bluuebunny/crossref_metadata_2025 huggingface dataset:
Lattice distortions and octahedral rotations in epitaxially strained LaNiO3/LaAlO3 superlattices
Authors: Kinyanjui M. K. , Lu Y. , Gauquelin N. , Wu M. , Frano A. , Wochner P. , Reehuis M. , Christiani G. , Logvenov G. , Habermeier H.-U. , Botton G. A. , Kaiser U. , Keimer B. , Benckiser E.
Published: June 2014

Using a complementary combination of x-ray diffraction and atomically resolved imaging we investigated the lattice structure of epitaxial LaNiO3/LaAlO3 superlattices grown on a compressive-strain inducing LaSrAlO4 (001) substrate. A refinement of the structure obtained from the x-ray data revealed the monoclinic I 2/c 1 1 space group. The (Ni/Al)O6 octahedral rotation angle perpendicular to the superlattice plane is enhanced, and the one parallel to the plane is reduced with respect to the corresponding bulk values. High-angle annular dark field imaging was used to determine the lattice parameters within the superlattice unit cell. High-resolution electron microscopy images of the oxygen atoms are consistent with the x-ray results.
Localized modes in mini-gaps opened by periodically modulated intersite coupling in two-dimensional nonlinear lattices
Authors: Gligorić Goran , Maluckov Aleksandra , Hadžievski Ljupčo , Malomed Boris A.
Published: June 2014

Spatially periodic modulation of the intersite coupling in two-dimensional (2D) nonlinear lattices modifies the eigenvalue spectrum by opening mini-gaps in it. This work aims to build stable localized modes in the new bandgaps. Numerical analysis shows that single-peak and composite two- and four-peak discrete static solitons and breathers emerge as such modes in certain parameter areas inside the mini-gaps of the 2D superlattice induced by the periodic modulation of the intersite coupling along both directions. The single-peak solitons and four-peak discrete solitons are stable in a part of their existence domain, while unstable stationary states (in particular, two-soliton complexes) may readily transform into robust localized breathers.
Note: Experimental study on feasibility of a flexural traveling wave piezoelectric device for biomedical micro-electromechanical system
Authors: Marinozzi F. , Bini F.
Published: June 2014

The aim of this paper is to experimentally show that polyvinylidene fluoride biaxially oriented in bimorph configuration is a suitable flexural traveling wave device. Piezoelectric ceramic is promising, however the lack biocompatibility is the main drawback for biomedical micro-electromechanical system. A prototype of 20 mm diameter was designed, constructed, and tested via an optical method. A first investigation was performed on two standing waves which were excited to generate the traveling wave. The findings of amplitude and phase have revealed a B31vibration mode at 7.2 kHz and a maximum amplitude of roughly 40 nm. The flexural traveling wave was confirmed experimentally.
The quaternionic affine group and related continuous wavelet transforms on complex and quaternionic Hilbert spaces
Authors: Ali S. Twareque , Thirulogasanthar K.
Published: June 2014

By analogy with the real and complex affine groups, whose unitary irreducible representations are used to define the one- and two-dimensional continuous wavelet transforms, we study here the quaternionic affine group and construct its unitary irreducible representations. These representations are constructed both on a complex and on a quaternionic Hilbert space. As in the real and complex cases, the representations for the quaternionic group also turn out to be square-integrable. Using these representations we construct quaternionic wavelets and continuous wavelet transforms on both the complex and quaternionic Hilbert spaces.
Ferroelectric switching in epitaxial GeTe films
Authors: Kolobov A. V. , Kim D. J. , Giussani A. , Fons P. , Tominaga J. , Calarco R. , Gruverman A.
Published: June 2014

In this paper, using a resonance-enhanced piezoresponse force microscopy approach supported by density functional theory computer simulations, we have demonstrated the ferroelectric switching in epitaxial GeTe films. It has been shown that in films with thickness on the order of several nanometers reversible reorientation of polarization occurs due to swapping of the shorter and longer Ge-Te bonds in the interior of the material. It is also hinted that for ultra thin films consisting of just several atomic layers weakly bonded to the substrate, ferroelectric switching may proceed through exchange of Ge and Te planes within individual GeTe layers.
Effect of fluid medium on mechanical behavior of carbon nanotube foam
Authors: Misra Abha , Kumar Praveen , Raney Jordan R. , Singhal Anish , Lattanzi Ludovica , Daraio Chiara
Published: June 2014

This study reports the constitutive response and energy absorption capabilities of fluid-impregnated carbon nanotube (CNT) foams under compressive loading as a function of fluid viscosity and loading rates. At all strain rates tested, we observe two characteristic regimes: below a critical value, increasing fluid viscosity increases the load bearing and energy absorption capacities; after a critical value of the fluid's viscosity, we observe a rapid decrease in the systems' mechanical performance. For a given fluid viscosity, the load bearing capacity of the structure slightly decreases with strain rate. A phenomenological model, accounting for fluid-CNT interaction, is developed to explain the observed mechanical behavior.
Strong electron emission from antiferroelectric PLZT(2/95/5) films
Authors: Yaseen Muhammad , Lou Xiaojie , Chen Xiaofeng , Ren Wei , Liu Yang , Feng Yujun , Shi Peng , Wu Xiaoqing
Published: June 2014

