Aberrantly Expressed CeRNAs Account for Missing Genomic Variability of Cancer Genes via MicroRNA-Mediated Interactions

There is growing evidence that RNAs compete for binding and regulation by a finite pool of microRNAs (miRs), thus regulating each other through a competing endogenous RNA (ceRNA) mechanism. My dissertation work focused on systematically studying ceRNA interactions in cancer by reverse-engineering context-specific miR-RNA interactions and ceRNA regulatory interactions across multiple tumor types and study the effects of these interactions in cancer. I attempted to use ceRNA interactions to explain how genetic and epigenetic alterations are propagated to target established drivers of tumorigenesis. Using bioinformatics analysis of primary tumor samples and experimental validation in cell lines, I have investigated the roles that mRNAs and noncoding RNAs can play in tumorigenesis via ceRNA interactions. Specifically, I studied how RNAs target tumor-suppressors and oncogenes as ceRNAs, and attempted to accounting for some of the missing genomic variability in tumors

Scheduling of flexible manufacturing systems with automated guided vehicles using petri net models

In this thesis, Petri net models for Flexible Manufacturing Systems (EMS) are constructed. A firing sequence of the Petri net from the initial marking to the final marking can be seen as a schedule of the modeled FMS. By using the branch-and-bound algorithm, an optimal schedule of the FMS can be obtained. Automated Guided Vehicle Systems (AGVS) are increasingly used for material handling in factories and warehouses. An AGVS can reduce labor costs and is ready to be integrated into an automated factory. This thesis presents two AGVS models (shared and duty) which integrate the control of AGVS with the control of part processing facilities. Both types of AGVS are modeled by Petri nets. We want to compare the two AGVS in terms of systems performance and discuss which application is more suitable for each AGVS type. We also want to consider and solve AGV jam problems. The objective of the AGV jam-free control module is to guarantee a jam-free condition among AGVs in an EMS. Results have been obtained and analyzed

The Dual-mediation Effect of Perceived Accuracy and Perceived Connectedness on Consumer Attitude Toward Social Network Advertising

Drawing on the stimulus-organism-response (S-O-R) model, this paper investigates the dual mediation effect of perceived accuracy and perceived connectedness in the effect of endorsement from satisfied customers, review credibility, and social influence on consumers’ social media advertising attitudes. A study was conducted and received 1597 returned surveys with 1031 valid surveys. The results show that endorsement from satisfied customers, review credibility, and social influence are antecedents of perceived accuracy and perceived connectedness. These five variables are also antecedents of consumer attitude toward social network advertising. Furthermore, perceived accuracy and connectedness are partially mediating these relationships between endorsement from satisfied customers/review credibility/social influence and consumer attitude toward social network advertising

Protein subcellular localization prediction based on compartment-specific features and structure conservation

BACKGROUND: Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins. RESULTS: We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM) model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%. CONCLUSION: Our results demonstrate that biological features derived from Gram-negative bacteria translocation pathways yield a significant improvement. The biological features are interpretable and can be applied in advanced analyses and experimental designs. Moreover, the overall accuracy of combining the structural homology approach is further improved, which suggests that structural conservation could be a useful indicator for inferring localization in addition to sequence homology. The proposed method can be used in large-scale analyses of proteomes

The Number Of Titrated Microrna Species Dictates Cerna Regulation

microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many targets. We modeled ceRNA and simulated its effects using established parameters for miRNA/mRNA interaction kinetics while accounting for co-regulation by multiple miRNAs with many targets. Our simulations suggested that co-regulation by many miRNA species is more likely to produce physiologically relevant context-independent couplings. To test this, we studied the overlap of inferred ceRNA networks from four tumor contexts-our proposed pan-cancer ceRNA interactome (PCI). PCI was composed of interactions between genes that were coregulated by nearly three-times as many miRNAs as other inferred ceRNA interactions. Evidence from expression-profiling datasets suggested that PCI interactions are predictive of gene expression in 12 independent tumor-and non-tumor contexts. Biochemical assays confirmed ceRNA couplings for two PCI subnetworks, including oncogenes CCND1, HIF1A and HMGA2, and tumor suppressors PTEN, RB1 and TP53. Our results suggest that PCI is enriched for context-independent interactions that are coupled by many miRNA species and are more likely to be context independent

