Medical and Health Sciences

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3D surface reconstruction for lower limb prosthetic model using modified radon transform
(Universiti Teknologi Malaysia, 2017) Mohd. Sobani, Siti Syazalina
Computer vision has received increased attention for the research and innovation on three-dimensional surface reconstruction with aim to obtain accurate results. Although many researchers have come up with various novel solutions and feasibility of the findings, most require the use of sophisticated devices which is computationally expensive. Thus, a proper countermeasure is needed to resolve the reconstruction constraints and create an algorithm that is able to do considerably fast reconstruction by giving attention to devices equipped with appropriate specification, performance and practical affordability. This thesis describes the idea to realize three-dimensional surface of the residual limb models by adopting the technique of tomographic imaging coupled with the strategy based on multiple-views from a digital camera and a turntable. The surface of an object is reconstructed from uncalibrated two-dimensional image sequences of thirty-six different projections with the aid of Radon transform algorithm and shape-from-silhouette. The results show that the main objective to reconstruct three-dimensional surface of lower limb model has been successfully achieved with reasonable accuracy as the starting point to reconstruct three-dimensional surface and extract digital reading of an amputated lower limb model where the maximum percent error obtained from the computation is approximately 3.3 % for the height whilst 7.4%, 7.9% and 8.1% for the diameters at three specific heights of the objects. It can be concluded that the reconstruction of three-dimensional surface for the developed method is particularly dependent to the effects the silhouette generated where high contrast two-dimensional images contribute to higher accuracy of the silhouette extraction. The advantage of the concept presented in this thesis is that it can be done with simple experimental setup and the reconstruction of three-dimensional model neither involves expensive equipment nor require any service by an expert to handle sophisticated mechanical scanning system
Adaptive nonlinear multivariate brain connectivity analysis of motor imagery movements using graph theory
(Universiti Teknologi Malaysia, 2016) Hamedi, Mahyar
Recent studies on motor imagery (MI)-based brain computer interaction (BCI) reported that the interaction of spatially separated brain areas in forms of functional or effective connectivity leads to a better insight of brain neural patterns during MI movements and can provide useful features for BCIs. However, existing studies suffer from unrealistic assumptions or technical weaknesses for processing brain signals, such as stationarity, linearity and bivariate analysis framework. Besides, volume conduction effect as a critical challenge in this area and the role of subcortical regions in connectivity analysis have not been considered and studied well. In this thesis, the neurophysiological connectivity patterns of healthy human brain during different MI movements are deeply investigated. At first, an adaptive nonlinear multivariate statespace model known as dual extended Kalman filter is proposed for connectivity pattern estimation. Several frequency domain functional and effective connectivity estimators are developed for nonlinear non-stationary signals. Evaluation results show superior parameter tracking performance and hence more accurate connectivity analysis by the proposed model. Secondly, source-space time-varying nonlinear multivariate brain connectivity during feet, left hand, right hand and tongue MI movements is investigated in a broad frequency range by using the developed connectivity estimators. Results reveal the similarities and the differences between MI tasks in terms of involved regions, density of interactions, distribution of interactions, functional connections and information flows. Finally, organizational principles of brain networks of MI movements measured by all considered connectivity estimators are extensively explored by graph theoretical approach where the local and global graph structures are quantified by computing different graph indexes. Results report statistical significant differences between and within the MI tasks by using the graph indexes extracted from the networks formed particularly by normalized partial directed coherence. This delivers promising distinctive features of the MI tasks for non-invasive BCI applications
Andrographis paniculata crude extract and its polymeric nanoparticles fraction for inhibition of cervix cancer cells
(Universiti Teknologi Malaysia, 2018) Sanati, Parisa
Cervix cancer contributes to high mortality rate around the world and various efforts have been done to identify suitable treatments and remedies, including the use of Andrographis paniculata, a plant rich in andrographolide (AG) with remarkable anti-cancer properties. AG in the form of nanoparticles has been proven to increase the efficiency and bioavailability of the herbal medicine. So far, no studies have been reported on the use of spontaneous emulsion solvent diffusion (SESD) method to produce polymeric nanoparticles (PNPs) of AG. Therefore, this study was conducted to produce crude extract and AG rich fraction, and SESD method was used to prepare the extracts into PNPs, which were then characterized and tested on cervix cancer cells. The crude extract and AG rich fraction were prepared by reflux technique, followed by successive soxhlet extraction. Polyvinyl alcohol (1%) was found to be the best concentration of emulsifier to prepare the PNPs at 2400 rpm for 5 min in a homogenizer. The nanomization achieved 80 % encapsulation efficiency with the particle size, 149.38 and 163.40 nm for crude extract and AG rich fraction, respectively. The low polydispersity index (0.23-0.38) also revealed uniform crude extract and AG rich fraction PNPs. The zeta potential values -37.30 and -57.85 mV for crude extract and AG rich fraction, respectively indicated stables PNPs. No significant chemical interaction was found between AG and polylactic-co-glycolic acid polymer on attenuated total reflection images. In vitro AG release showed a high initial burst release for both PNPs. The AG extracts, as well as their PNPs showed dose and time dependent anti-proliferative activities against hela cells. AG rich fraction exhibited higher anti-cancer activity than crude extract. Both extracts and their PNPs did not have any inhibition effect on proliferation of normal cells. Therefore, AG rich fraction PNPs was selective against the growth of cervix cancer cells. The findings of this study will be beneficial for relevant healthcare and therapeutic industries
Anti-inflammatory and cytoprotective effects of 5, 7-dimethoxyflavone and 4', 5-7 - trimethoxyflavone on human umbilical vein endothelial cells
(Universiti Teknologi Malaysia, 2016) Nadri, Muhammad Helmi
Previous cell culture-based studies have shown potential health benefits of polyphenolic compounds conveyed by fruit and vegetables. However, most of these studies have rather tested higher concentrations of polyphenols than those maximum plasma concentrations, which is rarely exceed 10 µM, attained after a consumption of polyphenol-rich diet. Therefore, the present in vitro study investigates the antiinflammatory and cytoprotective effects of 5,7-dimethoxyflavone (DMF) and 4’,5,7- trimethoxyflavone (TMF) at both physiological and supraphysiological concentrations. DMF and TMF were tested for inhibitory activities on cyclooxygenase-2 (COX-2) and 15-lipoxygenase (15-LOX), both play important role in inflammation, using direct enzyme inhibition assay. DMF at concentrations of 0.01-10 µM were also used to treat oxidative stress-induced human umbilical vein endothelial cells (HUVEC), to assess effects on the expression of markers related to increased vasodilation and inflammation. Particularly, markers for vasodilation including endothelial nitric oxide synthase (eNOS) and endothelin-1 (ET-1), and markers for inflammation such as intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1), were assayed using qRT-PCR. DMF and TMF strongly inhibit prostaglandins production through direct suppression of COX-2 activity, nearly equivalent to indomethacin with the mechanism mimicked current used drug, diclofenac based on molecular docking. Physiological and supraphysiological concentrations of DMF and TMF have been found to effectively abolish the effect of hydrogen peroxide (H2O2)-induced cell death in HUVEC independent of antioxidant activities. Furthermore, DMF at supraphysiological concentration was found to regulate eNOS expression at transcription rather than translational level in H2O2-induced HUVEC. In addition, H2O2 was found to increase ET-1, ICAM-1 and VCAM-1 mRNA expression in HUVEC culture and these negative effects was reversed by DMF at supraphysiological concentration. Since tested markers are the key molecules involved in the early atherogenic process, the present study emphasize a novel mechanism by which DMF may exert antiatherogenic activities under oxidative stress condition.
Automatic white matter lesions detection and segmentation of brain magnetic resonance images
(Universiti Teknologi Malaysia, 2019) Ong, Kok Haur
White matter lesions (WML) are frequently associated with neuronal degeneration in ageing and can be an important indicator of stroke, multiple sclerosis, dementia and other brain-related disorders. WML can be readily detected on Magnetic Resonance Imaging (MRI), but manual delineation of lesions by neuroradiologists is a time consuming and laborious task. Furthermore, MRI intensity scales are not standardised and do not have tissue-specific interpretation, leading to WML quantification inaccuracies and difficulties in interpreting their pathological relevance. Numerous studies have shown tremendous advances in WML segmentation, but flow artefact, image noise, incomplete skull stripping and inaccurate WML classification continue to yield False Positives (FP) that have limited the reliability and clinical utility of these approaches. The present study proposed a new MRI intensity standardisation and clustered texture feature method based on the K-means clustering algorithm. Enhanced clustered texture features and histogram features were constructed based on the proposed standardisation method to significantly reduce FP through a Random Forest algorithm. Subsequently, a local outlier identification method further refined the boundary of WML for the final segmentation. The method was validated with a test set of 32 scans (279 images), with a significant correlation coefficient (R=0.99574, p-value < 0.001) between the proposed method and manual delineation by a neuroradiologist. Furthermore, comparison against three state-of-the-art methods for the 32 scans demonstrated that the proposed method outperformed five of seven well-known evaluation metrics. This improved specificity in WML segmentation may thus improve the quantification of clinical WML burden to assess for correlations between WML load and distribution with neurodenegerative disease.
Autonomy support, motivations, value and natural content belief on herbal medicine product consumptions amongst emerging adults
(Universiti Teknologi Malaysia, 2020) Tam, Yin Ling @ Adeline Tam
Global and local herbal medicine product markets experienced recorded growth, while emerging adults are one of the fastest growing markets for health-related products in Malaysia. However, emerging adults are turning to non-herbal products. Although marketing herbal medicines to emerging adults would provide significant contributions, empirical study on herbal medicine product consumption was limited. Underpinned by Self-Determination Theory (SDT), this study addressed the practical and literature gaps by investigating the effects of perceived autonomy support, motivations, consumer perceived value, and natural content belief on herbal medicines products consumption stages. Consumer perceived value is included as the mediator on the relationship between autonomous motivation and consumption stages, while natural content belief is included to moderate the relationship between motivations and consumption stages. Multi-method quantitative research, using cross-sectional survey questionnaire and experiment, were conducted. Natural content belief was tested with experiment, while other variables were examined with survey. Samples of this research were emerging adults studying in local universities. Data were collected from Universiti Malaysia Sabah and Universiti Teknologi Malaysia. A total of 363 usable samples collected, in which 184 were in experiment group and the rest were in controlled group. Partial Least Square Structural Equation Modelling technique is applied to analyse a model and eight hypotheses. The last hypothesis was analysed with profile analysis, a person-centred approach, to understand consumer profile. Analysis of the results confirmed that perceived autonomy support significantly influenced motivations, as well as autonomous motivation significantly predicted consumption stages. Mediation effects of autonomous motivation and consumer perceived value were also found significant, respectively. However, moderation effects of natural content belief were rejected. Profile analysis provided insights on the herbal medicine consumer profiles. Meanwhile a model predicting herbal medicine consumption is confirmed theoretically. Mediation effect of consumer perceived value is another important theoretical implication. Findings of this study also contributed practically by confirming that herbal medicine product users appreciated perceived benefits and multi-dimensional values.
Biocompatible, adsorptive and antibacterial polysulfone hollow fibre membrane incorporated with silica alpha mangostin for uremic toxins removal
(Universiti Teknologi Malaysia, 2021) Mansur, Sumarni
Kidney failure patients rely on haemodialysis treatment to survive. However, unlike the kidney, this treatment cannot remove protein bound uremic toxins effectively and its long exposure to dialysis fluid poses risk of bacterial contamination. Hence, the main objective of this study is to develop a biocompatible, adsorptive and antibacterial polysulfone (PSf) based dual-layer hollow fibre (DLHF) membrane for efficient uremic toxins removal. In the first phase of the study, a silica nanoparticle with adsorption property was hybrid with α-mangostin via sol-gel technique, to enhance its biocompatibility. The synthesized nanoparticle had the Santa Barbara Amorphous-15 (SBA-15) mesoporous silica characteristic with particle size range of 15-25 nm, as confirmed by Fourier transform infrared spectroscopy (FTIR), particle size analysis, X-ray powder diffraction (XRD) and transmission electron microscopy (TEM). An adsorption study of a protein bound uremic toxin, namely p-cresol, and an antioxidant activity study were conducted, where the effect of α-mangostin addition was investigated. Silica nanoparticle showed the highest p-cresol adsorption capacity of 198 mg/g, followed by silica nanoparticles containing 5 wt% α-mangostin (186 mg/g) and 2 wt% α-mangostin (179 mg/g), respectively. Silica nanoparticle with 5 wt% α-mangostin prolonged the blood clotting time by 21.5% and inhibited the formation of reactive oxygen species by 36% compared to silica nanoparticle. The addition of 5 wt% α-mangostin enhanced the antioxidant property and maintained the good p-cresol adsorption capacity of silica nanoparticle. In the second phase of the study, 2 wt% silica and 1-2 wt% silica/α-mangostin nanoparticles were incorporated into PSf membrane, individually, where their effects on the surface properties, the adsorption capacity and the biocompatibility of the membrane were determined. Results showed that the membrane incorporated with 2 wt% silica/α-mangostin nanoparticle had a reduced water contact angle by 12.5%, indicating its improved surface hydrophilicity. Besides, the incorporation of silica/α-mangostin nanoparticle enhanced the p-cresol adsorption capacity of the membrane by 20.9% with the value of 56 mg/g. The silica/α-mangostin also improved the scavenging activity of hydrogen peroxide and nitrogen oxide by 61.8% and 36%, respectively and inhibited the formation of human complement fragment 5a (C5a) by 27.3%. In the final phase of the study, DLHF membranes consisting different combinations of inner and outer layers were prepared. 2 wt% of silica and activated carbon (AC) was incorporated in the outer layer of the membrane, individually, to impart antibacterial property to the membrane. Compared to the single layer hollow fibre membrane, the DLHF membranes showed 6-8% improvement of bovine serum albumin (BSA) rejection. DLHF membrane with the combination of silica/α-mangostin nanoparticle in the inner layer and AC in the outer layer possessed the highest removal of urea and creatinine throughout the 4-hour filtration. The silica/α-mangostin nanoparticle promoted the membrane’s interaction with urea and creatinine via chemisorption. Moreover, the AC in the outer layer of DLHF membrane successfully filtered bacteria via bacteria entrapment. The membrane displayed the highest antibacterial capability against Escherichia coli and Staphylococcus aureus, by having an antibacterial rate of 68% and 75%, respectively. The biocompatible and adsorptive DLHF membrane was successfully developed for safe and effective removal of uremic toxins in haemodialysis application.
Biomechanical evaluation and new improvement on ankle external fixator
(Universiti Teknologi Malaysia, 2015) Ramlee, Muhammad Hanif
An ankle external fixator is a medical device that can be used for temporary fixation in order to limit movement during treatment. This device has been effectively proven in clinical studies to promote the healing process. The stability of the construct could also be attributed to clinical outcomes. However, this knowledge is limited in the literature. Therefore, the main purpose of this study was to biomechanically evaluate and optimise the external fixator with the aim of producing a better construct for the improvement of stress distribution. In this project, the biomechanical study using a finite element method involved several analyses of the effects of external fixator designs as well as its material properties. In order to do that, first and foremost, a three-dimensional ankle model was reconstructed using CT data images which consisted of tibia, fibula, talus, calcaneus, navicular, three cuneiform, cuboid and five metatarsal bones. The cartilages were developed with an estimated uniform thickness of 1 mm. A total of 34 ligaments and 3 plantar fascias were also modelled. Two pathological conditions of ankle problems were simulated with the external fixator by applying axial compression loads based on the swing and stance phase. The results of the finite element study showed that the Delta frame configuration had better stability in terms of relative micromovement, displacement and von Mises stress as compared to the Mitkovic and Unilateral external fixators. In addition, the use of 6 mm pin and 11 mm connecting bar were more favourable options to provide a stable construction. However, the use of extra pins at cuboid and medial cuneiform bone did not contribute to enhance stability. For better improvement of the external fixator, additional hollow cylinder fitted at the pin was considered to decrease stress.
