Initiation and evolution of phase separation in heteroepitaxial InAlAs films

We have investigated the initiation and evolution of phase separation in heteroepitaxial InAlAs films. In misfit-free InAlAs layers, cross-sectional scanning tunneling microscopy (XSTM) reveals the presence of isotropic nanometer-sized clusters. For lattice-mismatched InAlAs layers with 1.2% misfit, quasiperiodic contrast modulations perpendicular to the growth direction are apparent. Interestingly, these lateral modulations are apparently initiated within the first few bilayers of film growth, and both the amplitude and wavelength of the modulations increase with film thickness. The saturation value of the modulation wavelength determined from XSTM coincides with the lateral superlattice period determined from (002) x-ray reciprocal space maps, suggesting that the lateral modulation wavelength represents a periodic composition variation. Together, these results suggest that phase separation in the heteroepitaxial InAlAs thin-film system is a misfit-driven kinetic process initiated by random compositional nonuniformities, which later develop into coupled compositional and surface morphological variations. © 2002 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69359/2/APPLAB-80-18-3292-1.pd

Enterohemorrhagic Escherichia coli O157∶H7 Gene Expression Profiling in Response to Growth in the Presence of Host Epithelia

BACKGROUND: The pathogenesis of enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection is attributed to virulence factors encoded on multiple pathogenicity islands. Previous studies have shown that EHEC O157:H7 modulates host cell signal transduction cascades, independent of toxins and rearrangement of the cytoskeleton. However, the virulence factors and mechanisms responsible for EHEC-mediated subversion of signal transduction remain to be determined. Therefore, the purpose of this study was to first identify differentially regulated genes in response to EHEC O157:H7 grown in the presence of epithelial cells, compared to growth in the absence of epithelial cells (that is, growth in minimal essential tissue culture medium alone, minimal essential tissue culture medium in the presence of 5% CO(2), and Penassay broth alone) and, second, to identify EHEC virulence factors responsible for pathogen modulation of host cell signal transduction. METHODOLOGY/PRINCIPAL FINDINGS: Overnight cultures of EHEC O157:H7 were incubated for 6 hr at 37 degrees C in the presence or absence of confluent epithelial (HEp-2) cells. Total RNA was then extracted and used for microarray analyses (Affymetrix E. coli Genome 2.0 gene chips). Relative to bacteria grown in each of the other conditions, EHEC O157:H7 cultured in the presence of cultured epithelial cells displayed a distinct gene-expression profile. A 2.0-fold increase in the expression of 71 genes and a 2.0-fold decrease in expression of 60 other genes were identified in EHEC O157:H7 grown in the presence of epithelial cells, compared to bacteria grown in media alone. CONCLUSION/SIGNIFICANCE: Microarray analyses and gene deletion identified a protease on O-island 50, gene Z1787, as a potential virulence factor responsible for mediating EHEC inhibition of the interferon (IFN)-gamma-Jak1,2-STAT-1 signal transduction cascade. Up-regulated genes provide novel targets for use in developing strategies to interrupt the infectious process

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

<p>Abstract</p> <p>Background</p> <p>Adherent and invasive <it>Escherichia coli </it>(AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated <it>E. coli </it>pathotype.</p> <p>Results</p> <p>We sequenced the complete genome of <it>E. coli </it>NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic <it>E. coli </it>causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal <it>E. coli </it>allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype.</p> <p>Conclusions</p> <p>Up to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease.</p

Linear and Second-order Optical Response of the III-V Mono-layer Superlattices

We report the first fully self-consistent calculations of the nonlinear optical properties of superlattices. The materials investigated are mono-layer superlattices with GaP grown on the the top of InP, AlP and GaAs (110) substrates. We use the full-potential linearized augmented plane wave method within the generalized gradient approximation to obtain the frequency dependent dielectric tensor and the second-harmonic-generation susceptibility. The effect of lattice relaxations on the linear optical properties are studied. Our calculations show that the major anisotropy in the optical properties is the result of strain in GaP. This anisotropy is maximum for the superlattice with maximum lattice mismatch between the constituent materials. In order to differentiate the superlattice features from the bulk-like transitions an improvement over the existing effective medium model is proposed. The superlattice features are found to be more pronounced for the second-order than the linear optical response indicating the need for full supercell calculations in determining the correct second-order response.Comment: 9 pages, 4 figures, submitted to Phy. Rev.

