bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystallographic dependence of the lateral undercut wet etch rate of Al0.5In0.5P in diluted HCl for III–V sacrificial release
Authors: Ansbæk Thor , Semenova Elizaveta S. , Yvind Kresten , Hansen Ole
Published: December 2012

The authors investigated the use of InAlP as a sacrificial layer lattice-matched to GaAs when diluted hydrochloric acid is used for sacrificial etching. They show that InAlP can be used to fabricate submicrometer air gaps in micro-opto-electro-mechanical systems and that a selectivity toward GaAs larger than 500 is achieved. This selectivity enables fabrication control of the nanometer-size structures required in photonic crystal and high-index contrast subwavelength grating structures. The crystallographic dependence of the lateral etch rate in InAlP is shown to be symmetric around the 〈110〉 directions where an etch rate of 0.5 μm/min is obtained at 22 °C in HCl:2H2O. Since the etch rate in the 〈100〉 directions exceeds by ten times that of the 〈110〉 directions, InAlP may be used in sacrificial release of high-aspect ratio structures. Free-hanging structures with length to air-gap aspect ratios above 600 are demonstrated by use of critical point drying following the sacrificial etch.
Ion implantation synthesis and conduction of tantalum oxide resistive memory layers
Authors: Bishop Seann M. , Briggs Benjamin D. , Rice Phillip Z. , Capulong Jihan O. , Bakhru Hassaram , Cady Nathaniel C.
Published: December 2012

In this paper, the ion implantation synthesis of tantalum oxide resistive memory material is introduced, the salient switching properties are described, and the results from an analysis of the off- and on-state conduction are presented. The tantalum oxide layers were synthesized by oxygen ion implanting (5 × 1016/cm2 O+ ions at 30 keV) tantalum metal. From composition-depth profiling, the oxygen implant profile is estimated to peak at ∼20 at. %. The properties of memory devices fabricated from the implantation-synthesized oxide were investigated through endurance testing. A stable 2× memory window was obtained for >103 switching cycles with low SET and RESET voltages <|1|. Both the on- and off-state resistance decreased inversely with the current used during programming. Analyses of the current–voltage data show that the platinum-tantalum oxide Schottky barrier factors largely into the resistance difference between memory states. Lastly, defect-related conduction dominated the current of the off-state resistance at high voltages. At >2 V, Frenkel-Poole emission current was identified; thus, trap states that may be induced by the implantation process impact high voltage conduction in this memory state.
Atomic layer deposition of ZnO on Cu-nanoclusters for methanol synthesis
Authors: Zhang Ziyu , Patterson Matthew , Ren Maoming , Wang Ying , Flake John C. , Sprunger Phillip T. , Kurtz Richard L.
Published: December 2012

The properties of ALD-grown ZnO thin films on Cu clusters supported on ZnO(101¯0) have been studied with scanning tunneling and scanning electron microscopy in combination with angle-resolved x-ray photoelectron spectroscopy. Deposition at room temperature of two monolayers of Cu on ZnO(101¯0) results in metallic Cu0 clusters ∼8 nm wide by 1.4 nm high. Higher coverages of 15 ML results in a similar morphology, with slightly larger cluster sizes. Following air-exposure and ALD-growth of two cycles of ZnO, the Cu exhibits Cu+ species characteristic of Cu2O and the thin ZnO coating is hydroxylated. Electrochemical studies of ALD ZnO coatings on Cu suggest that they are more active for CO2 reduction.
Fabrication of indium tin oxide bump/pit structures on GaN-based light emitting diodes
Authors: Liu Zhe , Wang Yujin , Yang Haifang , Yin Hongxing , Quan Baogang , Xia Xiaoxiang , Li Wuxia , Gu Changzhi
Published: December 2012

In the past several decades, significant progress has been made to improve the performance of semiconducting light emitting diodes (LEDs), which has resulted in a wide number of applications for LEDs in the information and energy fields. However, light extraction efficiency is limited due to remarkable total internal reflection on the device's surface due to the large refractive index of GaN and indium tin oxides (ITO). In this work, ITO bump and pit patterns were fabricated on the LED surface using an ion beam etching method via metal or resist masks, respectively. By changing the incident angle of the ion beam and the material of the masks, the effects of faceting and redeposition can be properly controlled, resulting in well-controlled manipulation of the shape of the fabricated bump/pit structures. By altering the etching time, the over-etched structures have a much smoother surface compared with the under-etched/in-etched structures. These bump/pit structures could have potential applications in LED light emitting enhancement and optical devices.
Direct comparison of spectroscopic data with cluster calculations of plutonium dioxide and uranium dioxide
Authors: Tobin J. G. , Yu S.-W. , Chung B. W. , Ryzhkov M. V. , Mirmelstein A.
Published: December 2012

The density of states predicted by cluster calculations of PuO2 and UO2 is directly compared to the results from soft x-ray spectroscopy. Remarkably good agreement between the experimentally measured spectroscopic peaks and the calculated density of states of the central part of the cluster is observed.
The Si3N4/TiN Interface: 3. Si3N4/TiN(001) Grown with a −150 V Substrate Bias and Analyzed In situ using Angle-resolved X-ray Photoelectron Spectroscopy
Authors: Haasch Richard T. , Patscheider Jörg , Hellgren Niklas , Petrov Ivan , Greene J. E.
Published: December 2012

