bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of dynamically induced variability in the recent warming trend slowdown over the Northern Hemisphere
Authors: Guan Xiaodan , Huang Jianping , Guo Ruixia , Lin Pu
Published: July 2015

Since the slowing of the trend of increasing surface air temperature (SAT) in the late 1990 s, intense interest and debate have arisen concerning the contribution of human activities to the warming observed in previous decades. Although several explanations have been proposed for the warming-trend slowdown (WTS), none has been generally accepted. We investigate the WTS using a recently developed methodology that can successfully identify and separate the dynamically induced and radiatively forced SAT changes from raw SAT data. The dynamically induced SAT changes exhibited an obvious cooling effect relative to the warming effect of the adjusted SAT in the hiatus process. A correlation analysis suggests that the changes are dominated primarily by the North Atlantic Oscillation (NAO), Pacific Decadal Oscillation (PDO) and Atlantic Multidecadal Oscillation (AMO). Our results confirm that dynamically induced variability caused the WTS. The radiatively forced SAT changes are determined mainly by anthropogenic forcing, indicating the warming influence of greenhouse gases (GHGs), which reached levels of 400 ppm during the hiatus period. Therefore, the global SAT will not remain permanently neutral. The increased radiatively forced SAT will be amplified by increased dynamically induced SAT when the natural mode returns to a warming phase in the next period.
A Sensor Array Using Multi-functional Field-effect Transistors with Ultrahigh Sensitivity and Precision for Bio-monitoring
Authors: Kim Do-Il , Quang Trung Tran , Hwang Byeong-Ung , Kim Jin-Su , Jeon Sanghun , Bae Jihyun , Park Jong-Jin , Lee Nae-Eung
Published: July 2015

Mechanically adaptive electronic skins (e-skins) emulate tactition and thermoception by cutaneous mechanoreceptors and thermoreceptors in human skin, respectively. When exposed to multiple stimuli including mechanical and thermal stimuli, discerning and quantifying precise sensing signals from sensors embedded in e-skins are critical. In addition, different detection modes for mechanical stimuli, rapidly adapting (RA) and slowly adapting (SA) mechanoreceptors in human skin are simultaneously required. Herein, we demonstrate the fabrication of a highly sensitive, pressure-responsive organic field-effect transistor (OFET) array enabling both RA- and SA- mode detection by adopting easily deformable, mechano-electrically coupled, microstructured ferroelectric gate dielectrics and an organic semiconductor channel. We also demonstrate that the OFET array can separate out thermal stimuli for thermoreception during quantification of SA-type static pressure, by decoupling the input signals of pressure and temperature. Specifically, we adopt piezoelectric-pyroelectric coupling of highly crystalline, microstructured poly(vinylidene fluoride-trifluoroethylene) gate dielectric in OFETs with stimuli to allow monitoring of RA- and SA-mode responses to dynamic and static forcing conditions, respectively. This approach enables us to apply the sensor array to e-skins for bio-monitoring of humans and robotics.
Detection of cardiovascular drugs and marine toxins using a multifunctional cell-based impedance biosensor system
Authors: Li Hongbo , Zou Quchao , Zou Ling , Wang Qin , Su Kaiqi , Hu Ning , Wang Ping
Published: July 2015

The system structure of the CIB detection instrument: cell-based impedance biosensor units, hardware module, and data processing module.
Recent developments in molecularly imprinted polymer nanofibers and their applications
Authors: Zaidi Shabi Abbas
Published: July 2015

Molecularly imprinted polymers (MIPs) have been potential and versatile candidates for analyte detection.
Crystal-to-crystal transformation of fishnet-like layered compounds: a self-locking structure with position-variable intercalated molecules
Authors: Nishio Masaki , Motokawa Natsuko , Miyasaka Hitoshi
Published: July 2015

Fishnet-like layered compounds crystallized with anthracene (ANT) molecules between their layers and crystallization solvents at their hexagonal columnar pores; these complexes undergo a solvent-release crystal-to-crystal transformation involving the migration of a portion of the ANT molecules from between the layers to the hexagonal pores.
Evidence for the existence of Li2S2 clusters in lithium–sulfur batteries: ab initio Raman spectroscopy simulation
Authors: Partovi-Azar Pouya , Kühne Thomas D. , Kaghazchi Payam
Published: July 2015

