MapCores 2013-2014 Assessment Report

This is a report showing the assessment results for the MapCores (MAthematics, Physics, COmputer science REsearch Scholars) program at the College of Saint Benedict. Started in 2009, MapCores is a cohort-based program designed to increase women\u27s interest and achievement in mathematics, physics, computer science and engineering. The report was submitted for the National Science Foundation grant number 0965705

pKWmEB: integration of Kruskal-Wallis test with empirical bayes under polygenic background control for multi-locus genome-wide association study

Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal–Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait. Finally, all the selected markers were placed into multi-locus model, these effects were estimated by empirical Bayes, and all the nonzero effects were further identified by a likelihood ratio test for true QTN detection. This method, named pKWmEB, was validated by a series of Monte Carlo simulation studies. As a result, pKWmEB effectively controlled false positive rate, although a less stringent significance criterion was adopted. More importantly, pKWmEB retained the high power of Kruskal–Wallis test, and provided QTN effect estimates. To further validate pKWmEB, we re-analyzed four flowering time related traits in Arabidopsis thaliana, and detected some previously reported genes that were not identified by the other methods

A Women in Mathematics, Computer Science, and Physics Course

Increasing women\u27s participation is a concern in disciplines beyondphysics. As part of our Mathematics, Physics, Computer ScienceResearch Scholars (MapCores) program, we teach a women in scienceclass covering these three areas. Our course is a special version ofour college\u27s first year seminar, which is a course designed toprepare our students to read, write, and speak at a college-level. Westructure our FYS to promote academic confidence and interest in ourdisciplines for the women in MapCores. It covers not only contributionsthat women have made and barriers that women face in thesedisciplines, but also research frontiers and science policy issues inthese disciplines. While the women in MapCores find covering thesetopics beneficial, the most important benefit of the course is the supportive cohort that develops from it

Objective Comparison of Toolmarks from the Cutting Surfaces of Slip-Joint Pliers

Experimental results from a statistical analysis algorithm for objectively comparing toolmarks via data files obtained using optical profilometry data are described. The algorithm employed has successfully been used to compare striated marks produced by screwdrivers. In this study, quasi-striated marks produced by the cutting surfaces of slip-joint pliers were examined. Marks were made by cutting both copper and lead wire. Data files were obtained using an optical profilometer that uses focus variation to determine surface roughness. Early efforts using the comparative algorithm yielded inconclusive results when the comparison parameters used were the same as those employed successfully for screw-driver marks. Further experiments showed that the algorithm could successfully be used to separate known matches from non-matches by changing the comparison parameters. Results are presented from the analysis of the copper wires

Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method

Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes

CO₂ gasification of bio-char derived from conventional and microwave pyrolysis

Thermal-chemical processing of biomass is expected to provide renewable and clean energy and fuels in the future. Due to the nature of endothermic reactions, microwave and conventional heating have been applied to this technology. However, more studies need to be carried out to clarify the difference between these two heating technologies. In this work, we investigated two bio-char samples produced from conventional pyrolysis of wood biomass (yield of bio-char: 38.48 and 59.70 wt.%, respectively) and one bio-char produced from microwave pyrolysis with a yield of 45.16 wt.% from the same biomass sample at different process conditions. Various methodologies have been used to characterise the bio-chars. CO₂ gasification of bio-char has also been studied using a thermogravimetric analyser (TGA) and a fixed-bed reaction system. The results show that volatile and carbon contents of the bio-char derived from microwave pyrolysis were between the two conventional bio-chars. However, the microwave bio-char is more reactive for CO₂ gasification, as more CO was released during TGA experiments, and the CO release peak was narrower compared with the CO₂ gasification of the conventional bio-chars. It is suggested that the conventional bio-char is less reactive due to the presence of more secondary chars which are produced from secondary reactions of volatiles during the conventional biomass pyrolysis. While the microwave pyrolysis generates more uniform bio-chars with less secondary char, and therefore, has advantages of producing bio-char for downstream char gasification

Identification of non‐reported bupropion metabolites in human plasma

Bupropion and its three active metabolites exhibit clinical efficacy in the treatment of major depression, seasonal depression and smoking cessation. The pharmacokinetics of bupropion in humans is highly variable. It is not known if there are any non‐reported metabolites formed in humans in addition to the three known active metabolites. This paper reports newly identified and non‐reported metabolites of bupropion in human plasma samples. Human subjects were dosed with a single oral dose of 75 mg of an immediate release bupropion HCl tablet. Plasma samples were collected and analysed by LC–MS/MS at 0, 6 and 24 h. Two non‐reported metabolites (M1 and M3) were identified with mass‐to‐charge (m/z) ratios of 276 (M1, hydration of bupropion) and 258 (M3, hydroxylation of threo/erythrohydrobupropion) from human plasma in addition to the known hydroxybupropion, threo/erythrohydrobupropion and the glucuronidation products of the major metabolites (M2 and M4–M7). These new metabolites may provide new insight and broaden the understanding of bupropion’s variability in clinical pharmacokinetics. © 2016 The Authors Biopharmaceutics & Drug Disposition Published by John Wiley & Sons Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134787/1/bdd2046_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134787/2/bdd2046.pd

Orsay virus CP-δ adopts a novel β-bracelet structural fold and incorporates into virions as a head fiber

Fiber proteins are commonly found in eukaryotic and prokaryotic viruses, where they play important roles in mediating viral attachment and host cell entry. They typically form trimeric structures and are incorporated into virions via noncovalent interactions. Orsay virus, a small RNA virus which specifically infects the laboratory model nematod