bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of n-type versus p-type AlGaN electron-blocking layer on InGaN/GaN multiple quantum wells light-emitting diodes
Authors: Ji Yun , Zhang Zi-Hui , Kyaw Zabu , Tiam Tan Swee , Gang Ju Zhen , Liang Zhang Xue , Liu Wei , Wei Sun Xiao , Volkan Demir Hilmi
Published: August 2013

The effect of n-AlGaN versus p-AlGaN electron-blocking layers (EBLs) on the performance of InGaN/GaN light-emitting diodes is studied in this work. Experimental results suggest that the n-type EBL leads to higher optical output power and external quantum efficiency, compared to the devices with p-AlGaN EBL, which is commonly used today. Numerical simulations on the carrier distribution and energy band diagram reveal that the n-AlGaN EBL is more efficient in preventing electron overflow, while not blocking the hole injection into the active region, hence leading to higher radiative recombination rate within the multiple quantum wells active region.
Multiple broadband magnetoelectric response in thickness-controlled Ni/[011] Pb(Mg1/3Nb2/3)O3-Pb(Zr,Ti)O3 single crystal/Ni laminates
Authors: Rajaram Patil Deepak , Kambale Rahul C. , Chai Yisheng , Yoon Woon-Ha , Jeong Dae-Yong , Park Dong-Soo , Kim Jong-Woo , Choi Jong-Jin , Ahn Cheol-Woo , Hahn Byung-Dong , Zhang Shujun , Hoon Kim Kee , Ryu Jungho
Published: August 2013

We report the realization of a multiple, broadband, magnetoelectric (ME) response using Ni/[011]-Pb(Mg1/3Nb2/3)O3-Pb(Zr,Ti)O3 (PMN-PZT) single crystal/Ni laminates that take advantage of the multiple mechanical resonances inherent to laminates with anisotropic piezoelectric properties. The ME voltage coefficient of the laminates showed three distinct resonance frequencies and large in-plane anisotropy in its sign and magnitude owing to the anisotropic planar piezoelectric coefficient of [011]-oriented PMN-PZT single crystals. Upon serially connecting three such laminates with different thickness ratios between the Ni and PMN-PZT layers, we observed two distinct frequency windows with bandwidths of ∼60 kHz showing flat, giant ME responses of over 16 V/cm Oe, which suggests that these ME laminates are good candidates for application in broadband field sensors or energy harvesters.
Resonant enhancement of third-order nonlinear optical susceptibilities of Cd-free chalcopyrite nanocrystals within quantum confinement regime
Authors: Hamanaka Yasushi , Ogawa Tetsuya , Tsuzuki Masakazu , Kuzuya Toshihiro , Sumiyama Kenji
Published: August 2013

Third-order nonlinear optical susceptibilities (χ(3)) have been investigated for chalcopyrite CuInS2 and AgInS2 nanocrystals within a strong confinement regime. The imaginary part of χ(3) (Imχ(3)) of 2.0- and 4.9-nm-sized CuInS2 nanocrystals and 2.6- and 4.3-nm-sized AgInS2 nanocrystals are negative and exhibit resonant enhancement around the absorption between the highest quantized levels of valence band and the lowest conduction band due to the state-filling effect. Figure of merit of |Imχ(3)| ranges 10−20–10−19 m3/V2, which is comparable to those of CdSSe nanocrystals.
Detecting response of microelectromechanical resonators by microwave reflectometry
Authors: Legrand B. , Ducatteau D. , Théron D. , Walter B. , Tanbakuchi H.
Published: August 2013

Microwave reflectometry is proposed as an effective technique to detect the vibration of capacitively transduced microelectromechanical resonators. The transducer capacitor is probed by an incident wave, which is reflected being modulated by the time variations of the resonator displacement. Calculations demonstrate that the sensitivity of the technique is maximum for a given microwave frequency depending on the transducer total capacitance. Experimental data show that capacitance variations as low as 3 zF/√Hz are measurable at 4 GHz for the studied devices. Such a performance corresponds to a sub-picometer resolution in vibration amplitude of the microelectromechanical resonator. The measurement technique is particularly appropriate for resonant sensors when high signal-to-noise ratio and fully electrical detection are required. It can be used for device resonance frequency up to several hundreds of MHz.
Shock response of low-density silica aerogel in the multi-Mbar regime
Authors: Knudson M. D. , Lemke R. W.
Published: August 2013

Low-density silica aerogels have found several applications in high-pressure research due to the ability for aerogel to be made over a wide range of initial densities with very small and uniform pore sizes. Here, we present plate-impact, shock wave experiments on nominally 110 and 200 mg/cc silica aerogel over the pressure range of ∼30-100 and ∼30-200 GPa, respectively. Direct measurement of the shock velocity in the aerogel using velocity interferometry enabled the Hugoniot to be inferred with very high precision, more than an order of magnitude improvement with respect to previously reported data for similar density silica aerogel. These results establish aerogel as a useful low impedance shock wave standard and provide data at high-entropy, high-pressure, and relatively low-density states to aid in the development of wide range equations of state for silica, a major constituent in the Earth's crust and mantle. Such models are crucial for accurate simulations of high-velocity giant impacts that are thought to be prevalent in the final stages of terrestrial planet formation.
Second harmonic generation in free-standing lithium niobate photonic crystal L3 cavity
Authors: Diziain Séverine , Geiss Reinhard , Zilk Matthias , Schrempel Frank , Kley Ernst-Bernhard , Tünnermann Andreas , Pertsch Thomas
Published: August 2013

