bluuebunny/crossref_metadata_2025 huggingface dataset:
Ionic liquid directed syntheses of water-stable Eu– and Tb–organic-frameworks for aqueous-phase detection of nitroaromatic explosives
Authors: Qin Jian-Hua , Ma Bing , Liu Xiao-Fei , Lu Hong-Lin , Dong Xi-Yan , Zang Shuang-Quan , Hou Hongwei
Published: July 2015

Ionic liquid directed syntheses of water-stable Eu– and Tb–organic-frameworks for aqueous-phase detection of nitroaromatic explosives.
Treatment of indium-tin-oxide etching wastewater and recovery of In, Mo, Sn and Cu by liquid–liquid extraction and wet chemical reduction: a laboratory scale sustainable commercial green process
Authors: Swain Basudev , Mishra Chinmayee , Hong Hyun Seon , Cho Sung-Soo
Published: July 2015

A sustainable commercial green process for treatment and recovery of ITO etching wastewater by liquid–liquid extraction and wet chemical reduction.
3(2H)-Furanone as a promising scaffold for the synthesis of novel fluorescent organic dyes: an experimental and theoretical investigation
Authors: Varghese Beena , Al-Busafi Saleh N. , Suliman FakhrEldin O. , Al-Kindy Salma M. Z.
Published: July 2015

Novel 3(2H)-furanone compounds have been synthesised and characterized. Experimental and theoretical studies indicated that these compounds exhibit interesting solvatochromic effects.
Photodegradation of Rhodamine B over a novel photocatalyst of feather keratin decorated CdS under visible light irradiation
Authors: Wang Qizhao , Lian Juhong , Ma Qiong , Bai Yan , Tong Jinhui , Zhong Junbo , Wang Rongmin , Huang Haohao , Su Bitao
Published: July 2015

Natural polymer feather keratin was employed as a composite material for enhancing the photocatalytic activity of CdS for the degradation of Rhodamine B dye.
Structural diversification and photocatalytic properties of zinc(ii) polymers modified by auxiliary N-containing ligands
Authors: Yin Wen-Yu , Huang Zuo-Long , Tang Xiao-Yan , Wang Jun , Cheng Hong-Jian , Ma Yun-Sheng , Yuan Rong-Xin , Liu Dong
Published: July 2015

Four zinc coordination polymers with different architectures based on 5-(1H-benzoimidazol-2-ylsulfanylmethyl)-isophthalic acid have been prepared. Their photoluminescence and photocatalytic properties were also investigated.
A polyaniline–zeolite nanocomposite material based acetylcholinesterase biosensor for the sensitive detection of acetylcholine and organophosphates
Authors: Kaur Balwinder , Srivastava Rajendra
Published: July 2015

A nanoporous polyaniline film formed on high surface area Nano-ZSM-5 is responsible for excellent bio-sensing ability.
A highly selective and sensitive single click novel fluorescent off–on sensor for copper and sulfide ions detection directly in aqueous solution using curcumin nanoparticles
Authors: Bhopate Dhanaji P. , Mahajan Prasad G. , Garadkar Kalyanrao M. , Kolekar Govind B. , Patil Shivajirao R.
Published: July 2015

Graphical representation of the binding of CURNPs to Cu2+(fluorescence off) and release of CURNPs (fluorescence on) by the reaction of S2−with copper bound to CURNPs.
Theoretical study on homolytic C(sp2)–O cleavage in ethers and phenols
Authors: Ding Lanlan , Zheng Wenrui , Wang Yingxing
Published: July 2015

The C(sp2)–O BDEs and the substituent effect of ethers/phenols were investigated in detail by the wB97 method.
Leishmania cell wall as a potent target for antiparasitic drugs. A focus on the glycoconjugates
Authors: Cabezas Yari , Legentil Laurent , Robert-Gangneux Florence , Daligault Franck , Belaz Sorya , Nugier-Chauvin Caroline , Tranchimand Sylvain , Tellier Charles , Gangneux Jean-Pierre , Ferrières Vincent
Published: July 2015

The basic structure of membrane glycoconjugates inLeishmaniastill inspires therapeutic drugs fighting against this parasite.
The first proton sponge-based amino acids: synthesis, acid–base properties and some reactivity
Authors: Ozeryanskii Valery A. , Gorbacheva Anastasia Yu. , Pozharskii Alexander F. , Vlasenko Marina P. , Tereznikov Alexander Yu. , Chernov'yants Margarita S.
Published: July 2015

The first hybrid bases constructed from 1,8-bis(dimethylamino)naphthalene and glycine or alanine residues were synthesised and structurally characterised and unusual channels of their reactivity revealed.
Influence of rare earth doping on the structural and electro-magnetic properties of SmFeAsO0.7F0.3 iron pnictide
Authors: Anooja J. B. , Aswathy P. M. , Varghese Neson , Chandrakanth C. K. , Devendra Kumar N. , Sundaresan A. , Syamaprasad U.
Published: July 2015

The effect of Gd and Ce doping on the structural and transport properties of the (Sm,RE)FeAsO0.7F0.3 superconductor.
Antibacterial properties of Ag–TiO2 composite sol–gel coatings
Authors: Albert E. , Albouy P. A. , Ayral A. , Basa P. , Csík G. , Nagy N. , Roualdès S. , Rouessac V. , Sáfrán G. , Suhajda Á. , Zolnai Z. , Hórvölgyi Z.
Published: July 2015

