A Project Based Approach to Statistics and Data Science

In an increasingly data-driven world, facility with statistics is more important than ever for our students. At institutions without a statistician, it often falls to the mathematics faculty to teach statistics courses. This paper presents a model that a mathematician asked to teach statistics can follow. This model entails connecting with faculty from numerous departments on campus to develop a list of topics, building a repository of real-world datasets from these faculty, and creating projects where students interface with these datasets to write lab reports aimed at consumers of statistics in other disciplines. The end result is students who are well prepared for interdisciplinary research, who are accustomed to coping with the idiosyncrasies of real data, and who have sharpened their technical writing and speaking skills

Marginal likelihoods in phylogenetics: a review of methods and applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.Comment: 33 pages, 3 figure

Legislative Note: Micigan\u27s Criminal Sexual Assault Law

Under increasing pressure from women\u27s rights groups and other reform organizations, the Michigan legislature has re-evaluated its centenarian rape statute, found it inadequate for the realities of the mid-twentieth century, and enacted a new sexual assault act. While people may refer to the act as the new rape law, it should be noted at the outset that the statute is intended to prohibit a variety of sexual acts which involve criminal assault. Michigan\u27s new criminal sexual assault law was formulated to distinguish among degrees of violence as motivated by hostility rather than passion; rape, like other crimes, is more heinous in certain contexts than others. The new law acknowledges that criminal sexual conduct is generally a premeditated crime of violence rather than a crime provoked by the victim\u27s behavior. The victim is no longer required to resist. Where force is used, it is now presumed that the victim did not consent. Similarly, evidence is limited to that which applies to the specific crime rather than evidence concerning the victim\u27s past sexual behavior. This note will analyze the specific provisions of the new bill and discuss the policies behind the evidentiary changes

Experimentally Constrained Molecular Relaxation: The Case of Glassy GeSe2

An ideal atomistic model of a disordered material should contradict no experiments,and should also be consistent with accurate force fields (either {\it ab initio}or empirical). We make significant progress toward jointly satisfying {\it both} of these criteria using a hybrid reverse Monte Carlo approach in conjunction with approximate first principles molecular dynamics. We illustrate the method by studying the complex binary glassy material g-GeSe$_2$. By constraining the model to agree with partial structure factors and {\it ab initio} simulation, we obtain a 647-atom model in close agreement with experiment, including the first sharp diffraction peak in the static structure factor. We compute the electronic state densities and compare to photoelectron spectroscopies. The approach is general and flexible.Comment: 6 pages, 4 figure

Geologic Descriptions and Coal Analyses for 1982 Coal Drilling in the Daniel Boone National Forest, Eastern Kentucky

This report contains core descriptions, lithologic logs, and analyses of coal from 21 stratigraphic test holes drilled in 1982 in the Daniel Boone National Forest, including the Redbird Purchase Unit, in eastern Kentucky. The test holes ranged in depth from 85 to 1,988 feet and averaged about 700 feet. A total of 89 coal samples were analyzed. Results of analyses (on the as-received basis) showed the following ranges: ash, 2.37 to 28.8 percent; sulfur, 0.3 to 8.4 percent; and Btu, 9,017 to 14,550 per pound

Characterization of Simulated Low Earth Orbit Space Environment Effects on Acid-spun Carbon Nanotube Yarns

The purpose of this study is to quantify the detrimental effects of atomic oxygen and ultraviolet (UV) C radiation on the mechanical properties, electrical conductivity, and piezoresistive effect of acid-spun carbon nanotube (CNT) yarns. Monotonic tensile tests with in-situ electrical resistance measurements were performed on pristine and exposed yarns to determine the effects of the atomic oxygen and UVC exposures on the yarn’s material properties. Both type of exposures were performed under vacuum to simulate space environment conditions. The CNT yarns’ mechanical properties did not change significantly after being exposed to UV radiation, but were significantly degraded by the atomic oxygen exposure. The electrical conductivity of the yarn was not significantly affected by either exposure. The piezoresistive effect did not significantly change due to atomic oxygen exposure, but was significantly enhanced as a result of the UV exposure. Scanning electron microscopy revealed significant erosion due to atomic oxygen exposure, but the UV exposure did not significantly change the appearance of the yarn’s external surface. Raman spectroscopy showed that both exposure types induced significant structural disorder in the surface level CNTs. Focused ion beam milling of a UVC exposed yarn revealed that the depth of the induced disorder was very shallow

