bluuebunny/crossref_metadata_2025 huggingface dataset:
Ferroelectric nanostructures
Authors: Vrejoiu Ionela , Alexe Marin , Hesse Dietrich , Gösele Ulrich
Published: February 2009

Device miniaturization poses not only technological and manufacturing challenges, it also requires the understanding of the phenomena occurring at nanoscale in condensed matter and at the involved interfaces. Herein, the authors present a summary of their results in fabricating and understanding the properties of ultrathin films and nanometer-size dots of ferroelectric perovskite and layered-perovskite oxides.
Leakage current effects on C-V plots of high-k metal-oxide-semiconductor capacitors
Authors: Lu Y. , Hall S. , Tan L. Z. , Mitrovic I. Z. , Davey W. M. , Raeissi B. , Engström O. , Cherkaoui K. , Monaghan S. , Hurley P. K. , Gottlob H. D. B. , Lemme M. C.
Published: February 2009

With the employment of ultrathin, high dielectric constant gate materials in advanced semiconductor technology, the conventional capacitance-voltage measurement technique exhibits a series of anomalies. In particular, a nonsaturating increase in the accumulation capacitance with reducing measurement frequency is frequently observed, which has not been adequately explained to our knowledge. In this article, the authors provide an explanation for this anomaly and hence set a criterion for the lower bound on measurement frequency. We then present a model which allows the easy extraction of the required parameters and apply it to an experimental set of data.
Deprotection blur in extreme ultraviolet photoresists: Influence of base loading and post-exposure bake temperature
Authors: Anderson Christopher N. , Naulleau Patrick P.
Published: February 2009

The deprotection blur of Rohm and Haas XP 5435, XP 5271, and XP 5496 extreme ultraviolet photoresists has been determined as their base weight percent is varied. The authors have also determined the deprotection blur of TOK EUVR P1123 photoresist as the post-exposure bake temperature is varied from 80to120°C. In Rohm and Haas XP 5435 and XP 5271 resists seven times and three times (respective) increases in base weight percent reduce the size of successfully patterned 1:1 line-space features by 16 and 8nm with corresponding reductions in deprotection blur of 7 and 4nm. In XP 5496 a seven times increase in base weight percent reduces the size of successfully patterned 1:1 line-space features from 48to38nm without changing deprotection blur. In TOK EUVR P1123 resist, a reduction in post-exposure bake temperature from 100to80°C reduces deprotection blur from 21to10nm and reduces patterned line-edge roughness from 4.8to4.1nm.
Improved characterization of Fourier transform infrared spectra analysis for post-etched ultra-low-κ SiOCH dielectric using chemometric methods
Authors: Oszinda Thomas , Beyer Volkhard , Schaller Matthias , Fischer Daniel , Bartsch Christin , Schulz Stefan E.
Published: February 2009

The structural changes due to post-ash and post-ash treatments on chemical vapor deposited ultra-low-κ (ULK) SiOCH dielectric films were studied by Auger electron spectroscopy (AES) and Fourier transform infrared spectroscopy (FTIR). Changes in the ULK layer with respect to the carbon content were analyzed. For the application of different plasma gases for photoresist removal and further post-clean and anneal treatments first a reduction of carbon was observed. Using AES it was found that the carbon was removed up to ∼140nm. Accompanied with the carbon loss a modification of chemical bonds was observed with FTIR, whereas the analysis of FTIR spectra was improved by means of chemometric methods. A principle component analysis was applied for qualitative analysis, which focuses on changes of infrared vibration peaks. This provides a fast assessment of chemical bond modifications. A partial least square regression was used to correlate the carbon loss with the infrared spectra. It is shown that the regression method allows a prediction of the carbon loss. For both methods the applicability and their limitations with respect to FTIR spectra are discussed.
Some peculiarities of resist-profile simulation for positive-tone chemically amplified resists in electron-beam lithography
Authors: Vutova K. , Koleva E. , Mladenov G. , Kostic I.
Published: February 2009

In the present work, we numerically modeled the processes of exposure and development of the CAMP6 chemically amplified resist during electron-beam lithography. The radial distributions of the absorbed electron energy in the resist for a zero-width δ-function 30keV electron beam are obtained by Monte Carlo simulation. These distributions (discrete data) are approximated by an analytical function (sum of double Gaussian and an exponential function). The values of the parameters of the function are calculated using an original Monte Carlo technique, and their dependencies on the resist thickness (d=100, 200, 600, 1000, and 1500nm) at two resist depths are presented. Using these parameters’ values, we performed a computer simulation of the process of developing the resist taking into account its peculiarities due to the complicated mechanism of resist removal from soluble resist areas. We obtained profiles at various development times of a single 100nm line.
Absorber stack with transparent conductive oxide layer for extreme ultraviolet lithography
Authors: Kang Hee Young , Hwangbo Chang Kwon
Published: February 2009

In this study, the authors propose transparent conductive oxide layer as a new absorber for extreme ultraviolet lithography mask. The optical constant of indium tin oxide (ITO) at 13.5nm is calculated and the extinction coefficient of ITO is found to be 1.55 times higher than that of TaN, resulting in higher absorption in the absorbing stack. Using an ITO layer in the absorber stack enables to design the attenuated phase-shift masks with smaller height difference of only 32.1nm than the conventional TaN absorber stack of about 80nm between high reflecting and absorbing stacks in extreme ultraviolet lithography, indicating that the geometric shadow effect can be significantly reduced.
Fabrication of nanoscale bioarrays for the study of cytoskeletal protein binding interactions using nanoimprint lithography
Authors: Schvartzman M. , Nguyen K. , Palma M. , Abramson J. , Sable J. , Hone J. , Sheetz M. P. , Wind S. J.
Published: February 2009

The authors describe a high-throughput patterning process used to create arrays of molecular-scale features for the study of cytoskeletal protein binding interactions. The process uses a shadow-evaporated metal mask to facilitate lift-off of features defined by nanoimprint lithography. This simple and robust approach alleviates difficulties in pattern transfer of ultrasmall features and results in arrays of highly ordered sub-10 nm features which are then functionalized with extracellular matrix proteins. Application of these arrays is demonstrated in cell spreading assays.
Hafnium oxide thin films: Effect of growth parameters on oxygen and hafnium vacancies
Authors: Hildebrandt E. , Kurian J. , Zimmermann J. , Fleissner A. , von Seggern H. , Alff L.
Published: February 2009

Thin films of hafnium oxide were grown by reactive molecular beam epitaxy. The growth parameters, substrate temperature, and oxidation conditions were varied in a wide range in order to investigate their influence on the thin film characteristics. The oxidation conditions during growth were decisive to hafnium oxide film orientation on c-cut sapphire substrates; it was possible to grow single oriented (00l) or (−111) oriented hafnium oxide films depending upon the oxidation conditions. The authors could successfully grow hafnium oxide thin films with oxygen or hafnium vacancies, depending on the oxidation conditions during growth, evident from optical band gap measurements. All the hafnium oxide thin films investigated in this study, irrespective of oxygen/hafnium vacancies, failed to show any ferromagnetic characteristics.
Frequency dispersion and dielectric relaxation of La2Hf2O7
Authors: Zhao C. Z. , Taylor S. , Werner M. , Chalker P. R. , Gaskell J. M. , Jones A. C.
Published: February 2009

Thin films of La2Hf2O7 have been deposited by liquid injection atomic layer deposition and post-deposition annealed at 900°C. The dielectric frequency dispersion was more serious for thinner films which is attributed to the effect of a lossy interfacial layer between the La2Hf2O7 dielectric and silicon substrate. The effect of the interfacial layer was modeled based on a dual-frequency measurement technique. The dielectric relaxation of the La2Hf2O7 thin films was modelled using both the Curie-von Schweidler and Havriliak-Negami relationships. Post deposition annealing in nitrogen at 900°C for 15min improved dielectric relaxation and reduced the dielectric loss.
Study of interface degradation of Hf-silicate gate dielectrics during thermal nitridation process
Authors: Son S. Y. , Jang J. H. , Kumar P. , Singh R. K. , Yuh J. H. , Cho H. , Kang C. J.
Published: February 2009

An evaluation of the effect of nitridation temperature on interface layer (IL) quality of Hf-silicate gate dielectric prepared by the atomic layer deposition method has been reported. An increase in IL density and IL roughness was observed by x-ray reflectivity as the nitridation temperature was increased. X-ray photoelectron spectroscopy showed preferential interface reaction at the dielectric-Si interface at higher temperatures. The progressive increase in IL roughness finally led to degradation of the breakdown voltage, a shift in flat band voltage (∼0.54V), and deterioration of electron channel mobility by ∼20% in samples nitrided at 850°C.
Structure and defects of epitaxial Si(111) layers on Y2O3(111)/Si(111) support systems
Authors: Borschel C. , Ronning C. , Hofsäss H. , Giussani A. , Zaumseil P. , Wenger Ch. , Storck P. , Schroeder T.
Published: February 2009

Single crystalline epitaxial Si(111)/Y2O3(111)/Si(111) heterostructures were grown by molecular beam epitaxy and the morphology, structure, and defects were characterized in detail. The growth of a closed and smooth layer system is demonstrated by means of reflection high energy electron diffraction measurements. X-ray reflectometry and high resolution Rutherford backscattering (RBS) experiments show low surface and interface roughnesses. Channeling RBS as well as x-ray diffraction pole figure studies demonstrate the type A/B/A epitaxy relationship of the Si(111)/Y2O3(111)/Si(111) heterostructure and reveal the existence of defects in the epitaxial Si(111) layer. These defects are studied in detail with high resolution transmission electron microscopy, disclosing microtwin formation and type B Si grains as the major defects.
Ti
0.94
Fe
0.06
O
2
∕
Ti
0.94
Mn
0.06
O
2
superlattice films deposited on atomic-scale flattened sapphire substrates for dilute magnetic semiconductor applications
Authors: Seong Nak-Jin , Jiang Juan , Yoon Soon-Gil
Published: February 2009

20 - nm -thick Ti0.94Fe0.06O2∕Ti0.94Mn0.06O2 (TFO/TMO) superlattice films, where each alternating layer is about 0.27nm thick, were prepared at 500°C by pulsed-laser deposition on (11¯02)-sapphire substrates with and without atomic flatness. The authors then investigated structural and ferromagnetic properties of these TFO/TMO superlattice films. The superlattice films deposited on atomically flattened sapphire substrates exhibit an excellent crystallinity, smoother surface morphology, and higher saturation magnetization and coercive field than the films deposited on sapphire substrates without atomic flatness. The superlattice films exhibit no segregated impurity phase and obey a three-dimensional spin wave model, indicating a ferromagnetic property.
Forbidden pitch improvement using modified illumination in lithography
Authors: Ling M. L. , Tay C. J. , Quan C. , Chua G. S. , Lin Q.
Published: February 2009