We report on second harmonic generation in a photonic crystal L3 cavity drilled in a thin self-suspended lithium niobate membrane. The cavity, resonant for the pump beam in the telecom wavelength range, exhibits a quality factor of around 500. Second harmonic generation has been measured with a low power continuous laser. A conversion efficiency of 6.4×10−9 has been estimated with an input coupled power of 53 μW.
Optical emission spectroscopy measurements within a single microdischarge of a dielectric barrier discharge actuator
Authors: Stanfield S. A. , Menart J.
Published: August 2013

This paper reports optical emission spectroscopy measurements resolved laterally within a single microdischarge during the negative half-cycle of a sinusoidally driven dielectric barrier discharge. The maximum values of the reduced electric field, vibrational temperature of N2(C3Πu), and rotational temperature of N2+(B2Σu+) were approximately 300 Td, 3500 K, and 1200 K, respectively. These values were correlated to the outer-edges of the microdischarge near the plasma-dielectric surface interface. These maximum values were significantly greater than measurements made elsewhere within the microdischarge and suggest a strong sheath at the outer-edges of the microdischarge.
Experimental verification of enhancement of evanescent waves inside a wire medium
Authors: Slobozhanyuk Alexey P. , Melchakova Irina V. , Simovski Constantin R. , Belov Pavel A.
Published: August 2013

A theoretically revealed effect [Belov et al., Opt. Lett. 34, 527 (2009)] of the significant enhancement of evanescent harmonics inside a wire medium slab is experimentally verified in the microwave frequency range. The phenomenon originates from resonant pumping of standing waves into which evanescent waves are converted inside the slab. We find a good agreement between experimental data, numerical simulations and theory.
Dependence of doubly curved regions on drying method in the fabrication of long-side rolled-up III-V microtubes
Authors: Li Bochang , Wang Qi , Wang Eryang , Jia Zhigang , Yan Yingce , Bian Zhiqiang , Ren Xiaomin , Cai Shiwei , Huang Yongqing
Published: August 2013

Through improving fabrication process, short-side rolling phenomenon has been eliminated, and well-aligned long-side rolled-up III-V microtube arrays have been achieved. Finite element method (FEM) has been exploited to simulate the evolution of strain energy in the entire self-rolling process, showing that the difference of strain-released regions is the major factor that determines the rolling direction. Meanwhile, the doubly curved regions have been observed around the openings of air-dried microtubes but do not exist on the microtubes dried in critical point dryer, which demonstrates this structural deformation results not from the release of residual strain energy but from the surface tension.
Electronic structure and transport properties of Si nanotubes
Authors: Li Jing , Gu Tang , Delerue Christophe , Niquet Yann-Michel
Published: August 2013

The electronic structure and the transport properties of Si nanotubes with outer diameter between 2 and 20 nm are investigated using fully atomistic simulations. A formula is given for the energy of the band edges versus diameter and thickness. The phonon-limited mobility of electrons and holes is calculated and is compared to the case of Si nanowires. It is found that the thickness of the nanotubes is the main parameter controlling the shape of the band structure and the values of the effective masses. Configurations with expected best carrier mobilities are discussed.
Photon shot noise limited detection of terahertz radiation using a quantum capacitance detector
Authors: Echternach P. M. , Stone K. J. , Bradford C. M. , Day P. K. , Wilson D. W. , Megerian K. G. , Llombart N. , Bueno J.
Published: August 2013

We observed a sweep rate dependence of the quantum capacitance in a single Cooper-Pair box used as the readout of a Quantum Capacitance Detector. A model was developed that fits the data over five orders of magnitude in sweep rate and optical signal power and provides a natural calibration of the absorbed power. We are thereby able to measure the noise equivalent power of the detector as a function of absorbed power. We find that it is shot-noise-limited in detecting 1.5 THz photons with absorbed power ranging from 1 × 10−22 W to 1 × 10−17 W.
The insulator to correlated metal phase transition in molybdenum oxides
Authors: Smith G. B. , Golestan D. , Gentle A. R.
Published: August 2013

In sub-stoichiometric MoO3, electrical and optical responses across the solar spectrum are tunable and manifest a sharp phase transition in thin films at a specific oxygen content. Models of optical response in insulating and conducting regimes have been developed. Oxygen vacancies induce semiconducting response exactly proportional to the observed concentration of gap d-states until the transition. Ionization potential is thus tunable. Metallic thin films are never plasmonic at any stoichiometry and their conductivity, Hall mobility, carrier density, and plasma frequency are consistent, but either loss rate or effective mass mean metallic conduction is correlated rather than classical.
Experimental realization of epsilon-near-zero metamaterial slabs with metal-dielectric multilayers
Authors: Gao Jie , Sun Lei , Deng Huixu , Mathai Cherian J. , Gangopadhyay Shubhra , Yang Xiaodong
Published: August 2013

Epsilon-near-zero (ENZ) metamaterial slabs at visible frequencies based on metal-dielectric multilayers are experimentally realized. Transmission, reflection, and absorption spectra are measured and used to determine the complex refractive indices and the effective permittivities of the ENZ slabs, which agree with the results obtained from both the numerical simulations and the optical nonlocalities analysis. Furthermore, light propagation in ENZ slabs and directional emission from ENZ prisms are also analyzed. The accurate determination of the ENZ wavelength for metal-dielectric multilayer metamaterial slabs is important for realizing many unique applications, such as phase front manipulation and enhancement of photonic density of states.
Same-wavelength cascaded-transition quantum cascade laser
Authors: Huang Xue , Zhang Jingyuan L. , Tokranov Vadim , Oktyabrsky Serge , Gmachl Claire F.
Published: August 2013

