bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary instability of Jeans mode in a gravitating fluid with uniform rotation
Authors: Chakrabarti Nikhil
Published: June 2011

An axisymmetric rotating gas in a gravitational field is examined for its stability to two dimensional disturbances with first azimuthal mode. It is shown that a quasi-equilibrium is established when pressure and Coriolis force act against primary Jeans instability. A linear perturbation on this inhomogeneous equilibrium gives rise to secondary instability, which grows differently from homogeneous case. A stationary phase integral method demonstrates that the instability grows algebraically due to the free energy associated with the axisymmetric equilibrium. This secondary Jeans instability may have some bearing with the structure formations in the universe.
Enhanced performance of room-temperature-grown epitaxial thin films of vanadium dioxide
Authors: Nag Joyeeta , Payzant E. Andrew , More Karren L. , Haglund Richard F.
Published: June 2011

Vanadium dioxide (VO2) in bulk, thin-film, and nanostructured forms exhibits an insulator-to-metal transition accompanied by structural reorganization, induced by temperature, light, electric fields, doping, or strain. We have grown epitaxial films of VO2 on c-cut (0001) sapphire following two different procedures: (1) room-temperature growth followed by annealing and (2) direct high-temperature growth. We find that variations in strain at the film-substrate interface in the two protocols leads to differences in morphologies and transition characteristics. Our results show that room-temperature-grown epitaxial films have smoother morphologies and better switching contrast, analogous to the enhanced performance of epitaxially grown compound semiconductors.
A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. II. Coulomb interaction effects in single conjugated polymer chains
Authors: Miranda R. P. , Fisher A. J. , Stella L. , Horsfield A. P.
Published: June 2011

Conjugated polymers have attracted considerable attention in the last few decades due to their potential for optoelectronic applications. A key step that needs optimisation is charge carrier separation following photoexcitation. To understand better the dynamics of the exciton prior to charge separation, we have performed simulations of the formation and dynamics of localised excitations in single conjugated polymer strands. We use a nonadiabatic molecular dynamics method which allows for the coupled evolution of the nuclear degrees of freedom and of multiconfigurational electronic wavefunctions. We show the relaxation of electron-hole pairs to form excitons and oppositely charged polaron pairs and discuss the modifications to the relaxation process predicted by the inclusion of the Coulomb interaction between the carriers. The issue of charge photogeneration in conjugated polymers in dilute solution is also addressed.
Flexible drift-compensation system for precise 3D force mapping in severe drift environments
Authors: Rahe Philipp , Schütte Jens , Schniederberend Werner , Reichling Michael , Abe Masayuki , Sugimoto Yoshiaki , Kühnle Angelika
Published: June 2011

The acquisition of dense 3D data sets is of great importance, but also a challenge for scanning probe microscopy (SPM). Thermal drift often induces severe distortions in the data, which usually constrains the acquisition of dense data sets to experiments under ultra-high vacuum and low-temperature conditions. Atom tracking is an elegant approach to compensate for thermal drift and to position the microscope tip with highest precision. Here, we present a flexible drift compensation system which can easily be connected to existing SPM hardware. Furthermore, we describe a 3D data acquisition and position correction protocol, which is capable of handling large and non-linear drift as typically present in room temperature measurements. This protocol is based on atom-tracking for precise positioning of the tip and we are able to acquire dense 3D data sets over several hours at room temperature. The performance of the protocol is demonstrated by presenting 3D data taken on a ${\rm CaCO}_\text{3}$ CaCO 3$(10\overline{1}4)$(101¯4) surface with the data density being as large as 85×85×500 pixel.
30-band k⋅p method for quantum semiconductor heterostructures
Authors: Boyer-Richard S. , Raouafi F. , Bondi A. , Pédesseau L. , Katan C. , Jancu J.-M. , Even J.
Published: June 2011

We illustrate how the linear combination of zone center bulk bands combined with the full-zone k⋅p method can be used to accurately compute the electronic states in semiconductor nanostructures. To this end we consider a recently developed 30-band model which carefully reproduces atomistic calculations and experimental results of bulk semiconductors. The present approach is particularly suited both for short-period superlattices and large nanostructures where a three-dimensional electronic structure is required. This is illustrated by investigating ultrathin GaAs/AlAs superlattices.
Effects of disordered interchain interactions on polaron dynamics in semiconducting polymers
Authors: Yuan Xiao-Juan , Dong Xian-Feng , Li Dong-Mei , Liu De-Sheng
Published: June 2011

Polaron dynamics in a system of two randomly coupled polymer chains is simulated using a nonadiabatic evolution method. The simulations are performed within the framework of the Su-Schrieffer-Heeger model modified to include disordered interchain interactions and an external electric field. By analysing the polaron velocity statistically, we find that the polaron motion is determined by the competition between the electric field and the disordered interchain interactions. Polaron dynamics are classified into two types, weak-coupling dynamics and strong-coupling dynamics. It is found that the strength of interchain interactions is the dominant factor controlling charge propagation in weak-coupling dynamics, whereas the effects of disorder are dominant in strong-coupling dynamics. The charge carriers tend to have higher mobility for stronger interchain coupling, and interchain coupling disorder can be favorable for charge transport depending on the coupling strength and the electric field.
Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: Effect of changes in bond-stretching force-field terms
Authors: Pereverzev Andrey , Sewell Thomas D.
Published: June 2011

