714 research outputs found

    Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments

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    A two-groups mixed-effects model for the comparison of (normalized) microarray data from two treatment groups is considered. Most competing parametric methods that have appeared in the literature are obtained as special cases or by minor modification of the proposed model. Approximate maximum likelihood fitting is accomplished via a fast and scalable algorithm, which we call LEMMA (Laplace approximated EM Microarray Analysis). The posterior odds of treatment ×\times gene interactions, derived from the model, involve shrinkage estimates of both the interactions and of the gene specific error variances. Genes are classified as being associated with treatment based on the posterior odds and the local false discovery rate (f.d.r.) with a fixed cutoff. Our model-based approach also allows one to declare the non-null status of a gene by controlling the false discovery rate (FDR). It is shown in a detailed simulation study that the approach outperforms well-known competitors. We also apply the proposed methodology to two previously analyzed microarray examples. Extensions of the proposed method to paired treatments and multiple treatments are also discussed.Comment: Published in at http://dx.doi.org/10.1214/10-STS339 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

    Factors influencing the energy requirements of native ponies living outdoors in the United Kingdom

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    The purpose of this study was to determine the daily energy requirements of ponies native to the U.K., living on upland areas. This information can be used to improve the management of ponies kept under these conditions.The objectives of this thesis were to i) determine the effects of speed and terrain on the energy costs of ponies when walking, ii) measure seasonal differences in the hair coat, iii) estimate the effect of a wet winter coat on metabolic rate, iv) determine the proportion of a day spent by free-living ponies in feeding, walking, standing and lying, v) estimate the total distance moved daily by these ponies, and vi) describe the relationship between weather conditions and the behaviour and location of ponies.In the first study, the energy costs of walking were measured in four Shetland and two Exmoor ponies by using open-circuit, indirect calorimetry. The energy cost of activity, above that for standing, was independent of speed and averaged 1.02 J/kg liveweight/m travelled. An Oxylog, a portable breath-by-breath oxygen analyser, was used to determine effects of terrrain on the energy cost of walking using five Shetland ponies. The mean (s.e.) energy expenditures (J/kg/m) were:- grass 1.7 (0.07); concrete 2.9 (0.15); 12 cm of mud 5.9 (0.21); uphill (+5.8°) 5.5 (0.31); downhill (-5.8°) 3.3 (0.23) J/kg/m.In the second study, physical parameters of the winter and summer hair coats of six Shetland ponies were compared. Also, metabolic rate was monitored as a means of assessing the effect of wetting ponies in winter coat. Coat density in the winter 2 • 2 averaged 96.2 (s.e. 8.01) mg/cm , 3.24 times the summer value of 29.5 (3.37) mg/cm . Fibre diameter differed significantly between ponies within season. For some ponies there were seasonal changes in fibre diameter. The number of fibres/cm" did not differ significantly between seasons. Metabolic rate (determined by open-circuit, indirect calorimetry) and body temperature were unaffected by wetting (to the skin) the dorsal surface of Shetland ponies in winter coat. However, there were decreases in skin temperature over the wetted area which suggested local vasoconstrictionIn the third study, six Exmoor pony mares, kept in an enclosed area of fell in Cumbria, were observed in late winter (W) when they were pregnant, and in summer (S) when they were lactating. There were significant seasonal differences in the time spent feeding 17.2 h (W), 13.5 h (S); walking 0.5 h (W), 1.2 h (S); and standing 4.6 h (W), 6.2 h (S); but not in lying 1.3 h (W & S). The total distance moved by the mares in 24 h; 3.1 - 5.7 km (W) and 3.7 - 4.9 km (S), was calculated as the sum of the distances moved whilst grazing and walking. In winter, ponies preferentially grazed facing directly into or away from the wind at all wind speeds, and preferred to stand in areas where wind viii speed was reduced. In the summer, the same orientations to the wind became evident at wind speeds of 5 m/s. Ponies stood in the most exposed areas during the hottest parts of the day, but stood in sheltered areas at night. Grazing speed and bite rate were significantly greater (P<0.05) in the winter than in the summerThe results showed that the energy costs of activity (walking and grazing) were greater in winter than in summer. Therefore, seasonal adjustments in energy requirements are needed to allow for changes in activity as well as changes in heat loss. Recommendations are made regarding the management strategies for ponies kept outdoors

    An exploration of Doctor's perceptions and the provision of Palliative Care at a Private Hospital in Gauteng, South Africa.

