Ex vivo culture of patient tissue and examination of gene delivery

Gene therapy has emerged as a realistic prospect for the treatment of cancer due to its potential for selective tumour cell targeting. The greatest challenge gene delivery vectors face is the ability to safely and efficiently deliver genes into target cells. The overall objectives of this thesis are to evaluate the efficacy of various gene delivery methods in a clinically relevant tumour model and to also investigate potential strategies for tumour selective delivery. We began with the development of a tumour slice model system using patient waste tissue. This model involves the use of fresh human tumour tissue, cut into thin slices and maintained ex vivo and is universally applicable to gene delivery methods, using a real-time luminescence detection method to assess gene delivery. The nature of the ex vivo culture system permitted examination of specific physiological variables, the influence of intratumoural factors and tissue specific effects on vector expression. Adenoviral vectors under the control of the human CXCR4 promoter demonstrated a 'tumour on' and 'normal off' expression profile when compared with the ubiquitously active CMV promoter when tested in patient tumour tissue. In addition, we developed an ex vivo system of changing oxygenation using the hypoxia inducer, cobalt, to mimic the transient hypoxic conditions found in solid tumours. We found that Adenoviral transgene expression was robust in the cycling hypoxic conditions relevant to solid tumours and re-oxygenation of chronically hypoxic tissue enhanced transgene expression. Finally, we demonstrated an AAV-based tumour targeting strategy using a tumour-selective promoter allowing for the efficient targeting of AAV vectors to cancer cells and the sparing of normal tissue in both murine metastatic liver tumours models and patient tissue. The thesis highlights the importance of indepth preclinical assessment of novel therapeutics and may serve as a platform for further testing of novel gene delivery approaches

Techno-economic Assessment of Optimised Vacuum Swing Adsorption for Post-Combustion CO2 capture from Steam-Methane Reformer Flue Gas

This study focuses on the techno-economic assessment integrated with detailed optimisation of a four step vacuum swing adsorption (VSA) process for post-combustion CO2 capture and storage (CCS) from steam-methane reformer dried flue gas containing 20 mol% CO2. The comprehensive techno-economic optimisation model developed herein takes into account VSA process model, peripheral component models, vacuum pump performance, scale-up, process scheduling and a thorough cost model. Three adsorbents, namely, Zeolite 13X (current benchmark material for CO2 capture) and two metal–organic frameworks, UTSA-16 (widely studied metal–organic framework for CO2 capture) and IISERP MOF2 (good performer in recent findings) are optimised to minimise the CO2 capture cost. Monoethanolamine (MEA)-based absorption technology serves as a baseline case to assess and compare optimal techno-economic performances of VSA technology for three adsorbents. The results show that the four step VSA process with IISERP MOF2 outperforms other two adsorbents with a lowest CO2 capture cost (including flue gas pre-treatment) of 33.6 € per tonne of CO2 avoided and an associated CO2 avoided cost of 73.0 € per tonne of CO2 avoided. Zeolite 13X and UTSA-16 resulted in CO2 avoided costs of 90.9 and 104.9 € per tonne of CO2 avoided, respectively. The CO2 avoided costs obtained for the VSA technology remain higher than that of the baseline MEA-based absorption process which was found to be 66.6 € per tonne of CO2 avoided. The study also demonstrates the importance of using cost as means of evaluating the separation technique compared to the use of process performance indicators. Accounting for the efficiency of vacuum pumps and the cost of novel materials such as metal–organic frameworks is highlighted. © 2020 Elsevier B.V.acceptedVersio

Learning Linear Causal Representations from Interventions under General Nonlinear Mixing

We study the problem of learning causal representations from unknown, latent interventions in a general setting, where the latent distribution is Gaussian but the mixing function is completely general. We prove strong identifiability results given unknown single-node interventions, i.e., without having access to the intervention targets. This generalizes prior works which have focused on weaker classes, such as linear maps or paired counterfactual data. This is also the first instance of causal identifiability from non-paired interventions for deep neural network embeddings. Our proof relies on carefully uncovering the high-dimensional geometric structure present in the data distribution after a non-linear density transformation, which we capture by analyzing quadratic forms of precision matrices of the latent distributions. Finally, we propose a contrastive algorithm to identify the latent variables in practice and evaluate its performance on various tasks.Comment: 38 page

Lithium modulates autophagy in esophageal and colorectal cancer cells and enhances the efficacy of therapeutic agents in vitro and in vivo