Terahertz (THz) active normal-mode relaxation in crystalline pentaerythritol tetranitrate (PETN) was studied using classical molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Two modifications to the fully flexible non-reactive force field due to Borodin et al. [J. Phys. Chem. B 112, 734 (2008)]10.1021/jp076149f used in a previous study of THz-active normal-mode relaxation in PETN [J. Chem. Phys. 134, 014513 (2011)]10.1063/1.3518423 were considered to assess the sensitivity of the earlier predictions to details of the covalent bond-stretching terms in the force field. In the first modification the harmonic bond-stretching potential was replaced with the Morse potential to study the effect of bond anharmonicity on the THz-region mode relaxation. In the second modification the C-H and nitro-group N-O bond lengths were constrained to constant values to mimic lower quantum occupation numbers for those high-frequency modes. The results for relaxation times of the initially excited modes were found to be insensitive to either force-field modification. Overall time scales for energy transfer to other modes in the system were essentially unaffected by the force-field modifications, whereas the detailed pathways by which the energy transfer occurs are more complicated for the Morse potential than for the harmonic-bond and fixed-bond cases. Terahertz infrared absorption spectra constructed using calculated normal-mode frequencies, transition dipoles, and relaxation times for THz-active modes were compared to the spectra obtained from the Fourier transform of the dipole-dipole time autocorrelation function (DDACF). Results from the two approaches are in near agreement with each other and with experimental results in terms of main peak positions. Both theoretical methods yield narrower peaks than observed experimentally and in addition predict a weaker peak at ω ∼ 50 cm−1 that is weak or absent experimentally. Peaks obtained using the DDACF approach are broader than those obtained from the normal-mode relaxation method.
Subcell I-V characteristic analysis of GaInP/GaInAs/Ge solar cells using electroluminescence measurements
Authors: Roensch Sebastian , Hoheisel Raymond , Dimroth Frank , Bett Andreas W.
Published: June 2011

The I-V characteristics of the individual subcells of a monolithic Ga0.50In0.50P/Ga0.99In0.01As/Ge triple-junction solar cell have been extracted from measurements of the electroluminescence peak intensity as a function of the electroluminescence injection current. By using the spectral reciprocity relation between the electroluminescence and the quantum efficiency, the individual subcell I-V characteristics were derived. It is shown that the subcell dark I-V characteristics and the subcell illuminated I-V characteristics are accessible under variable spectral illumination conditions.
Mictomagnetic behavior of structurally disordered melt-spun DyMn6−xGe6−xFexAlx (0 ≤ x ≤ 6) alloys
Authors: Śniadecki Z. , Grenèche J.-M. , Idzikowski B.
Published: June 2011

The presence of magnetic clusters with different chemical and/or geometric order (e.g., regions with various Fe atoms content) in some of the melt-spun DyMn6−xGe6−xFexAlx (0 ≤ x ≤ 6) alloys of amorphous structure is indicated. This statement is based on macroscopic magnetic measurements M(T), M(H), ac susceptibility, as well as those of microscopic 57Fe Mössbauer spectrometry. With decreasing Fe content, an increase in the hyperfine field strength Bhyp as well as that in the volume of the magnetic fraction in the alloy is observed. The Mössbauer effect investigations on the DyMn3Ge3Fe3Al3 alloy suggest the presence of magnetic fluctuations because the magnetic component increases after applying an external field. ac susceptibility measurements confirm the presence of spin dynamics. There is a cusp in the temperature dependence of the real part of magnetic susceptibility χ′(T) with a significant shift in freezing temperature Tf measured at different frequencies. The Vogel-Fulcher law and critical slowing-down power law were used to characterize the spin dynamics. The analysis suggests the presence of mictomagnetic order in the alloys investigated.
Large-area uniform graphene-like thin films grown by chemical vapor deposition directly on silicon nitride
Authors: Sun Jie , Lindvall Niclas , Cole Matthew T. , Teo Kenneth B. K. , Yurgens August
Published: June 2011

Large-area uniform carbon films with graphene-like properties are synthesized by chemical vapor deposition directly on Si3N4/Si at 1000 °C without metal catalysts. The as deposited films are atomically thin and wrinkle- and pinhole-free. The film thickness can be controlled by modifying the growth conditions. Raman spectroscopy confirms the sp2 graphitic structures. The films show ohmic behavior with a sheet resistance of ∼2.3–10.5 kΩ/◻ at room temperature. An electric field effect of ∼2–10% (VG=−20 V) is observed. The growth is explained by the self-assembly of carbon clusters from hydrocarbon pyrolysis. The scalable and transfer-free technique favors the application of graphene as transparent electrodes.
Hybrid organic-inorganic light-emitting electrochemical cells using fluorescent polymer and ionic liquid blend as an active layer
Authors: Lee Hyun Jung , Lee Bo Ram , Park Ji Sun , Kim Sang Ouk , Kim Jin Young , Song Myoung Hoon
Published: June 2011

