Development of a Reality-Based, Haptics-Enabled Simulator for Tool-Tissue Interactions

The advent of complex surgical procedures has driven the need for finite element based surgical training simulators which provide realistic visual and haptic feedback throughout the surgical task. The foundation of a simulator stems from the use of accurate, reality-based models for the global tissue response as well as the tool-tissue interactions. To that end, ex vivo and in vivo tests were conducted for soft-tissue probing and in vivo tests were conducted for soft-tissue cutting for the purpose of model development. In formulating a surgical training system, there is a desire to replicate the surgical task as accurately as possible for haptic and visual realism. However, for many biological tissues, there is a discrepancy between the mechanical characteristics of ex vivo and in vivo tissue. The efficacy of utilizing an ex vivo model for simulation of in vivo probing tasks on porcine liver was evaluated by comparing the simulated probing task to an identical in vivo probing experiment. The models were then further improved upon to better replicate the in vivo response. During the study of cutting modeling, in vivo cutting experiments were performed on porcine liver to derive the force-displacement response of the tissue to a scalpel blade. Using this information, a fracture mechanics based approach was applied to develop a fully defined cohesive zone model governing the separation properties of the liver directly in front of the scalpel blade. Further, a method of scaling the cohesive zone parameters was presented to minimize the computational expense in an effort to apply the cohesive based cutting approach to real-time simulators. The development of the models for the global tissue response and local tool-tissue interactions for probing and cutting of soft-tissue provided the framework for real-time simulation of basic surgical skills training. Initially, a pre-processing approach was used for the development of reality-based, haptics enabled simulators for probing and cutting of soft tissue. Then a real-time finite element based simulator was developed to simulate the probing task without the need to know the tool path prior to simulation

A measurement system for and the measurement system of single particle energies in quantum dots

This thesis describes the design, development, construction and performance of an instrumentation system suitable for the measurement of single electron quantum dot devices. The inaugural measurement with this new system produced fascinating experimental data from a novel magnetic spectrometer device. This data, presented in chapter 5, suggests that it is possible to measure the single particle spacing in a 500nm quantum dot device independent of the Coulomb blockade energy and within an electron mean free path. Devices were defined on a GaAs/AlGaAs heterostructure, the interface of which formed a 2 dimensional electron gas (2DEG). The surface was patterned with metallic surface gates. On the application of a potential to the gates, the electrons were depleted from beneath the gate and the pattern was transferred to the 2DEG. The devices were fabricated in a Hall bar geometry using standard nanofabrication techniques. Measurements were performed using a 3He/4He Kelvinox 25 dilution refrigerator unit at a lattice temperature of TL45mK. Prior to the work detailed in this thesis the lowest effective electron temperature available to quantum transport researchers at Glasgow had been 1.2 Kelvin. This was achieved with the use of a pumped 4He variable temperature insert (VTI), for which 1.2K represented the lowest working temperature. Although a 3He/4He dilution unit had been available for some time, the unit had exhibited an effective electron temperature of Te>7K. As a direct result of the work contained within this thesis (detailed in chapter 4), the lower limit of the effective electron temperature range available was extended down to 250mK. This represents an improvement of more than an order of magnitude over the lowest effective electron temperature previously available and an improvement of >20 over that previously available within the dilution limit. In order to achieve this improvement a systems approach was adopted. The individual subsystems associated with the design of the new measurement system were designed to work in conjunction with one another. Great care was taken with respect to referencing potentials, shielding, intrinsic noise of the electronic components used and vibration isolation in order that the measurement system imposed the minimum induced electron heating on the device under test. Measurements were performed on quantum dot devices in the Coulomb blockade regime. Periodic peaks in the conductance of a quantum dot were observed. These conductance peaks were seen in response to an applied gate voltage, and are referred to as Coulomb oscillations. Such oscillations are a result of classical charging effects due to the addition or subtraction of a single electron to, or from, the quantum dot. These effects are a direct result of the quantisation of charge. Energy quantisation due to the confinement of the electrons wave-function, also plays a role in quantum dot devices. In the devices studied the classical charging energy, that gives rise to the Coulomb oscillations is generally an order of magnitude greater than the quantum mechanical effects that give rise to the single particle spectrum

How well do high resolution models reproduce tropical convection?

