Bayesian algorithms with applications

Advances in algorithms for approximate sampling from a multivariable target function have led to solutions to challenging statistical inference problems that would otherwise not be considered by the applied scientist. Such sampling algorithms are particularly relevant to Bayesian statistics, since the target function is the posterior distribution of the unobservables given the observables. In this thesis we develop, adapt and apply Bayesian algorithms, whilst addressing substantive applied problems in biology and medicine as well as other applications. For an increasing number of high-impact research problems, the primary models of interest are often sufficiently complex that the likelihood function is computationally intractable. Rather than discard these models in favour of inferior alternatives, a class of Bayesian "likelihoodfree" techniques (often termed approximate Bayesian computation (ABC)) has emerged in the last few years, which avoids direct likelihood computation through repeated sampling of data from the model and comparing observed and simulated summary statistics. In Part I of this thesis we utilise sequential Monte Carlo (SMC) methodology to develop new algorithms for ABC that are more efficient in terms of the number of model simulations required and are almost black-box since very little algorithmic tuning is required. In addition, we address the issue of deriving appropriate summary statistics to use within ABC via a goodness-of-fit statistic and indirect inference. Another important problem in statistics is the design of experiments. That is, how one should select the values of the controllable variables in order to achieve some design goal. The presences of parameter and/or model uncertainty are computational obstacles when designing experiments but can lead to inefficient designs if not accounted for correctly. The Bayesian framework accommodates such uncertainties in a coherent way. If the amount of uncertainty is substantial, it can be of interest to perform adaptive designs in order to accrue information to make better decisions about future design points. This is of particular interest if the data can be collected sequentially. In a sense, the current posterior distribution becomes the new prior distribution for the next design decision. Part II of this thesis creates new algorithms for Bayesian sequential design to accommodate parameter and model uncertainty using SMC. The algorithms are substantially faster than previous approaches allowing the simulation properties of various design utilities to be investigated in a more timely manner. Furthermore the approach offers convenient estimation of Bayesian utilities and other quantities that are particularly relevant in the presence of model uncertainty. Finally, Part III of this thesis tackles a substantive medical problem. A neurological disorder known as motor neuron disease (MND) progressively causes motor neurons to no longer have the ability to innervate the muscle fibres, causing the muscles to eventually waste away. When this occurs the motor unit effectively ‘dies’. There is no cure for MND, and fatality often results from a lack of muscle strength to breathe. The prognosis for many forms of MND (particularly amyotrophic lateral sclerosis (ALS)) is particularly poor, with patients usually only surviving a small number of years after the initial onset of disease. Measuring the progress of diseases of the motor units, such as ALS, is a challenge for clinical neurologists. Motor unit number estimation (MUNE) is an attempt to directly assess underlying motor unit loss rather than indirect techniques such as muscle strength assessment, which generally is unable to detect progressions due to the body’s natural attempts at compensation. Part III of this thesis builds upon a previous Bayesian technique, which develops a sophisticated statistical model that takes into account physiological information about motor unit activation and various sources of uncertainties. More specifically, we develop a more reliable MUNE method by applying marginalisation over latent variables in order to improve the performance of a previously developed reversible jump Markov chain Monte Carlo sampler. We make other subtle changes to the model and algorithm to improve the robustness of the approach.

Modeling and detection of complex attacks

A complex attack is a sequence of temporally and spatially separated legal and illegal actions each of which can be detected by various IDS but as a whole they constitute a powerful attack. IDS fall short of detecting and modeling complex attacks therefore new methods are required. This paper presents a formal methodology for modeling and detection of complex attacks in three phases: (1) we extend basic attack tree (AT) approach to capture temporal dependencies between components and expiration of an attack, (2) using enhanced AT we build a tree automaton which accepts a sequence of actions from input message streams from various sources if there is a traversal of an AT from leaves to root, and (3) we show how to construct an enhanced parallel automaton that has each tree automaton as a subroutine. We use simulation to test our methods, and provide a case study of representing attacks in WLANs.

