Assessing Methods for Assigning SNPs to Genes in Gene-Based Tests of Association Using Common Variants

Gene-based tests of association are frequently applied to common SNPs (MAF>5%) as an alternative to single-marker tests. In this analysis we conduct a variety of simulation studies applied to five popular gene-based tests investigating general trends related to their performance in realistic situations. In particular, we focus on the impact of non-causal SNPs and a variety of LD structures on the behavior of these tests. Ultimately, we find that non-causal SNPs can significantly impact the power of all gene-based tests. On average, we find that the “noise” from 6–12 non-causal SNPs will cancel out the “signal” of one causal SNP across five popular gene-based tests. Furthermore, we find complex and differing behavior of the methods in the presence of LD within and between non-causal and causal SNPs. Ultimately, better approaches for a priori prioritization of potentially causal SNPs (e.g., predicting functionality of non-synonymous SNPs), application of these methods to sequenced or fully imputed datasets, and limited use of window-based methods for assigning inter-genic SNPs to genes will improve power. However, significant power loss from non-causal SNPs may remain unless alternative statistical approaches robust to the inclusion of non-causal SNPs are developed.

Mean field evolution in an open quantum system

In this thesis, we consider N quantum particles coupled to collective thermal quantum environments. The coupling is energy conserving and scaled in the mean field way. There is no direct interaction between the particles, they only interact via the common reservoir. It is well known that an initially disentangled state of the N particles will remain disentangled at times in the limit N -> [infinity]. In this thesis, we evaluate the η-body reduced density matrix (tracing over the reservoirs and the N - η remaining particles). We identify the main disentangled part of the reduced density matrix and obtain the first order correction term in 1/N. We show that this correction term is entangled. We also estimate the speed of convergence of the reduced density matrix as N -> [infinity]. Our model is exactly solvable and it is not based on numerical approximation.

Studies in asymmetric and heterocyclic synthesis: I. chiral ketones II. Quinolones III. Trifluoromethylated pyrones

This thesis is split into three sections based on three different areas of research. In the first section, investigations into the α-alkylation of ketones using a novel chiral auxiliary is reported. This chiral auxiliary was synthesised containing a pyrrolidine ring in the chiral arm and was applied in the preparation of α-alkylated ketones which were obtained in up to 92% ee and up to 63% yield over two steps. Both 3-pentanone and propiophenone based ketones were used in the investigation with a variety of both alkyl and benzyl based electrophiles. The novel chiral auxiliary was also successful when applied to Michael and aldol reactions. A diamine precursor en route to the chiral auxiliary was also applied as an organocatalyst in a Michael reaction, with the product obtained in excellent enantioselectivity. In the second section, investigations into potential anti-quorum sensing molecules are reported. The bacteria Pseudomonas aeruginosa is an antibiotic-resistant pathogen that demonstrates cooperative behaviours and communicates using small chemical molecules in a process termed quorum sensing. A variety of C-3 analogues of the quorum sensing molecules used by P. aeruginosa were synthesised. Expanding upon previous research within the group, investigations were carried out into alternative protecting group strategies of 2-heptyl-4-(1H)- quinolone with the aim of improving the yields of products of cross-coupling reactions. In the third section, investigations into fluorination and trifluoromethylation of 2-pyrones, pyridones and quinolones is reported. The incorporation of a fluorine atom or a trifluoromethyl group into a molecule is important in pharmaceutical drug discovery programmes as it can lead to increased lipophilicity and bioavailability, however late-stage incorporation is rarely reported. Both direct fluorination and trifluoromethylation were attempted. Eight trifluoromethylated 2-pyrones, five trifluoromethylated 2-pyridones and a trifluoromethylated 2-quinolone were obtained in a late-stage synthesis from their respective iodinated precursors using methyl fluorosulfonyldifluoroacetate as a trifluoromethylating reagent.

