bluuebunny/crossref_metadata_2025 huggingface dataset:
Laser field and electric field effects on exciton states and optical properties in zinc-blende GaN/AlGaN quantum well
Authors: Xia Congxin , Chen Xiaoyang , Wei Shuyi , Jia Yu
Published: June 2013

Based on the effective mass approximation, the combined effects of the laser field and electric field on exciton states and optical properties in the zinc-blende GaN/AlGaN quantum well (QW) are investigated by means of a variational method. Numerical results show that when the applied electric field is weak, the laser field reduces the exciton binding energy and oscillator strength in the QW; however, when the applied electric field is strong, the exciton binding energy and oscillator strength have a maximum with the variation of the laser field. Moreover, the laser field increases the interband transition energy and the energy position of the linear optical susceptibility peak.
Spin-polarized electrons in bilayer graphene ribbons
Authors: Orellana P. A. , Rosales L. , Chico L. , Pacheco M.
Published: June 2013

We show that a bilayer graphene ribbon deposited above a ferromagnetic insulator can behave as a spin-filtering device. The ferromagnetic material induces exchange splitting in the graphene ribbon, and due to the Fano antiresonances occurring in the transmission of the graphene ribbon as a function of ribbon length and energy, it is possible to obtain a net spin current. This happens when an antiresonance for one spin channel coincides with a maximum transmission for the opposite spin. We propose these structures as a means to obtain spin-polarized currents and spin filters in graphene-based systems.
Magnetic properties and magnetocaloric effect in Fe90−xNixZr10 alloy ribbons
Authors: Dang Thanh Tran , Yu Yikyung , Thanh P. T. , Yen N. H. , Dan N. H. , Phan The-Long , Grishin A. M. , Yu S. C.
Published: June 2013

We report magnetic properties and magnetocaloric (MC) effect in Fe90−xNixZr10 (x = 0, 5, 10, and 15) alloy ribbons prepared by rapid-quenching method. We found the Curie temperature (TC) of the alloy ribbons depends strongly on Ni-doping concentration (x) increasing from 245 K for (x = 0), through 306 K (for x = 5) up to TC = 403 (for x = 15). Also, the dependence of the maximum magnetic entropy change (|ΔSmax|) on Ni content was readily apparent. Indeed, for the x = 0 and 5 samples that have TC around room temperature, the |ΔSmax| values increment under magnetic field changes of 10, 20, and 40 kOe was found to be as high as 0.87, 1.76, and 3.04 J·kg−1·K−1 for x = 0, and 1.03, 1.90, and 3.26 J·kg−1·K−1 for x = 5, respectively. These values correspond to refrigerant capacity in the range of 86-334 J·kg−1 and are comparable to other known MC materials. High magnetocaloric performance in rare-earth-free non-expensive metallic alloys indicates that these materials could be competitive candidate for active magnetic refrigeration at room temperature.
Electron scattering in GaAs/InGaAs quantum wells subjected to an in-plane magnetic field
Authors: Jin Dong-Dong , Yang Shao-Yan , Zhang Liu-Wan , Li Hui-jie , Zhang Heng , Wang Jian-xia , Yang Tao , Xiang-LinLiu  , Zhu Qin-Sheng , Wang Zhan-Guo
Published: June 2013

We study theoretically the effect of the in-plane magnetic field on two-dimensional electron gas transport in GaAs/InGaAs single quantum well structure. Our results show that, due to the scatterers (GaSb quantum dots) are one-side distributed, the in-plane magnetic field leads to an anisotropic scattering probability, which results in a higher mobility along the direction perpendicular to the magnetic field. Besides, compared with the no magnetic field case, the mobility shows a parabolic increasing trend as the in-plane magnetic field strength increases.
Design, fabrication, and measurement of highly sub-wavelength double negative metamaterials at high frequencies
Authors: Li Long , Fan Yingchun , Yu Shixing , Zhu Cheng , Liang Changhong
Published: June 2013

In this paper, a highly sub-wavelength double negative (DNG) metamaterial for operation at high frequencies is designed, fabricated, and measured. A dual layer design that consists of a planar spiral on one side and a meander line touching with narrow metallic strips on the other side produces the properties of effective negative permittivity and permeability simultaneously, i.e., negative refractive index (NRI). The size of the unit cell of DNG metamaterials is about 253 times smaller than the operation wavelength at 15.2 MHz. The strong coupling between the topological structures on two sides makes a contribution to the miniaturization of the proposed metamaterials. A simple probe method is used to measure the transmission and reflection coefficients, and the comparison of effective medium parameters retrieved from transverse electromagnetic waveguide simulation and the probe method is given to verify the effectiveness and correctness. The measured results from one cell show a good agreement with simulated results. The measured effective real index of refraction n = −6.9 with a total loss that is less than 0.45 dB/cm at 15.2 MHz. The NRI bandwidth was > 10% in the neighborhood of 15.2 MHz.
Thermal (Kapitza) resistance of interfaces in compositional dependent ZnO-In2O3 superlattices
Authors: Liang Xin , Baram Mor , Clarke David R.
Published: June 2013