In lithography, forbidden pitch refers to pitch that suffers degradation in the process window due to the application of off-axis illumination (OAI). Destructive light field interference of diffracted light from a mask at forbidden pitch causes reduction in image contrast and depth of focus (DOF) and limits the pitch range to be patterned. In this paper, a modification to conventional OAI shape is proposed to minimize the effect of forbidden pitch. The modification is based on the interaction of illumination source with pattern density. The modified source employs double annular illumination. Simulation is carried out to investigate the effect of the modified source for one dimensional line and space pattern with a pitch varying from 130to500nm. Results shows that the maximum critical dimension fluctuation is around 3% compared to 13% in conventional annular illumination. Furthermore, the degradation in DOF is within 21% of DOF compared to 49% in conventional annular illumination.
Contact etch stop a-SixNy:H layer: A key factor for single polysilicon flash memory data retention
Authors: Beylier G. , Benoit D. , Mora P. , Bruyère S. , Ghibaudo G.
Published: February 2009

The silicon nitride (a-SixNy:H) contact etch stop layer strongly affects data retention performances in single polysilicon nonvolatile memories by acting on the initial charge loss phenomenon. Its improvement has required an analysis of influent plasma enhanced chemical vapor deposition process parameters through a design of experiment approach. The a-SixNy:H physico-electrical analysis points out that silicon rich compositions especially of its interfacial layer must be avoided to reduce a-SixNy:H charge amount and as a result to improve the data retention. Indeed, the a-SixNy:H being near the floating gate, its charges modulation could act as a parasitic memory screening charges stored in the floating gate by capacitive effects.
Low frequency noise analysis in HfO2∕SiO2 gate oxide fully depleted silicon on insulator transistors
Authors: Zafari L. , Jomaah J. , Ghibaudo G. , Faynot O.
Published: February 2009

In this article, low frequency noise in HfO2∕SiO2 metal-oxide-semiconductor devices with TiN metal gate on fully depleted silicon on insulator technology is analyzed. The drain current noise in linear regime is presented to determine the noise sources in such devices. The impact of different gate stack parameters such as interfacial oxide layer thickness, high-κ layer thickness, and the oxide deposit techniques on the noise level is studied.
Oral Live Vaccine Strain-Induced Protective Immunity against PulmonaryFrancisella tularensisChallenge Is Mediated by CD4+T Cells and Antibodies, Including Immunoglobulin A
Authors: Ray Heather J. , Cong Yu , Murthy Ashlesh K. , Selby Dale M. , Klose Karl E. , Barker Jeffrey R. , Guentzel M. Neal , Arulanandam Bernard P.
Published: February 2009

Francisella tularensisis an intracellular gram-negative bacterium and the etiological agent of pulmonary tularemia. Given the high degrees of infectivity in the host and of dissemination of bacteria following respiratory infection, immunization strategies that target mucosal surfaces are critical for the development of effective vaccines against this organism. In this study, we have characterized the efficacy of protective immunity against pneumonic tularemia following oral vaccination withF. tularensisLVS (live vaccine strain). Mice vaccinated orally with LVS displayed colocalization of LVS with intestinal M cells, with subsequent enhanced production of splenic antigen-specific gamma interferon and of systemic and mucosal antibodies, including immunoglobulin A (IgA). LVS-vaccinated BALB/c mice were highly protected against intranasal (i.n.) SCHU S4 challenge and exhibited significantly less bacterial replication in the lungs, liver, and spleen than mock-immunized animals. Depletion of CD4+T cells significantly abrogated the protective immunity, and mice deficient in B cells or IgA displayed partial protection against SCHU S4 challenge. These results suggest that oral vaccination with LVS induces protective immunity against i.n. challenge withF. tularensisSCHU S4 by a process mediated cooperatively by CD4+T cells and antibodies, including IgA.
Ertapenem Resistance among Extended-Spectrum-β-Lactamase-Producing
Klebsiella pneumoniae
Isolates
Authors: Leavitt Azita , Chmelnitsky Inna , Colodner Raul , Ofek Itzhak , Carmeli Yehuda , Navon-Venezia Shiri
Published: February 2009

Ertapenem resistance in
Klebsiella pneumoniae
is rare. We report on an ertapenem-nonsusceptible phenotype among 25 out of 663 (3.77%) extended-spectrum-β-lactamase (ESBL)-producing
K. pneumoniae
isolates in a multicenter Israeli study. These isolates originated from six different hospitals and were multiclonal, belonging to 12 different genetic clones. Repeat testing using Etest and agar dilution confirmed ertapenem nonsusceptibility in only 15/663 (2.3%) of the isolates. The molecular mechanisms of ertapenem resistance in seven single-clone resistant isolates was due to the presence of ESBL genes (CTX-M-2 in four isolates, CTX-M-10 and OXA-4 in one isolate, SHV-12 in one isolate, and SHV-28 in one isolate) combined with the absence of OMPK36. Seven of 10 isolates initially reported as ertapenem nonsusceptible and subsequently classified as susceptible showed an inoculum effect with ertapenem but not with imipenem or meropenem. Population analysis detected the presence of an ertapenem-resistant subpopulation at a frequency of 10
−6
. These rare resistant subpopulations carried multiple ESBL genes, including TEM-30, SHV-44, CTX-M-2, and CTX-M-10, and they lacked OMPK36. The clinical and diagnostic significance of the results should be further studied.
Evaluation of Phenotypic Tests for Detection of Metallo-β-Lactamase-Producing
Pseudomonas aeruginosa
Strains in China
Authors: Qu Ting-ting , Zhang Jun-li , Wang Jie , Tao Jing , Yu Yun-song , Chen Ya-gang , Zhou Jian-ying , Li Lan-juan
Published: February 2009