Strong emission current of 500 mA/cm2 was observed in sol-gel derived antiferroelectric (AFE) PLZT (2/95/5) thick films at a trigger voltage of 150 V and a dc extraction voltage of 50 V. The PLZT emitters were found to be fatigue-free up to 106 emission cycles. Electron emission from our samples is believed to originate from the antiferroelectric-ferroelectric phase transition in the PLZT film emitters. Our results therefore indicate that PLZT could be a promising candidate for flat panel applications because of its higher saturated polarization and fatigue-free properties as compared to its ferroelectric counterparts.
On exact statistics and classification of ergodic systems of integer dimension
Authors: Guralnik Zachary , Pehlevan Cengiz , Guralnik Gerald
Published: June 2014

We describe classes of ergodic dynamical systems for which some statistical properties are known exactly. These systems have integer dimension, are not globally dissipative, and are defined by a probability density and a two-form. This definition generalizes the construction of Hamiltonian systems by a Hamiltonian and a symplectic form. Some low dimensional examples are given, as well as a discretized field theory with a large number of degrees of freedom and a local nearest neighbor interaction. We also evaluate unequal-time correlations of these systems without direct numerical simulation, by Padé approximants of a short-time expansion. We briefly speculate on the possibility of constructing chaotic dynamical systems with non-integer dimension and exactly known statistics. In this case there is no probability density, suggesting an alternative construction in terms of a Hopf characteristic function and a two-form.
The effect of Ta interface on the crystallization of amorphous phase change material thin films
Authors: Ghezzi G. E. , Noé P. , Marra M. , Sabbione C. , Fillot F. , Bernier N. , Ferrand J. , Maîtrejean S. , Hippert F.
Published: June 2014

The crystallization of amorphous GeTe and Ge2Sb2Te5 phase change material films, with thickness between 10 and 100 nm, sandwiched between either Ta or SiO2 layers, was investigated by optical reflectivity. Ta cladding layers were found to increase the crystallization temperature, even for films as thick as 100 nm. X-Ray diffraction investigations of crystallized GeTe films showed a very weak texture in Ta cladded films, in contrast with the strong texture observed for SiO2 cladding layers. This study shows that crystallization mechanism of phase change materials can be highly impacted by interface effects, even for relatively thick films.
Modulating resonance behaviors by noise recycling in bistable systems with time delay
Authors: Sun Zhongkui , Yang Xiaoli , Xiao Yuzhu , Xu Wei
Published: June 2014

In this paper, the impact of noise recycling on resonance behaviors is studied theoretically and numerically in a prototypical bistable system with delayed feedback. According to the interior cooperating and interacting activity of noise recycling, a theory has been proposed by reducing the non-Markovian problem into a two-state model, wherein both the master equation and the transition rates depend on not only the current state but also the earlier two states due to the recycling lag and the feedback delay. By virtue of this theory, the formulae of the power spectrum density and the linear response function have been found analytically. And the theoretical results are well verified by numerical simulations. It has been demonstrated that both the recycling lag and the feedback delay play a crucial role in the resonance behaviors. In addition, the results also suggest an alternative scheme to modulate or control the coherence or stochastic resonance in bistable systems with time delay.
Physical principles of microwave assisted magnetic recording
Authors: Rivkin Kirill , Benakli Mourad , Tabat Ned , Yin Huaqing
Published: June 2014

While the basic physics of Microwave Assisted Magnetization Reversal (MAMR) phenomenon is well established both theoretically and experimentally, its application in a practical magnetic recording environment was so far studied primarily with the help of micromagnetic recording models. In this work, we instead attempt to use analytical formulation and simple numerical models to understand the main challenges as well as benefits that are associated with such a system. It appears that the main difference between the previously introduced theory [G. Bertotti et al., Phys. Rev. Lett. 86, 724 (2001); K. Rivkin et al., Appl. Phys. Lett. 92, 153104 (2008); S. Okamoto et al., J. Appl. Phys. 107, 123914 (2010).] and recording environment is that both the RF and DC magnetic fields are applied at a substantial angle to the anisotropy axis. While the associated symmetry breaking prevents one from describing the reversal process explicitly, it is possible to approximate the solutions well enough to satisfactorily match numerical models both in the case of wire and Spin Torque Oscillator generated RF fields. This approach allows for physical explanation of various effects associated with MAMR such as high gradient of writeable anisotropy and reduction of track width, and offers a clear guidance regarding future optimization of MAMR recording.
Magnetic and dielectric behavior in YMn1−xFexO3 (x ≤ 0.5)
Authors: Sharma Neetika , Das A. , Mishra S. K. , Prajapat C. L. , Singh M. R. , Meena S. S.
Published: June 2014