Using density functional theory calculations and ab initio molecular dynamics simulations, we have observed a clear evidence of Li2S4 → Li2S2 transition by studying systematic changes in the simulated Raman spectra of (Li2S4)n, n = 1, 4, and 8, towards that of (Li2S2)8.
Effects of oxygen impurities and nitrogen vacancies on the surface properties of the Ta3N5photocatalyst: a DFT study
Authors: Wang Jiajia , Ma Aibin , Li Zhaosheng , Jiang Jinghua , Feng Jianyong , Zou Zhigang
Published: July 2015

DFT calculations were performed to study Ta3N5(100), (010) and (001) surfaces with oxygen impurities and nitrogen vacancies. The effects of oxygen impurities and nitrogen vacancies on the surface stability and electronic structures of Ta3N5surfaces were put forward.
Ethanol photocatalysis on rutile TiO2(110): the role of defects and water
Authors: Walenta Constantin A. , Kollmannsberger Sebastian L. , Kiermaier Josef , Winbauer Andreas , Tschurl Martin , Heiz Ueli
Published: July 2015

In this work we present a stoichiometric reaction mechanism for the photocatalytic ethanol oxidation on TiO2(110).
General cooperative effects of single atom ligands on a metal: a195Pt NMR chemical shift as a function of coordinated halido ligands’ ionic radii overall sum
Authors: Benedetti M. , de Castro F. , Antonucci D. , Papadia P. , Fanizzi F. P.
Published: July 2015

An inverse linear relationship between the experimentally observed195Pt NMR signals and the overall sum of coordinated halido X ligands’ ionic radii was discovered in Pt(ii) and Pt(iv) complexes.
Chiral probe development for circularly polarised luminescence: comparative study of structural factors determining the degree of induced CPL with four heptacoordinate europium(iii) complexes
Authors: Neil Emily R. , Fox Mark A. , Pal Robert , Pålsson Lars-Olof , O'Sullivan Benjamin A. , Parker David
Published: July 2015

Induced CPL signatures arising from the reversible binding of chiral carboxylates allow their absolute configuration and enantiomeric purity to be assessed.
Quantitative single molecule FRET efficiencies using TIRF microscopy
Authors: Hildebrandt Lasse L. , Preus Søren , Birkedal Victoria
Published: July 2015

Förster resonance energy transfer (FRET) microscopy at the single molecule level has the potential to yield information on intra and intermolecular distances within the 2–10 nm range of molecules or molecular complexes that undergo frequent conformation changes. A pre-requirement for obtaining accurate distance information is to determine quantitative instrument independent FRET efficiency values. Here, we applied and evaluated a procedure to determine quantitative FRET efficiencies directly from individual fluorescence time traces of surface immobilized DNA molecules without the need for external calibrants. To probe the robustness of the approach over a wide range of FRET efficiencies we used a set of doubly labelled double stranded DNA samples, where the acceptor position was varied systematically. Interestingly, we found that fluorescence contributions arising from direct acceptor excitation following donor excitation are intrinsically taken into account in these conditions as other correction factors can compensate for inaccurate values of these parameters. We give here guidelines, that can be used through tools within the iSMS software (http://www.isms.au.dk), for determining quantitative FRET and assess uncertainties linked with the procedure. Our results provide insights into the experimental parameters governing quantitative FRET determination, which is essential for obtaining accurate structural information from a wide range of biomolecules.
The effect of reaction atmosphere and growth duration on the size and morphology of boron nitride nanotubes
Authors: Ahmad Pervaiz , Khandaker Mayeen Uddin , Amin Yusoff Mohd , Muhammad Nawshad , Usman Ahmed Rufai , Amin Muhammad
Published: July 2015

Observations of BNNTs grown in the reaction atmosphere of argon, ammonia and nitrogen.
Vanadium-based nanostructure materials for secondary lithium battery applications
Authors: Tan Hui Teng , Rui Xianhong , Sun Wenping , Yan Qingyu , Lim Tuti Mariana
Published: July 2015

In this review, we will be casting light on the recent advances in the synthesis of nanostructured vanadium-based cathodes, such as V2O5, LiV3O8, VO2(B) and Li3V2(PO4)3.
Preparation of multiformable supramolecular gels through helical complexation by amylose in vine-twining polymerization
Authors: Kadokawa Jun-ichi , Tanaka Kazuya , Hatanaka Daisuke , Yamamoto Kazuya
Published: July 2015