Angle-resolved x-ray photoelectron spectroscopy (AR-XPS) was used to analyze Si3N4/TiN(001) bilayers grown by ultrahigh vacuum reactive magnetron sputter deposition onto MgO(001), with a substrate potential of −150 V, in mixed 1:1 Ar/N2 discharges maintained at a total pressure of 0.5 Pa (3.75 × 10−3 Torr). The TiN(001) films were grown at 600 °C and the 4-ML-thick Si3N4 overlayers at room temperature. AR-XPS spectra were obtained using incident monochromatic Al Kα x-radiation at 0.83401 nm. Si3N4/TiN(001) Ti 2p spectra reveal enhanced unscreened final-state satellite peaks, compared to Ti 2p spectra obtained from uncapped TiN(001), due to decreased electronic screening induced by Si3N4/TiN(001) bilayer interfacial polarization.
The Si3N4/TiN Interface: 4. Si3N4/TiN(001) Grown with a −250 V Substrate Bias and Analyzed In situ using Angle-resolved X-ray Photoelectron Spectroscopy
Authors: Haasch Richard T. , Patscheider Jörg , Hellgren Niklas , Petrov Ivan , Greene J. E.
Published: December 2012

Angle-resolved x-ray photoelectron spectroscopy (AR-XPS) was used to analyze Si3N4/TiN(001) bilayers grown by ultrahigh vacuum reactive magnetron sputter deposition onto MgO(001), with a substrate potential of −250 V, in mixed 1:1 Ar/N2 discharges maintained at a total pressure of 0.5 Pa (3.75 × 10−3 Torr). The TiN(001) films were grown at 600 °C and the 4-ML-thick Si3N4 overlayers at room temperature. AR-XPS spectra were obtained using incident monochromatic Al Kα X-radiation at 0.83401 nm. Si3N4/TiN(001) Ti 2p spectra reveal enhanced unscreened final-state satellite peaks, compared to Ti 2p spectra obtained from uncapped TiN(001), due to decreased electronic screening induced by Si3N4/TiN(001) bilayer interfacial polarization.
The Si3N4/TiN Interface: 5. TiN/Si3N4 Grown and Analyzed In situ using Angle-resolved X-ray Photoelectron Spectroscopy
Authors: Haasch Richard T. , Patscheider Jörg , Hellgren Niklas , Petrov Ivan , Greene J. E.
Published: December 2012

Angle-resolved x-ray photoelectron spectroscopy (AR-XPS) was used to analyze TiN/Si3N4 bilayers grown by ultrahigh vacuum reactive magnetron sputter deposition onto Si(001), with an electrically floating substrate potential of 7 V, in mixed 1:1 Ar/N2 discharges maintained at a total pressure of 0.5 Pa (3.75 × 10−3 Torr). The Si3N4 layers were deposited at room temperature and the 4-ML thick TiN overlayers were grown at 600 °C. AR-XPS spectra were obtained using incident monochromatic Al Kα x-radiation at 0.83401 nm. TiN/Si3N4 Ti 2p spectra reveal an unscreened final-state satellite intensity that lies between that of clean TiN(001) and Si3N4/TiN(001).
The Si3N4/TiN Interface: 7. Ti/TiN(001) Grown and Analyzed In situ using X-ray Photoelectron Spectroscopy
Authors: Haasch Richard T. , Patscheider Jörg , Hellgren Niklas , Petrov Ivan , Greene J. E.
Published: December 2012

X-ray photoelectron spectroscopy (XPS) was used to analyze Ti/TiN(001) bilayers grown by ultrahigh vacuum reactive magnetron sputter deposition on MgO(001), with an electrically floating substrate potential of 7 V, in mixed 1:1 Ar/N2 discharges maintained at a total pressure of 0.5 Pa (3.75 × 10−3 Torr). The TiN(001) films were grown at 600 °C and the 4-ML-thick Ti overlayers at room temperature. XPS spectra were obtained using incident monochromatic Al Kα x-radiation at 0.83401 nm. Ti/TiN(001) Ti 2p spectra reveal reduced unscreened final-state satellite peaks compared to Ti 2p spectra obtained from uncapped TiN(001) due to increased electronic screening.
Normal and shear strain imaging using 2D deformation tracking on beam steered linear array datasets
Authors: Xu Haiyan , Varghese Tomy
Published: December 2012

Purpose:

Previous publications have reported on the use of one‐dimensional cross‐correlation analysis with beam‐steered echo signals. However, this approach fails to accurately track displacements at larger depths (>4.5 cm) due to lower signal‐to‐noise. In this paper, the authors present the use of adaptive parallelogram shaped two‐dimensional processing blocks for deformation tracking.

Methods:

Beam‐steered datasets were acquired using a VFX 9L4 linear array transducer operated at a 6 MHz center frequency for steered angles from −15 to 15° in increments of 1°, on both uniformly elastic and single‐inclusion tissue‐mimicking phantoms. Echo signals were acquired to a depth of 65 mm with the focus set at 40 mm corresponding to the center of phantom. Estimated angular displacements along and perpendicular to the beam direction are used to compute axial and lateral displacement vectors using a least‐squares approach. Normal and shear strain tensor component are then estimated based on these displacement vectors.

Results:

Their results demonstrate that parallelogram shaped two‐dimensional deformation tracking significantly improves spatial resolution (factor of 7.79 along the beam direction), signal‐to‐noise (5 dB improvement), and contrast‐to‐noise (8–14 dB improvement) associated with strain imaging using beam steering on linear array transducers.

Conclusions:

Parallelogram shaped two‐dimensional deformation tracking is demonstrated in beam‐steered radiofrequency data, enabling its use in the estimation of normal and shear strain components.
Real‐time automatic fiducial marker tracking in low contrast cine‐MV images
Authors: Lin Wei‐Yang , Lin Shu‐Fang , Yang Sheng‐Chang , Liou Shu‐Cheng , Nath Ravinder , Liu Wu
Published: December 2012

Purpose:

To develop a real‐time automatic method for tracking implanted radiographic markers in low‐contrast cine‐MV patient images used in image‐guided radiation therapy (IGRT).

Methods:

Intrafraction motion tracking using radiotherapy beam‐line MV images have gained some attention recently in IGRT because no additional imaging dose is introduced. However, MV images have much lower contrast than kV images, therefore a robust and automatic algorithm for marker detection in MV images is a prerequisite. Previous marker detection methods are all based on template matching or its derivatives. Template matching needs to match object shape that changes significantly for different implantation and projection angle. While these methods require a large number of templates to cover various situations, they are often forced to use a smaller number of templates to reduce the computation load because their methods all require exhaustive search in the region of interest. The authors solve this problem by synergetic use of modern but well‐tested computer vision and artificial intelligence techniques; specifically the authors detect implanted markers utilizing discriminant analysis for initialization and use mean‐shift feature space analysis for sequential tracking. This novel approach avoids exhaustive search by exploiting the temporal correlation between consecutive frames and makes it possible to perform more sophisticated detection at the beginning to improve the accuracy, followed by ultrafast sequential tracking after the initialization. The method was evaluated and validated using 1149 cine‐MV images from two prostate IGRT patients and compared with manual marker detection results from six researchers. The average of the manual detection results is considered as the ground truth for comparisons.

Results:

The average root‐mean‐square errors of our real‐time automatic tracking method from the ground truth are 1.9 and 2.1 pixels for the two patients (0.26 mm/pixel). The standard deviations of the results from the 6 researchers are 2.3 and 2.6 pixels. The proposed framework takes about 128 ms to detect four markers in the first MV images and about 23 ms to track these markers in each of the subsequent images.

Conclusions:

The unified framework for tracking of multiple markers presented here can achieve marker detection accuracy similar to manual detection even in low‐contrast cine‐MV images. It can cope with shape deformations of fiducial markers at different gantry angles. The fast processing speed reduces the image processing portion of the system latency, therefore can improve the performance of real‐time motion compensation.
Reflection of a polarized light cone
Authors: Brody Jed , Weiss Daniel , Berland Keith
Published: December 2012

We introduce a visually appealing experimental demonstration of Fresnel reflection. In this simple optical experiment, a polarized light beam travels through a high numerical-aperture microscope objective, reflects off a glass slide, and travels back through the same objective lens. The return beam is sampled with a polarizing beam splitter and produces a surprising geometric pattern on an observation screen. Understanding the origin of this pattern requires careful attention to geometry and an understanding of the Fresnel coefficients for S and P polarized light. We demonstrate that in addition to a relatively simple experimental implementation, the shape of the observed pattern can be computed both analytically and by using optical modeling software. The experience of working through complex mathematical computations and demonstrating their agreement with a surprising experimental observation makes this a highly educational experiment for undergraduate optics or advanced-lab courses. It also provides a straightforward yet non-trivial system for teaching students how to use optical modeling software.
Conductance quantization: A laboratory experiment in a senior-level nanoscale science and technology course
Authors: Tolley R. , Silvidi A. , Little C. , Eid K. F.
Published: December 2012

We describe a simple, inexpensive, and robust undergraduate lab experiment that demonstrates the emergence of quantized conductance as a macroscopic gold wire is broken and unbroken. The experiment utilizes a mechanically controlled break junction and demonstrates how conductance quantization can be used to understand the importance of quantum mechanics at the nanoscale. Such an experiment can be integrated into the curriculum of a course on nanoscale science or contemporary physics at the junior and senior levels.
Robust and low complexity localization algorithm based on head-related impulse responses and interaural time difference
Authors: Wan Xinwang , Liang Juan
Published: December 2012

This article introduces a biologically inspired localization algorithm using two microphones, for a mobile robot. The proposed algorithm has two steps. First, the coarse azimuth angle of the sound source is estimated by cross-correlation algorithm based on interaural time difference. Then, the accurate azimuth angle is obtained by cross-channel algorithm based on head-related impulse responses. The proposed algorithm has lower computational complexity compared to the cross-channel algorithm. Experimental results illustrate that the localization performance of the proposed algorithm is better than those of the cross-correlation and cross-channel algorithms.
How We Got Here: An Inquiry-Based Activity About Human Evolution
Authors: Price Rebecca M.
Published: December 2012

How We Got Here, an IBI prize—winning module, utilizes iterative cycles of inquiry to help students learn about evolution.
Comment on “The Local Structure of Amorphous Silicon”
Authors: Roorda Sjoerd , Lewis Laurent J.
Published: December 2012