The role of doping Fe on the structural, magnetic, and dielectric properties of frustrated antiferromagnet YMn1−xFexO3 (x ≤ 0.5) has been investigated. The neutron diffraction analysis shows that the structure of these polycrystalline samples changes from hexagonal phase (space group P63cm) to orthorhombic phase (space group Pnma) for x > 0.2. The frustration parameter decreases with Fe substitution. All the compounds are antiferromagnetic, and the magnetic structure is described as a mixture of Γ3 and Γ4 irreducible representation (IR) in the hexagonal phase, and the ratio of these two IRs is found to vary with Fe doping (x ≤ 0.2). A continuous spin reorientation as a function of temperature is observed in these samples. The magnetic ground state in the orthorhombic phase of the higher doped samples (x ≥ 0.3) is explained by taking Γ1 (GxCyAz) representation of Pnma setting. In YMnO3 suppression of dielectric constant ε′ is observed below TN indicative of magnetoelectric coupling. This anomalous behavior reduces in Fe doped samples. The dielectric constant is found to be correlated with the magnetic moment (M) obtained from neutron diffraction experiments and follows a M2 behavior close to TN in agreement with Landau theory.
Ultrafast electron diffraction using an ultracold source
Authors: van Mourik M. W. , Engelen W. J. , Vredenbregt E. J. D. , Luiten O. J.
Published: June 2014

The study of structural dynamics of complex macromolecular crystals using electrons requires bunches of sufficient coherence and charge. We present diffraction patterns from graphite, obtained with bunches from an ultracold electron source, based on femtosecond near-threshold photoionization of a laser-cooled atomic gas. By varying the photoionization wavelength, we change the effective source temperature from 300 K to 10 K, resulting in a concomitant change in the width of the diffraction peaks, which is consistent with independently measured source parameters. This constitutes a direct measurement of the beam coherence of this ultracold source and confirms its suitability for protein crystal diffraction.
Effects of emitted electron temperature on the plasma sheath
Authors: Sheehan J. P. , Kaganovich I. D. , Wang H. , Sydorenko D. , Raitses Y. , Hershkowitz N.
Published: June 2014

It has long been known that electron emission from a surface significantly affects the sheath surrounding that surface. Typical fluid theory of a planar sheath with emitted electrons assumes that the plasma electrons follow the Boltzmann relation and the emitted electrons are emitted with zero energy and predicts a potential drop of 1.03Te/e across the sheath in the floating condition. By considering the modified velocity distribution function caused by plasma electrons lost to the wall and the half-Maxwellian distribution of the emitted electrons, it is shown that ratio of plasma electron temperature to emitted electron temperature significantly affects the sheath potential when the plasma electron temperature is within an order of magnitude of the emitted electron temperature. When the plasma electron temperature equals the emitted electron temperature the emissive sheath potential goes to zero. One dimensional particle-in-cell simulations corroborate the predictions made by this theory. The effects of the addition of a monoenergetic electron beam to the Maxwellian plasma electrons were explored, showing that the emissive sheath potential is close to the beam energy only when the emitted electron flux is less than the beam flux.
The role of Nb in intensity increase of Er ion upconversion luminescence in zirconia
Authors: Smits K. , Sarakovskis A. , Grigorjeva L. , Millers D. , Grabis J.
Published: June 2014

It is found that Nb co-doping increases the luminescence and upconversion luminescence intensity in rare earth doped zirconia. Er and Yb-doped nanocrystalline samples with or without Nb co-doping were prepared by sol-gel method and thermally annealed to check for the impact of phase transition on luminescence properties. Phase composition and grain sizes were examined by X-ray diffraction; the morphology was checked by scanning- and high-resolution transmission electron microscopes. Both steady-state and time-resolved luminescence were studied. Comparison of samples with different oxygen vacancy concentrations and different Nb concentrations confirmed the known assumption that oxygen vacancies are the main agents for tetragonal or cubic phase stabilization. The oxygen vacancies quench the upconversion luminescence; however, they also prevent agglomeration of rare-earth ions and/or displacement of rare-earth ions to grain surfaces. It is found that co-doping with Nb ions significantly (>20 times) increases upconversion luminescence intensity. Hence, ZrO2:Er:Yb:Nb nanocrystals may show promise for upconversion applications.
On-chip lectin microarray for glycoprofiling of different gastritis types and gastric cancer
Authors: Roy Bibhas , Chattopadhyay Gautam , Mishra Debasish , Das Tamal , Chakraborty Suman , Maiti Tapas K.
Published: June 2014