Recycling failed photoelectrons via tertiary photoemission

A key insight of Einstein's theory of the photoelectric effect is that a minimum energy is required for photoexcited electrons to escape from a material. For the past century it has been assumed that photoexcited electrons of lower energies make no contribution to the photoemission spectrum. Here we demonstrate the conceptual possibility that the energy of these 'failed' photoelectrons-primary or secondary-can be partially recycled to generate new 'tertiary' electrons of energy sufficient to escape. Such a 'recycling' step goes beyond the traditional three steps of the photoemission process (excitation, transport, and escape), and, as we illustrate, it can be realized through a novel Auger mechanism that involves three distinct minority electronic states in the material. We develop a phenomenological three-band model to treat this mechanism within a revised four-step framework for photoemission, which contains robust features of linewidth narrowing and population inversion under strong excitation, reminiscent of the lasing phenomena. We show that the conditions for this recycling mechanism are likely satisfied in many quantum materials with multiple flat bands properly located away from the Fermi level, and elaborate on the representative case of SrTiO3 among other promising candidates. We further discuss how this mechanism can explain the recent observation of anomalous intense coherent photoemission from a SrTiO3 surface, and predict its manifestations in related experiments, including the 'forbidden' case of photoemission with photon energies lower than the work function. Our study calls for paradigm shifts across a range of fundamental and applied research fields, especially in the areas of photoemission, photocathodes, and flat-band materials.Comment: 45 Pages, 14 Figure

Identification of genes related to the development of bamboo rhizome bud

Bamboo (Phyllostachys praecox) is one of the largest members of the grass family Poaceae, and is one of the most economically important crops in Asia. However, complete knowledge of bamboo development and its molecular mechanisms is still lacking. In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified. The rice cross-species microarray hybridization showed a total of 318 up-regulated and 339 down-regulated genes, including those involved in regulation and signalling, metabolism, and stress, and also cell wall-related genes, in the bamboo rhizome buds versus the leaves. By referring to the functional dissection of the homologous genes from Arabidopsis and rice, the putative functions of the 52 up-regulated genes in the bamboo rhizome bud were described. Six genes related to the development of the bamboo rhizome bud were further cloned and sequenced. These show 66–90% nucleotide identity and 68–98% amino acid identity with the homologous rice genes. The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets. Furthermore, in situ hybridization showed that the PpRLK1 gene is expressed in the procambium and is closely related to meristem development of bamboo shoots. The PpHB1 gene is expressed at the tips of bamboo shoots and procambium, and is closely related to rhizome bud formation and procambial development. To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development

S9, a Novel Anticancer Agent, Exerts Its Anti-Proliferative Activity by Interfering with Both PI3K-Akt-mTOR Signaling and Microtubule Cytoskeleton

