Mechanical Engineering - Research Publications
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ItemNo Preview AvailableConversion of Upper-Limb Inertial Measurement Unit Data to Joint Angles: A Systematic Review.(MDPI AG, 2023-07-19)Inertial measurement units (IMUs) have become the mainstay in human motion evaluation outside of the laboratory; however, quantification of 3-dimensional upper limb motion using IMUs remains challenging. The objective of this systematic review is twofold. Firstly, to evaluate computational methods used to convert IMU data to joint angles in the upper limb, including for the scapulothoracic, humerothoracic, glenohumeral, and elbow joints; and secondly, to quantify the accuracy of these approaches when compared to optoelectronic motion analysis. Fifty-two studies were included. Maximum joint motion measurement accuracy from IMUs was achieved using Euler angle decomposition and Kalman-based filters. This resulted in differences between IMU and optoelectronic motion analysis of 4° across all degrees of freedom of humerothoracic movement. Higher accuracy has been achieved at the elbow joint with functional joint axis calibration tasks and the use of kinematic constraints on gyroscope data, resulting in RMS errors between IMU and optoelectronic motion for flexion-extension as low as 2°. For the glenohumeral joint, 3D joint motion has been described with RMS errors of 6° and higher. In contrast, scapulothoracic joint motion tracking yielded RMS errors in excess of 10° in the protraction-retraction and anterior-posterior tilt direction. The findings of this study demonstrate high-quality 3D humerothoracic and elbow joint motion measurement capability using IMUs and underscore the challenges of skin motion artifacts in scapulothoracic and glenohumeral joint motion analysis. Future studies ought to implement functional joint axis calibrations, and IMU-based scapula locators to address skin motion artifacts at the scapula, and explore the use of artificial neural networks and data-driven approaches to directly convert IMU data to joint angles.
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ItemEffect Of Arm Deweighting Using End-Effector Based Robotic Devices On Muscle Activity.(IEEE, 2018)Deweighting of the limb is commonly performed for patients with a neurological injury, such as stroke, as it allows these patients with limited muscle activity to perform movements. Deweighting has been implemented in exoskeletons and other multi-contact devices, but not on an end-effector based device with single contact point between the assisting robot and the human limb being assisted. This study inves-tigates the effects of deweighting using an end-effector based device on healthy subjects. The muscle activity of five subjects was measured in both static postures and dynamic movements. The results indicate a decrease in the activity of muscles which typically act against gravity - such as the anterior deltoid and the biceps brachii - but also suggest an increase in activity in muscles which act with gravity - such as the posterior deltoid and the lateral triceps. This can be explained by both the change in required muscle-generated torques and a conscious change in approach by the participants. These observations have implications for neurorehabilitation, particularly with respect to the muscle activation patterns which are trained through rehabilitation exercises.
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ItemUnicortical and bicortical plating in the fixation of comminuted fractures of the clavicle: a biomechanical study(WILEY, 2017-11)BACKGROUND: Intraoperative neurovascular complications with clavicle fracture fixation are often due to far cortex penetration by drills and screws, but could be avoided using a unicortical construct. The objective of this study was to compare the bending and torsional strength of a unicortical locking screw plate construct and a hybrid (with central locked and outer non-locked long oblique screws) unicortical plate construct for clavicle fracture fixation with that of a conventional bicortical locking screw construct of plate fixation. METHODS: Twenty-four human clavicle specimens were harvested and fractured in a comminuted mid-shaft butterfly configuration. Clavicles were randomly allocated to three surgical fixation groups: unicortical locking screw, bicortical locking screw and hybrid unicortical screw fixation. Clavicles were tested in torsion and cantilever bending. Construct bending and torsional stiffness were measured, as well as ultimate strength in bending. RESULTS: There were no significant differences in bending stiffness or ultimate bending moment between all three plating techniques. The unicortical locked construct had similar torsional stiffness compared with the bicortical locked construct; however, the hybrid technique was found to have significantly lower torsional stiffness to that of the bicortical locking screw construct (mean difference: 87.5 Nmm/degree, P = 0.028). CONCLUSIONS: Unicortical locked screw plate fixation and hybrid unicortical plating fixation with centrally locked screws and outer long, oblique screws may alleviate far cortex penetration, protecting nearby anatomical structures, and may ease implant removal and conversion to bicortical fixation for revision surgery; however, use of long oblique screws may increase the risk of early loosening under torsion.
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ItemMechanical properties of normal and osteoarthritic human articular cartilage(ELSEVIER, 2016-08)Isotropic hyperelastic models have been used to determine the material properties of normal human cartilage, but there remains an incomplete understanding of how these properties may be altered by osteoarthritis. The aims of this study were to (1) measure the material constants of normal and osteoarthritic human knee cartilage using isotropic hyperelastic models; (2) determine whether the material constants correlate with histological measures of structure and/or cartilage tissue damage; and (3) quantify the abilities of two common isotropic hyperelastic material models, the neo-Hookean and Yeoh models, to describe articular cartilage contact force, area, and pressure. Small osteochondral specimens of normal and osteoarthritic condition were retrieved from human cadaveric knees and from the knees of patients undergoing total knee arthroplasty and tested in unconfined compression at loading rates and large strains representative of weight-bearing activity. Articular surface contact area and lateral deformation were measured concurrently and specimen-specific finite element models then were used to determine the hyperelastic material constants. Structural parameters were measured using histological techniques while the severity of cartilage damage was quantified using the OARSI grading scale. The hyperelastic material constants correlated significantly with OARSI grade, indicating that the mechanical properties of cartilage for large strains change with tissue damage. The measurements of contact area described anisotropy of the tissue constituting the superficial zone. The Yeoh model described contact force and pressure more accurately than the neo-Hookean model, whereas both models under-predicted contact area and poorly described the anisotropy of cartilage within the superficial zone. These results identify the limits by which isotropic hyperelastic material models may be used to describe cartilage contact variables. This study provides novel data for the mechanical properties of normal and osteoarthritic human articular cartilage and enhances our ability to model this tissue using simple isotropic hyperelastic materials.
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ItemAssessing Species Diversity Using Metavirome Data: Methods and Challenges(ELSEVIER SCIENCE BV, 2017)Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.
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ItemCoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision(BMC, 2017-12-28)BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains. RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome. CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.