An on-chip lectin microarray based glycomic approach is employed to identify glyco markers for different gastritis and gastric cancer. Changes in protein glycosylation have impact on biological function and carcinogenesis. These altered glycosylation patterns in serum proteins and membrane proteins of tumor cells can be unique markers of cancer progression and hence have been exploited to diagnose various stages of cancer through lectin microarray technology. In the present work, we aimed to study the alteration of glycan structure itself in different stages of gastritis and gastric cancer thoroughly. In order to perform the study from both serum and tissue glycoproteins in an efficient and high-throughput manner, we indigenously developed and employed lectin microarray integrated on a microfluidic lab-on-a-chip platform. We analyzed serum and gastric biopsy samples from 8 normal, 15 chronic Type-B gastritis, 10 chronic Type-C gastritis, and 6 gastric adenocarcinoma patients and found that the glycoprofile obtained from tissue samples was more distinctive than that of the sera samples. We were able to establish signature glycoprofile for the three disease groups, that were absent in healthy normal individuals. In addition, our findings elucidated certain novel signature glycan expression in chronic gastritis and gastric cancer. In silico analysis showed that glycoprofile of chronic gastritis and gastric adenocarcinoma formed close clusters, confirming the previously hypothesized linkage between them. This signature can be explored further as gastric cancer marker to develop novel analytical tools and obtain in-depth understanding of the disease prognosis.
Frustrated total internal reflection and critical coupling in a thick plasmonic grating with narrow slits
Authors: Mattiucci N. , D'Aguanno G. , Bloemer M. J. , Alù A.
Published: June 2014

We demonstrate the possibility of critical coupling through frustrated total internal reflection in a thick plasmonic grating below the first diffraction order. Differently from conventional approaches relying on the excitation of surface plasmon-polaritons, here we exploit the light coupling with the leaky modes supported by the grating. This mechanism entails a wide-angle coupling and effectively access spectral bands that would otherwise be difficult to probe using conventional plasmonic critical coupling techniques, such as the Otto configuration. Our finding may pave the way to efficient plasmonic bio-sensor devices.
Tunable ultracompact chip-integrated multichannel filter based on plasmon-induced transparencies
Authors: Yang Xiaoyu , Hu Xiaoyong , Chai Zhen , Lu Cuicui , Yang Hong , Gong Qihuang
Published: June 2014

Nanoscale multichannel filter is realized in plasmonic circuits directly, which consists of four plasmonic nanocavities coupled via a plasmonic waveguide etched in a gold film. The feature device size is only 1.35 μm, which is reduced by five orders of magnitude compared with previous reports. The optical channels are formed by transparency windows of plasmon-induced transparencies. A shift of 45 nm in the central wavelengths of optical channels is obtained when the plasmonic coupled-nanocavities are covered with a 100-nm-thick poly(methyl methacrylate) layer. This work opens up the possibility for the realization of solid quantum chips based on plasmonic circuits.
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
Authors: Parker Hilary S. , Leek Jeffrey T. , Favorov Alexander V. , Considine Michael , Xia Xiaoxin , Chavan Sameer , Chung Christine H. , Fertig Elana J.
Published: June 2014

Motivation: Sample source, procurement process and other technical variations introduce batch effects into genomics data. Algorithms to remove these artifacts enhance differences between known biological covariates, but also carry potential concern of removing intragroup biological heterogeneity and thus any personalized genomic signatures. As a result, accurate identification of novel subtypes from batch-corrected genomics data is challenging using standard algorithms designed to remove batch effects for class comparison analyses. Nor can batch effects be corrected reliably in future applications of genomics-based clinical tests, in which the biological groups are by definition unknown a priori.

Results: Therefore, we assess the extent to which various batch correction algorithms remove true biological heterogeneity. We also introduce an algorithm, permuted-SVA (pSVA), using a new statistical model that is blind to biological covariates to correct for technical artifacts while retaining biological heterogeneity in genomic data. This algorithm facilitated accurate subtype identification in head and neck cancer from gene expression data in both formalin-fixed and frozen samples. When applied to predict Human Papillomavirus (HPV) status, pSVA improved cross-study validation even if the sample batches were highly confounded with HPV status in the training set.

Availability and implementation: All analyses were performed using R version 2.15.0. The code and data used to generate the results of this manuscript is available from https://sourceforge.net/projects/psva .

Contact:  ejfertig@jhmi.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ABRA: improved coding indel detection via assembly-based realignment
Authors: Mose Lisle E. , Wilkerson Matthew D. , Hayes D. Neil , Perou Charles M. , Parker Joel S.
Published: June 2014

Motivation: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative.

Results: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation.

Availability and implementation: ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra .

Contact:  lmose@unc.edu ; parkerjs@email.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
Authors: Kim Jihoon , Levy Eric , Ferbrache Alex , Stepanowsky Petra , Farcas Claudiu , Wang Shuang , Brunner Stefan , Bath Tyler , Wu Yuan , Ohno-Machado Lucila
Published: June 2014

Summary: MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. MAGI’s salient features are (i) transfer of large input files in native FASTA with Qualities (FASTQ) format through drag-and-drop operations, (ii) rapid prediction of microRNA target genes leveraging parallel computing with GPU devices, (iii) all-in-one analytics with novel feature extraction, statistical test for differential expression and diagnostic plot generation for quality control and (iv) interactive visualization and exploration of results in web reports that are readily available for publication.