Biomedical diagnostic tools for in vivo local and systemic assessments
(Universiti Teknologi Malaysia, 2016) Ulum, Mokhamad Fakhrul
Novel bioactive-degradable metals for a temporary medical implant may have improved tissue-implant reaction properties. Although several diagnostic tools are available, in details, most of them have difficulties in tracing the properties. Therefore, a deep fundamental understanding on the local and systemic responses is needed for the development of new diagnostic tools. This research project consists of two parts. The first part explored the ability of conventionally available diagnostic tools to locally monitor tissue-implant reaction due to insertion of novel iron-bioceramic composites in sheeps. The clinical radiology, visual inspection, and histological imaging indicated biodegradation and tissueimplant interaction, locally. The second part assessed the systemic body responses to implants. The results also indicated increasing biomarkers level (inflammatory cells, plasma ion, and sex-steroid hormones) in blood circulation. This project then focused on the fabrication of simple, quick, and low-cost cotton-based microfluidic analytical device for systemic assessment, as well as for other applications through the development of one-step whole blood processing and assay using EDTA-treated cotton-thread microfluidic analytical device (µTAD). A further advance improvement of the EDTA-treated µTAD to be pipette-less integrated system using mosquito proboscis-inspired needle with µTAD (p(-)µCAD) for sampling-to-answer diagnostic was also performed in this project. The p(-)µCAD was able to collect whole blood, plasma separation, and albumin detection with its calibration. As a conclusion, this research has contributed in the development of a new bio-inspired diagnostic tool using a versatile, abundant, and affordable material for systemic body fluid assessment
Characterisation of Malaysian honeys and electrochemical detection of gallotannin for pure honey identification
(Universiti Teknologi Malaysia, 2017) Ismail, Norjihada Izzah
Seventeen samples (n = 17) of Malaysian gelam, acacia, nanas, tualang and kelulut honeys were analysed for their physicochemical, biochemical and phytochemical properties to evaluate their influence on floral source and bee type. Comparisons were also made with synthetic honeys to determine a suitable measure for fast identification of pure honey from synthetic honey. Solid phase extraction (SPE) was utilised for isolation of phenolic compounds in honey samples. The phenolic compounds present in the samples were analysed using high performance liquid chromatography-diode array detector (HPLC-DAD) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Three electrode systems were utilised for rapid identification of pure Malaysian honeys. Properties of honey were shown to be influenced by the floral source and bee type to the lesser extent. Kelulut honeys were observed of having lower pH, higher free acid, moisture and ash contents as well as higher electrical conductivity (EC), the properties that distinguish Trigona honey from the common Apis honey. Antioxidant properties were different for the five types of honey with Trigona honey dominating most of the antioxidant tests. Up to 16 phenolic compounds were identified using HPLC-DAD system. Similar dominant compounds were observed between tualang and acacia honeys, and between kelulut and gelam honeys, suggesting that the floral source of unifloral honey is an equally important food source for the analysed multifloral honey. More phenolic compounds were detected spectrometrically using full scan method and multiple reaction monitoring (MRM). Plant gallotannin, penta-ο-galloyl-β-D-glucose (PGG) was successfully detected at low potential 0.173 V vs Ag/AgCl in pH 7 phosphate buffer solution using glassy carbon electrode (GCE) without any prior electrode activation, chemical modification and pre-concentration at the GCE. The PGG detection in blank pure honey and via standard addition approach in the Malaysian honeys revealed its presence only in the pure honeys. The present study suggested that electrochemical detection of PGG using GCE could be used as a tool for pure honey identification through a rapid and simple method rather than other conventional, highly-technical, expensive and time-consuming analytical techniques
Characterization of a novel bacterial dehalogenase isolated from cow dung
(Universiti Teknologi Malaysia, 2018) Ismail, Siti Nurul Fasehah
The large quantities of the halogenated compound for example 2,2- dichloropropionic acid (2,2DCP) in the environment may lead to health problems in humans and pollution due to their toxicity and recalcitrance, respectively. Interestingly, previous studies have indicated that cow dung was proven to degrade pollutants. Hence, such animals feeding on a daily diet of halogen contaminated forage may influence the microflora in their digestive tract. Bacterial species from cow dung able to utilize 2,2DCP is yet to be reported. Therefore, the purpose of this study was to isolate, identify and characterize dehalogenase bacteria from cow dung. Four bacteria were isolated which are SN1, SN2, SN3, and SN4. Strain SN1 was observed with rapid growth in 20 mM 2,2DCP liquid minimal media, and was used for further experiments such as growth in different concentration of 2,2DCP, High-performance liquid chromatography (HPLC), Biolog GENIII, 16S rRNA analysis, characterization of purified enzyme, kinetic analysis, Liquid Chromatography-Mass Spectrometry (LC-MS/MS) and amplification of dehalogenase gene. The growth of strain SN1 in various concentrations (10 mM, 20 mM, 30 mM and 40 mM) of the substance was evaluated. The study found the bacteria grew particularly well in 20 mM 2,2DCP with the highest chloride ion released (39.5 μmolCIˉ/mL) while exhibiting a remarkably short doubling time of 3.85 h. The utilization of 2,2DCP was also confirmed by detection of 20 mM 2,2DCP depletion in the growth medium containing strain SN1 measured using HPLC. The result showed 98.6 % utilization of 2,2DCP in the growth medium. Species identification via Biolog GENIII system and 16S rRNA analysis was performed and identified strain SN1 as Bacillus cereus. Further investigations on dehalogenase enzyme were done by using purified enzyme of Bacillus cereus SN1. The molecular weight of the purified enzyme was 25 kDa by SDS-PAGE. The enzyme characteristics revealed it was optimum at pH 6 and 30 °C. It also has low Km value of 0.2 mM. The dehalogenase peptide was identified by LC-MS/MS with 18% sequence coverage to haloacid dehalogenase, Bacillus cereus (strain 03BB102). Moreover, Group I and Group II dehalogenase primers were used to amplify dehalogenase gene and the band only appeared for Group I. The dehalogenase gene fragment amplified was designated “DehSN1” and belongs to Group I dehalogenase since it has 75 % similarity with Group I dehalogenase (DehE). Five conserved residues were identified as Asn33, Tyr117, Cys42, Ala120 and Asp136. As a conclusion, this is the first reported case of a Bacillus sp. isolated from cow dung capable of utilizing 2,2DCP. Therefore, further assessment of its ability to degrade other types of haloalkanoic acids merits special consideration