This study reveals the connection between the silver-doping method, the resulting nature and amount of the silver dopant together with the structural properties and the long-term antibacterial activity of composite coatings.
Diketopyrrolopyrroles disubstituted with alkylated thiophenes: effect of the donor unit size and solubilizing substituents on their redox, photo- and electroluminescence properties
Authors: Wiosna-Salyga Gabriela , Gora Monika , Zagorska Malgorzata , Toman Petr , Luszczynska Beata , Pfleger Jiri , Glowacki Ireneusz , Ulanski Jacek , Mieczkowski Jozef , Pron Adam
Published: July 2015

Diketopyrrolopyrroles disubstituted with thiophene derivatives can be used as effective luminophores in guest/host type light emitting diodes.
Packing directed beneficial role of 3-D rigid alicyclic arms on the templated molecular aggregation problem
Authors: Kumar Sunil , Singh Punita , Srivastava Ritu , Ghosh Subrata
Published: July 2015

Tuning of solid state emission by controlling intermolecular interactions and spacing.
Sorption behavior of tylosin and sulfamethazine on humic acid: kinetic and thermodynamic studies
Authors: Guo Xuetao , Ge Jianhua , Yang Chen , Wu Renren , Dang Zhi , Liu Shaomin
Published: July 2015

Sorption and transport of TYL and SMT in soils is complicated and the transportation abilities of TYL and SMT might be weak for the soils rich in organic matter.
Electrochemical–thermal modeling for a ternary lithium ion battery during discharging and driving cycle testing
Authors: Huo Weiwei , He Hongwen , Sun Fengchun
Published: July 2015

The 3D modeling of the thermal behavior for a lithium ion battery is presented.
Marine integrated culture of carbohydrate rich Ulva rigida for enhanced production of bioethanol
Authors: Korzen Leor , Pulidindi Indra Neel , Israel Alvaro , Abelson Avigdor , Gedanken Aharon
Published: July 2015

Macro algal seaweeds are a promising feedstock for biofuels production.
Graphene and chiral nematic liquid crystals: a focus on lasing
Authors: Khan Ammar A. , Bin-Kamarudin Muhammad A. , Kidambi Piran. R. , Hofmann Stephan , Wilkinson Timothy D. , Qasim Malik M.
Published: July 2015

This work presents the interaction of self-assembled liquid crystalline unidimensional photonic structures on the surface of CVD grown graphene. Further, this surface effect is characterised through POM and laser emission features.
Hydroxyl-containing non-viral lipidic gene vectors with macrocyclic polyamine headgroups
Authors: Wang Hai-Jiao , He Xi , Zhang Yang , Zhang Ji , Liu Yan-Hong , Yu Xiao-Qi
Published: July 2015

The gene transfection abilities and structure–activity relationship of the newly designed hydroxyl-containing cationic lipids were studied in detail.
Photophysical and theoretical studies of peripherally halogenated octaphenoxyphthalocyanines
Authors: Makhseed Saad , Ghazal Basma , Abdelmoniem Amr Mohamed , Novakova Veronika , Zimcik Petr
Published: July 2015

Computational studies validated the experimental results and revealing details about the electronic structures of novel halogenated phthalocyanines. Fluorescence and singlet oxygen quantum yields analysis revealed two-dimensional heavy atom effect.
Photocatalytic conversion of glucose in aqueous suspensions of heteropolyacid–TiO2 composites
Authors: Bellardita M. , García-López E. I. , Marcì G. , Megna B. , Pomilla F. R. , Palmisano L.
Published: July 2015

Commercial and home prepared TiO2 samples were functionalized with a commercial Keggin heteropolyacid (HPA) H3PW12O40 (PW12) or with a hydrothermally home prepared K7PW11O39 salt (PW11).
In situ investigation of dissociation and migration phenomena at the Pt/electrolyte interface of an electrochemical cell
Authors: Law Yeuk Ting , Zafeiratos Spyridon , Neophytides Stylianos G. , Orfanidi Alin , Costa Dominique , Dintzer Thierry , Arrigo Rosa , Knop-Gericke Axel , Schlögl Robert , Savinova Elena R.
Published: July 2015

Using near ambient pressure X-ray photoelectron spectroscopy we probe in situ the double layer at the Pt/liquid electrolyte interface.
Water stabilization of Zr6-based metal–organic frameworks via solvent-assisted ligand incorporation
Authors: Deria Pravas , Chung Yongchul G. , Snurr Randall Q. , Hupp Joseph T. , Farha Omar K.
Published: July 2015

Water stability in metal–organic frameworks (MOFs) is critical for several practical applications; we report here fundamental understanding how capillary forces induce damage to MOFs and highlight that metal node functionalization as a strategy to create vapor-stable and recyclable MOFs.
Modified template synthesis and electrochemical performance of a Co3O4/mesoporous cathode for lithium–oxygen batteries
Authors: Wang Shaofeng , Sha Yujing , Zhu Yinlong , Xu Xiaomin , Shao Zongping
Published: July 2015

A Co3O4/mesoporous carbon (Co3O4/C) composite was successfully prepared for high performance nonaqueous lithium–oxygen batteries.
Hydrogen-bonding-mediated structural stability and electrochemical performance of iron fluoride cathode materials
Authors: Li Zuosheng , Wang Beizhou , Li Chilin , Liu Jianjun , Zhang Wenqing
Published: July 2015