A total of 264 nonduplicate strains of imipenem (IPM)-nonsusceptible
Pseudomonas aeruginosa
were isolated from hospitals in 16 different regions throughout China. These 264 IPM-nonsusceptible clinical isolates of
P. aeruginosa
were examined by PCR, a metallo-β-lactamase (MBL) Etest, a double-disk synergy test (DDST), and a test using combined IPM disks supplemented with various amounts of EDTA. A total of 24 strains positive for MBLs were confirmed by PCR and DNA sequence analysis: 10 strains positive for the
bla
VIM-2
gene, 13 strains positive for the
bla
IMP-9
gene, and 1 strain positive for the
bla
IMP-1
gene. Real-time reverse transcriptase PCR (RT-PCR) was used to verify whether the isolates harboring MBL genes produced the enzyme and was considered the standard for evaluation of the methodology in this study. Of these 24 MBL-positive stains, 21 were confirmed as MBL-producing strains by real time RT-PCR for MBL expression and the other 3 had no expression of MBLs. The sensitivities, specificities, and positive and negative predictive values for the MBL Etest, the DDST, and the combined disk (CD) assay were evaluated. The best method for screening for MBL production in
P. aeruginosa
strains from China was the CD assay (IMP-EDTA) using 750 μg of EDTA/disk with a breakpoint of ≥6 mm. In the CD assay (IPM-EDTA) with 290 μg and 750 μg EDTA, the zone diameter increases for VIM-2-producing
P. aeruginosa
isolates were greater than those for IMP-9-producing
P. aeruginosa
isolates (
P
= 0.00).
Identification of
Staphylococcus
Species Directly from Positive Blood Culture Broth by Use of Molecular and Conventional Methods
Authors: Mehta Maitry S. , Paule Suzanne M. , Thomson Richard B. , Kaul Karen L. , Peterson Lance R.
Published: February 2009

We compared two real-time PCR assays (both by the use of melting curve analysis) for their ability to identify
Staphylococcus
species directly from 200 positive blood culture bottles. The PCR assays correctly identified 83% to 94% of the
Staphylococcus
isolates to species clusters. Molecular testing significantly outperformed commercially available latex tests (sensitivity for both latex tests, <15%) when it was used directly with broth from signal-positive blood cultures.
Attenuated Foot-and-Mouth Disease Virus RNA Carrying a Deletion in the 3′ Noncoding Region Can Elicit Immunity in Swine
Authors: Rodríguez Pulido Miguel , Sobrino Francisco , Borrego Belén , Sáiz Margarita
Published: February 2009

We constructed foot-and-mouth disease virus (FMDV) mutants bearing independent deletions of the two stem-loop structures predicted in the 3′ noncoding region of viral RNA, SL1 and SL2, respectively. Deletion of SL2 was lethal for viral infectivity in cultured cells, while deletion of SL1 resulted in viruses with slower growth kinetics and downregulated replication associated with impaired negative-strand RNA synthesis. With the aim of exploring the potential of an RNA-based vaccine against foot-and-mouth disease using attenuated viral genomes, full-length chimeric O1K/C-S8 RNAs were first inoculated into pigs. Our results show that FMDV viral transcripts could generate infectious virus and induce disease in swine. In contrast, RNAs carrying the ΔSL1 mutation on an FMDV O1K genome were innocuous for pigs but elicited a specific immune response including both humoral and cellular responses. A single inoculation with 500 μg of RNA was able to induce a neutralizing antibody response. This response could be further boosted by a second RNA injection. The presence of the ΔSL1 mutation was confirmed in viruses isolated from serum samples of RNA-inoculated pigs or after transfection and five passages in cell culture. These findings suggest that deletion of SL1 might contribute to FMDV attenuation in swine and support the potential of RNA technology for the design of new FMDV vaccines.
Human Immunodeficiency Virus Integrates Directly into Naïve Resting CD4+T Cells but Enters Naïve Cells Less Efficiently than Memory Cells
Authors: Dai Jihong , Agosto Luis M. , Baytop Clifford , Yu Jianqing J. , Pace Matthew J. , Liszewski Megan K. , O'Doherty Una
Published: February 2009

Resting CD4+T cells restrict human immunodeficiency virus (HIV) infection at or before reverse transcription, resulting in slower kinetics of reverse transcription. In a previous study, we showed that, despite this restriction at reverse transcription, HIV integration occurs in resting CD4+T cells, albeit with slower kinetics. In that study, the resting T cells were a mixture of memory and naïve cells. Here we asked whether the more quiescent naïve cell subset could be directly infected by HIV and, if so, whether the level of integration in naïve cells was comparable to that in memory cells. We found that HIV integrates in the naïve subset of resting CD4+T cells without prior activation of the cells. The level of integration (proviruses/cell) in naïve cells was lower than that in memory cells. This difference between naïve and memory cells was observed whether we inoculated the cells with R5 or X4 HIV and could not be explained solely by differences in coreceptor expression. The presence of endogenous dendritic cells did not change the number of proviruses/cell in memory or naïve cells, and deoxynucleoside pools were equally limiting. Our results instead indicate the existence of a novel restriction point in naïve T cells at viral fusion that results in reduced levels of fusion to naïve CD4+T cells. We conclude that HIV can integrate into both naïve and memory cells directly. Our data further support our hypothesis that integrated proviral infection of resting T cells can be established without T-cell activation.
Gamma Interferon-Induced Interferon Regulatory Factor 1-Dependent Antiviral Response Inhibits Vaccinia Virus Replication in Mouse but Not Human Fibroblasts
Authors: Trilling Mirko , Le Vu Thuy Khanh , Zimmermann Albert , Ludwig Holger , Pfeffer Klaus , Sutter Gerd , Smith Geoffrey L. , Hengel Hartmut
Published: February 2009

