bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of T-Cell Receptor Repertoire Breadth to the Dominance of Epitope-Specific CD8+T-Lymphocyte Responses
Authors: Manuel Edwin R. , Charini William A. , Sen Pritha , Peyerl Fred W. , Kuroda Marcelo J. , Schmitz Jörn E. , Autissier Patrick , Sheeter Dennis A. , Torbett Bruce E. , Letvin Norman L. 
Published: November 2006

ABSTRACTDominant epitope-specific CD8+T-lymphocyte responses play a central role in controlling viral spread. We explored the basis for the development of this focused immune response in simian immunodeficiency virus (SIV)- and simian-human immunodeficiency virus (SHIV)-infected rhesus monkeys through the use of two dominant (p11C and p199RY) and two subdominant (p68A and p56A) epitopes. Using real-time PCR to quantitate T-cell receptor (TCR) variable region beta (Vβ) family usage, we show that CD8+T-lymphocyte populations specific for dominant epitopes are characterized by a diverse Vβ repertoire, whereas those specific for subdominant epitopes employ a dramatically more focused Vβ repertoire. We also demonstrate that dominant epitope-specific CD8+T lymphocytes employ TCRs with multiple CDR3 lengths, whereas subdominant epitope-specific cells employ TCRs with a more restricted CDR3 length. Thus, the relative dominance of an epitope-specific CD8+T-lymphocyte response reflects the clonal diversity of that response. These findings suggest that the limited clonal repertoire of subdominant epitope-specific CD8+T-lymphocyte populations may limit the ability of these epitope-specific T-lymphocyte populations to expand and therefore limit the ability of these cell populations to contribute to the control of viral replication.
Retrotransposon Suicide: Formation of Ty1 Circles and Autointegration via a Central DNA Flap
Authors: Garfinkel David J. , Stefanisko Karen M. , Nyswaner Katherine M. , Moore Sharon P. , Oh Jangsuk , Hughes Stephen H. 
Published: November 2006

ABSTRACT

Despite their evolutionary distance, the
Saccharomyces cerevisiae
retrotransposon Ty1 and retroviruses use similar strategies for replication, integration, and interactions with their hosts. Here we examine the formation of circular Ty1 DNA, which is comparable to the dead-end circular products that arise during retroviral infection. Appreciable levels of circular Ty1 DNA are present with one-long terminal repeat (LTR) circles and deleted circles comprising major classes, while two-LTR circles are enriched when integration is defective. One-LTR circles persist when homologous recombination pathways are blocked by mutation, suggesting that they result from reverse transcription. Ty1 autointegration events readily occur, and many are coincident with and dependent upon DNA flap structures that result from DNA synthesis initiated at the central polypurine tract. These results suggest that Ty1-specific mechanisms minimize copy number and raise the possibility that special DNA structures are a targeting determinant.
Increased Frequency of Circulating CCR5+CD4+T Cells in Human Immunodeficiency Virus Type 2 Infection
Authors: Soares Rui , Foxall Russell , Albuquerque Adriana , Cortesão Catarina , Garcia Miguel , Victorino Rui M. M. , Sousa Ana E. 
Published: November 2006

ABSTRACTCCR5 expression determines susceptibility to infection, cell tropism, and the rate of human immunodeficiency virus type 1 (HIV-1) disease progression. CCR5 is also considered the major HIV-2 coreceptor in vivo, in spite of broad coreceptor use in vitro. Here we report a significantly increased proportion of memory-effector CD4 T cells expressing CCR5 in HIV-2-infected patients correlating with CD4 depletion. Moreover, HIV-2 proviral DNA was essentially restricted to memory-effector CD4, suggesting that this is the main target for HIV-2. Similar levels of proviral DNA were found in the two infection categories. Thus, the reduced viremia and slow rate of CD4 decline that characterize HIV-2 infection seem to be unrelated to coreceptor availability.
The Betaretrovirus Mason-Pfizer Monkey Virus Selectively Excludes Simian APOBEC3G from Virion Particles
Authors: Doehle Brian P. , Bogerd Hal P. , Wiegand Heather L. , Jouvenet Nolwenn , Bieniasz Paul D. , Hunter Eric , Cullen Bryan R. 
Published: November 2006