Compositionally dependent superlattices, In2O3(ZnO)k, form in the ZnO-rich portion of the ZnO-In2O3 phase diagram, decreasing thermal conductivity and altering both the electron conductivity and Seebeck coefficient over a wide range of composition and temperature. With increasing indium concentration, isolated point defects first form in ZnO and then superlattice structures with decreasing interface spacing evolve. By fitting the temperature and indium concentration dependence of the thermal conductivity to the Klemens-Callaway model, incorporating interface scattering and accounting for conductivity anisotropy, the Kapitza resistance due to the superlattice interfaces is found to be 5.0 ± 0.6 × 10−10 m2K/W. This finding suggests that selecting oxides with a compositionally dependent superlattice structure can be a viable approach, unaffected by grain growth, to maintaining low thermal conductivity at high temperatures.
X-ray photoelectron spectroscopy and X-ray diffraction studies on tin sulfide films grown by sulfurization process
Authors: Reddy M. V. , Babu P. , Ramakrishna Reddy K. T. , Miles R. W.
Published: June 2013

Tin sulfide (SnS) thin films were grown by single zone sulfurization process using sputtered tin layers. Metallic tin (Sn) layers were grown on molybdenum (Mo) coated soda-lime glass substrates by DC magnetron sputtering. The sputtered Sn layers along with sulfur flakes were kept in a graphite box and sulfurized using a closed single zone quartz tube furnace at different temperatures that vary in the range of 200–350 °C for a fixed sulfurization time of 2 h. The X-ray photoelectron spectroscopy studies on these layers revealed approximately stoichiometric ratio of Sn/S at a sulfurization temperature of 350 °C. The X-ray diffraction studies revealed the presence of secondary phases such as SnS2 and Sn2S3 at lower sulfurization temperatures that got suppressed with the rise of temperature. All the layers showed the (111) plane as preferential orientation with orthorhombic structure and its intensity increased with the increase of sulfurization temperature. The evaluated crystallite size of the layers was found to increase with the increase of sulfurization temperature.
Characterization of polymer:fullerene solar cells by low-frequency noise spectroscopy
Authors: Landi G. , Barone C. , De Sio A. , Pagano S. , Neitzert H. C.
Published: June 2013

A detailed electric noise investigation of polymer:fullerene solar cells, at 300 K under dark conditions, is reported. The experimental noise results are interpreted in terms of a model taking into account the device capacitance and recombination resistance. Relevant parameters of the solar cells can be computed through fluctuation spectroscopy, and the results have been compared with those obtained by alternative techniques. After a thermal treatment at 340 K, a modification of the voltage-spectral traces has been observed and related to a strong cell resistance reduction.
Exploration on pressure-induced phase transition of cerium mononitride from first-principles calculations
Authors: Zhang Meiguang , Yan Haiyan , Wei Qun , Wang Hui
Published: June 2013

Recently, pressure-induced phase transition of CeN from ambient B1 phase to the B2 phase has been experimentally reported at the pressure of 65–70 GPa. Nevertheless, the full transformation of the high-pressure B2 phase has not been observed in the experiment as the authors said. Here we predict an unexpected anti-B10 high-pressure phase which is energetically more preferable than the B2 phase at the studied pressure range, disproving the experimental result. Our argument has been supported by the softening of both elastic constant C44 in B1 phase and transverse acoustic mode at the zone boundary M point of B2 phase.
Electrical conductivity of multi-walled carbon nanotubes-SU8 epoxy composites
Authors: Grimaldi Claudio , Mionić Marijana , Gaal Richard , Forró László , Magrez Arnaud
Published: June 2013

We have characterized the electrical conductivity of the composite which consists of multi-walled carbon nanotubes dispersed in SU8 epoxy resin. Depending on the processing conditions of the epoxy (ranging from non-polymerized to cross-linked), we obtained tunneling and percolating-like regimes of the electrical conductivity of the composites. We interpret the observed qualitative change of the conductivity behavior in terms of reduced separation between the nanotubes induced by polymerization of the epoxy matrix.
Field emission characteristics of pristine and N-doped graphene measured by in-situ transmission electron microscopy
Authors: Kashid Ranjit V. , Zamri Yusop Mohd , Takahashi Chisato , Kalita Golap , Panchakarla Leela S. , Joag Dilip S. , More Mahendra A. , Tanemura Masaki
Published: June 2013

We report the field emission characteristics of a few-layer pristine and N-doped graphene by the in-situ transmission electron microscopy. The measurements were performed with a Pt-Ir nanoprobe and at a vacuum gap of 400 nm. The turn on voltage, required to draw an emission current of 1 nA from pristine and N-doped graphene, was found to be 230 and 110 V, respectively. The lower turn on voltage for the N-doped graphene can be explained from the improved electrical conductivity and up-shift of the Fermi level with nitrogen doping. Structural deformation/contraction/buckling of the N-doped graphene sheet was observed with the field emission current exceeding ∼6.9 μA, which can be attributed to the Joule heating.
Photocatalytic degradation mechanisms of self-assembled rose-flower-like CeO2 hierarchical nanostructures
Authors: Sabari Arul N. , Mangalaraj D. , Whan Kim Tae
Published: June 2013