Conventional Quantum Cascade (QC) lasers are based on intersubband transitions in repeated stages of precisely engineered quantum wells, with one electron emitting at most one photon in each stage. Here, we report on a same-wavelength cascaded-transition (SWCT) QC structure, with two subsequent optical transitions emitting at the same wavelength (λ ∼ 14.2 μm) in each stage. This SWCT QC gain medium was inserted between two conventional QC stacks, also at ∼14.2 μm. The measured laser power shows a quasi-saturation region with a 46% increase in slope efficiency after it. This quasi-saturation region is attributed to different current injection mechanisms.
A bright continuous-wave laser source at 193 nm
Authors: Scholz Matthias , Opalevs Dmitrijs , Leisching Patrick , Kaenders Wilhelm , Wang Guiling , Wang Xiaoyang , Li Rukang , Chen Chuangtian
Published: August 2013

This Letter reports on the realization of a highly coherent light source at 193 nm. By frequency-quadrupling an amplified diode laser, over 15 mW of laser emission could be generated using the nonlinear crystal potassium fluoro-beryllo-borate. The high stability of the setup was proven in an 80 h-measurement, and the impact of the crystal transmission on the output power was thoroughly studied. This laser source is an ideal tool for photoemission spectroscopy and reaches the power level to replace excimer lasers in metrological applications.
Metamorphic InAsSb-based barrier photodetectors for the long wave infrared region
Authors: Wang Ding , Donetsky Dmitry , Kipshidze Gela , Lin Youxi , Shterengas Leon , Belenky Gregory , Sarney Wendy , Svensson Stefan
Published: August 2013

InAs0.6Sb0.4/Al0.75In0.25Sb-based barrier photodetectors were grown metamorphically on compositionally graded Ga1−xInxSb buffer layers and GaSb substrates by molecular beam epitaxy. At the wavelength of 8 μm and T = 150 K, devices with 1-μm thick absorbers demonstrated an external quantum efficiency of 18% under a bias voltage of 0.45 V.
Temperature dependence of the electrical resistivity of LaxLu1-xAs
Authors: Rahimi S. , Krivoy E. M. , Lee J. , Michael M. E. , Bank S. R. , Akinwande D.
Published: August 2013

We investigate the temperature-dependent resistivity of single-crystalline films of LaxLu1-xAs over the 5–300 K range. The resistivity was separated into lattice, carrier and impurity scattering regions. The effect of impurity scattering is significant below 20 K, while carrier scattering dominates at 20–80 K and lattice scattering dominates above 80 K. All scattering regions show strong dependence on the La content of the films. While the resistivity of 600 nm LuAs films agree well with the reported bulk resistivity values, 3 nm films possessed significantly higher resistivity, suggesting that interfacial roughness significantly impacts the scattering of carriers at the nanoscale limit.
On the efficiency droop of top-down etched InGaN/GaN nanorod light emitting diodes under optical pumping
Authors: Zhang Shaofei , Li Yukun , Fathololoumi Saeed , Nguyen Hieu Pham Trung , Wang Qi , Mi Zetian , Li Qiming , Wang George T.
Published: August 2013

The optical performance of top-down etched InGaN/GaN nanorod light emitting diodes (LEDs) was studied using temperature variable photoluminescence spectroscopy with a 405 nm pump laser. Efficiency droop is measured from such nanorod structures, which is further enhanced with decreasing temperature. Through detailed rate equation analysis of the temperature-dependent carrier distribution and modeling of the quantum efficiency, this unique phenomenon can be largely explained by the interplay and dynamics between carrier radiative recombination in localized states and nonradiative recombination via surface states/defects.
Carbon nanotube-ZnO nanowire hybrid architectures as multifunctional devices
Authors: Singh L. T. , Sugavaneshwar R. P. , Nanda K. K.
Published: August 2013

We report on multifunctional devices based on CNT arrays-ZnO nanowires hybrid architectures. The hybrid structure exhibit excellent high current Schottky like behavior with ZnO as p-type and an ideality factor close to the ideal value. Further the CNT-ZnO hybrid structures can be used as high current p-type field effect transistors that can deliver currents of the order of milliamperes and also can be used as ultraviolet detectors with controllable current on-off ratio and response time. The p-type nature of ZnO and possible mechanism for the rectifying characteristics of CNT-ZnO has been presented.
Predictions of watertable depth and soil salinity levels for land capability assessment using site indicator species
Authors: Bennett Sarita Jane , Barrett-Lennard E. G.
Published: August 2013

