Development of a tool for automatic segmentation of the cerebellum in MR images of children

The human cerebellar cortex is a highly foliated structure that supports both motor and complex cognitive functions in humans. Magnetic Resonance Imaging (MRI) is commonly used to explore structural alterations in patients with psychiatric and neurological diseases. The ability to detect regional structural differences in cerebellar lobules may provide valuable insights into disease biology, progression and response to treatment, but has been hampered by the lack of appropriate tools for performing automated structural cerebellar segmentation and morphometry. In this thesis, time intensive manual tracings by an expert neuroanatomist of 16 cerebellar regions on high-resolution T1-weighted MR images of 18 children aged 9-13 years were used to generate the Cape Town Pediatric Cerebellar Atlas (CAPCA18) in the age-appropriate National Institute of Health Pediatric Database (NIHPD) asymmetric template space. An automated pipeline was developed to process the MR images and generate lobule-wise segmentations, as well as a measure of the uncertainty of the label assignments. Validation in an independent group of children with ages similar to those of the children used in the construction of the atlas, yielded spatial overlaps with manual segmentations greater than 70% in all lobules, except lobules VIIb and X. Average spatial overlap of the whole cerebellar cortex was 86%, compared to 78% using the alternative Spatially Unbiased Infra-tentorial Template (SUIT), which was developed using adult images

Revisiting Robustness in Priced Timed Games

Priced timed games are optimal-cost reachability games played between two players---the controller and the environment---by moving a token along the edges of infinite graphs of configurations of priced timed automata. The goal of the controller is to reach a given set of target locations as cheaply as possible, while the goal of the environment is the opposite. Priced timed games are known to be undecidable for timed automata with $3$ or more clocks, while they are known to be decidable for automata with $1$ clock. In an attempt to recover decidability for priced timed games Bouyer, Markey, and Sankur studied robust priced timed games where the environment has the power to slightly perturb delays proposed by the controller. Unfortunately, however, they showed that the natural problem of deciding the existence of optimal limit-strategy---optimal strategy of the controller where the perturbations tend to vanish in the limit---is undecidable with $10$ or more clocks. In this paper we revisit this problem and improve our understanding of the decidability of these games. We show that the limit-strategy problem is already undecidable for a subclass of robust priced timed games with $5$ or more clocks. On a positive side, we show the decidability of the existence of almost optimal strategies for the same subclass of one-clock robust priced timed games by adapting a classical construction by Bouyer at al. for one-clock priced timed games

Combining Hindu Philosophy and Scientific Concepts in a Children’s Picture Book

Faculty Advisor: Mark Borello; Art Advisor: Lisa Van DrasekThis research was supported by the Undergraduate Research Opportunities Program (UROP)

DIRECT REPEATS AND DELETIONS IN MITOCHONDRIAL DNA: CASUAL AND EVOLUTIONARY ASPECTS

Ph.DDOCTOR OF PHILOSOPH

Caste, class and education: the social construction of capabilities in a Tamil village

Venkataraman LN. Caste, class and education: the social construction of capabilities in a Tamil village. Bielefeld: Bielefeld University Library; 2013.India as an ethnographic museum is known for its national notion of unity in diversity. It is a country of many religions, further divided in terms of diverse social hierarchies. The socio-economic reality, for instance, is not simply based on class dynamics as prevailing in many other countries. The intersectional factors like caste play an important role. The stratification of Hindu social system based on caste places individuals hierarchically according to their birth. The inheritance based on birth in caste structure most often plays a ‘fixed’ identity where the social mobility is discouraged. The broader classification of varnashrma dharma divides people in terms of Brahmins, Kshatriyas, Vaishyas and Shudras. This ascriptive social order based on the Hindu scriptures places Brahmins (or the “higher” castes) above “others”. Kshatriyas who are traditionally known for martial valor and managerial roles are in the next layers of social stratification. Third, the Vaishyas who are known for their trade and commercial activities are above to the last layer of the “lower” castes. In the fourfold ascriptive division of labour, the “lower” castes are often addressed as Shudras (or Dalits or Harijans). The ascriptive nature of caste system is, thus, unique in the stratification where social status is mostly determined by birth. In this backdrop, the current research attempts to analyze the intersections between caste, class and education. This intersectionality is conceptualized in terms of the social construction of the “mutually constitutive relations among social identities…” (Shields 2008: 301)

Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?

Non D-loop direct repeats (DRs) in mitochondrial DNA (mtDNA) have been commonly implicated in the mutagenesis of mtDNA deletions associated with neuromuscular disease and ageing. Further, these DRs have been hypothesized to put a constraint on the lifespan of mammals and are under a negative selection pressure. Using a compendium of 294 mammalian mtDNA, we re-examined the relationship between species lifespan and the mutagenicity of such DRs. Contradicting the prevailing hypotheses, we found no significant evidence that long-lived mammals possess fewer mutagenic DRs than short-lived mammals. By comparing DR counts in human mtDNA with those in selectively randomized sequences, we also showed that the number of DRs in human mtDNA is primarily determined by global mtDNA properties, such as the bias in synonymous codon usage (SCU) and nucleotide composition. We found that SCU bias in mtDNA positively correlates with DR counts, where repeated usage of a subset of codons leads to more frequent DR occurrences. While bias in SCU and nucleotide composition has been attributed to nucleotide mutational bias, mammalian mtDNA still exhibit higher SCU bias and DR counts than expected from such mutational bias, suggesting a lack of negative selection against non D-loop DR