Genetic regulation of mouse liver metabolite levels.

We profiled and analyzed 283 metabolites representing eight major classes of molecules including Lipids, Carbohydrates, Amino Acids, Peptides, Xenobiotics, Vitamins and Cofactors, Energy Metabolism, and Nucleotides in mouse liver of 104 inbred and recombinant inbred strains. We find that metabolites exhibit a wide range of variation, as has been previously observed with metabolites in blood serum. Using genome-wide association analysis, we mapped 40% of the quantified metabolites to at least one locus in the genome and for 75% of the loci mapped we identified at least one candidate gene by local expression QTL analysis of the transcripts. Moreover, we validated 2 of 3 of the significant loci examined by adenoviral overexpression of the genes in mice. In our GWAS results, we find that at significant loci the peak markers explained on average between 20 and 40% of variation in the metabolites. Moreover, 39% of loci found to be regulating liver metabolites in mice were also found in human GWAS results for serum metabolites, providing support for similarity in genetic regulation of metabolites between mice and human. We also integrated the metabolomic data with transcriptomic and clinical phenotypic data to evaluate the extent of co-variation across various biological scales

Remote Health Monitor

The goal of the Remote Health Monitor (RHM) is to collect a patient’s health data and manage them. Patients can be monitored from anywhere there is internet access. The RHM measures parameters such as temperature and pulse, and transmits the information to the database located in the hospital. The database can be accessed through a software application that will be provided along with the purchase of RHM. The application can be logged in to either as a doctor or as a patient, thus allowing the care providers to monitor a patient’s health condition and the patients to review their own medical history.  Our goal in implementing RHM is to provide chronic disease patients with an easy to use device that will help them track health information without going to the hospital, and to allow doctors to review the patient data with a software application that organizes and updates information automatically.&nbsp

Flavin containing monooxygenase 3 exerts broad effects on glucose and lipid metabolism and atherosclerosis

We performed silencing and overexpression studies of flavin containing monooxygenase (FMO) 3 in hyperlipidemic mouse models to examine its effects on trimethylamine N-oxide (TMAO) levels and atherosclerosis. Knockdown of hepatic FMO3 in LDL receptor knockout mice using an antisense oligonucleotide resulted in decreased circulating TMAO levels and atherosclerosis. Surprisingly, we also observed significant decreases in hepatic lipids and in levels of plasma lipids, ketone bodies, glucose, and insulin. FMO3 overexpression in transgenic mice, on the other hand, increased hepatic and plasma lipids. Global gene expression analyses suggested that these effects of FMO3 on lipogenesis and gluconeogenesis may be mediated through the PPARα and Kruppel-like factor 15 pathways. In vivo and in vitro results were consistent with the concept that the effects were mediated directly by FMO3 rather than trimethylamine/TMAO; in particular, overexpression of FMO3 in the human hepatoma cell line, Hep3B, resulted in significantly increased glucose secretion and lipogenesis. Our results indicate a major role for FMO3 in modulating glucose and lipid homeostasis in vivo, and they suggest that pharmacologic inhibition of FMO3 to reduce TMAO levels would be confounded by metabolic interactions

Relative Alignment between the Magnetic Field and Molecular Gas Structure in the Vela C Giant Molecular Cloud Using Low- and High-density Tracers

We compare the magnetic field orientation for the young giant molecular cloud Vela C inferred from 500 μm polarization maps made with the BLASTPol balloon-borne polarimeter to the orientation of structures in the integrated line emission maps from Mopra observations. Averaging over the entire cloud we find that elongated structures in integrated line-intensity or zeroth-moment maps, for low-density tracers such as 12CO and 13CO J → 1 – 0, are statistically more likely to align parallel to the magnetic field, while intermediate- or high-density tracers show (on average) a tendency for alignment perpendicular to the magnetic field. This observation agrees with previous studies of the change in relative orientation with column density in Vela C, and supports a model where the magnetic field is strong enough to have influenced the formation of dense gas structures within Vela C. The transition from parallel to no preferred/perpendicular orientation appears to occur between the densities traced by 13CO and by C18O J → 1 – 0. Using RADEX radiative transfer models to estimate the characteristic number density traced by each molecular line, we find that the transition occurs at a molecular hydrogen number density of approximately 103 cm−3. We also see that the Centre Ridge (the highest column density and most active star-forming region within Vela C) appears to have a transition at a lower number density, suggesting that this may depend on the evolutionary state of the cloud

GPU and cell phone-aided multimedia processing

Computing technology has been evolving rapidly during the past decades. New ideas and inventions are constantly developed to improve usability and processing power of applications. This thesis develops a multimedia processing system that uses GPU and cell phone to improve speed and user experience. The CUDA framework developed by NVIDIA turns the GPU into a manycore coprocessor of the CPU. We show in this thesis that by taking advantage of GPU computing, algorithms such as image encoding and resolution upconversion can be up to five times as fast. We also develop algorithms to use accelerometer-equipped cell phone as a remote controller to improve user interaction. When user performs various actions, input command is sent to the PC via Bluetooth and identified using motion detection algorithms. Some applications of these tools are presented, including image slideshow, multiview video viewer, as well as cell phone aided Google Map application and web browser