Supramolecular hydrogels with macroscopic interfacial healing behavior were obtained through helical complexation by amylose in vine-twining polymerization using poly(γ-glutamic acid-graft-ε-caprolactone), which were further converted into cryo- and ion gels.
Synthesis, characterization and the effect of temperature on different physicochemical properties of protic ionic liquids
Authors: Ullah Zahoor , Bustam M. Azmi , Man Zakaria , Muhammad Nawshad , Khan Amir Sada
Published: July 2015

In this work, eleven protic ionic liquids (PILs) containing different cations and anions were prepared and their physicochemical properties were measured.
Nanocomposites of graphene/polymers: a review
Authors: Chee W. K. , Lim H. N. , Huang N. M. , Harrison I.
Published: July 2015

Graphene-based nanofillers and their applications. Fabrication methods of graphene-based nanocomposites. Interaction and dispersion of graphene-based fillers in polymer matrices. Current trends and prospects of graphene-based nanocomposites.
Upgrading of anaerobic digestion of waste activated sludge by a hyper-thermophilic–mesophilic temperature-phased process with a recycle system
Authors: Wu L. J. , Qin Y. , Hojo T. , Li Y. Y.
Published: July 2015

A hyper-thermophilic–mesophilic temperature-phased anaerobic digestion with a recycle system effectively upgraded the mesophilic digestion of waste activated sludge.
Endogenous Cu and Zn nanocluster-regulated soy protein isolate films: excellent hydrophobicity and flexibility
Authors: Li Kuang , Chen Hui , Li Ying , Li Jianzhang , He Jing
Published: July 2015

Special bio-films from SPI regulated by endogenous Cu and Zn nanoclusters have excellent hydrophobicity and flexibility.
Site and stereoselectivity in sulfa-Michael addition to equivocally activated conjugated dienes
Authors: Kowalczyk Rafał , Boratyński Przemysław J. , Wierzba Aleksandra J. , Bąkowicz Julia
Published: July 2015

Two terminally-linked Michael acceptors can react in either a 1,4- or 1,6-fashion with thiols depending on the choice of activation method.
Graphene-decorated porous ceramics for efficient removal of Cr(vi)
Authors: Wang Shi , Yang Wen , Chen Guohua
Published: July 2015

Porous ceramics (such as activated alumina (AA)) is a common adsorbent material in water purification.
Preparation of a P(THF-co-PO)-b-PB-b-P(THF-co-PO) triblock copolymer via cationic ring-opening polymerization and its use as a thermoset polymer
Authors: Zhang Wanbin , Fan Xiaodong , Tian Wei , Chen Heng , Zhu Xiuzhong , Zhang Haitao
Published: July 2015

Triblock copolymer P(THF-co-PO)-b-PB-b-P(THF-co-PO) with gradient copolyether segments was synthesized, and its elastomer exhibited excellent dynamic mechanical properties.
β-Cyclodextrin/chitosan–magnetic graphene oxide–surface molecularly imprinted polymer nanocomplex coupled with chemiluminescence biosensing of bovine serum albumin
Authors: Duan Huimin , Li Leilei , Wang Xiaojiao , Wang Yanhui , Li Jianbo , Luo Chuannan
Published: July 2015

In this report, a sensitive and selective chemiluminescence biosensor for bovine serum albumin coupled with surface molecularly imprinted nanocomplex using β-cyclodextrin/chitosan–magnetic graphene oxide as backbone material was investigated.
Optimization of an analytical method for the spectrophotometric determination of copper in tea and water samples after ultrasonic assisted cloud point extraction using a benzothiazole fluorescein derivative complexing agent
Authors: Fan Chunlei , Luo Shengxu , Liu Rong
Published: July 2015

BTF is exists with spirolactone species with adding Cu2+, which leads to the absorbance intensity is decreased gradually and the decrease of the absorbance value is linear for Cu2+.
Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters
Authors: Church Andrew T. , Hughes Zak E. , Walsh Tiffany R.
Published: July 2015

We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca2+, and introduce a modification that can recover experimentally-determined binding free energies for these systems.
Selective protein purification by PEG–IDA-functionalized iron oxide nanoparticles
Authors: Bloemen M. , Vanpraet L. , Ceulemans M. , Parac-Vogt T. N. , Clays K. , Geukens N. , Gils A. , Verbiest T.
Published: July 2015