Availability and implementation: MAGI relies on the Node.js JavaScript framework, along with NVIDIA CUDA C, PHP: Hypertext Preprocessor (PHP), Perl and R. It is freely available at http://magi.ucsd.edu .

Contact:  j5kim@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Improving upon the efficiency of complete case analysis when covariates are MNAR
Authors: Bartlett Jonathan W. , Carpenter James R. , Tilling Kate , Vansteelandt Stijn
Published: June 2014

Missing values in covariates of regression models are a pervasive problem in empirical research. Popular approaches for analyzing partially observed datasets include complete case analysis (CCA), multiple imputation (MI), and inverse probability weighting (IPW). In the case of missing covariate values, these methods (as typically implemented) are valid under different missingness assumptions. In particular, CCA is valid under missing not at random (MNAR) mechanisms in which missingness in a covariate depends on the value of that covariate, but is conditionally independent of outcome. In this paper, we argue that in some settings such an assumption is more plausible than the missing at random assumption underpinning most implementations of MI and IPW. When the former assumption holds, although CCA gives consistent estimates, it does not make use of all observed information. We therefore propose an augmented CCA approach which makes the same conditional independence assumption for missingness as CCA, but which improves efficiency through specification of an additional model for the probability of missingness, given the fully observed variables. The new method is evaluated using simulations and illustrated through application to data on reported alcohol consumption and blood pressure from the US National Health and Nutrition Examination Survey, in which data are likely MNAR independent of outcome.
Biomass consumption by breeding seabirds in the western Indian Ocean: indirect interactions with fisheries and implications for management
Authors: Danckwerts D. K. , McQuaid C. D. , Jaeger A. , McGregor G. K. , Dwight R. , Le Corre M. , Jaquemet S.
Published: June 2014

Fisheries potentially affect seabirds both directly and indirectly. Well-documented direct effects have resulted in significant losses to seabird populations, but indirect effects are less well known. One way in which tropical seabirds may be indirectly affected is through overexploitation of large subsurface predators. Tropical seabirds must forage over wide areas to attain sufficient prey and have evolved various methods of increasing foraging efficiency. One strategy is their association with surface-feeding tunas. When feeding, these predators drive prey to the surface, making them available to seabirds feeding from above. Losses in predator biomass will reduce prey accessibility (but not necessarily prey abundance) for seabirds, contributing to declines in bird populations. To explore indirect fisheries effects, we compared estimates of the magnitude and spatial distributions of consumption by breeding seabirds with fisheries offtake in the western Indian Ocean (WIO). Data from the literature were compared with Indian Ocean Tuna Commission longline and purse seine landings of selected tuna and billfish species from between 2000 and 2009. Breeding seabird populations (adults and immature birds) were estimated at ∼19 million individuals, assuming 50% breeding success. Based on the literature, these birds will consume between 150 000 and 500 000 metric tonnes (t) of prey; values that are of the same magnitude as mean annual longline (904±632 t) and purse seine (349 861±61 820 t) landings for the region. Spatial overlap between fisheries and seabirds is high, especially around the Seychelles, suggesting that the indirect impacts of fisheries on seabird populations may be great. Sooty Tern (Onychoprion fuscatus) is by far the dominant seabird in the study area, accounting for over 80% of numbers and consumption estimates. Our results highlight the importance of seabirds within WIO marine trophic webs and emphasize the potential indirect effects of industrial tuna fisheries on their populations.
A novel mucosal vaccine targeting Peyer’s patch M cells induces protective antigen-specific IgA responses
Authors: Shima Hideaki , Watanabe Takashi , Fukuda Shinji , Fukuoka Shin-Ichi , Ohara Osamu , Ohno Hiroshi
Published: June 2014

Mucosal vaccines can induce mucosal immunity, including antigen-specific secretory IgA production, to protect from invasion by pathogens and to neutralize toxins at mucosal surfaces. We established an effective antigen-delivering fusion protein, anti-GP2-SA, as a mucosal vaccine. The anti-GP2-SA consists of streptavidin (SA) fused to the antigen-binding fragment region from a mAb against glycoprotein 2 (GP2), an antigen-uptake receptor specifically expressed on M cells. Anti-GP2-SA targets antigen-sampling M cells in the follicle-associated epithelium covering Peyer’s patches. Immunofluorescence showed that anti-GP2-SA specifically bound to M cells. Orally administered biotinylated ovalbumin peptide (bOVA) conjugated with anti-GP2-SA more efficiently induced OVA-specific fecal IgA secretion compared with bOVA alone or bOVA conjugated with SA. Furthermore, mice immunized by oral administration of the biotinylated Salmonella enterica serovar Typhimurium (S. Typhimurium) lysate conjugated with anti-GP2-SA were significantly better protected from subsequent infection by virulent S. Typhimurium than mice treated with the bacterial lysate alone or conjugated with SA. These results suggest that anti-GP2-SA-based M-cell-targeting vaccines are a novel strategy for inducing efficient mucosal immunity.
Dark matter–baryons separation at the lowest mass scale: the Bullet Group★
Authors: Gastaldello F. , Limousin M. , Foëx G. , Muñoz R. P. , Verdugo T. , Motta V. , More A. , Cabanac R. , Buote D. A. , Eckert D. , Ettori S. , Fritz A. , Ghizzardi S. , Humphrey P. J. , Meneghetti M. , Rossetti M.
Published: June 2014