Vaccinia virus (VACV) replicates in mouse and human fibroblasts with comparable kinetics and efficiency, yielding similar titers of infectious progeny. Here we demonstrate that gamma interferon (IFN-γ) but not IFN-α or IFN-β pretreatment of mouse fibroblasts prior to VACV infection induces a long-lasting antiviral state blocking VACV replication. In contrast, high doses of IFN-γ failed to establish an antiviral state in human fibroblasts. In mouse fibroblasts, IFN-γ impeded the viral replication cycle at the level of late gene transcription and blocked the multiplication of VACV genomes. The IFN-γ-induced antiviral state invariably prevented the growth of different VACV strains but was not effective against the replication of ectromelia virus. The IFN-γ effect required intact IFN-γ receptor signaling prior to VACV infection through Janus kinase 2 (Jak2) and signal transducer and activator of transcription 1 (STAT1). The permissive state of IFN-γ-treated human cells was unrelated to the VACV-encoded IFN decoy receptors B8 and B18 and associated with a complete disruption of STAT1 homodimer formation and DNA binding. Unlike human fibroblasts, mouse cells responded with long-lasting STAT1 activation which was preserved after VACV infection. The deletion of the IFN regulatory factor 1 (IRF-1) gene from mouse cells rescued efficient VACV replication, demonstrating that IRF-1 target genes have a critical role in VACV control. These data have implications for the understanding of VACV pathogenesis and identify an incongruent IFN-γ response between the human host and the mouse model.
Identification of a Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Variant Resistant to Cold Inactivation
Authors: Kassa Aemro , Finzi Andrés , Pancera Marie , Courter Joel R. , Smith Amos B. , Sodroski Joseph
Published: February 2009

The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein trimer consists of gp120 and gp41 subunits and undergoes a series of conformational changes upon binding to the receptors, CD4 and CCR5/CXCR4, that promote virus entry. Surprisingly, we found that the envelope glycoproteins of some HIV-1 strains are functionally inactivated by prolonged incubation on ice. Serial exposure of HIV-1 to extremes of temperature, followed by expansion of replication-competent viruses, allowed selection of a temperature-resistant virus. The envelope glycoproteins of this virus resisted cold inactivation due to a single passage-associated change, H66N, in the gp120 exterior envelope glycoprotein. Histidine 66 is located within the gp41-interactive inner domain of gp120 and, in other studies, has been shown to decrease the sampling of the CD4-bound conformation by unliganded gp120. Substituting asparagine or other amino acid residues for histidine 66 in cold-sensitive HIV-1 envelope glycoproteins resulted in cold-stable phenotypes. Cold inactivation of the HIV-1 envelope glycoproteins occurred even at high pH, indicating that protonation of histidine 66 is not necessary for this process. Increased exposure of epitopes in the ectodomain of the gp41 transmembrane envelope glycoprotein accompanied cold inactivation, but shedding of gp120 did not. An amino acid change in gp120 (S375W) that promotes the CD4-bound state or treatment with soluble CD4 or a small-molecule CD4 mimic resulted in increased cold sensitivity. These results indicate that the CD4-bound intermediate of the HIV-1 envelope glycoproteins is cold labile; avoiding the CD4-bound state increases temperature stability.
Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis
Authors: Victoria Joseph G. , Kapoor Amit , Li Linlin , Blinkova Olga , Slikas Beth , Wang Chunlin , Naeem Asif , Zaidi Sohail , Delwart Eric
Published: February 2009

We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the
Picornaviridae
family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel
Picornaviridae
genus and four new viral species (members of the
Dicistroviridae
,
Nodaviridae
, and
Circoviridae
families and the
Bocavirus
genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel
Enterovirus
genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.
Four Major Envelope Proteins of White Spot Syndrome Virus Bind To Form a Complex
Authors: Zhou Qing , Xu Limei , Li Hui , Qi Yi-Peng , Yang Feng
Published: February 2009

Early events in white spot syndrome virus (WSSV) morphogenesis, particularly the formation of viral membranes, are poorly understood. The major envelope proteins of WSSV are VP28, VP26, VP24, and VP19. Our previous results indicated that VP28 interacts with VP26 and VP24. In the present study, we used coimmunoprecipitation assays and pull-down assays to confirm that the four major proteins in the WSSV envelope can form a multiprotein complex. Yeast two-hybrid assays were also used to test for interactions among the four proteins. In summary, three pairwise protein interactions (VP19-VP28, VP19-VP24, and VP24-VP26) and one self-association (VP24-VP24) were identified for the first time.
Genomic Epidemiology of a Dengue Virus Epidemic in Urban Singapore
Authors: Schreiber Mark J. , Holmes Edward C. , Ong Swee Hoe , Soh Harold S. H. , Liu Wei , Tanner Lukas , Aw Pauline P. K. , Tan Hwee Cheng , Ng Lee Ching , Leo Yee Sin , Low Jenny G. H. , Ong Adrian , Ooi Eng Eong , Vasudevan Subhash G. , Hibberd Martin L.
Published: February 2009

