Molecular genetic analysis of DNA alterations in Irish colorectal cancer

Colorectal cancer is the most common cause of death due to malignancy in nonsmokers in the western world. In 1995 there were 1,757 cases of colon cancer in Ireland. Most colon cancer is sporadic, however ten percent of cases occur where there is a previous family history of the disease. In an attempt to understand the tumorigenic pathway in Irish colon cancer patients, a number of genes associated with colorectal cancer development were analysed in Irish sporadic and HNPCC colon cancer patients. The hereditary forms of colon cancer include Familial adenomatous polyposis coli (FAP) and Hereditary Non-Polyposis Colon Cancer (HNPCC). Genetic analysis of the gene responsible for FAP, (the APC gene) has been previously performed on Irish families, however the genetic analysis of HNPCC families is limited. In an attempt to determine the mutation spectrum in Irish HNPCC pedigrees, the hMSH2 and hMLHl mismatch repair genes were screened in 18 Irish HNPCC families. Using SSCP analysis followed by DNA sequencing, five mutations were identified, four novel and a previously reported mutation. In families where a mutation was detected, younger asyptomatic members were screened for the presence of the predisposing mutation (where possible). Detection of mutations is particularly important for the identification of at risk individuals as the early diagnosis of cancer can vastly improve the prognosis. The sensitive and efficient detection of multiple different mutations and polymorphisms in DNA is of prime importance for genetic diagnosis and the identification of disease genes. A novel mutation detection technique has recently been developed in our laboratory. In order to assess the efficacy and application of the methodology in the analysis of cancer associated genes, a protocol for the analysis of the K-ras gene was developed and optimised. Matched normal and tumour DNA from twenty sporadic colon cancer patients was analysed for K-ras mutations using the Glycosylase Mediated Polymorphism Detection technique. Five mutations of the K-ras gene were detected using this technology. Sequencing analysis verified the presence of the mutations and SSCP analysis of the same samples did not identify any additional mutations. The GMPD technology proved to be highly sensitive, accurate and efficient in the identification of K-ras gene mutations. In order to investigate the role of the replication error phenomenon in Irish colon cancer, 3 polyA tract repeat loci were analysed. The repeat loci included a 10 bp intragenic repeat of the TGF-β-RII gene. TGF-β-RII is involved in the TGF-β epithelial cell growth pathway and mutation of the gene is thought to play a role in cell proliferation and tumorigenesis. Due to the presence of a repeat sequence within the gene, TGFB-RII defects are associated with tumours that display the replication error phenomenon. Analysis of the TGF-β-RII 10 bp repeat failed to identify mutations in any colon cancer patients. Analysis of the Bat26 and Bat 40 polyA repeat sequences in the sporadic and HNPCC families revealed that instability is associated with HNPCC tumours harbouring mismatch repair defects and with 20 % of sporadic colon cancer tumours. No correlation between K-ras gene mutations and the RER+ phenotype was detected in sporadic colon cancer tumours.

Financial modelling with 2-EPT probability density functions

The class of all Exponential-Polynomial-Trigonometric (EPT) functions is classical and equal to the Euler-d’Alembert class of solutions of linear differential equations with constant coefficients. The class of non-negative EPT functions defined on [0;1) was discussed in Hanzon and Holland (2010) of which EPT probability density functions are an important subclass. EPT functions can be represented as ceAxb, where A is a square matrix, b a column vector and c a row vector where the triple (A; b; c) is the minimal realization of the EPT function. The minimal triple is only unique up to a basis transformation. Here the class of 2-EPT probability density functions on R is defined and shown to be closed under a variety of operations. The class is also generalised to include mixtures with the pointmass at zero. This class coincides with the class of probability density functions with rational characteristic functions. It is illustrated that the Variance Gamma density is a 2-EPT density under a parameter restriction. A discrete 2-EPT process is a process which has stochastically independent 2-EPT random variables as increments. It is shown that the distribution of the minimum and maximum of such a process is an EPT density mixed with a pointmass at zero. The Laplace Transform of these distributions correspond to the discrete time Wiener-Hopf factors of the discrete time 2-EPT process. A distribution of daily log-returns, observed over the period 1931-2011 from a prominent US index, is approximated with a 2-EPT density function. Without the non-negativity condition, it is illustrated how this problem is transformed into a discrete time rational approximation problem. The rational approximation software RARL2 is used to carry out this approximation. The non-negativity constraint is then imposed via a convex optimisation procedure after the unconstrained approximation. Sufficient and necessary conditions are derived to characterise infinitely divisible EPT and 2-EPT functions. Infinitely divisible 2-EPT density functions generate 2-EPT Lévy processes. An assets log returns can be modelled as a 2-EPT Lévy process. Closed form pricing formulae are then derived for European Options with specific times to maturity. Formulae for discretely monitored Lookback Options and 2-Period Bermudan Options are also provided. Certain Greeks, including Delta and Gamma, of these options are also computed analytically. MATLAB scripts are provided for calculations involving 2-EPT functions. Numerical option pricing examples illustrate the effectiveness of the 2-EPT approach to financial modelling.

