Computational modelling for decision-making: where, why, what, who and how

In order to deal with an increasingly complex world, we need ever more sophisticated computational models that can help us make decisions wisely and understand the potential consequences of choices. But creating a model requires far more than just raw data and technical skills: it requires a close collaboration between model commissioners, developers, users and reviewers. Good modelling requires its users and commissioners to understand more about the whole process, including the different kinds of purpose a model can have and the different technical bases. This paper offers a guide to the process of commissioning, developing and deploying models across a wide range of domains from public policy to science and engineering. It provides two checklists to help potential modellers, commissioners and users ensure they have considered the most significant factors that will determine success. We conclude there is a need to reinforce modelling as a discipline, so that misconstruction is less likely; to increase understanding of modelling in all domains, so that the misuse of models is reduced; and to bring commissioners closer to modelling, so that the results are more useful

An Abundant Dysfunctional Apolipoprotein A1 in Human Atheroma

Recent studies have indicated that high-density lipoproteins (HDLs) and their major structural protein, apolipoprotein A1 (apoA1), recovered from human atheroma are dysfunctional and are extensively oxidized by myeloperoxidase (MPO). In vitro oxidation of either apoA1 or HDL particles by MPO impairs their cholesterol acceptor function. Here, using phage display affinity maturation, we developed a high-affinity monoclonal antibody that specifically recognizes both apoA1 and HDL that have been modified by the MPO-H2O2-Cl− system. An oxindolyl alanine (2-OH-Trp) moiety at Trp72 of apoA1 is the immunogenic epitope. Mutagenesis studies confirmed a critical role for apoA1 Trp72 in MPO-mediated inhibition of the ATP-binding cassette transporter A1 (ABCA1)-dependent cholesterol acceptor activity of apoA1 in vitro and in vivo. ApoA1 containing a 2-OH-Trp72 group (oxTrp72-apoA1) is in low abundance within the circulation but accounts for 20% of the apoA1 in atherosclerosis-laden arteries. OxTrp72-apoA1 recovered from human atheroma or plasma is lipid poor, virtually devoid of cholesterol acceptor activity and demonstrated both a potent proinflammatory activity on endothelial cells and an impaired HDL biogenesis activity in vivo. Elevated oxTrp72-apoA1 levels in subjects presenting to a cardiology clinic (n = 627) were associated with increased cardiovascular disease risk. Circulating oxTrp72-apoA1 levels may serve as a way to monitor a proatherogenic process in the artery wall

An Abundant Dysfunctional Apolipoprotein A1 in Human Atheroma

Recent studies have indicated that high-density lipoproteins (HDLs) and their major structural protein, apolipoprotein A1 (apoA1), recovered from human atheroma are dysfunctional and are extensively oxidized by myeloperoxidase (MPO). In vitro oxidation of either apoA1 or HDL particles by MPO impairs their cholesterol acceptor function. Here, using phage display affinity maturation, we developed a high-affinity monoclonal antibody that specifically recognizes both apoA1 and HDL that have been modified by the MPO-H2O2-Cl− system. An oxindolyl alanine (2-OH-Trp) moiety at Trp72 of apoA1 is the immunogenic epitope. Mutagenesis studies confirmed a critical role for apoA1 Trp72 in MPO-mediated inhibition of the ATP-binding cassette transporter A1 (ABCA1)-dependent cholesterol acceptor activity of apoA1 in vitro and in vivo. ApoA1 containing a 2-OH-Trp72 group (oxTrp72-apoA1) is in low abundance within the circulation but accounts for 20% of the apoA1 in atherosclerosis-laden arteries. OxTrp72-apoA1 recovered from human atheroma or plasma is lipid poor, virtually devoid of cholesterol acceptor activity and demonstrated both a potent proinflammatory activity on endothelial cells and an impaired HDL biogenesis activity in vivo. Elevated oxTrp72-apoA1 levels in subjects presenting to a cardiology clinic (n = 627) were associated with increased cardiovascular disease risk. Circulating oxTrp72-apoA1 levels may serve as a way to monitor a proatherogenic process in the artery wall