Tunable H2O–F− hydrogen bonding is crucial to the structural stability and electrochemical performance of FeF3·0.33H2O cathode materials.
Molecular beacon-loaded polymeric nanoparticles for non-invasive imaging of mRNA expression
Authors: Wiraja Christian , Yeo David C. , Chew Sing Yian , Xu Chenjie
Published: July 2015

Assessment of intracellular mRNA expression is invaluable for understanding cellular signaling activities, identifying disease stages, and monitoring the gene expression pattern of therapeutic cells during their culture, expansion and/or differentiation process.
Geometry-induced high performance ultraviolet photodetectors in kinked SnO2nanowires
Authors: Gan Lin , Liao Meiyong , Li Huiqiao , Ma Ying , Zhai Tianyou
Published: July 2015

Kinked structure improves the photoresponse of nanowire both in photocurrent and response rate.
How does the multiple constituent affect the carrier generation and charge transport in multicomponent TCOs of In–Zn–Sn oxide
Authors: Lu Ying-Bo , Yang T. L. , Ling Z. C. , Cong Wei-Yan , Zhang Peng , Li Y. H. , Xin Y. Q.
Published: July 2015

In multicomponent TCOs of In–Zn–Sn oxide, the modulation of constituent elements on carrier generation and charge transport is interpreted.
Spatially inhomogeneous, stepwise phase transitions in a thiazyl diradical: a structural mismatch induced by lattice transformation
Authors: Suizu Rie , Iwasaki Akito , Shuku Yoshiaki , Awaga Kunio
Published: July 2015

Bis(1,2,3,5-dithiadiazolyl)-4,4′-biphenylene exhibits spatially inhomogeneous, stepwise phase transitions, which are caused by a “bond frustration”, as seen in frustrated gear trains.
Active-core/active-shell nanostructured design: an effective strategy to enhance Nd3+/Yb3+ cascade sensitized upconversion luminescence in lanthanide-doped nanoparticles
Authors: Huang Xiaoyong , Lin Jun
Published: July 2015

Giant enhancement of Nd3+–Yb3+ cascade sensitized upconversion luminescence has been achieved in lanthanide-doped active-core/active-shell nanoparticles.
Flexible thermoelectric materials and device optimization for wearable energy harvesting
Authors: Bahk Je-Hyeong , Fang Haiyu , Yazawa Kazuaki , Shakouri Ali
Published: July 2015

In this paper, we review recent advances in the development of flexible thermoelectric materials and devices for wearable human body-heat energy harvesting applications.
Unusual morphology of equimolar Ar–Kr alloys
Authors: Danchuk V. V. , Solodovnik A. A. , Mysko N. S. , Strzhemechny M. A.
Published: July 2015

The transmission high electron energy diffraction (THEED) technique was employed for studying the structure of the equimolar Ar–Kr alloy, in which the thermodynamics predicts the maximum feasibility of phase separation. Deposition of preliminarily cooled gas mixtures was performed onto substrates cooled to 6 or 20 K. All diffraction patterns contained several sets of reflections against an appreciable background. Analysis of the data obtained during a warm-up from 6 to 33 K (at which the major part of argon was removed due to sublimation) as well as of the diffraction pattern from the “sandwich” (two successively deposited film of pure Ar and Kr) provided reliable arguments for the following conclusions. Actually, we have documented for the first time a phase separation of an Ar–Kr mixture, manifestations of which turned out to be oddly asymmetric as far as the behavior of the components involved is concerned. Upon deposition both onto 6 or 20 K the emerging sample contained two crystal phases of virtually pure argon with a small admixture of krypton. One of the Ar phases (fcc) did not cause a surprise, whereas the other was hcp with the a/c ratio close to the ideal value. The krypton component separated as a fine-grained glass-like state, possibly, with a low admixture of argon.
Poisson's ratio in cryocrystals under pressure
Authors: Freiman Yu. A. , Grechnev Alexei , Tretyak S. M. , Goncharov Alexander F. , Gregoryanz Eugene
Published: July 2015

We present results of lattice dynamics calculations of Poisson's ratio (PR) for solid hydrogen and rare gas solids (He, Ne, Ar, Kr and Xe) under pressure. Using two complementary approaches—the semi-empirical many-body calculations and the first-principle density-functional theory calculations we found three different types of pressure dependencies of PR. While for solid helium PR monotonically decreases with rising pressure, for Ar, Kr, and Xe it monotonically increases with pressure. For solid hydrogen and Ne the pressure dependencies of PR are nonmonotonic displaying rather deep minimums. The role of the intermolecular potentials in this diversity of patterns is discussed.
On dissociation in weakly doped ice
Authors: Chikina I. , Shikin V.
Published: July 2015

Currently, there is some ambiguity in the problem of decay of a single donor into charged fragments. Thus, in the well-known Ostwald approximation used for semiconductors (ice being one of them) the donor dissociation degree of tends to its maximum value (i.e., unity) as the doping impurity concentration approaches zero. At the same time, the statistical theory of atom reveals within the Thomas–Fermi (or Debye–Hückel) approximation the existence of a thermodynamically equilibrium state of a single multi-electron atom (donor) where charged nucleus keeps the number of counterions just necessary for its neutralization. These scenarios do not show the atom dissociation at all. Discussed in the present paper is the alternative between the full dissociation of a single donor (i.e., dissociation degree equals unity) in a semiconducting media (ice, water, semiconductor) and zero dissociation degree.
Wave turbulence on the surface of liquid hydrogen in restricted geometry: The influence of the boundary conditions
Authors: Brazhnikov M. Yu. , Levchenko A. A. , Mezhov-Deglin L. P. , Remizov I. A.
Published: July 2015