We report on the X-ray observation of a strong lensing selected group, SL2S J08544-0121, with a total mass of 2.4 ± 0.6 × 1014 M⊙ which revealed a separation of 124 ± 20 kpc between the X-ray emitting collisional gas and the collisionless galaxies and dark matter (DM), traced by strong lensing. This source allows to put an order of magnitude estimate to the upper limit to the interaction cross-section of DM of 10 cm2 g−1. It is the lowest mass object found to date showing a DM–baryons separation, and it reveals that the detection of bullet-like objects is not rare and confined to mergers of massive objects opening the possibility of a statistical detection of DM–baryons separation with future surveys.
Analyzing ion distributions around DNA
Authors: Lavery Richard , Maddocks John H. , Pasi Marco , Zakrzewska Krystyna
Published: June 2014

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.
Substantial Overlap Between Incarceration and Tuberculosis in Atlanta, Georgia, 2011
Authors: Haddad Maryam B. , Foote Mary K. , Ray Susan M. , Maggio David M. , Sales Rose-Marie F. , Kim Min Jung , Kempker Russell R. , Spaulding Anne C.
Published: June 2014

Standard tuberculosis case reporting captures incarceration at diagnosis only. This retrospective analysis of 106 US-born adults with prevalent tuberculosis in 2011 found that 46.2% had documented histories of being in jail or prison, including 16.0% during the year before diagnosis.
Disparities in CD4+ T-Lymphocyte Monitoring Among Human Immunodeficiency Virus-Positive Medicaid Beneficiaries: Evidence of Differential Treatment at the Point of Care
Authors: Davis Anna C. , Watson Greg , Pourat Nadereh , Kominski Gerald F. , Roby Dylan H.
Published: June 2014

Background.  Monitoring of immune function, measured by CD4+ T-lymphocyte (CD4) cell count, is an essential service for people with human immunodeficiency virus (HIV). Prescription of antiretroviral (ARV) medications is contingent on CD4 cell count; patients without regular CD4 monitoring are unlikely to receive ARVs when indicated. This study assesses disparities in CD4 monitoring among HIV-positive Medicaid beneficiaries.

Methods.  In this retrospective observational study, we examined 24 months of administrative data on 2250 HIV-positive, continuously enrolled, fee-for-service, Medicaid beneficiaries with at least 2 outpatient healthcare encounters. We used logistic regression to evaluate the association of patient demographics (age, gender, race or ethnicity, and language) with receipt of at least 1 CD4 test per year, controlling for other potentially confounding variables.

Results.  Having a history of ARV therapy was positively associated with receipt of CD4 tests. We found racial or ethnic, gender, and age disparities in CD4 testing. Among individuals with a history of ARV use, all racial or ethnic groups were significantly less likely to have CD4 tests than White non-Latinos (African Americans, odds ratio [OR] = 0.35, P < .0001; Asian or Pacific Islanders, OR = 0.31, P = .0047; and Latinos, OR = 0.42, P < .0001).

Conclusions.  We identified disparities in receipt of CD4 tests, a finding that may elucidate one potential pathway for previously reported disparities in ARV treatment. Further qualitative and quantitative research is needed to identify the specific factors that account for these disparities, so that appropriate interventions can be implemented.
Development of ALMA Band 4 (125–163 GHz) receiver
Authors: Asayama Shin’ichiro , Takahashi Toshikazu , Kubo Kouichi , Ito Tetsuya , Inata Motoko , Suzuki Takakiyo , Wada Toru , Soga Tomio , Kamada Chiyoshi , Karatsu Miki , Fujii Yumi , Obuchi Yoshiyuki , Kawashima Susumu , Iwashita Hiroyuki , Uzawa Yoshinori
Published: June 2014