Finite element shoulder models

Shoulder joint is a complex integration of soft and hard tissues. It plays an important role in performing daily activities and can be considered as a perfect compromise between mobility and stability. However, shoulder is vulnerable to complications such as dislocations and osteoarthritis. Finite element (FE) models have been developed to understand shoulder injury mechanisms, implications of disease on shoulder complex and in assessing the quality of shoulder implants. Further, although few, Finite element shoulder models have also been utilized to answer important clinical questions such as the difference between a normal and osteoarthritic shoulder joint. However, due to the absence of experimental validation, it is questionable whether the constitutive models applied in these FE models are adequate to represent mechanical behaviors of shoulder elements (Cartilages, Ligaments, Muscles etc), therefore the confidence of using current models in answering clinically relevant question. The main objective of this review is to critically evaluate the existing FE shoulder models that have been used to investigate clinical problems. Due concern is given to check the adequacy of representative constitutive models of shoulder elements in drawing clinically relevant conclusion. Suggestions have been given to improve the existing shoulder models by inclusion of adequate constitutive models for shoulder elements to confidently answer clinically relevant questions.

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010 : a systematic analysis for the Global Burden of Disease Study 2010

Background Non-fatal health outcomes from diseases and injuries are a crucial consideration in the promotion and monitoring of individual and population health. The Global Burden of Disease (GBD) studies done in 1990 and 2000 have been the only studies to quantify non-fatal health outcomes across an exhaustive set of disorders at the global and regional level. Neither effort quantified uncertainty in prevalence or years lived with disability (YLDs). Methods Of the 291 diseases and injuries in the GBD cause list, 289 cause disability. For 1160 sequelae of the 289 diseases and injuries, we undertook a systematic analysis of prevalence, incidence, remission, duration, and excess mortality. Sources included published studies, case notification, population-based cancer registries, other disease registries, antenatal clinic serosurveillance, hospital discharge data, ambulatory care data, household surveys, other surveys, and cohort studies. For most sequelae, we used a Bayesian meta-regression method, DisMod-MR, designed to address key limitations in descriptive epidemiological data, including missing data, inconsistency, and large methodological variation between data sources. For some disorders, we used natural history models, geospatial models, back-calculation models (models calculating incidence from population mortality rates and case fatality), or registration completeness models (models adjusting for incomplete registration with health-system access and other covariates). Disability weights for 220 unique health states were used to capture the severity of health loss. YLDs by cause at age, sex, country, and year levels were adjusted for comorbidity with simulation methods. We included uncertainty estimates at all stages of the analysis. Findings Global prevalence for all ages combined in 2010 across the 1160 sequelae ranged from fewer than one case per 1 million people to 350 000 cases per 1 million people. Prevalence and severity of health loss were weakly correlated (correlation coefficient −0·37). In 2010, there were 777 million YLDs from all causes, up from 583 million in 1990. The main contributors to global YLDs were mental and behavioural disorders, musculoskeletal disorders, and diabetes or endocrine diseases. The leading specific causes of YLDs were much the same in 2010 as they were in 1990: low back pain, major depressive disorder, iron-deficiency anaemia, neck pain, chronic obstructive pulmonary disease, anxiety disorders, migraine, diabetes, and falls. Age-specific prevalence of YLDs increased with age in all regions and has decreased slightly from 1990 to 2010. Regional patterns of the leading causes of YLDs were more similar compared with years of life lost due to premature mortality. Neglected tropical diseases, HIV/AIDS, tuberculosis, malaria, and anaemia were important causes of YLDs in sub-Saharan Africa. Interpretation Rates of YLDs per 100 000 people have remained largely constant over time but rise steadily with age. Population growth and ageing have increased YLD numbers and crude rates over the past two decades. Prevalences of the most common causes of YLDs, such as mental and behavioural disorders and musculoskeletal disorders, have not decreased. Health systems will need to address the needs of the rising numbers of individuals with a range of disorders that largely cause disability but not mortality. Quantification of the burden of non-fatal health outcomes will be crucial to understand how well health systems are responding to these challenges. Effective and affordable strategies to deal with this rising burden are an urgent priority for health systems in most parts of the world. Funding Bill & Melinda Gates Foundation.