We demonstrate enhanced device performance by using a blend of emissive polymer and mobile ionic liquid molecules in hybrid organic-inorganic polymeric light-emitting electrochemical cells with high air stability. The mobile anions and cations redistributed near each electrode/active layer interface make ohmic contacts, thereby enhancing current density and electroluminescence efficiency at relatively low operating voltage.
Pop-up archival satellite tagging of Carcharias taurus: movements and depth/temperature-related use of south-eastern Australian waters
Authors: Otway N. M. , Ellis M. T.
Published: June 2011

Knowledge of migratory movements and depth/temperature-related use of coastal waters by sharks can lead to more sustainable fisheries and assist in managing the long-term conservation of those species now considered threatened. Pop-up archival satellite tags (PATs) provide an alternative to conventional tagging for documenting migratory movements. This study focussed on the migratory movements of Carcharias taurus, a critically endangered shark found along the east coast of Australia. From October 2003 to July 2008, 15 C. taurus individuals were tagged with PATs with varying deployments (60–150 days) and acoustic tags linked to an acoustic monitoring system providing accurate geo-location. Distances moved by C. taurus individuals ranged from 5 to 1550 km and varied according to sex and season. Migrations north and south were punctuated en route by occupation of sites for varying periods of time. The deepest depth recorded was 232 m off South West Rocks on the New South Wales mid-north coast. On average, C. taurus males and females spent at least 71% of their time in waters <40 m and 95% of their time in waters 17–24°C. By mainly occupying inshore waters, C. taurus is exposed to potentially adverse fishing-related interactions that may be difficult to mitigate.
Fine-scale spatial and seasonal partitioning among large sharks and other elasmobranchs in south-eastern Queensland, Australia
Authors: Taylor Stephen , Sumpton Wayne , Ham Tony
Published: June 2011

Our understanding of the ecological role of larger elasmobranchs is limited by a lack of information on their spatial and seasonal abundance. Analysis of 14 years of gill-net catch data in south-eastern Queensland, Australia, revealed that the species composition of large sharks and other elasmobranchs significantly differed among beaches and seasons. Spinner sharks (Carcharhinus brevipinna) and hammerhead sharks (Sphyrna spp.) comprised nearly half the catch of all elasmobranchs. Although the distribution of these sharks overlapped, spatial variation existed in their abundance. Spinner sharks characterised the catch at Sunshine Coast beaches, whereas the catch at Gold Coast beaches was dominated by hammerhead sharks. Seasonal differences in elasmobranch community structure were also apparent, driven largely by a lower abundance of many species during the winter and the predominance of species such as spinner sharks and hammerheads in spring and summer. The present study provides the first quantitative data for numerous species of Carcharhiniformes in south-eastern Queensland and demonstrates that analysis of catch-rate data can improve our understanding of how larger sharks partition resources.
Description of the mechanoreceptive lateral line and electroreceptive ampullary systems in the freshwater whipray, Himantura dalyensis
Authors: Marzullo Teagan A. , Wueringer Barbara E. , Jnr Lyle Squire , Collin Shaun P.
Published: June 2011

Mechanoreceptive and electroreceptive anatomical specialisations in freshwater elasmobranch fishes are largely unknown. The freshwater whipray, Himantura dalyensis, is one of a few Australian elasmobranch species that occur in low salinity (oligohaline) environments. The distribution and morphology of the mechanoreceptive lateral line and the electroreceptive ampullae of Lorenzini were investigated by dissection and compared with previous studies on related species. The distribution of the pit organs resembles that of a marine ray, Dasyatis sabina, although their orientation differs. The lateral line canals of H. dalyensis are distributed similarly compared with two marine relatives, H. gerrardi and D. sabina. However, convolutions of the ventral canals and proliferations of the infraorbital canal are more extensive in H. dalyensis than H. gerrardi. The intricate nature of the ventral, non-pored canals suggests a mechanotactile function, as previously demonstrated in D. sabina. The ampullary system of H. dalyensis is not typical of an obligate freshwater elasmobranch (i.e. H. signifer), and its morphology and pore distribution resembles those of marine dasyatids. These results suggest that H. dalyensis is euryhaline, with sensory systems adapted similarly to those described in marine and estuarine species.
Rediscovery and redescription of the smoothtooth blacktip shark, Carcharhinus leiodon (Carcharhinidae), from Kuwait, with notes on its possible conservation status
Authors: Moore Alec B. M. , White William T. , Ward Robert D. , Naylor Gavin J. P. , Peirce Richard
Published: June 2011