We have developed a dual-polarization receiver for Band 4 of the Atacama Large Millimeter/submillimeter Array (ALMA). Band 4, which covers the 125 to 163 GHz spectral window, is one of the ten bands that form the ALMA Front End. The Band 4 receiver consists of three elements: a warm optics, a cold cartridge assembly, and a warm cartridge assembly. The cold cartridge includes a feed horn, an orthomode transducer, sideband-separating (2SB) superconductor–insulator–superconductor mixers, cold intermediate frequency (IF) amplifiers, IF isolators, bias-protection circuit boards, and component interconnections. The IF bandwidth is 4–8 GHz. The first eight receivers manufactured as preproduction models have demonstrated excellent performance within the stringent ALMA requirements. Stable astronomical fringes and closure phase have been successfully achieved during field performance tests of the Band 4 receivers installed in the ALMA antennas. Our well-established Band 4 receivers will contribute to various fields of astronomical research, such as the detection of high-redshift galaxies, characterization of cold molecular medium in normal field galaxies, and astrochemistry including observations of deuterated species.
A comparative study of infrared asteroid surveys: IRAS, AKARI, and WISE
Authors: Usui Fumihiko , Hasegawa Sunao , Ishiguro Masateru , Müller Thomas G. , Ootsubo Takafumi
Published: June 2014

We present a comparative study of three infrared asteroid surveys based on the size and albedo data from the Infrared Astronomical Satellite (IRAS), the Japanese infrared satellite AKARI, and the Wide-field Infrared Survey Explorer (WISE). Our study showed that: (i) the total number of asteroids detected with diameter and albedo information with these three surveyors is 138285, which is largely contributed by WISE; (ii) the diameters and albedos measured by the three surveyors for 1993 commonly detected asteroids are in good agreement, and within ±10% in diameter and ±22% in albedo at 1 σ deviation level. It is true that WISE offers size and albedo of a large fraction (> 20%) of known asteroids down to bodies of a few km, but we would suggest that the IRAS and AKARI catalogs compensate for larger asteroids up to several hundred km, especially in the main belt region. We discuss the complementarity of these three catalogs in order to facilitate the use of these data sets for characterizing the physical properties of minor planets.
Cyclosporine Protects the Heart during Aortic Valve Surgery
Authors: Chiari Pascal , Angoulvant Denis , Mewton Nathan , Desebbe Olivier , Obadia Jean-François , Robin Jacques , Farhat Fadi , Jegaden Olivier , Bastien Olivier , Lehot Jean-Jacques , Ovize Michel
Published: June 2014

Background:

Part of the myocardial damage occurring during cardiac surgery is a consequence of reperfusion injury. Cyclosporine, a potent inhibitor of the opening of the mitochondrial permeability transition pore, attenuates reperfusion injury in patients with acute ST-segment elevation myocardial infarction. This study investigated whether the administration of cyclosporine just before the aortic cross-unclamping would reduce myocardial injury in patients undergoing aortic valve surgery.

Methods:

This study was a monocentric, prospective, randomized, single-blinded, controlled trial. Sixty-one patients, scheduled for elective aortic valve surgery, were randomly assigned (computer-generated randomization sequence) to receive either an intravenous bolus of cyclosporine (2.5 mg/kg, cyclosporine group, n = 30) or normal saline (control group, n = 31) 10 min before aortic cross-unclamping. The primary endpoint was the 72-h area under the curve for cardiac troponin I.

Results:

Both groups were similar with respect to baseline characteristics and aortic cross-clamping duration. A significant 35% reduction of area under the curve for cardiac troponin I was observed in the cyclosporine group compared with the control group (242 ± 225 vs. 155 ± 71 arbitrary units, mean ± SD; mean difference, −86.2 ± 42.5; 95% CI, −172.3 to −0.1; P = 0.03). Cyclosporine beneficial effect remained significant after adjustment for aortic cross-clamping duration in each group (mean difference, −88 ± 34, 95% CI, −157 to −19; P = 0.01). None of the treated patients had significant side effects (odds ratio, 0.64; 95% CI, 0.16 to 2.55; P = 0.52).

Conclusions:

Cyclosporine administration at the time of reperfusion protects against reperfusion injury in patients undergoing aortic valve surgery. The clinical benefit of this protection requires confirmation in a larger clinical trial.
Effects of Dexamethasone on Cognitive Decline after Cardiac Surgery
Authors: Ottens Thomas H. , Dieleman Jan M. , Sauër Anne-Mette C. , Peelen Linda M. , Nierich Arno P. , de Groot Welmer J. , Nathoe Hendrik M. , Buijsrogge Marc P. , Kalkman Cor J. , van Dijk Diederik
Published: June 2014

Background:

Cardiac surgery can be complicated by postoperative cognitive decline (POCD), which is characterized by impaired memory function and intellectual ability. The systemic inflammatory response that is induced by major surgery and cardiopulmonary bypass may play an important role in the etiology of POCD. Prophylactic corticosteroids to attenuate the inflammatory response may therefore reduce the risk of POCD. The authors investigated the effect of intraoperative high-dose dexamethasone on the incidence of POCD at 1 month and 12 months after cardiac surgery.