Dengue is one of the most important emerging diseases of humans, with no preventative vaccines or antiviral cures available at present. Although one-third of the world's population live at risk of infection, little is known about the pattern and dynamics of dengue virus (DENV) within outbreak situations. By exploiting genomic data from an intensively studied major outbreak, we are able to describe the molecular epidemiology of DENV at a uniquely fine-scaled temporal and spatial resolution. Two DENV serotypes (DENV-1 and DENV-3), and multiple component genotypes, spread concurrently and with similar epidemiological and evolutionary profiles during the initial outbreak phase of a major dengue epidemic that took place in Singapore during 2005. Although DENV-1 and DENV-3 differed in viremia and clinical outcome, there was no evidence for adaptive evolution before, during, or after the outbreak, indicating that ecological or immunological rather than virological factors were the key determinants of epidemic dynamics.
Fewer Latent Herpes Simplex Virus Type 1 and Cytotoxic T Cells Occur in the Ophthalmic Division than in the Maxillary and Mandibular Divisions of the Human Trigeminal Ganglion and Nerve
Authors: Hüfner Katharina , Horn Anja , Derfuss Tobias , Glon Christine , Sinicina Inga , Arbusow Viktor , Strupp Michael , Brandt Thomas , Theil Diethilde
Published: February 2009

Following primary infection of the mouth, herpes simplex virus type 1 (HSV-1) travels retrogradely along the maxillary (V2) or mandibular (V3) nerve to the trigeminal ganglion (TG), where it establishes lifelong latency. Symptomatic HSV-1 reactivations frequently manifest as herpes labialis, while ocular HSV-1 disease is rare. We investigated whether these clinical observations are mirrored by the distribution of latent HSV-1 as well as cytotoxic T-cell infiltration around the nerve cell bodies and in the nerve fibers. The three divisions of the TG were separated by using neurofilament staining and carbocyanine dye Di-I tracing and then screened by in situ hybridization for the presence of HSV-1 latency-associated transcript (LAT). The T-cell distribution and the pattern of cytolytic molecule expression were evaluated by immunohistochemistry. The Di-I-labeled neurons were largely confined to the nerve entry zone of the traced nerve branches. Very few Di-I-labeled neurons were found in adjacent divisions due to traversing fiber bundles. LAT was abundant in the V2 and V3 divisions of all TG but was scarce or totally absent in the ophthalmic (V1) division. CD8
+
T cells were found in all three divisions of the TG and in the respective nerves, clearly clustering in V2 and V3, which is indicative of a chronic inflammation. Only T cells surrounding neurons in the V2 and V3 ganglionic divisions expressed granzyme B. In conclusion, the large accumulation of LAT and cytotoxic T cells in the V2 and V3 but not in the V1 division of the TG reflects the sites supplied by the sensory fibers and the clinical reactivation patterns.
Reducing the Risk of Adeno-Associated Virus (AAV) Vector Mobilization with AAV Type 5 Vectors
Authors: Hewitt F. Curtis , Li Chengwen , Gray Steven J. , Cockrell Shelley , Washburn Michael , Samulski R. Jude
Published: February 2009

Current adeno-associated virus (AAV) gene therapy vectors package a transgene flanked by the terminal repeats (TRs) of AAV type 2 (AAV2). Although these vectors are replication deficient, wild-type (wt) AAV2 prevalent in the human population could lead to replication and packaging of a type 2 TR (TR2)-flanked transgene in
trans
during superinfection by a helper virus, leading to “mobilization” of the vector genome from treated cells. More importantly, it appears likely that the majority of currently characterized AAV serotypes as well as the majority of new novel isolates are capable of rescuing and replicating AAV2 vector templates. To investigate this possibility, we flanked a green fluorescent protein transgene with type 2 and, the most divergent AAV serotype, type 5 TRs (TR2 or TR5). Consistent with AAV clades, AAV5 specifically replicated TR5 vectors, while AAV2 and AAV6 replicated TR2-flanked vectors. To exploit this specificity, we created a TR5 vector production system for Cap1 to Cap5. Next, we showed that persisting recombinant AAV genomes flanked by TR2s or TR5s were mobilized in vitro after addition of the cognate AAV Rep (as well as Rep6 for TR2) and adenoviral helper. Finally, we showed that a cell line containing a stably integrated wt AAV2 genome resulted in mobilization of a TR2-flanked vector but not a TR5-flanked vector upon adenoviral superinfection. Based on these data and the relative prevalence of wt AAV serotypes in the population, we propose that TR5 vectors have a significantly lower risk of mobilization and should be considered for clinical use.
Impact of Epitope Escape on PD-1 Expression and CD8 T-Cell Exhaustion during Chronic Infection
Authors: Blattman Joseph N. , Wherry E. John , Ha Sang-Jun , van der Most Robbert G. , Ahmed Rafi
Published: February 2009

