Recognition of Promoters in DNA Sequences Using Weightily Averaged One-dependence Estimators

AbstractThe completion of the human genome project in the last decade has generated a strong demand in computational analysis techniques in order to fully exploit the acquired human genome database. The human genome project generated a perplexing mass of genetic data which necessitates automatic genome annotation. There is a growing interest in the process of gene finding and gene recognition from DNA sequences. In genetics, a promoter is a segment of a DNA that marks the starting point of transcription of a particular gene. Therefore, recognizing promoters is a one step towards gene finding in DNA sequences. Promoters also play a fundamental role in many other vital cellular processes. Aberrant promoters can cause a wide range of diseases including cancers. This paper describes a state-of-the-art machine learning based approach called weightily averaged one-dependence estimators to tackle the problem of recognizing promoters in genetic sequences. To lower the computational complexity and to increase the generalization capability of the system, we employ an entropy-based feature extraction approach to select relevant nucleotides that are directly responsible for promoter recognition. We carried out experiments on a dataset extracted from the biological literature for a proof-of-concept. The proposed system has achieved an accuracy of 97.17% in classifying promoters. The experimental results demonstrate the efficacy of our framework and encourage us to extend the framework to recognize promoter sequences in various species of higher eukaryotes

A Control Method to Reduce Interferences and Collisions between Multiple RFID Tags and RFID Readers

Radio frequency identification technology (RFID) is one of the fastest developing technologies today. Although it has significant performance in use of Auto-ID applications, the presence of multiple tags in a RFID system can lead to interferences between each tags which is called Collision. There are many method to overcome this issue and this project introduces the use of DS-CDMA technique to overcome this issue. The Simulink simulation environment is used to simulate the use of DS-CDMA in RFID system. The results obtained clearly show the concept of this method is leading to a solution for RFID collision issues. However, the further improvement in simulations and concept of the method is most recommended in future project work

The Role of Cellular Architecture in Vascular Smooth Muscle Function and Mechanics

University of Minnesota Ph.D. dissertation. August 2017. Major: Biomedical Engineering. Advisor: Patrick Alford. 1 computer file (PDF); x, 98 pages.Recently, there has been a push towards clinical translation of biomechanical models of tissues by developing patient-specific models to predict disease outcomes. To accomplish this, it is necessary to understand the functional and mechanical properties of all the tissue components, including individual cells. In vasculature, tissues and cells have different structures based on their functional role. The principle goal of this work is to determine how cellular architecture influences function and mechanical properties. To test our hypotheses, we have developed in vitro models to study the relationship between structure and function at the tissue and cellular scale. We have developed microfluidic capture array device (MCAD) technology to study cell structure and function in 2D engineered vascular smooth muscle tissue and have developed cellular micro-biaxial stretching (CμBS) microscopy to determine single cell mechanical properties. First, using MCAD technology we were able to vary initial cell-cell contact during seeding to bias the cellular architecture in confluent vascular smooth muscle tissues. We found that tissues seeded using initially higher cell–cell contact conditions yielded tissues with more elongated cellular architecture which lead to greater contractile function in engineered tissues. We then used CμBS microscopy to determine the elastic anisotropic mechanical properties of individual cells, given by the strain energy density (SED) function. We found that smooth muscle cells (VSMCs) with native-like architectures are highly anisotropic and can be described by a SED based on the actin cytoskeletal organization. Then, we utilized CμBS microscopy to characterize loading and unloading mechanics of VSMCs. We found that VSMCs exhibit architecture-dependent anisotropic hysteresis where highly structured VSMCs exhibit typical hysteresis associated with viscous loss when stretched in the direction of actin fiber alignment but exhibit reverse hysteresis when stretched in the direction orthogonal to actin fiber alignment. We then modeled the observed hysteresis using two models: a quasi-linear (QLV) model and a Hill-type active fiber model and found that the QLV model was insufficient to characterize the anisotropic hysteresis but the Hill-type active fiber model was able to predict the anisotropic hysteresis in highly-organized VSMCs

Graphene is neither Relativistic nor Non-Relativistic case: Thermodynamics Aspects

Discovery of electron hydrodynamics in graphene system has opened a new scope of analytic calculations in condensed matter physics, which was traditionally well cultivated in science and engineering as a non-relativistic hydrodynamics and in high energy nuclear and astro physics as relativistic hydrodynamics. Electrons in graphene follow neither non-relativistic nor relativistic hydrodynamics and thermodynamics. Present article has gone through systematic microscopic calculations of thermodynamical quantities like pressure, energy density, etc. of electron-fluid in graphene and compared with corresponding estimations for non-relativistic and ultra-relativistic cases. Identifying the Dirac fluid and Fermi liquid domains, we have sketched the transition of temperature and Fermi energy dependency of electron thermodynamics for graphene and other cases. An equivalent transition for quark matter is also discussed. The most exciting part is the general expression of specific heat, whose Fermi to Dirac fluid domain transition can be realized as a transition from a solid-based to a fluid-based picture. This understanding may be connected to the experimentally observed Wiedemann-Franz Law violation in the Dirac fluid domain of graphene system.Comment: 16 pages, 13 figure

A Control Method to Reduce Interferences and Collisions between Multiple RFID Tags and RFID Readers

Radio frequency identification technology (RFID) is one of the fastest developing technologies today. Although it has significant performance in use of Auto-ID applications, the presence of multiple tags in a RFID system can lead to interferences between each tags which is called Collision. There are many method to overcome this issue and this project introduces the use of DS-CDMA technique to overcome this issue. The Simulink simulation environment is used to simulate the use of DS-CDMA in RFID system. The results obtained clearly show the concept of this method is leading to a solution for RFID collision issues. However, the further improvement in simulations and concept of the method is most recommended in future project work

CANCER RECOGNITION FROM DNA MICROARRAY GENE EXPRESSION DATA USING AVERAGED ONE- DEPENDENCE ESTIMATORS

ABSTRAC

Development of a New Method to Estimate Ionospheric TEC Distribution by Single Frequency Measurements of GPS Signals

13301甲第4569号博士（工学）金沢大学博士論文要旨Abstract 以下に掲載：International Journal of Advanced Computer Science and Applications 7(12) pp.1-6 2016. The Science and Information Orgnization (SAI). 共著者：Win Zaw Hein, Yoshitaka Goto, Yoshiya Kasahar

Development of a New Method to Estimate Ionospheric TEC Distribution by Single Frequency Measurements of GPS Signals

13301甲第4569号博士（工学）金沢大学博士論文本文Full 以下に掲載：International Journal of Advanced Computer Science and Applications 7(12) pp.1-6 2016. The Science and Information Orgnization (SAI). 共著者：Win Zaw Hein, Yoshitaka Goto, Yoshiya Kasahar