Hierarchical rose-flower-like CeO2 nanostructures were formed by using solvothermal and thermal annealing processes. The CeCO3OH thin film was transformed into CeO2 roses due to thermal annealing. CeO2 nanostructured roses exhibited excellent photocatalytic activity with a degradation rate of 65% for the azo dye acid orange 7 (AO7) under ultraviolet illumination. The fitting of the absorbance maximum versus time showed that the degradation of AO7 obeyed pseudo-first-order reaction kinetics. The enhancement of the photocatalytic activity for the CeO2 roses was attributed to the high adsorptivity resulting from the surface active sites and special 4f electron configuration.
High-quality electron beam from laser wake-field acceleration in laser produced plasma plumes
Authors: Sanyasi Rao Bobbili , Moorti Anand , Rathore Ranjana , Ali Chakera Juzer , Anant Naik Prasad , Dass Gupta Parshotam
Published: June 2013

Generation of highly collimated (θdiv ∼10 mrad), quasi-monoenergetic electron beam with peak energy 12 MeV and charge ∼50 pC has been experimentally demonstrated from self-guided laser wake-field acceleration (LWFA) in a plasma plume produced by laser ablation of solid nylon (C12H22N2O2)n target. A 7 TW, 45 fs Ti:sapphire laser system was used for LWFA, and the plasma plume forming pulse was derived from the Nd:YAG pump laser of the same system. The results show that a reproducible, high quality electron beam could be produced from this scheme which is simple, low cost and has the capability for high repetition rate operation.
Mn substitution-modified polar phase in the Bi1−xNdxFeO3 multiferroics
Authors: Khomchenko V. A. , Karpinsky D. V. , Pereira L. C. J. , Kholkin A. L. , Paixão J. A.
Published: June 2013

Room-temperature crystal structure and multiferroic properties of the Bi0.92Nd0.08Fe1−xMnxO3 (x ≤ 0.3) ferromanganites have been studied to reveal the effect of Mn doping on the magnetic and ferroelectric behaviors of the lanthanide-modified compound representing a polar (space group R3c) predominantly antiferromagnetic phase of the Bi1−xLnxFeO3 perovskites. B-site substitution tends to suppress existing polar displacements and induces a ferroelectric-to-antiferroelectric transition near x = 0.2. The threshold concentration inducing the structural transformation does not coincide with that required to change the dominant magnetic interaction, so a weak ferromagnetic/ferroelectric state unusual for the Bi1−xLnxFeO3 and BiFe1−xMnxO3 series appears in the intermediate concentration range near the polar/nonpolar phase boundary.
Introduction
Authors: Ramet Sabrina P.
Published: June 2013

Reading the psychological literature on memory, there is little doubt who plays the leading roles on this stage. The radiant hero in the limelight is Remembering, attracting all attention, support and sympathy. The shady villain is Forgetting, the trouble maker who is lurking behind the scenes, always ready to counteract Remembering and thwart its achievement. There are various scenarios in which this plot is acted out. Typically, Remembering is forced to use all kinds of tricks to resist the villain's assaults and to guard the treasure – the accumulated wealth of past experience and knowledge. While Remembering strives to defend this precious treasure, maintaining it as untouched as possible, Forgetting never tires of trying to steal and destroy it (or at least to damage or, insidiously, to distort and falsify it). In this way, the conflict about the treasure of the past takes on still another dramatic dimension: it becomes a struggle for truth. (Brockmeier 2002, 15)
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data
Authors: Larson Nicholas B. , Fridley Brooke L.
Published: June 2013

Summary: We have developed a novel Bayesian method, PurBayes, to estimate tumor purity and detect intratumor heterogeneity based on next-generation sequencing data of paired tumor-normal tissue samples, which uses finite mixture modeling methods. We demonstrate our approach using simulated data and discuss its performance under varying conditions.

Availability: PurBayes is implemented as an R package, and source code is available for download through CRAN at http://cran.r-project.org/package=PurBayes.

Contact:  larson.nicholas@mayo.edu

Supplementary information:  Supplementary data are available online at Bioinformatics online.
SVGenes: a library for rendering genomic features in scalable vector graphic format
Authors: Etherington Graham J. , MacLean Daniel
Published: June 2013

Motivation: Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements.

Results: SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion.

Availability: The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License.

Contact:  dan.maclean@tsl.ac.uk
Network2Canvas: network visualization on a canvas with enrichment analysis
Authors: Tan Christopher M. , Chen Edward Y. , Dannenfelser Ruth , Clark Neil R. , Ma’ayan Avi
Published: June 2013

Motivation: Networks are vital to computational systems biology research, but visualizing them is a challenge. For networks larger than ∼100 nodes and ∼200 links, ball-and-stick diagrams fail to convey much information. To address this, we developed Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using simulated annealing to maximize local connections where a node’s brightness is made proportional to its local fitness. The interactive canvas is implemented in HyperText Markup Language (HTML)5 with the JavaScript library Data-Driven Documents (D3). We applied N2C to visualize 30 canvases made from human and mouse gene-set libraries and 6 canvases made from the Food and Drug Administration (FDA)-approved drug-set libraries. Given lists of genes or drugs, enriched terms are highlighted on the canvases, and their degree of clustering is computed. Because N2C produces visual patterns of enriched terms on canvases, a trained eye can detect signatures instantly. In summary, N2C provides a new flexible method to visualize large networks and can be used to perform and visualize gene-set and drug-set enrichment analyses.

Availability: N2C is freely available at http://www.maayanlab.net/N2C and is open source.

Contact:  avi.maayan@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
NOA: a cytoscape plugin for network ontology analysis
Authors: Zhang Chao , Wang Jiguang , Hanspers Kristina , Xu Dong , Chen Luonan , Pico Alexander R.
Published: June 2013

Summary: The Network Ontology Analysis (NOA) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges. The plugin facilitates the annotation and analysis of one or more networks in Cytoscape according to user-defined parameters. In addition to tables, the NOA plugin also presents results in the form of heatmaps and overview networks in Cytoscape, which can be exported for publication figures.

Availability: The NOA plugin is an open source, Java program for Cytoscape version 2.8 available via the Cytoscape App Store (http://apps.cytoscape.org/apps/noa) and plugin manager. A detailed user manual is available at http://nrnb.org/tools/noa.

Contact: apico@gladstone.ucsf.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas
Authors: Labrenz Matthias , Grote Jana , Mammitzsch Kerstin , Boschker Henricus T. S. , Laue Michael , Jost Günter , Glaubitz Sabine , Jürgens Klaus
Published: June 2013

A psychro- and aerotolerant bacterium was isolated from the sulfidic water of a pelagic redox zone of the central Baltic Sea. The slightly curved rod- or spiral-shaped cells were motile by one polar flagellum or two bipolar flagella. Growth was chemolithoautotrophic, with nitrate or nitrite as electron acceptor and either a variety of sulfur species of different oxidation states or hydrogen as electron donor. Although the bacterium was able to utilize organic substances such as acetate, pyruvate, peptone and yeast extract for growth, these compounds yielded considerably lower cell numbers than obtained with reduced sulfur or hydrogen; in addition, bicarbonate supplementation was necessary. The cells also had an absolute requirement for NaCl. Optimal growth occurred at 15 °C and at pH 6.6–8.0. The predominant fatty acid of this organism was 16 : 1ω7c, with 3-OH 14 : 0, 16 : 0, 16 : 1ω5c+t and 18 : 1ω7c present in smaller amounts. The DNA G+C content was 33.6 mol%. As determined in 16S rRNA gene sequence phylogeny analysis, the isolate belongs to the genus

Sulfurimonas

, within the class

Epsilonproteobacteria

, with 93.7 to 94.2 % similarity to the other species of the genus

Sulfurimonas

,

Sulfurimonas autotrophica

,

Sulfurimonas paralvinellae

and

Sulfurimonas denitrificans

. However, the distinct physiological and genotypic differences from these previously described taxa support the description of a novel species, Sulfurimonas gotlandica sp. nov. The type strain is GD1T ( = DSM 19862T = JCM 16533T). Our results also justify an emended description of the genus

Sulfurimonas

.
Geodermatophilus

taihuensis sp. nov., isolated from the interfacial sediment of a eutrophic lake
Authors: Qu Jian-Hang , Hui Ming , Qu Jian-Ying , Wang Fu-Fang , Li Hai-Feng , Hu Yuan-Sen , Luo Yu , Cai Jing-Ping
Published: June 2013

A novel actinobacterial strain, 3-wff-81T, was isolated from interfacial sediment of the eutrophic Taihu Lake in Jiangsu Province (China) and subjected to polyphasic taxonomic characterization. The strain formed pale orange-pigmented colonies comprising rod-shaped cells on R2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain 3-wff-81T belonged to the genus

Geodermatophilus

, with

Geodermatophilus soli

PB34T (99.1 % similarity) and

Geodermatophilus terrae

PB261T (98.3 % similarity) as closest relatives. The major fatty acids were 16 : 0 iso, 15 : 0 iso, 17 : 1ω8c and 14 : 0 iso. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The genomic DNA G+C content was 73.2 mol%. DNA–DNA relatedness values with

G. soli

PB34T and

G. terrae

PB261T were 42.8 % and 39.6 %, respectively. Based on the physiological, biochemical and chemotaxonomic data, it is proposed that strain 3-wff-81T represents a novel species named

Geodermatophilus

taihuensis sp. nov. with 3-wff-81T ( = CGMCC 1.12303T = NBRC 109416T) as the type strain.
Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge
Authors: Alves J. I. , van Gelder A. H. , Alves M. M. , Sousa D. Z. , Plugge C. M.
Published: June 2013

A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-OT, was isolated from anaerobic sludge from a municipal solid waste digester. Cells were straight rods, 0.6–1 µm in diameter and 2–3 µm in length and grew as single cells or in pairs. Cells formed round terminal endospores. The temperature range for growth was 50–70 °C, with an optimum at 65 °C. The pH range for growth was 5.7–8.0, with an optimum at 7.5. Strain E3-OT had the ability to ferment various sugars, such as fructose, galactose, glucose, mannose, raffinose, ribose, sucrose and xylose, producing mainly H2 and acetate. In addition, the isolate was able to grow with CO as the sole carbon and energy source. CO oxidation was coupled to H2 and CO2 formation. The G+C content of the genomic DNA was 54.6 mol%. Based on 16S rRNA gene sequence analysis, this bacterium is most closely related to

Moorella glycerini

(97 % sequence identity). Based on the physiological features and phylogenetic analysis, it is proposed that strain E3-OT should be classified in the genus

Moorella

as a representative of a novel species, Moorella
stamsii. The type strain of Moorella stamsii is E3-OT ( = DSM 26271T = CGMCC 1.5181T).
Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater
Authors: Wang Hui , Li Junde , Zheng Tianling , Hill Russell T. , Hu Xiaoke
Published: June 2013

A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family

Flammeovirgaceae

in the phylum

Bacteroidetes

, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1ω6c/C16 : 1ω7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycolipids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T ( = CICC 10659T = KCTC 32399T).
Formosa

undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida
Authors: Park Sooyeon , Lee Jung-Sook , Lee Keun-Chul , Yoon Jung-Hoon
Published: June 2013

A strain of Gram-staining-negative, aerobic, non-flagellated, non-gliding and rod-shaped bacteria, designated WS-MY3T, was isolated from a brown algae reservoir in South Korea. Strain WS-MY3T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain WS-MY3T fell within the cluster comprising the type strains of species of the genus

Formosa

, clustering coherently with the type strains of

Formosa agariphila

and

Formosa algae

. It exhibited 16S rRNA gene sequence similarity values of 98.7, 97.9 and 96.8 % to the type strains of F. agariphila, F. algae and

Formosa spongicola

, respectively. Strain WS-MY3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C16 : 0 3-OH, iso-C15 : 1 G and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids of strain WS-MY3T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain WS-MY3T was 37.3 mol% and its DNA–DNA relatedness values with F. agariphila KCTC 12365T and F. algae KCTC 12364T were 23 % and 17 %, respectively. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WS-MY3T is separate from the three recognized species of the genus

Formosa

. On the basis of the data presented, strain WS-MY3T is considered to represent a novel species of the genus

Formosa

, for which the name

Formosa

undariae sp. nov. is proposed. The type strain is WS-MY3T ( = KCTC 32328T = CECT 8286T).
Natronobacterium texcoconense sp. nov., a haloalkaliphilic archaeon isolated from soil of a former lake
Authors: Ruiz-Romero Erick , Sánchez-López Katia Berenice , Coutiño-Coutiño María de los Angeles , González-Pozos Sirenia , Bello-López Juan Manuel , López-Ramírez María Patricia , Ramírez-Villanueva Daniel Alejandro , Dendooven Luc
Published: June 2013

A novel haloalkaliphilic archaeon, strain B23T was isolated from the former lake Texcoco in Mexico. The strain was Gram-stain-negative, the cells coccoid to ovoid rods, red pigmented and aerobic. Strain B23T grew in 1.7–4.3 M NaCl, at pH 6.5–9.5 and at 25–45 °C with optimal growth at 2.6–3.4 M NaCl, pH 7.5–8.5 and 37 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain B23T was most closely related to

Natronobacterium gregoryi

SP2T with 97.3 % sequence similarity. The polar lipids of strain B23T were phosphatidylglycerol and several unidentified phospholipids. The G+C content of the DNA of the strain was 62.5 mol%. Levels of DNA–DNA relatedness between strain B23T and

Natronobacterium gregoryi

DSM 3393T was 32.3 %. The name Natronobacterium texcoconense sp. nov. is proposed. The type strain is B23T ( = CECT 8068T = JCM 17655T).
Characterization of AtSTOP1 Orthologous Genes in Tobacco and Other Plant Species
Authors: Ohyama Yoshinao , Ito Hiroki , Kobayashi Yuriko , Ikka Takashi , Morita Akio , Kobayashi Masatomo , Imaizumi Ryujiro , Aoki Toshio , Komatsu Kenji , Sakata Yoichi , Iuchi Satoshi , Koyama Hiroyuki
Published: June 2013

Aluminum (Al) and proton (H+) tolerances are essential traits for plants to adapt to acid soil environments. In Arabidopsis (Arabidopsis thaliana), these tolerances are mediated by a zinc-finger transcription factor, SENSITIVE TO PROTON RHIZOTOXICITY1 (AtSTOP1), which regulates the transcription of multiple genes critical for tolerance to both stressors. Here, the functions of orthologous proteins (STOP1-like proteins) in other plant species were characterized by reverse genetics analyses and in planta complementation assays. RNA interference of a gene for NtSTOP1 repressed Al and H+ tolerances of tobacco (Nicotiana tabacum) roots. Tobacco roots released citrate in response to Al, concomitant with the up-regulated transcription of an ortholog of an Al tolerance gene encoding a citrate-transporting multidrug and toxic compound extrusion protein. The RNA interference repression of NtSTOP1 blocked this process and also repressed the transcription of another orthologous gene for Al tolerance, ALUMINUM SENSITIVE3, which encodes a prokaryote-type transporter. These results demonstrated that NtSTOP1 regulates Al tolerance in tobacco through the transcriptional regulation of these genes. The in planta complementation assays revealed that other plant species, including woody plants, a legume, and a moss (Physcomitrella patens), possess functional STOP1-like proteins that can activate several H+ and Al-tolerance genes in Arabidopsis. Knocking out the gene encoding the STOP1-like protein decreased the Al tolerance of P. patens. Together, our results strongly suggest that transcriptional regulation by STOP1-like proteins is evolutionarily conserved among land plants and that it confers the ability to survive in acid soils through the transcriptional regulation of Al- and H+-tolerance genes.
Nuclear Calcium Signaling in Plants
Authors: Charpentier Myriam , Oldroyd Giles E.D.
Published: June 2013

Plant cell nuclei can generate calcium responses to a variety of inputs, tantamount among them the response to signaling molecules from symbiotic microorganisms.
Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales
Authors: Kleessen Sabrina , Klie Sebastian , Nikoloski Zoran
Published: June 2013

Plant behaviors across levels of cellular organization, from biochemical components to tissues and organs, relate and reflect growth habitats. Quantification of the relationship between behaviors captured in various phenotypic characteristics and growth habitats can help reveal molecular mechanisms of plant adaptation. The aim of this article is to introduce the power of using statistics originally developed in the field of geographic variability analysis together with prominent network models in elucidating principles of biological organization. We provide a critical systematic review of the existing statistical and network-based approaches that can be employed to determine patterns of covariation from both uni- and multivariate phenotypic characteristics in plants. We demonstrate that parameter-independent network-based approaches result in robust insights about phenotypic covariation. These insights can be quantified and tested by applying well-established statistics combining the network structure with the phenotypic characteristics. We show that the reviewed network-based approaches are applicable from the level of genes to the study of individuals in a population of Arabidopsis thaliana. Finally, we demonstrate that the patterns of covariation can be generalized to quantifiable biological principles of organization. Therefore, these network-based approaches facilitate not only interpretation of large-scale data sets, but also prediction of biochemical and biological behaviors based on measurable characteristics.
Multiscale measurement of cardiac energetics
Authors: Goo Soyeon , Pham Toan , Han Jun‐Chiew , Nielsen Poul , Taberner Andrew , Hickey Anthony , Loiselle Denis
Published: June 2013

Herein we describe our laboratories' experimental methods for interrogating cardiac energetics at the organ (whole heart), tissue (trabecula) and perforated fibre (mitochondrial) levels.

In whole heart and trabecula experiments, we focus on measuring pressure–volume (force–length) work and oxygen consumption (heat production) from which mechanical efficiency is derived. In both preparations (i.e. across scales differing by three orders of magnitude) we find efficiency values of 10%–15%.

Mitochondrial experiments invoke a trio of titration protocols to yield information on oxygen consumption, ATP flux, membrane potential, electron leak and reactive oxygen species production, the latter two of which index energy transfer inefficiencies.
The effect of enriching milk‐based beverages with plant sterols or stanols on the fatty acid composition of the products
Authors: Garcia‐Llatas Guadalupe , Cilla Antonio , Higueras Laura , Pons María , Ripollés Susana , Bañuls Celia , Lagarda María Jesús
Published: June 2013

Five plant sterol (PS)‐enriched dairy products from the Spanish market were characterised for fatty acids (FA), volatile compounds and lipid stability. The ingredients used for PS enrichment by the food industry may come from different sources, thus influencing the composition and stability of the lipid fraction. In this study, the FA profile proved highly variable among samples, not agreeing with the nutritional labelling of the products. The volatile profile was characterised. A total of 55 volatile compounds were identified in the samples by GC–MS. Concentrations of hexanal (from 1.1 to 7.5 ng/g), nonanal (from 0.9 to 1.2 ng/g) and decane (from n.d. to 11.9 ng/g) indicated a low lipid oxidation extent. Peroxide value, ranking between 0.7 and 3.2 meq of active oxygen per kilogram of fat, except sample with fish oil, where peroxide value was 7.7 meq of active oxygen per kilogram of fat, and thiobarbituric acid reactive species, from 2 to 21 μg malondialdehyde (MDA)/g of fat, were in the lower limits of the ranges found in the literature.
Interferon‐gamma release assays versus tuberculin skin testing in patients with rheumatoid arthritis
Authors: Song Gwan Gyu , Bae Sang‐Cheol , Lee Young Ho
Published: June 2013

Objective

The aim of this study was to analyze the results of interferon‐gamma release assays (IGRAs) and tuberculin skin tests (TST) performed to detect latent tuberculosis infection (LTBI) in patients with rheumatoid arthritis (RA).

Methods

Interferon‐γ release assays and TST test results were summarized and systematically reviewed.

Results

Four hundred and five RA patients and 339 controls that underwent IGRA and/or TST were identified in seven studies. Five studies were case‐control studies and two were cross‐sectional studies. Among RA patients, the IGRA positivity rate was 31.6% (89/282; range 11.4%–44.6%), and the TST positivity rate was 23.0% (78/339; range from 14.60% to 45%). Concordance rates ranged from 40% to 76% and discordance rates from 24% to 29.7%. Agreement between IGRAs and TST in RA was poor (69.6%, k = 0.33, 95% CI 0.188–0.478). The IGRA positivity rate was 31.0% in RA and 40.0% in controls, which was not significant (relative risk [RR] 0.802, 95% CI 0.629–1.023, P = 0.075). The TST positivity rate was 24.7% in RA and 50.5% in controls, and this difference was not significant (RR 0.680, 95% CI 0.331–1.339, P = 0.295).

Conclusions

Positivity rates of IGRA and TST were 31.6 and 23.0%, respectively, in RA patients. Agreement between IGRA and TST results in RA was poor. Our data suggest that both IGRA and TST are needed to detect LTBI in RA.
Urbanization and poverty reduction: the role of rural diversification and secondary towns1
Authors: Christiaensen Luc , De Weerdt Joachim , Todo Yasuyuki
Published: June 2013

A rather unique panel tracking more than 3,300 individuals from households in rural Kagera, Tanzania, during 1991/1994–2010 shows that about one out of two individuals/households who exited poverty did so by transitioning out of agriculture into the rural nonfarm economy or secondary towns. Only one out of seven exited poverty by migrating to the big cities, even though those moving to the city experienced on average faster consumption growth. Further analysis of a much larger cross‐country panel of 51 developing countries cannot reject that rural diversification and secondary town development lead to more inclusive growth patterns than metropolitization. Indications are that this follows because more of the poor find their way to the rural nonfarm economy and secondary towns, than to distant cities. The development discourse would benefit from shifting beyond the rural–urban dichotomy and focusing more instead on how best to urbanize and develop its rural nonfarm economy and secondary towns.
Nonfarm diversification, poverty, economic mobility, and income inequality: a case study in village India
Authors:   Himanshu, Lanjouw Peter , Murgai Rinku , Stern Nicholas
Published: June 2013

This article assembles data at the all‐India level and for the village of Palanpur, Uttar Pradesh, to document the growing importance, and influence, of the nonfarm sector in the rural economy between the early 1980s and late 2000s. The suggestion from the combined National Sample Survey and Palanpur data is of a slow process of nonfarm diversification, whose distributional incidence, on the margin, is increasingly pro‐poor. The village‐level analysis documents that the nonfarm sector is not only increasing incomes and reducing poverty, but appears as well to be breaking down long‐standing barriers to mobility among the poorest segments of rural society. Efforts by the government of India to accelerate the process of diversification could thus yield significant returns in terms of declining poverty and increased income mobility. The evidence from Palanpur also shows, however, that at the village‐level a significant increase in income inequality has accompanied diversification away from the farm. A growing literature argues that such a rise in inequality could affect the fabric of village society, the way in which village institutions function and evolve, and the scope for collective action at the village level. Failure to keep such inequalities in check could thus undermine the pro‐poor impacts from the process of structural transformation currently underway in rural India.
Consumer preferences for new technology: apples enriched with antioxidant coatings in Uzbekistan
Authors: Zaikin Andrey A. , McCluskey Jill J.
Published: June 2013

Food markets in developing countries are experiencing an expansion of new functional products. Even though their market share is small, these food products are usually imported and post a higher price compared to local products. In this article, we investigate the consumer response toward new functional food products in Uzbekistan by focusing on the incorporation of apples enriched with antioxidant coating in the food market. We conduct consumer surveys with two different information treatments. We utilize a dichotomous‐choice contingent valuation methodology to estimate willingness to pay for this product and analyze factors that affect consumer choice. The results suggest that the average Uzbek respondent is willing to purchase functional apples with a 6% discount. The effect of information regarding the potential health benefits of antioxidants is positive and statistically significant. We compare the findings with a previous U.S. study of the same product and discuss how the delivery method provides an additional hurdle in the Uzbek market.
Sparkling wine choice from supermarket shelves: the impact of certification of origin and production practices
Authors: Thiene Mara , Scarpa Riccardo , Galletto Luigi , Boatto Vasco
Published: June 2013

We report the results of a study based on revealed and stated preference data on choice of Prosecco wines in retail stores close to the origin of production in Northern Italy. Emphasis is placed on ability to reconcile the utility structure of stated preference data with that underlying revealed preference data. We extend the analysis to cover nonattendance of key attributes, such as price and certification of origin, while controlling for the large range of brand effects.
Evaluating the Predictivity of Virtual Screening for Abl Kinase Inhibitors to Hinder Drug Resistance
Authors: Gani Osman A. B. S. M. , Narayanan Dilip , Engh Richard A.
Published: June 2013