Treacy and Borisenko (Reports, 24 February 2012, p. 950) argue from reverse Monte Carlo modeling of electron diffraction and fluctuation electron microscopy data that amorphous silicon is paracrystalline and not described by a continuous random network. However, their models disagree with high-resolution x-ray measurements and other evidence, whereas the agreement with fluctuation electron microscopy is at best qualitative.
Sign-Problem–Free Quantum Monte Carlo of the Onset of Antiferromagnetism in Metals
Authors: Berg Erez , Metlitski Max A. , Sachdev Subir
Published: December 2012

Getting Rid of Negativity

Problems in condensed matter physics involving strong interactions are notoriously hard to tackle analytically, and physicists often resort to numerical methods such as quantum Monte Carlo (QMC). However, in the most interesting cases, this method becomes computationally intractable because partition sums for fermionic systems generally involve integration over an oscillatory function with both negative and positive values.

Berg
et al.

(p.
1606
) find a way around this problem for a two-dimensional metal in the vicinity of an antiferromagnetic quantum phase transition, which is of relevance to electron-doped cuprates, iron-based superconductors, and heavy fermion compounds. Their lattice theory results in a positive integrand for the partition sums; thus, avoiding the sign problem; and yields the expected competition between antiferromagnetic order and unconventional superconductivity near the critical point.
Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
Authors: Merkin Jason , Russell Caitlin , Chen Ping , Burge Christopher B.
Published: December 2012

Whence Species Variation?

Vertebrates have widely varying phenotypes that are at odds with their much more limited proteincoding genotypes and conserved messenger RNA expression patterns. Genes with multiple exons and introns can undergo alternative splicing, potentially resulting in multiple protein isoforms (see the Perspective by

Papasaikas and Valcárcel

).

Barbosa-Morais
et al.

(p.
1587
) and

Merkin
et al.

(p.
1593
) analyzed alternative splicing across the genomes of a variety of vertebrates, including human, primates, rodents, opossum, platypus, chicken, lizard, and frog. The findings suggest that the evolution of alternative splicing has for the most part been very rapid and that alternative splicing patterns of most organs more strongly reflect the identity of the species rather than the organ type. Species-classifying alternative splicing can affect key regulators, often in disordered regions of proteins that may influence protein-protein interactions, or in regions involved in protein phosphorylation.
Of Chymists and Kings

The Secrets of Alchemy
by Lawrence M. Principe

University of Chicago Press, Chicago, 2013. 295 pp. $25, £16. ISBN 9780226682952.
Authors: Grafton Anthony
Published: December 2012

Principe's concise survey explores the practices and influences of alchemy in their historical and cultural contexts.
Keith Campbell (1954–2012)
Authors: Wilmut Ian
Published: December 2012

A cell biologist interested in the cell division cycle worked on Dolly the sheep, the first cloned mammal.
NIF Report Asks for More Time to Achieve Ignition
Authors: Clery Daniel
Published: December 2012

The National Ignition Facility faces an uncertain future after its managers admitted to Congress this month that they need at least another 3 years to try to identify what has prevented the giant laser fusion lab in California from achieving ignition.
Sutter's Mill Meteorite Produces Mother Lode of Research
Authors: Underwood Emily
Published: December 2012

The Sutter's Mill meteorite is the most pristine sample yet collected of a rare type of carbonaceous chondrite, and possibly a sneak preview of a primitive asteroid to which NASA might one day send astronauts.
No Lake Mud for Curiosity Rover to Investigate?
Authors: Kerr Richard
Published: December 2012

Gale crater's central mound seemed irresistible, offering the prospect of analyzing ancient lake sediments and posing as the ideal place to find remains of any early martian life. But at the meeting, a pair of researchers put a damper on those hopes.
Tying Megaeruptions to a Mass Extinction Long After the Fact
Authors: Kerr Richard
Published: December 2012

Geochronologists who measure the passage of time in the steady ticking of radioactive decay presented convincing evidence that massive eruptions at the opening of the Atlantic Ocean 201 million years ago drove the mass extinction that cleared the way for the rise of the dinosaurs.
Buildup to Quakes Spied in Both Model And Real World
Authors: Kerr Richard A.
Published: December 2012

Seismologists hoping to discover how earthquakes work may be one small step closer.
The Discovery of the Higgs Boson
Authors: Cho Adrian
Published: December 2012

Science
has chosen the finding of the Higgs boson as its Breakthrough of the Year.
Italian Quake Verdicts Rattle Researchers
Authors: Malakoff David
Published: December 2012

Can scientists risk talking publicly about risk—especially when lives are on the line? It's a question that many researchers are asking after seven defendants were accused of conducting superficial analyses and making misleading public statements, then convicted of manslaughter.
A Year On, the H5N1 Debate Remains Infectious, With No End in Sight
Authors: Malakoff David
Published: December 2012

Two controversial studies that showed how to make the H5N1 avian influenza virus transmissible among mammals have left scientists wondering which kinds of studies are worth the risk and how potentially dangerous results should be reviewed and safely communicated to the public and public health experts.
Characterization of Recombinant Per a 10 from Periplaneta americana
Authors: Govindaraj Dhanapal , Gaur Shailendra Nath , Arora Naveen
Published: December 2012