Formation of low frequency harmonics on turbulent distribution in the system of waves on the surface of liquid hydrogen has been studied in the frequency range 1–100 Hz (capillary-gravity waves). It is shown that the geometry of the experimental cell has a significant influence on the direct cascade of capillary waves generated by monochromatic force as well as on the direction of the wave energy transfer from the range of pumping towards that of dissipation. Besides a direct turbulent cascade, single half-frequency harmonic generation was observed in a cylindrical cell under high pump power. In a square cell we observed not only a half-frequency harmonic but a number of low frequency harmonics below the driving frequency generated by the nonlinear three-wave interaction. In the case of a rectangular cell we observed formation of incommensurate low frequency harmonics caused by the three-wave interaction of capillary waves and generation of a wave mode of ∼1 Hz in the frequency range of gravity waves which could be attributed to the four-wave interaction.
Investigations of thermal conductivity of simple van der Waals crystal-based nanocomposites
Authors: Nikonkov R. V. , Stachowiak P. , Romanova T. V. , Jeżowski A. , Sumarokov V. V.
Published: July 2015

The experimental setup for obtaining and determination of the thermal conductivity of simple van der Waals crystal-based nanocomposites is described. Preliminary thermal conductivity results of measurements carried out in the temperature range 1–40 K on two samples of methane crystals containing nanoparticles of hydroxyapatite are presented. These results confirm usability of the setup and its suitability as a proper experimental method for investigations of the thermal conductivity of the nanocomposites.
Velocity map imaging with non-uniform detection: Quantitative molecular axis alignment measurements via Coulomb explosion imaging
Authors: Underwood Jonathan G. , Procino I. , Christiansen L. , Maurer J. , Stapelfeldt H.
Published: July 2015

We present a method for inverting charged particle velocity map images which incorporates a non-uniform detection function. This method is applied to the specific case of extracting molecular axis alignment from Coulomb explosion imaging probes in which the probe itself has a dependence on molecular orientation which often removes cylindrical symmetry from the experiment and prevents the use of standard inversion techniques for the recovery of the molecular axis distribution. By incorporating the known detection function, it is possible to remove the angular bias of the Coulomb explosion probe process and invert the image to allow quantitative measurement of the degree of molecular axis alignment.
Acoustic whispering gallery modes within the theory of elasticity
Authors: Sturman Boris , Breunig Ingo
Published: July 2015

Investigations of nonlinear phenomena in optical whispering gallery mode (WGM) microresonators are booming because of rich physics and applications. Stimulated Brillouin scattering is one of the strongest processes in these devices. Here, the optical WGMs interact with acoustic counterparts. The acoustic WGMs are well known for resonators based on liquids and gases, where the sound waves are longitudinal. The situation with solid-state resonators is different because of the presence of the longitudinal (l) and transverse (t) sound waves with substantially different velocities vl,t. Moreover, the l- and t-parts of the acoustic displacement are coupled at the resonator surface breaking the separation of modes into longitudinal and transverse. Investigation of the acoustic WGMs is of high priority. Here, analytically and numerically we investigate the resonant frequencies and the eigenfunctions (displacement vector distributions) for acoustic WGMs in microresonators made of isotropic solid-state materials. Cylindrical and spherical resonators are considered. Each mode has the azimuth, radial, and orbital (for sphere) numbers m, q, and ℓ; its properties are controlled also by the ratio vl/vt. All modes are either transverse (t) or hybrid transverse-longitudinal (tl). Pure l-modes, providing the strongest interaction with optical modes in fibers and bulk crystals, are absent. The tl-modes include distorted Rayleigh waves, the modes with q∼1 and dominating t-part, and pseudo-longitudinal modes with q≫1, closely spaced frequencies, and weakly localized t-part. They have no analogies to the optical WGMs and are of high relevance for Brillouin lasing in optical microresonators. The actual values of ℓ and m are 102−105, and the lasing thresholds lie in the μW range. Our findings include exact dispersion equations for acoustic WGMs, which can be solved numerically for ℓ,m≲104, asymptotic tools for ℓ,m≳103, and particular illustrations.
Line-tension-induced scenario of heterogeneous nucleation on a spherical substrate and in a spherical cavity
Authors: Iwamatsu Masao
Published: July 2015

Line-tension-induced scenario of heterogeneous nucleation is studied for a lens-shaped nucleus with a finite contact angle nucleated on a spherical substrate and on the bottom of the wall of a spherical cavity. The effect of line tension on the free energy of a critical nucleus can be separated from the usual volume term. By comparing the free energy of a lens-shaped critical nucleus of a finite contact angle with that of a spherical nucleus, we find that a spherical nucleus may have a lower free energy than a lens-shaped nucleus when the line tension is positive and large, which is similar to the drying transition predicted by Widom [B. Widom, J. Phys. Chem. 99, 2803 (1995)]. Then, the homogeneous nucleation rather than the heterogeneous nucleation will be favorable. Similarly, the free energy of a lens-shaped nucleus becomes negative when the line tension is negative and large. Then, the barrier-less nucleation with no thermal activation called athermal nucleation will be realized.
Angle-resolved spin wave band diagrams of square antidot lattices studied by Brillouin light scattering
Authors: Gubbiotti G. , Montoncello F. , Tacchi S. , Madami M. , Carlotti G. , Giovannini L. , Ding J. , Adeyeye A. O.
Published: July 2015