The smoothtooth blacktip shark, Carcharhinus leiodon, is one of the rarest whaler shark species of the genus Carcharhinus, previously known only from the holotype collected over 100 years ago from the Arabian Sea coast of Yemen. Recent market surveys in the Persian (Arabian) Gulf rediscovered 25 specimens (~2% of individual sharks recorded) in Kuwait, ~3000 km away from the type location. This study combined morphometric and molecular approaches to provide a detailed redescription of this species based on new material, as well as the first information on fresh colouration, size range and maturity. Sequences from two separate regions of the mitochondrial genome (COI and ND2) support the identity of C. leiodon as a distinct species, closely related to C. limbatus, C. amblyrhynchoides and C. tilstoni. Carcharhinus leiodon is superficially similar to, but clearly distinct from, C. melanopterus and C. amblyrhynchoides. The previously uncertain type locality of C. leiodon is considered to be correct, and the narrow range and unusual disjunct distribution, relatively rare for a marine carcharhinid, is discussed. The Kuwait population of C. leiodon, including juveniles, is subject to fisheries by-catch and is in an area of extensive habitat alteration. As a result, C. leiodon is considered vulnerable, requiring urgent conservation action.
Changing patterns of shark attacks in Australian waters
Authors: West John G.
Published: June 2011

Although infrequent, shark attacks attract a high level of public and media interest, and often have serious consequences for those attacked. Data from the Australian Shark Attack File were examined to determine trends in unprovoked shark attacks since 1900, particularly over the past two decades. The way people use the ocean has changed over time. The rise in Australian shark attacks, from an average of 6.5 incidents per year in 1990–2000, to 15 incidents per year over the past decade, coincides with an increasing human population, more people visiting beaches, a rise in the popularity of water-based fitness and recreational activities and people accessing previously isolated coastal areas. There is no evidence of increasing shark numbers that would influence the rise of attacks in Australian waters. The risk of a fatality from shark attack in Australia remains low, with an average of 1.1 fatalities year–1 over the past 20 years. The increase in shark attacks over the past two decades is consistent with international statistics of shark attacks increasing annually because of the greater numbers of people in the water.
Activation-induced cytidine deaminase mediates central tolerance in B cells
Authors: Kuraoka Masayuki , Holl T. Matt , Liao Dongmei , Womble Mandy , Cain Derek W. , Reynolds Alexander E. , Kelsoe Garnett
Published: June 2011

TheAicdagene product, activation-induced cytidine deaminase (AID), initiates somatic hypermutation, class-switch recombination, and gene conversion of Ig genes by the deamination of deoxycytidine, followed by error-prone mismatch- or base-excision DNA repair. These processes are crucial for the generation of genetically diverse, high affinity antibody and robust humoral immunity, but exact significant genetic damage and promote cell death. In mice, physiologically significant AID expression was thought to be restricted to antigen-activated, mature B cells in germinal centers. We now demonstrate that low levels of AID in bone marrow immature and transitional B cells suppress the development of autoreactivity.Aicda−/−mice exhibit significantly increased serum autoantibody and reduced capacity to purge autoreactive immature and transitional B cells. In vitro, AID deficient immature/transitional B cells are significantly more resistant to anti-IgM–induced apoptosis than their normal counterparts. Thus, early AID expression plays a fundamental and unanticipated role in purging self-reactive immature and transitional B cells during their maturation in the bone marrow.
Hikma muta‘aliya in Qajar Iran: Locating the Life and Work of Mulla Hadi Sabzawari (d. 1289/1873)
Authors: Rizvi Sajjad H.
Published: June 2011

The Qajar period witnessed a revival of traditional Islamic philosophy based on the philosophical method of the Safavid sage Mulla Sadra Shirazi. This was philosophy as a way of life, an ethical commitment born of a method that combined both rational discourse and mystical intuition, deployed to defend the intellectual and cultural norms of the old learning against the new European inspired centers in Qajar Iran. A prominent figure in this process of revival was Mulla Hadi Sabzavari, who trained in the seminaries of Mashhad and Isfahan and became the most famous teacher of the works of Mulla Sadra and of philosophy in the second half of the nineteenth century. This paper examines his life and intellectual and pedagogical contribution, and traces some lines of his impact on seminarian philosophy into the twentieth century through the many students who came to study with him in his hometown, including his influence on modern trends within Shi‘i jurisprudence and legal theory.
The German Other: Nasir al-Din Shah's Perceptions of Difference and Gender during his Visits to Germany, 1873–89
Authors: Motadel David
Published: June 2011

The article examines the travelogues kept by the Qajar ruler Nasir al-Din Shah during his European tours in 1873, 1878 and 1889. To the monarch, Europe appeared to be an exotic and at times troubling place and he recorded his experiences with delight, criticism and humor. Focusing on his notes on Germany, the article explores Nasir al-Din Shah's encounters with people on the streets and at court, and in particular his perception of the female sex. Scholarship has either neglected the diaries or rejected them as a historical source, referring to the strong influence of literary convention and the Shah's alleged lack of understanding of the political, social and cultural conditions in Europe. Drawing on the uncensored versions of the diaries, the article argues that a closer look at the texts reveals fruitful, often amusing, insight into the monarch's experiences with social roles and cultural patterns alien to him. It suggests that a more careful reading of the diaries will also be beneficial in regard to the Shah's perception of European history and monuments, technology and scientific innovations, and landscape.
Combustion-assisted plasma in fuel conversion
Authors: Gutsol A , Rabinovich A , Fridman A
Published: June 2011

