Graphical User Interface and Microprocessor Control Enhancement of a Pseudorandom Code Generator

Modern digital communication techniques often require the generation of pseudorandom numbers or sequences. The ability to quickly and easily produce various codes such as maximal length codes, Gold codes, Jet Propulsion Laboratory ranging codes, syncopated codes, and non-linear codes in a laboratory environment is essential. This thesis addresses the issue of providing automated computer control to previously built, manually controlled hardware incorporating the Stanford Telecom STEL-1032 Pseudo-Random Number (PRN) Coder. By incorporating a microcontroller into existing hardware, the STEL-1032 can now be conveniently controlled from a MATLAB Graphical User Interface (GUI). The user can quickly create, save, and recall various setups for the STEL-1032 in an easy to use GUI environment. In addition to having complete control of the STEL-1032\u27s internal actions, the microcontroller adds an extra measure of control possibilities by using various signals as possible interrupt sources. The microcontroller can sample the STEL-1032\u27s various outputs at a rate up to 320 kHz and the data can be imported directly into MATLAB for further analysis

Dart Athwart the Mountain Torrents: The Introduction of Brown Trout to New Zealand

From the mid-1860s onwards, British settlers introduced brown trout to New Zealand in an attempt to recreate aspects of Britain, to improve upon New Zealand’s existing resources and to realise their own social aspirations. These introductions were primarily facilitated by organised acclimatisation societies, based upon a British model, located in urban and country centres around New Zealand. Acclimatisation societies received almost unanimous support from the Pākehā populace, particularly with regard to the introduction of British fish, and their every action was reported in detail in local newspapers. Following the first introduction of brown trout, from Tasmania to Canterbury in 1867, societies established breeding facilities and propagated and distributed trout throughout New Zealand. Within ten years brown trout were established in New Zealand sufficiently that settlers were able to fish for trout some 22,000km from their native range. Today they are one of New Zealand’s most popular recreational species and a major source of international tourism. This thesis examines the introduction of brown trout to New Zealand, while situating it in its colonial context and in the environmental ethos of the nineteenth-century. Through constructing an in-depth narrative history of the introduction of trout to the major regions of New Zealand, subtle regional, ethnic, religious and environmental differences come to light. Though some ethno-religious differences are present, environmental conditions between the regions prove by far the most significant cause of difference. This study demonstrates that the introduction of brown trout is inherently linked to the British colonisation of New Zealand, and that trout played the roles of both a product and an agent of colonisation. The colonial connection is affirmed by transnational comparisons with Australia and the United States of America. This thesis further establishes that the introduction of brown trout was a part of the same movement that resulted in the wider environmental transformation of New Zealand in the nineteenth-century to improve the environment and render it more productive for British settlers. In making this argument, the history of the introduction of brown trout provides a greater understanding of New Zealand’s broader environmental history. This thesis further provides historical context to the scientific assessments of the ecological impacts of brown trout, particularly with regard to their displacement of native freshwater species. Many of these species were important food sources for Māori and in this capacity the introduction of brown trout provides insight into the Māori-Pākehā dynamic regarding resource management and fishing. In particular, the imposition of regulatory conditions on trout fishing highlights a fundamental dichotomy between Māori and Pākehā. This thesis establishes an argument for viewing brown trout as a part of the colonial machinery that resulted in Māori alienation from their lands and resources. Finally, this study demonstrates that British settlers prioritised introduced species over native species through legislation, the intentional destruction of native species, and a systematic transformation of the environment that favoured introduced species. This prioritisation is informed by the Eurocentric belief of settlers that their familiar species were inherently superior to New Zealand’s native species. These practices stand in direct contrast to the value modern society attributes to native species, and are testament to the transition in environmental philosophy that has taken place in the past 150 years

Genz and Mendell-Elston Estimation of the High-Dimensional Multivariate Normal Distribution

Statistical analysis of multinomial data in complex datasets often requires estimation of the multivariate normal (MVN) distribution for models in which the dimensionality can easily reach 10–1000 and higher. Few algorithms for estimating the MVN distribution can offer robust and efficient performance over such a range of dimensions. We report a simulation-based comparison of two algorithms for the MVN that are widely used in statistical genetic applications. The venerable Mendell- Elston approximation is fast but execution time increases rapidly with the number of dimensions, estimates are generally biased, and an error bound is lacking. The correlation between variables significantly affects absolute error but not overall execution time. The Monte Carlo-based approach described by Genz returns unbiased and error-bounded estimates, but execution time is more sensitive to the correlation between variables. For ultra-high-dimensional problems, however, the Genz algorithm exhibits better scale characteristics and greater time-weighted efficiency of estimation

Contribution of Inbred Singletons to Variance Component Estimation of Heritability and Linkage

Objectives: An interesting consequence of consanguinity is that the inbred singleton becomes informative for genetic variance. We determine the contribution of an inbred singleton to variance component analysis of heritability and linkage. Methods: Statistical theory for the power of variance component analysis of quantitative traits is used to determine the expected contribution of an inbred singleton to likelihood-ratio tests of heritability and linkage. Results: In variance component models an inbred singleton contributes relatively little to a test of heritability, but can contribute substantively to a test of linkage. For small to moderate QTL effects and a level of inbreeding comparable to matings between first cousins (the preferred form of union in many human populations), an inbred singleton can carry nearly 25% the information of a non-inbred sibpair. In more highly inbred contexts available with experimental animal populations, nonhuman primate colonies, and some human subpopulations, the contribution of an inbred singleton relative to a sibpair can exceed 50%. Conclusions: Inbred individuals, even in isolation from other members of a sample, can contribute to variance component estimation and tests of heritability and linkage. Under certain conditions the informativeness of the inbred singleton can approach that of non-inbred sibpair

