Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.

Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites

An ECOOP web portal for visualising and comparing distributed coastal oceanography model and in situ data

As part of a large European coastal operational oceanography project (ECOOP), we have developed a web portal for the display and comparison of model and in situ marine data. The distributed model and in situ datasets are accessed via an Open Geospatial Consortium Web Map Service (WMS) and Web Feature Service (WFS) respectively. These services were developed independently and readily integrated for the purposes of the ECOOP project, illustrating the ease of interoperability resulting from adherence to international standards. The key feature of the portal is the ability to display co-plotted timeseries of the in situ and model data and the quantification of misfits between the two. By using standards-based web technology we allow the user to quickly and easily explore over twenty model data feeds and compare these with dozens of in situ data feeds without being concerned with the low level details of differing file formats or the physical location of the data. Scientific and operational benefits to this work include model validation, quality control of observations, data assimilation and decision support in near real time. In these areas it is essential to be able to bring different data streams together from often disparate locations

Glaciology in Aberdeen

Thanks to David Sugden, Doug Benn, Nick Spedding, Doug Mair, Alastair Dawson, Rob Bingham and Tim Lane for providing photographs and images.Peer reviewedPostprin

Climate Related Mortality and Morbidity in Scotland: Modelling Time Series of Counts

Earlier research has demonstrated that excess winter mortality is greater in the countries of the United Kingdom than in those on comparable latitudes elsewhere in Europe. The purpose of this thesis was to provide an up-to-date analysis of excess winter mortality in Scotland. This involved exploring the relationships between mortality, morbidity (as reflected in rates of emergency hospital admissions), climate, influenza epidemics, and socio-demographic variables. The majority of the analysis was concerned with temporal relationships between these variables, however, latterly spatial relationships were also considered. Chapter 1 reviews the literature in support of seasonal patterns in health and assesses the merits of the various statistical techniques that have been used to demonstrate these patterns. Much of the previous analyses have used simple descriptive statistical methods with few acknowledging the Poisson time series nature of the data. In chapter 2 the seasonal pattern of mortality and morbidity from three main disease groups was described using a generalised linear model with Poisson errors incorporating a cosine term. The method was used to analyse the seasonal pattern by sex, age group, social class, deprivation category and health board. In chapter 3 the effect of climate on mortality and morbidity is explored. This chapter is chiefly concerned with the comparison of possible methods of analysis. Firstly the problems with summary methods are demonstrated before the principles of time series methodology are introduced. The final comparison involves three methods, ARIMA time series methods, Poisson regression and Zeger's method. Zeger's method is as a time series regression method for Poisson data. The methods are compared by assessing the effect of temperature on weekly deaths from respiratory disease. Examination of the residuals and the standard errors of the model coefficients reveal that Zeger's method is the most appropriate for this type of analysis. Zeger's method is used in Chapter 4 to assess the relationship between temperature and mortality and morbidity in more detail, by considering the effects of age, socio-economic deprivation and city of residence. This chapter also includes a detailed examination of the effects on mortality of a variety of different temperature patterns. In chapter 5 the spatial aspect of the data is included in the analysis. Space-time variations in emergency admissions for respiratory disease are assessed at various levels of aggregation. Overall there is no clear evidence of space-time patterns in emergency respiratory admissions over the time period, however spatial relationships are demonstrated. Finally, methods which account for spatial autocorrelation are used in an analysis of the relationship between emergency admissions and socio-economic deprivation in Glasgow. This analysis demonstrates, as with the previous temporal analysis, that if autocorrelation exists it is vital to account for this in any modelling procedure. Chapter 6 provides a summary of the main findings of the analysis in terms of both the epidemiological results and the methodological concerns. The limitations of the study concerning problems associated with the use of routinely collected data are also recognised. The thesis has demonstrated that seasonal patterns in mortality and morbidity are still a significant public health problem in Scotland and that Zeger's method is the most appropriate method to use when assessing the direct relationship between climate and ill health

4H-SiC Schottky diodes with Ni2Si contacts for X-ray detection

4H-SiC Schottky photodiodes, with epitaxial layers, employing thin (20 nm) Ni2Si Schottky contacts, were investigated for high temperature photon counting X-ray spectroscopy. Important X-ray photodiode detector parameters were extracted from electrical characterization within the temperature range 160 °C to 0 °C. The devices were found to be fully depleted at an applied electric field of 20 kV/cm; a leakage current density of 33 nA cm 1 nA cm−2 at 160 °C, was measured for one of the devices. The detectors were subsequently connected to low-noise photon counting readout electronics and investigated for their spectral performance at temperatures up to 100 °C. With the charge-sensitive preamplifier operated at the same temperature as the detector the best energy resolution (Full Width at Half Maximum at 5.9 keV) obtained decreased from 2.20 keV 0.04 keV (120 e rms 2 e rms) at 100 C to 1.20 keV 0.03 keV (65 e rms 2 e rms) at 0 C. The dominant source of noise broadening the 55Fe X-ray photopeak was found to be the dielectric noise, except for the spectra accumulated at 100 °C and long shaping times (>), in those case the main source of photopeak broadening was the white parallel noise

mtDNA polymorphism and metabolic inhibition affect sperm performance in conplastic mice

This is the author accepted manuscript. The final version is available from BioScientifica via the DOI in this record.A broad link exists between nucleotide substitutions in the mitochondrial genome (mtDNA) and a range of metabolic pathologies, but the exploration of the effect of specific mtDNA genotypes is on-going. Mitochondrial DNA mutations are of particular relevance for reproductive traits, because they are expected to have profound effects on male specific processes as a result of the strict maternal inheritance of mtDNA. Sperm motility is crucially dependent on ATP in most systems studied. However, the importance of mitochondrial function in the production of the ATP necessary for sperm function remains uncertain. In this study, we test the effect of mtDNA polymorphisms upon mouse sperm performance and bioenergetics by using five conplastic inbred strains that share the same nuclear background while differing in their mitochondrial genomes. We found that, while genetic polymorphisms across distinct mtDNA haplotypes are associated with modification in sperm progressive velocity, this effect is not related to ATP production. Furthermore, there is no association between the number of mtDNA polymorphisms and either (a) the magnitude of sperm performance decrease, or (b) performance response to specific inhibition of the main sperm metabolic pathways. The observed variability between strains may be explained in terms of additive effects of single nucleotide substitutions on mtDNA coding sequences, which have been stabilized through genetic drift in the different laboratory strains. Alternatively, the decreased sperm performance might have arisen from the disruption of the nuclear DNA / mtDNA interactions that have co-evolved during the radiation of Mus musculus subspecies.This work was supported by a Smart Ideas grant from the Ministry of Business, Innovation and Employment (MBIE), New Zealand Government (NJG, DMT, DKD), grants from the Spanish Ministry of Economy and Competitiveness (CGL2011-26341, and CGL2016-80577-P to ERSR), and from the German Science Foundation grant (ExC 306/2 to MH and SI)

OAO-3 end of mission tests report

Twelve engineering type tests were performed on several subsystems and experiment(s) of the OAO 3 spacecraft near its end of mission. The systems tested include: Princeton experiment package (PEP), fine error system guidance, inertial reference unit, star trackers, heat pipes, thermal control coatings, command and data handling, solar array; batteries, and onboard processor/power boost regulator. Generally, the systems performed well for the 8 1/2 years life of OAO 3, although some degradation was noted in the sensitivity of PEP and in the absorptivity of the skin coatings. Battery life was prolonged during the life of the mission in large part by carefully monitoring the charge-discharge cycle with careful attention not to overcharge