bluuebunny/crossref_metadata_2025 huggingface dataset:
Cellular geography of IP3 receptors, STIM and Orai: a lesson from secretory epithelial cells
Authors: Dingsdale Hayley , Voronina Svetlana , Haynes Lee , Tepikin Alexei , Lur Gyorgy
Published: January 2012

Pancreatic acinar cells exhibit a remarkable polarization of Ca2+ release and Ca2+ influx mechanisms. In the present brief review, we discuss the localization of channels responsible for Ca2+ release [mainly IP3 (inositol 1,4,5-trisphosphate) receptors] and proteins responsible for SOCE (store-operated Ca2+ entry). We also place these Ca2+-transporting mechanisms on the map of cellular organelles in pancreatic acinar cells, and discuss the physiological implications of the cellular geography of Ca2+ signalling. Finally, we highlight some unresolved questions stemming from recent observations of co-localization and co-immunoprecipitation of IP3 receptors with Orai channels in the apical (secretory) region of pancreatic acinar cells.
Targeting phosphoinositide 3-kinase δ for allergic asthma
Authors: Rowan Wendy C. , Smith Janet L. , Affleck Karen , Amour Augustin
Published: January 2012

Chronic inflammation in the lung has long been linked to the pathogenesis of asthma. Central to this airway inflammation is a T-cell response to allergens, with Th2 cytokines driving the differentiation, survival and function of the major inflammatory cells involved in the allergic cascade. PI3Kδ (phosphoinositide 3-kinase δ) is a lipid kinase, expressed predominantly in leucocytes, where it plays a critical role in immune receptor signalling. A selective PI3Kδ inhibitor is predicted to block T-cell activation in the lung, reducing the production of pro-inflammatory Th2 cytokines. PI3Kδ is also involved in B-cell and mast cell activation. Therefore the inhibition of PI3Kδ should dampen down the inflammatory cascade involved in the asthmatic response through a wide breadth of pharmacology. Current anti-inflammatory therapies, which are based on corticosteroids, are effective in controlling inflammation in mild asthmatics, but moderate/severe asthmatic patients remain poorly controlled, experiencing recurrent exacerbations. Corticosteroids have no effect on mast cell degranulation and do not act directly on B-cells, so, overall, a PI3Kδ inhibitor has the potential to deliver improvements in onset of action, efficacy and reduced exacerbations in moderate/severe asthmatics. Additionally, PI3Kδ inhibition is expected to block effects of Th17 cells, which are increasingly implicated in steroid-insensitive asthma.
Generalization of H-pseudoalgebraic structures
Authors: Sun Qinxiu
Published: January 2012

The goal of this paper is to study Hom-H-pseudoalgebraic structures generalizing H-pseudoalgebras of associative and Lie type. We provide examples of the new structures and present some properties and construction theorems. Similar to the case of H-pseudoalgebras, the annihilator algebras are also discussed. We also describe the equivalent definitions of Hom-H-pseudoalgebra. Finally, we consider the cohomology theory of Hom-H-pseudoalgebra with coefficients in an arbitrary module. Furthermore, the connection between the cohomology of Hom-Lie H-pseudoalgebra and its corresponding annihilator algebra is depicted.
Mechanism of drag generation by surface corrugation
Authors: Mohammadi A. , Floryan J. M.
Published: January 2012

Drag generated by periodic corrugation has been determined analytically in the limit of long corrugation wavelength. Three physical mechanisms have been identified, i.e., the additional shear drag due to an increase of the wetted area and the re-arrangement of the shear stress distribution, the pressure form drag associated with the mean pressure gradient, and the pressure interaction drag associated with the phase difference between the surface geometry and the periodic part of the pressure field. The total drag increases rapidly with increase of the corrugation amplitude, with the form and interaction drags contributing up to 45% and 30% of this increase, respectively.
Semiconductor disk laser at 2.05 μm wavelength with <100 kHz linewidth at 1 W output power
Authors: Kaspar Sebastian , Rattunde Marcel , Töpper Tino , Manz Christian , Köhler Klaus , Wagner Joachim
Published: January 2012

We report on an optically pumped single-mode GaSb-based semiconductor disk laser (SDL) emitting at 2.05 μm at an output power of 960 mW (1100 mW) with a side-mode suppression of better than 30 dB (20 dB). A linewidth of 60 kHz (sampling time: 100 μs) was measured at an output power of 960 mW. This improvement in output power over previous reports, which was achieved via a careful design of the SDL cavity paying close attention to the spatial overlap between cavity mode and pump spot, makes this class of SDL particularly attractive for remote sensing and optical free-space communication.
A comparative density functional study of the low pressure phases of solid ZnX, CdX, and HgX: Trends and relativistic effects
Authors: Biering S. , Schwerdtfeger P.
Published: January 2012