The long history of plasma application for fuel conversion shows that reasonably low specific energy requirement has been achieved in most cases using non-equilibrium systems with relatively high local temperature (‘warm’ plasmas). Analysis of reasons for this trend presented in this paper indicates that transitional warm plasma discharge systems are optimal for large-scale fuel processing. This analysis also reveals one specific feature of warm discharges that was not discussed earlier: warm discharge-based plasma-chemical systems are very sensitive to gas temperature and chemical reactions. When temperature reaches the level that is high enough to support chemical reactions in a particular system (ignition temperature), chemical reactions produce high concentration of excited molecules, and these molecules form a basis for stepwise ionization. This results in a significant drop in the energy necessary to support electric discharge in the system for two reasons. First, stepwise ionization that requires relatively low electron energy overcomes direct ionization that is typical for low-temperature non-equilibrium plasmas and requires much higher ionization energy. Second, high temperature of surrounding gas reduces heat losses from the discharge channel, while a significant portion of the discharge energy in warm plasma systems should be spent to compensate these losses. Thus, an intensive chemical reaction, e.g. combustion, supports the existence of a warm electric discharge.
Coke-free dry reforming of model diesel fuel by a pulsed spark plasma at low temperatures using an exhaust gas recirculation (EGR) system
Authors: Sekine Yasushi , Furukawa Naotsugu , Matsukata Masahiko , Kikuchi Eiichi
Published: June 2011

Dry reforming of diesel fuel, an endothermic reaction, is an attractive process for on-board hydrogen/syngas production to increase energy efficiency. For operating this dry reforming process in a vehicle, we can use the exhaust gas from an exhaust gas recirculation (EGR) system as a source of carbon dioxide. Catalytic dry reforming of heavy hydrocarbon is a very difficult reaction due to the high accumulation of carbon on the catalyst. Therefore, we attempted to use a non-equilibrium pulsed plasma for the dry reforming of model diesel fuel without a catalyst. We investigated dry reforming of model diesel fuel (n-dodecane) with a low-energy pulsed spark plasma, which is a kind of non-equilibrium plasma at a low temperature of 523 K. Through the reaction, we were able to obtain syngas (hydrogen and carbon monoxide) and a small amount of C2 hydrocarbon without coke formation at a ratio of CO2/Cfuel = 1.5 or higher. The reaction can be conducted at very low temperatures such as 523 K. Therefore, it is anticipated as a novel and effective process for on-board syngas production from diesel fuel using an EGR system.
Gaia: automated quality assessment of protein structure models
Authors: Kota Pradeep , Ding Feng , Ramachandran Srinivas , Dokholyan Nikolay V.
Published: June 2011

Motivation: Increasing use of structural modeling for understanding structure–function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.

Results: In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement.

Availability and Implementation: We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures.

Contact:  dokh@unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
Authors: Wrzodek Clemens , Dräger Andreas , Zell Andreas
Published: June 2011

Summary: The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms.

We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those.

Availability: KEGGtranslator is freely available as a Java™ Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application.

Contact:  clemens.wrzodek@uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
HIV: Long-Term Management and Palliative Care
Authors: Rigg Carolyn
Published: June 2011

The advent of antiretroviral therapy has radically changed the prognosis of human immunodeficiency virus (HIV) infection. HIV is now a treatable medical condition and is increasingly managed as a chronic disease. The majority of those living with the virus remain fit and well on treatment. However, those living with HIV are at risk of adverse effects due to antiretroviral treatment and increased risk of cardiovascular disease.
A probabilistic disease-gene finder for personal genomes
Authors: Yandell Mark , Huff Chad , Hu Hao , Singleton Marc , Moore Barry , Xing Jinchuan , Jorde Lynn B. , Reese Martin G.
Published: June 2011

VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds on existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and noncoding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. Here we demonstrate its ability to identify damaged genes using small cohorts (n = 3) of unrelated individuals, wherein no two share the same deleterious variants, and for common, multigenic diseases using as few as 150 cases.
B73-Mo17 Near-Isogenic Lines Demonstrate Dispersed Structural Variation in Maize
Authors: Eichten Steven R. , Foerster Jillian M. , de Leon Natalia , Kai Ying , Yeh Cheng-Ting , Liu Sanzhen , Jeddeloh Jeffrey A. , Schnable Patrick S. , Kaeppler Shawn M. , Springer Nathan M.
Published: June 2011

Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.
CESA5 Is Required for the Synthesis of Cellulose with a Role in Structuring the Adherent Mucilage of Arabidopsis Seeds
Authors: Sullivan Stuart , Ralet Marie-Christine , Berger Adeline , Diatloff Eugene , Bischoff Volker , Gonneau Martine , Marion-Poll Annie , North Helen M.
Published: June 2011