Cockroach allergen is a major risk factor for IgE-mediated allergic response and asthma in sensitized individuals. Serine proteases have been identified from various sources and characterized as major allergens. The present study was aimed to express and characterize recombinant allergen Per a 10 (rPer a 10) from
Periplaneta americana.
rPer a 10 was expressed in
Escherichia coli
and purified in soluble form, yielding 0.75 mg/liter of culture. Homology of the Per a 10 protein sequence exhibited 27 to 38% similarity to the mite serine protease and 41 to 52% similarity to other insect trypsins. The purified rPer a 10 protein resolved at 28 kDa on SDS-PAGE and was recognized by cockroach-hypersensitive patients' sera by immunoblotting and enzyme-linked immunosorbent assay (ELISA). In competitive ELISA, rPer a 10 required 96 ng of purified protein for 50% inhibition of IgE binding, whereas 34 ng of native protein (nPer a 10) was required for the same inhibition. rPer a 10 and nPer a 10 induced basophil histamine release in the range of 47 to 64% and 60 to 85%, respectively, when sensitized with cockroach-hypersensitive patients' sera. In conclusion, Per a 10 was subcloned, and the protein was purified to homogeneity. rPer a 10 showed reduced IgE binding and histamine release and showed no proteolytic activity. These data suggest that rPer a 10 has potential for immunotherapy.
Single Real-Time Reverse Transcription-PCR Assay for Detection and Quantification of Genetically Diverse HIV-1, SIVcpz, and SIVgor Strains
Authors: Etienne Lucie , Eymard-Duvernay Sabrina , Aghokeng Avelin , Butel Christelle , Monleau Marjorie , Peeters Martine
Published: December 2012

Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (
n
= 190; 1.68 to 7.78 log
10
copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra- and interassay variation (<5%) and a limit of quantification of <2.50 log
10
copies/ml, with a 200-μl plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (
r
= 0.95,
P
< 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (
n
= 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants.
An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of
vif
mRNA
Authors: Widera Marek , Erkelenz Steffen , Hillebrand Frank , Krikoni Aikaterini , Widera Darius , Kaisers Wolfgang , Deenen René , Gombert Michael , Dellen Rafael , Pfeiffer Tanya , Kaltschmidt Barbara , Münk Carsten , Bosch Valerie , Köhrer Karl , Schaal Heiner
Published: December 2012

Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3′ splice site (3′ss) A1 but lack splicing at 5′ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3′ss A1 and repression of D2, respectively, determine the levels of
vif
mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3′ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5′ss D2. Here we show that an intronic G run (G
I2
-1) represses the use of a second 5′ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G
I2
-1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of
vif
mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vif-to-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here.
Effects of an Early Conformational Switch Defect during ϕX174 Morphogenesis Are Belatedly Manifested Late in the Assembly Pathway
Authors: Gordon Emile B. , Fane Bentley A.
Published: December 2012

C-terminal, aromatic amino acids in the ϕX174 internal scaffolding protein B mediate conformational switches in the viral coat protein. These switches direct the coat protein through early assembly. In addition to the aromatic amino acids, two acidic residues, D111 and E113, form salt bridges with basic, coat protein side chains. Although salt bridge formation did not appear to be critical for assembly, the substitution of an aromatic amino acid for D111 produced a lethal phenotype. This side chain is uniquely oriented toward the center of the coat-scaffolding binding pocket, which is heavily dominated by aromatic ring-ring interactions. Thus, the D111Y substitution may restructure pocket contacts. Previously characterized
B
−
mutants blocked assembly before procapsid formation. However, the D111Y mutant produced an assembled particle, which contained the structural and external scaffolding proteins but lacked protein B and DNA. A suppressor within the external scaffolding protein, which mediates the later stages of particle morphogenesis, restored viability. The unique formation of a postprocapsid particle and the novel suppressor may be indicative of a novel B protein function. However, genetic data suggest that the particle represents the delayed manifestation of an early assembly error. This seemingly late-acting defect was rescued by previously characterized suppressors of early, preprocapsid,
B
−
assembly mutations, which act on the level of coat protein flexibility. Likewise, the newly isolated suppressor in the external scaffolding protein also exhibited a global suppressing phenotype. Thus, the off-pathway product isolated from infected cells may not accurately reflect the temporal nature of the initial defect.
Tropism and Infectivity of Influenza Virus, Including Highly Pathogenic Avian H5N1 Virus, in Ferret Tracheal Differentiated Primary Epithelial Cell Cultures
Authors: Zeng Hui , Goldsmith Cynthia S. , Maines Taronna R. , Belser Jessica A. , Gustin Kortney M. , Pekosz Andrew , Zaki Sherif R. , Katz Jacqueline M. , Tumpey Terrence M.
Published: December 2012