A comprehensive density functional study of the group 12 chalcogenides has been carried out to study the impact of relativistic effects on the solid-state and electronic structure of the mercury chalcogenides in order to explain their unique behavior compared to the lighter group 12 congeners. For this, we present scalar-relativistic and nonrelativistic density functional calculations for several crystal structures commonly occurring in ZnX, CdX, and HgX (X = S, Se, and Te). The cohesive energies and other ground-state properties (at the zero-temperature limit) are obtained to identify the low-pressure phases and to discuss relativistic effects. Relativistic crucially influences the crystal structure in HgS, an effect less pronounced in the heavier chalcogenides HgSe and HgTe. However, for HgSe and HgTe we find that relativistic effects have a major impact on the electronic structure, where the change upon neglect of relativity goes as far as to the restoration of semiconducting properties.
Theoretical predictions of properties and gas-phase chromatography behaviour of bromides of group-5 elements Nb, Ta, and element 105, Db
Authors: Pershina V. , Anton J.
Published: January 2012

Fully relativistic, four-component density functional theory electronic structure calculations were performed for MBr5, MOBr3, MBr6−, KMBr6, and MBr5Cl− of group-5 elements Nb, Ta, and element 105, Db, with the aim to predict adsorption behaviour of the bromides in gas-phase chromatography experiments. It was shown that in the atmosphere of HBr/BBr3, the pentabromides are rather stable, and their stability should increase in the row Nb < Db < Ta. Several mechanisms of adsorption were considered. In the case of adsorption by van der Waals forces, the sequence in volatility of the pentabromides should be Nb < Ta < Db, being in agreement with the sublimation enthalpies of the Nb and Ta pentabromides. In the case of adsorption by chemical forces (on a quartz surface modified with KBr/KCl), formation of the MBr5L− (L = Cl, Br) complex should occur, so that the volatility should change in an opposite way, i.e., Nb > Ta > Db. This sequence is in agreement with the one observed in the “one-atom-at-a-time” chromatography experiments. Some other scenarios, such as surface oxide formation were also considered but found to be irrelevant.
Observation of quantum beat oscillations and ultrafast relaxation of excitons confined in GaAs thin films by controlling probe laser pulses
Authors: Ohta Shohei , Kojima Osamu , Kita Takashi , Isu Toshiro
Published: January 2012

We study the quantum beats and relaxation dynamics of exciton center-of-mass motion confined in GaAs thin films by a reflection-type pump-probe technique. By using spectrally narrowed probe pulses with energies comparable with the exciton energy separation, oscillations caused by quantum beats between the confined excitons and ultrafast responses which are shorter than their lifetime appear. This appearance of quantum beats does not result from the so-called detection process. Our results demonstrate that the reduction of the destructive interference of the probe pulse in the sample is a key factor to observe the excitonic quantum beats.
A dynamical theory of nucleation for colloids and macromolecules
Authors: Lutsko James F.
Published: January 2012

A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential equations for the evolution of order parameters are given. The conditions under which the elements of classical nucleation theory are recovered are determined. The theory provides a justification and extension of more heuristic equilibrium approaches based solely on the free energy. It is illustrated by application to the low-concentration/high-concentration transition in globular proteins, where a novel two-step mechanism is identified, where the first step involves the formation of long-wavelength density fluctuations, and the second step is the actual nucleation event occurring within the fluctuation.
A new method of semigrand canonical ensemble to calculate first-order phase transitions for binary mixtures
Authors: Tang Yiping
Published: January 2012

First-order phase transitions of binary mixtures at the given pressure (P) and temperature (T) are studied by taking into account the composition fluctuations. Isothermal-isobaric semigrand canonical ensemble is adopted to find the relations among the total number of molecules, the composition fluctuations and Gibbs free energy density. By combining two identical subsystems of mixtures successively, the free energy density is transformed until being stable and its linear segments represent phase transitions. A new method is developed to calculate the phase equilibriums of binary mixtures. The method handles multiple types and number of phase equilibriums at single time and its solutions are physically justified. One example is shown for calculating the phase diagram of binary Lennard-Jones mixture. It demonstrates that the fluctuations of the total number of molecules in mixtures are fundamental behind phase transitions and the van der Waals loops in Gibbs free energy are reasonable.
Nuclear dynamics for a three-state Jahn–Teller model system
Authors: Krause Pascal , Matsika Spiridoula
Published: January 2012

We report wavepacket dynamics on a model system with a three-state conical intersection. Quantum wavepacket dynamics using the multiconfigurational time-dependent Hartree method have been carried out for the T ⊗ (e + t2) Jahn–Teller problem, using a Jahn–Teller vibronic model Hamiltonian. The effects of the magnitude of the coupling parameters and of the initial position of the wavepacket on the dynamics around the three-state conical intersection have been considered. It was found that the effect of the coupling strength is not dramatic for the population transfer in most cases, but the details of the dynamics and the involvement of the different modes are affected by it.
Note: Development of target changeable palm-top pyroelectric x-ray tube
Authors: Imashuku Susumu , Kawai Jun
Published: January 2012

A target changeable palm-top size x-ray tube was realized using pyroelectric crystal and detachable vacuum flanges. The target metals can be exchanged easily by attaching them on the brass stage with carbon tape. When silver and titanium palates (area: 10 mm2) were used as targets, silver Lα and titanium K lines were clearly observed by bombarding electrons on the targets for 90 s. The intensities were the same or higher than those of previously reported pyroelectric x-ray tubes. Chromium, iron, nickel, copper, and zinc K lines in the x-ray tube (stainless steel and brass) disappeared by replacing the brass stage and the stainless steel vacuum flange with a carbon stage and a glass tube, respectively.
41 GHz and 10.6 GHz low threshold and low noise InAs/InP quantum dash two-section mode-locked lasers in L band
Authors: Dontabactouny M. , Piron R. , Klaime K. , Chevalier N. , Tavernier K. , Loualiche S. , Le Corre A. , Larsson D. , Rosenberg C. , Semenova E. , Yvind K.
Published: January 2012

This paper reports recent results on InAs/InP quantum dash–based, two-section, passively mode-locked lasers pulsing at 41 GHz and 10.6 GHz and emitting at 1.59 μm at 20 °C. The 41-GHz device (1 mm long) starts lasing at 25 mA under uniform injection and the 10.6 GHz (4 mm long) at 71 mA. Their output pulses are significantly chirped. The 41-GHz laser exhibits 7 ps pulses after propagation in 60 m of a single-mode fiber. The 10.6-GHz laser generates one picosecond pulses with 545 m of a single-mode fiber. Its single side-band phase noise does not exceed –80 dBc/Hz at 100 kHz offset, leading to an average timing jitter of 800 fs.
Microwave-induced thermoacoustic computed tomography with a clinical contrast agent of NMG2[Gd(DTPA)]
Authors: Qin Huan , Yang Sihua , Xing Da
Published: January 2012

NMG2[Gd(DTPA)], a clinical contrast agent, was investigated for microwave-induced thermoacoustic computed tomography (CT). Due to ionic conduction and magnetic dipole rotation in the presence of microwave field, microwave energy absorbed by NMG2[Gd(DTPA)] would be transformed to thermoacoustic signals based on the thermoelastic effect. The experimental results demonstrated that NMG2[Gd(DTPA)] at a concentration of 10 mM provided effective enhancement compared with water. The enhancement of NMG2[Gd(DTPA)] for thermoacoustic CT was further demonstrated in invivo tumor-bearing mouse. The theory and experimental results indicate that the clinically available NMG2[Gd(DTPA)] will promote the medical applications of thermoacoustic CT.
Room temperature ferromagnetism in transparent Fe-doped In2O3 films
Authors: Kim H. , Osofsky M. , Miller M. M. , Qadri S. B. , Auyeung R. C. Y. , Piqué A.
Published: January 2012

Fe-doped In2O3 thin films were deposited on MgO substrates by pulsed laser deposition (PLD). The linear decrease in lattice constant with increasing Fe concentration of up to 18% suggests the incorporation of Fe atoms into In2O3 lattice matrix. The PLD grown films exhibited ferromagnetism at room temperature with a strong magnetic anisotropy. The observed anomalous Hall effect (AHE) indicates that spin polarized charge carriers play an important role in the origin of ferromagnetism in these oxides. Our observations, including AHE, magnetic anisotropy, and structural analysis provide strong evidence of intrinsic ferromagnetism at room temperature in these materials.
High power and low critical current spin torque oscillation from a magnetic tunnel junction with a built-in hard axis polarizer
Authors: Zhang Yisong , Zhao Hui , Lyle Andrew , Crowell Paul A. , Wang Jian-Ping
Published: January 2012

The microwave power and the critical current of spin torque oscillator (STO) devices with a built-in hard axis polarizer have been studied. This design allows for an external-field-free STO. The time domain oscillation signals give direct evidence of higher output from the hard axis polarizer STO, which agrees with spectroscopic results. The hard axis polarizer STO generates a higher power because of the larger slope of the magnetoresistance-angle curve at the lowest energy potential. Furthermore, the hard axis polarizer STO shows a low critical current indicating the large spin torque effect when two magnetic layers are in the 90° configuration.
Morphology control of Fe films using ordered termination on SrTiO3 surfaces
Authors: Chien TeYu , Freeland John W. , Guisinger Nathan P.
Published: January 2012

Long-range nanometer-scale stripe patterns of alternating termination on fractured Nb-doped SrTiO3 surfaces were used as templates to control the Fe film morphology. The as deposited Fe film consisted of a uniform layer of small Fe clusters (∼4 nm) randomly distributed on the surface. After annealing, two distinct morphologies were formed and were directly correlated to the underlying SrO and TiO2 terminated stripes. This behavior is consistent with a higher interfacial energy of the Fe/SrO interface than that of the Fe/TiO2 interface.
Tunneling time and Hartman effect in a ferromagnetic graphene superlattice
Authors: Sattari Farhad , Faizabadi Edris
Published: January 2012

