Search results for: Wenyu Guo

Authors: Guo Wenyu, Qu Youli

Abstract:

A practical and simple self-indexing data structure, Partitioned Elias-Fano (PEF) - Compressed Suffix Arrays (CSA), is built in linear time for the CSA based on PEF indexes. Moreover, the PEF-CSA is compared with two classical compressed indexing methods, Ferragina and Manzini implementation (FMI) and Sad-CSA on different type and size files in Pizza & Chili. The PEF-CSA performs better on the existing data in terms of the compression ratio, count, and locates time except for the evenly distributed data such as proteins data. The observations of the experiments are that the distribution of the φ is more important than the alphabet size on the compression ratio. Unevenly distributed data φ makes better compression effect, and the larger the size of the hit counts, the longer the count and locate time.

Keywords: compressed suffix array, self-indexing, partitioned Elias-Fano, PEF-CSA

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Authors: Junhong Feng, Wenyu Lu, Xinhong Cheng, Li Zheng, Yuehui Yu

Abstract:

The effects of proton irradiation on the properties of gate oxide were evaluated by monitoring the static parameters (such as threshold voltage and on-resistance) and dynamic parameters (Miller plateau time) of 1700V SiC VDMOS before and after proton irradiation. The incident proton energy was 3MeV, and the doses were 5 × 10¹² P / cm², 1 × 10¹³ P / cm², respectively. The results show that the threshold voltage of MOS exhibits negative drift under proton irradiation, and the near-interface traps in the gate oxide layer are occupied by holes generated by the ionization effect of irradiation, thus forming more positive charges. The basis for selecting TMiller is that the change time of Vgs is the time when Vds just shows an upward trend until it rises to a stable value. The degradation of the turn-off time of the Miller platform verifies that the capacitance Cgd becomes larger, reflecting that the gate oxide layer is introduced into the trap by the displacement effect caused by proton irradiation, and the interface state deteriorates. As a more sensitive area in the irradiation process, the gate oxide layer will be optimized for its parameters (such as thickness, type, etc.) in subsequent studies.

Keywords: SiC VDMOS, proton radiation, Miller time, gate oxide

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Authors: Christine Y. Yeh, Brian D. Piening, Sarah M. Totten, Kimberly Kukurba, Wenyu Zhou, Kevin P. F. Contrepois, Gucci J. Gu, Sharon Pitteri, Michael Snyder

Abstract:

Three million deaths worldwide are attributed to obesity. However, the biomolecular mechanisms that describe the link between adiposity and subsequent disease states are poorly understood. Insulin resistance characterizes approximately half of obese individuals and is a major cause of obesity-mediated diseases such as Type II diabetes, hypertension and other cardiovascular diseases. This study makes use of longitudinal quantitative and high-throughput multi-omics (genomics, epigenomics, transcriptomics, glycoproteomics etc.) methodologies on blood samples to develop multigenic and multi-analyte signatures associated with weight gain and insulin resistance. Participants of this study underwent a 30-day period of weight gain via excessive caloric intake followed by a 60-day period of restricted dieting and return to baseline weight. Blood samples were taken at three different time points per patient: baseline, peak-weight and post weight loss. Patients were characterized as either insulin resistant (IR) or insulin sensitive (IS) before having their samples processed via longitudinal multi-omic technologies. This comparative study revealed a wealth of biomolecular changes associated with weight gain after using methods in machine learning, clustering, network analysis etc. Pathways of interest included those involved in lipid remodeling, acute inflammatory response and glucose metabolism. Some of these biomolecules returned to baseline levels as the patient returned to normal weight whilst some remained elevated. IR patients exhibited key differences in inflammatory response regulation in comparison to IS patients at all time points. These signatures suggest differential metabolism and inflammatory pathways between IR and IS patients. Biomolecular differences associated with weight gain and insulin resistance were identified on various levels: in gene expression, epigenetic change, transcriptional regulation and glycosylation. This study was not only able to contribute to new biology that could be of use in preventing or predicting obesity-mediated diseases, but also matured novel biomedical informatics technologies to produce and process data on many comprehensive omics levels.

Keywords: insulin resistance, multi-omics, next generation sequencing, proteogenomics, type ii diabetes

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Authors: Wenyu Guo, Malachy O’Rourke, Mark Bowkett, Michael Gilchrist

Abstract:

Many devices for real-time monitoring of surface water have been developed in the past few years to provide early warning of pollutions and so to decrease the risk of environmental pollution efficiently. One of the most common methodologies used in the detection system is a colorimetric process, in which a container with fixed volume is filled with target ions and reagents to combine a colorimetric dye. The colorimetric ions can sensitively absorb a specific-wavelength radiation beam, and its absorbance rate is proportional to the concentration of the fully developed product, indicating the concentration of target nutrients in the pre-mixed water samples. In order to achieve precise and rapid detection effect, channels with dimensions in the order of micrometers, i.e., microfluidic systems have been developed and introduced into these diagnostics studies. Microfluidics technology largely reduces the surface to volume ratios and decrease the samples/reagents consumption significantly. However, species transport in such miniaturized channels is limited by the low Reynolds numbers in the regimes. Thus, the flow is extremely laminar state, and diffusion is the dominant mass transport process all over the regimes of the microfluidic channels. The objective of this present work has been to analyse the mixing effect and chemistry kinetics in a stop-flow microfluidic device measuring Nitride concentrations in fresh water samples. In order to improve the temporal resolution of the Nitride microfluidic sensor, we have used computational fluid dynamics to investigate the influence that the effectiveness of the mixing process between the sample and reagent within a microfluidic device exerts on the time to completion of the resulting chemical reaction. This computational approach has been complemented by physical experiments. The kinetics of the Griess reaction involving the conversion of sulphanilic acid to a diazonium salt by reaction with nitrite in acidic solution is set in the Laminar Finite-rate chemical reaction in the model. Initially, a methodology was developed to assess the degree of mixing of the sample and reagent within the device. This enabled different designs of the mixing channel to be compared, such as straight, square wave and serpentine geometries. Thereafter, the time to completion of the Griess reaction within a straight mixing channel device was modeled and the reaction time validated with experimental data. Further simulations have been done to compare the reaction time to effective mixing within straight, square wave and serpentine geometries. Results show that square wave channels can significantly improve the mixing effect and provides a low standard deviations of the concentrations of nitride and reagent, while for straight channel microfluidic patterns the corresponding values are 2-3 orders of magnitude greater, and consequently are less efficiently mixed. This has allowed us to design novel channel patterns of micro-mixers with more effective mixing that can be used to detect and monitor levels of nutrients present in water samples, in particular, Nitride. Future generations of water quality monitoring and diagnostic devices will easily exploit this technology.

Keywords: nitride detection, computational fluid dynamics, chemical kinetics, mixing effect

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