Protein secondary structure prediction using BLAST and relaxed threshold rule induction from coverings

Protein structure prediction has always been an important research area in bioinformatics and biochemistry. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q₃ accuracy of various computational prediction methods rarely has exceeded 75%; this status has changed little since 2003 when Rost stated that the currently best methods reach a level around 77% three-state per-residue accuracy. The application of artificial neural network methods to this problem is revolutionary in the sense that those techniques employ the homologues of proteins for training and prediction. In this dissertation, a different approach, RT-RICO (Relaxed Threshold Rule Induction from Coverings), is presented that instead uses association rule mining. This approach still makes use of the fundamental principle that structure is more conserved than sequence. However, rules between each known secondary structure element and its neighboring amino acid residues are established to perform the predictions. This dissertation consists of five research articles that discuss different prediction techniques and detailed rule-generation algorithms. The most recent prediction approach, BLAST-RT-RICO, achieved a Q₃ accuracy score of 89.93% on the standard test dataset RS126 and a Q₃ score of 87.71% on the standard test dataset CB396, an improvement over comparable computational methods. Herein one research article also discusses the results of examining those RT-RICO rules using an existing association rule visualization tool, modified to account for the non-Boolean characterization of protein secondary structure --Abstract, page iv

Real Exchange Rate Behavior: New Evidence with Linear and Non-linear Endogenous Break(s)

Using monthly frequency data from 1981 to 2005, we test for the potential mean reversion of Japan-US real exchange rates using newly improved unit root tests allowing for endogenous (unknown) break(s) in the linear as well as non-linear manner. Both countries have contributed vital proportion in global trading on top of being the major trading partner to each other since 1960s. We identify structural breaks in 1985 and 1994 respectively via the Lumsdaine and Papell (1997)’s linear test, but the results were against the PPP hypothesis. The Saikkonen and LÄutkepohl, (2002)’s test, however, provides sufficient supports for non-linear adjustment of real exchange towards long run PPP. In addition, stronger evidence for PPP is found in the post-1994 period, in conjunction with the small persistence of real exchange deviations (half-life less than a year). Also, the exchange rate misalignment is less evident after the Plaza Accord 1985. In brief, our findings reveal that the Japanese authority has shown some form of PPP-oriented rule as a basis for their exchange rate policies, in the presence of structural break(s) and non-linearity.Real Exchange Rates, Endogenous Breaks, Non-linearity, Half-life

Precipitation of amorphous ferromagnetic semiconductor phase in epitaxially grown Mn-doped Ge thin films

We investigated the origin of ferromagnetism in epitaxially grown Mn-doped Ge thin films. Using low-temperature molecular beam epitaxy, Mn-doped Ge films were successfully grown without precipitation of ferromagnetic Ge-Mn intermetallic compounds, such as Mn5Ge3. Magnetic circular dichroism measurements revealed that the epitaxially grown Mn-doped Ge films exhibited clear ferromagnetic behavior, but the Zeeman splitting observed at the critical points was not induced by the s,p-d exchange interactions. High-resolution transmission electron microscopy and energy dispersive X-ray spectroscopy analyses show phase separation of amorphous Ge1-xMnx clusters with high Mn content from a Mn-free monocrystalline Ge matrix. Since amorphous Ge1-xMnx was characterized as a homogeneous ferromagnetic semiconductor, the precipitation of the amorphous Ge1-xMnx clusters is the origin of the ferromagnetic semiconductor behavior of the epitaxially grown Mn-doped Ge films.Comment: 12pages, 4figure

Course Time Table Scheduling for a Local College

This study dive into the field of course time table scheduling for a local institution. The subject of the study will be a local college in Malaysia, in particular on the SEGi College branch in Penang. This covers the development of the prototype software which will enable the simulation of the course time table for both the students and lecturers. The prototype software will be on a local search approach with reference to Hill Climbing with Random Walk algorithm and Best First Search algorithm. This research enables users to increase efficiency and performance in developing a course time table. Later,this research will be proposed for implementation to the management of SEGi College branch in Penang

A Study On Saturation Flow Rates Of Through Vehicles At Signalised Intersections Based On Malaysian Road Conditions. [HE336.T7 L583 2004 f rb] [Microfiche 7668]

Aliran tepu merupakan satu parameter yang penting dalam analisis kapasiti persimpangan berlampu isyarat. Saturation flow is an important parameter in the capacity analysis of signalised intersections

The impact of dividend tax changes on the performance of Malaysian REITs

This is the first empirical research examining the effects of dividend taxes on the performance of real estate investment trusts (REITs) in Malaysia. The Malaysian government’s announcement of remissions of dividend tax for the REIT sector under the 2007, 2009 and 2011 budgets, provide an excellent but rare opportunity to examine the impact of taxation on stock price performance and stock liquidity. It can be concluded that dividend tax cut announcements made in 2006 and 2008 resulted in a positive stock price reaction from the stock market. The cumulative average abnormal returns (CAARs) are significant at the 10% level across the three event windows. The CAARs for dividend tax remission announced in 2011, on the other hand, are not significantly different from zero. These results support the hypothesis that the announcement of dividend tax reductions increases the wealth of REITs because tax is a form of transaction cost. The insignificance of third announcement CAARs could possible due to lack of new information as it merely extended the dividend tax benefits for another 4 years until 2016. It is also verified that there were no evidence to support the hypothesis that dividend tax cuts will increase the liquidity of REIT shares as proxied by shares trading volum

Characteristics of Firms Going Private in the Malaysian Stock Exchange

The study empirically investigates the financial characteristics that discriminate firms that went private and firms that remain publicly traded. Based on the results of logit and probit model, companies that reverted to the private domain are characterized as having higher cash balance, higher degree of undervaluation, higher operating profit margin, lower dividend payout rate, and lower free float compared to public counterparts. The classification accuracy rates for in-sample and holdout sample are 69.17% and 65.38% respectively.Going Private, Public-to-Private Transaction, Stock Market, Target Prediction, Firm Characteristics

Malmquist Indices of Pre and Post-Deregulation Productivity, Efficiency and Technological Change in the Singaporean Banking Sector

By the end of the 1990s, the Singaporean government had recognised the need to open up its banking sector so as to remain competitive in the global economy. The Monetary Authority of Singapore thus began deregulation of the banking sector in 1999 to strengthening the competitiveness of local banks relative to their foreign competition through mergers. This paper employs a nonparametric Malmquist productivity index to provide measure of productivity, technological change and efficiency gains over the period 1995-2005. The findings reveal some total factor productivity growth associated with deregulation and scale efficiency improvement largely from mergers amongst the local banks.Efficiency, productivity; deregulation; Malmquist indices; banking