Modeling a mixture of ordinal treatment response and natural response. A Bayesian approach

Only abstract. Paper copies of master’s theses are listed in the Helka database (http://www.helsinki.fi/helka). Electronic copies of master’s theses are either available as open access or only on thesis terminals in the Helsinki University Library.Vain tiivistelmä. Sidottujen gradujen saatavuuden voit tarkistaa Helka-tietokannasta (http://www.helsinki.fi/helka). Digitaaliset gradut voivat olla luettavissa avoimesti verkossa tai rajoitetusti kirjaston opinnäytekioskeilla.Endast sammandrag. Inbundna avhandlingar kan sökas i Helka-databasen (http://www.helsinki.fi/helka). Elektroniska kopior av avhandlingar finns antingen öppet på nätet eller endast tillgängliga i bibliotekets avhandlingsterminaler.Bacterial meningitis (inflammation of brain lining) caused by Neisseria meningitidis (meningococcus) may be life-threatening, meningococcus of serogroup B being the predominant agent of disease in industrialized countries. Natural immunity against disease develops with age associated with an increase in serum bactericidal activity. Although bacterial MenB meningitis is relatively rare, its severity and possible sequelae necessitate search for efficient vaccine. Since human clinical trials are costly and are often limited by ethical considerations there is a need for animal model, in which disease development and protection would depend on the same mechanism as in humans. This experiment is part of the study to access the relevance of infant rat animal model. The experiment was randomised at two levels: human volunteers were randomly assigned Norwegian, Cuban, or placebo vaccines and outbred rat pups were randomly assigned into 6-rat groups. Each day of the trial 1 group was injected with saline solution and 1-3 groups were injected with heated human serum samples taken before and after the vaccination with interval of 6 month. Thus two sources of random variation must to be taken into account: the human sera variation and variation between rat pups. It is often the case in dose response studies, that the observed effect is a combination of latent natural and treatment responses, where the treatment effect is of interest. A common way to model a binary situation is Abbott's formula. It can be extended to account for a situation with ordinal response. The treatment effect was assigned proportional odds model with strain and treatment covariates, and a full Bayesian model with vague priors was set-up. Two outcomes were examined: the proportion of protected rats (binary) and proportional reduction of bacteremia (ordinal). Both models were estimated using programme WinBUGS12beta. Large variability was apparent both between human sera and between individual rats. Probability of natural response occurrence was high in both models, but no significant treatment effects was found. In order to access the relevancy of this infant rat model to human sera protective immunity, the results of this experiment should be compared with the results of human clinical trials

Effect of Indian clubbell exercises on cricket fast bowlers’ shoulder kinematics

Background: The glenohumeral joint’s rotational range of motion (ROM) and muscle strength are essential to execute the cricket bowling action. Performing shoulder rotation exercises may increase the rotator cuff muscle strength and rotational ROM.  Objectives: The aim of this study was to test the effect of a six-week exercise programme on shoulder rotational ROM and muscle strength. Methods: Twenty-one healthy male cricket fast bowlers were recruited, ranked and pair-matched on initial shoulder rotator muscle strength and assigned to either a shoulder exercise (SE) group or cricket training (CT) only group. The SE group incorporated Indian clubbell exercises in addition to their cricket training. Results: Bowlers in both groups displayed a large increase on the dominant shoulder’s internal rotation (IR) ROM, but only the SE group’s bowlers displayed ROM improvements (p<0.001) bilaterally for both internal and external rotation. The CT group’s fast bowler’s non-dominant shoulder IR ROM significantly decreased (p=0.02) during the six weeks. Between groups, only the SE group’s bowler’s internal rotator muscle strength improved (p<0.001) bilaterally. The observed kinematic changes were statistically significantly greater at a 5% level for the SE group’s bowlers (bilateral internal rotators muscle strength, non-dominant shoulder IR ROM and horizontal adduction ROM). Conclusion: Maintenance of the shoulder’s rotational ROM and muscle strength is vital for a fast bowler. Cricket bowlers who perform regular clubbell exercises might increase their shoulder’s ROM and internal rotator cuffs’ muscle strength, which may aid in stabilising their glenohumeral joint while bowling.