Development of germanium/silicon integration for near infrared detection

Silicon (Si) is the base material for electronic technologies and is emerging as a very attractive platform for photonic integrated circuits (PICs). PICs allow optical systems to be made more compact with higher performance than discrete optical components. Applications for PICs are in the area of fibre-optic communication, biomedical devices, photovoltaics and imaging. Germanium (Ge), due to its suitable bandgap for telecommunications and its compatibility with Si technology is preferred over III-V compounds as an integrated on-chip detector at near infrared wavelengths. There are two main approaches for Ge/Si integration: through epitaxial growth and through direct wafer bonding. The lattice mismatch of ~4.2% between Ge and Si is the main problem of the former technique which leads to a high density of dislocations while the bond strength and conductivity of the interface are the main challenges of the latter. Both result in trap states which are expected to play a critical role. Understanding the physics of the interface is a key contribution of this thesis. This thesis investigates Ge/Si diodes using these two methods. The effects of interface traps on the static and dynamic performance of Ge/Si avalanche photodetectors have been modelled for the first time. The thesis outlines the original process development and characterization of mesa diodes which were fabricated by transferring a ~700 nm thick layer of p-type Ge onto n-type Si using direct wafer bonding and layer exfoliation. The effects of low temperature annealing on the device performance and on the conductivity of the interface have been investigated. It is shown that the diode ideality factor and the series resistance of the device are reduced after annealing. The carrier transport mechanism is shown to be dominated by generation–recombination before annealing and by direct tunnelling in forward bias and band-to-band tunnelling in reverse bias after annealing. The thesis presents a novel technique to realise photodetectors where one of the substrates is thinned by chemical mechanical polishing (CMP) after bonding the Si-Ge wafers. Based on this technique, Ge/Si detectors with remarkably high responsivities, in excess of 3.5 A/W at 1.55 μm at −2 V, under surface normal illumination have been measured. By performing electrical and optical measurements at various temperatures, the carrier transport through the hetero-interface is analysed by monitoring the Ge band bending from which a detailed band structure of the Ge/Si interface is proposed for the first time. The above unity responsivity of the detectors was explained by light induced potential barrier lowering at the interface. To our knowledge this is the first report of light-gated responsivity for vertically illuminated Ge/Si photodiodes. The wafer bonding approach followed by layer exfoliation or by CMP is a low temperature wafer scale process. In principle, the technique could be extended to other materials such as Ge on GaAs, or Ge on SOI. The unique results reported here are compatible with surface normal illumination and are capable of being integrated with CMOS electronics and readout units in the form of 2D arrays of detectors. One potential future application is a low-cost Si process-compatible near infrared camera.

