A direct manipulation object-oriented environment to support methodology-independent CASE tools : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Computer Science at Massey University

The aim of the thesis is research into application of direct-manipulable OO graphical environments to the development of methodology-independent CASE tools. In this thesis, a Methodology-Independent Graphical OO CASE Environment (M1GOCE) is proposed. MIGOCE consists of three parts: OO Notation Workshop, OO Notation Repository and Universal OO Diagramming Tool. OO Notation Workshop is an OO graphical editor which is used to design existing and new notations; OO Notation Repository is a notation database that stores different notations designed by the notation workshop; Universal OO Diagramming Tool is an upper-CASE graphical environment, by which a user can draw arbitrary OO diagrams of different methodologies. The MIGOCE database management system provides OO notation sets management, OOA/OOD diagrams management and OO repository management for data integrity and sharing. MIGOCE has three outstanding characteristics: Methodology-independence, Directly-manipulable graphical environment and Easily-expanded program structure MIGOCE is completely methodology-independent. It not only supports existing OO methodologies, but also supports users' own notation designs. It provides support for mixing, updating existing methodologies or defining new ones. It typically allows the user to switch quickly different OO notation sets supported by corresponding methodologies for designing diagrams. Direct manipulation interfaces of MIGOCE enable it more flexible and distinctive. The user can easily add, delete, edit or show notation shapes, and get the system feedback very quick on the screen. The MIGOCE system itself is programmed using object-oriented programming language - C++. Its program structure enable the functions of itself easy to be modified and expanded. Although MIGOCE is a prototype, it provides a new way to develop the real methodology-independent OO CASE environment. So far, the way and style taken by MIGOCE have not been found in OO CASE literatures. This system gives a complete possibility of implementing a methodology-independent OO CASE tool and shows distinct effectiveness of such a tool in practice

Strategies of reducing input sample volume for extracting circulating cell-free nuclear DNA and mitochondrial DNA in plasma

Background: Circulating cell-free (ccf) DNA in blood has been suggested as a potential biomarker in many conditions regarding early diagnosis and prognosis. However, misdiagnosis can result due to the limited DNA resources in Biobank's plasma samples or insufficient DNA targets from a predominant DNA background in genetic tests. This study explored several strategies for an efficient DNA extraction to increase DNA amount from limited plasma input. Methods: Ccf plasma DNA was extracted with three different methods, a phenol-chloroform-isoamylalcohol (PCI) method, a High Pure PCR Template Preparation Kit method and a method used for single cell PCR in this group. Subsequently, the total DNA was measured by Nanodrop and the genome equivalents (GE) of the GAPDH housekeeping gene and MTATP 8 gene were measured using a multiplex real-time quantitative PCR for the quantitative assessment of nDNA and mtDNA. Results: Instead of 400-800 μL (routine input in the laboratory), 50 μLof plasma input enabled the extraction of ccf DNA sufficient for quantitative analysis. Using the PCI method and the kit method, both nDNA and mtDNA could be successfully detected in plasma samples, but nDNA extracted using protocol for single cell PCR was not detectable in 25% of plasma samples. In comparison to the other two methods, the PCI method showed lower DNA purity, but higher concentrations and more GE of nDNA and mtDNA. Conclusions: The PCI method was more efficient than the other two methods in the extraction of ccf DNA in plasma. Limited plasma is available for ccf DNA analysi

HIV-1 Tat Triggers Nuclear Localization of ZO-1 via Rho Signaling and cAMP Response Element-Binding Protein Activation

The human immunodeficiency virus (HIV)-specific protein trans-activator of transcription (Tat) can contribute to the dysfunction of brain endothelial cells and HIV trafficking into the brain by disrupting tight junction (TJ) integrity at the blood–brain barrier (BBB) level. Specific TJ proteins, such as zonula occludens (ZO) proteins, localize not only at the cell–cell borders but are also present in the nuclei. The objective of the present study was to evaluate the mechanisms and significance of Tat-induced nuclear localization of ZO-1. Treatment of a brain endothelial cell line (hCMEC/D3 cells) with Tat resulted in a decrease in total levels of ZO-1 but significantly upregulated ZO-1 protein expression in the nuclei. In addition, exposure to Tat stimulated Rho signaling and induced phosphorylation and activity of transcription factor cAMP response element-binding protein (CREB), binding sites that have been identified in the proximal region of the ZO-1 promoter. Interestingly, inhibition of the Rho cascade protected against Tat-induced upregulation of ZO-1 in the nuclei and activation of CREB. Depletion of CREB by infection of cells with specific shRNA lentiviral particles attenuated both Tat-induced Rho signaling and nuclear targeting of ZO-1. A decrease in CREB levels also attenuated Tat-induced endothelial and BBB hyperpermeability as well as transendothelial migration of monocytic cells. The role of CREB in Tat-mediated alterations of ZO-1 was confirmed in brain microvessels in mice with CREB shRNA lentiviral particles injected into the cerebral circulation. The present results indicate the crucial role of Rho signaling and CREB in modulation of nuclear localization of ZO-1 and maintaining the integrity of endothelial monolayers

Rainbow tensor model with two tensors of rank three

We give the keystone operators and construct a graded ring with tree and loop operators. In terms of the keystones operators, connected tree and loop operators in the ring, we construct the rainbow tensor model with two tensors of rank-3 and present its $W$-representation. Moreover we derive the compact expressions of correlators from the $W$-representation and analyze the free energy in large $N$ limit. In addition, we establish the correspondence between two colored Dyck walks in the Fredkin spin chain and tree operators in the ring. Based on the classification Dyck walks, we give the number of tree operators with the given level. Furthermore, for the entanglement entropy of the Fredkin spin chain, we show the entanglement scaling beyond logarithmic scaling in the ordinary critical systems from the viewpoint of tensor model.Comment: 27 pages, 15 figures, 1 tabl