Salt-affected land varies spatially and seasonally in terms of soil salinity and depth to the watertable. This paper asks whether native and naturalised species growing on saltland can be used as ‘indicators’ of saltland capability. The percentage cover of native and naturalised species was recorded in spring 2004 and 2005 across saltland transects on three sites in Western Australia. The presence of these plants was related to average soil salinity (ECe) at depth (25–50 cm), and depth to the watertable in spring. Eight naturalised species occurred with ≥40% cover on the sites. Species preferences varied, with some such as samphire (Tecticornia pergranulata) and puccinellia (Puccinellia ciliata) only occurring with shallow watertables (<0.7 m deep) and with ECe values >16 dS/m. Other species such as capeweed (Arctotheca calendula) and annual ryegrass (Lolium rigidum) were dominant where watertables were deeper (>1.3 m) and salinity levels lower (ECe values 2–8 and 4–16 dS/m, respectively). Our data suggest that some of the species recorded can be used as indicators of saltland capability and, further, can predict the most productive species to sow in that area. Other species were found not to be good indicators as they displayed more opportunistic habitat requirements.
Size-resolved elemental composition of aerosol particles in greater Sydney in 2002–2003
Authors: Hallal Taleb , Box Gail P. , Cohen David D. , Stelcer Eduard
Published: August 2013

Environmental context
Atmospheric aerosols may either scatter or absorb solar radiation, potentially cooling or warming the planet. The warming–cooling effects of aerosols are determined by their optical properties, which depend on chemical composition. To better predict aerosol effects we need a good understanding of aerosol chemistry across a wide size range and geographic area. We report results of a study designed to increase understanding of the chemical composition of fine and coarse aerosols in Sydney.

Abstract
Between November 2002 and December 2003 samples of PM2.5 and PM10 (particulate matter less than 2.5- and 10-μm aerodynamic diameter) aerosols were collected at four sites in the Sydney Basin in order to determine the spatial and seasonal variation of size-resolved aerosol chemical composition in the Sydney region and relate this to aerosol optical properties. Accelerator-based ion beam analysis was used to determine the elemental composition and black carbon (BC) was determined using the laser integrating plate method. Aerosol species were determined by multiplying a marker element by a factor based on molecular weight ratios. Mass concentrations at the rural sites were lower than at the urban sites with an average PM2.5/PM10 mass ratio of 0.5–0.6 for all sites although at the urban sites it was 0.2–0.25 in summer. For all sites BC was the dominant element, followed by Na. For the urban sites this was followed by Cl suggesting sea salt and then the soil elements Al and Si. For the rural sites the soil elements Al, Si and Ca were more important than Cl, which was found to decrease away from the coast. Analysis of aerosol species shows that BC accounts for a larger portion of PM2.5 than PM10 and sea salt and sulfate levels are higher in summer than in winter.
Aggregation kinetics and surface charge of CuO nanoparticles: the influence of pH, ionic strength and humic acids
Authors: Sousa Vânia Serrão , Teixeira Margarida Ribau
Published: August 2013

Environmental context
The high demand and use of nanomaterials in commercial products have led to increased concerns about their effect on the environment and human health. Because CuO nanoparticles are widely used in several products, it is necessary to understand and predict their behaviour and fate in the environment. We report a study on the aggregation and surface charge of CuO nanoparticles under environmentally relevant conditions to better predict the mobility and bioavailability of these materials in natural waters.

Abstract
In this study, the role of pH, ionic strength and humic acids (HAs) on the aggregation kinetics and surface charge of commercial copper oxide (CuO) nanoparticles were examined. Results show that the aggregation of CuO nanoparticles is favoured near pH 10, which was determined as the isoelectric point where the hydrodynamic diameter of the aggregates is the greatest. The aggregation of CuO nanoparticles is also ionic strength dependent. The increase in the ionic strength reduces the zeta potential, which leads to an increase in aggregation until 0.15M. After this point an increase in ionic strength has no influence on aggregation. In the presence of HA for concentrations below 4mgCL–1, aggregation was enhanced for acidic to neutral pH, whereas for higher concentrations, at all pH tested, aggregation does not change. The influence of HA on CuO nanoparticles is due to steric and electrostatic interactions. The sedimentation rates of CuO nanoparticles showed a relation between particle diameter and zeta potentials values confirmed by Derjaguin–Landau–Verwey–Overbeek calculations. The results obtained have important implications for predicting the stability and fate of CuO nanoparticles in natural water.
MC1R and cAMP signaling inhibit cdc25B activity and delay cell cycle progression in melanoma cells
Authors: Lyons Jesse , Bastian Boris C. , McCormick Frank
Published: August 2013

The melanocortin 1 receptor (MC1R) mediates the tanning response through induction of cAMP and downstream pigmentary enzymes. Diminished function alleles of MC1R are associated with decreased tanning and increased melanoma risk, which has been attributed to increased rates of mutation. We have found that MC1R or cAMP signaling also directly decreases proliferation in melanoma cell lines. MC1R overexpression, treatment with the MC1R ligand, or treatment with small-molecule activators of cAMP signaling causes delayed progression from G2 into mitosis. This delay is caused by phosphorylation and inhibition of cdc25B, a cyclin dependent kinase 1-activating phosphatase, and is rescued by expression of a cdc25B mutant that cannot be phosphorylated at the serine 323 residue. These results show that MC1R and cAMP signaling can directly inhibit melanoma growth through regulation of the G2/M checkpoint.
Promotion and selection by serum growth factors drive field cancerization, which is anticipated in vivo by type 2 diabetes and obesity
Authors: Rubin Harry
Published: August 2013