Inquiring into perspective transformation in university education

My Portfolio of Exploration tackles the difficult question as to whether adult mental development can be accelerated and if so how. Rooted in constructive-developmental ideas, adult mental development is explained as an evolutionary unfolding of human capability. Going beyond this I look at the possibility of advancing development as transformational growth in adulthood in the belief that a broader perspective leads to increased effectiveness in professional life. Initially I explored my own meaning making, to make sense of my experiences, knowledge, relationships and my own motivations. This exploration has provided me with a ‘developmental bridge’ between my current way of knowing and a new more enlightened way. I have come to view my way of making meaning in the world as an evolving and progressive sequence of emotional and cognitive development. Through the formation of new stretching experiences, increased self - awareness and reflection my previous perspective has been overtaken by a more complex form of being aware of myself, others and the world. I refer to this process of growth as transformation. As part of my own transformational work I have conducted an inquiry into transformational growth and learning in the early academic life of university undergraduates. The result shows how accelerated adult mental development can be achieved in an academic environment ably preparing students for the workplace. This new model of education is part of a truly unique and exciting model signalling ground-breaking change for the undergraduate experience. The overhaul of a traditional BA degree in Economics into a world-class transformational programme is discussed through-out my Portfolio. Central to my broadening awareness is the challenge and nurturing required to awaken the student’s ‘internal authority’ . This involves stimulating students to take ownership for their own thinking, steering them away from the passivity and complacency of thinking through the minds of others. In doing so, the ultimate aim of renewing the BA is to narrow the developmental ‘mismatch’ which exists for m any college students between them and the world of work, by encouraging and inviting them to take on the challenge of thinking independently. Mindfulness, awareness, and personal authority are treated with reverence throughout the exploration as I consider them core parts of the students engaging with development. Engagement is construed as an active and open-minded process of awareness involving planning and reviewing one’s own goals and performance, engaging in constructive feedback, reflection and new action. I conclude with a view that the journey of adult mental development is relentless and that undergraduate education represents a crucial beginning. The value and relevance of transformational education rooted in developmental principles provides a significant opportunity in advancing development and perspectives at the start of adult life.

Developing executive capability — banking and beyond

The transition to becoming a leader is perhaps the least understood and most difficult in business. This Portfolio of Exploration examines the development of conscious awareness and meaning complexity as key transformational requirements to operate competently at leadership level and to succeed in a work environment characterised by change and complexity. It recognises that developing executive leadership capability is not just an issue of personality increasing what we know or expertise. It requires development of complexity in terms of how we know ourselves, relate to others, construe leadership and organisation, problem solve in business and understand the world as a whole. The exploration is grounded in the theory of adult mental development as outlined by Robert Kegan (1982, 1994) and in his collaborations with Lisa Laskow Lahey (2001, 2009). The theory points to levels of consciousness which impact on how we make meaning of and experience the world around us and respond to it. Critically it also points to transformational processes which enable us to evolve how we make meaning of our world as a means to close the mismatch between the demands of this world and our ability to cope. The exploration is laid out in three stages. Using Kegan’s (1982, 1994) theory as a framework it begins with a reflection of my career to surface how I made meaning of banking, management and subsequently leadership. In stage two I engage with a range of source thinkers in the areas of leadership, decision making, business, organisation, growth and complexity in a transformational process of developing greater conscious and complex understanding of organisational leadership (also recognising ever increasing complexity in the world). Finally, in stage three, I explore how qualitative changes as a result of this transformational effort have benefitted my professional, leadership and organisational capabilities.

Reliability of antitransglutaminase antibodies as predictors of gluten-free diet compliance in adult celiac disease.

