Chemical and Biomedical Engineering - Research Publications
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ItemThe impact of inter-observer variation in delineation on robustness of radiomics features in non-small cell lung cancer(NATURE PORTFOLIO, 2022-07-27)Artificial intelligence and radiomics have the potential to revolutionise cancer prognostication and personalised treatment. Manual outlining of the tumour volume for extraction of radiomics features (RF) is a subjective process. This study investigates robustness of RF to inter-observer variation (IOV) in contouring in lung cancer. We utilised two public imaging datasets: 'NSCLC-Radiomics' and 'NSCLC-Radiomics-Interobserver1' ('Interobserver'). For 'NSCLC-Radiomics', we created an additional set of manual contours for 92 patients, and for 'Interobserver', there were five manual and five semi-automated contours available for 20 patients. Dice coefficients (DC) were calculated for contours. 1113 RF were extracted including shape, first order and texture features. Intraclass correlation coefficient (ICC) was computed to assess robustness of RF to IOV. Cox regression analysis for overall survival (OS) was performed with a previously published radiomics signature. The median DC ranged from 0.81 ('NSCLC-Radiomics') to 0.85 ('Interobserver'-semi-automated). The median ICC for the 'NSCLC-Radiomics', 'Interobserver' (manual) and 'Interobserver' (semi-automated) were 0.90, 0.88 and 0.93 respectively. The ICC varied by feature type and was lower for first order and gray level co-occurrence matrix (GLCM) features. Shape features had a lower median ICC in the 'NSCLC-Radiomics' dataset compared to the 'Interobserver' dataset. Survival analysis showed similar separation of curves for three of four RF apart from 'original_shape_Compactness2', a feature with low ICC (0.61). The majority of RF are robust to IOV, with first order, GLCM and shape features being the least robust. Semi-automated contouring improves feature stability. Decreased robustness of a feature is significant as it may impact upon the features' prognostic capability.
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ItemPlease Place Your Seat in the Full Upright Position: A Technical Framework for Landing Upright Radiation Therapy in the 21st Century(FRONTIERS MEDIA SA, 2022-03-03)Delivering radiotherapy to patients in an upright position can allow for increased patient comfort, reduction in normal tissue irradiation, or reduction of machine size and complexity. This paper gives an overview of the requirements for the delivery of contemporary arc and modulated radiation therapy to upright patients. We explore i) patient positioning and immobilization, ii) simulation imaging, iii) treatment planning and iv) online setup and image guidance. Treatment chairs have been designed to reproducibly position seated patients for treatment and can be augmented by several existing immobilisation systems or promising emerging technologies such as soft robotics. There are few solutions for acquiring CT images for upright patients, however, cone beam computed tomography (CBCT) scans of upright patients can be produced using the imaging capabilities of standard Linacs combined with an additional patient rotation device. While these images will require corrections to make them appropriate for treatment planning, several methods indicate the viability of this approach. Treatment planning is largely unchanged apart from translating gantry rotation to patient rotation, allowing for a fixed beam with a patient rotating relative to it. Rotation can be provided by a turntable during treatment delivery. Imaging the patient with the same machinery as used in treatment could be advantageous for online plan adaption. While the current focus is using clinical linacs in existing facilities, developments in this area could also extend to lower-cost and mobile linacs and heavy ion therapy.
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ItemNo Preview AvailableAdsorption Behavior of Divalent Metal Ions onto Surface-functionalized Mesoporous Silicate MCM-41 Having Schiff Base Structure(SPRINGERNATURE, 2021-04)Surface functionalized mesoporous silicates, MCM-41s, having 3-(2-pyridylmethylideneimino)propyl group (PI-MCM-41) or 3-(2-quinolylmethylideneimino)propyl group (QI-MCM-41) were prepared via Schiff base reaction, and the adsorption behavior of metal ions onto the modified MCM-41s was investigated. The function groups on the modified MCM-41 surface were confirmed by Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), and elemental analysis. The metal ions examined, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Pb2+, were quantitatively adsorbed on the PI-MCM-41 and QI-MCM-41, except for Mn2+. In the complexation with these metal ions, it was suggested that imine-N and heterocyclic-N atoms act as donor atoms. In addition, it was considered that the hydrophobicity derived from the organo-functional groups modified on MCM-41 contributed to improving the adsorption ability.