Design and operation of the Chicago air shower array

The Chicago Air Shower Array (CASA) is a large‐area surface scintillator array designed to study PeV sources of cosmic rays. The complete detector will consist of 1089 detector stations, distributed on a square 15 m grid. We have operated an array of 49 stations for much of the 1989 calendar year, an array of 529 stations for much of 1990, and the balance of the 1089 stations will be operating in early 1991. This surface array, together with the University of Michigan underground muon detectors (MIA), and the University of Utah atmospheric Čerenkov telescopes and Fly’s Eye air fluorescence detector, constitute a uniquely powerful instrument, dubbed the Utah Michigan Chicago (UMC) experiment, for the study of PeV sources. We report here the performance and current status of these detectors.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87431/2/111_1.pd

Preliminary results from the Chicago air shower array and the Michigan muon array

The Chicago Air Shower Array (CASA) is a large area surface array designed to detect extensive air showers (EAS) produced by primaries with energy ∼100 TeV. It operates in coincidence with the underground Michigan Muon Array (MIA). Preliminary results are presented from a search for steady emission and daily emission from three astrophysical sources: Cygnus X‐3, Hercules X‐1, and the Crab nebula and pulsar. There is no evidence for a significant signal from any of these sources in the 1989 data.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87432/2/122_1.pd

A search for astrophysical point sources of 100 TeV gamma rays by the UMC collaboration

The CASA‐MIA experiment is a very large extensive air shower detector with good angular resolution. This instrument has been used to search the entire visible sky for astrophysical point sources of 100 TeV gamma rays. Approximately 90% of the isotropic charged cosmic ray background is rejected by measuring the muon content of the showers. Stringent limits are placed on the possible flux of 100 TeV sources across a large part of the Northern sky.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87711/2/1203_1.pd

Impact of national guidelines on use of BRCA1/2 germline testing, risk management advice given to women with pathogenic BRCA1/2 variants and uptake of advice

Background: This nationwide study assessed the impact of nationally agreed cancer genetics guidelines on use of BRCA1/2 germline testing, risk management advice given by health professionals to women with pathogenic BRCA1/2 variants and uptake of such advice by patients. Methods: Clinic files of 883 women who had initial proband screens for BRCA1/2 pathogenic variants at 12 familial cancer clinics between July 2008–July 2009 (i.e. before guideline release), July 2010–July 2011 and July 2012–July 2013 (both after guideline release) were audited to determine reason given for genetic testing. Separately, the clinic files of 599 female carriers without a personal history of breast/ovarian cancer who underwent BRCA1/2 predictive genetic testing and received their results pre- and post-guideline were audited to ascertain the risk management advice given by health professionals. Carriers included in this audit were invited to participate in a telephone interview to assess uptake of advice, and 329 agreed to participate. Results: There were no significant changes in the percentages of tested patients meeting at least one published indication for genetic testing - 79, 77 and 78% of files met criteria before guideline, and two-, and four-years post-guideline, respectively (χ = 0.25, p = 0.88). Rates of documentation of post-test risk management advice as per guidelines increased significantly from pre- to post-guideline for 6/9 risk management strategies. The strategies with the highest compliance amongst carriers or awareness post-release of guidelines were annual magnetic resonance imaging plus mammography in women 30–50 years (97%) and annual mammography in women > 50 years (92%). Of women aged over 40 years, 41% had a risk-reducing bilateral mastectomy. Amongst women aged > 40 years, 75% had a risk-reducing salpingo-oophorectomy. Amongst women who had not had a risk-reducing bilateral mastectomy, only 6% took risk-reducing medication. Fear of side-effects was cited as the main reasons for not taking these medicines by 73% of women. Conclusions: Guidelines did not change the percentages of tested patients meeting genetic testing criteria but improved documentation of risk management advice by health professionals. Effective approaches to enhance compliance with guidelines are needed to improve risk management and quality of care