Methods:

This multicenter, randomized, double-blind, placebo-controlled trial is a preplanned substudy of the DExamethasone for Cardiac Surgery trial. A total of 291 adult patients undergoing cardiac surgery with cardiopulmonary bypass were recruited in three hospitals and randomized to receive dexamethasone 1 mg/kg (n = 145) or placebo (n = 146). The main outcome measures were incidence of POCD at 1- and 12-month follow-up, defined as a decline in neuropsychological test performance beyond natural variability, as measured in a control group.

Results:

At 1-month follow-up, 19 of 140 patients in the dexamethasone group (13.6%) and 10 of 138 patients in the placebo group (7.2%) fulfilled the diagnostic criteria for POCD (relative risk, 1.87; 95% CI, 0.90 to 3.88; P = 0.09). At 12-month follow-up, 8 of 115 patients in the dexamethasone group (7.0%) and 4 of 114 patients (3.5%) in the placebo group had POCD (relative risk, 1.98; 95% CI, 0.61 to 6.40; P = 0.24).

Conclusion:

Intraoperative high-dose dexamethasone did not reduce the risk of POCD after cardiac surgery.
Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae
Authors: Zhou En-Min , Yu Tian-Tian , Liu Lan , Ming Hong , Yin Yi-Rui , Dong Lei , Tseng Min , Nie Guo-Xing , Li Wen-Jun
Published: June 2014

Strains YIM 77562T and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50–55 °C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family

Thermoactinomycetaceae

. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the

Thermoactinomycetaceae

were 88.33–93.24 %; the highest sequence similarity was with

Hazenella coriacea

DSM 45707T. In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562T and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA–DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562T ( = CCTCC AA 2011022T = JCM 18057T).
Chitinimonas
prasina sp. nov., isolated from lake water
Authors: Li Yi , Zhu Hong , Lai Qiliang , Lei Xueqian , Chen Zhangran , Zhang Huajun , Tian Yun , Zheng Wei , Zheng Tianling
Published: June 2014

A Gram-stain-negative, elongated rod-shaped, motile by gliding, green-pigmented, aerobic bacterial strain, designated LY03T, was isolated from lake water in Xiamen, Fujian Province, China. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus

Chitinimonas

, which belongs to the family

Burkholderiaceae

. Strain LY03T was most closely related to

Chitinimonas taiwanensis

LMG 22011T (96.02 % 16S rRNA gene sequence similarity), followed by

Chitinimonas koreensis

KACC 11467T (94.85 %), and the three strains formed a distinct lineage from other strains in the phylogenetic analyses. Optimum conditions for growth were 37 °C, pH 7–9 and without NaCl. The major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C10 : 0 3-OH. The DNA G+C content of strain LY03T was 63.6 mol% and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown polar lipids and unidentified phospholipids. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LY03T from all other members of the genus

Chitinimonas

. On the basis of its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain LY03T represents a novel species of the genus

Chitinimonas

, for which the name Chitinimonas prasina sp. nov. is proposed. The type strain is LY03T ( = MCCC 1F01209T = KCTC 32574T).
Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota
Authors: Stieglmeier Michaela , Klingl Andreas , Alves Ricardo J. E. , Rittmann Simon K.-M. R. , Melcher Michael , Leisch Nikolaus , Schleper Christa
Published: June 2014

A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76T, was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6–0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76Thad an S-layer with p3 symmetry, so far only reported for members of theSulfolobales. Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids. The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively. The genome of strain EN76Thad a DNA G+C content of 52.7 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain EN76Tis affiliated with the recently proposed phylumThaumarchaeota, sharing 85 % 16S rRNA gene sequence identity with the closest cultivated relative ‘CandidatusNitrosopumilus maritimus’ SCM1, a marine ammonia-oxidizing archaeon, and a maximum of 81 % 16S rRNA gene sequence identity with members of the phylaCrenarchaeotaandEuryarchaeotaand any of the other recently proposed phyla (e.g. ‘Korarchaeota’ and ‘Aigarchaeota’). We propose the nameNitrososphaera viennensisgen. nov., sp. nov. to accommodate strain EN76T. The type strain ofNitrososphaera viennensisis strain EN76T( = DSM 26422T = JMC 19564T).Additionally, we propose the familyNitrososphaeraceaefam. nov., the orderNitrososphaeralesord. nov. and the classNitrososphaeriaclassis nov.
Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus
Authors: Sharma Avinash , Dhar Sunil Kumar , Prakash Om , Vemuluri Venkata Ramana , Thite Vishal , Shouche Yogesh S.
Published: June 2014

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111Tthat forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111Tgrew well on seawater agar at pH 6–10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade withDomibacillus robiginosusWS 4628T( = DSM 25058T). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA–DNA relatedness toD. robiginosusDSM 25058T. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0and iso-C16 : 0and MK-6 was the predominant quinone. The polar lipid profile of strain SD111Tconsisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall containedmeso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111Trepresents a novel species of the genusDomibacillusfor which the nameDomibacillus indicussp. nov. is proposed. The type strain is SD111T( = MCC 2255T = DSM 28032T).