Individuals suffering from type 2 diabetes or obesity exhibit a significant increase in the incidence of various types of cancer. It is generally accepted that those conditions arise from overnutrition and a sedentary lifestyle, which lead to insulin resistance characterized by overproduction of insulin acting as a growth factor. There is a consensus based largely on epidemiological data that chronic overproduction of insulin is responsible for the increased incidence of cancer. A model system in culture of NIH 3T3 cells induces the collective effects of serum growth factors on progression through the stages of field cancerization. It shows that the driving force of progression is promotion of cell growth under selection at high cell density, with no requirement for exogenous carcinogenic agents. The early effect is gradual selection among many preexisting, low-penetrance preneoplastic mutations or stable epigenetic variants, followed by sporadic, high-penetrance transforming variants, all dependent on endogenous processes. The significance of the results for cancer in diabetic and obese individuals is that the initial stages of the process involve multiorgan metabolic interactions that produce a systemic insulin resistance with chronic overproduction of insulin and localized field cancerization. Hypomagnesemia is prevalent in the foregoing metabalo/systemic disorders, and may also provide a selective microenvironment for tumor development.
Toward a syntactic phylogeny of modern Indo-European languages
Authors: Longobardi Giuseppe , Guardiano Cristina , Silvestri Giuseppina , Boattini Alessio , Ceolin Andrea
Published: August 2013

The Parametric Comparison Method (PCM, Guardiano & Longobardi 2005, Longobardi & Guardiano 2009) is grounded on the assumption that syntactic parameters are more appropriate than other traits for use as comparanda for historical reconstruction, because they are able to provide unambiguous correspondences and objective measurements, thus guaranteeing wide-range applicability and quantitative exactness. This article discusses a set of experiments explicitly designed to evaluate the impact of parametric syntax in representing historical relatedness, and performed on a selection of 26 contemporary Indo-European varieties. The results show that PCM is in fact able to correctly identify genealogical relations even from modern languages only, performing as accurately as lexical methods, and that its effectiveness is not limited by interference effects such as ‘horizontal’ transmission. PCM is thus validated as a powerful tool for the analysis of historical relationships not only on a long-range perspective (as suggested by Longobardi & Guardiano 2009), but even on more focused, though independently well-known domains.
Imagined communities and othering processes
Authors: Marzorati Roberta
Published: August 2013

The article explores discourses, which, strongly marked by the association between immigration and security/safety issues, shape conflicts between groups in the urban spaces. More specifically, the article analyses daily interactions in a neighbourhood located in a semi-central area of the city of Milan and the discursive strategies of established Italian residents in dealing with neighbours, shopkeepers and public space users of immigrant origin. It focuses on the specific case of a small park which, claimed by the Italian residents in the neighbourhood, is currently a space of different activities by different groups and constitutes a core of an intergroup conflict. Referring to the existent Italian literature on the social construction of immigration as a problem related to security and urban safety issues, the article focuses on how such a discourse is produced and reproduced at the local level in established residents’ discourses and practices and their imagination/s of the community of ‘us’. While the article analyses how established residents account for the changes that have occurred in their area, discursive strategies about the nature of the place and its ‘legitimate’ users as well as social practices of appropriation and control are examined in order to show the interrelation between the processes of othering and place-identity making.
Stable birational equivalence and geometric Chevalley-Warning
Authors: Liao Xia
Published: August 2013

We propose a “geometric Chevalley-Warning” conjecture, that is, a motivic extension of the Chevalley-Warning theorem in number theory. Its statement is equivalent to a recent question raised by F. Brown and O. Schnetz. In this paper we show that the conjecture is true for linear hyperplane arrangements, quadratic and singular cubic hypersurfaces of any dimension, and cubic surfaces in

P

3

\mathbb {P}^3

. The last section is devoted to verifying the conjecture for certain special kinds of hypersurfaces of any dimension. As a by-product, we obtain information on the Grothendieck classes of the affine “Potts model” hypersurfaces considered by Aluffi and Marcolli.
Sections of surface bundles and Lefschetz fibrations
Authors: Baykur R. , Korkmaz Mustafa , Monden Naoyuki
Published: August 2013

We investigate the possible self-intersection numbers for sections of surface bundles and Lefschetz fibrations over surfaces. When the fiber genus

g
g

and the base genus

h
h

are positive, we prove that the adjunction bound

2
h
−
2

2h-2

is the only universal bound on the self-intersection number of a section of any such genus

g
g

bundle and fibration. As a side result, in the mapping class group of a surface with boundary, we calculate the precise value of the commutator lengths of all powers of a Dehn twist about a boundary component, concluding that the stable commutator length of such a Dehn twist is

1

/

2

1/2

. We furthermore prove that there is no upper bound on the number of critical points of genus–

g
g

Lefschetz fibrations over surfaces with positive genera admitting sections of maximal self-intersection, for

g
≥
2

g \geq 2

.
SPNConverter: a new link between static and dynamic complex network analysis
Authors: Dent Jennifer E. , Yang Xinyi , Nardini Christine
Published: August 2013

Summary: The signaling Petri net (SPN) simulator, designed to provide insights into the trends of molecules’ activity levels in response to an external stimulus, contributes to the systems biology necessity of analyzing the dynamics of large-scale cellular networks. Implemented into the freely available software, BioLayout Express3D, the simulator is publicly available and easy to use, provided the input files are prepared in the GraphML format, typically using the network editing software, yEd, and standards specific to the software. However, analysis of complex networks represented using other systems biology formatting languages (on which popular software, such as CellDesigner and Cytoscape, are based) requires manual manipulation, a step that is prone to error and limits the use of the SPN simulator in BioLayout Express3D. To overcome this, we present a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible.