Tropism and adaptation of influenza viruses to new hosts is partly dependent on the distribution of the sialic acid (SA) receptors to which the viral hemagglutinin (HA) binds. Ferrets have been established as a valuable
in vivo
model of influenza virus pathogenesis and transmission because of similarities to humans in the distribution of HA receptors and in clinical signs of infection. In this study, we developed a ferret tracheal differentiated primary epithelial cell culture model that consisted of a layered epithelium structure with ciliated and nonciliated cells on its apical surface. We found that human-like (α2,6-linked) receptors predominated on ciliated cells, whereas avian-like (α2,3-linked) receptors, which were less abundant, were presented on nonciliated cells. When we compared the tropism and infectivity of three human (H1 and H3) and two avian (H1 and H5) influenza viruses, we observed that the human influenza viruses primarily infected ciliated cells and replicated efficiently, whereas a highly pathogenic avian H5N1 virus (A/Vietnam/1203/2004) replicated efficiently within nonciliated cells despite a low initial infection rate. Furthermore, compared to other influenza viruses tested, VN/1203 virus replicated more efficiently in cells isolated from the lower trachea and at a higher temperature (37°C) compared to a lower temperature (33°C). VN/1203 virus infection also induced higher levels of immune mediator genes and cell death, and virus was recovered from the basolateral side of the cell monolayer. This ferret tracheal differentiated primary epithelial cell culture system provides a valuable
in vitro
model for studying cellular tropism, infectivity, and the pathogenesis of influenza viruses.
CD4 T-Cell Memory Responses to Viral Infections of Humans Show Pronounced Immunodominance Independent of Duration or Viral Persistence
Authors: Jing Lichen , Schiffer Joshua T. , Chong Tiana M. , Bruckner Joseph J. , Davies D. Huw , Felgner Phillip L. , Haas Juergen , Wald Anna , Verjans G. M. G. M. , Koelle David M.
Published: December 2012

Little is known concerning immunodominance within the CD4 T-cell response to viral infections and its persistence into long-term memory. We tested CD4 T-cell reactivity against each viral protein in persons immunized with vaccinia virus (VV), either recently or more than 40 years ago, as a model self-limited viral infection. Similar tests were done with persons with herpes simplex virus 1 (HSV-1) infection as a model chronic infection. We used an indirect method capable of counting the CD4 T cells in blood reactive with each individual viral protein. Each person had a clear CD4 T-cell dominance hierarchy. The top four open reading frames accounted for about 40% of CD4 virus-specific T cells. Early and long-term memory CD4 T-cell responses to vaccinia virus were mathematically indistinguishable for antigen breadth and immunodominance. Despite the chronic intermittent presence of HSV-1 antigen, the CD4 T-cell dominance and diversity patterns for HSV-1 were identical to those observed for vaccinia virus. The immunodominant CD4 T-cell antigens included both long proteins abundantly present in virions and shorter, nonstructural proteins. Limited epitope level and directex vivodata were also consistent with pronounced CD4 T-cell immunodominance. We conclude that human memory CD4 T-cell responses show a pattern of pronounced immunodominance for both chronic and self-limited viral infections and that this pattern can persist over several decades in the absence of antigen.
A Short
cis
-Acting Motif in the M112-113 Promoter Region Is Essential for IE3 To Activate M112-113 Gene Expression and Is Important for Murine Cytomegalovirus Replication
Authors: Perez Kareni J. , Martínez Francisco Puerta , Cosme-Cruz Ruth , Perez-Crespo Neysa M. , Tang Qiyi
Published: December 2012

Immediate-early 3 (IE3) gene products are required to activate early (E)-stage gene expression of murine cytomegaloviruses (MCMV). The first early gene activated by IE3 is the M112-113 gene (also called E1), although a complete understanding of the activation mechanism is still lacking. In this paper, we identify a 10-bp
cis
-regulating motif upstream of the M112-113 TATA box as important for IE3 activation of M112-113 expression. Results from DNA affinity assays and chromatin immunoprecipitation assays show that the association of IE3 with the M112-113 gene promoter was eliminated by deletion of the 10-bp DNA sequence, now named IE3AM (for IE3
a
ctivating
m
otif). In addition, IE3 interacts with TATA box binding protein (TBP), a core protein of TFIID (transcription initiation) complexes. Finally, we created an IE3AM-deleted MCMV (MCMVdIE3AM) using a bacterial artificial chromosome system. The mutant virus can still replicate in NIH 3T3 cells but at a significantly lower level. The defectiveness of the MCMVdIE3AM infection can be rescued in an M112-113-complemented cell line. Our results suggest that the interactions of IE3 with IE3AM and with TBP stabilize the TFIID complex at the M112-113 promoter such that M112-113 gene expression can be activated and/or enhanced.
Euforia-induced acute hepatitis in a patient with scleroderma
Authors: Jiménez-Encarnación Esther , Ríos Grissel , Muñoz-Mirabal Angel , Vilá Luis M
Published: December 2012

Euforia, a supplement containing a variety of natural ingredients, is widely used as an antioxidant and anti-inflammatory formula. It is not approved by the US Food and Drug Administration and its side effects are unknown. We report a 45-year-old woman with limited systemic sclerosis who presented with jaundice and marked elevation of serum transaminases. One month before, she started taking Euforia juice. A liver biopsy disclosed submassive hepatocellular necrosis with histopathological changes consistent with toxic hepatitis. The patient's symptoms resolved with cessation of Euforia. Six months later, she persisted with abnormal liver function tests, but these resolved 18 months after discontinuation of Euforia. The mechanism by which Euforia causes liver injury is unknown. Some ingredients contained in this supplement (green tea, Aloe vera, noni and goji) are linked to hepatic injury. To our knowledge, this is the first report of hepatotoxicity associated with Euforia.
Postcardiotomy syndrome: recurrent cardiac tamponade and an exquisite steroid response
Authors: Fink Douglas , Frigiola Alessandra , Cullen Shay
Published: December 2012