Cascade is a multi-institution project studying the temporal and spatial organization of tropical convective systems. While cloud resolving numerical models can reproduce the observed diurnal cycle of such systems they are sensitive to the chosen resolution. As part of this effort, we are comparing results from the Met. Office Unified Model to data from the Global Earth Radiation Budget satellite instrument over the African Monsoon Interdisciplinary Analyses region of North Africa. We use a variety of mathematical techniques to study the outgoing radiation and the evolution of properties such as the cloud size distribution. The effectiveness of various model resolutions is tested with a view to determining the optimum balance between resolution and the need to reproduce the observations

Assessing the farm-scale impacts of cover crops and non-inversion tillage regimes on nutrient losses from an arable catchment

The efficacy of cover crops and non-inversion tillage regimes at minimising farm-scale nutrient losses were assessed across a large, commercial arable farm in Norfolk, UK. The trial area, covering 143 ha, was split into three blocks: winter fallow with mouldboard ploughing (Block J); shallow non-inversion tillage with a winter oilseed radish (Raphanus sativus) cover crop (Block P); and direct drilling with a winter oilseed radish cover crop (Block L). Soil, water and vegetation chemistry across the trial area were monitored over the 2012/13 (pre-trial), 2013/14 (cover crops and non-inversion tillage) and 2014/15 (non-inversion tillage only) farm years. Results revealed oilseed radish reduced nitrate (NO3¬¬-N) leaching losses in soil water by 75–97% relative to the fallow block, but had no impact upon phosphorus (P) losses. Corresponding reductions in riverine NO3¬¬-N concentrations were not observed, despite the trial area covering 20% of the catchment. Mean soil NO3¬¬-N concentrations were reduced by ~77% at 60–90 cm depth beneath the cover crop, highlighting the ability of deep rooting oilseed radish to scavenge nutrients from deep within the soil profile. Alone, direct drilling and shallow non-inversion tillage were ineffective at reducing soil water NO3¬¬-N and P concentrations relative to conventional ploughing. Applying starter fertiliser to the cover crop increased radish biomass and nitrogen (N) uptake, but resulted in net N accumulation within the soil. There was negligible difference between the gross margins of direct drilling (£731 ha-1) and shallow non-inversion tillage (£758 ha-1) with a cover crop and conventional ploughing with fallow (£745 ha-1), demonstrating farm productivity can be maintained whilst mitigating diffuse pollution. The results presented here support the wider adoption of winter oilseed radish cover crops to reduce NO3¬¬-N leaching losses in arable systems, but caution that it may take several years before catchment-scale impacts downstream are detected

Chemical Tuning Enhances Both Potency Toward Nrf2 and In Vitro Therapeutic Index of Triterpenoids

The transcription factor Nrf2 protects against a number of experimental pathologies, and is a promising therapeutic target. The clinical investigation of a potent Nrf2-inducing agent, the triterpenoid (TP) bardoxolone methyl (BARD), was recently halted due to adverse cardiovascular events in chronic kidney disease patients, although the underlying mechanisms are yet to be resolved. The majority of small molecule Nrf2 inducers are electrophilic and trigger Nrf2 accumulation via the chemical modification of its redox-sensitive repressor Keap1. Therefore, it is pertinent to question whether the therapeutic targeting of Nrf2 could be hindered in many cases by the inherent reactivity of a small molecule inducer toward unintended cellular targets, a key mechanism of drug toxicity. Using H4IIE-ARE8L hepatoma cells, we have examined the relationship between (a) Nrf2 induction potency, (b) toxicity and (c) in vitro therapeutic index (ratio of b:a) for BARD and a number of other small molecule activators of Nrf2. We show that BARD exhibits the highest potency toward Nrf2 and the largest in vitro therapeutic index among compounds that have been investigated clinically (namely BARD, sulforaphane and dimethylfumarate). Through further examination of structurally related TPs, we demonstrate that an increase in potency toward Nrf2 is associated with a relatively smaller increase in toxicity, indicating that medicinal chemistry can be used to enhance the specificity of a compound as an inducer of Nrf2 signaling whilst simultaneously increasing its therapeutic index. These findings will inform the continuing design and development of drugs targeting Nrf

Application of high-resolution telemetered sensor technology to develop conceptual models of catchment hydrogeological processes