OBJECTIVE: Strict lifelong compliance to a gluten-free diet (GFD) minimizes the long-term risk of mortality, especially from lymphoma, in adult celiac disease (CD). Although serum IgA antitransglutaminase (IgA-tTG-ab), like antiendomysium (IgA-EMA) antibodies, are sensitive and specific screening tests for untreated CD, their reliability as predictors of strict compliance to and dietary transgressions from a GFD is not precisely known. We aimed to address this question in consecutively treated adult celiacs. METHODS: In a cross-sectional study, 95 non-IgA deficient adult (median age: 41 yr) celiacs on a GFD for at least 1 yr (median: 6 yr) were subjected to 1) a dietician-administered inquiry to pinpoint and quantify the number and levels of transgressions (classified as moderate or large, using as a cutoff value the median gluten amount ingested in the overall noncompliant patients of the series) over the previous 2 months, 2) a search for IgA-tTG-ab and -EMA, and 3) perendoscopic duodenal biopsies. The ability of both antibodies to discriminate celiacs with and without detected transgressions was described using receiver operating characteristic curves and quantified as to sensitivity and specificity, according to the level of transgressions. RESULTS: Forty (42%) patients strictly adhered to a GFD, 55 (58%) had committed transgressions, classified as moderate (< or = 18 g of gluten/2 months; median number 6) in 27 and large (>18 g; median number 69) in 28. IgA-tTG-ab and -EMA specificity (proportion of correct recognition of strictly compliant celiacs) was 0.97 and 0.98, respectively, and sensitivity (proportion of correct recognition of overall, moderate, and large levels of transgressions) was 0.52, 0.31, and 0.77, and 0.62, 0.37, and 0.86, respectively. IgA-tTG-ab and -EMA titers were correlated (p < 0.001) to transgression levels (r = 0.560 and R = 0.631, respectively) and one to another (p < 0.001) in the whole patient population (r = 0.834, N = 84) as in the noncompliant (r = 0.915, N = 48) group. Specificity and sensitivity of IgA-tTG-ab and IgA-EMA for recognition of total villous atrophy in patients under a GFD were 0.90 and 0.91, and 0.60 and 0.73, respectively. CONCLUSIONS: In adult CD patients on a GFD, IgA-tTG-ab are poor predictors of dietary transgressions. Their negativity is a falsely secure marker of strict diet compliance.

Attentional Biases in Value-Based Decision-Making

Humans make decisions in highly complex physical, economic and social environments. In order to adaptively choose, the human brain has to learn about- and attend to- sensory cues that provide information about the potential outcome of different courses of action. Here I present three event-related potential (ERP) studies, in which I evaluated the role of the interactions between attention and reward learning in economic decision-making. I focused my analyses on three ERP components (Chap. 1): (1) the N2pc, an early lateralized ERP response reflecting the lateralized focus of visual; (2) the feedback-related negativity (FRN), which reflects the process by which the brain extracts utility from feedback; and (3) the P300 (P3), which reflects the amount of attention devoted to feedback-processing. I found that learned stimulus-reward associations can influence the rapid allocation of attention (N2pc) towards outcome-predicting cues, and that differences in this attention allocation process are associated with individual differences in economic decision performance (Chap. 2). Such individual differences were also linked to differences in neural responses reflecting the amount of attention devoted to processing monetary outcomes (P3) (Chap. 3). Finally, the relative amount of attention devoted to processing rewards for oneself versus others (as reflected by the P3) predicted both charitable giving and self-reported engagement in real-life altruistic behaviors across individuals (Chap. 4). Overall, these findings indicate that attention and reward processing interact and can influence each other in the brain. Moreover, they indicate that individual differences in economic choice behavior are associated both with biases in the manner in which attention is drawn towards sensory cues that inform subsequent choices, and with biases in the way that attention is allocated to learn from the outcomes of recent choices.

Improvement in visual search with practice: mapping learning-related changes in neurocognitive stages of processing.

Practice can improve performance on visual search tasks; the neural mechanisms underlying such improvements, however, are not clear. Response time typically shortens with practice, but which components of the stimulus-response processing chain facilitate this behavioral change? Improved search performance could result from enhancements in various cognitive processing stages, including (1) sensory processing, (2) attentional allocation, (3) target discrimination, (4) motor-response preparation, and/or (5) response execution. We measured event-related potentials (ERPs) as human participants completed a five-day visual-search protocol in which they reported the orientation of a color popout target within an array of ellipses. We assessed changes in behavioral performance and in ERP components associated with various stages of processing. After practice, response time decreased in all participants (while accuracy remained consistent), and electrophysiological measures revealed modulation of several ERP components. First, amplitudes of the early sensory-evoked N1 component at 150 ms increased bilaterally, indicating enhanced visual sensory processing of the array. Second, the negative-polarity posterior-contralateral component (N2pc, 170-250 ms) was earlier and larger, demonstrating enhanced attentional orienting. Third, the amplitude of the sustained posterior contralateral negativity component (SPCN, 300-400 ms) decreased, indicating facilitated target discrimination. Finally, faster motor-response preparation and execution were observed after practice, as indicated by latency changes in both the stimulus-locked and response-locked lateralized readiness potentials (LRPs). These electrophysiological results delineate the functional plasticity in key mechanisms underlying visual search with high temporal resolution and illustrate how practice influences various cognitive and neural processing stages leading to enhanced behavioral performance.