Using transfer-matrix and stationary phase methods, we study the tunneling time (group delay time) in a ferromagnetic monolayer graphene superlattice. The system we peruse consists of a sequence of rectangular barriers and wells, which can be realized by putting a series of electronic gates on the top of ferromagnetic graphene. The magnetization in the two ferromagnetic layers is aligned parallel. We find out that the tunneling time for normal incident is independent of spin state of electron as well as the barrier height and electron Fermi energy while for the oblique incident angles the tunneling time depends on the spin state of electron and has an oscillatory behavior. Also the effect of barrier width on tunneling time is also investigated and shown that, for normal incident, the Hartman effect disappears in a ferromagnetic graphene superlattice but it appears for oblique incident angles when the x component of the electron wave vector in the barrier is imaginary.
Contactless monitoring of Ge content and B concentration in ultrathin single and double layer Si1-xGex epitaxial films using multiwavelength micro-Raman spectroscopy
Authors: Chang Chun-Wei , Hong Min-Hao , Lee Wei-Fan , Lee Kuan-Ching , Jang Jian Shiu-Ko , Chuang Yen , Fan Yu-Ta , Hasuike Noriyuki , Harima Hiroshi , Ueda Takeshi , Ishigaki Toshikazu , Kang Kitaek , Sik Yoo Woo
Published: January 2012

Non-contact monitoring of Ge content and B concentration in single and double Si1-xGex epitaxial layers on Si(100) device wafers was attempted using high-resolution, multiwavelength micro-Raman spectroscopy. The Ge content and B concentration determined by secondary ion mass spectroscopy (SIMS) depth profiling showed very strong correlation with the position and full-width-at-half-maximum of the Si-Si peak from the Si1-xGex epitaxial layers as determined by Raman measurements. High resolution X-ray diffraction (HRXRD) characterization was done for all wafers to determine Ge and B sensitivity and form comparisons with Raman and SIMS analysis. The non-destructive, in-line monitoring of Ge content and B concentration of single and double Si1-xGex epitaxial layers with thickness ranging from 5 ∼ 120 nm, on small area monitoring pads, was successfully demonstrated by multiwavelength micro-Raman spectroscopy during epitaxial process optimization, material property verification, and quality control applications.
Determination of critical current density from arbitrary flux relaxation process
Authors: Ma Rongchao
Published: January 2012

The current-carrying ability of a type-II superconductor is generally represented by its critical current density. This can be determined by measuring a flux relaxation process starting with a testing current density that is greater than or equal to the critical value. Here we show that a flux relaxation process starting with an intermediate current density can be converted into a process starting with the critical current density by introducing a virtual time interval. Therefore, one may calculate the critical current density from the flux relaxation process starting with a current density below the critical value. The exact solutions of the time dependence of current density in the flux relaxation process were also discussed.
Polyaniline nano-composites with large negative dielectric permittivity
Authors: Hsieh Chia-Hung , Lee An-Hung , Liu Cheng-Dar , Han Jin-Lin , Hsieh Kuo-Huang , Lee Sung-Nung
Published: January 2012

Two polyaniline (PANI)/polymer nano-composites exhibiting huge negative dielectric permittivity have been synthesized for the first time. These novel chemical processes open a new approach for fabrication of the negative index materials (NIMs), since most of the NIMs prepared today are obtained by a structural approach – by putting together two structured materials that exhibit separately a negative permittivity and a negative permeability. We found the negative permittivity of these nano-composites is a function of the content of the dopant (i.e., PANI) as well as of the frequency. The generation of huge negative permittivity can be rationalized by the well-dispersed PANI-DBSA nano-particles which form a pseudo-continuous conductive pathway in these nano-composites.
“On the Network, off the Map”: Developing Intervillage and Intragender Differentiation in Rural Water Supply
Authors: Birkenholtz Trevor
Published: January 2012

Despite decades of water-supply development programs in the Global South, their effect on gendered access to water remains both unclear and contradictory. This paper addresses this lacuna by examining the expansion of a rural water-supply network aimed at reducing household water scarcity in the arid zone of Rajasthan, India. Specifically, the Indira Gandhi Canal was conceived and constructed during the green revolution to ‘green the Thar Desert’. But now, through a complex network of reservoirs, treatment facilities, distribution centers, and supply pipelines, it connects much of rural and urban western Rajasthan to a drinking water-supply network. The paper examines the interaction of water-supply technologies, social power relations and dynamic socioecological change operating within these development processes. To do so it draws on household surveys, interviews with water users and government engineers, and participant observation with women and children water collectors. The paper finds that this ongoing water development project rendered the water provision landscape technical on the surface, but that uneven flows of water between villages and people reveal a more complex water provision landscape. The expansion of the network based on a technical reimagining of water supply has resulted in intervillage scarcity, intragender differential access, usurious private water markets, the abandonment and then the proposed rehabilitation of traditional water bodies, and urban water logging. In the conclusion I argue for a rethinking of water-supply development programs through a political ecology approach that focuses on the emergent capacities of water-supply technologies to redirect existing socioecological associations in unanticipated ways. Looking at the relationship between nature—society and technology may illuminate the possible ruptures in these associations and the ways that they may be rearticulated to produce less differentiating modes of accessing water.
Independent modulation of defect modes in fractal potential patterned graphene superlattices with multiple defect layers
Authors: Yu-ping Zhang , Ying Gao , Hui-yun Zhang
Published: January 2012

Independent modulation of defect modes in one-dimensional fractal potential patterned graphene superlattices with multiple defect layers is performed theoretically. It is found that the fractal structure with defect layers possesses an unusual tunnelling state existing inside the forbidden gap, and the defect modes are compatible with the corresponding defect layer. As a result, the same kind of tunnelling modes corresponding to a certain defect layer could be tuned independently by changing the width of the defect layer. Moreover, altering the period number of self-similar defects could result in a change in the energy interval of the corresponding defect modes. This interesting phenomenon may be beneficial to further experimental studies on graphene-based electronic devices.
FX: an RNA-Seq analysis tool on the cloud
Authors: Hong Dongwan , Rhie Arang , Park Sung-Soo , Lee Jongkeun , Ju Young Seok , Kim Sujung , Yu Saet-Byeol , Bleazard Thomas , Park Hyun-Seok , Rhee Hwanseok , Chong Hyonyong , Yang Kap-Seok , Lee Yeon-Su , Kim In-Hoo , Lee Jin Soo , Kim Jong-Il , Seo Jeong-Sun
Published: January 2012

Summary: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface.

Availability: FX is freely available on the web at (http://fx.gmi.ac.kr), and can be installed on local Hadoop clusters. Guidance for the installation and operation of FX can be found under the ‘Documentation’ menu on the website.

Contact:  jeongsun@snu.ac.kr; jongil@snu.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exact coalescent simulation of new haplotype data from existing reference haplotypes
Authors: Kang Chul Joo , Marjoram Paul
Published: January 2012

Motivation: We introduce a coalescent-based method (RECOAL) for the simulation of new haplotype data from a reference population of haplotypes. A coalescent genealogy for the reference haplotype data is sampled from the appropriate posterior probability distribution, then a coalescent genealogy is simulated which extends the sampled genealogy to include new haplotype data. The new haplotype data will, therefore, contain both some of the existing polymorphic sites and new polymorphisms added based on the structure of the simulated coalescent genealogy. This allows exact coalescent simulation of new haplotype data, compared with other methods which are more approximate in nature.

Results: We demonstrate the performance of our method using a variety of data simulated under a coalescent model, before applying it to data from the 1000 Genomes project.

Availability: The source code is freely available for download at ftp://popgen.usc.edu

Contact:  chulkang@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Release of filamentous and spherical influenza A virus is not restricted by tetherin
Authors: Bruce Emily A. , Abbink Truus E. , Wise Helen M. , Rollason Ruth , Galao Rui Pedro , Banting George , Neil Stuart J. , Digard Paul
Published: January 2012

The cellular protein tetherin is thought to act as a ‘leash’ that anchors many enveloped viruses to the plasma membrane and prevents their release. We found that replication of multiple strains of influenza A virus was generally insensitive to alteration of tetherin levels, as assessed by output titre or scanning electron microscopy of cell-associated virions. This included human, swine, avian and equine isolates, strains that form filamentous or spherical particles and viruses that lack the M2 or NS1 proteins. Levels of cell-surface tetherin were not reduced by influenza infection, but tetherin and the viral haemagglutinin co-localized on the plasma membrane. However, tetherin could not be detected in filamentous virions, suggesting that influenza may possess a mechanism to exclude it from virions. Overall, if influenza does encode a specific antagonist of tetherin, it is not M2 or NS1 and we find no evidence for a role in host range specificity.
Beet necrotic yellow vein virus subgenomic RNA3 is a cleavage product leading to stable non-coding RNA required for long-distance movement
Authors: Peltier Claire , Klein Elodie , Hleibieh Kamal , D’Alonzo Massimiliano , Hammann Philippe , Bouzoubaa Salah , Ratti Claudio , Gilmer David
Published: January 2012

Beet necrotic yellow vein virus (BNYVV) is a multipartite RNA virus. BNYVV RNA3 does not accumulate in non-host transgenic Arabidopsis thaliana plants when expressed using a 35S promoter. However, a 3′-derivative species has been detected in transgenic plants and in transient expression assays conducted in Nicotiana benthamiana and Beta macrocarpa. The 3′-derivative species is similar to the previously reported subgenomic RNA3 produced during virus infection. 5′ RACE revealed that the truncated forms had identical 5′ ends. The 5′ termini carried the coremin motif also present on BNYVV RNA5, beet soil-borne mosaic virus RNA3 and 4, and cucumber mosaic virus group 2 RNAs. This RNA3 species lacks a m7Gppp at the 5′ end of the cleavage products, whether expressed transiently or virally. Mutagenesis revealed the importance of the coremin sequence for both long-distance movement and stabilization of the cleavage product in vivo and in vitro. The isolation of various RNA3 5′-end products suggests the existence of a cleavage between nt 212 and 1234 and subsequent exonucleolytic degradation, leading to the accumulation of a non-coding RNA. When RNA3 was incubated in wheatgerm extracts, truncated forms appeared rapidly and their appearance was protein- and divalent ion-dependent.
General stress sigma factor RpoS influences time required to enter the viable but non‐culturable state in Salmonella enterica
Authors: Kusumoto Akiko , Asakura Hiroshi , Kawamoto Keiko
Published: January 2012

In stressful conditions, bacteria enter into the viable but non‐culturable (VBNC) state; in this state, they are alive but fail to grow on conventional media on which they normally grow and develop into colonies. The molecular basis underlying this state is unknown. We investigated the role of the alternative sigma factor RpoS (σ38) in the VBNC induction using Salmonella Dublin, Salmonella Oranienburg and Salmonella Typhimurium LT2. VBNC was induced by osmotic stress in LT2 and Oranienburg. Dublin also entered the VBNC state, but more slowly than LT2 and Oranienburg did. The LT2 rpoS gene was initiated from an alternative initiation codon, TTG; therefore, LT2 had smaller amounts of RpoS than Dublin and Oranienburg. Oranienburg had a single amino acid substitution (D118N) in RpoS (RpoSSO). Disruption of rpoS caused rapid VBNC induction. VBNC induction was significantly delayed by Dublin‐type RpoS (RpoSSD), but only slightly by RpoSSO. These results indicate that RpoS delays VBNC induction and that the rapid induction of VBNC in LT2 and Oranienburg may be due to lower levels of RpoS and to the D118N amino acid substitution, respectively. Reduced RpoS intracellular level was observed during VBNC induction. During the VBNC induction, Salmonella might regulate RpoS which is important for maintenance of culturablity under stresses.
Meta‐analysis: oral anti‐viral agents in adults with decompensated hepatitis B virus cirrhosis
Authors: Singal A. K. , Fontana R. J.
Published: January 2012

Background

The optimal oral anti‐viral agent to use in patients with decompensated HBV cirrhosis remains unclear.

Aim

We performed a meta‐analysis of the oral nucleos(t)ide analogues in patients with decompensated HBV cirrhosis.

Methods

One year efficacy and safety outcomes in 22 studies published in English between95 and 2010 were analysed.

Results

Substantial heterogeneity was noted in the inclusion/exclusion criteria, controls, and sensitivity of the HBV DNA assay used. Pooled 1‐year data showed benefit favouring lamivudine (LAM) vs. untreated controls for Child‐Turcotte‐Pugh (CTP) score improvement by ≥2 (OR: 117 (15 921), P ≤ 0.0001) and transplant‐free survival (OR: 3.2 (1.2, 9), P = 0.022). Adefovir (ADV) led to undetectable HBV DNA at 1‐year in 41% compared to 83% with LAM and 80% with entecavir (ETV). Overall, 1‐year transplant‐free survival rates varied from 78% with LAM to 95% and 94% with Tenofovir (TDF) and Telbivudine (TBV), respectively. The 1‐year incidence of drug resistant HBV was 0% with ADV, ETV and TDF and 11% with LAM although TBV was associated with a 29% incidence at 2 years. Drug‐related adverse events were infrequently reported.

Conclusions

All the oral anti‐viral agents were associated with improved virological, biochemical and clinical parameters at 1‐year. However, the efficacy of lamivudine and telbivudine is limited by drug resistance, and adefovir is limited by its potency and slower onset of action. Additional studies of tenofovir and entecavir are needed to determine the optimal agent(s) for treatment naïve patients and in those with drug‐resistant decompensated HBV cirrhosis.
The evolution of the high‐elevated depocenters of the northern Sierras Pampeanas (ca. 28˚ SL), Argentine broken foreland, South‐Central Andes: the Pipanaco Basin
Authors: Dávila Federico M. , Giménez Mario E. , Nóbile Julieta C. , Martínez M. Patricia
Published: January 2012

The Pipanaco Basin, in the southern margin of the Andean Puna plateau at ca. 28°SL, is one of the largest and highest intermontane basins within the northernmost Argentine broken foreland. With a surface elevation >1000 m above sea level, this basin represents a strategic location to understand the subsidence and subsequent uplift history of high‐elevation depositional surfaces within the distal Andean foreland. However, the stratigraphic record of the Pipanaco Basin is almost entirely within the subsurface, and no geophysical surveys have been conducted in the region. A high‐resolution gravity study has been designed to understand the subsurface basin geometry. This study, together with stratigraphic correlations and flexural and backstripping analysis, suggests that the region was dominated by a regional subsidence episode of ca. 2 km during the Miocene‐Pliocene, followed by basement thrusting and ca. 1–1.5 km of sediment filling within restricted intermontane basin between the Pliocene‐Pleistocene. Based on the present‐day position of the basement top as well as the Neogene‐Present sediment thicknesses across the Sierras Pampeanas, which show slight variations along strike, sediment aggradation is not the most suitable process to account for the increase in the topographic level of the high‐elevation, close‐drainage basins of Argentina. The close correlation between the depth to basement and the mean surface elevations recorded in different swaths indicates that deep‐seated geodynamic process affected the northern Sierras Pampeanas. Seismic tomography, as well as a preliminary comparison between the isostatic and seismic Moho, suggests a buoyant lithosphere beneath the northern Sierras Pampeanas, which might have driven the long‐wavelength rise of this part of the broken foreland after the major phase of deposition in these Andean basins.
Generalist predation on forest tent caterpillar varies with forest stand composition: an experimental study across multiple life stages
Authors: NIXON AMY E. , ROLAND JENS
Published: January 2012

1. Generalist enemies can regulate low‐density forest insect populations, and are widely considered to cause greater mortality in more diverse habitats. Forest tent caterpillars (Malacosoma disstria Hübner; FTC) are a major defoliator of aspen (Populus tremuloides Micheaux) in the boreal forest, a region with a mosaic of forest stand types. This heterogeneity may influence FTC outbreaks if generalist predation or parasitism differs among stands of different tree composition.

2. Using exclusion experiments we estimate predation and parasitism of FTC across multiple life‐history stages in low‐density populations occupying both aspen (low diversity) and mixedwood stands (high diversity).

3. Arthropod and avian generalist predators were responsible for most natural enemy‐caused mortality of immature FTC, but their relative impacts varied among FTC life‐history stages. Contrary to expectation, predation on late instar larvae and pupae was higher in the less diverse aspen stands and early instar mortality did not differ.

4. By considering multiple life‐history stages, our results provide a more comprehensive view of natural enemy‐caused morality of immature FTC. Because generalist predation on FTC was higher in aspen than in mixedwood stands, we suggest that FTC populations may be slower to reach outbreak levels in aspen stands.
Non‐consumptive effects of a natural enemy on a non‐prey herbivore population
Authors: FILL ANDREW , LONG ELIZABETH Y. , FINKE DEBORAH L.
Published: January 2012

1. Predator–prey interactions have traditionally focused on the consumptive effects that predators have on prey. However, predators can also reduce the abundance of prey through behaviourally‐mediated non‐consumptive effects. For example, pea aphids (Acyrthosiphon pisum Harris) drop from their host plants in response to the risk of attack, reducing population sizes as a consequence of lost feeding opportunities.

2. The objective of the present study was to determine whether the non‐consumptive effects of predators could extend to non‐prey herbivore populations as a result of non‐lethal incidental interactions between herbivores and foraging natural enemies.

3. Polyculture habitats consisting of green peach aphids (Myzus persicae Sulzer) feeding on collards and pea aphids feeding on fava beans were established in greenhouse cages. Aphidius colemani Viereck, a generalist parasitoid that attacks green peach aphids but not pea aphids, was released into half of the cages and the abundance of the non‐host pea aphid was assessed.

4. Parasitoids reduced the population growth of the non‐host pea aphid by increasing the frequency of defensive drops; but this effect was dependent on the presence of green peach aphids.

5. Parasitoids probably elicited the pea aphid dropping behaviour through physical contact with pea aphids while foraging for green peach aphids. It is unlikely that pea aphids were responding to volatile alarm chemicals emitted by green peach aphids in the presence of the parasitoid.

6. In conclusion, the escape response of the pea aphid provided the opportunity for a parasitoid to have non‐target effects on an herbivore with which it did not engage in a trophic interaction. The implication is that natural enemies with narrow diet breadths have the potential to influence the abundance of a broad range of prey and non‐prey species via non‐consumptive effects.
What shapes local density? The importance of migration rates and local growth for density‐patch size relationships in two Cionus weevils
Authors: ANDERSSON PETTER , HAMBÄCK PETER A.
Published: January 2012

1. The relative effect of migration and local growth on the spatio‐temporal density‐distribution of two co‐existing herbivorous weevils, Cionus scrophulariae L. and C. tuberculosus Scop., in 32 host plant Scrophularia nodosa L. patches of varying sizes was investigated.

2. Predictions of the temporal development of the slope in the density‐patch size relationships were derived from a basic population model with scale‐dependent migration rates. The model indicated that the slopes in the density‐patch size relationships during the early season should be reflected by the net scaling of immigration and emigration rates, whereas the slopes during the later season should increase as a result of local growth.

3. Emigration rates of the weevils were estimated in a field experiment, were the weevils coexisted in space and time. These results were then combined with a previous estimate of immigration rates in order to determine the net scaling of migration rates.

4. The emigration rate differed between species, caused by different movement rates in small patches, which could explain differences in the general slope of the density‐patch size relationships of the weevils in the natural figwort patches throughout the summer. The slopes in the relationships in the early season were largely predicted by the net scaling of migration rates. The slope also increased in the later season for C. tuberculosus, whereas the slope decreased for C. scrophulariae.

5. It was concluded that the understanding of both inter‐ and intra‐specific variations in density‐patch size relationships of insect herbivores can be improved using population models incorporating scale‐dependent migration and local growth.
A seed parasitoid wasp prevents berries from changing their colour, reducing their attractiveness to frugivorous birds
Authors: TAKAGI ETSURO , IGUCHI KAZUNOBU , SUZUKI MASANORI , TOGASHI KATSUMI
Published: January 2012

1. Frugivorous and seed‐feeding insects may alter the traits of fruits, such as shape and size, which may influence fruit attractiveness to frugivorous birds. Consequently, trait‐mediated interactions may occur in systems where plants, seed‐dispersing frugivorous vertebrates, and frugivorous or seed‐feeding insects interact. We investigated colour manipulation in Ilex integra Thunb. berries caused by the seed parasitoid wasp Macrodasyceras hirsutum Kamijo and how that manipulation relates to fruit attractiveness for frugivorous birds.

2. In winter, the colour of I. integra berries varied from green to red, but most berries were greenish, indicating that the berries were immature. Berry dissection indicated that the number of live parasitoid larvae present within each berry was closely related to berry colour – the greater the number of live larvae, more intense is the green colour of the berry. However, the wasp larvae did not modify the shape or size of the berries. More than 98% of berries that were protected from the insects by gauze bags ripened and turned red. In the present study, berries with unfertilised seeds alone turned red. Field‐feeding preference tests showed that the brown‐eared bulbul Hypsipetes amaurotis Temminck preferred red berries to green berries.

