Chemical and Biomedical Engineering - Research Publications
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ItemNo Preview AvailableSeizure occurrence is linked to multiday cycles in diverse physiological signals(WILEY, 2023-06)OBJECTIVE: The factors that influence seizure timing are poorly understood, and seizure unpredictability remains a major cause of disability. Work in chronobiology has shown that cyclical physiological phenomena are ubiquitous, with daily and multiday cycles evident in immune, endocrine, metabolic, neurological, and cardiovascular function. Additionally, work with chronic brain recordings has identified that seizure risk is linked to daily and multiday cycles in brain activity. Here, we provide the first characterization of the relationships between the cyclical modulation of a diverse set of physiological signals, brain activity, and seizure timing. METHODS: In this cohort study, 14 subjects underwent chronic ambulatory monitoring with a multimodal wrist-worn sensor (recording heart rate, accelerometry, electrodermal activity, and temperature) and an implanted responsive neurostimulation system (recording interictal epileptiform abnormalities and electrographic seizures). Wavelet and filter-Hilbert spectral analyses characterized circadian and multiday cycles in brain and wearable recordings. Circular statistics assessed electrographic seizure timing and cycles in physiology. RESULTS: Ten subjects met inclusion criteria. The mean recording duration was 232 days. Seven subjects had reliable electroencephalographic seizure detections (mean = 76 seizures). Multiday cycles were present in all wearable device signals across all subjects. Seizure timing was phase locked to multiday cycles in five (temperature), four (heart rate, phasic electrodermal activity), and three (accelerometry, heart rate variability, tonic electrodermal activity) subjects. Notably, after regression of behavioral covariates from heart rate, six of seven subjects had seizure phase locking to the residual heart rate signal. SIGNIFICANCE: Seizure timing is associated with daily and multiday cycles in multiple physiological processes. Chronic multimodal wearable device recordings can situate rare paroxysmal events, like seizures, within a broader chronobiology context of the individual. Wearable devices may advance the understanding of factors that influence seizure risk and enable personalized time-varying approaches to epilepsy care.
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ItemNo Preview AvailableWildfire-related PM2.5 and DNA methylation: An Australian twin and family study(PERGAMON-ELSEVIER SCIENCE LTD, 2023-01-01)BACKGROUND: Wildfire-related fine particulate matter (PM2.5) has many adverse health impacts, but its impacts on human epigenome are unknown. We aimed to evaluate the associations between long-term exposure to wildfire-related PM2.5 and blood DNA methylation, and whether the associations differ from those with non-wildfire-related PM2.5. METHODS: We studied 479 Australian women comprising 132 twin pairs and 215 of their sisters. Blood-derived DNA methylation was measured using the HumanMethylation450 BeadChip array. Data on 3-year (year of blood collection and previous two years) average wildfire-related and non-wildfire-related PM2.5 at 0.01°×0.01° spatial resolution were created by combining information from satellite observations, chemical transport models, and ground-based observations. Exposure data were linked to each participant's home address, assuming the address did not change during the exposure window. For DNA methylation of each cytosine-guanine dinucleotide (CpG), and for global DNA methylation represented by the average of all measured CpGs or CpGs in repetitive elements, we evaluated their associations with wildfire- or non-wildfire-related PM2.5 using a within-sibship analysis controlling for factors shared between siblings and other important covariates. Differentially methylated regions (DMRs) were defined by comb-p and DMRcate. RESULTS: The 3-year average wildfire-related PM2.5 (range: 0.3 to 7.6 µg/m3, mean: 1.6 µg/m3) was negatively, but not significantly (p-values greater than 0.05) associated with all seven global DNA methylation measures. There were 26 CpGs and 33 DMRs associated with wildfire-related PM2.5 (Bonferroni adjusted p-value < 0.05) mapped to 47 genes enriched for pathways related to inflammatory regulation and platelet activation. These genes have been related to many human diseases or phenotypes e.g., cancer, mental disorders, diabetes, obesity, asthma, blood pressure. These CpGs, DMRs and enriched pathways did not overlap with the 1 CpG and 7 DMRs associated with non-wildfire-related PM2.5. CONCLUSIONS: Long-term exposure to wildfire-related PM2.5 was associated with various blood DNA methylation signatures in Australian women, and these were distinct from those associated with non-wildfire-related PM2.5.
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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.