BACKGROUND: Deregulation of the phosphatidylinositol 3-kinases (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway plays a central role in tumor formation and progression, providing validated targets for cancer therapy. S9, a hybrid of alpha-methylene-gamma-lactone and 2-phenyl indole compound, possessed potent activity against this pathway. METHODOLOGY/PRINCIPAL FINDINGS: Effects of S9 on PI3K-Akt-mTOR pathway were determined by Western blot, immunofluorescence staining and in vitro kinas assay. The interactions between tubulin and S9 were investigated by polymerization assay, CD, and SPR assay. The potential binding modes between S9 and PI3K, mTOR or tubulin were analyzed by molecular modeling. Anti-tumor activity of S9 was evaluated in tumor cells and in nude mice bearing human cancer xenografts. S9 abrogated EGF-activated PI3K-Akt-mTOR signaling cascade and Akt translocation to cellular membrane in human tumor cells. S9 possessed inhibitory activity against both PI3K and mTOR with little effect on other tested 30 kinases. S9 also completely impeded hyper-phosphorylation of Akt as a feedback of inhibition of mTOR by rapamycin. S9 unexpectedly arrested cells in M phase other than G1 phase, which was distinct from compounds targeting PI3K-Akt-mTOR pathway. Further study revealed that S9 inhibited tubulin polymerization via binding to colchicine-binding site of tubulin and resulted in microtubule disturbance. Molecular modeling indicated that S9 could potentially bind to the kinase domains of PI3K p110alpha subunit and mTOR, and shared similar hydrophobic interactions with colchicines in the complex with tubulin. Moreover, S9 induced rapid apoptosis in tumor cell, which might reflect a synergistic cooperation between blockade of both PI3-Akt-mTOR signaling and tubulin cytoskeleton. Finally, S9 displayed potent antiproliferative activity in a panel of tumor cells originated from different tissue types including drug-resistant cells and in nude mice bearing human tumor xenografts. CONCLUSIONS/SIGNIFICANCE: Taken together, S9 targets both PI3K-Akt-mTOR signaling and microtubule cytoskeleton, which combinatorially contributes its antitumor activity and provides new clues for anticancer drug design and development

The Influences of H2Plasma Pretreatment on the Growth of Vertically Aligned Carbon Nanotubes by Microwave Plasma Chemical Vapor Deposition

The effects of H2flow rate during plasma pretreatment on synthesizing the multiwalled carbon nanotubes (MWCNTs) by using the microwave plasma chemical vapor deposition are investigated in this study. A H2and CH4gas mixture with a 9:1 ratio was used as a precursor for the synthesis of MWCNT on Ni-coated TaN/Si(100) substrates. The structure and composition of Ni catalyst nanoparticles were investigated using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The present findings showed that denser Ni catalyst nanoparticles and more vertically aligned MWCNTs could be effectively achieved at higher flow rates. From Raman results, we found that the intensity ratio of G and D bands (ID/IG) decreases with an increasing flow rate. In addition, TEM results suggest that H2plasma pretreatment can effectively reduce the amorphous carbon and carbonaceous particles. As a result, the pretreatment plays a crucial role in modifying the obtained MWCNTs structures

Intra-Arterial Chemotherapy with Doxorubicin and Cisplatin Is Effective for Advanced Hepatocellular Cell Carcinoma

Advanced hepatocellular carcinoma (HCC) remains a fatal disease even in the era of targeted therapies. Intra-arterial chemotherapy (IACT) can provide therapeutic benefits for patients with locally advanced HCC who are not eligible for local therapies or are refractory to targeted therapies. The aim of this retrospective study was to analyze the effect of IACT with cisplatin and doxorubicin on advanced HCC. Methods. Patients with advanced HCC who were not eligible for local therapies or were refractory to sorafenib received doxorubicin (50 mg/m2) and cisplatin (50 mg/m2) infusions into the liver via the transhepatic artery. Between January 2005 and December 2011, a total of 50 patients with advanced HCC received this treatment regimen. The overall response rate (ORR) was 22% in all treated patients. In patients who received at least 2 cycles of IACT, the ORR was 36.7%, and the disease control rate was 70%. Survival rate differed significantly between patients who received only one cycle of IACT (group I) and those who received several cycles (group II). The median progression-free survival was 1.3 months and 5.8 months in groups I and II, respectively (P<0.0001). The median overall survival was 8.3 months for all patients and was 3.1 months and 12.0 months in groups I and II, respectively (P<0.0001). The most common toxicity was alopecia. Four patients developed grade 3 or 4 leukopenia. Worsening of liver function, nausea, and vomiting were uncommon side effects. This study demonstrated clinical efficacy and tolerable side effects of repeated IACT with doxorubicin and cisplatin in advanced HCC. Our regimen can be an alternative choice for patients with adequate liver function who do not want to receive continuous infusion of IACT