A new heterobifunctional PEG ligand was developed for efficient magnetic purification of His-tagged proteins.
Ammonium ionic liquids with anions of natural origin
Authors: Pernak Juliusz , Łęgosz Bartosz , Walkiewicz Filip , Klejdysz Tomasz , Borkowski Andrzej , Chrzanowski Łukasz
Published: July 2015

Ammonium ionic liquids with anions of natural origin are biodegradable agents with antifeedant and anti-microbial activity.
A new rhodamine based chemodosimeter for Ni2+ with high sensitivity and selectivity
Authors: Zhang Ivan , Wang Yi , Wan Chao , Xing Zhen , Li Wen , Li Minjie , Zhang Sean Xiao-An
Published: July 2015

A new spirocyclic rhodamine derivative for colorimetric sensing of Ni2+.
Stability of graphene-based heterojunction solar cells
Authors: Singh Eric , Nalwa Hari Singh
Published: July 2015

The long-term environmental stability and degradation of graphene-based heterojunction solar cells under different atmospheric conditions such as air, humidity, temperature, and light illumination for commercial applications are discussed.
Role of basicity and the catalytic activity of KOH loaded MgO and hydrotalcite as catalysts for the efficient synthesis of 1-[(2-benzothiazolylamino)arylmethyl]-2-naphthalenols
Authors: Sahu Pramod K. , Sahu Praveen K. , Agarwal Dau D.
Published: July 2015

Novel KOH-loaded MgO and hydrotalcite as basic catalysts have been synthesized and were characterized by XRD, SEM and their basicity.
Zinc induced polyelectrolyte coacervate bioadhesive and its transition to a self-healing hydrogel
Authors: Wang Weina , Xu Yisheng , Li Ang , Li Tao , Liu Miaomiao , von Klitzing Regine , Ober Christopher K. , Kayitmazer A. Basak , Li Li , Guo Xuhong
Published: July 2015

High performance Dopa-modified poly(acrylic acid) adhesives formed under the assistance of zinc ions can transform to a self-recovery polymer hydrogel with a pH trigger.
Insight into the limited electrochemical activity of NaVP2O7
Authors: Kee Yongho , Dimov Nikolay , Staikov Aleksandar , Barpanda Prabeer , Lu Ying-Ching , Minami Keita , Okada Shigeto
Published: July 2015

Recently, LiVP2O7 has been investigated as a possible high-voltage substitute for Li2FeP2O7.
Synthesis, characterization and applications of selenocysteine-responsive nanoprobe based on dinitrobenzene sulfonyl-modified poly(carbonate) micelles
Authors: Nan Yanxia , Zhao Wenjie , Xu Xinhua , Au Chak-Tong , Qiu Renhua
Published: July 2015

Dinitrobenzenesulfonyl-modified micelles can be used for selenocysteine detection in cells and tissues.
Mono- and tri-β-substituted unsymmetrical metalloporphyrins: synthesis, structural, spectral and electrochemical properties
Authors: Prakash Kamal , Kumar Ravi , Sankar Muniappan
Published: July 2015

Mono-/tri-β-substituted metalloporphyrins have been synthesized and characterized. Dramatic reduction in the HOMO–LUMO gap with tunable electronic, spectral and electrochemical redox potentials were observed as the number of electron withdrawing groups increased.
The impact of lignin source on its self-assembly in solution
Authors: Ratnaweera Dilru R. , Saha Dipendu , Pingali Sai Venkatesh , Labbé Nicole , Naskar Amit K. , Dadmun Mark
Published: July 2015

The assembly of lignin molecules from a variety of sources is followed using small angle neutron scattering. The degree of branching of the lignin molecule, which varies with source, plays a crucial role in determining their association behavior.
Hierarchically structured catalyst layer for the oxygen reduction reaction fabricated by electrodeposition of platinum on carbon nanotube coated carbon fiber
Authors: Sharma Raghunandan , Kar Kamal K.
Published: July 2015

Hierarchically structured fuel cell cathode catalysts consisting of Pt-nanoparticle clusters coated on a CNT-based, ORR active catalyst support were synthesized.
Metal-free one-pot sequential direct diarylation of pyrazolin-5-ones with diaryliodonium salts
Authors: Huang Tao , Ji Xinfei , Wu Wei , Liang Fang , Cao Song
Published: July 2015