ABSTRACT
The APOBEC3 protein family can constitute a potent barrier to the successful infection of mammalian species by retroviruses. Therefore, any retrovirus that has evolved the ability to replicate in a given animal must have developed mechanisms that allow it to avoid or inhibit the APOBEC3 proteins expressed in that animal. Here, we demonstrate that Mason-Pfizer monkey virus (MPMV) is resistant to inhibition by the APOBEC3G protein expressed in its normal host, the rhesus macaque, but highly susceptible to inhibition by murine APOBEC3 (mA3). MPMV virion particles fail to package rhesus APOBEC3G (rA3G), and MPMV Gag binds rA3G poorly in coexpressing cells. In contrast, MPMV virions package mA3 efficiently and MPMV Gag-mA3 complexes are readily detected. Moreover, mA3, but not rA3G, partially colocalizes with MPMV Gag in the cytoplasm of coexpressing cells. Previously, we have demonstrated that murine leukemia virus also escapes inhibition by APOBEC3 proteins by avoiding virion incorporation of its cognate APOBEC3 protein, mA3, yet is inhibited by primate APOBEC3G proteins, which it packages effectively (B. P. Doehle, A. Schäfer, H. L. Wiegand, H. P. Bogerd, and B. R. Cullen, J. Virol. 79:8201-8207, 2005). The finding that two essentially unrelated beta- and gammaretroviruses use similar mechanisms to escape inhibition by the APOBEC3 proteins found in their normal host species suggests that the selective exclusion of APOBEC3 proteins from virion particles may be a general mechanism used by simple mammalian retroviruses.
Proviral Progeny of Heterodimeric Virions Reveal a High Crossover Rate for Human Immunodeficiency Virus Type 2
Authors: Mukherjee Sayandip , Lee Hui-Ling Rose , Ron Yacov , Dougherty Joseph P. 
Published: November 2006

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1), the causative agent of AIDS in humans, exhibits a very high rate of recombination. Bearing in mind the significant epidemiological and clinical contrast between HIV-2 and HIV-1 as well as the critical role that recombination plays in viral evolution, we examined the nature of HIV-2 recombination. Towards this end, a strategy was devised to measure the rate of crossover of HIV-2 by evaluating recombinant progeny produced exclusively by heterodimeric virions. The results showed that HIV-2 exhibits a crossover rate similar to that of HIV-1 and murine leukemia virus, indicating that the extremely high rate of crossover is a common retroviral feature.
Linker Insertion Mutations in the Herpes Simplex Virus Type 1 UL28 Gene: Effects on UL28 Interaction with UL15 and UL33 and Identification of a Second-Site Mutation in the UL15 Gene That Suppresses a Lethal UL28 Mutation
Authors: Jacobson Jennie G. , Yang Kui , Baines Joel D. , Homa Fred L. 
Published: November 2006

ABSTRACT
The UL28 protein of herpes simplex virus type 1 (HSV-1) is one of seven viral proteins required for the cleavage and packaging of viral DNA. Previous results indicated that UL28 interacts with UL15 and UL33 to form a protein complex (terminase) that is presumed to cleave concatemeric DNA into genome lengths. In order to define the functional domains of UL28 that are important for DNA cleavage/packaging, we constructed a series of HSV-1 mutants with linker insertion and nonsense mutations in UL28. Insertions that blocked DNA cleavage and packaging were found to be located in two regions of UL28: the first between amino acids 200 to 400 and the second between amino acids 600 to 740. Insertions located in the N terminus or in a region located between amino acids 400 and 600 did not affect virus replication. Insertions in the carboxyl terminus of the UL28 protein were found to interfere with the interaction of UL28 with UL33. In contrast, all of the UL28 insertion mutants were found to interact with UL15 but the interaction was reduced with mutants that failed to react with UL33. Together, these observations were consistent with previous conclusions that UL15 and UL33 interact directly with UL28 but interact only indirectly with each other. Revertant viruses that formed plaques on Vero cells were detected for one of the lethal UL28 insertion mutants. DNA sequence analysis, in combination with genetic complementation assays, demonstrated that a second-site mutation in the UL15 gene restored the ability of the revertant to cleave and package viral DNA. The isolation of an intergenic suppressor mutant provides direct genetic evidence of an association between the UL28 and UL15 proteins and demonstrates that this association is essential for DNA cleavage and packaging.
Human Papillomavirus Type 5 E6 Oncoprotein Represses the Transforming Growth Factor β Signaling Pathway by Binding to SMAD3
Authors: Mendoza Jose-Andres , Jacob Yves , Cassonnet Patricia , Favre Michel 
Published: November 2006