Availability and implementation: Distributed under the GNU General Public License Version 3 athttp://apps.cytoscape.org/apps/spnconverter.

Contact:  christine@picb.ac.cn
Enterococcus diestrammenae sp. nov., isolated from the gut of Diestrammena coreana
Authors: Kim Joon Yong , Shin Na-Ri , Na Hong-Kyung , Hyun Dong-Wook , Whon Tae Woong , Kim Pil Soo , Yun Ji-Hyun , Bae Jin-Woo
Published: August 2013

A novel Gram-stain-positive, facultatively anaerobic, non-motile and lactic-acid-producing bacterium, designated strain ORL-24T, was isolated from the gut of the camel cricket,Diestrammena coreana. Optimal growth occurred at 37 °C, pH 8 and with 0 % (w/v) NaCl. The ratio ofl-lactate tod-lactate in strain ORL-24Twas 96 : 4. Lancefield antigen D was not detected. The strain was negative for oxidase activity and catalase activity. According to a phylogenetic analysis based on 16S rRNA gene sequences, strain ORL-24Twas most closely related to the type strain ofEnterococcus asini(96.9 % similarity). ComparativepheSandrpoAsequence analyses of strain ORL-24Tindicated that the strain belonged to the genusEnterococcus. The major fatty acids were C16 : 0and C18 : 1ω9c. The DNA G+C content was 41.3 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain ORL-24Trepresents a novel species of the genusEnterococcus, for which the nameEnterococcus diestrammenaeis proposed. The type strain is ORL-24T( = KACC 16708T = JCM 18359T).
Corynebacterium frankenforstense sp. nov. and Corynebacterium lactis sp. nov., isolated from raw cow milk
Authors: Wiertz Raika , Schulz Stefanie Christine , Müller Ute , Kämpfer Peter , Lipski André
Published: August 2013

Two groups of Gram-stain positive, aerobic bacterial strains were isolated from raw cow’s milk, from a milking machine and from bulk tank milk. Based on their 16S rRNA gene sequences these isolates formed two distinct groups within the genusCorynebacterium. The sequence similarities of the isolates to the type strains of species of the genusCorynebacteriumwere below 98.4 %. The presence of menaquinones MK-8(H2) and MK-9(H2), the predominant fatty acid 18 : 1cis9 and a polar lipid pattern with several phospholipids but without aminolipids was in accord with the characteristics of this genus. The results of DNA–DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from all known species of the genusCorynebacterium. Therefore, the isolates were assigned to two novel species of this genus for which the namesCorynebacterium frankenforstensesp. nov. (type strain ST18T = DSM 45800T = CCUG 63371T), andCorynebacterium lactissp. nov. (type strain RW2-5T = DSM 45799T = CCUG 63372T) are proposed, respectively.
Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.
Authors: Killer J. , Ročková Š. , Vlková E. , Rada V. , Havlík J. , Kopečný J. , Bunešová V. , Benada O. , Kofroňová O. , Pechar R. , Profousová I.
Published: August 2013

A novel bacterial strain, designated M8T, was isolated from milk of a female macaque bred in captivity. The strain was Gram-stain-positive, anaerobic, irregular coccoid–rod-shaped without catalase activity. Analysis of 16S rRNA gene sequence similarity revealed that the isolate was most closely related toAlloscardovia omnicolensCCUG 31649T(96.4 %) andMetascardovia cricetiOMB105T(96.6 %). Sequences ofhsp60,fusA, andxfpgenes also confirmed that the strain was most closely related to the type strains ofA. omnicolensandM. criceti. The isolate produced fructose-6-phosphate phosphoketolase which is in agreement with classification within the familyBifidobacteriaceae. The major fatty acids were C18 : 1ω9c(35.8 %), C16 : 1(6.2 %) and C14 : 0(5.7 %). Polar lipid analysis revealed five different glycolipids, two unidentified phospholipids and diphosphatidylglycerol. The peptidoglycan was of the type A4αl-Lys–d-Asp with the presence ofd(l)-alanine,d-glutamine,d-asparagine andl-lysine. The DNA G+C content of strain M8Twas 50.1 mol%. On the basis of genetic, phylogenetic and phenotypic data, strain M8Trepresents a novel species of the genusAlloscardoviafor which the nameAlloscardovia macacaesp. nov. is proposed. The type strain is M8T( = DSM 24762T = CCM 7944T). In addition, our results also revealed thatAlloscardovia omnicolensDSM 21503TandMetascardovia cricetiDSM 17774Tdo not belong to different genera within the familyBifidobacteriaceae. We therefore propose to reclassifyMetascardovia cricetiasAlloscardovia criceticomb. nov. An emended description of the genusAlloscardoviais also provided.
Chryseobacterium gwangjuense sp. nov., isolated from soil
Authors: Park Yong Jin , Son Heung-Min , Lee Eun-Hee , Kim Ju Han , Mavlonov Gafurjon T. , Choi Ki Ju , Shin Hun-Sub , Kook MooChang , Yi Tae-Hoo
Published: August 2013

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterial strain, THG-A18T, was isolated from soil of Gwangju province in South Korea. Strain THG-A18T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the absence of NaCl. Strain THG-A18T displayed β-glucosidase activity, which enabled it to convert ginsenoside Rb1 to Rd. According to 16S rRNA gene sequence analysis, strain THG-A18T was shown to belong to the genus