A novel and efficient one-pot sequential C4-diarylation of pyrazolin-5-ones with diaryliodonium salts at room temperature in the absence of a metal catalyst was reported.
Room temperature synthesis of an amorphous MoS2 based composite stabilized by N-donor ligands and its light-driven photocatalytic hydrogen production
Authors: Niefind Felix , Djamil John , Bensch Wolfgang , Srinivasan Bikshandarkoil R. , Sinev Ilya , Grünert Wolfgang , Deng Mao , Kienle Lorenz , Lotnyk Andriy , Mesch Maria B. , Senker Jürgen , Dura Laura , Beweries Torsten
Published: July 2015

An amorphous molybdenum sulfide based composite has been synthesized at room temperature applying a kinetically controlled reaction. The new material exhibits an extraordinary performance in the visible light driven hydrogen evolution reaction.
Continuous-flow focusing of microparticles using induced-charge electroosmosis in a microfluidic device with 3D AgPDMS electrodes
Authors: Jia Yankai , Ren Yukun , Jiang Hongyuan
Published: July 2015

Efficient continuous-flow focusing of microparticles using induced-charge electroosmosis is presented and 3D AgPDMS electrodes are employed to avoid the negative effects of alternating current electroosmosis and dielectrophoresis.
Fast mass interdiffusion in ceria/alumina composite
Authors: Teocoli F. , Ni D. W. , Sanna S. , Thydén K. , Fonseca F. C. , Esposito V.
Published: July 2015

Gadolinium-doped ceria (CGO) presents unique processes at low oxygen partial pressure (pO2 < 10−12 atm) and low temperatures (T > 800 °C) such as faster mass diffusion, which are not observed in conventional sintering under ambient air conditions. These effects lead to fast elemental interdiffusion in ceria/alumina composites.
WO3based solid solution oxide – promising proton exchange membrane fuel cell anode electro-catalyst
Authors: Patel Prasad Prakash , Jampani Prashanth H. , Datta Moni Kanchan , Velikokhatnyi Oleg I. , Hong Daeho , Poston James A. , Manivannan Ayyakkannu , Kumta Prashant N.
Published: July 2015

Nanostructured (W1-xIrx)Oy(x= 0.3) electro-catalyst exhibits excellent electrochemical activity and stability similar to that of Pt/C, which is in agreement with the results of the theoretical first principles studies.
Investigation of ultra-thin titania films as hole-blocking contacts for organic photovoltaics
Authors: Kim Hyungchul , Ou Kai-Lin , Wu Xin , Ndione Paul F. , Berry Joseph , Lambert Yannick , Mélin Thierry , Armstrong Neal R. , Graham Samuel
Published: July 2015

Ultra-thin (0.5–10 nm) plasma-enhanced atomic layer deposited titanium oxide (TiOx) films deposited on indium-tin-oxide contacts, are investigated as hole-blocking interlayers using conventional electrochemistry, Si-diodes, and heterojunction (P3HT:PCBM) organic photovoltaics (OPVs).
Synthesis and photovoltaic properties of an n-type two-dimension-conjugated polymer based on perylene diimide and benzodithiophene with thiophene conjugated side chains
Authors: Zhang Youdi , Wan Qun , Guo Xia , Li Wanbin , Guo Bing , Zhang Maojie , Li Yongfang
Published: July 2015

A novel n-type two-dimensional (2D) conjugated polymer based on bithienyl-benzodithiophene (BDT) and perylene diimide (PDI), P(PDI-BDT-T), is synthesized by Stille coupling for applications in all-polymer solar cells (PSCs).
A novel microwave stimulus remote controlled anticancer drug release system based on Fe3O4@ZnO@mGd2O3:Eu@P(NIPAm-co-MAA) multifunctional nanocarriers
Authors: Qiu Hongjin , Cui Bin , Zhao Weiwei , Chen Ping , Peng Hongxia , Wang Yaoyu
Published: July 2015

A novel thermally responsive nanocarrier with mesoporous surfaces has been successfully prepared and developed for microwave stimulus remote controlled anticancer drug release.
Assembly, organization and regulation of cell-surface receptors by lectin–glycan complexes
Authors: Elola María T. , Blidner Ada G. , Ferragut Fátima , Bracalente Candelaria , Rabinovich Gabriel A.
Published: July 2015

