Fast GPU-Based Two-Way Continuous Collision Handling

Step-and-project is a popular way to simulate non-penetrated deformable bodies in physically-based animation. First integrating the system in time regardless of contacts and post resolving potential intersections practically strike a good balance between plausibility and efficiency. However, existing methods could be defective and unsafe when the time step is large, taking risks of failures or demands of repetitive collision testing and resolving that severely degrade performance. In this paper, we propose a novel two-way method for fast and reliable continuous collision handling. Our method launches the optimization at both ends of the intermediate time-integrated state and the previous intersection-free state, progressively generating a piecewise-linear path and finally reaching a feasible solution for the next time step. Technically, our method interleaves between a forward step and a backward step at a low cost, until the result is conditionally converged. Due to a set of unified volume-based contact constraints, our method can flexibly and reliably handle a variety of codimensional deformable bodies, including volumetric bodies, cloth, hair and sand. The experiments show that our method is safe, robust, physically faithful and numerically efficient, especially suitable for large deformations or large time steps

Invited - Droplets driving and sensing pixel circuits for thin film transistor-based digital microfluidics

Thin film transistor-based active-matrix digital microfluidics (AM-DMF) is an emerging and promising technology for large-scale parallel biological sample handling. With electrowetting-on-dielectric (EWOD) method, DMF chip can realize accurately controlling discrete droplets, thus it has great application prospects in biology, chemistry, and drug discovery. With the rapid development of micro-analysis and detection requirements, the precise control of droplets in DMF chips is increasingly required, so it is necessary to conduct the real-time sensing of droplet position. Figure 1 shows the designed droplet position detection unit circuit. The circuit consists of six thin film transistors, T1-T6. The input signals mainly include the enable signal Ven, the reverse enable signal Venb, the discharge signal Vdischarge, the detection signal Vdetect, and the ground signal Vgnd. The signal Vdrive is the driving voltage applied for driving electrode. Cpixel is the equivalent capacitance between the two plates of a pixel electrode in a microfluidic chip. Vout is the output voltage signal. Please click Download on the upper right corner to see the full abstract

Systems level analysis of two-component signal transduction systems in Erwinia amylovora: Role in virulence, regulation of amylovoran biosynthesis and swarming motility

<p>Abstract</p> <p>Background</p> <p>Two-component signal transduction systems (TCSTs), consisting of a histidine kinase (HK) and a response regulator (RR), represent a major paradigm for signal transduction in prokaryotes. TCSTs play critical roles in sensing and responding to environmental conditions, and in bacterial pathogenesis. Most TCSTs in <it>Erwinia amylovora </it>have either not been identified or have not yet been studied.</p> <p>Results</p> <p>We used a systems approach to identify TCST and related signal transduction genes in the genome of <it>E. amylovora</it>. Comparative genomic analysis of TCSTs indicated that <it>E. amylovora </it>TCSTs were closely related to those of <it>Erwinia tasmaniensis</it>, a saprophytic enterobacterium isolated from apple flowers, and to other enterobacteria. Forty-six TCST genes in <it>E. amylovora </it>including 17 sensor kinases, three hybrid kinases, 20 DNA- or ligand-binding RRs, four RRs with enzymatic output domain (EAL-GGDEF proteins), and two kinases were characterized in this study. A systematic TCST gene-knockout experiment was conducted, generating a total of 59 single-, double-, and triple-mutants. Virulence assays revealed that five of these mutants were non-pathogenic on immature pear fruits. Results from phenotypic characterization and gene expression experiments indicated that several groups of TCST systems in <it>E. amylovora </it>control amylovoran biosynthesis, one of two major virulence factors in <it>E. amylovora</it>. Both negative and positive regulators of amylovoran biosynthesis were identified, indicating a complex network may control this important feature of pathogenesis. Positive (non-motile, EnvZ/OmpR), negative (hypermotile, GrrS/GrrA), and intermediate regulators for swarming motility in <it>E. amylovora </it>were also identified.</p> <p>Conclusion</p> <p>Our results demonstrated that TCSTs in <it>E. amylovora </it>played major roles in virulence on immature pear fruit and in regulating amylovoran biosynthesis and swarming motility. This suggested presence of regulatory networks governing expression of critical virulence genes in <it>E. amylovora</it>.</p

Crucial Role for Early Growth Response-1 in the Transcriptional Regulation of miR-20b in Breast Cancer

Transcriptional regulation of miRNAs that control the pathogenesis of breast cancer remains largely unknown. Here, we showed that ionizing radiation, a known breast carcinogen, triggered the differential expression of miR-20b in mammary tissues. We identified several GC-rich consensus binding motifs for the zinc finger transcription factor early growth response-1 (EGR1) in miR-20b promoter. miR-20b was upregulated by IR and its upregulation correlated with EGR1 expression in the breast cancer cell line HCC1806. Therefore, we used HCC1806 cells as a model system to explore the role of EGR1 in miR-20b transcription. siRNA knockdown of EGR1 attenuated miR-20b expression. Luciferase assays showed that whereas EGR1 stimulated luciferase activity driven by the wild-type miR-20b promoter, this induction was abolished in the mutant miR-20 promoter construct. We noted significant enrichment of EGR1 at miR-20b promoter in HCC1806 cells compared with normal human mammary epithelial cells. Suppression of miR-20b significantly inhibited HCC1806 cell proliferation and migration, and led to G 0/G 1 and S phase arrest. In vitro RNA-pull down assays indicated that miR-20b targets numerous tumor suppressors, including PTEN and BRCA1, which were downregulated in HCC1806. Conversely, suppression of miR-20b increased PTEN and BRCA1 levels. Moreover, immunohistochemical and FISH analyses showed that the miR-20b expression correlated significantly with EGR1 levels in breast cancer tissues. Our findings thus demonstrate for the first time that EGR1 is a key player in the transcriptional control of miR-20b, and miR-20b may in turn function as an oncogene by contributing to breast tumorigenesis via tumor suppressor targeting