Many epithelial cancers, particularly gastrointestinal tract cancers, remain poor prognosis diseases, due to resistance to cytotoxic therapy and local or metastatic recurrence. We have previously shown that apoptosis incompetent esophageal cancer cells induce autophagy in response to chemotherapeutic agents and this can facilitate their recovery. However, known pharmacological inhibitors of autophagy could not enhance cytotoxicity. In this study, we have examined two well known, clinically approved autophagy inducers, rapamycin and lithium, for their effects on chemosensitivity in apoptosis incompetent cancer cells. Both lithium and rapamycin were shown to induce autophagosomes in esophageal and colorectal cancer cells by western blot analysis of LC3 isoforms, morphology and FACS quantitation of Cyto-ID or mCherry-GFP-LC3. Analysis of autophagic flux indicates inefficient autophagosome processing in lithium treated cells, whereas rapamycin treated cells showed efficient flux. Viability and recovery was assessed by clonogenic assays. When combined with the chemotherapeutic agent 5-fluorouracil, rapamycin was protective. In contrast, lithium showed strong enhancement of non-apoptotic cell death. The combination of lithium with 5-fluorouracil or oxaliplatin was then tested in the syngenic mouse (balb/c) colorectal cancer model-CT26. When either chemotherapeutic agent was combined with lithium a significant reduction in tumor volume was achieved. In addition, survival was dramatically increased in the combination group (p 50% of animals achieving long term cure without re-occurrence (> 1 year tumor free). Thus, combination treatment with lithium can substantially improve the efficacy of chemotherapeutic agents in apoptosis deficient cancer cells. Induction of compromised autophagy may contribute to this cytotoxicity

A Pilot Study on Argument Simplification in Stance-Based Opinions

Prior work has investigated the problem mining arguments from online reviews by classifying opinions based on the stance expressed explicitly or implicitly. An implicit opinion has the stance left unexpressed linguistically while an explicit opinion has the stance expressed explicitly. In this paper, we propose a bipartite graph-based approach to relate a given set of explicit opinions as simplified arguments for a given set of implicit opinions using three different features (a) sentence similarity, (b) sentiment and (c) target. Experiments are carried out on a manually annotated set of explicit-implicit opinions and show that unsupervised sentence representations can be used to accurately match arguments with their corresponding simplified versions

Towards Continuous Acoustic Tactile Soft Sensing

Acoustic Soft Tactile (AST) skin is a novel sensing technology that uses deformations of the acoustic channels beneath the sensing surface to predict static normal forces and their contact locations. AST skin functions by sensing the changes in the modulation of the acoustic waves travelling through the channels as they deform due to the forces acting on the skin surface. Our previous study tested different AST skin designs for three discrete sensing points and selected two designs that better predicted the forces and contact locations. This paper presents a study of the sensing capability of these two AST skin designs with continuous sensing points with a spatial resolution of 6 mm. Our findings indicate that the AST skin with a dual-channel geometry outperformed the single-channel type during calibration. The dual-channel design predicted more than 90% of the forces within a ± 3 N tolerance and was 84.2% accurate in predicting contact locations with ± 6 mm resolution. In addition, the dual-channel AST skin demonstrated superior performance in a real-time pushing experiment over an off-the-shelf soft tactile sensor. These results demonstrate the potential of using AST skin technology for real-time force sensing in various applications, such as human-robot interaction and medical diagnosis

Towards Autonomous Selective Harvesting: A Review of Robot Perception, Robot Design, Motion Planning and Control

This paper provides an overview of the current state-of-the-art in selective harvesting robots (SHRs) and their potential for addressing the challenges of global food production. SHRs have the potential to increase productivity, reduce labour costs, and minimise food waste by selectively harvesting only ripe fruits and vegetables. The paper discusses the main components of SHRs, including perception, grasping, cutting, motion planning, and control. It also highlights the challenges in developing SHR technologies, particularly in the areas of robot design, motion planning and control. The paper also discusses the potential benefits of integrating AI and soft robots and data-driven methods to enhance the performance and robustness of SHR systems. Finally, the paper identifies several open research questions in the field and highlights the need for further research and development efforts to advance SHR technologies to meet the challenges of global food production. Overall, this paper provides a starting point for researchers and practitioners interested in developing SHRs and highlights the need for more research in this field.Comment: Preprint: to be appeared in Journal of Field Robotic