The Brillouin light scattering technique has been exploited to study the angle-resolved spin wave band diagrams of squared Permalloy antidot lattice. Frequency dispersion of spin waves has been measured for a set of fixed wave vector magnitudes, while varying the wave vector in-plane orientation with respect to the applied magnetic field. The magnonic band gap between the two most dispersive modes exhibits a minimum value at an angular position, which exclusively depends on the product between the selected wave vector magnitude and the lattice constant of the array. The experimental data are in very good agreement with predictions obtained by dynamical matrix method calculations. The presented results are relevant for magnonic devices where the antidot lattice, acting as a diffraction grating, is exploited to achieve multidirectional spin wave emission.
Ferromagnetic effects for nanofluid venture through composite permeable stenosed arteries with different nanosize particles
Authors: Akbar Noreen Sher , Mustafa M. T.
Published: July 2015

In the present article ferromagnetic field effects for copper nanoparticles for blood flow through composite permeable stenosed arteries is discussed. The copper nanoparticles for the blood flow with water as base fluid with different nanosize particles is not explored upto yet. The equations for the Cu-water nanofluid are developed first time in literature and simplified using long wavelength and low Reynolds number assumptions. Exact solutions have been evaluated for velocity, pressure gradient, the solid volume fraction of the nanoparticles and temperature profile. Effect of various flow parameters on the flow and heat transfer characteristics are utilized.
Rapid, one-step fabrication and loading of nanoscale 1,2-distearoyl-sn-glycero-3-phosphocholine liposomes in a simple, double flow-focusing microfluidic device
Authors: Tien Sing Young Ryan V. , Tabrizian Maryam
Published: July 2015

Liposomes are currently well-established as biocompatible delivery vehicles for numerous compounds. However, conventional manufacturing tends to rely on time-consuming processes, costly equipment, unstable reaction parameters, and numerous pre- and post-processing steps. Herein, we demonstrate a microscope-slide-sized alternative: a double flow-focusing microfluidic geometry capable of sub-hour synthesis and controlled loading of tunable liposomes. Using phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine as the bilayer constituent, the effect of varying the dissolved lipid concentration and flow rate ratio on synthesized liposome diameters was investigated and the encapsulation of fluorescent hydrophobic drug model ergost-5,7,9(11),22-tetraen-3β-ol was performed to ascertain the potential of this device as a loading platform.
Efimov trimers imaged for the first time
Authors: Miller Johanna L.
Published: July 2015

The exotic molecules, though composed of three identical atoms, have an asymmetric structure.
Artificial eardrums get real
Authors: Wilson R. Mark
Published: July 2015

Three-dimensional printing can fabricate polymer scaffolds that mimic the orientation of collagen in the tympanic membrane.
Renewal of Sino–US nuclear accord in question
Authors: Kramer David
Published: July 2015

Blanket approval for fuel reprocessing and China’s adapting US civil reactor technology for military use are key concerns for lawmakers.
Watching a roundworm develop with a sheet of light
Authors: Kumar Abhishek , Colón-Ramos Daniel A. , Shroff Hari
Published: July 2015

Light-sheet fluorescence microscopy allows neurobiologists to observe fundamental biological processes in real time.
Climate change and adaptive capacity in the Western Australian rangelands: a review of current institutional responses
Authors: Shaw Ellena , Witt G. Bradd
Published: July 2015

This research analysed contemporary publications concerning climate change adaptation in the agricultural systems of the Western Australian rangelands. The term ‘systems’ refers to the supportive economic and social systems as well as agricultural industries. The aim of the study was to evaluate how the adaptive capacity of agricultural systems is supported given the anticipated challenges of climatic changes. The conceptual framework of adaptive capacity was employed to evaluate progress towards improving adaptation and resilience. Eight key indicators of adaptive capacity formed the evaluative criteria, and were applied to a wide range of publicly available documents relevant to the Western Australian rangelands. Progress towards building adaptive capacity was also evaluated by classifying the documents as ‘aspirational’, ‘in action’ or ‘assessed’. The institutional support for adaptive capacity was found to be adequate, as there was sufficient evidence that relevant institutions were providing mechanisms for social, economic and environmental adaptation in the face of climate change. The viability of the agricultural systems of the Western Australian rangelands has been in decline for some time and, therefore, the degree to which efforts to improve adaptive capacity have been successful was difficult to assess. There were methodological limitations of this research due to the limited breadth of available data and subjectivity within the data analysis process, which may have inhibited the accuracy of the findings and recommendations. Also difficulties inherent in quantifying social, economic and environmental processes at differing geographic and temporal scales, were apparent. This raises important questions regarding the extent to which the literature is able to appropriately reflect actual adaptation within the rangelands, and the extent to which stakeholders (community, pastoralists and regional organisations) perceive that adequate institutional support is being provided.
Grassland soil carbon and nitrogen stocks under temperate livestock grazing
Authors: Cui Junfang , Askari Mohammad Sadegh , Holden Nicholas M.
Published: July 2015

