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Search Results: 1 - 10 of 53052 matches for " David Crouse "
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Examining large-scale time-use files through graphic representation
William Michelson,David Crouse
Electronic International Journal of Time Use Research , 2004,
Abstract: The objective of this paper is to demonstrate the utility of graphic means to add to the comprehension of time-use analysis. The paper traces the development of several graphic approaches, from the logic of plotting a single case in multidimensional space to several ways of examining time-use dynamics graphically without limitations on sample size. It draws on pilot studies from the FAMITEL researchproject on telecommuting and extends to Statistics Canada’s General Social Survey in 1998 with time-use data (GSS12). The examples of graphic development focus on aspects of the daily lives of teleworkers, to illustrate in this context how graphic representation can illuminate much-discussed differences between the complex pattern of daily life characterizing of these workers in comparison to conventional workers, regardless of the size of samples and subsamples. The graphic techniques discussed advance understanding of these phenomena by presenting visual evidence of differential patterns reflecting the interrelations between the several components of time-use as well as reflecting the different times in the day in which phenomena occur, within and between analytic subgroups. As in many other analyses, gender can be literally seen in the graphics as an important differentiating factor, even within occupationalsituations.
Introduction to the Mid-Atlantic Education Review
Kevin Crouse
Mid-Atlantic Education Review , 2013,
Abstract: The Mid-Atlantic Education Review is a peer-reviewed, online journal that provides a forum for studies pertaining to educational issues of interest to educators and researchers in the Mid-Atlantic region. The Review publishes articles that contribute to the knowledge base of researchers, policy-makers, teachers, and administrators. To appeal to a broad educational audience, articles cover a spectrum in their level of analysis, subject focus, and methodological approach.
An effective cavity resonance model for enhanced optical transmission through arrays of subwavelength apertures in metal films
Eli Lansey,Isroel M. Mandel,Jonah N. Gollub,David T. Crouse
Physics , 2013,
Abstract: We present a novel theoretical approach for modeling the resonant properties of transmission through subwavelength apertures penetrating metal films. We show that cavity mode theory applies to an effective resonant cavity whose dimensions are determined by the aperture's geometry and the evanescent decay lengths of the associated diffracted waves. This method suggests a concrete physical mechanism for the enhanced transmission observed in periodic aperture arrays, namely it is the evanescently scattered light, localized in the near field of metal surface, which couples into the apertures. Furthermore, it analytically predicts the frequencies of peaks in enhanced transmission, the quality factor of the peaks, and explains their dependence on variation in the hole radius, periodicity, and the film thickness over a wide range of geometries. This model demonstrates strong correlation to simulation and existing results with a high degree of accuracy.
High-power Yb-doped Fibre Laser for Cutting Dry Pine Wood
Juan Carlos Hernandez,Philippus Crouse,Lin Li
Lecture Notes in Engineering and Computer Science , 2007,
Different Roles of Eukaryotic MutS and MutL Complexes in Repair of Small Insertion and Deletion Loops in Yeast
Nina V. Romanova,Gray F. Crouse
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003920
Abstract: DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors. In order to understand how this fidelity is maintained, it is important to uncover the relative specificities of the different components of mismatch repair. There are two major mispair recognition complexes in eukaryotes that are homologues of bacterial MutS proteins, MutSα and MutSβ, with MutSα recognizing base-base mismatches and small loop mispairs and MutSβ recognizing larger loop mispairs. Upon recognition of a mispair, the MutS complexes then interact with homologues of the bacterial MutL protein. Loops formed on the primer strand during replication lead to insertion mutations, whereas loops on the template strand lead to deletions. We show here in yeast, using oligonucleotide transformation, that MutSα has a strong bias toward repair of insertion loops, while MutSβ has an even stronger bias toward repair of deletion loops. Our results suggest that this bias in repair is due to the different interactions of the MutS complexes with the MutL complexes. Two mutants of MutLα, pms1-G882E and pms1-H888R, repair deletion mispairs but not insertion mispairs. Moreover, we find that a different MutL complex, MutLγ, is extremely important, but not sufficient, for deletion repair in the presence of either MutLα mutation. MutSβ is present in many eukaryotic organisms, but not in prokaryotes. We suggest that the biased repair of deletion mispairs may reflect a critical eukaryotic function of MutSβ in mismatch repair.
