase terms. Thus, targets with constant acceleration will undergo full motion compensation and their point scatterers will each be localised. It should be noted that the source of the quadratic term can come not only from acceleration, but also from non-uniform rotational motion and the cosine term in wide-angle imaging. The method is also computationally simple, requiring only slight modifications to the existing FT-based algorithm. The effectiveness of the S-method is demonstrated through application to simulated and experimental data sets.     

Analysis of Genomics and Proteomics Using DSP Techniques

With the enormous amount of data that is available in the public domain, signal processing concepts are playing an important role in genomic and proteomic data processing. The binary sequence method is well known in the literature for genomic signal processing. As an alternative to the binary sequence method, this paper presents a new view to the genomic sequence processing with the electron–ion interaction potential (EIIP) values for nulcleotides. The efficacy of the EIIP values-based method is demonstrated through implementation results for the prediction of the gene F56F11.4 with five exons and for cystic-fibrosis gene identification. The biological function of a protein is determined by the amino-acid sequence within the protein. Identification of the amino acids (hot spots) that contribute to the characteristic frequency characterizing a particular biological function is an important task in the protein sequence analysis. Hence, using EIIP values for amino acids, this paper presents a continuous-wavelet transform approach using the modified Morlet wavelet for the identification of active sites (hot spots) in a protein sequence. The efficacy of the approach is illustrated through implementation results on hemoglobin human $alpha $, human immunodeficiency virus, and oncogene protein sequences.      

溶液中微米级异物目标视觉检测技术

提出了一种利用机器视觉技术对溶液中μm级异物微粒进行检测并统计粒径信息的新方法。首先,建立溶液离心旋转急停后其中异物粒子的运动轨迹数学模型;然后,提取溶液视觉图像序列中每个可能目标的有效特征,通过特征匹配得到帧间若干可能目标的运动轨迹,根据异物目标与背景噪声等伪目标轨迹的差异进行甄别检测;最后,对视觉系统进行标定,确定检测到的异物目标粒径大小及各区间微粒数量。实验表明,该技术检测精度能够到达10μm,且具有较高的检测准确率。     

Solution of large dense complex matrix equations using a fastFourier transform (FFT)-based wavelet-like methodology

Wavelet-like transformations have been used in the past to compress dense large matrices into a sparse system. However, they generally are implemented through a finite impulse response filter realized through the formulation of Daubechies (1992). A method is proposed to use a very high order filter (namely an ideal one) and use the computationally efficient fast Fourier transform (FFT) to carry out the multiresolution analysis. The goal here is to reduce the redundancy in the system and also guarantee that the wavelet coefficients drop off much faster. Hence, the efficiency of the new procedure becomes clear for very high order filters. The advantage of the FFT-based procedure utilizing ideal filters is that it can be computationally efficient and for very large matrices may yield a sparse matrix. However, this is achieved, as well known in the literature, at the expense of robustness, which may lead to a larger reconstruction error due to the presence of the Gibb's phenomenon. Numerical examples are presented to illustrate the efficiency of this procedure as conjectured in the literature     

Functional assays for identifying ligands at orphan G protein-coupled receptors

The superfamily of G protein-coupled receptors (GPCRs; 7TMs) is one of the largest families of genes identified in humans, and has a proven history of being an excellent source of drug targets. The near completion of the human genome sequencing project has allowed the identification of a plethora of sequences encoding "orphan" GPCRs--putative receptors whose natural ligand(s) remain to be discovered. In many cases, the level of sequence homology with known receptors is insufficient to be able to predict the natural ligand for these orphan receptors, although it is usually possible to determine the likely nature of the cognate ligand e.g. peptide, lipid, nucleotide etc. Deorphanizing these novel GPCRs and evaluating their biological function has become a major target of many of the major pharmaceutical companies as well as several academic groups. Since 1995 more than 50 ligands for orphan GPCRs have been discovered by using the orphan receptor as a biosensor and screening candidate compounds looking for a biological response (the so-called "reverse pharmacology" approach). Identification of the natural ligands for these receptors marks the beginning of the process of understanding the biology of these newly discovered signalling systems and the development of novel therapies targeted at them. This article will focus on the functional assays which have been used to discover ligands for orphan GPCRs.     