Role of Dicer Enzyme in the Regulation of Store Operated Calcium Entry (SOCE) in CD4+ T Cells

Background/Aims: Activation of T cell receptors (TCRs) in CD4+ T cells leads to a cascade of signalling reactions including increase of intracellular calcium (Ca2+) levels with subsequent Ca2+ dependent stimulation of gene expression, proliferation, cell motility and cytokine release. The increase of cytosolic Ca2+ results from intracellular Ca2+ release with subsequent activation of store-operated Ca2+ entry (SOCE). Previous studies suggested miRNAs are required for the development and functions of CD4+ T cells. An enzyme called Dicer is required during the process of manufacturing mature miRNAs from the precursor miRNAs. In this study, we explored whether loss of Dicer in CD4+ T cells affects SOCE and thus Ca2+ dependent regulation of cellular functions. Methods: We tested the expression of Orai1 by q-RT-PCR and flow cytometry. Further, we measured SOCE by an inverted phase-contrast microscope with the Incident-light fluorescence illumination system using Fura-2. Intracellular Ca2+ was also measured by flow cytometry using Ca2+ sensitive dye Fluo-4. Results: We found that in Dicer deficient (DicerΔ/Δ) mice Orai1 was downregulated at mRNA and protein level in CD4+ T cells. Further, SOCE was significantly smaller in DicerΔ/Δ CD4+ T cells than in CD4+ T cells isolated from wild-type (Dicerfl/fl) mice. Conclusion: Our data suggest that miRNAs are required for adequate Ca2+ entry into CD4+ T cells and thus triggering of Ca2+ sensitive immune functions

E-Cigarettes: Prevalence and Attitudes in Great Britain

Introduction: Electronic cigarettes (e-cigarettes) are a means of recreational nicotine use that can potentially eliminate the need to smoke tobacco. Little is known about the prevalence of use or smokers' attitudes toward e-cigarettes. This study describes use of and attitudes toward e-cigarettes in Britain. Methods: Respondents from three surveys were recruited from a panel of adults in Britain. Preliminary online and face-to-face qualitative research informed the development of a smokers' survey (486 smokers who had used e-cigarettes and 894 smokers who had not). Representative samples of adults in Britain were then constructed from the panel for population surveys in 2010 (12,597 adults, including 2,297 smokers) and 2012 (12,432 adults, including 2,093 smokers), generating estimates of the prevalence of e-cigarette use and trial in Great Britain. Results: Awareness, trial, and current use increased between 2010 and 2012; for example, current use more than doubled from 2.7% of smokers in 2010 to 6.7% in 2012. The proportion of ever-users currently using e-cigarettes was around one-third in both years. In 2012, 1.1% of ex-smokers reported current e-cigarette use, and a further 2.7% reported past use. Approximately 0.5% of never-smokers reported having tried e-cigarettes. Conclusions: While we found evidence supporting the view that e-cigarette use may be a bridge to quitting, we found very little evidence of e-cigarette use among adults who had never smoked. British smokers would benefit from information about the effective use, risks, and benefits of e-cigarettes, as this might enable the use of e-cigarettes to improve public health

Quantifying the Effects of Hyperthermal Atomic Oxygen and Thermal Fatigue Environments on Carbon Nanotube Sheets for Space-Based Applications

The effects of atomic oxygen and thermal fatigue on two different types of carbon nanotube sheets were studied. One set was treated with nitric acid, while the other set was left untreated. Monotonic tensile tests were performed before and after exposure to determine the effects of either exposure type on the sheets’ mechanical properties. Electrical conductivity and electromagnetic interference measurements were recorded to determine the effects of AO-exposure and thermal cycling on the sheets’ electrical properties. Neither exposure type affected the sheets’ specific strengths. Both exposure types increased the sheets’ specific stiffnesses and decreased the sheets’ strains at failure. The electrical conductivity of both sheets decreased due to the different exposure types, while the EMI shielding effectiveness was unaffected. Scanning electron microscopy was used to observe any changes in the sheets’ surface morphologies, while energy-dispersive X-ray spectroscopy was used to determine the effects of AO on the sheets’ chemical makeup