ABSTRACT
Mechanisms of cellular transformation associated with human papillomavirus type 5 (HPV5), which is responsible for skin carcinomas in epidermodysplasia verruciformis (EV) patients, are poorly understood. Using a yeast two-hybrid screening and molecular and cellular biology experiments, we found that HPV5 oncoprotein E6 interacts with SMAD3, a key component in the transforming growth factor β1 (TGF-β1) signaling pathway. HPV5 E6 inhibits SMAD3 transactivation by destabilizing the SMAD3/SMAD4 complex and inducing the degradation of both proteins. Interestingly, the E6 protein of nononcogenic EV HPV9 failed to interact with SMAD3, suggesting that downregulation of the TGF-β1 signaling pathway could be a determinant in HPV5 skin carcinogenesis.
High-k Gate Stack Engineering and Low Frequency Noise Performance
Authors: Luna-Sánchez Rosa María , González-Martínez Ignacio 
Published: November 2006

Gate stack engineering for deep submicron CMOS has been extensively studied, so that high-k dielectrics in combination with metal gate or FUSI electrodes are implemented in research lines. Much effort concentrated on the optimization of gate stacks from a viewpoint of dielectric properties and reliability. Less information is available on the low frequency noise performance of these gate stacks. This review demonstrates the necessity of gate stack engineering for achieving a low 1/f noise performance.	The impact of processing parameters, such as thickness of the interfacial layer and the high-k oxide, bulk properties of the high-k layer, post deposition anneals, choice of gate electrode material will be addressed. Such a systematic study forms the basis for noise modeling as for these gate-dielectrics the standard noise models are no longer applicable. The impact on the noise of strain engineering to boost up the carrier mobility is also briefly discussed.
300 mm SOI for High Volume Manufacturing
Authors: Pfeiffer Gerd , Haag M. , Schmidt M. , Krause R. , Tsai P. , Lee J.D. 
Published: November 2006

300 mm SOI for leading edge CMOS applications has been moving into high volume manufacturing recently but little information on the quality of these wafers is available. This paper reviews key characteristics of 300 mm SOI and how they compare to the status from several years ago.	For physical characteristics, Si layer thickness and uniformity, surface quality and defects, flatness, surface roughness, metal contamination and slip are surveyed. Electron mobility, buried oxide charge and interface state density data obtained from pseudo MOSFET measurements are employed to monitor the electrical characteristics of the SOI structure.
Analysis of Nanoscale Stress in Strained Silicon Materials and Microelectronics Devices by Energy-Filtered Convergent Beam Electron Diffraction
Authors: Zhang Peng , Istratov Andrei , He Haifeng , Ager Joel , Nelson Chris , Stach Eric , Mardinly John , Kisielowski Christian , Weber Eicke , Spence John 
Published: November 2006

The convergent beam electron diffraction (CBED) technique of transmission electron microscopy (TEM) has excellent capabilities for strain detection at high spatial resolution. Here we report strain measurements in a bulk s-Si/SiGe/Si wafer and in a strained 35nm PMOS device in which SiGe acts as the source and drain. CBED measurements of the composition of the relaxed SiGe buffer are in quantitative agreement with Raman spectroscopy. For the PMOS device, CBED measured a uniaxial compressive stress of 1.12GPa in the channel.	However, it was found that even in the cross-sectional TEM samples with thicknesses greater than 300nm, the intrinsic surface strain relaxation was often so severe that no recognizable high-order Laue zone lines in the CBED patterns could be collected. The amorphorization of both free surfaces of the TEM sample to a range of about 80nm is proposed to minimize the impact of surface strain relaxation for future study.
XPS, Static SIMS and NEXAFS Spectroscopic Investigation of Thiol Adsorption on Metals and Metal Sulfides
Authors: Buckley Alan N. , Goh Siew Wei , Lamb Robert , Fan Liang-Jen , Yang Yaw-Wen 
Published: November 2006

Examples are presented of the complementary nature of conventional XPS, synchrotron XPS, ToF-SIMS and NEXAFS spectroscopy when applied to the adsorption of MBT on metals and metal sulfides. Conventional XPS could detect chemisorption via S 2p spectra, detect the onset of multilayer formation via the relevant metal Auger or core level photoelectron spectra, and determine metal thiolate stoichiometry from thick multilayers. Surface-optimised synchrotron XPS allowed precise chemisorbed MBT S 2p binding energies to be obtained. Angle-dependent N and C NEXAFS spectra revealed adsorbate orientation, even for an abraded but relatively smooth surface.	Cu L3-edge spectra detected some Cu(II) and hence Cu(MBT)2 in multilayers on chalcocite. Static SIMS data confirmed the interaction of both N and exocyclic S with surface metal atoms for silver metal and chalcocite.
Surface Products on Gold Leached in Ammoniacal Copper(II) Thiosulfate Solution
Authors: Watling Kym , Hope Gregory A. , Jeffrey Matthew I. , Woods R. 
Published: November 2006