Imbibed Arabidopsis (Arabidopsis thaliana) seeds are encapsulated by mucilage that is formed of hydrated polysaccharides released from seed coat epidermal cells. The mucilage is structured with water-soluble and adherent layers, with cellulose present uniquely in an inner domain of the latter. Using a reverse-genetic approach to identify the cellulose synthases (CESAs) that produce mucilage cellulose, cesa5 mutants were shown to be required for the correct formation of these layers. Expression of CESA5 in the seed coat was specific to epidermal cells and coincided with the accumulation of mucilage polysaccharides in their apoplast. Analysis of sugar composition showed that although total sugar composition or amounts were unchanged, their partition between layers was different in the mutant, with redistribution from adherent to water-soluble mucilage. The macromolecular characteristics of the water-soluble mucilage were also modified. In accordance with a role for CESA5 in mucilage cellulose synthesis, crystalline cellulose contents were reduced in mutant seeds and birefringent microfibrils were absent from adherent mucilage. Although the mucilage-modified5 mutant showed similar defects to cesa5 in the distribution of sugar components between water-soluble and adherent mucilage, labeling of residual adherent mucilage indicated that cesa5 contained less cellulose and less pectin methyl esterification. Together, the results demonstrate that CESA5 plays a major and essential role in cellulose production in seed mucilage, which is critical for the establishment of mucilage structured in layers and domains.
Severe adverse cutaneous drug eruptions: epidemiological and clinical features
Authors: Zaraa Inès , Jones Meriem , Trojjet Sondes , Cheikh Rouhou Rym , El Euch Dalenda , Mokni Mourad , Ben Osman Amel
Published: June 2011

Introduction  Adverse cutaneous drug reactions (ACDR) are common, and some can be lethal. The aim of our study was to discuss the epidemiological and clinical features of severe ACDR.

Materials and methods  We retrospectively analyzed 100 cases of ACDR from 1981 to 2007, collected in the Department of Dermatology of the La Rabta Hospital in Tunis, which is located in the north of Tunisia. Severity was defined on three criteria: hospitalization; visceral involvement; and severity markers.

Results  Characteristics of the 54 included cases were: women (70%); mean age: 44.8 years; responsible drugs: anticonvulsants (28%), antibiotics (28%), and nonsteroidal anti‐inflammatory drugs (15%). The most common dermatoses were maculopapular rash (50%). We observed fever (76%), lymphadenopathy (31.5%), eosinophilia (35%), and visceral involvement (50%). Twelve patients died directly related to the ACDR.

Conclusion  This study underlines the polymorphous clinical presentation of ACDR and the importance of researching some severity markers, which have important practical implications.
Stress and quality of life in psoriasis: an update
Authors: Basavaraj Kabbur H. , Navya Mysore Ashok , Rashmi Ramesh
Published: June 2011

Psoriasis is a chronic, relapsing, cutaneous condition with 1–2% prevalence in the general population. There are many factors involved in the induction and/or exacerbation of psoriasis of which stress is a well‐known trigger factor in the appearance or exacerbation of psoriasis. Stress reaction in patients with psoriasis is probably mediated by the hypothalamic–pituitary–adrenal relationship with immunologic effects. Stress response involves increased levels of neuroendocrine hormones and autonomic neurotransmitters. Psychological stress or an abnormal response to stressors has been found to modify the evolution of skin disorders such as psoriasis. It can also have substantial psychological, and psychosocial impact on a patient’s quality of life. Treatment regimens include stress‐reduction strategies, such as biofeedback, meditation, yoga, and self‐help approaches. This review focuses the relationship between psoriasis and stress, especially relating to psychosocial, psychological, and emotional stress aspects.
DIRECT PERORAL CHOLANGIOSCOPY AND PANCREATOSCOPY FOR DIAGNOSIS OF A PANCREATOBILIARY FISTULA CAUSED BY AN INTRADUCTAL PAPILLARY MUCINOUS NEOPLASM OF THE PANCREAS: A CASE REPORT
Authors: SUNG KAI‐FENG , CHU YIN‐YI , LIU NAI‐JEN , HUNG CHIEN‐FU , CHEN TSE‐CHING , CHEN JINN‐SHIUN , LIN CHENG‐HUI
Published: June 2011

