Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better

Heritability of risk-taking in adolescence: A longitudinal twin study

Adolescents are prone to risk-taking behaviors leading to adverse consequences such as substance abuse, accidents, violence, and victimization. However, little is known about the contribution of genetic and environmental factors to individual differences in the propensity for risk-taking. This study investigated developmental changes, longitudinal stability, and heritability of risk-taking using data from 752 adolescent twins including 169 MZ and 203 DZ pairs. The Balloon Analogue Risk Task (BART), an experimental behavioral measure of risk taking, was administered to the twins at age 12 and then re-administered to a part of this sample at age 14. Risk-taking increased with age, but individual differences showed a significant longitudinal stability. Genetic model fitting showed that at age 12, heritability of risk-taking was modest but significant in both sexes, whereas at age 14, heritability increased to 55% in males and became non-significant in females. The findings suggest that propensity for risk-taking as measured by BART can be a useful endophenotype for genetic studies of adolescent externalizing psychopathology, however, the utility of this measure may be limited by sex differences in heritability

The complexity of finding minimal Voronoĭ covers with applications to machine learning

Abstract Our goal in this paper is to examine the application of Voronoi diagrams, a fundamental concept of computational geometry, to the nearest neighbor algorithm used in machine learning. We consider the question "Given a planar polygonal tessellation T and an integer k, is there a set of k points whose Voronoi diagram contains every edge in T?" We show that this question is NP-hard. We encountered this problem while studying a learning model in which we seek the minimum sized set of training examples needed to teach a given geometric concept to a nearest neighbor learning program. That is, given a concept which can be described by a planar tessellation, we are seeking to construct the smallest set of points whose Voronoi diagram is consistent with the given tessellation. In a sense, this question captures the difficulty of teaching the nearest neighbor algorithm a simple structure, using a minimal number of examples. In addition, we consider the natural inverse to the problem of computing Voronoi diagrams. Given a planar polygonal tessellation T, we describe an algorithm to find a set of points whose Voronoi diagram is T, if such a set exists

Estimating the potential yield of small building-mounted wind turbines

The wind profile in the urban boundary layer is described as following a logarithmic curve above the mean building height and an exponential curve below it. By considering the urban landscape to be an array of cubes, a method is described for calculating the surface roughness length and displacement height of this profile. Firstly, a computational fluid dynamics (CFD) model employing a k-ϵ turbulence model is used to simulate the flow around a cube. The results of this simulation are compared with wind tunnel measurements in order to validate the code. Then, the CFD model is used to simulate the wind flow around a simple pitched-roof building, using a semi-logarithmic inflow profile. An array of similar pitched-roof houses is modelled using CFD to determine the flow characteristics within an urban area. Mean wind speeds at potential turbine mounting points are studied, and optimum mounting points are identified for different prevailing wind directions. A methodology is proposed for estimating the energy yield of a building-mounted turbine from simple information such as wind atlas wind speed and building density. The energy yield of a small turbine on a hypothetical house in west London is estimated. The energy yield is shown to be very low, particularly if the turbine is mounted below rooftop height. It should be stressed that the complexity of modelling such urban environments using such a computational model has limitations and results can only be considered approximate, but nonetheless, gives an indication of expected yields within the built environment

