Open Science Research Excellence

D Lim

Publications

4

Publications

4
4182
Comparison of Phylogenetic Trees of Multiple Protein Sequence Alignment Methods
Abstract:
Multiple sequence alignment is a fundamental part in many bioinformatics applications such as phylogenetic analysis. Many alignment methods have been proposed. Each method gives a different result for the same data set, and consequently generates a different phylogenetic tree. Hence, the chosen alignment method affects the resulting tree. However in the literature, there is no evaluation of multiple alignment methods based on the comparison of their phylogenetic trees. This work evaluates the following eight aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN, ProbCons and Align-m, based on their phylogenetic trees (test trees) produced on a given data set. The Neighbor-Joining method is used to estimate trees. Three criteria, namely, the dNNI, the dRF and the Id_Tree are established to test the ability of different alignment methods to produce closer test tree compared to the reference one (true tree). Results show that the method which produces the most accurate alignment gives the nearest test tree to the reference tree. MUSCLE outperforms all aligners with respect to the three criteria and for all datasets, performing particularly better when sequence identities are within 10-20%. It is followed by T-Coffee at lower sequence identity (30%), trees scores of all methods become similar.
Keywords:
Multiple alignment methods, phylogenetic trees, Neighbor-Joining method, Robinson-Foulds distance.
3
8615
Benefits and Issues of Open-Cut Coal Mining on the Socio-Economic Environment - The Iban Community in Mukah, Sarawak, Malaysia
Authors:
Abstract:

This paper deals principally with the socio-economic impact on the local Iban community in Mukah Division, Sarawak; with the commencement of the open-cut coal mining industry since 2003. To-date there are no actual studies being carried out by either the public or private sector to truly analyze how the Iban community is coping with the advent of a large influx of cash into their society. The Iban community has traditionally been practicing shifting cultivation and farming of domesticated animals; with a portion of the younger generation working as laborers and professional. This paper represents the views and observations of the author supported by some statistical facts extracted from published articles and non-published reports. The paper deals primarily in the following areas: • Background of the coal mining industry in Mukah Division, Sarawak; • Benefits of the coal mining industry towards the Iban community; • Issues / Problems arise in the Iban community because of the presence of the coal mining industry; and • Possible actions that need to be taken to overcome these issues/ problems.

Keywords:
Coal Mining, Iban Community, Malaysia, Sub-Bituminous Coal.
2
9088
A Feasibility-study of a Micro- Communications Sonobuoy Deployable by UAV Robots
Abstract:
This paper describes a feasibility study that is included with the research, development and testing of a micro communications sonobuoy deployable by Maritime Fixed wing Unmanned Aerial Vehicles (M-UAV) and rotor wing Quad Copters which are both currently being developed by the University of Adelaide. The micro communications sonobuoy is developed to act as a seamless communication relay between an Autonomous Underwater Vehicle (AUV) and an above water human operator some distance away. Development of such a device would eliminate the requirement of physical communication tethers attached to submersible vehicles for control and data retrieval.
Keywords:
Autonomous Underwater Vehicle, AUV, Maritime, Unmanned Aerial Vehicle, UAV, Micro Sonobuoy, Communication.
1
10003353
Optical Flow Technique for Supersonic Jet Measurements
Abstract:

This paper outlines the development of an experimental technique in quantifying supersonic jet flows, in an attempt to avoid seeding particle problems frequently associated with particle-image velocimetry (PIV) techniques at high Mach numbers. Based on optical flow algorithms, the idea behind the technique involves using high speed cameras to capture Schlieren images of the supersonic jet shear layers, before they are subjected to an adapted optical flow algorithm based on the Horn-Schnuck method to determine the associated flow fields. The proposed method is capable of offering full-field unsteady flow information with potentially higher accuracy and resolution than existing point-measurements or PIV techniques. Preliminary study via numerical simulations of a circular de Laval jet nozzle successfully reveals flow and shock structures typically associated with supersonic jet flows, which serve as useful data for subsequent validation of the optical flow based experimental results. For experimental technique, a Z-type Schlieren setup is proposed with supersonic jet operated in cold mode, stagnation pressure of 4 bar and exit Mach of 1.5. High-speed singleframe or double-frame cameras are used to capture successive Schlieren images. As implementation of optical flow technique to supersonic flows remains rare, the current focus revolves around methodology validation through synthetic images. The results of validation test offers valuable insight into how the optical flow algorithm can be further improved to improve robustness and accuracy. Despite these challenges however, this supersonic flow measurement technique may potentially offer a simpler way to identify and quantify the fine spatial structures within the shock shear layer.

Keywords:
Schlieren, optical flow, supersonic jets, shock shear layer.