Galectins are a family of β-galactoside-binding lectins carrying at least one consensus sequence in the carbohydrate-recognition domain. Properties of glycosylated ligands, such as N- and O-glycan branching, LacNAc (N-acetyl-lactosamine) content and the balance of α2,3- and α2,6-linked sialic acid dramatically influence galectin binding to a preferential set of counter-receptors. The presentation of specific glycans in galectin-binding partners is also critical, as proper orientation and clustering of oligosaccharide ligands on multiple carbohydrate side chains increase the binding avidity of galectins for particular glycosylated receptors. When galectins are released from the cells, they typically concentrate on the cell surface and the local matrix, raising their local concentration. Thus galectins can form their own multimers in the extracellular milieu, which in turn cross-link glycoconjugates on the cell surface generating galectin–glycan complexes that modulate intracellular signalling pathways, thus regulating cellular processes such as apoptosis, proliferation, migration and angiogenesis. Subtle changes in receptor expression, rates of protein synthesis, activities of Golgi enzymes, metabolite concentrations supporting glycan biosynthesis, density of glycans, strength of protein–protein interactions at the plasma membrane and stoichiometry may modify galectin–glycan complexes. Although galectins are key contributors to the formation of these extended glycan complexes leading to promotion of receptor segregation/clustering, and inhibition of receptor internalization by surface retention, when these complexes are disrupted, some galectins, particularly galectin-3 and -4, showed the ability to drive clathrin-independent mechanisms of endocytosis. In the present review, we summarize the data available on the assembly, hierarchical organization and regulation of conspicuous galectin–glycan complexes, and their implications in health and disease.
Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis
Authors: Ramos-Alvarado Bladimir , Kumar Satish , Peterson G. P.
Published: July 2015

The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability.
Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion
Authors: Albert Julian , Falge Mirjam , Gomez Sandra , Sola Ignacio R. , Hildenbrand Heiko , Engel Volker
Published: July 2015

We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.
Growth of epitaxial orthorhombic YO1.5-substituted HfO2 thin film
Authors: Shimizu Takao , Katayama Kiliha , Kiguchi Takanori , Akama Akihiro , Konno Toyohiko J. , Funakubo Hiroshi
Published: July 2015

YO1.5-substituted HfO2 thin films with various substitution amounts were grown on (100) YSZ substrates by the pulsed laser deposition method directly from the vapor phase. The epitaxial growth of film with different YO1.5 amounts was confirmed by the X-ray diffraction method. Wide-area reciprocal lattice mapping measurements were performed to clarify the crystal symmetry of films. The formed phases changed from low-symmetry monoclinic baddeleyite to high-symmetry tetragonal/cubic fluorite phases through an orthorhombic phase as the YO1.5 amount increased from 0 to 0.15. The additional annular bright-field scanning transmission electron microscopy indicates that the orthorhombic phase has polar structure. This means that the direct growth by vapor is of polar orthorhombic HfO2-based film. Moreover, high-temperature X-ray diffraction measurements showed that the film with a YO1.5 amount of 0.07 with orthorhombic structure at room temperature only exhibited a structural phase transition to tetragonal phase above 450 °C. This temperature is much higher than the reported maximum temperature of 200 °C to obtain ferroelectricity as well as the expected temperature for real device application. The growth of epitaxial orthorhombic HfO2-based film helps clarify the nature of ferroelectricity in HfO2-based films (186 words/200 words).
Photoinduced Cycloadditions in the Diversity-Oriented Synthesis Toolbox: Increasing Complexity with Straightforward Post-Photochemical Modifications
Authors: Umstead Weston J. , Mukhina Olga A. , Kumar N. N. Bhuvan , Kutateladze Andrei G.
Published: July 2015

Rapid growth of complexity and unprecedented molecular architectures is realised via the excited state intramolecular proton transfer (ESIPT) in o-acylamidobenzaldehydes and ketones followed by [4+2] or [4+4] cycloadditions with subsequent post-photochemical modifications. The approach is congruent with diversity-oriented synthesis, whereby photoprecursors are synthesised in a modular fashion allowing for up to four diversity inputs. The complexity of the primary photoproducts is further enhanced using straightforward and high-yielding post-photochemical modification steps such as reactions with nitrile oxides and nitrones, and Povarov and oxa-Diels–Alder reactions.
Effect of mastication and other mechanical treatments on fuel structure in chaparral
Authors: Brennan Teresa J. , Keeley Jon E.
Published: July 2015