Here, we report a case of a pancreatobiliary (PB) fistula caused by an intraductal papillary mucinous neoplasm (IPMN) of the pancreas. The PB fistula was suspected after endoscopic retrograde cholangiopancreatography (ERCP) and diagnosed after direct visualization with a direct peroral cholangioscopy and pancreatoscopy by using an ultra‐slim endoscope. No previous reports exist on the precise diagnosis of a PB fistula with direct peroral cholangioscopy and pancreatoscopy. In our case report, a 69‐year‐old man underwent an ERCP because of a pancreatic head mass and biliary tract obstruction. During ERCP, a fistula between the common bile duct (CBD) and main pancreatic duct (MPD) was suspected. After endoscopic sphincterotomy, we examined both the CBD and MPD with an ultra‐slim videoendoscope (GIF‐N260; Olympus Optical Co, Tokyo, Japan) under direct visualization and biopsy of the mass. The analysis of the biopsy specimen confirmed this mass to be an IPMN of the pancreas. When we examined the CBD, one fistula with copious mucin secretion was identified at the distal CBD. In conclusion, direct peroral cholangioscopy and pancreatoscopy using the ultra‐slim endoscope is an efficient tool for diagnosis of PB fistula and pancreatic IPMN.
Serum markers for necroinflammatory activity in patients with chronic viral hepatitis and normal or mildly elevated aminotransferase levels
Authors: Cheong Jae Y. , Kim Dong J. , Hwang Seong G. , Yang Jin M. , Kim Young B. , Park Young N. , Cho Sung W.
Published: June 2011

Background: Reports on the usefulness of serum markers for predicting liver necroinflammation are limited. The aim of this study was to determine the serum markers that predict significant inflammation in patients with chronic hepatitis B (CHB) and C (CHC) and normal or mildly elevated serum aminotransferase levels.

Methods: Two hundred twenty‐seven patients with CHB or CHC with normal or mildly elevated serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels (≤60 IU/L) were enrolled in this study. Significant inflammation was defined as inflammatory grade ≥3 activities using the Batt–Ludwig scoring system. The correlation between liver histology and serum markers of liver inflammation was analysed.

Results: Forty‐eight (21.1%) and eight patients (3.5%) had grade 3 and 4 inflammation respectively. Univariate analysis revealed that age, platelet coun, and AST, ALT, γ‐glutamyl transpeptidase, alkaline phosphatase, hyaluronic acid, haptoglobin, apolipoprotein A1 and procollagen III N‐terminal peptide levels were significantly different between the patients with and without significant inflammation. There were no significant differences in the cytokeratin‐18 fragment levels between the two groups. On the basis of multivariate analysis, the AST and apolipoprotein A1 levels and stage of fibrosis were highly predictive of significant inflammation. Using AST and apolipoprotein cut‐off values ≥44 IU/L and ≤100 ng/ml, respectively, the presence of significant inflammation was predicted with high specificity (96.5%) and with a negative predictive value of 76.3%.

Conclusion: The AST and apolipoprotein A1 levels were shown to be independent predictors of significant inflammatory activities in patients with CHB and CHC and normal or mildly elevated aminotransferase levels.
Evaluation of the Regional Cerebral Blood Flow Changes during Long‐Term Donepezil Therapy in Patients with Alzheimer's Disease Using 3DSRT
Authors: Kimura Noriyuki , Kumamoto Toshihide , Masuda Teruaki , Hanaoka Takuya , Okazaki Toshio , Arakawa Ryuki
Published: June 2011

BACKGROUND

We attempt to evaluate objectively the regional cerebral blood flow (rCBF) changes during long‐term donepezil therapy and the relationship between the clinical response and rCBF change in patients with Alzheimer's disease (AD).

PATIENTS AND METHODS

Thirty‐one patients with mild‐to‐moderate AD (11 men, 20 female; mean age, 76.2 ± 6.7 years) were treated with donepezil and underwent brain perfusion single‐photon emission computed tomography (SPECT) twice with an interval of 24.5 ± 4.2 months. The rCBF was calculated using 3‐dimensional stereotaxic region of interest template, a fully automated each region of interest technique. We compared the differences in rCBF between baseline and follow‐up SPECT studies. Moreover, all patients were divided into stabilized (n= 14) and nonstabilized subgroups (n= 17) based on Mini‐Mental State Examination (MMSE) score changes and the changes in rCBF were compared between two subgroups.

RESULTS

The mean MMSE score significantly decreased from 20.7 ± 4.6 at baseline to 16.5 ± 6.5 after 2 years. The mean rCBF significantly decreased in the widespread brain regions between the baseline and follow‐up SPECT studies. The nonstabilized subgroup showed a significant decrease in rCBF of the parietal and temporal segments compared to the stabilized subgroup.

CONCLUSION

The progression of cognitive deterioration may be related to rCBF affected by the neuropathologic changes of AD.
Neocortical Atrophy in Machado‐Joseph Disease: A Longitudinal Neuroimaging Study
Authors: D’Abreu Anelyssa , França Jr. Marcondes C. , Yasuda Clarissa L. , Campos Bruno A. G. , Lopes‐Cendes Iscia , Cendes Fernando
Published: June 2011

BACKGROUND/PURPOSE

Previous imaging studies in the Machado‐Joseph disease (MJD/SCA3) have mostly concentrated on the cerebellum and brainstem. Our goal was to perform a whole brain longitudinal evaluation.