During some persistent viral infections, virus-specific T-cell responses wane due to the antigen-specific deletion or functional inactivation (i.e., exhaustion) of responding CD8 T cells. T-cell exhaustion often correlates with high viral load and is associated with the expression of the inhibitory receptor PD-1. In other infections, functional T cells are observed despite high levels of pathogen persistence. The reasons for these different T-cell fates during chronic viral infections are not clear. Here, we tracked the fate of virus-specific CD8 T cells in lymphocytic choriomeningitis virus (LCMV)-infected mice during viral clearance, the persistence of wild-type virus, or the selection and persistence of a viral variant that abrogates the presentation of a single epitope. Viral clearance results in PD-1
lo
functional virus-specific CD8 T cells, while the persistence of wild-type LCMV results in high PD-1 levels and T-cell exhaustion. However, following the emergence of a GP35V→A variant virus that abrogates the presentation of the GP33 epitope, GP33-specific CD8 T cells remained functional, continued to show low levels of PD-1, and reexpressed CD127, a marker of memory T-cell differentiation. In the same animals and under identical environmental conditions, CD8 T cells recognizing nonmutated viral epitopes became physically deleted or were PD-1
hi
and nonfunctional. Thus, the upregulation of PD-1 and the functional inactivation of virus-specific T cells during chronic viral infection is dependent upon continued epitope recognition. These data suggest that optimal strategies for vaccination should induce high-magnitude broadly specific T-cell responses that prevent cytotoxic T-lymphocyte escape and highlight the need to evaluate the function of vaccine-induced T cells in the context of antigens presented during virus persistence.
JC Virus-Specific Immune Responses in Human Immunodeficiency Virus Type 1 Patients with Progressive Multifocal Leukoencephalopathy
Authors: Khanna Nina , Wolbers Marcel , Mueller Nicolas J. , Garzoni Christian , Du Pasquier Renaud A. , Fux Christoph A. , Vernazza Pietro , Bernasconi Enos , Viscidi Raphael , Battegay Manuel , Hirsch Hans H.
Published: February 2009

Progressive multifocal leukoencephalopathy (PML) is a frequently fatal disease caused by uncontrolled polyomavirus JC (JCV) in severely immunodeficient patients. We investigated the JCV-specific cellular and humoral immunity in the Swiss HIV Cohort Study. We identified PML cases (
n
= 29), as well as three matched controls per case (
n
= 87), with prospectively cryopreserved peripheral blood mononuclear cells and plasma at diagnosis. Nested controls were matched according to age, gender, CD4
+
T-cell count, and decline. Survivors (
n
= 18) were defined as being alive for >1 year after diagnosis. Using gamma interferon enzyme-linked immunospot assays, we found that JCV-specific T-cell responses were lower in nonsurvivors than in their matched controls (
P
= 0.08), which was highly significant for laboratory- and histologically confirmed PML cases (
P
= 0.004). No difference was found between PML survivors and controls or for cytomegalovirus-specific T-cell responses. PML survivors showed significant increases in JCV-specific T cells (
P
= 0.04) and immunoglobulin G (IgG) responses (
P
= 0.005). IgG responses in survivors were positively correlated with CD4
+
T-cell counts (
P
= 0.049) and negatively with human immunodeficiency virus RNA loads (
P
= 0.03). We conclude that PML nonsurvivors had selectively impaired JCV-specific T-cell responses compared to CD4
+
T-cell-matched controls and failed to mount JCV-specific antibody responses. JCV-specific T-cell and IgG responses may serve as prognostic markers for patients at risk.
Exercising with reserve: exercise regulation by perceived exertion in relation to duration of exercise and knowledge of endpoint
Authors: Swart J , Lamberts R P , Lambert M I , Lambert E V , Woolrich R W , Johnston S , Noakes T D
Published: February 2009

Objective:

The purpose of this study was to examine ratings of perceived exertion (RPE) and performance during repetitive maximal effort 40 km time trials as well as after an intervention that aimed to decrease certainty about the remaining distance of the exercise bout. In addition, we examined the RPE during exercise bouts of markedly different duration.

Methods:

Part 1: 12 well-trained, competitive-level cyclists completed five 40 km time trials. During the final time trial all feedback was withheld until the final kilometre. In addition, to cause confusion about the remaining distance, they were asked to report their RPE at random intervals from 18 km to 38 km. Part 2: 6 well-trained, recreation-level cyclists randomly completed a 5 km, 10 km, 40 km and 100 km time trial.

Results:

Part 1: Mean RPE increased during the first four trials and decreased during the final trial. The rate of RPE progression increased in linearity during the first four trials and became more conservative in the final trial. These changes were directly related to performance. Part 2: Mean RPE for longer duration trials (40 km, 100 km) were lower during the first half of trial duration but matched those of shorter trials in the final 20%.

Conclusions:

Increased familiarity of the exercise bout and certainty about its endpoint are associated with a more aggressive RPE strategy that produces a superior exercise performance. Certainty about the endpoint and the duration of exercise affect both the RPE strategy and performance.
Would you dope? A general population test of the Goldman dilemma
Authors: Connor J M , Mazanov J
Published: February 2009

Objective:

To test Goldman's dilemma on a general population sample by asking whether they would take the Faustian bargain of a drug that guaranteed sporting success but would result in their death in 5 years' time. Between 1982 and 1995 a bi-annual survey using this dilemma suggested half of all elite athletes would take the drug.

Design:

A random telephone survey of 250 members of the Australian general public, with counterbalanced presentation of success and death.

Main outcome measures:

Respondents gave age, gender, sports engagement and response to the dilemma (yes/no).