Mechanical fuel treatments are a common pre-fire strategy for reducing wildfire hazard that alters fuel structure by converting live canopy fuels to a compacted layer of dead surface fuels. Current knowledge concerning their effectiveness, however, comes primarily from forest-dominated ecosystems. Our objectives were to quantify and compare changes in shrub-dominated chaparral following crushing, mastication, re-mastication and mastication-plus-burning treatments, and to assess treatment longevity. Results from analysis of variance (ANOVA) identified significant differences in all fuel components by treatment type, vegetation type and time since treatment. Live woody fuel components of height, cover and mass were positively correlated with time since treatment, whereas downed woody fuel components were negatively correlated. Herbaceous fuels, conversely, were not correlated, and exhibited a 5-fold increase in cover across treatment types in comparison to controls. Average live woody fuel recovery was 50% across all treatment and vegetation types. Differences in recovery between time-since-treatment years 1–8 ranged from 32–65% and exhibited significant positive correlations with time since treatment. These results suggest that treatment effectiveness is short term due to the rapid regrowth of shrubs in these systems and is compromised by the substantial increase in herbaceous fuels. Consequences of not having a full understanding of these treatments are serious and leave concern for their widespread use on chaparral-dominated landscapes.
Code-switching at the auxiliary-VP boundary
Authors: Giancaspro David
Published: July 2015

While early code-switching research (i.e., Poplack, 1980) focused on the possibility of universal constraints on switching, MacSwan’s (2010, 2014) “Constraint-Free” research program centers on the notion that code-switching is only constrained by the interaction of a bilingual’s two grammars. In following with this proposal, the current study examines whether two types of Spanish-English bilinguals are equally sensitive to the (un)grammaticality of Spanish-English code-switching at the subject-predicate and auxiliary-verb phrase boundaries. Twenty-five heritage Spanish speakers and forty-four L2 Spanish learners completed an Audio Naturalness Judgment Task in which they judged grammatical and ungrammatical Spanish-English code-switching at these two syntactic junctions. Results indicate that the L2 Spanish speakers and the heritage bilinguals, regardless of their self-reported exposure to code-switching, correctly differentiated between grammatical and ungrammatical switches, suggesting that they have implicit knowledge of code-switching grammaticality which falls out from syntactic knowledge of the two languages.
Tīa 'toe' and Old Gutnish Sources of Long ī
Authors: Vrieland Seán D.
Published: July 2015

Explanations of the long ī in the Old Gutnish tīa ‘toe’ (>ModGu täiå) have been put forward that posit different ablaut grades than the Proto-Germanic *taihwōn which underlies the forms found in other Germanic languages. This is because it was thought the Old Gutnish form could not reflect the standard proto-form. This paper concludes on the basis of the parallel development of *slaihwōn ‘sloe berry’, which appears as ModGu släiå, that long ī can in fact continue the Proto-Germanic sequence *-aihw- as the result of regular sound development.
American Water Willow Mediates Survival and Antipredator Behavior of Juvenile Largemouth Bass
Authors: Stahr Kristopher J. , Shoup Daniel E.
Published: July 2015

State and federal agencies typically introduce aquatic vegetation to increase the recruitment of sport fishes, particularly Largemouth Bass Micropterus salmoides. However, due to frequent turbidity and water‐level fluctuations, managers in the southern United States are often left to introduce emergent macrophytes instead of submersed macrophytes. Emergent macrophytes have less underwater structural complexity than most submersed macrophytes and therefore may not be as effective in reducing the predation risk of Largemouth Bass. Therefore, the objective of this study was to determine if American water willow Justicia americana, a common emergent macrophyte species introduced in reservoirs, increases the survival of juvenile Largemouth Bass when exposed to predation. Predator–prey interactions between 10 juvenile and 1 adult Largemouth Bass were observed in tanks with natural densities of American water willow and compared with similar trials in vegetation‐free control tanks. Each adult Largemouth Bass was tested once in each treatment (vegetation present or absent). Water willow significantly reduced the capture‐to‐attack ratio of adult Largemouth Bass and decreased the amount of time spent searching and the number of captures, resulting in significantly higher juvenile survival in the vegetated trials. Although water willow provided a similar increase in survival compared with previous studies using submersed macrophytes, the mechanism underlying this change differed, likely resulting from the more rigid stem design of water willow. We conclude water willow is an excellent candidate for establishment in reservoirs because it is easier to establish than many other macrophyte species yet still reduces predation risk on juvenile Largemouth Bass.
Improved Ability to Characterize Recruitment of Gray Snapper in Three Florida Estuaries along the Gulf of Mexico through Targeted Sampling of Polyhaline Seagrass Beds
Authors: Flaherty‐Walia Kerry E. , Switzer Theodore S. , Winner Brent L. , J. Tyler‐Jedlund Amanda , Keenan Sean F.
Published: July 2015

