Self-Immolation In Tibet: Beyond The Lens Of The Western Media

This thesis provides a critique of Western media articles concerning self-immolation in Tibet. I begin by illustrating how the Western media provides reductionist accounts of Tibetan self-immolation by depicting the act solely as a form of political protest in response to Chinese occupation. I argue that these limited portrayals of self-immolation can be attributed to the Shangri-La imagery that characterizes much of the Western conceptions of Tibet. Through Shangri-La imagery, both Tibetans and their Buddhist religion are portrayed as utopic, peaceful, and able to provide the antidote to solving Western problems relating to modernization and consumerism. After illustrating the ways in which Shangri-La imagery influences Western media portrayals of Tibetan self-immolation, this thesis explores the commonly disregarded Buddhist dimensions of the act. Looking to Buddhist doctrine, scripture, and history, this thesis establishes a clear relationship between self-immolation and Buddhism, which situates the act as being more complicated than mere political protest. I argue that these limited portrayals given by the Western media are problematic because they overlook a fundamental aspect of self-immolation, thus potentially misrepresenting Tibetans. This thesis explores the Buddhist dimensions of self-immolation as a possible way to further understand what has led more than one hundred Tibetans to perform this act during the time of political crisis.

SNP array profiling of childhood adrenocortical tumors reveals distinct pathways of tumorigenesis and highlights candidate driver genes

Childhood adrenocortical tumors (ACT) are rare malignancies, except in southern Brazil, where a higher incidence rate is associated to a high frequency of the founder R337H TP53 mutation. To date, copy number alterations in these tumors have only been analyzed by low-resolution comparative genomic hybridization.

Combined pars plana phacofragmentation, vitrectomy, and Artisan lens implantation for traumatic subluxated cataracts

PURPOSE: To report on the outcome of combined pars plana phacofragmentation, vitrectomy, and Artisan lens implantation in the management of subluxated cataracts. METHODS: This prospective, interventional, nonrandomized case series included nine eyes of seven consecutive adult patients with traumatic lens subluxation. Pre- and postoperative data (complete manifest refraction, best spectacle-corrected visual acuity, slit-lamp examination findings, intraocular pressure, fundus status, numerical density of endothelial cells, corneal thickness, and complications) were collected prospectively for all patients. RESULTS: After a median postoperative follow-up of 12 months (range, 8-18 months), a mean spherical equivalent of -0.50 +/- 0.87 diopter (range, +1 to -1.50 diopter) was achieved. The mean logarithm of the minimum angle of resolution visual acuity improved from 1 (preoperatively) to 0.1 (postoperatively) (P = 0.007, Wilcoxon test). Median endothelial cell losses of 15 +/- 8% (P = 0.008) and 14 +/- 16% (P = 0.011) were registered at follow-ups of 1 month and 12 months, respectively. Postoperative complications included chronic intraocular inflammation and superior corectopia. CONCLUSIONS: Our procedure appears to be a safe, accurate, stable, and efficacious option for the management of traumatic subluxated cataracts in adults. However, longer-term data are needed to evaluate the corneal endothelium.

Influence of intraocular lens material on the development of acute endophthalmitis after cataract surgery?

PurposeTo investigate the causal relationship between acute postoperative endophthalmitis (POE) after cataract surgery and the biomaterial properties of the intraocular lens (IOLs) implanted.MethodsThis retrospective cohort study included all patients who had undergone cataract surgery with IOL implantation at the Lyon Croix-Rousse University Hospital between 1st January 1994 and 31st December 2004. Details respecting the type of IOL implanted (material and manufacturer) were meticulously recorded. The number of patients presenting with POE within 6 weeks of cataract surgery was documented together with their medical characteristics. These data were then compared, and Fisher's exact test was used to establish the significance of any apparent associations.ResultsEight of the 5837 eyes manifested acute POE (0.14%). Seven of these were composed of polymethylmethacrylate (PMMA) and one of heparinized PMMA. Patients with PMMA IOLs carried a higher risk of developing POE than did those implanted with either heparinized PMMA (P=0.001), hydrophilic acrylic, or hydrophobic acrylic IOLs (P=0.002).ConclusionsThe incidence of acute POE after cataract surgery in our hospital is similar to that currently reported for other institutions in developed countries. Our results add further evidence that IOL material and type are factors contributing to the risk to develop an acute POE after cataract surgery, and that PMMA IOLs may be associated with an increased risk of POE.Eye advance online publication, 15 September 2006; doi:10.1038/sj.eye.6702544.