Characterization of arsenate reduction by arsenic tolerant microbacterium foliorum strain SZ1 isolated from gold ores
(Universiti Teknologi Malaysia, 2016) Mohd. Bahari, Zaratulnur
Arsenic is a metalloid of global concern that primarily exists in two inorganic forms of severe toxicity, As (III) and As (V). The reduction of As (V) to As (III) increases toxicity, mobility and bioavailability of arsenic. Understanding how microorganisms reduce As (V) is important to elucidate As (V) reduction mechanism and inevitably, discover approaches to minimise its toxic impact on the environment. This study was aimed at investigating the capability of arsenic tolerant Microbacterium foliorum strain SZ1 isolated from gold ores to undergo As (V) reduction to As (III). This strain demonstrated complete reduction of 1 mM As (V) achieved within 120 hours under aerobic condition indicating a possible mechanism of detoxification through regulation of ars operon. Further optimization of factors enhancing As (V) reduction capacity of strain SZ1 resulted in complete reduction of 1 mM As (V) achieved within 36 hours in Tris minimal medium supplemented with 10 mM sucrose and 0.1 % (w/v) tryptone at pH 7. The effect of cell adaptation or acclimation towards As (V) reduction was investigated. Well-adapted strain SZ1 recorded complete reduction of 0.5 mM As (V) to 3 mM As (V) within 18 hours to 42 hours incubation. Exopolysaccharides (EPS) was observed to be secreted during reduction of As (V) and subjected to further characterization through chemical analysis of neutral carbohydrate and protein contents and Fourier transform infra-red (FT-IR) analysis. As As (V) concentration increased, so did the protein and carbohydrates concentration of EPS, indicating that EPS played an important role in enabling strain SZ1 to resist and reduce arsenic. Haldane inhibition model was used to fit the reduction rate at different initial As (V) concentrations and the parameters µmax, Ks and Ki were determined to be 0.14 h-1, 0.39 mM and 35.3 mM, respectively. In addition, presence of As (III) as the final product was further confirmed by detection through high performance liquid chromatography (HPLC) analysis. Field emission scanning electron microscopy analysis (FESEM) showed that cells grown in the presence of As (V) exhibited distinct changes in cell morphology and presence of EPS. Exploration of the draft genome of M. foliorum SZ1 identified the presence of ars operon (arsC-arsC-ACR3-arsT-arsC-arsR-arsC) and another two stand-alone genes, arsC and arsB which further confirmed SZ1’s tolerance towards high concentration of arsenic. From the screening of plant growth promoting (PGP) traits, strain SZ1 was able to produce siderophores and indole acetic acid which highlighted its potential use in microbe-assisted arsenic phytoremediation. This is the first study that elucidates the characterization of As (V) reduction by M. foliorum SZ1.
Characterization of dehalogenase for the degradation of 3-chloropropionic acid
(Universiti Teknologi Malaysia, 2017) Hassan Muslem, Wafaa
The use of herbicides that contain halogenated compounds, for example 3-chloropropionic acid (3-CP) poses significant environmental hazards as well as detrimental to human. The research detailed here investigated the isolation and identification of bacteria strains that could degrade 3-CP as its sole carbon source. Dehalogenase that can degrade 3-CP is rare in nature. In this study, two strains of dehalogenase producing bacteria capable of utilizing 3-CP were successfully isolated from abandoned agricultural land in Universiti Teknologi Malaysia. These bacteria were characterized by using 16S rRNA as well as biochemical analysis. Strain WH1 showed a 98 % sequence identity to Burkholderia cepacia with (accession number KU318403) whereas strain WH2 showed a 99% sequence identity to Bacillus cereus with (accession number KU721999). The results have shown that these bacteria were capable to grow in liquid minimal media supplied with 10 mM 3-CP as sole carbon source with doubling time of 43.62 h for WH1 and 14.75 h for WH2. Utilization of 3-CP was confirmed by detection of chloride ion released using halide ion assay technique for both strains which indicate their ability to degrade 3-CP. For further confirmation of 3-CP consumption, analysis by high performance liquid chromatography (HPLC) revealed that both B. cepacia WH1 and B. cereus WH2 effectively utilized ~100% of 10 mM 3-CP. This is the first report detailing both strains able to competently utilize 3-CP as their sole carbon source. Cell free extract of B. cereus strain WH2 was further characterized due to its faster growth on 3-CP compared to B. cepacia strain WH1. The intracellular dehalogenase from B. cereus WH2 was purified to homogeneity to afford a 2.5-fold (50 % yield) concentration with an estimated molecular mass of 37 kDa by SDS-PAGE analysis. Its highest enzyme activity was achieved at conditions of 30 oC and pH 7. While the activity of WH2 dehalogenase was substantially repressed by both Hg2+ and Ag2+, the enzyme was not inhibited by DTT and EDTA. Pertinently, kinetics evaluation revealed a higher affinity of the WH2 dehalogenase towards 3-CP than 3-chlorobutyric acid (3-CB), affording Km values of 0.32 mM (kcat 3.97 s-1) and 0.52 mM (kcat 4.35 s-1), respectively. The WH2 dehalogenase was ~1.6-fold catalytically more efficient (kcat/Km) in dehalogenating the three-carbon, 3-CP (12.4 mM-1 s-1) over the four-carbon, 3-CB (8.27 mM-1 s-1). From the data, it was identified that 3-CP degradation was not stimulated by co-factors, such as NAD+, NADH, NADP+, NADPH, FAD and CoA that did not affect the enzyme activity by demonstrating activities of <0.1 unite (g protein)-1. The amplified dehalogenase gene fragment was designated “deh-wh2” and subsequent analysis showed it belongs to Group II dehalogenase. Eight conserved residues that line the active site were identified: Asp10, Thr14, Ser117, Lys150, Tyr156, Ser174, Asn176 and Asp179. These residues are consistent with the residues found in the active site of DhlB, DehIVa and L-DEX. The product of 3-CP degradation was 3-hydroxypropionic acid based on HPLC. In conclusion, this study confirmed the presence of new dehalogenase isolated from various bacteria that have potential to utilize 3-CP, especially from contaminated environment
Characterization of novel marine bacterium vitellibacter aquimaris using polyphasic approach and genomic analyses
(Universiti Teknologi Malaysia, 2018) Thevarajoo, Suganthi