METHODS

We included 45 patients and 51 controls, who underwent two brain magnetic resonance imaging and magnetic resonance spectroscopy (mean interval of 12.5 ± 1.5 months). We used voxel‐based morphometry (VBM) and the MarsBar analysis toolbox to extract grey matter density (GMD) values from regions of interest. We used a linear regression model and a general linear model to correlate GMD with clinical markers, and paired t‐test for the longitudinal evaluation.

RESULTS

We observed decreased GMD (P < .01) at frontal, parietal, temporal and occipital lobes, subcortical grey matter, cerebellum, and brainstem. White matter atrophy was restricted to the cerebellum. Age, CAG, and disease duration predicted GMD in different areas, but age and CAG were the most important predictors. The longitudinal analysis failed to demonstrate changes. Changes in regions other than the cerebellum appeared to contribute significantly to the final International Cooperative Ataxia Rating Scale score.

CONCLUSION

We confirmed cortical involvement in MJD/SCA3. The most important factors in predicting GMD were age and CAG. The lack of progression of atrophy may indicate floor effect and/or short duration of follow‐up.
USE OF CONE‐BEAM COMPUTED TOMOGRAPHY TO CHARACTERIZE DAILY URINARY BLADDER VARIATIONS DURING FRACTIONATED RADIOTHERAPY FOR CANINE BLADDER CANCER
Authors: NIESET JESSICA R. , HARMON JOSEPH F. , LARUE SUSAN M.
Published: June 2011

Urinary bladder cancer is difficult to treat accurately with fractionated radiation therapy (RT) due to daily positional changes of the bladder and surrounding soft‐tissue structures. We quantified the daily motion experienced by the canine bladder with patients in dorsal vs. sternal vs. lateral recumbency. We also described the dose distribution for three different planning target volume expansions (5, 10, and 15 mm) for each of the three positions to ensure adequate bladder dose and minimize irradiation of nearby healthy tissues. Analysis was based on data from retrospective daily cone‐beam computed tomography (CT) (CBCT) images obtained for positioning of canine patients undergoing routine RT. Organs of interest were contoured on each CBCT data set and the images, along with the contours, were registered to the original planning CT. All measurements were made relative to the planning CT and dosimetric data for the organs of interest was determined using a dose volume histogram generated from sample parallel‐opposed beam configuration. There was a wide range in bladder position throughout treatment. The least amount of bladder variation and the lowest rectal dose was with dogs in lateral recumbency. It was also determined that a margin of 10 mm would allow for sufficient dose to be delivered to the bladder while minimizing rectal dose.
Racial Differences in Sexuality Profiles Among American, Japanese, and Japanese American Men with Localized Prostate Cancer
Authors: Namiki Shunichi , Carlile Robert G. , Namiki Thomas S. , Fukagai Takashi , Takegami Misa , Litwin Mark S. , Arai Yoichi
Published: June 2011

Introduction

Although there were marked racial differences in the clinical outcomes among Japanese men (JP), Caucasian men (CA), and Japanese American (JA) men with localized prostate cancer, the effect of race/ethnicity on sexual profiles remains unclear.

Aim

To determine differences of sexual profiles in JP, CA, and JA with localized prostate cancer.

Methods

A total of 412 JP, 352 CA, and 54 JA with clinically localized prostate cancer were enrolled in separate studies of health-related quality of life outcomes. We developed a collaborative study in each database.

Main Outcome Measure

Sexual function and bother were estimated before treatment with validated English and Japanese versions of the University of California in Los Angeles Prostate Cancer Index (UCLA PCI).

Results

The CA reported the highest sexual function score of all. Even after controlling for age, prostate specific antigen, clinical T stage, Gleason score and comorbidity, the JP were more likely than the CA to report poor sexual desire, poor erection ability, poor overall ability to function sexually, and poor ability to attain orgasm. With regard to sexual bother, however, no differences were reported between CA and JP. The JA reported sexual function closely approximate that of the JP, and they were less likely than the CA to report erection ability and intercourse. The JA were more likely to feel distress from their sexual function than the CA. When the JA were divided into two groups according to the ethnicity of their partners, UCLA PCI sexual function scores were equivalent between JA-partnered men and men partnered with other races. On the other hand, JA-partnered men were significantly less likely to report sexual bother scores than men partnered with other races.

Conclusion

We found significant interethnic variations among CA, JP, and JA with prostate cancer in terms of their sexual profiles. Ethnicity and/or country appear to modify some of these variables.
Why Larger Lenders Obtain Higher Returns: Evidence from Sovereign Syndicated Loans
Authors: Hallak Issam , Schure Paul
Published: June 2011

Lenders who make large funding commitments earn higher rates of return than those who make smaller commitments. We analyze a data set of sovereign syndicated loan contracts to document study and this phenomenon. We show that the “large lenders” in the lending syndicates earn a “return premium,” which is positively affected by the likelihood of future liquidity problems of the borrower. This finding suggests that the onus would be on the large lenders in particular to provide services, such as liquidity insurance and coordinating the workout. The return premium also increases in the fraction of banks among the larger syndicate members, suggesting that banks are special lenders in terms of addressing idiosyncratic liquidity problems.