Probing Nucleic Acid Structure with Nickel‐ and Cobalt‐Based Reagents

The use of nickel and cobalt reagents is presented for characterizing the solvent exposure of guanine residues in DNA and RNA. These reagents promote guanine oxidation in the presence of a peracid such as monopersulfate, and the extent of reaction indicates the steric and electronic environment surrounding the N7 and aromatic face of this residue. Since oxidation does not itself perturb target structure or induce strand scission, it is coupled with fragmentation by treatment with piperidine (for smaller polynucleotides) or termination of primer extension (for larger polynucleotides).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143767/1/cpnc0604.pd

Indiana state parks and the Hoosier imagination, 1916-1933

This dissertation focuses on changing conceptualizations of history and heritage to investigate how the burgeoning system of state parks in Indiana between 1916-1933 reflected the state’s own struggle against modernity. I argue that the parks were physical manifestations of the “Hoosier Imagination,” part of an on-going conceptual reframing of local identity. Fully a century ago, the people of Indiana successfully campaigned to protect certain portions of the state’s original domain and to keep these areas as a heritage passed down to future generations. During an era of constant change, the parks were imagined to be part of the collective memory of the people and a connection to a mythologized pastoral history of the state, though this history often ignored or marginalized culturally problematic parts of local history such as acknowledging the role of Native Americans. However, I argue that these seemingly “natural” sites cannot be seen as distinct from urban matters. Instead, Indiana’s state parks are inexorably linked to urban matters, dynamics, and systems. Close examination of archival source material and contemporary newspapers show that the parks were central to the dissemination and display of modern ideas about history, biology, technology, and personal health, as well as evolving cultural values concerning bureaucratic efficiency. These sites afforded Indiana space to position itself in the vanguard of Progressive Era social and economic growth, creating a veritable laboratory to consolidate the newly minted authority of the state. I further draw connections between local statecraft and large-scale imperial formations, an idea that I have coined called “local imperialism.” Ultimately, this study demonstrates that the Indiana State Parks were physical sites at which Hoosier residents and institutions could continually re-imagine the past, present, and future of the state

Learning Overlap Optimization for Domain Decomposition Methods

Abstract. The finite element method is a numerical simulation technique for solving partial differential equations. Domain decomposition provides a means for parallelizing the expensive simulation with modern computing architecture. Choosing the sub-domains for domain decomposition is a non-trivial task, and in this paper we show how this can be addressed with machine learning. Our method starts with a baseline decomposition, from which we learn tailored sub-domain overlaps from localized neighborhoods. An evaluation of 527 partial differential equations shows that our learned solutions improve the baseline decomposition with high consistency and by a statistically significant margin

Spitzer Planet Limits around the Pulsating White Dwarf GD66

We present infrared observations in search of a planet around the white dwarf, GD66. Time-series photometry of GD66 shows a variation in the arrival time of stellar pulsations consistent with the presence of a planet with mass > 2.4Mj. Any such planet is too close to the star to be resolved, but the planet's light can be directly detected as an excess flux at 4.5um. We observed GD66 with the two shorter wavelength channels of IRAC on Spitzer but did not find strong evidence of a companion, placing an upper limit of 5--7Mj on the mass of the companion, assuming an age of 1.2--1.7Gyr.Comment: 10 pages, accepted by Ap

A Multi-Epoch HST Study of the Herbig-Haro Flow from XZ Tauri

We present nine epochs of Hubble Space Telescope optical imaging of the bipolar outflow from the pre-main sequence binary XZ Tauri. Our data monitors the system from 1995-2005 and includes emission line images of the flow. The northern lobe appears to be a succession of bubbles, the outermost of which expanded ballistically from 1995-1999 but in 2000 began to deform and decelerate along its forward edge. It reached an extent of 6" from the binary in 2005. A larger and fainter southern counterbubble was detected for the first time in deep ACS images from 2004. Traces of shocked emission are seen as far as 20" south of the binary. The bubble emission nebulosity has a low excitation overall, as traced by the [S II]/H-alpha line ratio, requiring a nearly comoving surrounding medium that has been accelerated by previous ejections or stellar winds. Within the broad bubbles there are compact emission knots whose alignments and proper motions indicate that collimated jets are ejected from each binary component. The jet from the southern component, XZ Tau A, is aligned with the outflow axis of the bubbles and has tangential knot velocities of 70-200 km/s. Knots in the northern flow are seen to slow and brighten as they approach the forward edge of the outermost bubble. The knots in the jet from the other star, XZ Tau B, have lower velocities of ~100 km/s

Assimilation of SCIAMACHY Total Column CO Observations: Regional Analysis of Data Impact

Carbon monoxide (CO) total column observations from the SCanning Imaging Absorption SpectroMeter for Atmospheric CHartography (SCIAMACHY) on board ENVISAT are assimilated into the Global Modeling and Assimilation Office (GMAO) constituent assimilation system for the period July 18-October 31, 2004. This is the first assimilation of CO observations from a near infrared sounder. The impact of the assimilation on CO distribution is evaluated using independent Measurement of Ozone and Water vapor by Airbus In-service Aircraft (MOZAIC) in-situ CO profiles. Assimilation of satellite data improves agreement with MOZAIC CO globally, especially in the upper troposphere

Towards precision particle background estimation for future X-ray missions: correlated variability between Chandra ACIS and AMS

A science goal of many future X-ray observatories is mapping the cosmic web through deep exposures of faint diffuse sources. Such observations require low background and the best possible knowledge of the remaining unrejected background. The dominant contribution to the background above 1-2 keV is from Galactic Cosmic Ray protons. Their flux and spectrum are modulated by the solar cycle but also by solar activity on shorter timescales. Understanding this variability may prove crucial to reducing background uncertainty for ESA's Athena X-ray Observatory and other missions with large collecting area. We examine of the variability of the particle background as measured by ACIS on the Chandra X-ray Observatory and compare that variability to that measured by the Alpha Magnetic Spectrometer (AMS), a precision particle detector on the ISS. We show that cosmic ray proton variability measured by AMS is well matched to the ACIS background and can be used to estimate proton energies responsible for the background. We discuss how this can inform future missions.Comment: 11 pages, 8 figures, submitted to Proceedings of SPIE Astronomical Telescopes + Instrumentation 202

Multivariate analysis using high definition flow cytometry reveals distinct T cell repertoires between the fetal–maternal interface and the peripheral blood

The human T cell compartment is a complex system and while some information is known on repertoire composition and dynamics in the peripheral blood, little is known about repertoire composition at different anatomical sites. Here, we determine the T cell receptor beta variable (TRBV) repertoire at the decidua and compare it with the peripheral blood during normal pregnancy and pre-eclampsia. We found total T cell subset disparity of up to 58% between sites, including large signature TRBV expansions unique to the fetal–maternal interface. Defining the functional nature and specificity of compartment-specific T cells will be necessary if we are to understand localized immunity, tolerance, and pathogenesis

TopHat: discovering splice junctions with RNA-Seq

Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or ‘reads’, can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites