TmaDB: a repository for tissue microarray data

Background: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations ( at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data. Description: To analyse TMA output a relational database ( known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks ( from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK). Conclusion: TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray dat

Master of Science

thesisTraditionally, stratospheric sudden warming events (SSWs) are defined using a fixed threshold criterion. This criterion, however, may lead to spurious results if the climate of the underlying dataset is changing. In an attempt to overcome this potential shortcoming we develop alternative criteria to define such events and test these criteria using reanalysis and climate model data. Results show that under different future climate forcing scenarios the annual and monthly mean SSW frequency increase. This increase is most robust in early to mid-winter. We therefore conclude that under a changing climate there is a higher potential for winter cold air outbreaks for regions such as North America, Europe, and northern Asia

GRB Flares: UV/Optical Flaring (Paper I)

We present a new algorithm for the detection of flares in gamma-ray burst (GRB) light curves and use this algorithm to detect flares in the UV/optical. The algorithm makes use of the Bayesian Information Criterion (BIC) to analyze the residuals of the fitted light curve, removing all major features, and to determine the statistically best fit to the data by iteratively adding additional `breaks' to the light curve. These additional breaks represent the individual components of the detected flares: T_start, T_stop, and T_peak. We present the detection of 119 unique flaring periods detected by applying this algorithm to light curves taken from the Second Swift Ultraviolet/Optical Telescope (UVOT) GRB Afterglow Catalog. We analyzed 201 UVOT GRB light curves and found episodes of flaring in 68 of the light curves. For those light curves with flares, we find an average number of ~2 flares per GRB. Flaring is generally restricted to the first 1000 seconds of the afterglow, but can be observed and detected beyond 10^5 seconds. More than 80% of the flares detected are short in duration with Delta t/t of < 0.5. Flares were observed with flux ratios relative to the underlying light curve of between 0.04 to 55.42. Many of the strongest flares were also seen at greater than 1000 seconds after the burst.Comment: Submitted to ApJ. 20 pages (including 8 figures and 1 table

Severe Injury of the Thigh.

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Observation of Large Atomic-Recoil Induced Asymmetries in Cold Atom Spectroscopy

The atomic recoil effect leads to large (25 %) asymmetries in simple spectroscopic investigations of Ca atoms that have been laser-cooled to 10 microkelvin. Starting with spectra from the more familiar Doppler-broadened domain, we show how the fundamental asymmetry between absorption and stimulated emission of light manifests itself when shorter spectroscopic pulses lead to the Fourier transform regime. These effects occur on frequency scales much larger than the size of the recoil shift itself, and have not been observed before in saturation spectroscopy. These results are relevant to state-of-the-art optical atomic clocks based on freely expanding neutral atoms.Comment: 4 pages, 3 figure

Real-time Semiparametric Regression via Sequential Monte Carlo

We develop and describe online algorithms for performing real-time semiparametric regression analyses. Earlier work on this topic is in Luts, Broderick & Wand (J. Comput. Graph. Statist., 2014) where online mean field variational Bayes was employed. In this article we instead develop sequential Monte Carlo approaches to circumvent well-known inaccuracies inherent in variational approaches. Even though sequential Monte Carlo is not as fast as online mean field variational Bayes, it can be a viable alternative for applications where the data rate is not overly high. For Gaussian response semiparametric regression models our new algorithms share the online mean field variational Bayes property of only requiring updating and storage of sufficient statistics quantities of streaming data. In the non-Gaussian case accurate real-time semiparametric regression requires the full data to be kept in storage. The new algorithms allow for new options concerning accuracy/speed trade-offs for real-time semiparametric regression

Children's responses to traditional versus hybrid advertising formats

Research on the impact of advertising on children has failed to keep pace with the rapidly changing media environment. Using an experimental approach, children’s responses towards traditional (television advertisement) versus new, hybrid advertising techniques (trailer, advergame, and their combination), and the moderating role of persuasion knowledge, are investigated. Results show that children who played an advergame have more difficulty recalling the advertised brand than children who saw a traditional television advertisement. When confronted with integrated marketing communications (a trailer followed by an advergame), children without knowledge of persuasive intent developed a more positive brand attitude than children with persuasion knowledge. The implications of these results are discussed