The discovery of novel marine bacteria provides an opportunity in exploring new bioactive compounds and their significance. Extensive industrial applications of enzymes promote the search of the enzymes from the new source. In this study, a yellow-orange strain designated as D-24 was isolated from Desaru, Johor. The study aimed to taxonomically and genomically characterize strain D-24 through polyphasic approach and genome analyses, respectively. The 16S rRNA gene sequence of strain D-24 indicated that it belongs to genus Vitellibacter. Strain D-24 was distinct from the other Vitellibacter spp. in hydrolyse Tween 60 and tyrosine, composition of fatty acids, polar lipid profile and DNA–DNA relatedness. Hence, strain D-24 was proposed as a new type strain with the name of Vitellibacter aquimaris. Following, strain D-24 was characterized on its protease activity and extracellular protease encoding genes. The characterization of crude protease demonstrated optimum activity at 60 °C, 5 % (w/v) NaCl and pH 7. The draft genome sequence of V. aquimaris (3.1 Mbp) was generated using an Illumina MiSeq sequencer. Mining of genes revealed the presence of three metalloproteases, two serine proteases and a cysteine protease. Recently, genus Vitellibacter was suggested as the same genus of Aequorivita based on phylogenomic data with no further analyses. Therefore, the detailed comparative analyses were performed based on their phenotypic and genomic features. Analyses of 16S rRNA gene sequences, housekeeping genes, percentage of conserved proteins and phenotypic features supported both of them as same genus. Furthermore, the presence of proteases, glycoside hydrolases and denitrification genes in genome of Vitellibacter/Aequorivita revealed their role in detergent industry, food industry and in carbon mineralization. In a nutshell, this study has provided new knowledge on V. aquimaris and also the useful genes such as serine protease, beta-mannosidase and nitrous oxide reductase that could be further characterized
Clinical pathway evaluation model for ST elevation myocardial infarction optimal patient care
(Universiti Teknologi Malaysia, 2017) Al-Ashwal, Rania Hussien Ahmed
Recently, clinical pathway (CP) has been used to reduce the variation and optimise the ST-elevation myocardial infarction (STEMI) process of care. The evaluation domains of STEMI CP quality remain inconsistent information. The aim of this research is to develop an evaluation model to guide the decision making on the optimal STEMI clinical pathways content and design. A qualitative and quantitative (mixed method) was used to generate and analyse the data of this research. First, the initial research STEMI clinical pathway concept has been developed from theory and practice. Second, the concept was tested in subsequent questionnaires distributions (pilot and actual study). Third, a clinical pathway quality evaluation model for STEMI (STEMICPQ) has been proposed and then assessed by structural equation modelling (SEM) path analysis using smart PLS version 3.0 software. Fourth, the sensitivity and specificity of the proposed model were tested in comparison to three quality criteria performance in 138 retrospective trial records. The results of the two stages questionnaire demonstrated an agreement on the items grouping and classification by the experts on most of the items of the questionnaire. A total of 186 responses from the second questionnaire have been returned involving 84 specialists and 76 nurses. The items content validity index (ICVI) is greater than 80%, and the construct reliability (Cronbach Alpha) is 0.85. This research proposes a model consisted of three STEMI CP quality domains (Design and Content, Process and Activity, and Outcome and Variance) with total 30 items and 60 sub-items and proven its ability to evaluate the quality of STEMICP. The STEMICPQ model validation results have established strong composite reliability, predictive relevance and power of explanation. The hypothesis testing revealed that the outcome and variance is a strong predictor of the STEMI clinical pathway quality with path coefficient (β) = 0.65, t statistics (t) = 17.4 and item loadings significant (p) = 0.000. From a retrospective CP trial study, the overall predictive power of the STEMICPQ shows high sensitivity of 0.915, specificity of 0.942 and area under the curve accuracy (AUC) of 0.93 in comparison to the length of stay criterion (LOS) of STEMI patients. As a conclusion, this model revealed suitable to be implemented in the health care institution to improve the quality of healthcare for STEMI patients. Also, it provides the experts with a valid, feasible and practical decision-making tool to be used in the hospitals during the design stage of STEMI CP. This work does not cover the organisational or human factors
Convolution neural network for diabetic retinopathy classification with select enhancment algorithm
(Universiti Teknologi Malaysia, 2022) Mohammed Sheet, Sinan Salim
Diabetic retinopathy and retinal vascular occlusion are the most significant causes of vision loss. Physical examinations are no longer sufficient to detect early retinal diseases due to the rise in patients with diabetes and high blood pressure, making a multiclass automated detection system a necessity in the health care field. However, the majority of the previous proposed automated systems were designed to diagnose a specific case, single class, such as diabetic retinopathy or normal retina (no-diabetic retinopathy), where these previous automated systems require several complexes preprocessing steps, such as cropping the area of interest, which requires an expertise of ophthalmologist. Furthermore, the cropping method may result in the loss of important pieces of information about retina disease in the discarded area, so it is being a source of human error. Additionally, the new multiclass detection technique demands a high number of retina samples, which are tough to obtain in health care centres, in addition to mostly complex segmentation phases that should be done. In this thesis, a novel preprocessing strategy is proposed to replace the lengthy, complicated, and cumbersome preprocessing step in order to address the aforesaid issues and propose a high-precision multiclass retina identification system with a deep transfer learning method. Instead of applying contrast-enhancing to the whole fed retina picture database, this suggested solution uses a proposed single convolution neural network to decide the contrast-enhancing for the poor quality of retina photos. Furthermore, a unique picture enhancement filter has been introduced to increase the proposed multiclass model’s output classification accuracy. Finally, a unique augmentation approach has been created to expand the dataset's generality while reducing the impact of a lack of input samples. For each class, the samples were rotated eleven times by 30 degrees. The performance of the proposed model, which is based on fine-tuned and pre-trained ResNet101 and VGG19, was assessed using four databases: FIGSHARE, IDRID, MESSIDOR, and STARE. The FIGSHARE achieved a 100% classification accuracy, 100% sensitivity, 100% specificity, and 100% F1-score for FIGSHARE; while 92.6% classification accuracy, 94.15% precision, 92.62% sensitivity, 97.38% specificity, and 92.40% F1-score were achieved using MESSIDOR. The IDRID achieved a 93.6% classification accuracy, 92.74% precision, 94.05% sensitivity, 98% specificity, and 93.05% F1-score. Lastly, STARE obtained a 99.29% classification accuracy, 99.29% precision, 99.29% sensitivity, 100% specificity, and 99.29% F1-score. In comparison to the state-of-the-art research, the suggested model outperformed them by a significant margin of accuracy, sensitivity, and specificity for the retina classification. Therefore, this study is a promising retinal diseases diagnosis framework, which potentially supports the ophthalmologist in fast and precise diagnosis and treatment to stop vision impairment and loss.
Correlation reflected fast and slow waves with various cancellous bone models using pulse-echo ultrasound technique
(Universiti Teknologi Malaysia, 2020) Abd. Wahab, Muhamad Amin
Attenuation and velocity of an ultrasound wave parameter can be analyzed to estimate the quality of the bone. However, the bone quality evaluation using ultrasound is still not comparable with X-ray densitometry. Considering the parameters of the fast and slow waves perhaps develop the measurement accuracy of the ultrasound. Currently, fast and slow waves measured using through transmission (TT) technique. Nonetheless, this technique applied two transducers, which limited to certain parts of the skeletal structure. Based on pulse-echo (PE) technique which is much easier to use due to single transducer uses and analyse fast and slow waves might be able to solve the problems. Therefore, the objective of this study is to conduct simulation and experiment of the PE technique to study the correlation between fast and slow waves with various porosities and thicknesses of two-dimentional cancellous models and bone phantom (polyurethane (PU) foam) and comparing the result obtained to the result of the TT technique and previous works. The ultrasound wave measurement was done based on TT and PE technique for both simulation and experiment. The measurement also was repeated for every porosity and thickness. The “incident” and “reflected” waves then separated using bandlimited deconvolution method by estimating the time threshold between transfer function of the fast and slow waves. Then, the parameters for mix, fast and slow waves were calculated, plotted against porosity for several thicknesses and compared in terms of their correlation coefficient. There are two types of bone models orientation (parallel and perpendicular) and two types of materials in the simulation (bone and PU – to compare with experiment). The result showed some of the fast and slow waves were in good agreement with previous work in terms of the behaviour of the wave parameters against porosity for every thickness. Moreover, the bone orientations (simulation), frequency spectral content and domination of the wave can influence the behaviour of the fast and slow waves. The thickness factor influences the parameters of fast and slow waves. Nonetheless, the reaction varied depending on the porosity level. Based on the phase velocity parameters, the separation of the fast and slow waves are easier for the thicker samples for PU materials (simulation and experiment) but the same for bone materials. The overall correlation coefficient of the amplitude and signal loss parameters for the reflected wave was slightly lower compared to incident wave due to suffering additional propagation loss. Nevertheless, for the attenuation parameters, most incident and reflected fast and slow waves shows a consistent trends and good correlation coefficient for simulation and experiment (Bone – R2ßI/Rfast = 0.52/0.50average and R2ßIslow = 0.67average) (PU – R2ßI/Rfast = 0.86/0.61max) (Experiment – R2ßIfast = 0.88max and R2ßRfast = 0.58average, R2ßIslow = 0.65max and R2ßRslow = 0.70average). This indicates that, the reflected fast and slow wave showed similar behaviour as the incident fast and slow wave and feasible to be applied in PE measurement technique. The result from simulation (PU materials) was also in good agreement with the experiment. The overall result shows, considering reflected fast and slow waves especially the attenuation parameter to estimate bone quality, might be able to improve the measurement accuracy for PE technique.
Corrosion behavior and mechanical properties of silicon and zinc-oxide coated magnesium-based bionanocomposite with hydroxyapatite and titania additives
(Universiti Teknologi Malaysia, 2016) Khalajabadi, Shahrouz Zamani
Magnesium (Mg)-based alloys were emerged as potential biodegradable material for temporary implants. However, their fast degradation in the high chloride environment of the physiological solution is detrimental unless inhibited. These Mg-based implants lose their mechanical integrity before the tissue is being sufficiently healed. Furthermore, the accumulation of hydrogen gas upon fast degradation in a physiological solution restricted their clinical applications. In this view, the present research is targeted to improve the biocorrosion behavior and mechanical properties of pure Mg by alloying it with nanostructured hydroxyapatite (HA), MgO, and TiO2 through milling-pressing-sintering powder metallurgy route. Four different Mg-based bionanocomposites including Mg/HA, Mg/HA/MgO, Mg/HA/TiO2 and Mg/HA/TiO2/MgO were synthesized to evaluate their bioimplantation efficacy. The Mg/HA/TiO2/MgO bionanocomposite was further coated with nano-Si, nano-ZnO single-layer, and nano-Si/ZnO double-layers using radio frequency magnetron sputtering technique to achieve such goal. The influence of varying amounts of the additives, the ball milling duration, the annealing temperature, and the coating agents on the biocorrosion and mechanical properties of these bionanocomposites were evaluated using electrochemical, immersion and compression tests. The phase evolution of the synthesized bionanocomposites before and after immersing in the simulated body fluid (SBF) solution was characterized via X-ray diffraction, Fourier-transform infrared and X-ray photoelectron spectroscopy. The detailed microstructures were determined using field-emission scanning electron, transmission electron, and atomic force microscopies. The bionanocomposites wettability was measured via video contact angle method. Thermal gravimetric and differential thermal analysis were performed to evaluate the activation energy and the reaction kinetics of the prepared powder bionanocomposites. In vitro corrosion resistance was analysed using potentiodynamic polarization, immersion, pH variation, and hydrogen evolution tests. After 8 h of ball milling the corrosion resistance of Mg/xHA/10TiO2/10MgO (wt%) bionanocomposite for two different compositions of HA such as 12.5wt% and 27.5wt% was found to increase from 1.35 and 2.19 kΩ.cm2 to 2.25 and 4.78 kΩ.cm2, respectively. Meanwhile, by annealing at 630°C, these two bionanocomposites demonstrated reduced corrosion rates compared to those annealed at 500°C. Interestingly, the compression failure strain (ductility) of HA incorporated Mg was decreased by increasing milling time. The corrosion rate of Mg/12.5HA/10TiO2/10MgO coated with nano-Si/ZnO exhibited a significant reduction from 5.82 (uncoated) to 0.25 mm/year. The cell culture test authenticated that the Mg-based bionanocomposites appeared biocompatible in the presence of HA, MgO, TiO2 additives and nano-Si/ZnO coating. It is noticed that the synthesized Mg/12.5HA/10TiO2/10MgO coated with nano-Si/ZnO has a great potential to become a candidate for biodegradable implants
Detection of onset muscle fatigue based on joint analysis of surface electromyography spectrum and amplitude
(Universiti Teknologi Malaysia, 2017) Mohamad Ishak, Nurul Ain
Many studies have been conducted to track muscle fatigue and to understand the mechanisms that contribute to the deterioration of muscle performance. Electromyography fatigue threshold (EMGFT) and Integrated Electromyography (IEMG) are two techniques that have been applied to determine the Onset of Muscle Fatigue (OMF) by depending on the percentage force output and amplitude respectively. Nevertheless, force and amplitude are correlated with one another during fatigue. Joint Analysis of EMG Spectrum and Amplitude (JASA) is commonly used to discriminate force-related from fatigue induced EMG changes. However, the length of signal affects the performance of JASA in discriminating fatigue signal. Apart from that, JASA has not been used to detect OMF. Thus, the purpose of this study is to determine the OMF region by applying JASA on the segmented EMG signal. Surface EMG signals were recorded from 30 college students while they were performing isometric contractions of Biceps Brachii muscles for 2 minutes. Each recorded signal was segmented into 15-second time interval. Root Mean Square (RMS) and Mean Frequency (MNF) were used as the muscle fatigue indicators. The indicators were extracted from 3-second epoch length within each segment. A polynomial regression model was applied to describe the trends of the indicators in a segment. The first segment that simultaneously showed a decrease in the frequency and an increase in the amplitude of a sEMG signal with correlation coefficient r = 0.7 was classified as the region where the OMF occurred. Out of 30 subjects, 20 subjects (67%) either admitted to experience muscle discomfort and at the same time the OMF region was also detected or vice-versa. For the other 10 subjects, the OMF region was able to be detected in 90% of them but due to better endurance levels, they required longer time to experience muscle discomfort. The temporal-spectral fatigue indicator (Instantaneous Mean Frequency (iMNF)) was used to determine the reliability of the developed technique. The decrement of iMNF on the detected OMF region showed high correlation coefficient (r > 0.6). The subjects were also asked to perform dynamic contractions for 2 minutes. The proposed technique was applied to the recorded signals and the OMF was detected in 24 subjects. Eighteen of them (72%) acknowledged that they had experienced muscle discomfort. Fourteen out of 18 subjects felt muscle discomfort after OMF was detected. The results indicate that muscle discomfort develops gradually after the onset of muscle fatigue. For handwriting activity, 4 subjects were asked to write for 5 minutes while the sEMG signals were captured from Flexor Carpi Radialis muscle (small muscle). Out of 4 subjects, all of them showed an increment in pen pressure, and 75% of them showed an increment in the writing speed after detecting OMF region. This study concludes that the proposed technique is feasible to detect the OMF; not only during isometric contraction but also during dynamic contraction. The technique also has the potential to be applied to small muscle contraction
Deterministic model for West African Ebola epidemic growth dynamics
(Universiti Teknologi Malaysia, 2020) Datilo, Philemon Manliura
Previous models of Ebola epidemic growth in the affected populations of West Africa such as found in the literature have insufficient consideration of the preventive and control compartments for the models. This had led to inaccurate estimation of Ebola virus disease reproduction number and insufficient quantitative information for policy decision making of Ebola outbreak control. An improvement over those models by using additional class specifications that fully represent the Ebola epidemic dynamics is necessary. In this research, a new deterministic epidemic growth model which explains Ebola growth dynamics alongside preventive and control strategies was proposed. The Susceptible- Vaccined-Exposed-Quarantine-Infected-Hospitalised-Funeral-Recovered (SVEQIHFR) stability analysis showed that the disease-free equilibrium and the unique endemic equilibrium are asymptotically stable both locally and globally. Next generation matrix was used to determine the model threshold parameter. The threshold was found to represent the average individuals infected due to transmission from the community, hospitals and funeral events. The SVEQIHFR model was fitted to the Ebola cumulative incidence and death data of Guinea, Liberia and Sierra Leone outbreaks, collected from World Health Organization (WHO) and Center for Disease Control (CDC). Nonlinear least square method was used to estimate the model parameters and their confidence intervals were calculated using the bootstrapping method. Ebola epidemic growth threshold was estimated to be 1.28, 1.72 and 1.89 for outbreaks in Guinea, Liberia and Sierra Leone respectively. The model predicted the Ebola epidemic final size in Guinea, Liberia and Sierra Leone with 98%, 99.03% and 98.4% precision and Root Mean Square Error (RMSE) values of 0.1135, 0.1216 and 0.1167, respectively. Meanwhile the Mean Average Percentage Error (MAPE) were 22.1%, 33.2% and 20.2% for infected cases in the respective countries. Latin Hypercube Sampling (LHS) or Partial Rank Correlation Coefficient (PRCC) procedure was implemented to carry out uncertainty analysis for the model's estimated parameters of Ebola transmission and prevalence outcome variables. It was proven that transmission coefficients and effective isolation, safe burial, effective identification and tracking of Ebola victims are critical to breaking Ebola transmission and prevalence. This model has comprehensively represented the dynamics of Ebola virus disease growth in the populations. It can help international agencies and affected countries' public health administrators to plan for prevention and control of the spread of Ebola virus disease. The model can also be used to study similar outbreaks in the future.

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