An Abundant Dysfunctional Apolipoprotein A1 in Human Atheroma

Recent studies have indicated that high-density lipoproteins (HDLs) and their major structural protein, apolipoprotein A1 (apoA1), recovered from human atheroma are dysfunctional and are extensively oxidized by myeloperoxidase (MPO). In vitro oxidation of either apoA1 or HDL particles by MPO impairs their cholesterol acceptor function. Here, using phage display affinity maturation, we developed a high-affinity monoclonal antibody that specifically recognizes both apoA1 and HDL that have been modified by the MPO-H2O2-Cl− system. An oxindolyl alanine (2-OH-Trp) moiety at Trp72 of apoA1 is the immunogenic epitope. Mutagenesis studies confirmed a critical role for apoA1 Trp72 in MPO-mediated inhibition of the ATP-binding cassette transporter A1 (ABCA1)-dependent cholesterol acceptor activity of apoA1 in vitro and in vivo. ApoA1 containing a 2-OH-Trp72 group (oxTrp72-apoA1) is in low abundance within the circulation but accounts for 20% of the apoA1 in atherosclerosis-laden arteries. OxTrp72-apoA1 recovered from human atheroma or plasma is lipid poor, virtually devoid of cholesterol acceptor activity and demonstrated both a potent proinflammatory activity on endothelial cells and an impaired HDL biogenesis activity in vivo. Elevated oxTrp72-apoA1 levels in subjects presenting to a cardiology clinic (n = 627) were associated with increased cardiovascular disease risk. Circulating oxTrp72-apoA1 levels may serve as a way to monitor a proatherogenic process in the artery wall

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The modelling and design optimisation of tidal stream turbine arrays

Tidal stream turbines are devices that convert the momentum of tidally induced marine currents to electricity. Individual turbines typically have a rated power of up to a few megawatts, and thus power may be extracted on an industrial scale by installing arrays of dozens to hundreds of such devices. Accurately modelling such large arrays presents a formidable computational challenge, as the length scale of the problem varies from tenths of a meter (the scale of an individual turbine blade) to several kilometres (the scale of an array) to hundreds of kilometres (the scale of the ocean currents that govern the flow). In addition to this, the sites under consideration are chosen for their highly energetic, advection-dominated flow regimes. Since the power extracted by a turbine is proportional to the cube of the flow speed into which it is placed, the interaction between the turbines and the flow is both highly coupled and highly non-linear. `Array design' concerns determining the array size -- the number of turbines comprising the array -- and the micro-siting -- the locations of the turbines within the turbine site that has been leased by the array developer. For large arrays in real-world domains the micro-siting designer is faced with hundreds or thousands of control parameters that impact the farm performance through hydrodynamic interactions. Non-hydrodynamic factors such as technical, financial and practical engineering constraints can also have a significant impact upon the design decision. Thus, going beyond modelling such arrays to optimising their design adds an additional dimension of complexity to the problem. Manual optimisation over such large parameter spaces with complex nonlinear constraints is difficult, and there is little practical industrial experience to guide designs. As such the array design problem requires the deployment of specially designed computational tools which can balance the need for accurate evaluation of the hydrodynamics of the interactions between the flow and the array with a suitable optimisation strategy to achieve an efficient and scalable array design paradigm. This thesis documents work to develop and expand the utility of one such software tool; OpenTidalFarm, with the goal of developing a practical approach to array design optimisation and constructing a framework for the inclusion of wide ranging and disparate design criteria. OpenTidalFarm solves the Shallow-Water and associated adjoint equations to evaluate the power extracted by the array and the sensitivity of that power to the posisitions of the turbines. This work is aimed demonstrating that industrial sized turbine arrays may be designed within a broad range of constraints and optimised for complex and occasionally conflicting objectives. This is achieved through exploration of a collection of optimisation approaches including mixed fidelity hybrid global/local schemes for turbine layout, variable fidelity Bayesian optimisation for array size and integrating integer, routing optimisation for inclusion of location-based costs. The first chapter of this thesis introduces the engineering and practical aspects of the problem, while in the second chapter the numerical methods and optimisation techniques through which the problem can be tackled are presented. A family of alternate modelling and optimisation approaches are developed, tested and compared in Chapter 4, to understand how alternate approaches to the problem can be formulated by limiting the complexity of the problem, analysis or optimisation, and how this may successfully be done to suit the designer's available computational budget. In Chapter 5, a framework is presented in which costs over the lifespan of the array may be modelled and considered as part of the design optimisation process. Idealised scenarios are used to demonstrate the effects of a financial-return optimising design approach as contrasted with a power maximisation approach. The impact of non-hydrodynamic considerations on array design is shown to be potentially high. In Chapter 6 the broader question of array sizing is presented and a surrogate model is used to efficiently determine the optimal number of turbines to install on a given site based, once again, on a simple financial model. It is demonstrated that lower turbine densities on sites (between 20 % and 40 % of the maximum density the site could support) maximises the developer's profit on the installation and prevents diminishing returns on investment of additional turbines.Open Acces

Disclosure and sickle cell disorder: a mixed methods study of the young person with sickle cell at school