Chryseobacterium

. The closest phylogenetic neighbours were

Chryseobacterium ginsenosidimutans

THG 15T (97.9 % 16S rRNA gene sequence similariity),

C. defluvii

B2T (97.7 %),

C. daeguense

K105T (97.6 %),

C. taiwanense

BCRC 17412T (97.5 %),

C. indoltheticum

LMG 4025T (97.4 %),

C. gregarium

P 461/12T (97.4 %) and

C. lathyri

RBA2-6T (97.3 %), but DNA–DNA relatedness values between these strains and strain THG-A18T were below 41.9 %. The G+C content of the genomic DNA was 36.4 mol%. The major respiratory quinone (MK-6) and fatty acids [iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0)] supported the affiliation of strain THG-A18T with the genus

Chryseobacterium

. The polar lipids of strain THG-A18T were phosphatidylethanolamine, four unidentified aminolipids and seven unidentified lipids. A number of physiological and biochemical tests allowed phenotypic differentiation of strain THG-A18T from recognized species of the genus

Chryseobacterium

. The name Chryseobacterium gwangjuense sp. nov. is proposed, with THG-A18T ( = KACC 16227T = LMG 26579T) as the type strain.
Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012
Authors: Zhang Xiao-Mei , He Jie , Zhang Dao-Feng , Chen Wei , Jiang Zhao , Sahu Maloy Kumar , Sivakumar Kannan , Li Wen-Jun
Published: August 2013

A novel Gram-stain-positive bacterium, designated strain YIM M11385T, was isolated from a marine sediment sample collected from the South Bay, Little Andaman Island, India with a salinity of 35 p.p.m., pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M11385T belongs to the genus

Marininema

, supported by a bootstrap value of 100 %. The taxonomic position of this organism was further established by using a polyphasic approach. Strain YIM M11385T grew optimally at 28 °C, pH 7.0 and in the presence of 0–5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strain YIM M11385T and

Marininema mesophilum

SCSIO 10219T was 98.3 %. Strain YIM M11385T exhibited a quinone system with only MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major components, and the major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The level of DNA–DNA relatedness between strain YIM M11385T and

M. mesophilum

SCSIO 10219T was 59.36 %. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M11385T represents a novel species of the genus

Marininema

, for which the name Marininema halotolerans sp. nov. is proposed. The type strain is YIM M11385T ( = CCTCC AB 2012052T = DSM 45789T). In addition, we propose that the description of the genus

Marininema

should be further emended based on the results of the present study.
Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium
Authors: Montero-Calasanz Maria del Carmen , Göker Markus , Rohde Manfred , Spröer Cathrin , Schumann Peter , Busse Hans-Jürgen , Schmid Michael , Tindall Brian J. , Klenk Hans-Peter , Camacho Maria
Published: August 2013

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13T, isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15–40 °C, at pH 5.0–8.0 and with 0–4 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genusChryseobacterium. The DNA G+C content of the novel strain was 37.2 mol%. The strain had a polyamine pattern withsym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15 : 0, C17 : 1ω9cand iso-C17 : 03-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0–97.2 % sequence similarity with those of the members of the genusChryseobacterium. Based on chemotaxonomic and phenotypic traits, and DNA–DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species,Chryseobacterium hispalense, type strain AG13T( = DSM 25574T = CCUG 63019T). Emended descriptions of the speciesChryseobacterium defluvii,Chryseobacterium indologenes,Chryseobacterium wanjuenseandChryseobacterium gregariumare also provided.
A host cell RNA-binding protein, Staufen1, has a role in hepatitis C virus replication before virus assembly
Authors: Blackham Samantha L. , McGarvey Michael J.
Published: August 2013

Staufen1 is a dsRNA-binding protein involved in the regulation of translation and the trafficking and degradation of cellular RNAs. Staufen1 has also been shown to stimulate translation of human immunodeficiency virus type 1 (HIV-1) RNA, regulate HIV-1 and influenza A virus assembly, and there is also indication that it can interact with hepatitis C virus (HCV) RNA. To investigate the role of Staufen1 in the HCV replication cycle, the effects of small interfering RNA knockout of Staufen1 on HCV strain JFH-1 replication and the intracellular distribution of the Staufen1 protein during HCV infection were examined. Silencing Staufen1 in HCV-infected Huh7 cells reduced virus secretion by around 70 %, intracellular HCV RNA levels by around 40 %, and core and NS3 proteins by around 95 and 45 %, respectively. Staufen1 appeared to be predominantly localized in the endoplasmic reticulum at the nuclear periphery in both uninfected and HCV-infected Huh7 cells. However, Staufen1 showed significant co-localization with NS3 and dsRNA, indicating that it may bind to replicating HCV RNA that is associated with the non-structural proteins. Staufen1 and HCV core protein localized very closely to one another during infection, but did not appear to overlap, indicating that Staufen1 may not bind to core protein or localize to the core-coated lipid droplets, suggesting that it may not be directly involved in HCV virus assembly. These findings indicate that Staufen1 is an important factor in HCV replication and that it might play a role early in the HCV replication cycle, e.g. in translation, replication or trafficking of the HCV genome, rather than in virion morphogenesis.
Overexpression of microRNA gga-miR-1650 decreases the replication of avian leukosis virus subgroup J in infected cells
Authors: Wang Qi , Ji Xiaolin , Gao Yulong , Qi Xiaole , Wang Xiaojun , Wang Yongqiang , Qin Liting , Gao Honglei , Wang Xiaomei
Published: August 2013