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ItemAdvanced natural language processing technique to predict patient disposition based on emergency triage notes(WILEY, 2021-06)OBJECTIVE: To demonstrate the potential of machine learning and capability of natural language processing (NLP) to predict disposition of patients based on triage notes in the ED. METHODS: A retrospective cohort of ED triage notes from St Vincent's Hospital (Melbourne) was used to develop a deep-learning algorithm that predicts patient disposition. Bidirectional Encoder Representations from Transformers, a recent language representation model developed by Google, was utilised for NLP. Eighty percent of the dataset was used for training the model and 20% was used to test the algorithm performance. Ktrain library, a wrapper for TensorFlow Keras, was employed to develop the model. RESULTS: The accuracy of the algorithm was 83% and the area under the curve was 0.88. Sensitivity, specificity, precision and F1-score of the algorithm were 72%, 86%, 56% and 63%, respectively. CONCLUSION: Machine learning and NLP can be together applied to the ED triage note to predict patient disposition with a high level of accuracy. The algorithm can potentially assist ED clinicians in early identification of patients requiring admission by mitigating the cognitive load, thus optimises resource allocation in EDs.
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ItemClean Power Technology(Gaodeng Jiaoyu Chubanshe, 2020-12-01)It is timely that Engineering should devote a special issue to the topic of clean energy. The authors of the research articles and the views and comments cover much of what is a very diverse and controversial field. Responses to this topic cover a spectrum ranging from those that argue for emergency action to prevent the extinction of the human race to those that deny the existence of climate change. Before dismissing any group, it is informative for engineers and technologists to note that there is a fairly even distribution across this spectrum
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ItemCFD Simulation of Two-Phase Flow in a Hybrid Pulsed Sieve-Plate Solvent Extraction Column: Prediction of Holdup and Axial-dispersion Coefficients(Taylor & Francis, 2020-01-02)Two-phase computational fluid dynamics (CFD) models for a hybrid pulsed sieve-plate solvent extraction column, as well as a standard pulsed sieve-plate column, have been developed with commercial software ANSYS FLUENT. Hydrodynamic performance including two-phase distribution and velocity fields are generated with the models and comparisons are made between two columns. Important parameters including holdup and axial-dispersion coefficients are studied systematically, and CFD successfully predicts the higher holdup and lower axial-dispersion coefficients for the hybrid pulsed sieve-plate column as measured in the experiments. CFD also gives reasonable predictions for the effect of pulsation intensity, dispersed-phase velocity, and continuous-phase velocity on holdup, except for the effect of pulsation intensity in low pulsation region, and the cause has been discussed from the perspective of droplet breakage and coalescence. Comparison with literature data shows that CFD underestimates the holdup of hybrid pulsed sieve-plate column and standard pulsed sieve-plate column by 23.3% and 31.4%, respectively, and the cause has been discussed from the perspective of drag law. CFD gives good prediction of axial-dispersion coefficients for the hybrid pulsed sieve-plate column and the standard pulsed sieve-plate column with ARD of 12.0% and 14.3%, respectively. This study shows CFD to be a useful tool to predict performance for the novel hybrid pulsed sieve-plate column as well as the standard pulsed sieve-plate column.