Data driven decision making in chemistry first year subjects

ABSTRACT Background: Analytics is not a new area of endeavour with many industries and other professions are well ahead of the education sector in the uptake of advanced analytics methods and tools (Abdous, He, & Yen, 2012; Dziuban, Moskal, Cavanagh, & Watts, 2012). Wagner and Ice (2012) describe higher education as being on the early side of the analytics adoption curve when compared to retail, telecommunications, financial services and manufacturing. Analytics is often used in higher education institutions to identify and also predict individual students who may be ‘at risk’ (Fritz, 2011). Aims: The primary aim was the deployment of information technologies that provide learning analytic data on students enrolled in large chemistry first year subjects. These data contain valuable learning progression and experience information to academics, part-time teaching staff and professional staff on students engagement, motivation and progression in real time so that suitable interventions can be made on students at risk of failing the subject. Design and methods: Learning analytics (LA) is the measurement, collection, analysis and reporting of data about learners and their contexts, for purposes of understanding and optimising learning and the environments in which it occurs. No new data has been captured to get learning analytics started at UOW – existing information is being utilised from point‐of‐service information systems (PASS, Library and student management systems) and the Moodle grade book on the subject sites. As students make use of the subject Moodle sites, information is automatically gathered about learning resource use, time on task, assessment item activities and student involvement in online forums. Each student leaves ‘electronic breadcrumbs’ within these systems as they go about their student journey and these are consolidated in the learning analytics data warehouse. Learning Analytics then aims to draw data from these diverse systems to provide actionable intelligence visualisation for staff to make decisions on. Results: The learning analytics have been deployed in two first year subjects, which have a combined cohort of some 700 students and contain some 50 activities, assessments and resources to monitor. The study is approximately at the half way point, covering so far 13 weeks of teaching and with five visualisation reports having been created. The full study will have been completed by the time of the conference presentation, although not all data will have been analysed by that stage. Key findings so far are: • Bringing together information from multiple data sources to provide a more holistic picture of student engagement and activity within a subject is useful in broad terms but caution is required when interpreting data to avoid making assumptions, and drawing false conclusions. A mutual understanding from both learning analytics staff and academic staff is required in the decision making process. • Analytical insights can inform more tailored and focused student interventions that bring about a positive change in student resource utilisation and performance on assessment tasks. For example, this can reveal the value added of having or not having peer assisted study sessions (PASS) within a subject and developing a culture that uses data in making instructional curriculum design changes. Conclusions: The study so far has shown that learning analytics has been able identify a group of students early on in the semester at risk of failing, that interventions have been successful in preventing this, but that data noise is an issue that can obscure others whose performance drops off towards the end of the semester. REFERENCES 1. Buerck, J. P. (2014). A Resource-Constrained Approach to Implementing Analytics in an Institution of Higher Education: An Experience Report. Journal of Learning Analytics, 1(1), 129-139 2. Heath, J. (2014). Contemporary Privacy Theory Contribution to Learning Analytics Journal of Learning Analytics, 1(1), 140-149. 3. Macfadyen, L. P., & Dawson, S. (2012). Numbers Are Not Enough. Why e-Learning Analytics Failed to Inform an Institutional Strategic Plan. Educational Technology & Society, 15(3), 149-163

A Small Community Model for the Transmission of Infectious Diseases: Comparison of School Closure as an Intervention in Individual-Based Models of an Influenza Pandemic

BACKGROUND: In the absence of other evidence, modelling has been used extensively to help policy makers plan for a potential future influenza pandemic. METHOD: We have constructed an individual based model of a small community in the developed world with detail down to exact household structure obtained from census collection datasets and precise simulation of household demographics, movement within the community and individual contact patterns. We modelled the spread of pandemic influenza in this community and the effect on daily and final attack rates of four social distancing measures: school closure, increased case isolation, workplace non-attendance and community contact reduction. We compared the modelled results of final attack rates in the absence of any interventions and the effect of school closure as a single intervention with other published individual based models of pandemic influenza in the developed world. RESULTS: We showed that published individual based models estimate similar final attack rates over a range of values for R(0) in a pandemic where no interventions have been implemented; that multiple social distancing measures applied early and continuously can be very effective in interrupting transmission of the pandemic virus for R(0) values up to 2.5; and that different conclusions reached on the simulated benefit of school closure in published models appear to result from differences in assumptions about the timing and duration of school closure and flow-on effects on other social contacts resulting from school closure. CONCLUSION: Models of the spread and control of pandemic influenza have the potential to assist policy makers with decisions about which control strategies to adopt. However, attention needs to be given by policy makers to the assumptions underpinning both the models and the control strategies examined

Existence of equilibria in countable games: an algebraic approach

Although mixed extensions of finite games always admit equilibria, this is not the case for countable games, the best-known example being Wald's pick-the-larger-integer game. Several authors have provided conditions for the existence of equilibria in infinite games. These conditions are typically of topological nature and are rarely applicable to countable games. Here we establish an existence result for the equilibrium of countable games when the strategy sets are a countable group and the payoffs are functions of the group operation. In order to obtain the existence of equilibria, finitely additive mixed strategies have to be allowed. This creates a problem of selection of a product measure of mixed strategies. We propose a family of such selections and prove existence of an equilibrium that does not depend on the selection. As a byproduct we show that if finitely additive mixed strategies are allowed, then Wald's game admits an equilibrium. We also prove existence of equilibria for nontrivial extensions of matching-pennies and rock-scissors-paper. Finally we extend the main results to uncountable games