Symptom burden in chronic kidney disease : a review of recent literature

Background: People living with chronic kidney disease (CKD) experience multiple symptoms due to both the disease and its treatment, these symptoms are often under recognized. The majority of studies have focused on an individual symptom; however these symptoms rarely occur in isolation and may instead occur in clusters. Aim of review: This review investigated the total symptom burden in advanced CKD (stages 4 and 5) and identified the key instruments that are used to assess multiple symptoms. Methods: A literature search from 2006 to 2012 was undertaken and a total of 19 articles were included. Result: The most common CKD symptoms were fatigue or lack of energy, feeling drowsy, pain and pruritus. However, symptom assessment instruments varied between studies, often with inconsistent or inadequate symptom dimensions. Conclusion: People with CKD experience a high burden of symptom, although little is known about the burden for people with CKD stage 4 and for those with CKD stage 5 receiving PD. This review recommends that a full range of symptoms be assessed for those at different stages of CKD. Improved understanding of the burden of symptoms could be used as the basis for treatment choices and for identifying priorities which are likely to contribute to a better quality of life and improve the quality of care.

A review of the Ustilago-Sporisorium-Macalpinomyces complex

The fungal genera Ustilago, Sporisorium and Macalpinomyces represent an unresolved complex. Taxa within the complex often possess characters that occur in more than one genus, creating uncertainty for species placement. Previous studies have indicated that the genera cannot be separated by morphology alone. Here we chronologically review the history of the Ustilago-Sporisorium-Macalpinomyces complex, argue for its resolution and suggest methods to accomplish a stable taxonomy. A combined molecular and morphological approach is required to identify synapomorphic characters that underpin a new classification. Ustilago, Sporisorium and Macalpinomyces require explicit re-description and new genera, based on monophyletic groups, are needed to accommodate taxa that no longer fit the emended descriptions. A resolved classification will end the taxonomic confusion that surrounds generic placement of these smut fungi.

Preparing citizens for a complex world : the grand challenge of teaching socio-scientific issues in science education

The dawn of the twenty-first century encouraged a number of scientific and technological organisations to identify what they saw as ‘Grand Challenges and Opportunities’. Issues of environment and health featured very prominently in these quite short lists, as can be seen from a sample of these challenges in Table 1. Indeed, the first two lists of challenges in Table 1 were identified as for the environment and for health, respectively.

Soral synapomorphies are significant for the systematics of the Ustilago-Sporisorium-Macalpinomyces complex (Ustilaginaceae)

The genera Ustilago, Sporisorium and Macalpinomyces are a polyphyletic complex of plant pathogenic fungi. The four main morphological characters used to define these genera have been considered homoplasious and not useful for resolving the complex. This study re-evaluates character homology and discusses the use of these characters for defining monophyletic groups recovered from a reconstructed phylogeny using four nuclear loci. Generic delimitation of smut fungi based on their hosts is also discussed as a means for identifying genera within this group. Morphological characters and host specificity can be used to circumscribe genera within the Ustilago-Sporisorium-Macalpinomyces complex.

Approaches to designing for older adults' intuitive interaction with complex devices

Many older people have difficulties using modern consumer products due to increased product complexity both in terms of functionality and interface design. Previous research has shown that older people have more difficulty in using complex devices intuitively when compared to the younger. Furthermore, increased life expectancy and a falling birth rate have been catalysts for changes in world demographics over the past two decades. This trend also suggests a proportional increase of older people in the work-force. This realisation has led to research on the effective use of technology by older populations in an effort to engage them more productively and to assist them in leading independent lives. Ironically, not enough attention has been paid to the development of interaction design strategies that would actually enable older users to better exploit new technologies. Previous research suggests that if products are designed to reflect people's prior knowledge, they will appear intuitive to use. Since intuitive interfaces utilise domain-specific prior knowledge of users, they require minimal learning for effective interaction. However, older people are very diverse in their capabilities and domain-specific prior knowledge. In addition, ageing also slows down the process of acquiring new knowledge. Keeping these suggestions and limitations in view, the aim of this study was set to investigate possible approaches to developing interfaces that facilitate their intuitive use by older people. In this quest to develop intuitive interfaces for older people, two experiments were conducted that systematically investigated redundancy (the use of both text and icons) in interface design, complexity of interface structure (nested versus flat), and personal user factors such as cognitive abilities, perceived self-efficacy and technology anxiety. All of these factors could interfere with intuitive use. The results from the first experiment suggest that, contrary to what was hypothesised, older people (65+ years) completed the tasks on the text only based interface design faster than on the redundant interface design. The outcome of the second experiment showed that, as expected, older people took more time on a nested interface. However, they did not make significantly more errors compared with younger age groups. Contrary to what was expected, older age groups also did better under anxious conditions. The findings of this study also suggest that older age groups are more heterogeneous in their capabilities and their intuitive use of contemporary technological devices is mediated more by domain-specific technology prior knowledge and by their cognitive abilities, than chronological age. This makes it extremely difficult to develop product interfaces that are entirely intuitive to use. However, by keeping in view the cognitive limitations of older people when interfaces are developed, and using simple text-based interfaces with flat interface structure, would help them intuitively learn and use complex technological products successfully during early encounter with a product. These findings indicate that it might be more pragmatic if interfaces are designed for intuitive learning rather than for intuitive use. Based on this research and the existing literature, a model for adaptable interface design as a strategy for developing intuitively learnable product interfaces was proposed. An adaptable interface can initially use a simple text only interface to help older users to learn and successfully use the new system. Over time, this can be progressively changed to a symbols-based nested interface for more efficient and intuitive use.