Sustainable grassland management is critical to many agricultural economies because of the significant proportion of agricultural commodities derived from grass-fed livestock (milk and meat). Mismanagement will result in a cycle of soil quality deterioration and reduced productivity. This study estimated carbon (C) and nitrogen (N) stocks in relation to grazing management in Ireland, with a focus on understanding the role of management intensity derived from the interaction of stocking rate, N fertiliser rate and reseeding frequency. Soil samples were taken from depths 0–10, 10–20 and 20–30 cm. Soil physical properties, C and N concentrations, and microbial biomass C were measured. Significant increases in C and N concentrations were observed along the texture gradient: sandy loam < loam < sandy clay loam < clay loam < silty clay loam. However, there was little difference in C and N stock according to soil texture class. Soil with 10–20-year-old grass sward contained the lowest soil C and N content, indicating that proper reseeding is necessary to maintain soil C and N storage capacity. Increased chemical N fertiliser rate did not cause changes of soil C and N content, whereas intensified stocking rate caused great changes in soil C and N content by re-locating soil C and N at depth. Moderately intensive management was associated with significantly lower C and N stocks, and highly intensive management was associated with greater capacity of soil C and N, but no interaction between texture and management intensity was found.
Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape
Authors: Nguyen Lam T. , Gumbart James C. , Beeby Morgan , Jensen Grant J.
Published: July 2015

Significance

The rod shape of walled bacteria is determined by the peptidoglycan (PG) sacculus, but how rod shape is maintained as cells grow remains a fundamental question in bacterial cell biology. We have developed a coarse-grained modeling method to study rod shape maintenance. Individual PG remodeling enzymes, including transglycosylases, transpeptidases, and endopeptidases, are for the first time, to our knowledge, explicitly modeled to explore how they can coordinate to remodel a sacculus several orders of magnitude larger than the enzymes themselves. Rather than requiring top-down regulation of new PG insertion sites, our work shows that local coordination of the PG remodeling enzymes within discrete complexes can be sufficient to maintain the integrity and rod shape of the sacculus.
Finite-dimensional invariant subspace property and amenability for a class of Banach algebras
Authors: Lau Anthony , Zhang Yong
Published: July 2015

Motivated by a result of Ky Fan in 1965, we establish a characterization of a left amenable F-algebra (which includes the group algebra and the Fourier algebra of a locally compact group and quantum group algebras, or more generally the predual algebra of a Hopf von Neumann algebra) in terms of a finite-dimensional invariant subspace property. This is done by first revealing a fixed point property for the semigroup of norm one positive linear functionals in the algebra. Our result answers an open question posted in Tokyo in 1993 by the first author. We also show that the left amenability of an ideal in an F-algebra may determine the left amenability of the algebra.
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function
Authors: Pietal Michal J. , Bujnicki Janusz M. , Kozlowski Lukasz P.
Published: July 2015

Motivation: To date, only a few distinct successful approaches have been introduced to reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a 2D contact map). Current algorithms can infer structures from information-rich contact maps that contain a limited fraction of erroneous predictions. However, it is difficult to reconstruct 3D structures from predicted contact maps that usually contain a high fraction of false contacts.

Results: We describe a new, multi-step protocol that predicts protein 3D structures from the predicted contact maps. The method is based on a novel distance function acting on a fuzzy residue proximity graph, which predicts a 2D distance map from a 2D predicted contact map. The application of a Multi-Dimensional Scaling algorithm transforms that predicted 2D distance map into a coarse 3D model, which is further refined by typical modeling programs into an all-atom representation. We tested our approach on contact maps predicted de novo by MULTICOM, the top contact map predictor according to CASP10. We show that our method outperforms FT-COMAR, the state-of-the-art method for 3D structure reconstruction from 2D maps. For all predicted 2D contact maps of relatively low sensitivity (60–84%), GDFuzz3D generates more accurate 3D models, with the average improvement of 4.87 Å in terms of RMSD.

Availability and implementation: GDFuzz3D server and standalone version are freely available at http://iimcb.genesilico.pl/gdserver/GDFuzz3D/.

Contact:  iamb@genesilico.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites
Authors: Yang Jichen , Ramsey Stephen A.
Published: July 2015

Motivation: The position-weight matrix (PWM) is a useful representation of a transcription factor binding site (TFBS) sequence pattern because the PWM can be estimated from a small number of representative TFBS sequences. However, because the PWM probability model assumes independence between individual nucleotide positions, the PWMs for some TFs poorly discriminate binding sites from non-binding-sites that have similar sequence content. Since the local three-dimensional DNA structure (‘shape’) is a determinant of TF binding specificity and since DNA shape has a significant sequence-dependence, we combined DNA shape-derived features into a TF-generalized regulatory score and tested whether the score could improve PWM-based discrimination of TFBS from non-binding-sites.

Results: We compared a traditional PWM model to a model that combines the PWM with a DNA shape feature-based regulatory potential score, for accuracy in detecting binding sites for 75 vertebrate transcription factors. The PWM + shape model was more accurate than the PWM-only model, for 45% of TFs tested, with no significant loss of accuracy for the remaining TFs.

Availability and implementation: The shape-based model is available as an open-source R package at that is archived on the GitHub software repository at https://github.com/ramseylab/regshape/.

Contact:  stephen.ramsey@oregonstate.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cognitive Function Does Not Impact Self-reported Health-Related Quality of Life in Heart Failure Patients
Authors: Gathright Emily C. , Fulcher Michael J. , Dolansky Mary A. , Gunstad John , Redle Joseph D. , Josephson Richard , Moore Shirley M. , Hughes Joel W.
Published: July 2015

Background:

Adults with heart failure (HF) often demonstrate impairment across multiple domains of cognitive functioning and report poor health-related quality of life (HRQoL). Previous researchers have found that cognitive deficits were generally not associated with HRQoL in a carefully evaluated sample. The exception was memory, which was only weakly associated with HRQoL. However, cognitive deficits interfere with self-care and disease self-management, which could be expected to affect HRQoL.