Bayesian modeling of population variance for aggregated measurements

Growth curves are commonly used in modeling aimed at crop yield prediction. Fitting such curves often depends on availability of detailed observations, such as individual grape bunch weight or individual apple weight. However, in practice, aggregated weights (such as a bucket of grape bunches or apples) are available instead. While treating such bucket averages as if they were individual observations is tempting, it may introduce bias particularly with respect to population variance. In this paper we provide an elegant solution which enables estimation of individual weights using Dirichlet priors within Bayesian inferential framework.Comment: 9 pages, 3 figure

Potts model for haplotype associations

Bayesian spatial modeling has become important in disease mapping and has also been suggested as a useful tool in genetic fine mapping. We have implemented the Potts model and applied it to the Genetic Analysis Workshop 14 (GAW14) simulated data. Because the "answers" were known we have analyzed latent phenotype P1-related observed phenotypes affection status (genetically determined) and i (random) in the Danacaa population replicate 2. Analysis of the microsatellite/single-nucleotide polymorphism-based haplotypes at chromosomes 1 and 3 failed to identify multiple clusters of haplotype effects. However, the analysis of separately simulated data with postulated differences in the effects of the two clusters has yielded clear estimated division into the two clusters, demonstrating the correctness of the algorithm. Although we could not clearly identify the disease-related and the non-associated groups of haplotypes, results of both GAW14 and our own simulation encourage us to improve the efficiency and sensitivity of the estimation algorithm and to further compare the proposed method with more traditional methods

Recreational Road Accidents in New Zealand

This study investigates how the road safety in New Zealand is influenced by recreational factors, such as holiday weekends, alcohol and time/spatial patterns. The results of our analysis show that the number of accidents during holiday periods are similar to those on normal weekends. There are clear patterns of accidents during commuting times and accidents occurring under the influence on weekends. In recent years, accidents that occur with intoxicated drivers also occurs more frequently during the work week

Have LEGO Products Become More Violent?

Although television, computer games and the Internet play an important role in the lives of children they still also play with physical toys, such as dolls, cars and LEGO bricks. The LEGO company has become the world's largest toy manufacturer. Our study investigates if the LEGO company's products have become more violent over time. First, we analyzed the frequency of weapon bricks in LEGO sets. Their use has significantly increased. Second, we empirically investigated the perceived violence in the LEGO product catalogs from the years 1978-2014. Our results show that the violence of the depicted products has increased significantly over time. The LEGO Company's products are not as innocent as they used to be

How many people need to classify the same image? A method for optimizing volunteer contributions in binary geographical classifications

Involving members of the public in image classification tasks that can be tricky to automate is increasingly recognized as a way to complete large amounts of these tasks and promote citizen involvement in science. While this labor is usually provided for free, it is still limited, making it important for researchers to use volunteer contributions as efficiently as possible. Using volunteer labor efficiently becomes complicated when individual tasks are assigned to multiple volunteers to increase confidence that the correct classification has been reached. In this paper, we develop a system to decide when enough information has been accumulated to confidently declare an image to be classified and remove it from circulation. We use a Bayesian approach to estimate the posterior distribution of the mean rating in a binary image classification task. Tasks are removed from circulation when user-defined certainty thresholds are reached. We demonstrate this process using a set of over 4.5 million unique classifications by 2783 volunteers of over 190,000 images assessed for the presence/absence of cropland. If the system outlined here had been implemented in the original data collection campaign, it would have eliminated the need for 59.4% of volunteer ratings. Had this effort been applied to new tasks, it would have allowed an estimated 2.46 times as many images to have been classified with the same amount of labor, demonstrating the power of this method to make more efficient use of limited volunteer contributions. To simplify implementation of this method by other investigators, we provide cutoff value combinations for one set of confidence levels

Seasonality and ambient temperature at time of conception in term-born individuals - influences on cardiovascular disease and obesity in adult life

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