Surface-enhanced Raman scattering (SERS) spectroscopy has been applied in situ to identify species formed during gold leaching in copper(II) ammoniacal thiosulfate media. Species containing copper and sulfur develop on the gold surface and the coverage of these species was determined electrochemically. Vibrational modes due to sulfur-sulfur stretching at 382 cm-1 and symmetric sulfur-oxygen stretching at 1017 cm-1 develop during leaching.	These modes diminish and are replaced by a single band at 255 cm-1, assigned to a M-S stretch, when rinsed and examined in water.	In typical leach solutions, sulfur and copper coverages showed a 2:1 atomic ratio after leaching for 16 h. Ex situ ATR- FTIR and XPS studies show that ammonia is adsorbed to a surface copper sulfide.
Evaluation of the Effects of Additives, Pulsing, and Temperature on Morphologies of Copper Electrodeposited from Halide Media
Authors: Free Michael , Rodchanarowan Aphichart , Phadke Nikit , Bhide Ravindra 
Published: November 2006

Most of world's copper reserves are in the form of the mineral chalcopyrite (CuFeS2).	Traditional copper recovery from chalcopyrite is made by size reduction, flotation, smelting, and electrochemical purification. Alternative metal extraction technology using halide media allows for elimination of the smelting process. The use of halides has the additional advantage of reducing cell voltage and current requirements relative to sulfate based systems that are used in connection with copper extraction from oxide, silicate, hydroxide, and some sulfide minerals. The elimination of smelting and the reduction in energy utilization make this an attractive alternative for copper recovery. However, the halide based systems are more likely to produce irregular electrodeposits that cannot be removed by traditional methods. Halide solutions also present additional challenges related to the corrosive nature of the solutions. This study identifies the effects of additives, pulsing, and temperature on copper electrodeposit topography as characterized by root- mean-squared roughness for deposits made from halide media.
Cathode Guides for Conventional Copper Electrorefining Reactors Employing Starter Sheet Cathodes
Authors: Guerra Eduard , Shepherd Jeffrey 
Published: November 2006

Though employed in a large fraction of copper electrorefining reactors, the use of copper starter sheet as cathodes has inherent problems of poor alignment and wrap-around currents at cathode edges.	As an alternative to the use of reusable mother blanks, the design of electrically insulating cathode guides, similar to those developed for retrofitting of a nickel electrowinning plant, is examined. A procedure is outlined for designing cathode guides involving specific geometric considerations for facilitating installation and removal of electrodes. The design process is complimented by modeling the performance of the guides in terms of their ability to limit cathode misalignment and warping by solving for the corresponding primary current distributions for 2-D cross sections of the copper electrorefining cells. The potential use of cathode guides to decrease the energy consumption and improve the space-time-yield of conventional copper electrorefining is also discussed.
Development of Inert Anode Materials for Electrowinning in Calcium Chloride Melts
Authors: McGregor Katherine , Frazer Eric , Urban Andrew , Pownceby Mark , Deutscher Rex 
Published: November 2006

The electroreduction of solid titanium dioxide in a calcium chloride melt is an attractive method for the production of titanium metal. Several groups have proposed versions of this route, but no commercial process yet exists. In laboratory studies, consumable carbon anodes are used, and these can give rise to a number of cell design and operational issues. The replacement of the carbon anode with an inert anode offers numerous benefits that include: elimination of carbon dioxide emissions; more efficient cell operation and reduced electrode costs.	We have evaluated a wide range of candidate inert anode materials, including metals, alloys and conductive ceramics. The studies examined the chemical stability of these materials in a calcium chloride-based melt, and also performance in laboratory-scale electrolysis tests. All metals and alloys tested were either dissolved in the melt and/or formed a thick, highly resistive crust.	A conductive ceramic, chromium titanate, was the best-performed candidate and gave an acceptable cell voltage during a 24 h electrolysis test. This work was undertaken as part of the CSIRO Light Metals Flagship.
Materials Issues for the Heterogeneous Integration of III-V Compounds
Authors: Goorsky Mark , Hayashi Sumiko L. , Noori Atif , Bruno David 
Published: November 2006