Proteomic and bioinformatics tools to understand virulence mechanisms in Staphylococcus aureus

Staphylococcus aureus, one of the major pathogenic bacteria, is associated with substantial morbidity and mortality. The disease burden of staphylococcal infections is significant, which is primarily attributed to its adaptability and resistance to environmental stresses. S. aureus has the ability to develop multiple resistances to antimicrobial agents. These high resistances make pathogenicity of S. aureus one of the most complex mechanisms to understand and manage. Proteomic and bioinformatics approaches show great potential in exploring microbial adaptation strategies, ability to cause disease by pathogenic bacteria and the development of diagnostic tools. A summary of the latest developments in the application of ‘omics’ technologies to understand resistance mechanisms in S. aureus and their future role in antistaphylococcal vaccine and/or drug discovery is given here.

ECMO : the clinician’s view

Background: Extra corporeal membrane oxygenation (ECMO) is a complex rescue therapy used to provide cardiac and/or respiratory support for critically ill patients who have failed maximal conventional medical management. ECMO is based on a modified cardiopulmonary bypass (CPB) circuit, and can provide cardiopulmonary support for up-to several months. It can be used in a veno venous configuration for isolated respiratory failure, (VV-ECMO), or in a veno arterial configuration (VA-ECMO) where support is necessary for cardiac +/- respiratory failure. The ECMO circuit consists of five main components: large bore cannulae (access cannulae) for drainage of the venous system, and return cannulae to either the venous (in VV-ECMO) or arterial (in VA ECMO) system. An oxygenator, with a vast surface area of hollow filaments, allows addition of oxygen and removal of carbon dioxide; a centrifugal blood pump allows propulsion of blood through the circuit at upto 10 L/minute; a control module and a thermoregulatory unit, which allows for exact temperature control of the extra corporeal blood. Methods: The first successful use of ECMO for ARDS in adults occurred in 1972, and its use has become more commonplace over the last 30 years, supported by the improvement in design and biocompatibility of the equipment, which has reduced the morbidity associated with this modality. Whilst the use of ECMO in neonatal population has been supported by numerous studies, the evidence upon which ECMO was integrated into adult practice was substantially less robust. Results: Recent data, including the CESAR study (Conventional Ventilatory Support versus Extra corporeal membrane oxygenation for Severe Respiratory failure) has added a degree of evidence to the role of ECMO in such a patient population. The CESAR study analysed 180 patients, and confirmed that ECMO was associated with an improved rate of survival. More recently, ECMO has been utilized in numerous situations within the critical care area, including support in high-risk percutaneous interventions in cardiac catheter lab; the operating room, emergency department, as well in specialized inter-hospital retrieval services. The increased understanding of the risk:benefit profile of ECMO, along with a reduction in morbidity associated with its use will doubtless lead to a substantial rise in the utilisation of this modality. As with all extra-corporeal circuits, ECMO opposes the basic premises of the mammalian inflammation and coagulation cascade where blood comes into foreign circulation, both these cascades are activated. Anti-coagulation is readily dealt with through use of agents such as heparin, but the inflammatory excess, whilst less macroscopically obvious, continues un-abated. Platelet consumption and neutrophil activation occur rapidly, and the clinician is faced with balancing the need of anticoagulation for the circuit, against haemostasis in an acutely bleeding patient. Alterations in pharmacokinetics may result in inadequate levels of disease modifying therapeutics, such as antibiotics, hence paradoxically delaying recovery from conditions such as pneumonia. Key elements of nutrition and the innate immune system maysimilarly be affected. Summary: This presentation will discuss the basic features of ECMO to the nonspecialist, and review the clinical conundrum faced by the team treating these most complex cases.