Objective:

We sought to verify this counterintuitive finding in a large well-characterized sample of HF patients using a well-validated neuropsychological battery.

Methods:

Participants were 302 adults (63% male) predominately white (72.5%) HF patients (68.7 ± 9.6 years) recruited from 2 medical centers. Self-reported HRQoL was assessed using the Kansas City Cardiomyopathy Questionnaire. Participants completed a neuropsychological battery examining attention, executive function, memory, and visuospatial functioning. Hierarchical multiple linear regression was used for analyses.

Results:

Mild global cognitive impairment was observed in 29.5% of the sample (Modified Mini-Mental State [3MS] Examination score <90). Controlling for gender, depression, HF severity, premorbid IQ, comorbidities, and education, only executive function predicted HRQoL, β = .17, P < .05. However, executive function accounted for only 0.6% of the variance in HRQoL.

Conclusion:

Cognitive function generally did not predict HRQoL in HF patients. The correlates of HRQoL in HF do not appear to include mild cognitive impairment. Other factors may play a bigger role such as disease severity, age, and depressive symptoms. Future studies should investigate modifiable determinants of HRQoL in HF patients, toward the goal of finding interventions that preserve HRQoL during this chronic illness.
You talkin’ to me? Interactive playback is a powerful yet underused tool in animal communication research
Authors: King Stephanie L.
Published: July 2015

Over the years, playback experiments have helped further our understanding of the wonderful world of animal communication. They have provided fundamental insights into animal behaviour and the function of communicative signals in numerous taxa. As important as these experiments are, however, there is strong evidence to suggest that the information conveyed in a signal may only have value when presented interactively. By their very nature, signalling exchanges are interactive and therefore, an interactive playback design is a powerful tool for examining the function of such exchanges. While researchers working on frog and songbird vocal interactions have long championed interactive playback, it remains surprisingly underused across other taxa. The interactive playback approach is not limited to studies of acoustic signalling, but can be applied to other sensory modalities, including visual, chemical and electrical communication. Here, I discuss interactive playback as a potent yet underused technique in the field of animal behaviour. I present a concise review of studies that have used interactive playback thus far, describe how it can be applied, and discuss its limitations and challenges. My hope is that this review will result in more scientists applying this innovative technique to their own study subjects, as a means of furthering our understanding of the function of
signalling interactions
in animal communication systems.
Tuning the phase of circadian entrainment
Authors: Bordyugov Grigory , Abraham Ute , Granada Adrian , Rose Pia , Imkeller Katharina , Kramer Achim , Herzel Hanspeter
Published: July 2015

The circadian clock coordinates daily physiological, metabolic and behavioural rhythms. These endogenous oscillations are synchronized with external cues (‘zeitgebers’), such as daily light and temperature cycles. When the circadian clock is entrained by a zeitgeber, the phase difference
ψ
between the phase of a clock-controlled rhythm and the phase of the zeitgeber is of fundamental importance for the fitness of the organism. The phase of entrainment
ψ
depends on the mismatch between the intrinsic period
τ
and the zeitgeber period
T
and on the ratio of the zeitgeber strength to oscillator amplitude. Motivated by the intriguing complexity of empirical data and by our own experiments on temperature entrainment of mouse suprachiasmatic nucleus (SCN) slices, we present a theory on how clock and zeitgeber properties determine the phase of entrainment. The wide applicability of the theory is demonstrated using mathematical models of different complexity as well as by experimental data. Predictions of the theory are confirmed by published data on
Neurospora crassa
strains for different period mismatches
τ
−
T
and varying photoperiods. We apply a novel regression technique to analyse entrainment of SCN slices by temperature cycles. We find that mathematical models can explain not only the stable asymptotic phase of entrainment, but also transient phase dynamics. Our theory provides the potential to explore seasonal variations of circadian rhythms, jet lag and shift work in forthcoming studies.
An in-depth numerical study of the two-dimensional Kuramoto–Sivashinsky equation
Authors: Kalogirou A. , Keaveny E. E. , Papageorgiou D. T.
Published: July 2015

The Kuramoto–Sivashinsky equation in one spatial dimension (1D KSE) is one of the most well-known and well-studied partial differential equations. It exhibits spatio-temporal chaos that emerges through various bifurcations as the domain length increases. There have been several notable analytical studies aimed at understanding how this property extends to the case of two spatial dimensions. In this study, we perform an extensive numerical study of the Kuramoto–Sivashinsky equation (2D KSE) to complement this analytical work. We explore in detail the statistics of chaotic solutions and classify the solutions that arise for domain sizes where the trivial solution is unstable and the long-time dynamics are completely two-dimensional. While we find that many of the features of the 1D KSE, including how the energy scales with system size, carry over to the 2D case, we also note several differences including the various paths to chaos that are not through period doubling.
Multi-fidelity modelling via recursive co-kriging and Gaussian–Markov random fields
Authors: Perdikaris P. , Venturi D. , Royset J. O. , Karniadakis G. E.
Published: July 2015