基于网络药理学及分子对接探讨怀牛膝 治疗高血压的物质基础和作用机制

摘 要:目的 基于网络药理学方法探讨怀牛膝治疗高血压的作用机制。方法 通过中药系统药理学分析平台（TCMSP）筛选怀牛膝的有效成分及相应的靶蛋白，通过Genecards、OMIM数据库获取高血压的靶点，利用Venn在线软件获取怀牛膝 高血压交集靶点，运用Cytoscape 3.7.2软件构建“化合物 靶点 疾病”网络图。使用String数据库绘制蛋白互作（PPI）网络，利用David数据库和R语言3.6.3中clusterProfiler包对关键靶点进行GO功能富集及KEGG通路分析，通过分子对接技术将怀牛膝主要活性成分与关键靶点进行对接验证。结果 共筛选出怀牛膝潜在活性成分16个，有效作用靶点183个。通过Venn图获得76个药物疾病共同靶点，PPI网络发现IL6、AKT1、VEGFA、CCL2、MMP9、NOS3、PTGS2等可能是怀牛膝治疗高血压的关键靶点。GO分析共包含396条富集结果，其中生物过程307条，分子功能54条，细胞组成35条。KEGG通路分析发现60个条目。分子对接筛选得到与靶点有结合潜力的化合物。结论 怀牛膝通过“多成分 多靶点 多途径”发挥降压作用，为深入研究其物质基础及作用机制奠定了基础，也为后期实验验证和临床应用提供了相关依据。     

Random and pseudorandom inputs for Volterra filter identification

This paper studies input signals for the identification of nonlinear discrete-time systems modeled via a truncated Volterra series representation. A Kronecker product representation of the truncated Volterra series is used to study the persistence of excitation (PE) conditions for this model. It is shown that i.i.d. sequences and deterministic pseudorandom multilevel sequences (PRMS's) are PE for a truncated Volterra series with nonlinearities of polynomial degree N if and only if the sequences take on N+1 or more distinct levels. It is well known that polynomial regression models, such as the Volterra series, suffer from severe ill-conditioning if the degree of the polynomial is large. The condition number of the data matrix corresponding to the truncated Volterra series, for both PRMS and i.i.d. inputs, is characterized in terms of the system memory length and order of nonlinearity. Hence, the trade-off between model complexity and ill-conditioning is described mathematically. A computationally efficient least squares identification algorithm based on PRMS or i.i.d. inputs is developed that avoids directly computing the inverse of the correlation-matrix. In many applications, short data records are used in which case it is demonstrated that Volterra filter identification is much more accurate using PRMS inputs rather than Gaussian white noise inputs     

基于小波多尺度分析及Fisher分割的红外弱小目标检测

介绍一种新的红外图像序列中的弱小目标检测方法，利用小波多分辨特性，对图像进行预处理，以抑制背景杂波；利用改进的Fisher算法，对经预处理后的图像进行分割，最终将目标从背景中分离出来；对相邻帧进行差分运算，估计目标的运动轨迹采用本文方法与类别方差自动门限法，对大量的红外弱小目标进行了检测，实验对比结果表明了该算法的有效性。     

Three-level m sequences

Those properties of 3-level m sequences which are likely to prove useful in the crosscorrelation method of system dynamic analysis are listed. The use of 3-level m sequence signals in the identification of nonlinear systems is discussed, and it is shown that the number of crosscorrelation experiments required to determine the impulse response of the linear channel of a system with an amplitude nonlinearity is reduced by the use of these signals.     

Bent序列和Gold-like序列的构造

该文研究Bent序列和Gold-like序列, 设计了3类快速生成的Bent序列, 此外, 基于Klapper(1993)对几何序列相关性的分析, 递归地构造了一类Gold-like序列, 所得的Gold-like序列涵括了Khoo, Gong和Stinson(2002)递归生成的Gold-like序列。 根据Olsen, Scholtz和Welch(1982)给出的Bent序列簇的构造方法, 该文得到的Bent序列可以迅速地构造Bent序列簇。此外, 该文得到的Gold-like序列可以用来设计大周期的扩频序列簇。     

Transform domain approach for sequence design and its applications

Many communication and radar systems necessitate the use of sequences with desired autocorrelation (AC) and cross-correlation (CC) properties. This paper presents a systematic method based on the transform domain characterization of the AC and CC constraints to generate new families of sequences that meet the requirements. We demonstrate that some existing families can easily be generated by our approach. Our approach, however, renders new families of sequences with less constraints. The proposed approach is elementary and can easily be extended to synthesize two-dimensional arrays or even higher dimensional waveforms that possess the desired multidimensional correlation properties. A preamble structure based on our new sequence family is suggested and performance of frequency offset and channel estimation algorithms for a multiantenna orthogonal frequency-division multiplexing (OFDM) system that uses such a preamble is given.     

