FPGA Implementation of Efficient CFAR Algorithm for Radar Systems.

The constant false-alarm rate (CFAR) algorithm is essential for detecting targets during radar signal processing. It has been improved to accurately detect targets, especially in nonhomogeneous environments, such as multitarget or clutter edge environments. For example, there are sort-based and variable index-based algorithms. However, these algorithms require large amounts of computation, making them difficult to apply in radar applications that require real-time target detection. We propose a new CFAR algorithm that determines the environment of a received signal through a new decision criterion and applies the optimal CFAR algorithms such as the modified variable index (MVI) and automatic censored cell averaging-based ordered data variability (ACCA-ODV). The Monte Carlo simulation results of the proposed CFAR algorithm showed a high detection probability of 93.8% in homogeneous and nonhomogeneous environments based on an SNR of 25 dB. In addition, this paper presents the hardware design, field-programmable gate array (FPGA)-based implementation, and verification results for the practical application of the proposed algorithm. We reduced the hardware complexity by time-sharing sum and square operations and by replacing division operations with multiplication operations when calculating decision parameters. We also developed a low-complexity and high-speed sorter architecture that performs sorting for the partial data in leading and lagging windows. As a result, the implementation used 8260 LUTs and 3823 registers and took 0.6 µs to operate. Compared with the previously proposed FPGA implementation results, it is confirmed that the complexity and operation speed of the proposed CFAR processor are very suitable for real-time implementation.

FPGA Implementation of an Efficient FFT Processor for FMCW Radar Signal Processing.

This paper presents the design and implementation results of an efficient fast Fourier transform (FFT) processor for frequency-modulated continuous wave (FMCW) radar signal processing. The proposed FFT processor is designed with a memory-based FFT architecture and supports variable lengths from 64 to 4096. Moreover, it is designed with a floating-point operator to prevent the performance degradation of fixed-point operators. FMCW radar signal processing requires windowing operations to increase the target detection rate by reducing clutter side lobes, magnitude calculation operations based on the FFT results to detect the target, and accumulation operations to improve the detection performance of the target. In addition, in some applications such as the measurement of vital signs, the phase of the FFT result has to be calculated. In general, only the FFT is implemented in the hardware, and the other FMCW radar signal processing is performed in the software. The proposed FFT processor implements not only the FFT, but also windowing, accumulation, and magnitude/phase calculations in the hardware. Therefore, compared with a processor implementing only the FFT, the proposed FFT processor uses 1.69 times the hardware resources but achieves an execution time 7.32 times shorter.

Moving Object Detection Based on Optical Flow Estimation and a Gaussian Mixture Model for Advanced Driver Assistance Systems.

Most approaches for moving object detection (MOD) based on computer vision are limited to stationary camera environments. In advanced driver assistance systems (ADAS), however, ego-motion is added to image frames owing to the use of a moving camera. This results in mixed motion in the image frames and makes it difficult to classify target objects and background. In this paper, we propose an efficient MOD algorithm that can cope with moving camera environments. In addition, we present a hardware design and implementation results for the real-time processing of the proposed algorithm. The proposed moving object detector was designed using hardware description language (HDL) and its real-time performance was evaluated using an FPGA based test system. Experimental results demonstrate that our design achieves better detection performance than existing MOD systems. The proposed moving object detector was implemented with 13.2K logic slices, 104 DSP48s, and 163 BRAM and can support real-time processing of 30 fps at an operating frequency of 200 MHz.

Oxalobacter formigenes-Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells.

Hyperoxaluria is a major risk factor for kidney stones and has no specific therapy, although Oxalobacter formigenes colonization is associated with reduced stone risk. O. formigenes interacts with colonic epithelium and induces colonic oxalate secretion, thereby reducing urinary oxalate excretion, via an unknown secretagogue. The difficulties in sustaining O. formigenes colonization underscore the need to identify the derived factors inducing colonic oxalate secretion. We therefore evaluated the effects of O. formigenes culture conditioned medium (CM) on apical 14C-oxalate uptake by human intestinal Caco-2-BBE cells. Compared with control medium, O. formigenes CM significantly stimulated oxalate uptake (>2.4-fold), whereas CM from Lactobacillus acidophilus did not. Treating the O. formigenes CM with heat or pepsin completely abolished this bioactivity, and selective ultrafiltration of the CM revealed that the O. formigenes-derived factors have molecular masses of 10-30 kDa. Treatment with the protein kinase A inhibitor H89 or the anion exchange inhibitor 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid completely blocked the CM-induced oxalate transport. Knockdown of the oxalate transporter SLC26A6 also significantly restricted the induction of oxalate transport by CM. In a mouse model of primary hyperoxaluria type 1, rectal administration of O. formigenes CM significantly reduced (>32.5%) urinary oxalate excretion and stimulated (>42%) distal colonic oxalate secretion. We conclude that O. formigenes-derived bioactive factors stimulate oxalate transport in intestinal cells through mechanisms including PKA activation. The reduction in urinary oxalate excretion in hyperoxaluric mice treated with O. formigenes CM reflects the in vivo retention of biologic activity and the therapeutic potential of these factors.

Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia.

BACKGROUND: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue. FINDINGS: Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions. CONCLUSIONS: Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL.

Gene transfer efficiency and genome-wide integration profiling of Sleeping Beauty, Tol2, and piggyBac transposons in human primary T cells.

In this study, we compared the genomic integration efficiencies and transposition site preferences of Sleeping Beauty (SB or SB11), Tol2, and piggyBac (PB) transposon systems in primary T cells derived from peripheral blood lymphocytes (PBL) and umbilical cord blood (UCB). We found that PB demonstrated the highest efficiency of stable gene transfer in PBL-derived T cells, whereas SB11 and Tol2 mediated intermediate and lowest efficiencies, respectively. Southern hybridization analysis demonstrated that PB generated the highest number of integrants when compared to SB and Tol2 in both PBL and UCB T cells. Tol2 and PB appeared more likely to promote clonal expansion than SB, which may be in part due to the dysregulated expression of cancer-related genes near the insertion sites. Genome-wide integration analysis demonstrated that SB, Tol2, and PB integrations occurred in all the chromosomes without preference. Additionally, Tol2 and PB integration sites were mainly localized near transcriptional start sites (TSSs), CpG islands and DNaseI hypersensitive sites, whereas SB integrations were randomly distributed. These results suggest that SB may be a preferential choice of the delivery vector in T cells due to its random integration site preference and relatively high efficiency, and support continuing development of SB-mediated T-cell phase I trials.

Self-assembled nucleic acid nanoparticles capable of controlled disassembly in response to a single nucleotide mismatch.

We have demonstrated the self-assembled DNA nanoparticles capable of controlled disassembly in response to a single nucleotide change (SNC) in a target nucleic acid. The DNA nanoparticles (avg diameter=51+/-22 nm) were constructed by joining two types of streptavidin-DNA conjugates with 2 molar equiv of a linker strand that carries complementary sequences to both conjugates. Nanoparticle disassembly triggered by a target strand (i.e., a perfect complement to the linker) selectively over mismatched targets was achieved by kinetically controlled nucleation occurring at a 6-nt overhang in the linker. The disassembly process was shown to be dramatically slowed down when using mismatch targets in which the SNC was positioned at the fourth nucleotide from the 3'-end. To verify whether the controlled disassembly also works for a SNC located in the middle of a target strand, we tested a deleterious Z variant (G1024A) of human alpha(1)-antitrypsin as a mismatch target (60-nt) carrying the point mutation at position 39. The wild-type target completed the disassembly process in less than 10 min, whereas the mismatch Z-type target could not complete the disassembly even in 3 h. The DNA nanoparticles are promising for sequence-dependent controlled release of short nucleic acids, including siRNA and antisense oligonucleotides, and construction of smart nanomaterials capable of sensing and processing single-nucleotide polymorphisms.

The transcriptome of human CD34+ hematopoietic stem-progenitor cells.

Studying gene expression at different hematopoietic stages provides insights for understanding the genetic basis of hematopoiesis. We analyzed gene expression in human CD34(+) hematopoietic cells that represent the stem-progenitor population (CD34(+) cells). We collected >459,000 transcript signatures from CD34(+) cells, including the de novo-generated 3' ESTs and the existing sequences of full-length cDNAs, ESTs, and serial analysis of gene expression (SAGE) tags, and performed an extensive annotation on this large set of CD34(+) transcript sequences. We determined the genes expressed in CD34(+) cells, verified the known genes and identified the new genes of different functional categories involved in hematopoiesis, dissected the alternative gene expression including alternative transcription initiation, splicing, and adenylation, identified the antisense and noncoding transcripts, determined the CD34(+) cell-specific gene expression signature, and developed the CD34(+) cell-transcription map in the human genome. Our study provides a current view on gene expression in human CD34(+) cells and reveals that early hematopoiesis is an orchestrated process with the involvement of over half of the human genes distributed in various functions. The data generated from our study provide a comprehensive and uniform resource for studying hematopoiesis and stem cell biology.

Simplified DGS procedure for large-scale genome structural study.