Mitigating agricultural water pollution requires changes in land management practices and the implementation of on-farm measures to tackle the principal reasons for water quality failure. However, a paucity of robust empirical evidence on the hydrological functioning of river catchments can be a major constraint on the design of effective pollution mitigation strategies at the catchment-scale. In this regard, in 2010 the UK government established the Demonstration Test Catchment (DTC) initiative to evaluate the extent to which on-farm mitigation measures can cost-effectively reduce the impacts of agricultural water pollution on river ecology while maintaining food production capacity. A central component of the DTC platform has been the establishment of a comprehensive network of automated, web-based sensor technologies to generate high-temporal resolution empirical datasets of surface water, soil water, groundwater and meteorological parameters. In this paper, we demonstrate how this high-resolution telemetry can be used to improve our understanding of hydrological functioning and the dynamics of pollutant mobilisation and transport under a range of hydrometerological and hydrogeological conditions. Furthermore, we demonstrate how these data can be used to develop conceptual models of catchment hydrogeological processes and consider the implications of variable hydrological functioning on the performance of land management changes aimed at reducing agricultural water pollution

Chemical tuning enhances both potency toward Nrf2 and<em> in vitro</em> therapeutic index of triterpenoids

The transcription factor Nrf2 protects against a number of experimental pathologies, and is a promising therapeutic target. The clinical investigation of a potent Nrf2-inducing agent, the triterpenoid (TP) bardoxolone methyl (BARD), was recently halted due to adverse cardiovascular events in chronic kidney disease patients, although the underlying mechanisms are yet to be resolved. The majority of small molecule Nrf2 inducers are electrophilic and trigger Nrf2 accumulation via the chemical modification of its redox-sensitive repressor Keap1. Therefore, it is pertinent to question whether the therapeutic targeting of Nrf2 could be hindered in many cases by the inherent reactivity of a small molecule inducer toward unintended cellular targets, a key mechanism of drug toxicity. Using H4IIE-ARE8L hepatoma cells, we have examined the relationship between (a) Nrf2 induction potency, (b) toxicity and (c) in vitro therapeutic index (ratio of b:a) for BARD and a number of other small molecule activators of Nrf2. We show that BARD exhibits the highest potency toward Nrf2 and the largest in vitro therapeutic index among compounds that have been investigated clinically (namely BARD, sulforaphane and dimethylfumarate). Through further examination of structurally related TPs, we demonstrate that an increase in potency toward Nrf2 is associated with a relatively smaller increase in toxicity, indicating that medicinal chemistry can be used to enhance the specificity of a compound as an inducer of Nrf2 signaling whilst simultaneously increasing its therapeutic index. These findings will inform the continuing design and development of drugs targeting Nrf2.</p

Nrf2 is overexpressed in pancreatic cancer: implications for cell proliferation and therapy

<p>Abstract</p> <p>Background</p> <p>Nrf2 is a key transcriptional regulator of a battery of genes that facilitate phase II/III drug metabolism and defence against oxidative stress. Nrf2 is largely regulated by Keap1, which directs Nrf2 for proteasomal degradation. The Nrf2/Keap1 system is dysregulated in lung, head and neck, and breast cancers and this affects cellular proliferation and response to therapy. Here, we have investigated the integrity of the Nrf2/Keap1 system in pancreatic cancer.</p> <p>Results</p> <p>Keap1, Nrf2 and the Nrf2 target genes AKR1c1 and GCLC were detected in a panel of five pancreatic cancer cell lines. Mutation analysis of <it>NRF2 </it>exon 2 and <it>KEAP1 </it>exons 2-6 in these cell lines identified no mutations in <it>NRF2 </it>and only synonomous mutations in <it>KEAP1</it>. RNAi depletion of Nrf2 caused a decrease in the proliferation of Suit-2, MiaPaca-2 and FAMPAC cells and enhanced sensitivity to gemcitabine (Suit-2), 5-flurouracil (FAMPAC), cisplatin (Suit-2 and FAMPAC) and gamma radiation (Suit-2). The expression of Nrf2 and Keap1 was also analysed in pancreatic ductal adenocarcinomas (n = 66 and 57, respectively) and matching normal benign epithelium (n = 21 cases). Whilst no significant correlation was seen between the expression levels of Keap1 and Nrf2 in the tumors, interestingly, Nrf2 staining was significantly greater in the cytoplasm of tumors compared to benign ducts (P < 0.001).</p> <p>Conclusions</p> <p>Expression of Nrf2 is up-regulated in pancreatic cancer cell lines and ductal adenocarcinomas. This may reflect a greater intrinsic capacity of these cells to respond to stress signals and resist chemotherapeutic interventions. Nrf2 also appears to support proliferation in certain pancreatic adenocarinomas. Therefore, strategies to pharmacologically manipulate the levels and/or activity of Nrf2 may have the potential to reduce pancreatic tumor growth, and increase sensitivity to therapeutics.</p

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression