Image Processing Using Dataflow Techniques

Corner detection is an important task in digital image processing. Corner detection algorithms are widely used in pattern recognition, image mosaicing, motion detection, etc. The implementations of such algorithm in software/hardware can be challenging. One classical algorithm for finding corners in images is proposed by Harris and Stephens in 1988, commonly known as Harris corner detection algorithm; There have been different implementations of the algorithm in OpenCV and on FPGA. The implementations of the algorithm in hardware have been relatively less, and most importantly the architectures of the algorithm on FPGA have relatively been unexplored. LIDE, created at University of Maryland, College Park, is a light-weight dataflow environment for rapid prototyping of DSP systems using dataflow techniques. The framework in C programming language is called LIDE-C, in Verilog HDL is called LIDE-V. This light-weight framework makes modeling of DSPs easy in both software and hardware. It is platform- and language-agnostic. This thesis work models the application both in LIDE-C and LIDE-V, our emphasis is, however, to propose multi-architecture corner detection Harris algorithm in LIDE-V. In LIDE, computations are distributed to different computation nodes in dataflow graphs. Each node is called actor in LIDE, and each actor has different modes of computation. Depending on how we construct a dataflow graph for an application and how we design actors of a dataflow graph, we easily create different implementations for the same algorithm. In this thesis, different hardware architecture of the Harris algorithm will be proposed with different latency, resource usage, and throughput characteristics. Our preliminary results reveal, among other things, that unfolding for the non-max suppression actor not only improve performance but also decrease resource usage

Comparison of genetic impact on growth and wood traits between seedlings and clones from the same plus trees of Pinus koraiensis

To evaluate the relationships among clones and open pollinated families from the same plus trees and to select elite breeding materials, growth, and wood characteristics of 33-year-old Pinus koraiensis clones and families were measured and analyzed. The results show that growth and wood characters varied significantly. The variation due to clonal effects was higher than that of family effects. The ratio of genetic to phenotypic coefficient of variation of clones in growth and wood traits was above 90%, and the repeatability of these characteristics was more than 0.8, whereas the ratio of genetic to phenotypic coefficient of variation of families was above 90%. The broad-sense heritability of all characteristics exceeded 0.4, and the narrow-sense family heritability of growth traits was less than 0.3. Growth characteristics were positively correlated with each other, but most wood properties were weakly correlated in both clones and families. Fiber length and width were positively correlated between clones and families. Using the membership function method, eleven clones and four families were selected as superior material for improved diameter growth and wood production, and two families from clonal and open-pollinated trees showed consistently better performance. Generally, selection of the best clones is an effective alternative to deployment of families as the repeatability estimates from clonal trees were higher than narrow-sense heritability estimates from open pollinated families. The results provide valuable insight for improving P. koraiensis breeding programs and subsequent genetic improvement

The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04

The R (replicase) protein is the uniquely defined non-structural protein (NSP) responsible for RNA replication, mutation rate or fidelity, regulation of transcription in coronaviruses and many other ssRNA viruses. Based on our complete genome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China, we analyzed the structure and predicted functions of the R protein in comparison with 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF (open-reading frame) encodes for two major enzyme activities, RNA-dependent RNA polymerase (RdRp) and proteinase activities. The R polyprotein undergoes a complex proteolytic process to produce 15 function-related peptides. A hydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identified within NSP1. The substitution rate of the R protein is close to the average of the SARS-CoV genome. The functional domains in all NSPs of the R protein give different phylogenetic results that suggest their different mutation rate under selective pressure. Eleven highly conserved regions in RdRp and twelve cleavage sites by 3CLP (chymotrypsin-like protein) have been identified as potential drug targets. Findings suggest that it is possible to obtain information about the phylogeny of SARS-CoV, as well as potential tools for drug design, genotyping and diagnostics of SARS

A graphene oxide-based AIE biosensor with high selectivity toward bovine serum albumin

Graphene oxide (GO) was found to effectively enhance the selectivity of aggregation-induced emission (AIE) biosensors, and a new method based on GO and AIE molecules was proposed to detect bovine serum albumin (BSA) with high sensitivity and selectivity.National Natural Science Foundation of China[20974084]; NCET[NCET-08-0411]; National Fundamental Key Research Program[2011CB932702

DNp73 improves generation efficiency of human induced pluripotent stem cells

<p>Abstract</p> <p>Background</p> <p>Recent studies have found that p53 and its' associated cell cycle pathways are major inhibitors of human induced pluripotent stem (iPS) cell generation. In the same family as p53 is p73, which shares sequence similarities with p53. However, p73 also has distinct properties of its own, such as two alternative promoters to express transactivation of p73 (TAp73) and N terminal deleted p73 (DNp73). Functionally, TAp73 acts similarly to p53 in tumor suppression. However, DNp73, on the other hand acts as an oncogene to suppress p53 and p73 induced apoptosis. Therefore, how can p73 have opposing roles in human iPS cell generation?</p> <p>Results</p> <p>Transcription factors, Oct4, Sox2, Klf4 and cMyc (4TF, Yamanaka factors) are used as basal conditions to generate iPS cells. In addition, the factor of DNp73(actually alpha splicing DNp73, DNp73α) is used to generate iPS cells. The experiment found that the addition of DNp73 gene increases human iPS cell generation efficiency by 12.6 folds in comparison to human fibroblast cells transduced with only the basal conditions. Also, iPS cells generated with DNp73 expression are more resistant to <it>in vitro </it>and <it>in vivo </it>differentiation.</p> <p>Conclusions</p> <p>This study found DNp73, a family member of p53, is also involved in the human iPS cell generation. Specifically, that the involvement of DNp73 generates iPS cells that are more resistant to <it>in vitro </it>and <it>in vivo </it>differentiation. Therefore, this data may prove to be useful in future developmental studies and cancer researches.</p

HPV prevalence and genotype distribution in 2,306 patients with cervical squamous cell carcinoma in central and eastern China

BackgroundTo explore the positivity rate and genotype distribution of human papillomavirus (HPV) in cervical squamous cell carcinoma (CSCC) tissues in central and eastern China and to provide theoretical basis for cervical cancer screening and prophylactic HPV vaccine development in China.MethodsDNA was extracted from paraffin-embedded tissues of CSCC samples and exfoliated cervical cells of cervical cancer screening populations. 23 HPV genotypes were detected by combining polymerase chain reaction (PCR) and reverse dot hybridized gene chip detection technology in 2,306 CSCC tissues and 10,245 cervical cancer screening populations. The genotype distribution of HPV infection was analyzed.ResultsThe overall infection rate of HPVs in 2,306 CSCC patients was 92.71%. The frequency of single-type HPV infection and multiple-type HPV infection were 86.48% and 13.51%, respectively. The most common HPV genotypes detected in Chinese CSCC tissues were HPV-16, HPV-18, HPV-31, HPV-33, HPV-45, HPV-52, HPV-58, and HPV-59. The overall positivity rate of these eight high-risk HPV (HR-HPV) genotypes in HPV-positive CSCC was as high as 96.91%. Of which the positivity rate of seven HR-HPV genotypes related to nine-valent HPV vaccines in HPV-positive CSCC was 95.09%. Meanwhile, the overall infection rates of HR-HPV and low-risk HPV (LR-HPV) in female aged 35–64 years who underwent cervical cancer screening were 13.16% and 1.32%, respectively. The high-frequency HR-HPV genotypes in cervical cancer screening women were HPV-52, HPV-58, HPV-16, HPV-53, HPV-68, HPV-39, HPV-51, and HPV-56, with positivity rates of 2.25%, 1.60%, 1.31%, 1.22%, 0.93%, 0.92%, 0.78%, and 0.74%, respectively.ConclusionAmong women screened for cervical cancer in China, detecting the 8 high-frequency HR-HPV genotypes can reduce technical difficulty and reagent costs, while also improving the efficiency and effectiveness of cervical cancer screening. HPV genotyping assists gynecologists in assessing the risk of HR-HPV-positive cervical intraepithelial neoplasia and guiding them in implementing appropriate interventions. Furthermore, HPV genotyping is helpful for doctors to follow up HR-HPV-positive women and to evaluate the protective effect of HPV vaccine

A Novel Solid-Phase Site-Specific PEGylation Enhances the In Vitro and In Vivo Biostabilty of Recombinant Human Keratinocyte Growth Factor 1

Keratinocyte growth factor 1 (KGF-1) has proven useful in the treatment of pathologies associated with dermal adnexae, liver, lung, and the gastrointestinal tract diseases. However, poor stability and short plasma half-life of the protein have restricted its therapeutic applications. While it is possible to improve the stability and extend the circulating half-life of recombinant human KGF-1 (rhKGF-1) using solution-phase PEGylation, such preparations have heterogeneous structures and often low specific activities due to multiple and/or uncontrolled PEGylation. In the present study, a novel solid-phase PEGylation strategy was employed to produce homogenous mono-PEGylated rhKGF-1. RhKGF-1 protein was immobilized on a Heparin-Sepharose column and then a site-selective PEGylation reaction was carried out by a reductive alkylation at the N-terminal amino acid of the protein. The mono-PEGylated rhKGF-1, which accounted for over 40% of the total rhKGF-1 used in the PEGylation reaction, was purified to homogeneity by SP Sepharose ion-exchange chromatography. Our biophysical and biochemical studies demonstrated that the solid-phase PEGylation significantly enhanced the in vitro and in vivo biostability without affecting the over all structure of the protein. Furthermore, pharmacokinetic analysis showed that modified rhKGF-1 had considerably longer plasma half-life than its intact counterpart. Our cell-based analysis showed that, similar to rhKGF-1, PEGylated rhKGF-1 induced proliferation in NIH 3T3 cells through the activation of MAPK/Erk pathway. Notably, PEGylated rhKGF-1 exhibited a greater hepatoprotection against CCl4-induced injury in rats compared to rhKGF-1