Head-Up : co-designing novel neck orthosis for neck weakness in MND

Introduction : People with Motor Neurone Disease (MND) often develop weak neck muscles, leading to pain, restricted movement and problems with swallowing, breathing and communication. Ideally, a neck collar would help alleviate these. However, neck collars currently available are of limited use for people with MND and often rejected by patients. The same is true for patients with neck weakness due to other conditions. The Head-Up project is a 2 year study funded by the National Institute for Health Research's Invention for Innovation, or i4i, programme with a budget of £400k. Its principal aim is to develop a novel neck orthosis for neck weakness that supports whilst allowing freedom to move without negatively impacting quality of life. The research is a collaboration between clinicians, engineers, creative designers, patients and carer who will be working closely together is a co-design process. Manufacturers will be brought into this process at a later date. Ethical approval has been granted where necessary for all participatory elements. Methods The co-design process will inherently elicit subjective views. As such, prior to starting this workpackage, it was considered necessary to create a measure for this subjectivity and to give the design team a greater empathetic understanding of the inadequacies of current provision for this user group. This has been achieved by a combined clinical comfort assessment and engineering simulation. An engineering simulation of the head, neck and upper torso has been developed using Finite Element Analysis. This has been called the Neck Assessment Tool (NAT). Real body geometry was obtained via a 3D laser scan. The neck has been modelled without any structural integrity such that the head will drop without support. The body model has been meshed and constrained to represent this scenario. The geometry of different neck collar models were created in separate files and meshed. Individually they are imported into the body model, appropriate contact conditions applied and the model is processed. Each model tells the researchers where there is contact between body and collar and, relatively, the pressure of that contact. A clinical comfort assessment pilot study has been conducted using the design team members. This is based on location mapping from the McGill pain questionnaire and a Visual Analogue Scale. 5 different neck collars were identified based on common usage and distinct design differences. The members of the research team wore each collar for a day with recovery periods between. During each test period the participants recorded locations of pain/discomfort and perceptions of relative associated scales. They recorded other data relating to emotional reactions caused by the collars, impact on specific Activities of Daily Living (ADL's) and aesthetic considerations. Results The NAT has been conducted on 2 collars and the comfort assessment on 5, 2 of which are those tested in NAT. Comparisons between the comfort assessment and NAT demonstrate acceptable correlation, validating the simulation. The comfort assessment participant reporting forms have been refined and recruitment is under way to roll out to a wider population of health volunteers and use with MND volunteers to report about experiences of their specific collars as and when used. The design team reported significant differences in their perceptions of neck collars before and after the comfort assessment that will positively impact the co-design process. References 1. Ambrogio N et al, 'A Comparison of Three Types of Neck Support in Fibromyalgia Patients', Arthritis Care and Research (1998), v11, n5, pp 405-410 2. Bowen SJ, Chamberlain PM, 'Engaging the Ageing: Designing Artefacts to Provoke Dialogue', Designing Inclusive Futures (2008) Part I, 35-44, DOI: 10.1007/978-1-84800-211-1_4 3. Carlsson AM, 'Assessment of chronic pain. I. Aspects of the reliability and validity of the visual analogue scale', Pain (1983) v16, n1, pp 87–101 4. Escalante A, Lichtenstein MJ, Lawrence VA, Roberson M, Hazuda HP, ' Where does it hurt? Stability of recordings of pain location using the McGill Pain Map', The Journal of Rheumatology (1996) v23, n10, pp 1788-93 5. Huges TJR, 'The Finite Element Method: Linear Static and Dynamic Finite Element Analysis', Inform (2000), v682, n2, p 682, Publisher: Dover Publications, ISSN: 00457825, ISBN: 0486411818 6. Latimer N, Dixon S, Mcdermott C, Shaw P, McCarthy A, Tindale W, Heron N, 'Modelling the cost effectiveness of potential new neck collar for patients with motor neurone disease', http://www.sheffield.ac.uk/scharr/sections/heds/dps-2011 7. Miller RG et al, ' Practice Parameter update: The care of the patient with amyotrophic lateral sclerosis: Multidisciplinary care, symptom management and cognitive/behavioural impairment(an evidence based review)', Neurology (2009), v73, pp 1218-1225 8. Motor Neurone Disease Association, 'Head Supports', www.mndassociation.org/documents.rm?id=28 9. Thumbikat P, Bailey C and Datta D, 'Orthoses for neck control', ACNR (2006) v6, pp 18-19 10. Qing Hang Zhanga, Ee Chon Teoa, Hong Wan Nga, Vee Sin Lee, 'Finite element analysis of moment-rotation relationships for human cervical spine', Journal of Biomechanics (2006), v39, n1, pp1 89–19