MicroRNAs (miRNAs) are a class of small regulatory non-coding RNAs that modulate gene expression at the post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have demonstrated that a number of cellular miRNAs play a role during viral infection. In this study, a luciferase-reporter system carrying the 5′ untranslated region (5′ UTR) and 3′ UTR of avian leukosis virus subgroup J (ALV-J) was used to determine whether cellular miRNAs are involved in ALV-J infection. The miRNA gga-miR-1650 was screened for its potential interaction with the 5′ UTR of ALV-J and the ability to suppress luciferase-reporter activity. A mutational analysis of predicted gga-miR-1650-binding sites showed that the 5′ and 3′ ends of gga-miR-1650 contributed to the interaction between gga-miR-1650 and its target located at the 5′ UTR. Overexpression of miRNA gga-miR-1650 was shown to downregulate the expression of the Gag protein and influence the replication of ALV-J through binding to the 5′ UTR. Overall, this report provides the basis for the development of new strategies for anti-ALV-J intervention.
Mutations in hepatitis C virus p7 reduce both the egress and infectivity of assembled particles via impaired proton channel function
Authors: Bentham Matthew J. , Foster Toshana L. , McCormick Christopher , Griffin Stephen
Published: August 2013

Hepatitis C virus (HCV) p7 protein is critical for the efficient production of infectious virions in culture. p7 undergoes genotype-specific protein–protein interactions as well as displaying channel-forming activity, making it unclear whether the phenotypes of deleterious p7 mutations result from the disruption of one or both of these functions. Here, we showed that proton channel activity alone, provided in trans by either influenza virus M2 or genotype 1b HCV p7, was both necessary and sufficient to restore infectious particle production to genotype 2a HCV (JFH-1 isolate) carrying deleterious p7 alanine substitutions within the p7 dibasic loop (R33A, R35A), and the N-terminal trans-membrane region (N15 : C16 : H17/AAA). Both mutations markedly reduced mature p7 abundance, with those in the dibasic loop also significantly reducing levels of mature E2 and NS2. Interestingly, whilst M2 and genotype 1b p7 restored the same level of intracellular infectivity as JFH-1 p7, supplementing with the isogenic protein led to a further increase in secreted infectivity, suggesting a late-acting role for genotype-specific p7 protein interactions. Finally, cells infected by viruses carrying p7 mutations contained non-infectious core-containing particles with densities equivalent to WT HCV, indicating a requirement for p7 proton channel activity in conferring an infectious phenotype to virions.
Expression of the herpes simplex virus type 1 latency-associated transcripts does not influence latency establishment of virus mutants deficient for neuronal replication
Authors: Nicoll M. P. , Efstathiou S.
Published: August 2013

Herpes simplex virus type 1 establishes latency within neurons of the trigeminal ganglion. During latency, viral gene expression is largely restricted to the latency-associated transcripts (LATs), which, whilst not essential for any aspect of latency, function to suppress lytic gene expression and enhance the survival of virus-infected neurons. The latent cell population comprises primary-order neurons infected directly from peripheral tissues and cells infected following further virus spread within the ganglion. In order to assess the role of LAT expression on latency establishment within first-order neurons, we infected ROSA26R reporter mice with Cre recombinase-expressing recombinant viruses harbouring deletion of the thymidine kinase lytic gene and/or the core LAT promoter. We found that LAT expression did not impact on latency establishment in viruses unable to replicate in neurons, and under these conditions, it was not required for the survival of neurons between 3 and 31 days post-infection.
Specific fate decisions in adult hepatic progenitor cells driven by MET and EGFR signaling
Authors: Kitade Mitsuteru , Factor Valentina M. , Andersen Jesper B. , Tomokuni Akira , Kaji Kosuke , Akita Hirofumi , Holczbauer Agnes , Seo Daekwan , Marquardt Jens U. , Conner Elizabeth A. , Lee Seung-Bum , Lee Yun-Han , Thorgeirsson Snorri S.
Published: August 2013

The relative contribution of hepatocyte growth factor (HGF)/MET and epidermal growth factor (EGF)/EGF receptor (EGFR), two key signal transduction systems in the normal and diseased liver, to fate decisions of adult hepatic progenitor cells (HPCs) has not been resolved. Here, we developed a robust culture system that permitted expansion and genetic manipulation of cells capable of multilineage differentiation in vitro and in vivo to examine the individual roles of HGF/MET and EGF/EGFR in HPC self-renewal and binary cell fate decision. By employing loss-of-function and rescue experiments in vitro, we showed that both receptors collaborate to increase the self-renewal of HPCs through activation of the extracellular signal-regulated kinase (ERK) pathway. MET was a strong inducer of hepatocyte differentiation by activating AKT and signal transducer and activator of transcription (STAT3). Conversely, EGFR selectively induced NOTCH1 to promote cholangiocyte specification and branching morphogenesis while concomitantly suppressing hepatocyte commitment. Furthermore, unlike the deleterious effects of MET deletion, the liver-specific conditional loss of Egfr facilitated rather than suppressed progenitor-mediated liver regeneration by switching progenitor cell differentiation toward hepatocyte lineage. These data provide new insight into the mechanisms regulating the stemness properties of adult HPCs and reveal a previously unrecognized link between EGFR and NOTCH1 in directing cholangiocyte differentiation.