A 26-year-old woman presented moribund with fever and pleuritic chest pain 3 times in 4 months following elective aortic root surgery. She was admitted 41 days after surgery with cardiac tamponade requiring surgical drainage twice within 1 week. Despite this, she was re-admitted for a second time 4 days after discharge with persistent pericardial effusion. High fevers and an incidental regurgitant murmur were extensively investigated for and treated as possible endocarditis or graft infection without conclusive results. The patient spent a total of 61 days in hospital during this period, receiving seven different antibiotic courses. Her third admission, with most severe clinical features, nearly led to further surgery and removal of her aortic graft but instead culminated in a multidisciplinary team decision to initiate steroid therapy for postcardiotomy syndrome. A short course of oral prednisolone saw her pericardial effusion and symptoms resolve completely.
Solitaire FR device for treatment of dural sinus thrombosis
Authors: Pukenas Bryan Anthony , Kumar Monisha , Stiefel Michael , Smith Michelle , Hurst Robert
Published: December 2012

Dural venous sinus thrombosis is a rare and potentially devastating disease. Several predisposing factors exist, including oral contraceptive therapy and colitis. First-line therapy consists of systemic anticoagulation. If first-line therapies fail, more aggressive endovascular therapies may be performed. We report our initial experience with the Solitaire FR device for treatment of refractory symptomatic dural venous sinus thrombosis.
Initial experience of a novel sheath guide for transbrachial carotid artery stenting: technical note
Authors: Iwata Tomonori , Mori Takahisa , Miyazaki Yuichi , Nakazaki Masahito , Takahashi Yoichiro , Mizokami Koji
Published: December 2012

Background

The transfemoral approach has been a common technique for carotid artery stenting (CAS). When aortic or peripheral arterial conditions limit the transfemoral approach, the transbrachial approach may be used as an alternative. The purpose of our study was to report initial experiences of CAS with a novel sheath guide specifically designed for transbrachial carotid cannulation.

Methods

Patients who underwent transbrachial CAS with a novel sheath guide between May 2011 and July 2012 were analyzed. The sheath guide has an internal diameter of 6 Fr (2.24 mm, 0.088 inch) and is 90 cm long with a soft distal part and a particular distal shape like a modified Simmons catheter.

Results

Sixty-two patients underwent transbrachial CAS with the sheath guide. Transbrachial carotid cannulation was easy and successful and CAS procedures were performed easily through the sheath guide in every case. No sheath-related periprocedural complications occurred.

Conclusions

The sheath guide specifically designed for transbrachial carotid cannulation is useful for transbrachial CAS.
Enantioselective synthesis of 3-substituted tryptamines as core components of central nervous system drugs and indole natural products
Authors: Hanessian Stephen , Stoffman Elia J.L.
Published: December 2012

Application of the MacMillan iminium ion Michael and Friedel–Crafts type reactions to γ-amino α,β-unsaturated butanals led to the corresponding β-substituted butanals in good yields and high enantioselectivities. The products could be useful intermediates in the synthesis of indole-based central nervous system (CNS) drugs and natural products.
Studies of neodolastanes — Synthesis of the tricyclic core of the trichoaurantianolides
Authors: Williams David R. , Pinchman Joseph R.
Published: December 2012

Studies toward the synthesis of trichoaurantianolide C (5) are described. Stille cross-coupling reactions of (E)- and (Z)-β-stannyl-α,β-unsaturated esters with allylic acetate 32 provide for the stereocontrolled formation of nonconjugated 2,5-diene-1-ols. Studies of the asymmetric Sharpless epoxidation are utilized to establish diastereofacial selectivity for the preparation of a crucial C2tertiary allylic alcohol for subsequent esterification and ring-closing metathesis. SmI2reductive cyclization of the key butenolide precursor 49 led to formation of the central seven-membered ring of the tricyclic core of the natural product.
MOTT INSULATOR-SUPERFLUID TRANSITION IN A GENERALIZED BOSE–HUBBARD MODEL WITH TOPOLOGICALLY NONTRIVIAL FLAT-BAND
Authors: ZHANG XING-HAI , KOU SU-PENG
Published: December 2012

In this paper, we studied a generalized Bose–Hubbard model on a checkerboard lattice with topologically nontrivial flat-band. We used mean-field method to decouple the model Hamiltonian and obtained phase diagram by Landau theory of second-order phase transition. We further calculate the energy gap and the dispersion of quasi-particle or quasi-hole in Mott insulator phase and found that in strong interaction limit the quasi-particles or the quasi-holes also have flat-bands.
A MULTI-AGENT BASED SYSTEM FOR SENTIMENT ANALYSIS OF USER-GENERATED CONTENT
Authors: KECHAOU ZIED , AMMAR MOHAMED BEN , ALIMI ADEL M.
Published: December 2012