Analysis and identification of Android vulnerabilities and exploits

Android malware is a problem which users of the mobile operating system had to contend with. This project analysed 16 vulnerabilities from the Android framework to learn how to exploit them and developed proof-of-concept exploits for each of the vulnerabilities. The exploits were reverse engineered into Smali code using Apktool, and YARA rules were created based on unique patterns in Smali code to identify similar exploits. 82,389 published Android packages in the Google Play Store were then reverse engineered and scanned using Apktool and YARA using the rules created. The results from this project would be used for future Android vulnerability research.Bachelor of Engineering (Computer Science

An Autonomous, Self-Authenticating, and Self-Contained Secure Boot Process for Field-Programmable Gate Arrays

Secure booting within a field-programmable gate array (FPGA) environment is traditionally implemented using hardwired embedded cryptographic primitives and non-volatile memory (NVM)-based keys, whereby an encrypted bitstream is decrypted as it is loaded from an external storage medium, e.g., Flash memory. A novel technique is proposed in this paper that self-authenticates an unencrypted FPGA configuration bitstream loaded into the FPGA during the start-up. The internal configuration access port (ICAP) interface is accessed to read out configuration information of the unencrypted bitstream, which is then used as input to a secure hash function SHA-3 to generate a digest. In contrast to conventional authentication, where the digest is computed and compared with a second pre-computed value, we use the digest as a challenge to a hardware-embedded delay physical unclonable function (PUF) called HELP. The delays of the paths sensitized by the challenges are used to generate a decryption key using the HELP algorithm. The decryption key is used in the second stage of the boot process to decrypt the operating system (OS) and applications. It follows that any type of malicious tampering with the unencrypted bitstream changes the challenges and the corresponding decryption key, resulting in key regeneration failure. A ring oscillator is used as a clock to make the process autonomous (and unstoppable), and a novel on-chip time-to-digital-converter is used to measure path delays, making the proposed boot process completely self-contained, i.e., implemented entirely within the re-configurable fabric and without utilizing any vendor-specific FPGA features

Uroporphyrinogen decarboxylase as a potential target for specific components of traditional Chinese medicine: a virtual screening and molecular dynamics study.

Uroporphyrinogen decarboxylase (UROD) has been suggested as a protectant against radiation for head and neck cancer (HNC). In this study, we employed traditional Chinese medicine (TCM) compounds from TCM Database@Taiwan (http://tcm.cmu.edu.tw/) to screen for drug-like candidates with potential UROD inhibition characteristics using virtual screening techniques. Isopraeroside IV, scopolin, and nodakenin exhibited the highest Dock Scores, and were predicted to have good Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. Two common moieties, 2H-chromen-2-one and glucoside, were observed among the top TCM candidates. Cross comparison of the docking poses indicated that candidates formed stable interactions with key binding and catalytic residues of UROD through these two moieties. The 2H-chromen-2-one moiety enabled pi-cation interactions with Arg37 and H-bonds with Tyr164. The glucoside moiety was involved in forming H-bonds with Arg37 and Asp86. From our computational results, we propose isopraeroside IV, scopolin, and nodakenin as ligands that might exhibit drug-like inhibitory effects on UROD. The glucoside and 2H-chromen-2-one moieties may potentially be used for designing inhibitors of UROD

Solar Radiation Forecast Using Cloud Velocity for Photovoltaic Systems

Today, solar energy is used in a many different ways. One of the most popular technological developments for this purpose is photovoltaic conversion to electricity. However, power fluctuations due to the variability of solar energy are one of the challenges faced by the implementation of photovoltaic systems. To overcome this problem, forecasting solar radiation data several minutes in advance is needed. In this research, a methodology to forecast solar radiation using cloud velocity and cloud moving angle is proposed. Generally, a red-to-blue ratio (RBR) color model and correlation analysis are used for obtaining the cloud velocity and moving angle. Artificial neural network (ANN) forecast models with different input combinations are established. This methodology requires lower computational time since it only uses part of the pixels in the sky image. Based on R-squared analysis, it can be concluded that the ANN model with inputs of cloud velocity and moving angle and average solar radiation showed the highest accuracy among other combinations of inputs. The R-squared value was 0.59 with only a relatively small sample size of 42. The proposed model showed a highest improvement of 75.79% when compared to the ANN model based on historical solar radiation data only

H-bond interactions of UROD with top TCM candidates and Coproporphyrinogen III.

<p> <b>H-bond occupancy cutoff: 2.5 Å.</b></p