Design and implementation of a generalized laboratory data model
Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, Todd Hepler, Shin Leong, Lynn Carmichael, Mike Nhan, Benjamin J Oberkfell, Elaine R Mardis, LaDeana W Hillier, Richard K Wilson
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-362
Abstract: We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.Over the past several decades, many of the biomedical sciences have been transformed into what might be called "high-throughput" areas of study, e.g., DNA mapping and sequencing, gene expression, and proteomics. In a number of cases, the rate at which data can now be generated has increased by several orders of magnitude. This scale-up has contributed to the rise of "big biology" projects of the type that
Detection of Quadruplex DNA by Gold Nanoparticles
Heather F. Crouse,Alex Doudt,Cassie Zerbe,Swarna Basu
Journal of Analytical Methods in Chemistry , 2012, DOI: 10.1155/2012/327603
Abstract: Gold nanoparticles have been used as a probe to detect low (<10?ppb) concentrations of quadruplex DNA. These nanoparticles display a tendency to form aggregates in the presence of certain quadruplex forms, as observed via enhanced plasmon resonance light scattering (PRLS) signals. These nanoparticles showed differing degrees of interactions with different types of quadruplex and mixed sequences but no interaction with duplex DNA. Enhancement of PRLS signals greater than 50% was observed at nanomolar DNA concentration, and a lower limit of detection of 2.1?nM was established for three different quadruplex DNA sequences, including the thrombin-inhibiting single-stranded 15?mer aptamer DNA, d(GGTTGGTGTGGTTGG), and the double-stranded 12?mer DNA, d(G4T4G4). Two different sample preparation protocols were used for the PRLS experiments, and they yielded similar results. 1. Introduction Cost-effective and efficient methods for the selective detection of quadruplex structures present in many structural forms of DNA have been difficult to develop. A number of techniques have been used to monitor quadruplex formation. These techniques include, but are not limited to, nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), Raman spectroscopy, and absorption and fluorescence spectroscopy [1–6]. These methods consume large quantities of DNA, require expensive apparatus, or require elaborate sample preparation. Thus, there has been a lot of interest in the development of novel methodologies and probes for rapid and reliable detection of trace amounts of quadruplex DNA. Our research group has shown that a terbium chelate can detect small (20?ppb) amounts of both single-stranded and double-stranded quadruplex DNA and that the chelate might be binding to the DNA [7]. In this work, the ability of gold nanoparticles to detect low concentrations of DNA and distinguish between different quadruplex sequences is presented. Nanoparticles are a suitable probe for DNA detection due to their small size, optical and magnetic properties. A variety of biological applications, including drug and gene delivery, biodetection of pathogens, tissue engineering, and tumor destruction via heating, have been developed [8–10]. One important optical property that nanoparticles display is the ability to efficiently scatter light. Colloidal gold nanoparticles are known to display strong plasmon absorption bands due to electron oscillations induced by the incident light [11–13]. These strong absorption properties result in gold colloidal suspensions displaying intense colors. In
Transformation with Oligonucleotides Creating Clustered Changes in the Yeast Genome
Gina P. Rodriguez, Joseph B. Song, Gray F. Crouse
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042905
Abstract: We have studied single-strand oligonucleotide (oligo) transformation of yeast by using 40-nt long oligos that create multiple base changes to the yeast genome spread throughout the length of the oligos, making it possible to measure the portions of an oligo that are incorporated during transformation. Although the transformation process is greatly inhibited by DNA mismatch repair (MMR), the pattern of incorporation is essentially the same in the presence or absence of MMR, whether the oligo anneals to the leading or lagging strand of DNA replication, or whether phosphorothioate linkages are used at either end. A central core of approximately 15 nt is incorporated with a frequency of >90%; the ends are incorporated with a lower frequency, and loss of the two ends appears to be by different mechanisms. Bases that are 5–10 nt from the 5′ end are generally lost with a frequency of >95%, likely through a process involving flap excision. On the 3′ end, bases 5–10 nt from the 3′ end are lost about 1/3 of the time. These results indicate that oligos can be used to create multiple simultaneous changes to the yeast genome, even in the presence of MMR.
Multi-drug risk reduction strategy safe in peripheral artery disease
Lyford Joanna,Garg R,Elam MB,Crouse JR
Current Controlled Trials in Cardiovascular Medicine , 2000, DOI: 10.1186/cvm-2001-72058
In Vivo Bypass of 8-oxodG
Gina P. Rodriguez,Joseph B. Song,Gray F. Crouse
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003682
Abstract: 8-oxoG is one of the most common and mutagenic DNA base lesions caused by oxidative damage. However, it has not been possible to study the replication of a known 8-oxoG base in vivo in order to determine the accuracy of its replication, the influence of various components on that accuracy, and the extent to which an 8-oxoG might present a barrier to replication. We have been able to place a single 8-oxoG into the Saccharomyces cerevisiae chromosome in a defined location using single-strand oligonucleotide transformation and to study its replication in a fully normal chromosome context. During replication, 8-oxoG is recognized as a lesion and triggers a switch to translesion synthesis by Pol η, which replicates 8-oxoG with an accuracy (insertion of a C opposite the 8-oxoG) of approximately 94%. In the absence of Pol η, template switching to the newly synthesized sister chromatid is observed at least one third of the time; replication of the 8-oxoG in the absence of Pol η is less than 40% accurate. The mismatch repair (MMR) system plays an important role in 8-oxoG replication. Template switching is blocked by MMR and replication accuracy even in the absence of Pol η is approximately 95% when MMR is active. These findings indicate that in light of the overlapping mechanisms by which errors in 8-oxoG replication can be avoided in the cell, the mutagenic threat of 8-oxoG is due more to its abundance than the effect of a single lesion. In addition, the methods used here should be applicable to the study of any lesion that can be stably incorporated into synthetic oligonucleotides.
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