Routing, Driven Placement for ATMEL 6000 Architecture FPGAs

Based on the concept of Cell Binary Tree (CBT), a new technique for mapping combination circuits into ATMEL 6000 Architecture FPGAs is presented in this thesis. Cell Binary Tree (CBT) is a net-list representation of combinational circuits. For each node of CBT there is a distinguished variable associated with it, the node itself represents a certain logic function, which is selected according to target FPGA architecture. The proposed CBT placement algorithms preserve local connectivity and allow better mapping into ATMEL FPGA. Experiments reveal that the new mapping technique achieved reduction in a number buses used for routing comparing with previously proposed Modified Squashed Binary Tree (MSBT) approach and possibly reduction of area as well. In general, the new technique is realized through following four major steps: 1. Grouping and generating CBT: This is a step to read blifformat file, which is the result of logic synthesis, into a CBT data structure through grouping algorithm, which is a process of gathering logic functions into nodes for mapping based on a targeted FPGA architecture. The main objective of creating CBT is to generate a minimum number of nodes (or cells) to be mapped. 2. CBT placement: Upon getting the minimum number of nodes in CBT to be mapped, the next step is to map those nodes into cells in FPGA. The significance of the placement method in this thesis is to lineup the cells with the same variable into the same row in the FPGA. 3. Bus Assignment: The process of assigning variables to local buses, which run in two possible directions; horizontal and vertical. ATMEL 6000 has two horizontal buses and two vertical buses for each cell. The assignment is based on the number of times a variable appears in a row or column. 4. Routing: The last stage of the process is the connecting cells which have the same input variable. One of the important steps in the routing process is to choose connection bridge cells with the minimum impact on the area

Design and analysis of wireless diversity system

Ph.DDOCTOR OF PHILOSOPH

Identification of aromatic amino acid residues in conserved region VI of the large polymerase of vesicular stomatitis virus is essential for both guanine-N-7 and ribose 2'-O methyltransferases

AbstractNon-segmented negative-sense RNA viruses possess a unique mechanism for mRNA cap methylation. For vesicular stomatitis virus, conserved region VI in the large (L) polymerase protein catalyzes both guanine-N-7 (G-N-7) and ribose 2'-O (2'-O) methyltransferases, and the two methylases share a binding site for the methyl donor S-adenosyl-l-methionine. Unlike conventional mRNA cap methylation, the 2'-O methylation of VSV precedes subsequent G-N-7 methylation. In this study, we found that individual alanine substitutions in two conserved aromatic residues (Y1650 and F1691) in region VI of L protein abolished both G-N-7 and 2'-O methylation. However, replacement of one aromatic residue with another aromatic residue did not significantly affect the methyltransferase activities. Our studies provide genetic and biochemical evidence that conserved aromatic residues in region VI of L protein essential for both G-N-7 and 2'-O methylations. In combination with the structural prediction, our results suggest that these aromatic residues may participate in RNA recognition

Modeling Link-level Road Traffic Resilience to Extreme Weather Events Using Crowdsourced Data

Climate changes lead to more frequent and intense weather events, posing escalating risks to road traffic. Crowdsourced data offer new opportunities to monitor and investigate changes in road traffic flow during extreme weather. This study utilizes diverse crowdsourced data from mobile devices and the community-driven navigation app, Waze, to examine the impact of three weather events (i.e., floods, winter storms, and fog) on road traffic. Three metrics, speed change, event duration, and area under the curve (AUC), are employed to assess link-level traffic change and recovery. In addition, a user's perceived severity is computed to evaluate link-level weather impact based on crowdsourced reports. This study evaluates a range of new data sources, and provides insights into the resilience of road traffic to extreme weather, which are crucial for disaster preparedness, response, and recovery in road transportation systems

COVID-19 and Income Profile: How People in Different Income Groups Responded to Disease Outbreak, Case Study of the United States

Due to immature treatment and rapid transmission of COVID-19, mobility interventions play a crucial role in containing the outbreak. Among various non-pharmacological interventions, community infection control is considered to be a quite promising approach. However, there is a lack of research on improving community-level interventions based on a community's real conditions and characteristics using real-world observations. Our paper aims to investigate the different responses to mobility interventions between communities in the United States with a specific focus on different income levels. We produced six daily mobility metrics for all communities using the mobility location data from over 100 million anonymous devices on a monthly basis. Each metric is tabulated by three performance indicators: "best performance," "effort," and "consistency." We found that being high-income improves social distancing behavior after controlling multiple confounding variables in each of the eighteen scenarios. In addition to the reality that it is more difficult for low-income communities to comply with social distancing, the comparisons between scenarios raise concerns on the employment status, working condition, accessibility to life supplies, and exposure to the virus of low-income communities

Native and bone marrow-derived cell mosaicism in gastric carcinoma in H. pylori-infected p27-deficient mice

OBJECTIVE: Chronic Helicobacter pylori (H. pylori) infection promotes non-cardia gastric cancer. Some mouse models suggest that bone marrow derived cells (BMDC) contribute to Helicobacter-associated gastric carcinogenesis. We determined whether this increased susceptibility to Helicobacter-induced gastric carcinogenesis of p27-deficient mice is dependent upon their p27-null BMDC or their p27-null gastric epithelial cells. DESIGN: Female mice (recipients) were irradiated and transplanted with BMDC from male donors. Wild type (WT) mice in group 1 (control) received BMDC from male GFP-transgenic mice. Female WT and p27 KO mice were engrafted with male p27KO mice BMDC (Group 2) or GFP-transgenic WT BMDC (Group 3). Recipients were infected with H. pylori SS1 for one year. RESULTS: Mice lacking p27 in either the BM pool or gastric epithelium developed significantly more advanced gastric pathology, including high-grade dysplasia. Co-staining of donor BMDC in dysplastic gastric glands was confirmed by immunofluorescence. Gastric expression of IL-1 beta protein was reduced in groups 2 and 3 (p \u3c 0.05 vs control) whereas expression of IFN-gamma and chemokines MIP-1 beta, MIG, IP-10 and RANTES in group 2 were significantly higher than group 3. CONCLUSIONS: Both bone marrow-derived and gastric epithelial cells contribute to the increased gastric cancer susceptibility of p27-deficient H. pylori-infected mice

An Integrated Genomic and Immunoinformatic Approach to \u3cem\u3eH. pylori\u3c/em\u3e Vaccine Design

Background: One useful application of pattern matching algorithms is identification of major histocom-patability complex (MHC) ligands and T-cell epitopes. Peptides that bind to MHC molecules and interact with T cell receptors to stimulate the immune system are critical antigens for protection against infectious pathogens. We describe a genomes-to-vaccine approach to H. pylori vaccine design that takes advantage of immunoinformatics algorithms to rapidly identify T-cell epitope sequences from large genomic datasets. Results: To design a globally relevant vaccine, we used computational methods to identify a core genome comprised of 676 open reading frames (ORFs) from amongst seven genetically and phenotypically diverse H. pylori strains from around the world. Of the 1,241,153 9-mer sequences encoded by these ORFs, 106,791 were identical amongst all seven genomes and 23,654 scored in the top 5% of predicted HLA ligands for at least one of eight archetypal Class II HLA alleles when evaluated by EpiMatrix. To maximize the number of epitopes that can be assessed experimentally, we used a computational algorithm to in-crease epitope density in 20-25 amino acid stretches by assembling potentially immunogenic 9-mers to be identically positioned as they are in the native protein antigen. 1,805 immunogenic consensus sequences (ICS) were generated. 79% of selected ICS epitopes bound to a panel of 6 HLA Class II haplotypes, repre-senting \u3e90% of the global human population. Conclusions: The breadth of H. pylori genome datasets was computationally assessed to rapidly and care-fully determine a core set of genes. Application of immunoinformatics tools to this gene set accurately pre-dicted epitopes with promising properties for T cell-based vaccine development

Human Immune Responses to \u3cem\u3eH. pylori\u3c/em\u3e HLA Class II Epitopes Identified by Immunoinformatic Methods

H. pylori persists in the human stomach over decades and promotes several adverse clinical sequelae including gastritis, peptic ulcers and gastric cancer that are linked to the induction and subsequent evasion of chronic gastric inflammation. Emerging evidence indicates that H. pylori infection may also protect against asthma and some other immune-mediated conditions through regulatory T cell effects outside the stomach. To characterize the complexity of the CD4+ T cell response generated during H. pylori infection, computational methods were previously used to generate a panel of 90 predicted epitopes conserved among H. pylori genomes that broadly cover HLA Class II diversity for maximum population coverage. Here, these sequences were tested individually for their ability to induce in vitro responses in peripheral blood mononuclear cells by interferon-γ ELISpot assay. The average number of spot-forming cells/million PBMCs was significantly elevated in H. pylori-infected subjects over uninfected persons. Ten of the 90 peptides stimulated IFN-γ secretion in the H. pylori-infected group only, whereas two out of the 90 peptides elicited a detectable IFN-γ response in the H. pylori-uninfected subjects but no response in the H. pylori-infected group. Cytokine ELISA measurements performed using in vitro PBMC culture supernatants demonstrated significantly higher levels of TNF-α, IL-2, IL-4, IL-6, IL-10, and TGF-β1 in the H. pylori-infected subjects, whereas IL-17A expression was not related to the subjects H. pylori-infection status. Our results indicate that the human T cell responses to these 90 peptides are generally increased in actively H. pylori-infected, compared with H. pylori-naïve, subjects. This information will improve understanding of the complex immune response to H. pylori, aiding rational epitope-driven vaccine design as well as helping identify other H. pylori epitopes with potentially immunoregulatory effects