We propose a new framework for design under uncertainty based on stochastic computer simulations and multi-level recursive co-kriging. The proposed methodology simultaneously takes into account multi-fidelity in models, such as direct numerical simulations versus empirical formulae, as well as multi-fidelity in the probability space (e.g. sparse grids versus tensor product multi-element probabilistic collocation). We are able to construct response surfaces of complex dynamical systems by blending multiple information sources via auto-regressive stochastic modelling. A computationally efficient machine learning framework is developed based on multi-level recursive co-kriging with sparse precision matrices of Gaussian–Markov random fields. The effectiveness of the new algorithms is demonstrated in numerical examples involving a prototype problem inrisk-aversedesign, regression of random functions, as well as uncertainty quantification in fluid mechanics involving the evolution of a Burgers equation from a random initial state, and random laminar wakes behind circular cylinders.
Reclassification of Acetomicrobium faecale as Caldicoprobacter faecalis comb. nov.
Authors: Bouanane-Darenfed Amel , Ben Hania Wajdi , Cayol Jean-Luc , Ollivier Bernard , Fardeau Marie-Laure
Published: July 2015

Taking into account its phenotypical and genetic characteristics,Acetomicrobium faecalewas first recognized as a member of the genusAcetomicrobium, familyBacteroidaceae, orderBacteroidales, phylumBacteroidetes, withAcetomicrobium flavidumthe type species of the genus. However, it was found thatA. faecalehad 95.8 %, 97.6 % and 98.4 % similarity, respectively, withCaldicoprobacter guelmensis, Caldicoprobacter algeriensisandCaldicoprobacter oshimaiand only 82 % similarity withA. flavidum. The DNA G+C content ofA. faecaleis 45 mol , which is of the same order as the DNA G+C content of the three strains of species of the genusCaldicoprobacterand its main fatty acid is C16 : 0, with its second most prominent fatty acid, iso-C17 : 0, also common to strains of species of the genusCaldicoprobacter. On the basis of further phylogenetic, genetic and chemotaxonomic studies, we propose thatA. faecale(type strain DSM 20678T = JCM 30420T) be reclassified as Caldicoprobacterfaecaliscomb. nov.
Pantoea theicola sp. nov., isolated from black tea
Authors: Kato Tanaka Yuko , Horie Nobuhiro , Mochida Kaoru , Yoshida Yoshihiro , Okugawa Eri , Nanjo Fumio
Published: July 2015

A Gram-negative, facultatively anaerobic strain was isolated from black tea. On the basis of 16S rRNA gene sequence similarity comparisons, strain QC88-366T was grouped into the genus Pantoea, being related most closely to the type strains of Pantoea gaviniae (98.5 %) and Pantoea calida (98.3 %); sequence similarities were ≤ 97.0 % to the type strains of other species of the genus Pantoea. Multilocus sequence analysis based on partial sequences of the gyrB, rpoB, infB and atpD genes also revealed P. gaviniae and P. calida as the closest phylogenetic relatives. The fatty acid profile showed the major fatty acids of strain QC88-366T were C16 : 0, C16 : 1 and C18 : 1, the same as those of its closest related species. However, the ratio of C16 : 1, C17 : 0 cyclo, C18 : 1 and C18 : 2 differed slightly compared with those of the related neighbours. In addition, the results of physiological and biochemical tests also allowed the phenotypic differentiation of strain QC88-366T from its closest phylogenetic neighbours. The G+C content of the DNA was 57.2 mol%. Strain QC88-366T therefore represents a novel species of the genus Pantoea, for which the name Pantoea theicola sp. nov. is proposed. The type strain is QC88-366T ( = DSM 29212T = NBRC 110557T).
Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana
Authors: Fang Wei , Li Yong , Xue Han , Tian Guozhong , Wang Laifa , Guo Min-wei , Piao Chun-gen
Published: July 2015

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).
Lactobacillus vespulae sp. nov., isolated from gut of a queen wasp (Vespula vulgaris)
Authors: Hoang Van-An , Kim Yeon-Ju , Nguyen Ngoc-Lan , Kim Si-Kwan , Yang Deok-Chun
Published: July 2015

A Gram-stain-positive, oxidase- and catalase-negative, rod-shaped, facultatively anaerobic bacterial strain, DCY75T, was isolated from a queen wasp (Vespula vulgaris). Growth occurred at 4–37 °C (optimum, 30 °C), at pH 3.5–8.0 (optimum, pH 5.0–6.0) and with ≤ 7.0 % (w/v) NaCl. Strain DCY75T produced gas during growth on glucose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DCY75T belonged to the genus Lactobacillus and was closely related to Lactobacillus sanfranciscensis ATCC 27651T and Lactobacillus lindneri DSM 20690T at sequence similarities of 96.7 and 96.4 %, respectively. A comparison of two housekeeping genes, pheS and rpoA, revealed that strain DCT75T was well separated from other species of the genus Lactobacillus. Strain DCY75T produced d- and l-lactic acid isomers in a ratio of 22.5 : 77.5 (v/v). The major fatty acids were summed feature 8 (comprising C18 : 
1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω9c and C18 : 0.The peptidoglycan structure was of the A4α (l-Lys–d-Asp) type. Cell-wall sugars were glucose, galactose and ribose. The DNA G+C content was 35.5 ± 1.3 mol%. Based on phenotypic and genotypic properties, strain DCY75T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus vespulae sp. nov. is proposed. The type strain is DCY75T ( = KCTC 21023T = JCM 19742T).