Wetlands, climate zones and Barmah Forest virus disease in Queensland, Australia

Barmah Forest virus (BFV) disease is the second most common mosquito-borne disease in Australia, but the linkages of the wetlands and climate zones with BFV transmission remain unclear. We aimed to examine the relationship between the wetlands, climate zones and BFV risk in Queensland, Australia. Data on the wetlands, climate zones, population and BFV cases for the period 1992 to 2008 were obtained from relevant government agencies. BFV risk was grouped as low-, medium- and high-level based on BFV incidence percentiles. The buffer zones around each BFV case were made using 1, 5, 10, 15, 20, 25 and 50 km distances. We performed a discriminant analysis to determine the differences between wetland classes and BFV risk within each climate zone. The discriminant analyses show that saline 1, riverine and saline tidal influence were the most significant contributors to BFV risk in all climate and buffer zones, while lacustrine, palustrine, estuarine and saline 2 and saline 3 wetlands were less important. These models had classification accuracies of 76%, 98% and 100% for BFV risk in subtropical, tropical and temperate climate zones, respectively. This study demonstrates that BFV risk varies with wetland class and climate zone. The discriminant analysis is a useful tool to quantify the links between wetlands, climate zones and BFV risk.

Nutritional support and functional capacity in chronic obstructive pulmonary disease: A systematic review and meta-analysis

Currently there is confusion about the value of using nutritional support to treat malnutrition and improve functional outcomes in chronic obstructive pulmonary disease (COPD). This systematic review and meta-analysis of randomised controlled trials (RCTs) aimed to clarify the effectiveness of nutritional support in improving functional outcomes in COPD. A systematic review identified 12 RCTs (n = 448) in stable COPD patients investigating the effects of nutritional support [dietary advice (1 RCT), oral nutritional supplements (ONS; 10 RCTs), enteral tube feeding (1 RCT)] versus control on functional outcomes. Meta-analysis of the changes induced by intervention found that whilst respiratory function (FEV(1,) lung capacity, blood gases) was unresponsive to nutritional support, both inspiratory and expiratory muscle strength (PI max +3.86 SE 1.89 cm H(2) O, P = 0.041; PE max +11.85 SE 5.54 cm H(2) O, P = 0.032) and handgrip strength (+1.35 SE 0.69 kg, P = 0.05) were significantly improved, and associated with weight gains of ≥ 2 kg. Nutritional support produced significant improvements in quality of life in some trials, although meta-analysis was not possible. It also led to improved exercise performance and enhancement of exercise rehabilitation programmes. This systematic review and meta-analysis demonstrates that nutritional support in COPD results in significant improvements in a number of clinically relevant functional outcomes, complementing a previous review showing improvements in nutritional intake and weight.

Evidence supporting exercise interventions for persons in early-stage Alzheimer’s disease

The purpose of this article is to grade research evidence supporting exercise-based interventions for persons with early-stage dementias and to report the recommendations of a consensus panel. The search produced 11 data based articles testing the effects of exercise interventions on a variety of outcomes. The body of evidence to support exercise interventions in the prevention and treatment of Alzheimer’s disease is growing and has potential as a treatment modality following translational studies in recreation therapy and other fields.

Eyes on 3D-Current 3D biomimetic disease concept models and potential applications in age-related macular degeneration

Three dimensional cellular models that mimic disease are being increasingly investigated and have opened an exciting new research area into understanding pathomechanisms. The advantage of 3D in vitro disease models is that they allow systematic and in-depth studies of physiological and pathophysiological processes with less costs and ethical concerns that have arisen with animal models. The purpose of the 3D approach is to allow crosstalk between cells and microenvironment, and with cues from the microenvironment, cells can assemble their niche similar to in vivo conditions. The use of 3D models for mimicking disease processes such as cancer, osteoarthritis etc., is only emerging and allows multidisciplinary teams consisting of tissue engineers, biologist biomaterial scientists and clinicians to work closely together. While in vitro systems require rigorous testing before they can be considered as replicates of the in vivo model, major steps have been made, suggesting that they will become powerful tools for studying physiological and pathophysiological processes. This paper aims to summarize some of the existing 3D models and proposes a novel 3D model of the eye structures that are involved in the most common cause of blindness in the Western World, namely age-related macular degeneration (AMD).