Mechanical Engineering - Research Publications
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ItemOn Extremum Seeking in Bioprocesses with Multivalued Cost Functions(WILEY, 2009)Finding optimal operating modes for bioprocesses has been, for a long time, a relevant issue in bioengineering. The problem is of special interest when it implies the simultaneous optimization of competing objectives. In this paper, we address the problem of finding optimal steady states that achieve the best tradeoff between yield and productivity by using nonmodel-based extremum-seeking control with semiglobal practical stability and convergence properties. A special attention is paid to processes with multiple steady states and multivalued cost functions.
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ItemOn global extremum seeking in the presence of local extrema(PERGAMON-ELSEVIER SCIENCE LTD, 2009-01-01)We propose a global extremum seeking scheme which can seek the global optimal value in the presence of local extrema. It is shown that the proposed global extremum seeking scheme can converge to an arbitrarily small neighborhood of the global extremum from an arbitrarily large set of initial conditions if sufficient conditions are satisfied. A simple example illustrates the effectiveness of the proposed scheme.
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ItemOn the choice of dither in extremum seeking systems: A case study(PERGAMON-ELSEVIER SCIENCE LTD, 2008-05-01)We discuss how the choice of dither (excitation signal) affects the performance of extremum seeking using a benchmark situation: a static scalar map; and a simple scalar extremum seeking scheme. Our comparisons are based on the performance of the system with different dithers in terms of three performance indicators: the speed of convergence, domain of attraction and accuracy (i.e. the ultimate bound on trajectories). Our analysis explicitly shows how the dither shape affects each of these performance indicators. Our study suggests that the practitioners using extremum seeking control should consider the dither shape as an important design parameter. Computer simulations support our theoretical findings.
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ItemNo Preview AvailableInfluence of muscle-tendon wrapping on calculations of joint reaction forces in the equine distal forelimb(HINDAWI PUBLISHING CORPORATION, 2008)The equine distal forelimb is a common location of injuries related to mechanical overload. In this study, a two-dimensional model of the musculoskeletal system of the region was developed and applied to kinematic and kinetic data from walking and trotting horses. The forces in major tendons and joint reaction forces were calculated. The components of the joint reaction forces caused by wrapping of tendons around sesamoid bones were found to be of similar magnitude to the reaction forces between the long bones at each joint. This finding highlighted the importance of taking into account muscle-tendon wrapping when evaluating joint loading in the equine distal forelimb.
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ItemReliability and normative values for the foot mobility magnitude: a composite measure of vertical and medial-lateral mobility of the midfoot(BMC, 2009)BACKGROUND: A study was conducted to determine the reliability and minimal detectable change for a new composite measure of the vertical and medial-lateral mobility of the midfoot called the foot mobility magnitude. METHODS: Three hundred and forty-five healthy participants volunteered to take part in the study. The change in dorsal arch height between weight bearing and non-weight bearing as well as the change in midfoot width between weight bearing and non-weight bearing were measured at 50% of total foot length and used to calculate the foot mobility magnitude. The reliability and minimal detectable change for the measurements were then determined based on the assessment of the measurements by three raters with different levels of clinical experience. RESULTS: The change in dorsal arch height between weight bearing and non-weight bearing, midfoot width between weight bearing and non-weight bearing, and the foot mobility magnitude were shown to have high levels of intra-rater and inter-rater reliability. Normative data are provided for the left and right feet of both the female (n = 211) and male (n = 134) subjects. CONCLUSION: While the measurements of navicular drop and drift have been used as a clinical method to assess both the vertical and medial-lateral mobility of the midfoot, poor to fair levels of inter-rater reliability have been reported. The results of the current study suggest that the foot mobility magnitude provides the clinician and researcher with a highly reliable measure of vertical and medial-lateral midfoot mobility.
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ItemCan foot anthropometric measurements predict dynamic plantar surface contact area?(BIOMED CENTRAL LTD, 2009)BACKGROUND: Previous studies have suggested that increased plantar surface area, associated with pes planus, is a risk factor for the development of lower extremity overuse injuries. The intent of this study was to determine if a single or combination of foot anthropometric measures could be used to predict plantar surface area. METHODS: Six foot measurements were collected on 155 subjects (97 females, 58 males, mean age 24.5 +/- 3.5 years). The measurements as well as one ratio were entered into a stepwise regression analysis to determine the optimal set of measurements associated with total plantar contact area either including or excluding the toe region. The predicted values were used to calculate plantar surface area and were compared to the actual values obtained dynamically using a pressure sensor platform. RESULTS: A three variable model was found to describe the relationship between the foot measures/ratio and total plantar contact area (R2 = 0.77, p < 0.0001)). A three variable model was also found to describe the relationship between the foot measures/ratio and plantar contact area minus the toe region (R2 = 0.76, p < 0.0001). CONCLUSION: The results of this study indicate that the clinician can use a combination of simple, reliable, and time efficient foot anthropometric measurements to explain over 75% of the plantar surface contact area, either including or excluding the toe region.