Results:

Only two of a sample of 250 reported they would take the bargain offered by the dilemma.

Conclusions:

Athletes differ markedly from the general population in response to the dilemma. This raises significant practical and ethical dilemmas for athlete support personnel. The psychometry of the dilemma needs to be established more comprehensively for general and athlete populations.
MASS DEFORMATIONS OF SUPER YANG–MILLS THEORIES IN D = 2 + 1, AND SUPER-MEMBRANES: A NOTE
Authors: AGARWAL ABHISHEK
Published: February 2009

Mass deformations of supersymmetric Yang–Mills theories in three spacetime dimensions are considered. The gluons of the theories are made massive by the inclusion of a nonlocal gauge and Poincaré invariant mass term due to Alexanian and Nair, while the matter fields are given standard Gaussian mass-terms. It is shown that the dimensional reduction of such mass-deformed gauge theories defined on R3 or R × T2 produces matrix quantum mechanics with massive spectra. In particular, all known massive matrix quantum mechanical models obtained by the deformations of dimensional reductions of minimal super Yang–Mills theories in diverse dimensions are shown also to arise from the dimensional reductions of appropriate massive Yang–Mills theories in three spacetime dimensions. Explicit formulas for the gauge theory actions are provided.
FLUX COMPACTIFICATIONS AND SUPERSYMMETRY BREAKING IN 6D GAUGED SUPERGRAVITY
Authors: LEE HYUN MIN
Published: February 2009

We review on a recent construction of the on-shell supersymmetric brane action for the codimension-two branes with nonzero tension in the flux compactification of a 6D chiral gauged supergravity. On dimensionally reducing on 4D gauged supergravity for a new supersymmetric unwarped background with conical branes, we consider the modulus stabilization for determining the soft masses of the scalars localized on the branes and show that the bulk U (1)R provides a new mechanism for mediating the SUSY breaking.
Tissue inhibitor of metalloproteinase-3 inhibits neonatal mouse cardiomyocyte proliferation via EGFR/JNK/SP-1 signaling
Authors: Hammoud Lamis , Burger Dylan E. , Lu Xiangru , Feng Qingping
Published: February 2009

We have recently demonstrated that tissue inhibitor of metalloproteinase-3 (TIMP-3) decreases neonatal cardiomyocyte proliferation (Hammoud L, Xiang F, Lu X, Brunner F, Leco K, Feng Q. Cardiovasc Res 75: 359–368, 2007). The aim of the present study was to delineate a pathway through which TIMP-3 exerts its antiproliferative effect. Experiments were conducted on neonatal cardiomyocyte cultures and heart tissues isolated from wild-type (WT) and TIMP-3−/− mice. Deficiency in TIMP-3 decreased p27 expression and increased cardiomyocyte proliferation in cardiomyocytes and neonatal hearts. A TIMP-3/epidermal growth factor (EGF) receptor (EGFR)/c-Jun NH2-terminal kinase (JNK)/SP-1/p27 pathway was investigated. JNK phosphorylation and EGFR protein levels were increased in TIMP-3−/− cardiomyocytes and heart tissues. Treatment with recombinant TIMP-3 decreased JNK phosphorylation and EGFR expression/phosphorylation. Inhibition of JNK activity using SP-600125 decreased SP-1 phosphorylation, increased p27 expression, and decreased cardiomyocyte proliferation. Furthermore, treatment with the EGFR specific inhibitor PD-168393 or the EGF-neutralizing antibody decreased cardiomyocyte proliferation as well as phosphorylation of JNK and SP-1 in both WT and TIMP-3−/− cardiomyocytes. We conclude that TIMP-3 inhibits neonatal mouse cardiomyocyte proliferation by upregulating p27 expression. The effects of TIMP-3 are mediated via inhibition of EGFR expression/phosphorylation, and decreases in JNK and SP-1 signaling.
Membrane targeting and intracellular trafficking of the human sodium-dependent multivitamin transporter in polarized epithelial cells
Authors: Subramanian Veedamali S. , Marchant Jonathan S. , Boulware Michael J. , Ma Thomas Y. , Said Hamid M.
Published: February 2009

The human sodium-dependent multivitamin transporter (hSMVT) mediates sodium-dependent uptake of biotin in renal and intestinal epithelia. To date, however, there is nothing known about the structure-function relationship or targeting sequences in the hSMVT polypeptide that control its polarized expression within epithelia. Here, we focused on the role of the COOH-terminal tail of hSMVT in the targeting and functionality of this transporter. A full-length hSMVT-green fluorescent protein (GFP) fusion protein was functional and expressed at the apical membrane in renal and intestinal cell lines. Microtubule disrupting agents disrupted the mobility of trafficking vesicles and impaired cell surface delivery of hSMVT, which was also prevented in cells treated with dynamitin (p50), brefeldin, or monensin. Progressive truncation of the COOH-terminal tail impaired the functionality and targeting of the transporter. First, biotin transport decreased by approximately 20–30% on deletion of up to 15 COOH-terminal amino acids of hSMVT, a decrease mimicked solely by deletion of the terminal PDZ motif (TSL). Second, deletions into the COOH-terminal tail (between residues 584-612, containing a region of predicted high surface accessibility) resulted in a further drop in hSMVT transport (to ∼40% of wild-type). Third, apical targeting was lost on deletion of a helical-prone region between amino acids 570-584. We conclude that the COOH tail of hSMVT contains several determinants important for polarized targeting and biotin transport.