A Multiple Input-Multiple Output (MIMO) Adaptive Decision Feedback Equalizer (DFE) with Cancellation for Wideband Space-Time Communications

A new receiver structure able to deliver high data rates in a multiple input-multiple output (MIMO) frequency selective wireless environment is proposed and investigated in this paper. The optimal solution for the finite-length MIMO decision feedback equalizer (DFE) with cancellation is derived and used to illustrate the potential of this architecture for space-time communications. LMS and RLS adaptive algorithms are also presented for the MIMO architecture. The convergence and performance of these adaptive algorithms is analyzed through simulation results. The proposed adaptive solutions do not require channel identification, are less computationally intensive than their optimal solution counterpart, and allow the proposed MIMO receiver to seamlessly adapt to channel changes.     

数字混沌扩频序列的盲估计

混沌序列具有非线性、宽带类噪声、大的码族、任意长的周期且容易产生的特性,因此在扩频通信系统中很有实用价值。本文将文献[1]中对伪随机扩频序列盲估计的方法推广应用到混沌扩频通信中,并对其不足提出了改进方法。在只知道扩频码周期而无其它任何先验知识的条件下,利用特征值分析的方法可以对数字混沌直扩序列进行盲估计,仿真实验证明了该方法的有效性。     

Performance analysis of an automated E-pulse target discriminationscheme

An automated E-pulse scheme for target discrimination was initially presented by Ilavarasan et al. (1993) without an analytic performance evaluation. Assuming that target responses are contaminated with white Gaussian noise, an automated E-pulse scheme is rigorously analyzed to yield a reliable measure of performance. The discrimination performance of this automated E-pulse scheme is determined quantitatively through the use of energy discrimination numbers (EDNs). Statistics of the EDNs are evaluated analytically to derive the probability of correct identification. The probability of identification as a function of signal-to-noise ratio (SNR) is evaluated using the theoretical scattering data for all potential targets to predict the performance of the automated E-pulse scheme. These theoretical results are corroborated by direct simulation of the discrimination scheme. In addition, the probability density functions of the EDNs are presented providing new physical insights into E-pulse performance as a function of target geometries and SNR     

Multipath Diversity Reception of Spread-Spectrum Multiple-Access Communications

The analysis of a multipath-combining receiver for directsequence spread-spectrum communications through a specular multipath channel is developed. The analysis applies to systems that use quadriphase-shift-keyed, offset quadriphase-shift-keyed, minimum-shiftkeyed, or binary phase-shift-keyed modulation. The measures of performance are the signal-to-noise ratio and approximations to the error probability involving the signal-to-noise ratio. The performance of a multipath-combining receiver is determined not only for the case of a single transmitter, but also for the case of multiple interfering transmit, ters. Furthermore, the performance of the system is determined in terms of parameters of the signature sequences. These parameters can be used as guides in selecting signature sequences for the system. Results are also given for the case of randomly generated signature sequences.     

红外图像序列中运动弱小目标检测的方法研究

研究在红外图像序列中检测运动弱小目标的方法。首先通过高通或形态学滤波进行图像预处理，进一步用似然比检测分割出侯选目标，考虑到环境干扰造成的目标在某一帧暂时消失的情况，提出了利用目标运动特征通过选择合适的邻域判决条件并结合图像流分析提取运动弱小目标的一种方法。模拟实验表明该方法能够准确高效地检测出运动弱小目标。     

Effect of sequence selection on MAI suppression in limited spreading CDMA systems

Increasingly, spread spectrum systems are being proposed which support a range of data rates and traffic types in a band limited environment. One way to achieve a range of data rates with fixed bandwidth is to allow the use of different processing gains. If the range of data rates supported is large, the lower bound on the processing gain can become quite small. Receivers based on LMMSE algorithms offer high efficiency for CDMA systems through interference suppression, however at small processing gains, the sequence set correlation properties prove to be a significant limitation on the system efficiency. This paper provides examples of sets of short length spreading sequences which have good auto-correlation (AC) and cross-correlation (CC) properties which are essential to allow relatively high system efficiency. A CDMA system using an LMMSE receiver is examined with selected short length sets to demonstrate the application of the sequences. The sets proposed are compared to system performance when using well known sequence families. This revised version was published online in July 2006 with corrections to the Cover Date.