Sickle cell is a leading genetic condition, both globally and in England. Little research has been conducted into the experiences of young people with sickle cell at school. A mixed methods study (May 2007–September 2008) based on 569 questionnaires and 40 taped interviews with young people living with sickle cell disorder (SCD) in England found that students with SCD are faced with a dilemma as to whether or not to disclose their sickle cell to teachers and pupils: the latent and hidden characteristics of their symptoms make it possible, in Goffmanesque terms, to “pass”. However the variable and unpredictable course of sickle cell is a reminder of Goffman’s notion of being “discreditable”. We found that teacher or pupil knowledge that a young person has sickle cell is not statistically associated with reported better treatment of young people with SCD at school. Analysis of interviews suggests most young people favour disclosing their sickle cell status (on the basis that teachers will then know what actions to take in the face of bouts of illness and in terms of making allowances for illness or school absences). A minority disagreed because disclosure was felt to attract unwarranted attention or disabling attitudes. Attitudes to disclosing to peers were more varied: either for or against disclosure to peers, or ambivalent in that they felt a tension between acknowledging the reality of their sickle cell, and not wanting it to be a central part of their identity. Some health promotion advice appears to assume that teacher and/or peer awareness is the key to improving school experience for young people with SCD, but this is not borne out by this study. Rather a change in wider school environments is required such that young people with SCD are supported irrespective of whether they themselves foreground or play down their disabled identity

Disclosure and sickle cell disorder: A mixed methods study of the young person with sickle cell at school

Sickle cell is a leading genetic condition, both globally and in England. Little research has been conducted into the experiences of young people with sickle cell at school. A mixed methods study (May 2007-September 2008) based on 569 questionnaires and 40 taped interviews with young people living with sickle cell disorder (SCD) in England found that students with SCD are faced with a dilemma as to whether or not to disclose their sickle cell to teachers and pupils: the latent and hidden characteristics of their symptoms make it possible, in Goffmanesque terms, to "pass". However the variable and unpredictable course of sickle cell is a reminder of Goffman's notion of being "discreditable". We found that teacher or pupil knowledge that a young person has sickle cell is not statistically associated with reported better treatment of young people with SCD at school. Analysis of interviews suggests most young people favour disclosing their sickle cell status (on the basis that teachers will then know what actions to take in the face of bouts of illness and in terms of making allowances for illness or school absences). A minority disagreed because disclosure was felt to attract unwarranted attention or disabling attitudes. Attitudes to disclosing to peers were more varied: either for or against disclosure to peers, or ambivalent in that they felt a tension between acknowledging the reality of their sickle cell, and not wanting it to be a central part of their identity. Some health promotion advice appears to assume that teacher and/or peer awareness is the key to improving school experience for young people with SCD, but this is not borne out by this study. Rather a change in wider school environments is required such that young people with SCD are supported irrespective of whether they themselves foreground or play down their disabled identity.England Sickle cell Education School health Chronic illness Stigma Mixed methods Young people

Reported school experiences of young people living with sickle cell disorder in England

A survey of 569 young people with sickle cell disorder (SCD) in England has found such pupils miss considerable periods of time from school, typically in short periods of two or three days. One in eight has school absences equating to government-defined ‘persistent absence’. Students with SCD report that they are not helped to catch up after these school absences. Half the children reported not being allowed to use the toilet when needed and not being allowed water in class; a third reported being made to take unsuitable exercise and being called lazy when tired. Children perceived both physical environment (temperature, school furniture) and social environment (being upset by teachers or other pupils) as triggers to episodes of their illness. Policy initiatives on school absences; preventive measures to ensure maintenance of good health; and measures to prevent perceived social attitudes precipitating ill health would also support children with other chronic illnesses at school

presentation_1.PDF

Lysinuric protein intolerance (LPI) is a recessively inherited aminoaciduria caused by mutations of SLC7A7, the gene encoding y+LAT1 light chain of system y+L for cationic amino acid transport. The pathogenesis of LPI is still unknown. In this study, we have utilized a gene silencing approach in macrophages and airway epithelial cells to investigate whether complications affecting lung and immune system are directly ascribable to the lack of SLC7A7 or, rather, mediated by an abnormal accumulation of arginine in mutated cells. When SLC7A7/y+LAT1 was silenced in human THP-1 macrophages and A549 airway epithelial cells by means of short interference RNA (siRNA), a significant induction of the expression and release of the inflammatory mediators IL1β and TNFα was observed, no matter the intracellular arginine availability. This effect was mainly regulated at transcriptional level through the activation of NFκB signaling pathway. Moreover, since respiratory epithelial cells are the important sources of chemokines in response to pro-inflammatory stimuli, the effect of IL1β has been addressed on SLC7A7 silenced A549 cells. Results obtained indicated that the downregulation of SLC7A7/y+LAT1 markedly strengthened the stimulatory effect of the cytokine on CCL5/RANTES expression and release without affecting the levels of CXCL8/IL8. Consistently, also the conditioned medium of silenced THP-1 macrophages activated airway epithelial cells in terms of CCL5/RANTES expression due to the presence of elevated amount of proinflammatory cytokines. In conclusion, our results point to a novel thus far unknown function of SLC7A7/y+LAT1, that, under physiological conditions, besides transporting arginine, may act as a brake to restrain inflammation