The neural dynamics of stimulus and response conflict processing as a function of response complexity and task demands.

Both stimulus and response conflict can disrupt behavior by slowing response times and decreasing accuracy. Although several neural activations have been associated with conflict processing, it is unclear how specific any of these are to the type of stimulus conflict or the amount of response conflict. Here, we recorded electrical brain activity, while manipulating the type of stimulus conflict in the task (spatial [Flanker] versus semantic [Stroop]) and the amount of response conflict (two versus four response choices). Behaviorally, responses were slower to incongruent versus congruent stimuli across all task and response types, along with overall slowing for higher response-mapping complexity. The earliest incongruency-related neural effect was a short-duration frontally-distributed negativity at ~200 ms that was only present in the Flanker spatial-conflict task. At longer latencies, the classic fronto-central incongruency-related negativity 'N(inc)' was observed for all conditions, but was larger and ~100 ms longer in duration with more response options. Further, the onset of the motor-related lateralized readiness potential (LRP) was earlier for the two vs. four response sets, indicating that smaller response sets enabled faster motor-response preparation. The late positive complex (LPC) was present in all conditions except the two-response Stroop task, suggesting this late conflict-related activity is not specifically related to task type or response-mapping complexity. Importantly, across tasks and conditions, the LRP onset at or before the conflict-related N(inc), indicating that motor preparation is a rapid, automatic process that interacts with the conflict-detection processes after it has begun. Together, these data highlight how different conflict-related processes operate in parallel and depend on both the cognitive demands of the task and the number of response options.

Reliability analysis of flip chip designs via computer simulation

A flip chip component is a silicon chip mounted to a substrate with the active area facing the substrate. This paper presents the results of an investigation into the relationship between a number of important material properties and geometric parameters on the thermal-mechanical fatigue reliability of a standard flip chip design and a flip chip design with the use of microvias. Computer modeling has been used to analyze the mechanical conditions of flip chips under cyclic thermal loading where the Coffin-Manson empirical relationship has been used to predict the life time of the solder interconnects. The material properties and geometry parameters that have been investigated are the Young's modulus, the coefficient of thermal expansion (CTE) of the underfill, the out-of-plane CTE (CTEz) of the substrate, the thickness of the substrate, and the standoff height. When these parameters vary, the predicted life-times are calculated and some of the features of the results are explained. By comparing the predicted lifetimes of the two designs and the strain conditions under thermal loading, the local CTE mismatch has been found to be one of most important factors in defining the reliability of flip chips with microvias.

Modelling technology to predict flip-chip assembly

This paper describes modelling technology and its use in providing data governing the assembly of flip-chip components. Details are given on the reflow and curing stages as well as the prediction of solder joint shapes. The reflow process involves the attachment of a die to a board via solder joints. After a reflow process, underfill material is placed between the die and the substrate where it is heated and cured. Upon cooling the thermal mismatch between the die, underfill, solder bumps, and substrate will result in a nonuniform deformation profile across the assembly and hence stress. Shape predictions then thermal solidification and stress prediction are undertaken on solder joints during the reflow process. Both thermal and stress calculations are undertaken to predict phenomena occurring during the curing of the underfill material. These stresses may result in delamination between the underfill and its surrounding materials leading to a subsequent reduction in component performance and lifetime. Comparisons between simulations and experiments for die curvature will be given for the reflow and curing process

Experimental and modeling analysis of the reliability of the anisotropic conductive films