Materials integration can advance the performance of III-V semiconductor devices through the incorporation of wafer bonded template substrates. One example would be those with bulk high resistivity and with an appropriate lattice constant for large lattice parameter materials, and with compatible thermal expansion coefficients. The objective was to develop III-V based wafer bond templates for subsequent epitaxial growth of device structures using non-compliant layers. Issues of thermal-mismatch induced strain and stability during epitaxial growth were addressed.	A key component of this research is to quantify the formation of defects in wafer-bonded structures under different processing conditions.	In this study, InP and InAs layers are transferred to other III-V substrates using hydrogen ion exfoliation and wafer bonding.
High-Resolution Spectroscopic Measurements of InGaAs/GaAs Self-Assembled Quantum Dots
Authors: Silverman Kevin L. , Berry Joseph , Stevens Martin , Mirin Richard 
Published: November 2006

We report development of two absorption-based spectroscopic methods that have been adapted from atomic physics techniques to elucidate the basic physical properties of InGaAs/GaAs self-assembled quantum dots(SAQDs). Absorptive spectroscopic measurements allow the examination of the SAQDs optical transitions free from carrier relaxation effects. In addition, we employ these techniques to study SAQDs' optical transition with a level of spectral resolution not available using ultra-fast techniques.	The first of the two approaches we discuss is cavity ring-down spectroscopy (CRDS), which permits an absolute measurement of absorption.	We report on initial application of CRDS to SAQDs and present an assessment based on these measurements for single SAQD spectroscopy using this technique. The second method, spectral hole burning, is applied to SAQDs in a semiconductor ridge waveguide and permits the homogeneous linewidth of the SAQDs to be separated from the broad inhomogeneous spectrum.
Effect of Kinetics on the Morphology of Hydrogen Exfoliated Layers
Authors: Hayashi Sumiko L. , Sandhu Rajinder , Goorsky Mark 
Published: November 2006

The effect of different heat treatments during the exfoliation of a thin InP layer onto a GaAs substrate is investigated. Hydrogen implantation was carried out by implanting the InP with 5 x 1016 H2+/cm2 at 150 keV. Exfoliation occurred at either 150 {degree sign}C or 300 {degree sign}C. The extended annealing at lower temperature produced smoother surfaces, 2.8 nm, compared to the sample exfoliated at 300 {degree sign}C, 8.5 nm. This change in surface morphology exhibits a much larger impact than the effect of implantation energy (i.e. straggle) on the surface morphology.	The difference is attributed to the ability to trap hydrogen and form extended defects parallel to the surface at the lower temperature. Additionally, the exfoliation depth of the lower temperature specimen is slightly deeper than the specimen exfoliated at 300 {degree sign}C, indicating that the hydrogen diffuses towards the peak damage region at the higher temperatures.
Fuel Cell Catalyst Particle Size Growth Characterized by X-Ray Scattering Methods
Authors: Garzon F. H. , Davey John , Borup Rodney 
Published: November 2006

X-ray diffraction experiments coupled with whole profile pattern refinement and Warren Averbach data analysis methods were used to quantify Pt electrode crystallite growth in polymer membrane fuel cell cathode samples. Both X-ray data analysis methods produced similar results for average particle sizes.	The cycling of cathodes to cell potentials above 1 volt greatly increases the loss of Pt cathode surface area by Pt grain growth. The fuel cell anode catalysts exhibit little to no growth after potential cycling experiments. Changes in Pt to carbon peak integrated intensity ratios indicate carbon corrosion is occurring upon cycling to high potentials.
Screen-Printed Dense Yttria-Stabilized-Zirconia Electrolytes for Anode-Supported Solid Oxide Fuel Cells.
Authors: White Briggs M. , Grilli Maria Luisa , Traversa E. , Roncari Edoardo , Pittalis Francesco , Wachsman E. D. , Sanson Alessandra 
Published: November 2006

Further cost reductions are necessary for the commercialization of solid oxide fuel cells (SOFCs). The economically sensible methods of screen-printing and tape casting were used to fabricate green films that were subsequently sintered producing 5 cm x 5 cm planar Yittria- stabilized-Zirconia (YSZ)-based SOFCs.	An anode-interlayer was also included in the cell design that increased interfacial bonding between the electrolyte and anode.	The SOFCs were characterized using scanning electron microscopy and pressure drop measurements. The YSZ electrolytes were gas- tight and dense. These cells showed a maximum power density of 0.14 W/cm2 when tested using a methane-water vapor fuel source at 800{degree sign}C.