Conducting A/B Experiments with a Scalable Architecture

A/B experiments are commonly used in research to compare the effects of changing one or more variables in two different experimental groups - a control group and a treatment group. While the benefits of using A/B experiments are widely known and accepted, there is less agreement on a principled approach to creating software infrastructure systems to assist in rapidly conducting such experiments. We propose a four-principle approach for developing a software architecture to support A/B experiments that is domain agnostic and can help alleviate some of the resource constraints currently needed to successfully implement these experiments: the software architecture (i) must retain the typical properties of A/B experiments, (ii) capture problem solving activities and outcomes, (iii) allow researchers to understand the behavior and outcomes of participants in the experiment, and (iv) must enable automated analysis. We successfully developed a software system to encapsulate these principles and implement it in a real-world A/B experiment

Using Analytics on Student Created Data to Content Validate Pedagogical Tools

Conceptual and simulation models can function as useful pedagogical tools, however it is important to categorize different outcomes when evaluating them in order to more meaningfully interpret results. VERA is a ecology-based conceptual modeling software that enables users to simulate interactions between biotics and abiotics in an ecosystem, allowing users to form and then verify hypothesis through observing a time series of the species populations. In this paper, we classify this time series into common patterns found in the domain of ecological modeling through two methods, hierarchical clustering and curve fitting, illustrating a general methodology for showing content validity when combining different pedagogical tools. When applied to a diverse sample of 263 models containing 971 time series collected from three different VERA user categories: a Georgia Tech (GATECH), North Georgia Technical College (NGTC), and ``Self Directed Learners'', results showed agreement between both classification methods on 89.38\% of the sample curves in the test set. This serves as a good indication that our methodology for determining content validity was successful.Comment: 16 pages, preprin

Genes Contributing to Staphylococcus aureus Fitness in Abscess- and Infection-Related Ecologies

ABSTRACT Staphylococcus aureus is a leading cause of both community- and hospital-acquired infections that are increasingly antibiotic resistant. The emergence of S. aureus resistance to even last-line antibiotics heightens the need for the development of new drugs with novel targets. We generated a highly saturated transposon insertion mutant library in the genome of S. aureus and used Tn-seq analysis to probe the entire genome, with unprecedented resolution and sensitivity, for genes of importance in infection. We further identified genes contributing to fitness in various infected compartments (blood and ocular fluids) and compared them to genes required for growth in rich medium. This resulted in the identification of 426 genes that were important for S. aureus fitness during growth in infection models, including 71 genes that could be considered essential for survival specifically during infection. These findings highlight novel as well as previously known genes encoding virulence traits and metabolic pathways important for S. aureus proliferation at sites of infection, which may represent new therapeutic targets

Using genetic information from candidate gene and genome-wide association studies in risk prediction for alcohol dependence

Family-based and genome-wide association studies (GWAS) of alcohol dependence (AD) have reported numerous associated variants. The clinical validity of these variants for predicting AD compared with family history information has not been reported. Using the Collaborative Study on the Genetics of Alcoholism (COGA) and the Study of Addiction: Genes and Environment (SAGE) GWAS samples, we examined the aggregate impact of multiple single nucleotide polymorphisms (SNPs) on risk prediction. We created genetic sum scores by adding risk alleles associated in discovery samples, and then tested the scores for their ability to discriminate between cases and controls in validation samples. Genetic sum scores were assessed separately for SNPs associated with AD in candidate gene studies and SNPs from GWAS analyses that met varying P-value thresholds. Candidate gene sum scores did not exhibit significant predictive accuracy. Family history was a better classifier of case-control status, with a significant area under the receiver operating characteristic curve (AUC) of 0.686 in COGA and 0.614 in SAGE. SNPs that met less stringent P-value thresholds of 0.01-0.50 in GWAS analyses yielded significant AUC estimates, ranging from mean estimates of 0.549 for SNPs with P < 0.01 to 0.565 for SNPs with P < 0.50. This study suggests that SNPs currently have limited clinical utility, but there is potential for enhanced predictive ability with better understanding of the large number of variants that might contribute to risk

Nuclear-driven production of renewable fuel additives from waste organics

Non-intermittent, low-carbon energy from nuclear or biofuels is integral to many strategies to achieve Carbon Budget Reduction targets. However, nuclear plants have high, upfront costs and biodiesel manufacture produces waste glycerol with few secondary uses. Combining these technologies, to precipitate valuable feedstocks from waste glycerol using ionizing radiation, could diversify nuclear energy use whilst valorizing biodiesel waste. Here, we demonstrate solketal (2,2-dimethyl-1,3-dioxolane-4-yl) and acetol (1-hydroxypropan-2-one) production is enhanced in selected aqueous glycerol-acetone mixtures with γ radiation with yields of 1.5 ± 0.2 µmol J−1 and 1.8 ± 0.2 µmol J−1, respectively. This is consistent with the generation of either the stabilized, protonated glycerol cation (CH2OH-CHOH-CH2OH2+ ) from the direct action of glycerol, or the hydronium species, H3O+, via water radiolysis, and their role in the subsequent acid-catalyzed mechanisms for acetol and solketal production. Scaled to a hypothetically compatible range of nuclear facilities in Europe (i.e., contemporary Pressurised Water Reactor designs or spent nuclear fuel stores), we estimate annual solketal production at approximately (1.0 ± 0.1) × 104 t year−1. Given a forecast increase of 5% to 20% v/v% in the renewable proportion of commercial petroleum blends by 2030, nuclear-driven, biomass-derived solketal could contribute towards net-zero emissions targets, combining low-carbon co-generation and co-production