Ditag genome scanning (DGS) uses next-generation DNA sequencing to sequence the ends of ditag fragments produced by restriction enzymes. These sequences are compared to known genome sequences to determine their structure. In order to use DGS for large-scale genome structural studies, we have substantially revised the original protocol by replacing the in vivo genomic DNA cloning with in vitro adaptor ligation, eliminating the ditag concatemerization steps, and replacing the 454 sequencer with Solexa or SOLiD sequencers for ditag sequence collection. This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously.

Scanning the human genome at kilobase resolution.

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.

Genome-wide analysis of antisense transcription with Affymetrix exon array.

BACKGROUND: A large number of natural antisense transcripts have been identified in human and mouse genomes. Study of their potential functions clearly requires cost-efficient method for expression analysis. RESULTS: Here we show that Affymetrix Exon arrays, which were designed to detect conventional transcripts in the sense orientation, can be used to monitor antisense expression across all exonic loci in mammalian genomes. Through modification of the cDNA synthesis protocol, we labeled single-strand cDNA in the reverse orientation as in the standard protocol, thus enabling the detection of antisense transcripts using the same array. Applying this technique to human Jurkat cells, we identified antisense transcription at 2,088 exonic loci of 1,516 UniGene clusters. Many of these antisense transcripts were not observed previously and some were validated by orientation-specific RT-PCR. CONCLUSION: Our results suggest that with a modified protocol Affymetrix human, mouse and rat Exon arrays can be used as a routine method for genome-wide analysis of antisense transcription in these genomes.

Pan-genome isolation of low abundance transcripts using SAGE tag.

The SAGE (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human SAGE tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3' EST from SAGE tag for gene identification), we converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3' ESTs. We identified 3418 unique 3' ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3' ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3' ESTs were isolated by SAGE tag mis-priming to the non-parent transcripts. Replacing SAGE tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming.

A large quantity of novel human antisense transcripts detected by LongSAGE.

MOTIVATION: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632 813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts. RESULTS: Our study identified 45 321 tags that match the antisense strand of 9804 known mRNA sequences, 6606 of which contain antisense ESTs and 3198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database. CONCLUSIONS: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome.

Annotating nonspecific SAGE tags with microarray data.

SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags.

MOCVD of Bi2Te3 and Sb2Te3 on GaAs substrates for thin-film thermoelectric applications.

Metal organic chemical vapour deposition (MOCVD) has been investigated for growth of Bi2Te3 and Sb2Te3 films on (001) GaAs substrates using trimethylbismuth, triethylantimony and diisopropyltelluride as metal organic sources. The surface morphologies of Bi2Te3 and Sb2Te3 films were strongly dependent on the deposition temperatures as it varies from a step-flow growth mode to island coalescence structures depending on deposition temperature. In-plane carrier concentration and electrical Hall mobility were highly dependent on precursor ratio of VI/V and deposition temperature. By optimizing growth parameters, we could clearly observe an electrically intrinsic region of the carrier concentration over the 240 K in Bi2Te3 films. The high Seebeck coefficient (of -160 microVK(-1) for Bi2Te3 and +110 microVK(-1) for Sb2Te3 films, respectively) and good surface morphologies of these materials are promising for the fabrication of a few nm thick periodic Bi2Te3/Sb2Te3 super lattice structures for thin film thermoelectric device applications.

Mutants of Agrobacterium tumefaciens virG gene that activate transcription of vir promoter in Escherichia coli.

The virA and virG two-component regulatory system is essential for transcriptional activation of virulence (vir) genes in Agrobacterium tumefaciens in the presence of inducer molecules. The VirA/VirG mediated vir gene transcription depends on a specific interaction between the C-terminal domain of the alpha subunit (RpoA) of A. tumefaciens RNA polymerase (RNAP) and N-terminal domain of the VirG. However, such interaction does not occur between RNAP of E. coli and the VirG, thus vir gene activation in E. coli requires the presence of rpoA gene from A. tumefaciens. In this report, we describe VirG mutants that are capable of activating the expression of vir genes in E. coli in the absence of A. tumefaciens RpoA. The selected 45 VirG mutants exhibited a common amino acid substitution at position 56 and additional one or more substitutions at different positions; thus the amino acid at position 56 is likely to play a key role in the interaction with the RpoA of E. coli. Furthermore, two virG mutants, with amino acid substitutions of G56V/V7I/I106N and G56V/I77V, respectively, are capable of activating vir genes in E. coli in response to inducer acetosyringone in a virA-dependent manner, demonstrating that the interaction site between VirG and RpoA is separable from that of VirG and VirA. Therefore, it is possible to establish inducer-mediated vir gene expression in heterologous hosts using virG mutants that are capable of interacting with the RpoA of the respective bacterial hosts while retaining the ability to interact with the sensor VirA.