Biomedical Engineering - Research Publications
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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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ItemLoad response and gap formation in a single-row cruciate suture rotator cuff repair(WILEY, 2017-06)BACKGROUND: Double-row rotator cuff tendon repair techniques may provide superior contact area and strength compared with single-row repairs, but are associated with higher material expenses and prolonged operating time. The purpose of this study was to evaluate gap formation, ultimate tensile strength and stiffness of a single-row cruciate suture rotator cuff repair construct, and to compare these results with those of the Mason-Allen and SutureBridge repair constructs. METHODS: Infraspinatus tendons from 24 spring lamb shoulders were harvested and allocated to cruciate suture, Mason-Allen and SutureBridge repair groups. Specimens were loaded cyclically between 10 and 62 N for 200 cycles, and gap formation simultaneously measured using a high-speed digital camera. Specimens were then loaded in uniaxial tension to failure, and construct stiffness and repair strength were evaluated. RESULTS: Gap formation in the cruciate suture repair was significantly lower than that of the Mason-Allen repair (mean difference = 0.6 mm, P = 0.009) and no different from that of the SutureBridge repair (P > 0.05). Both the cruciate suture repair (mean difference = 15.7 N/mm, P = 0.002) and SutureBridge repair (mean difference = 15.8 N/mm, P = 0.034) were significantly stiffer than that of the Mason-Allen repair; however, no significant differences in ultimate tensile strength between repair groups were discerned (P > 0.05). CONCLUSION: The cruciate suture repair construct, which may represent a simple and cost-effective alternative to double-row and double-row equivalent rotator cuff repairs, has comparable biomechanical strength and integrity with that of the SutureBridge repair, and may result in improved construct longevity and tendon healing compared with the Mason-Allen repair.
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ItemAn intramedullary Echidna pin for fixation of comminuted clavicle fractures: a biomechanical study(BMC, 2017-08-11)BACKGROUND: Intramedullary fixation of comminuted mid-shaft clavicle fractures has traditionally been employed with satisfactory clinical outcomes; however, pins with smooth surfaces may protrude from the bone and are prone to migration, while some threaded pins are difficult to remove post-operatively. The aim of this proof-of-concept study was to develop and evaluate the biomechanical strength of a novel intramedullary Echidna pin device designed to maintain fracture reduction, resist migration and facilitate ease of post-operative removal. METHODS: Thirty human clavicle specimens were harvested and fractured in a comminuted mid-shaft butterfly configuration. Each specimen was randomly allocated to three surgical repair groups including intramedullary fixation using the Echidna pin and Herbert Cannulated Bone Screw System, as well as plate fixation using bi-cortical locking screws. Using a biomechanical testing apparatus, construct bending and torsional stiffness were measured, as well as ultimate bending strength. RESULTS: There was no significant difference in torsional stiffness and ultimate bending moment between the Echidna pin and Herbert screw repair constructs (p > 0.05); however, the Echidna pin construct demonstrated a significantly greater bending stiffness compared to that of the Herbert screw construct (mean difference 0.55 Nm/deg., p = 0.001). The plate construct demonstrated significantly greater torsional stiffness, bending stiffness and ultimate bending moment compared to those of the Herbert screw and Echidna pin (p < 0.05). CONCLUSIONS: An intramedullary Echidna pin device was designed to stabilize comminuted fractures of the clavicle, maintain fracture compression and provide ease of removal post-operatively. Since the results suggest equivalent or superior torsional and bending stability in the Echidna pin compared to that of the Herbert screw, the Echidna pin concept may represent an alternative fixation device to conventional intramedullary screws, nails and pins; however, superior plating using bi-cortical locking screws provides substantially higher construct structural rigidity than intramedullary devices, and may therefore be useful in cases of osteoporotic bone, or where high fracture stability is required.
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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.