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    Introduction: Palliative care is a core component of comprehensive health care across a person's life span. South Africa is currently in the process of integrating palliative care into all levels of the health care system. Doctors play a vital role in providing these services, but misconceptions about palliative care and who should be providing it, may prevent these services from being offered. Aim: The aim of this study was to discover doctor's perceptions and the current provision of palliative care in a private hospital. Objectives: The objectives of the study were: (1) to explore doctors' experiences of pain and symptom management in palliative care; (2) to explore doctors' perceptions of palliative care, goals of care and teamwork in palliative care; and (3) to explore the doctors' provision of palliative care at the hospital. Methodology: This was a qualitative study using a grounded theory approach. Semi-structured interviews were conducted with 14 participants, made up of doctors in oncology, physicians, surgeons, a cardiologist, an intensivist, a hematologist and a general practitioner. Interviews were recorded, transcribed and an inductive process was used for data analysis which allowed for categories to emerge from the data. Results: Eight themes emerged from the data analysis: improving the quality of life; palliative care as a role for oncologists; late referrals to palliative care, views on the World Health Organisation analgesic pain ladder; morphine a controversial means of pain control; team approach; family involvement and spiritual care. Conclusion: Palliative care was seen as an important intervention for a dying patient, but by introducing these services so late, patients are not benefitting from all that palliative care has to offer. Doctors did not always have a good understanding of when and how to provide palliative care. The following recommendations were made: (1) further research to be conducted in more private hospitals; (2)engage with management and doctors to begin the process of offering more formalised palliative care services at the hospital; (3) networking with available palliative care services, (4) organising palliative care training and workshops and (5) palliative care awareness campaigns

    Experience, action and affordance perception

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    The aim for this thesis is to motivate, critically evaluate and defend the claim that subjects are able to consciously perceive the affordances of objects. I will present my protagonist, the ‘Conscious Affordance Theorist’, with what are two main obstacles to this claim. The first of these is that affordance perception correctly understood refers only to a kind of subpersonal visual processing, and not to a kind of conscious visual experience. I claim that this results in an explanatory gap at the level of intentional action, which in order to correct we need to redefine the notion of affordance perception to include conscious as well as subpersonal affordance perception. Precisely, I claim that ‘affordance awareness’ has a crucial epistemological role to play, and that subjects must be able to consciously experience affordances in order to gain this awareness. In answer to this claim, I supplement the objection that affordance perception is defined as subpersonal perception to include the claim that any awareness subjects have of the affordances of objects they visually experience is due to them having thoughts about those affordances, and not visual experience of them. I then consider the Conscious Affordance Theorist’s response to this supplemented account. The second obstacle is the claim that conscious visual affordance perception is an impossible notion given that affordances are dispositional properties, and the dispositional properties of objects cannot be ‘seen’. In facing this objection I look to the supporting claims and motivations that lie behind it, in order to find a way for the Conscious Affordance Theorist to challenge its central claim that affordances cannot be seen. I end this thesis with an account of the Conscious Affordance Theorist’s own positive position, and a consideration of how his account has the ability to provide for conscious affordance perception in the case of non-human animals

    Feeling the benefit : fluctuating illness and the world of welfare

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    This article explores the experiences of people living with fluctuating long-term conditions, with a particular focus on the UK welfare benefits system. Respondents in this study suggested that this system constitutes a critical barrier to maintaining a positive work-based identity, being characterised by assessment and decision-making processes that are inappropriately focused and inflexibly implemented. Here, we report the findings from a cross sectional online study of people aged 18 to 75+, resident in the UK, with a self-reported diagnosis of lupus, arguably, the archetypal fluctuating condition. We explore some of the key themes respondents living with lupus identified in the context of striving to maintain a sense of themselves as productive and functional citizens. We conclude that there is a critical lack of attention afforded to the experience of fluctuating illness within the State benefits system and offer some strategies for better understanding, and addressing, this issue

    Going Global: A Faculty Connection between Peru and the United States

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    In 2003, the University System of Georgia sponsored the Peru Summer Institute for Faculty Development. A fortuitous meeting between Peruvian and U.S. faculty led to a faculty exchange with the shared goals of expanding cultural horizons, enhancing faculty through improved teaching and collaboration, and preparing students for the increasingly global reach of information technology. The experiences of this faculty exchange provide a framework for future collaboration between Peru’s information technology professionals and their colleagues in the United States. But perhaps more importantly, faculty and students discovered a synergy between designing information technology systems and the cultural contexts under which such systems operate

    Performance test of QU-fitting in cosmic magnetism study

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    QU-fitting is a standard model-fitting method to reconstruct distribution of magnetic fields and polarized intensity along a line of sight (LOS) from an observed polarization spectrum. In this paper, we examine the performance of QU-fitting by simulating observations of two polarized sources located along the same LOS, varying the widths of the sources and the gap between them in Faraday depth space, systematically. Markov Chain Monte Carlo (MCMC) approach is used to obtain the best-fit parameters for a fitting model, and Akaike and Bayesian Information Criteria (AIC and BIC, respectively) are adopted to select the best model from four fitting models. We find that the combination of MCMC and AIC/BIC works fairly well in model selection and estimation of model parameters in the cases where two sources have relatively small widths and a larger gap in Faraday depth space. On the other hand, when two sources have large width in Faraday depth space, MCMC chain tends to be trapped in a local maximum so that AIC/BIC cannot select a correct model. We discuss the causes and the tendency of the failure of QU-fitting and suggest a way to improve it.Comment: 8 pages, 9 figures, submitted to MNRA
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