Experiments as well as computer modeling methods have been used to investigate the effect of the solder reflow process on the electrical characteristics and reliability of anisotropic conductive film (ACF) interconnections. In the experiments, the contact resistance of the ACF interconnections was found to increase after a subsequent reflow and the magnitude of this increase was strongly correlated to the peak temperature of the reflow profile. In fact, nearly 40 percent of the joints were opened (i.e. lifted away from the pad) after the reflow with a peak temperature of 260 OC while no openings was observed when the peak temperature was 210 "C. It is believed that the CTE mismatch between the polymer particle and the adhesive matrix is the main cause of this contact degradation. To understand this phenomenon better, a 3-D model of an ACF joint structure was built and Finite Element Analysis was used to predict the stress distrihution in the conductive particles, adhesive matrix and metal pads during the reflow process. The effects of the peak temperature, the CTE of the adhesive matrix and the bump height on the reliability of the ACF interconnections were discussed.

Thermal, mechanical and optical modelling of VCSEL packaging

Hybrid OECB (Opto-Electrical Circuit Boards) are expected to make a significant impact in the telecomm switches arena within the next five years, creating optical backplanes with high speed point-to-point optical interconnects. OECB's incorporate short range optical interconnects, and are based on VCSEL (Vertical Cavity Surface Emitting Diode) and PD (Photo Diode) pairs, connected to each other via embedded waveguides in the OECB. The VCSEL device is flip-chip assembled onto an organic substrate with embedded optical waveguides. The performance of the VCSEL device is governed by the thermal, mechanical and optical characteristics of this assembly. During operation, the VCSEL device will heat up and the thermal change together with the CTE mismatch in the materials, will result in potential misalignment between the VCSEL apertures and the waveguide openings in the substrate. Any degree of misalignment will affect the optical performance of the package. This paper will present results from a highly coupled modelling analysis involving thermal, mechanical and optical models. The paper will also present results from an optimisation analysis based on Design of Experiments (DOE).

Effects of reflow process on the reliability of flip chip on flex interconnections using anisotropic conductive adhesives

In this paper, the effects of the solder reflow process on the reliability of anisotropic conductive film (ACF) interconnections for flip chip on flex (FCOF) applications are investigated. Experiments as well as computer modeling methods have been used. In the experiments, it was found that the contact resistance of ACF joints increased after the subsequent reflow process, and the magnitude of this increase was strongly correlated to the peak temperature of the reflow profile. Nearly 40% of the joints were opened (i.e. lifted away from the pad) after the reflow process with 260 °C peak temperature while no opening was observed when the peak temperature was 210 °C. It is believed that the CTE mismatch between the polymer particle and the adhesive matrix is the main cause of this contact degradation. It was also found that the ACF joints after the reflow process with 210 °C peak temperature showed a high ability to resist water absorption under steady state 85 °C/85%RH conditions, probably because the curing degree of the ACF was improved during the reflow process. To give a good understanding, a 3D model of an ACF joint structure was built and finite element analysis was used to predict the stress distribution in the conductive particles, adhesive matrix and metal pads during the reflow process.

VCSEL to waveguide coupling for optical backplanes

Hybrid OECB (Opto-Electrical Circuit Boards) are expected to make a significant impact in the telecomm switches arena within the next five years, creating optical backplanes with high speed point-to-point optical interconnects. The critical aspect in the manufacture of the optical backplane is the successful coupling between VCSEL (Vertical Cavity Surface Emitting Laser) device and embedded waveguide in the OECB. Optical performance will be affected by CTE mismatch in the material properties, and manufacturing tolerances. This paper will discuss results from a multidisciplinary research project involving both experimentation and modelling. Key process parameters are being investigated using Design of Experiments and Finite Element Modelling. Simulations have been undertaken that predict the temperature in the VCSEL during normal operation, and the subsequent misalignment that this imposes. The results from the thermomechanical analysis are being used with optimisation software and the experimental DOE (Design of Experiments) to identify packaging parameters that minimise misalignment. These results are also imported into an optical model which solves optical energy and attenuation from the VCSEL aperture into, and then through, the waveguide. Results from the thermomechanical and optical models will be discussed as will the experimental results from the DOE.