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ItemFoot orthoses and physiotherapy in the treatment of patellofemoral pain syndrome: A randomised clinical trial(BIOMED CENTRAL LTD, 2008-02-27)BACKGROUND: Patellofemoral pain syndrome is a highly prevalent musculoskeletal overuse condition that has a significant impact on participation in daily and physical activities. A recent systematic review highlighted the lack of high quality evidence from randomised controlled trials for the conservative management of patellofemoral pain syndrome. Although foot orthoses are a commonly used intervention for patellofemoral pain syndrome, only two pilot studies with short term follow up have been conducted into their clinical efficacy. METHODS/DESIGN: A randomised single-blinded clinical trial will be conducted to investigate the clinical efficacy and cost effectiveness of foot orthoses in the management of patellofemoral pain syndrome. One hundred and seventy-six participants aged 18-40 with anterior or retropatellar knee pain of non-traumatic origin and at least six weeks duration will be recruited from the greater Brisbane area in Queensland, Australia through print, radio and television advertising. Suitable participants will be randomly allocated to receive either foot orthoses, flat insoles, physiotherapy or a combined intervention of foot orthoses and physiotherapy, and will attend six visits with a physiotherapist over a 6 week period. Outcome will be measured at 6, 12 and 52 weeks using primary outcome measures of usual and worst pain visual analogue scale, patient perceived treatment effect, perceived global effect, the Functional Index Questionnaire, and the Anterior Knee Pain Scale. Secondary outcome measures will include the Lower Extremity Functional Scale, McGill Pain Questionnaire, 36-Item Short-Form Health Survey, Hospital Anxiety and Depression Scale, Patient-Specific Functional Scale, Physical Activity Level in the Previous Week, pressure pain threshold and physical measures of step and squat tests. Cost-effectiveness analysis will be based on treatment effectiveness against resource usage recorded in treatment logs and self-reported diaries. DISCUSSION: The randomised clinical trial will utilise high-quality methodologies in accordance with CONSORT guidelines, in order to contribute to the limited knowledge base regarding the clinical efficacy of foot orthoses in the management of patellofemoral pain syndrome, and provide practitioners with high-quality evidence upon which to base clinical decisions. TRIAL REGISTRATION: Australian Clinical Trials Registry ACTRN012605000463673ClinicalTrials.gov NCT00118521.
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ItemGene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages(BioMed Central, 2007-05-22)BACKGROUND: Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be easily analyzed by these methods. This work addresses these shortcomings and aims to provide an automated prediction system of gene function. RESULTS: We have developed a novel system called SynFPS to perform gene function prediction over completed genomes. The prediction system is initialized by clustering a large collection of weakly related genomes into groups based on their resemblance in gene distribution. From each individual group, data are then extracted and used to train a Support Vector Machine that makes gene function predictions. Experiments were conducted with 9 different gene functions over 296 bacteriophage genomes. Cross validation results gave an average prediction accuracy of ~80%, which is comparable to other genomic-context based prediction methods. Functional predictions are also made on 3 uncharacterized genes and 12 genes that cannot be identified by sequence alignment. The software is publicly available at http://www.synteny.net/. CONCLUSION: The proposed system employs genomic context to predict gene function and detect gene correspondence in whole-genome comparisons. Although our experimental focus is on bacteriophages, the method may be extended to other microbial genomes as they share a number of similar characteristics with phage genomes such as gene order conservation.
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ItemGenome classification by gene distribution: an overlapping subspace clustering approach(BioMed Central, 2008)BACKGROUND: Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods. RESULTS: We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2, Clostridium phi3626, Geobacillus GBSV1, and Listeria monocytogenes PSA. CONCLUSION: The method described in this paper can assist evolutionary study through objectively classifying genomes based on their resemblance in gene order, gene content and gene positions. The method is suitable for application to genomes with high genetic exchange and various conserved gene arrangement, as demonstrated through our application on phages.
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ItemFast splice site detection using information content and feature reduction(BioMed Central, 2008-12-12)BACKGROUND: Accurate identification of splice sites in DNA sequences plays a key role in the prediction of gene structure in eukaryotes. Already many computational methods have been proposed for the detection of splice sites and some of them showed high prediction accuracy. However, most of these methods are limited in terms of their long computation time when applied to whole genome sequence data. RESULTS: In this paper we propose a hybrid algorithm which combines several effective and informative input features with the state of the art support vector machine (SVM). To obtain the input features we employ information content method based on Shannon's information theory, Shapiro's score scheme, and Markovian probabilities. We also use a feature elimination scheme to reduce the less informative features from the input data. CONCLUSION: In this study we propose a new feature based splice site detection method that shows improved acceptor and donor splice site detection in DNA sequences when the performance is compared with various state of the art and well known methods.