Virtual screening methods are now widely used in early stages of drug discovery, aiming to rank potential inhibitors. However, any practical ligand set (of active or inactive compounds) chosen for deriving new virtual screening approaches cannot fully represent all relevant chemical space for potential new compounds. In this study, we have taken a retrospective approach to evaluate virtual screening methods for the leukemia target kinase ABL1 and its drug‐resistant mutant ABL1‐T315I. ‘Dual active’ inhibitors against both targets were grouped together with inactive ligands chosen from different decoy sets and tested with virtual screening approaches with and without explicit use of target structures (docking). We show how various scoring functions and choice of inactive ligand sets influence overall and early enrichment of the libraries. Although ligand‐based methods, for example principal component analyses of chemical properties, can distinguish some decoy sets from active compounds, the addition of target structural information via docking improves enrichment, and explicit consideration of multiple target conformations (i.e. types I and II) achieves best enrichment of active versus inactive ligands, even without assuming knowledge of the binding mode. We believe that this study can be extended to other therapeutically important kinases in prospective virtual screening studies.
The relationship between bone mass and body composition in children with hypothalamic and simple obesity
Authors: Shaikh M. Guftar , Crabtree Nicola , Kirk Jeremy M. W. , Shaw Nicholas J.
Published: June 2013

Introduction

Obesity has been associated with a positive influence on bone mass. This is thought to be due to a mechanical load exerted on the skeleton, together with various hormones and adipocytokines that control appetite and weight, such as leptin, some of which directly affect bone mass. However, there are conflicting reports of the association between fat mass and bone mass in children. Animal studies demonstrate increased bone mass where there is impaired central leptin signalling. Hypothalamic damage can cause abnormal central leptin action, which contributes to the development of obesity.

Objective

The objective of this study was to investigate the relationship between body composition and bone mass in hypothalamic and simple childhood obesity, in conjunction with the effect of the adipocytokines, leptin and adiponectin.

Design

This was a cross‐sectional study of three groups of children, those with hypothalamic obesity (HO), those with congenital hypopituitarism (CH) and those with simple obesity (SO).

Results

A total of 65 children (HO = 26 [11 males], CH = 17 [eight males] and SO = 22 [15 males]) had body composition assessed using dual‐energy X‐ray absorptiometry together with measurement of serum leptin and adiponectin. No significant differences were seen in bone mass once bone density (BMD) was adjusted for differences in body size between groups. Significantly elevated levels of leptin and adiponectin were seen in the HO group compared with the SO group (P < 0·01, P < 0·05, respectively).

Conclusion

Adiposity is associated with increased bone mass; however, this relationship is complex. Despite the presence of hyperleptinaemia, increased bone mass in the HO group was not seen. This may be due to the effects of other factors such as adiponectin, abnormal hypothalamic signalling, pituitary hormone deficiencies and disruption of normal homoeostatic mechanisms within the hypothalamus.
A ten‐year clinical update of a large RET p.Gly533Cys kindred with medullary thyroid carcinoma emphasizes the need for an individualized assessment of affected relatives
Authors: Signorini Priscila S. , França Maria Inez C. , Camacho Cleber P. , Lindsey Susan C. , Valente Flávia O. F. , Kasamatsu Teresa S. , Machado Alberto L. , Salim Camila P. , Delcelo Rosana , Hoff Ana O. , Cerutti Janete M. , Dias‐da‐Silva Magnus R. , Maciel Rui M. B.
Published: June 2013

Objective

Reviewing the clinical outcomes of a large kindred with a RET p.Gly533Cys mutation, 10 years after the first description of this kindred, has provided an important set of clinical data for healthcare decision‐making.

Design and Patients

We identified 728 RET533 Brazilian relatives, spread out over 7 generations. We performed clinical examination, biochemical and imaging analyses in the proband and in 103 carriers.

Measurement and Results

The proband has been followed without evidence of structural disease in the last 10 years but with elevated calcitonin. The clinical and surgical features of 60 thyroidectomized RET533 relatives were also described. Forty‐six patients had MTC (21–72 years), and 11 patients had C‐cell hyperplasia (CCH) (5–42 years). Twelve MTC patients with lymph node metastases had a tumour size of 0·7–2·8 cm. Calcitonin level and CEA were correlated with disease stage, and none of the patients presented with an altered PTH or metanephrine. A 63‐year‐old woman developed pheochromocytoma and breast cancer. Two other RET533 relatives developed lung squamous cell carcinoma and melanoma.

Conclusions

A vast clinical variability in RET533 presentation was observed, ranging from only an elevated calcitonin level (3%) to local metastatic disease (25%). Many individuals were cured (42%) and the majority had controlled chronic disease (56%), reinforcing the need for individualized ongoing risk stratification assessment. The importance of this update relies on the fact that it allows us to delineate the natural history of RET 533 MEN2A 10 years after its first description.