HELPING YOUTH WITH AUTISM SPECTRUM DISORDER DEVELOP SOCIAL COMPETENCE IN COMMUNITY-BASED SETTINGS

The purpose of the current dissertation is to identify the features of effective interventions by exploring the experiences of youth with ASD who participate in such interventions, through two intervention studies (Studies 1 and 2) and one interview study (Study 3). Studies 1 and 2 were designed to support the development of social competence of youth with ASD through Structured Play with LEGO TM (Study 1, 12 youths with ASD, ages 7–12) and Minecraft TM (Study 2, 4 youths with ASD, ages 11–13). Over the course of the sessions, the play of the youth developed from parallel play (children playing alone, without interacting) to co-operative play (playing together with shared objectives). The results of Study 2 showed that rates of initiations and levels of engagement increased from the first session to the final session. In Study 3, 12 youths with ASD (ages 10–14) and at least one of their parents were interviewed to explore what children and their parents want from programs designed to improve social competence, which activities and practices were perceived to promote social competence by the participants, and which factors affected their decisions regarding these programs. The adolescents and parents looked for programs that supported social development and emotional wellbeing, but did not always have access to the programs they would have preferred, with factors such as cost and location reducing their options. Three overarching themes emerged through analysis of the three studies: (a) interests of the youth; (b) structure, both through interactions and instruction; and (c) naturalistic settings. Adolescents generally engage more willingly in interventions that incorporate their interests, such as play with Minecraft TM in Study 2. Additionally, Structured Play and structured instruction were crucial components of providing safe and supportive contexts for the development of social competence. Finally, skills learned in naturalistic settings tend to be applied more successfully in everyday situations. The themes are analysed through the lens of Vygotsky’s (1978) perspectives on learning, play, and development. Implications of the results for practitioners and researchers are discussed.

Design and Implementation of Tools for STM Studies in UHV and at the Solid-Liquid Interface

This thesis presents details of the design and development of novel tools and instruments for scanning tunneling microscopy (STM), and may be considered as a repository for several years' worth of development work. The author presents design goals and implementations for two microscopes. First, a novel Pan-type STM was built that could be operated in an ambient environment as a liquid-phase STM. Unique features of this microscope include a unibody frame, for increased microscope rigidity, a novel slider component with large Z-range, a unique wiring scheme and damping mechanism, and a removable liquid cell. The microscope exhibits a high level of mechanical isolation at the tunnel junction, and operates excellently as an ambient tool. Experiments in liquid are on-going. Simultaneously, the author worked on designs for a novel low temperature, ultra-high vacuum (LT-UHV) instrument, and these are presented as well. A novel stick-slip vertical coarse approach motor was designed and built. To gauge the performance of the motor, an in situ motion sensing apparatus was implemented, which could measure the step size of the motor to high precision. A new driving circuit for stick-slip inertial motors is also presented, that o ffers improved performance over our previous driving circuit, at a fraction of the cost. The circuit was shown to increase step size performance by 25%. Finally, a horizontal sample stage was implemented in this microscope. The build of this UHV instrument is currently being fi nalized. In conjunction with the above design projects, the author was involved in a collaborative project characterizing N-heterocyclic carbene (NHC) self-assembled monolayers (SAMs) on Au(111) films. STM was used to characterize Au substrate quality, for both commercial substrates and those manufactured via a unique atomic layer deposition (ALD) process by collaborators. Ambient and UHV STM was then also used to characterize the NHC/Au(111) films themselves, and several key properties of these films are discussed. During this study, the author discovered an unexpected surface contaminant, and details of this are also presented. Finally, two models are presented for the nature of the NHC-Au(111) surface interaction based on the observed film properties, and some preliminary theoretical work by collaborators is presented.

Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis

Background: Esophageal adenocarcinoma (EA) is one of the fastest rising cancers in western countries. Barrett’s Esophagus (BE) is the premalignant precursor of EA. However, only a subset of BE patients develop EA, which complicates the clinical management in the absence of valid predictors. Genetic risk factors for BE and EA are incompletely understood. This study aimed to identify novel genetic risk factors for BE and EA.Methods: Within an international consortium of groups involved in the genetics of BE/EA, we performed the first meta-analysis of all genome-wide association studies (GWAS) available, involving 6,167 BE patients, 4,112 EA patients, and 17,159 representative controls, all of European ancestry, genotyped on Illumina high-density SNP-arrays, collected from four separate studies within North America, Europe, and Australia. Meta-analysis was conducted using the fixed-effects inverse variance-weighting approach. We used the standard genome-wide significant threshold of 5×10-8 for this study. We also conducted an association analysis following reweighting of loci using an approach that investigates annotation enrichment among the genome-wide significant loci. The entire GWAS-data set was also analyzed using bioinformatics approaches including functional annotation databases as well as gene-based and pathway-based methods in order to identify pathophysiologically relevant cellular pathways.Findings: We identified eight new associated risk loci for BE and EA, within or near the CFTR (rs17451754, P=4·8×10-10), MSRA (rs17749155, P=5·2×10-10), BLK (rs10108511, P=2·1×10-9), KHDRBS2 (rs62423175, P=3·0×10-9), TPPP/CEP72 (rs9918259, P=3·2×10-9), TMOD1 (rs7852462, P=1·5×10-8), SATB2 (rs139606545, P=2·0×10-8), and HTR3C/ABCC5 genes (rs9823696, P=1·6×10-8). A further novel risk locus at LPA (rs12207195, posteriori probability=0·925) was identified after re-weighting using significantly enriched annotations. This study thereby doubled the number of known risk loci. The strongest disease pathways identified (P<10-6) belong to muscle cell differentiation and to mesenchyme development/differentiation, which fit with current pathophysiological BE/EA concepts. To our knowledge, this study identified for the first time an EA-specific association (rs9823696, P=1·6×10-8) near HTR3C/ABCC5 which is independent of BE development (P=0·45).Interpretation: The identified disease loci and pathways reveal new insights into the etiology of BE and EA. Furthermore, the EA-specific association at HTR3C/ABCC5 may constitute a novel genetic marker for the prediction of transition from BE to EA. Mutations in CFTR, one of the new risk loci identified in this study, cause cystic fibrosis (CF), the most common recessive disorder in Europeans. Gastroesophageal reflux (GER) belongs to the phenotypic CF-spectrum and represents the main risk factor for BE/EA. Thus, the CFTR locus may trigger a common GER-mediated pathophysiology.

Behaviour change techniques in home-based cardiac rehabilitation: a systematic review

BACKGROUND: Cardiac rehabilitation (CR) programmes offering secondary prevention for cardiovascular disease (CVD) advise healthy lifestyle behaviours, with the behaviour change techniques (BCTs) of goals and planning, feedback and monitoring, and social support recommended. More information is needed about BCT use in home-based CR to support these programmes in practice.

AIM: To identify and describe the use of BCTs in home-based CR programmes.

DESIGN AND SETTING: Randomised controlled trials of home-based CR between 2005 and 2015 were identified by searching MEDLINE(®), Embase, PsycINFO, Web of Science, and Cochrane Database.

METHOD: Reviewers independently screened titles and abstracts for eligibility. Relevant data, including BCTs, were extracted from included studies. A meta-analysis studied risk factor change in home-based and comparator programmes.

RESULTS: From 2448 studies identified, 11 of good methodological quality (10 on post-myocardial infarction, one on heart failure, 1907 patients) were included. These reported the use of 20 different BCTs. Social support (unspecified) was used in all studies and goal setting (behaviour) in 10. Of the 11 studies, 10 reported effectiveness in reducing CVD risk factors, but one study showed no improvement compared to usual care. This study differed from effective programmes in that it didn't include BCTs that had instructions on how to perform the behaviour and monitoring, or a credible source.

CONCLUSION: Social support and goal setting were frequently used BCTs in home-based CR programmes, with the BCTs related to monitoring, instruction on how to perform the behaviour, and credible source being included in effective programmes. Further robust trials are needed to determine the relative value of different BCTs within CR programmes.

Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Quantum Dots

The purpose of this communication is to make a bibliographic review of Quantum Dots methods and their applications in the field of Biotechnology. Quantum dots (QDs) are a novel class of inorganic fluorophores, which are gaining widespread recognition as a result of their exceptional photophysical properties.

Quality of implementation in evidence-based positive parenting programs in Spain: Introduction to the special issue

The main contribution of this special issue is to present evaluation studies involving large-scale experiences of implementation of positive parenting programs delivered through home, group-based, and on-line formats in Spain. Two research questions were addressed: (1) what factors affect implementation; and (2) for whom and under which implementation conditions the programs lead to positive outcomes. Target populations were mainly families from low and middle socioeconomic backgrounds, and parents at psychosocial risk attending family support services in need of improving their parenting skills. All the programs fall under the umbrella of the positive parenting initiative launched by the Council of Europe, are evidence-based, follow a collaborative schema with national, regional, or local authorities, have multi-site implementation, and are supported by highly experienced researchers from Spanish universities. Special attention is given to the program adaptations to different contexts, the profile of parents who benefited most from the programs, analyses of the implementation process, and the assessment of parenting programs in the community. The information provided will help to increase our knowledge of evidence-based parenting programs in Spain, their implementation processes and results, and the future challenges that need to be addressed to continue the current expansion of evidence-based parenting programs.

FREQUENCY DOMAIN CHARACTERIZATION OF OPTIC FLOW AND VISION-BASED OCELLAR SENSING FOR ROTATIONAL MOTION

The structure of an animal’s eye is determined by the tasks it must perform. While vertebrates rely on their two eyes for all visual functions, insects have evolved a wide range of specialized visual organs to support behaviors such as prey capture, predator evasion, mate pursuit, flight stabilization, and navigation. Compound eyes and ocelli constitute the vision forming and sensing mechanisms of some flying insects. They provide signals useful for flight stabilization and navigation. In contrast to the well-studied compound eye, the ocelli, seen as the second visual system, sense fast luminance changes and allows for fast visual processing. Using a luminance-based sensor that mimics the insect ocelli and a camera-based motion detection system, a frequency-domain characterization of an ocellar sensor and optic flow (due to rotational motion) are analyzed. Inspired by the insect neurons that make use of signals from both vision sensing mechanisms, advantages, disadvantages and complementary properties of ocellar and optic flow estimates are discussed.

Stranski-Krastanov InN/InGaN quantum dots grown directly on Si(111)

The authors discuss and demonstrate the growth of InN surface quantum dots on a high-In-content In0.73Ga0.27N layer, directly on a Si(111) substrate by plasma-assisted molecular beam epitaxy. Atomic force microscopy and transmission electron microscopy reveal uniformly distributed quantum dots with diameters of 10–40 nm, heights of 2–4 nm, and a relatively low density of ∼7 × 109 cm−2. A thin InN wetting layer below the quantum dots proves the Stranski-Krastanov growth mode. Near-field scanning optical microscopy shows distinct and spatially well localized near-infrared emission from single surface quantum dots. This holds promise for future telecommunication and sensing devices.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

Development and scale-up studies of bio-based poly(ester-amide)s

Plastics are polymers of conventional and extensive use in our day-to-day life. This is due to their light weight, adaptability to different uses and low prices. A downside of such extensive use is the environmental pollution arising from plastic production and disposal. Indeed, many commodity polymers are produced from non-renewable resources while other do not bio-degrade after their end-of-life disposal. Consequently, the ideal polymer comes from renewable raw materials and bio-degrades after its disposal, meaning that it would do little or no harm to the environment from the beginning to the end of its life cycle. In this thesis project a class of bio-based and bio-degradable co-polymers, namely poly(ester-amide)s, was investigated because of their tunable mechanical and bio-degradation properties as well as their renewable origin. Such polymers were synthetized and characterized thermically and mechanically. Furthermore, a scale-up procedure was developed and applied to one polymer and processing trials were made with the material obtained after scale-up.