Trellis Decoding And Applications For Quantum Error Correction

Compact, graphical representations of error-correcting codes called trellises are a crucial tool in classical coding theory, establishing both theoretical properties and performance metrics for practical use. The idea was extended to quantum error-correcting codes by Ollivier and Tillich in 2005. Here, we use their foundation to establish a practical decoder able to compute the maximum-likely error for any stabilizer code over a finite field of prime dimension. We define a canonical form for the stabilizer group and use it to classify the internal structure of the graph. Similarities and differences between the classical and quantum theories are discussed throughout. Numerical results are presented which match or outperform current state-of-the-art decoding techniques. New construction techniques for large trellises are developed and practical implementations discussed. We then define a dual trellis and use algebraic graph theory to solve the maximum-likely coset problem for any stabilizer code over a finite field of prime dimension at minimum added cost. Classical trellis theory makes occasional theoretical use of a graph product called the trellis product. We establish the relationship between the trellis product and the standard graph products and use it to provide a closed form expression for the resulting graph, allowing it to be used in practice. We explore its properties and classify all idempotents. The special structure of the trellis allows us to present a factorization procedure for the product, which is much simpler than that of the standard products. Finally, we turn to an algorithmic study of the trellis and explore what coding-theoretic information can be extracted assuming no other information about the code is available. In the process, we present a state-of-the-art algorithm for computing the minimum distance for any stabilizer code over a finite field of prime dimension. We also define a new weight enumerator for stabilizer codes over F_2 incorporating the phases of each stabilizer and provide a trellis-based algorithm to compute it.Ph.D

Local Avian Density Influences Risk of Mortality from Window Strikes

Up to a billion birds die per year in North America as a result of striking windows. Both transparent and reflective glass panes are a cause for concern, misleading birds by either acting as invisible, impenetrable barriers to desired resources, or reflecting those resources over a large surface area. A high number of window strikes occur during migration, but little is known about the factors of susceptibility, or whether particular avian taxa are more vulnerable than others. We report on a study of window strikes and mist-netting data at the Virginia Zoological Park (Norfolk, Virginia, USA), conducted in the autumn of 2013 and 2014. We focused on three factors likely to contribute to an individual\u27s predisposition to collide with windows: (i) taxonomic classification, (ii) age, and (iii) migrant vs. resident status. Thrushes, dominated by the partial migrant American Robin (Turdus migratorius), were significantly less likely to strike glass than be sampled in mist nets (χ2 = 9.21, p = 0.002), while wood-warblers (Parulidae) were more likely to strike than expected (χ2 = 13.55, p \u3c 0.001). The proportion of juveniles striking windows (45.4%) was not significantly different (χ2 = 0.05, p = 0.827) than the population of juvenile birds naturally occurring at the zoo (48.8%). Migrants, however, were significantly more susceptible to window strikes than residents (χ2 = 6.35, p = 0.012). Our results suggest that resident birds are able to learn to avoid and thus reduce their likelihood of striking windows; this intrinsic risk factor may help explain the apparent susceptibility of certain taxa to window strikes

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function

The tyranny of the male preserve

Within this paper I draw on short vignettes and quotes taken from a two-year ethnographic study of boxing to think through the continuing academic merit of the notion of the male preserve. This is an important task due to evidence of shifts in social patterns of gender that have developed since the idea was first proposed in the 1970s. In aligning theoretical contributions from Lefebvre and Butler to discussions of the male preserve, we are able to add nuance to our understanding of how such social spaces are engrained with and produced by the lingering grasp of patriarchal narratives. In particular, by situating the male preserve within shifting social processes, whereby certain men’s power is increasingly undermined, I highlight the production of space within which narratives connecting men to violence, aggression and physical power can be consumed, performed and reified in a relatively unrestricted form. This specific case study contributes to gender theory as an illustration of a way in which we might explore and understand social enclaves where certain people are able to lay claim to space and power. As such, I argue that the notion of the male preserve is still a useful conceptual, theoretical and political device especially when considered as produced by the tyranny of gender power through the dramatic representation and reification of behaviours symbolically linked to patriarchal narrations of manhood

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency

Exploring the relationship between homosexuality and sport among the teammates of a small, Midwestern Catholic college soccer team.

Despite decreasing homophobia, openly gay male athletes are still rare in organized, competitive teamsports. In this action research, we explore two aspects of homosexuality and sport: (1) the effect of a gay male soccer player coming out to his teammates; and (2) the effect of having an openly gay researcher in the field. This is, therefore, the first-ever first-hand account of an athlete's coming-out process with researchers in the field. Even though this is action research and, therefore, not generalizable, we highlight that this research contributes to the body of literature on sexuality and sport because we document the interactions of straight athletes with a gay player and a gay researcher among the heterosexual players at a small, Catholic college in the American Midwest. We use interviews to show that players were accepting of homosexuality before the beginning of this research and show that discussions with these two gay men further promoted players' perspectives on homosexuality. This led to an increase in the team's social cohesion and a decrease in heteronormativity