The recent years have been marked by a rapid growth in the World Wide Web 2.0 applications such as blog posts, forums, mailing lists, and product-review websites. As a result, a special sentiment analysis field has sprung up relevant to the issue of people's responses to the diversity of available subjects. Hence, one might well wonder: how do people feel and react when dealing with certain topics? In this paper, a new automatic sentiment-processing model has been advanced, whereby the current problems faced by the prevalent existing models can be deciphered and more properly treated. The suggested approach consists in developing a multi-agent system based on a thorough linguistic analysis, meanwhile highlighting the major contributions provided by such a study in combination with the syntactic, semantic, and subjective analyses. Actually, the newly-devised framework enables to resolve the ambiguities and complexities of the natural evaluative language and to strengthen, as well as consolidate, the results achieved at the various analysis stages thereof.
WAVELET CHARACTERIZATIONS OF MULTI-DIRECTIONAL REGULARITY
Authors: SLIMANE MOURAD BEN
Published: December 2012

The study of d dimensional traces of functions of m several variables leads to directional behaviors. The purpose of this paper is two-fold. Firstly, we extend the notion of one direction pointwise Hölder regularity introduced by Jaffard to multi-directions. Secondly, we characterize multi-directional pointwise regularity by Triebel anisotropic wavelet coefficients (resp. leaders), and also by Calderón anisotropic continuous wavelet transform.
COMPLEXITY OF THE FIBONACCI SNOWFLAKE
Authors: MASSÉ ALEXANDRE BLONDIN , BRLEK SREČKO , LABBÉ SÉBASTIEN , FRANCE MICHEL MENDÈS
Published: December 2012

The object under study is a particular closed and simple curve on the square lattice ℤ2 related with the Fibonacci sequence Fn. It belongs to a class of curves whose length is 4F3n+1, and whose interiors tile the plane by translation. The limit object, when conveniently normalized, is a fractal line for which we compute first the fractal dimension, and then give a complexity measure.
MULTIFRACTAL CROSS-CORRELATION ANALYSIS BASED ON STATISTICAL MOMENTS
Authors: WANG JING , SHANG PENGJIAN , GE WEIJIE
Published: December 2012

We introduce a new method, multifractal cross-correlation analysis based on statistical moments (MFSMXA), to investigate the long-term cross-correlations and cross-multifractality between time series generated from complex system. Efficiency of this method is shown on multifractal series, comparing with the well-known multifractal detrended cross-correlation analysis (MFXDFA) and multifractal detrending moving average cross-correlation analysis (MFXDMA). We further apply this method on volatility time series of DJIA and NASDAQ indices, and find some interesting results. The MFSMXA has comparative performance with MFXDMA and sometimes perform slightly better than MFXDFA. Multifractal nature exists in volatility series. In addition, we find that the cross-multifractality of volatility series is mainly due to their cross-correlations, via comparing the MFSMXA results for original series with those for shuffled series.
AN APPLICATION OF MATTING LAPLACIAN MATRIX TO RANGE IMAGE SUPER-RESOLUTION
Authors: YANG YUXIANG , WANG ZENGFU
Published: December 2012

This paper describes a successful application of Matting Laplacian Matrix to the problem of generating high-resolution range images. The Matting Laplacian Matrix in this paper exploits the fact that discontinuities in range and coloring tend to co-align, which enables us to generate high-resolution range image by integrating regular camera image into the range data. Using one registered and potentially high-resolution camera image as reference, we iteratively refine the input low-resolution range image, in terms of both spatial resolution and depth precision. We show that by using such a Matting Laplacian Matrix, we can get high-quality high-resolution range images.
A PLATFORM FOR SERVICE PROVIDER TO ADVERTISE QUALITY OF SERVICE USING WSDL
Authors: PANDEY RAVI SHANKAR
Published: December 2012

Web services are programs which perform some elementary business process of an application and are distributed over the Internet. These services are described, discovered and executed using standard languages WSDL, SOAP and UDDI. Proliferation of web services has resulted in intense competition between providers, which provide the same service. To survive in such a competitive environment, they need to advertise the quality of their service. Web service description language does not provide support to describe quality attributes. Recently, DAmbrogio proposed QOS model of web services based on a meta model of WSDL. In this paper, we present a platform to advertise QOS as declared by the service provider. This tool generates a WSDL file from Java code along with its quality of service attributes. It accepts Java code and a file containing quality attributes. These attributes include reliability, availability, and operation demand and operation latency. These attributes are included in WSDL file as a content of description element.
Single-Photon Single-Ion Interaction in Free Space Configuration in Front of a Parabolic Mirror
Authors: Stobińska Magdalena , Alicki Robert
Published: December 2012

The efficient interaction between single photons and single matter objects in free space is of key importance for quantum technologies. An experimental setup for testing this possibility involves single two-level ion trapped at the focus of a parabolic metallic mirror. We study the conditions for the setup, under which the assumption about the free-space mode structure of the radiation field in the vicinity of the atom is justified. In our analysis we apply vectorial properties of light by including the polarization degree of freedom. We look for possible changes in the spontaneous emission rate of the atom resulting from the presence of the parabolic boundary conditions.
Some Coding Theorems Based on Three Types of the Exponential Form of Cost Functions
Authors: Kumar Satish , Choudhary Arun
Published: December 2012

In the present communication three generalizations of 'useful' mean length of codewords of memoryless source outputs are given. Lower and upper bounds are also derived for these generalized 'useful' mean lengths in terms of 'useful' R-norm entropy