A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal $t$-statistic with a permutation reference distribution to obtain the corresponding $p$-value. The number of computations required for the maximal test statistic is $O(N^2),$ where $N$ is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the $p$-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy'' package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the $p$-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Detection of erythropoietin in exhaled breath condensate of nonhypoxic subjects using a multiplex bead array

As a noninvasive method, exhaled breath condensate (EBC) has gained importance to improve monitoring of lung diseases and to detect biomarkers. The aim of the study was to investigate, whether erythropoietin (EPO) is detectable in EBC. EBC was collected from 22 consecutive patients as well as from healthy individuals. Using a multiplex fluorescent bead immunoassay, we detected EPO in EBC, as well as tumour necrosis factor-alpha (TNF-alpha) in 13 out of 22 patients simultaneously (EPO 0.21 +/- 0.03 in U/mL and TNF-alpha 34.6 +/- 4.2 in pg/mL, mean +/- SEM). No significant differences for EPO levels or correlation between EPO and TNF-alpha were found but TNF-alpha was significantly higher in patients with chronic obstructive pulmonary disease (COPD) than in non-COPD (obstructive sleep apnoea, OSA, and lung healthy patients). This is the first report of detection of EPO in EBC. Due to the small study size more data is needed to clarify the role of EPO in EBC.

Bayesian Hidden Markov Modeling of Array CGH Data

Genomic alterations have been linked to the development and progression of cancer. The technique of Comparative Genomic Hybridization (CGH) yields data consisting of fluorescence intensity ratios of test and reference DNA samples. The intensity ratios provide information about the number of copies in DNA. Practical issues such as the contamination of tumor cells in tissue specimens and normalization errors necessitate the use of statistics for learning about the genomic alterations from array-CGH data. As increasing amounts of array CGH data become available, there is a growing need for automated algorithms for characterizing genomic profiles. Specifically, there is a need for algorithms that can identify gains and losses in the number of copies based on statistical considerations, rather than merely detect trends in the data. We adopt a Bayesian approach, relying on the hidden Markov model to account for the inherent dependence in the intensity ratios. Posterior inferences are made about gains and losses in copy number. Localized amplifications (associated with oncogene mutations) and deletions (associated with mutations of tumor suppressors) are identified using posterior probabilities. Global trends such as extended regions of altered copy number are detected. Since the posterior distribution is analytically intractable, we implement a Metropolis-within-Gibbs algorithm for efficient simulation-based inference. Publicly available data on pancreatic adenocarcinoma, glioblastoma multiforme and breast cancer are analyzed, and comparisons are made with some widely-used algorithms to illustrate the reliability and success of the technique.

A Pseudolikelihood Approach for Simultaneous Analysis of Array Comparative Genomic Hybridizations (aCGH)

DNA sequence copy number has been shown to be associated with cancer development and progression. Array-based Comparative Genomic Hybridization (aCGH) is a recent development that seeks to identify the copy number ratio at large numbers of markers across the genome. Due to experimental and biological variations across chromosomes and across hybridizations, current methods are limited to analyses of single chromosomes. We propose a more powerful approach that borrows strength across chromosomes and across hybridizations. We assume a Gaussian mixture model, with a hidden Markov dependence structure, and with random effects to allow for intertumoral variation, as well as intratumoral clonal variation. For ease of computation, we base estimation on a pseudolikelihood function. The method produces quantitative assessments of the likelihood of genetic alterations at each clone, along with a graphical display for simple visual interpretation. We assess the characteristics of the method through simulation studies and through analysis of a brain tumor aCGH data set. We show that the pseudolikelihood approach is superior to existing methods both in detecting small regions of copy number alteration and in accurately classifying regions of change when intratumoral clonal variation is present.

EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA

In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data manipulations, referred to as preprocessing, can influence the quality of the ultimate measurements. In the last few years, the high-throughput measurement of gene expression is the most popular application of microarray technology. For this application, various groups have demonstrated that the use of modern statistical methodology can substantially improve accuracy and precision of gene expression measurements, relative to ad-hoc procedures introduced by designers and manufacturers of the technology. Currently, other applications of microarrays are becoming more and more popular. In this paper we describe a preprocessing methodology for a technology designed for the identification of DNA sequence variants in specific genes or regions of the human genome that are associated with phenotypes of interest such as disease. In particular we describe methodology useful for preprocessing Affymetrix SNP chips and obtaining genotype calls with the preprocessed data. We demonstrate how our procedure improves existing approaches using data from three relatively large studies including one in which large number independent calls are available. Software implementing these ideas are avialble from the Bioconductor oligo package.