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ItemSurface Modification of Spider Silk Particles to Direct Biomolecular Corona Formation.(American Chemical Society, 2020-05-20)In recent years, spider silk-based materials have attracted attention because of their biocompatibility, processability, and biodegradability. For their potential use in biomaterial applications, i.e., as drug delivery systems and implant coatings for tissue regeneration, it is vital to understand the interactions between the silk biomaterial surface and the biological environment. Like most polymeric carrier systems, spider silk material surfaces can adsorb proteins when in contact with blood, resulting in the formation of a biomolecular corona. Here, we assessed the effect of surface net charge of materials made of recombinant spider silk on the biomolecular corona composition. In-depth proteomic analysis of the biomolecular corona revealed that positively charged spider silk materials surfaces interacted predominantly with fibrinogen-based proteins. This fibrinogen enrichment correlated with blood clotting observed for both positively charged spider silk films and particles. In contrast, negative surface charges prevented blood clotting. Genetic engineering allows the fine-tuning of surface properties of the spider silk particles providing a whole set of recombinant spider silk proteins with different charges or peptide tags to be used for, for example, drug delivery or cell docking, and several of these were analyzed concerning the composition of their biomolecular corona. Taken together this study demonstrates how the surface net charge of recombinant spider silk surfaces affects the composition of the biomolecular corona, which in turn affects macroscopic effects such as fibrin formation and blood clotting.
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ItemModulating the Selectivity and Stealth Properties of Ellipsoidal Polymersomes through a Multivalent Peptide Ligand Display(Wiley, 2020-05-19)There is a need for improved nanomaterials to simultaneously target cancer cells and avoid non‐specific clearance by phagocytes. An ellipsoidal polymersome system is developed with a unique tunable size and shape property. These particles are functionalized with in‐house phage‐display cell‐targeting peptide to target a medulloblastoma cell line in vitro. Particle association with medulloblastoma cells is modulated by tuning the peptide ligand density on the particles. These polymersomes has low levels of association with primary human blood phagocytes. The stealth properties of the polymersomes are further improved by including the peptide targeting moiety, an effect that is likely driven by the peptide protecting the particles from binding blood plasma proteins. Overall, this ellipsoidal polymersome system provides a promising platform to explore tumor cell targeting in vivo.
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ItemHigh-Efficiency Biocatalytic Conversion of Thebaine to Codeine(American Chemical Society, 2020-04-28)An enzymatic biosynthesis approach is described for codeine, the most widely used medicinal opiate, providing a more environmentally sustainable alternative to current chemical conversion, with yields and productivity compatible with industrial production. Escherichia coli strains were engineered to express key enzymes from poppy, including the recently discovered neopinone isomerase, producing codeine from thebaine. We show that compartmentalization of these enzymes in different cells is an effective strategy that allows active spatial and temporal control of reactions, increasing yield and volumetric productivity and reducing byproduct generation. Codeine is produced at a yield of 64% and a volumetric productivity of 0.19 g/(L·h), providing the basis for an industrially applicable aqueous whole-cell biotransformation process. This approach could be used to redirect thebaine-rich feedstocks arising from the U.S. reduction of opioid manufacturing quotas or applied to enable total biosynthesis and may have broader applicability to other medicinal plant compounds.
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ItemOn-chip surface acoustic wave and micropipette aspiration techniques to assess cell elastic properties.(A I P Publishing LLC, 2020-01)The cytoskeletal mechanics and cell mechanical properties play an important role in cellular behaviors. In this study, in order to provide comprehensive insights into the relationship between different cytoskeletal components and cellular elastic moduli, we built a phase-modulated surface acoustic wave microfluidic device to measure cellular compressibility and a microfluidic micropipette-aspiration device to measure cellular Young's modulus. The microfluidic devices were validated based on experimental data and computational simulations. The contributions of structural cytoskeletal actin filament and microtubule to cellular compressibility and Young's modulus were examined in MCF-7 cells. The compressibility of MCF-7 cells was increased after microtubule disruption, whereas actin disruption had no effect. In contrast, Young's modulus of MCF-7 cells was reduced after actin disruption but unaffected by microtubule disruption. The actin filaments and microtubules were stained to confirm the structural alteration in cytoskeleton. Our findings suggest the dissimilarity in the structural roles of actin filaments and microtubules in terms of cellular compressibility and Young's modulus. Based on the differences in location and structure, actin filaments mainly contribute to tensile Young's modulus and microtubules mainly contribute to compressibility. In addition, different responses to cytoskeletal alterations between acoustophoresis and micropipette aspiration demonstrated that micropipette aspiration was better at detecting the change from actin cortex, while the response to acoustophoresis was governed by microtubule networks.