3. We demonstrated that the seed parasitoid wasp manipulates the berry colour, but not its shape or size, in a density‐dependent manner. Because green berries suffered less from bird foraging, we believe that this colour manipulation helps the wasps to avoid being killed by the birds. The present study indicates that manipulation by wasps may reduce the level of mutualism between the tree and seed‐dispersing birds.
The formation of P particle increased immunogenicity of norovirus P protein
Authors: Tan Ming , Jiang Xi
Published: January 2012

As a commentary on a recently published paper in Immunology, this article summaries the principle of norovirus P particle as a promising vaccine against noroviruses. It emphasizes the importance of P particle formation in the immune enhancement of the vaccine and methods for production/verification of high quality P particles which may be easily neglected by researchers.
Mutualistic cleaner fish initiate trait‐mediated indirect interactions by influencing the behaviour of coral predators
Authors: Adam Thomas C.
Published: January 2012

1. Indirect interactions resulting from changes in organismal traits such as behaviour [i.e. trait‐mediated indirect interactions (TMIIs)] are widespread in biological communities, yet few studies have explored the potential for mutualisms to initiate TMIIs.

2. This study used a combination of behavioural observations and manipulative field experiments to investigate potential TMIIs resulting from a mutualism between specialized cleaner fish and the ‘clients’ that visit cleaners for the removal of ectoparasites.

3. Behavioural observations indicate that the bluestreak cleaner wrasse, Labroides dimidiatus, increases local predation pressure on corals at cleaner stations by attracting corallivorous butterflyfish to their territories.

4. Observations of the ornate butterflyfish, Chaetodon ornatissimus, suggest a trade‐off between seeking cleaning and foraging; individuals decreased their foraging rate at cleaner stations and shifted their diet to include a greater proportion of less preferred prey items. Nonetheless, predation pressure on corals was higher at cleaner stations because the spatial response of butterflyfish to cleaners more than compensated for their lower foraging rates.

5. The results of a field experiment suggest that the greater predation pressure observed at cleaner stations may be sufficient to reduce the growth rate of the unpreferred coral Porites rus.

6. Together, these results emphasize the need to consider mutualists as potential initiators of TMIIs and highlight the importance of integrating individual movement into conceptual analyses of TMIIs.
Sodium intake and excretion in individuals with type 2 diabetes mellitus: a cross‐sectional analysis of overweight and obese males and females in Australia
Authors: Villani A. M. , Clifton P. M. , Keogh J. B.
Published: January 2012

How to cite this article
 Villani A.M., Clifton P.M. & Keogh J.B. (2012) Sodium intake and excretion in individuals with type 2 diabetes mellitus: a cross‐sectional analysis of overweight and obese males and females in Australia. J Hum Nutr Diet.25, 129–139

Background:  Hypertension is common in individuals with type 2 diabetes mellitus (T2DM). Dietary sodium plays an important regulatory role in blood pressure management. However, dietary sodium intakes and the major food sources of dietary sodium have yet to be thoroughly investigated in individuals with T2DM.

Methods:  In a cross‐sectional study sample of 88 overweight and obese men (n = 52) and women (n = 36) with T2DM in Adelaide, Australia, sodium intake and excretion was investigated using two different methodologies, including a 4‐day weighed food record and 24‐h urinary sodium excretion. The major dietary contributors to sodium intake in this population were also explored.

Results:  Mean (SD) 24‐h urinary sodium excretion was greater (P < 0.001) in males [195.1 (74.6) mmol] compared to females [144.3 (41.8) mmol]. Breads and cereals (B&Cs) were the largest contributors to dietary sodium intake (23% of intake). There was an association between sodium intake from B&Cs and 24‐h urinary sodium excretion (r = 0.235; P = 0.02); however, when controlled for gender, B&Cs were not associated with urinary sodium excretion (males, r = 0.134; P = 0.343; females, r = 0.102; P = 0.554).

Conclusions:  The findings of the present study show that sodium intake and excretion in individuals with T2DM is more than two‐fold greater than the current recommendations for chronic disease prevention. B&Cs were the major dietary contributors of sodium intake, suggesting that they are primary targets for a reduction in their sodium content.
Silica–rubber microstructure visualised in three dimensions by focused ion beam–scanning electron microscopy
Authors: TUNNICLIFFE L.B. , THOMAS A.G. , BUSFIELD J.J.C.
Published: January 2012

A focused ion beam–scanning electron microscope (FIB–SEM) technique for three‐dimensional reconstruction and representation of material microstructures was applied to a silica‐filled synthetic rubber for the first time. Backscattered electron imaging allowed differentiation between rubber matrix, silica filler and zinc oxide (used as an activator for the sulphur vulcanisation reaction). Subsequent image processing allowed three‐dimensional isosurface model generation of the particulate structure within the rubber composite and separation of zinc oxide from the silica filler. The potential for development and application of this technique using finite element analysis modelling is also highlighted.