Estuarine‐dependent Gray Snapper Lutjanus griseus support extensive recreational fisheries in estuarine and coastal waters throughout the eastern Gulf of Mexico. Multiyear fisheries‐independent monitoring data collected in three Florida estuaries can be used to estimate the strength of juvenile Gray Snapper recruitment, which has been critical to assessments of other fish populations. Earlier evaluation of these data indicated that Gray Snapper inhabit polyhaline seagrass beds, which are underrepresented in ongoing monitoring efforts. During this study, in addition to the routine monitoring of shorelines and channel habitats, sampling of shoal and deepwater polyhaline seagrass habitats was implemented using 183‐m haul seines and 6.1‐m otter trawls. The incorporation of polyhaline seagrass surveys from 2008 through 2011 allowed a more thorough sampling of the Gray Snapper population, resulting in improved catch rates, increased frequency of occurrence, and a substantial reduction of the coefficient of variation for CPUE in most years and estuarine systems. Habitat‐based sampling of polyhaline seagrass habitats also provided additional data for annual abundance indices and therefore improved the ability to characterize the strength of recruitment for Gray Snapper over time. These results demonstrated that periodically reevaluating habitat‐based stratification approaches to estimate fish abundance indices from long‐term surveys can lead to more precise estimates and greater numbers of measured individuals, which are key components of successful monitoring programs.
The cellular prion protein PrPcis a partner of the Wnt pathway in intestinal epithelial cells
Authors: Besnier Laura S. , Cardot Philippe , Da Rocha Barbara , Simon Anthony , Loew Damarys , Klein Christophe , Riveau Béatrice , Lacasa Michel , Clair Caroline , Rousset Monique , Thenet Sophie
Published: July 2015

We reported previously that the cellular prion protein (PrPc) is a component of desmosomes and contributes to the intestinal barrier function. We demonstrated also the presence of PrPcin the nucleus of proliferating intestinal epithelial cells. Here we sought to decipher the function of this nuclear pool. In human intestinal cancer cells Caco-2/TC7 and SW480 and normal crypt-like HIEC-6 cells, PrPcinteracts, in cytoplasm and nucleus, with γ-catenin, one of its desmosomal partners, and with β-catenin and TCF7L2, effectors of the canonical Wnt pathway. PrPcup-regulates the transcriptional activity of the β-catenin/TCF7L2 complex, whereas γ-catenin down-regulates it. Silencing of PrPcresults in the modulation of several Wnt target gene expressions in human cells, with different effects depending on their Wnt signaling status, and in mouse intestinal crypt cells in vivo. PrPcalso interacts with the Hippo pathway effector YAP, suggesting that it may contribute to the regulation of gene transcription beyond the β-catenin/TCF7L2 complex. Finally, we demonstrate that PrPcis required for proper formation of intestinal organoids, indicating that it contributes to proliferation and survival of intestinal progenitors. In conclusion, PrPcmust be considered as a new modulator of the Wnt signaling pathway in proliferating intestinal epithelial cells.
CFAP54 is required for proper ciliary motility and assembly of the central pair apparatus in mice
Authors: McKenzie Casey W. , Craige Branch , Kroeger Tiffany V. , Finn Rozzy , Wyatt Todd A. , Sisson Joseph H. , Pavlik Jacqueline A. , Strittmatter Lara , Hendricks Gregory M. , Witman George B. , Lee Lance
Published: July 2015

Motile cilia and flagella play critical roles in fluid clearance and cell motility, and dysfunction commonly results in the pediatric syndrome primary ciliary dyskinesia (PCD). CFAP221, also known as PCDP1, is required for ciliary and flagellar function in mice and Chlamydomonas reinhardtii, where it localizes to the C1d projection of the central microtubule apparatus and functions in a complex that regulates flagellar motility in a calcium-dependent manner. We demonstrate that the genes encoding the mouse homologues of the other C. reinhardtii C1d complex members are primarily expressed in motile ciliated tissues, suggesting a conserved function in mammalian motile cilia. The requirement for one of these C1d complex members, CFAP54, was identified in a mouse line with a gene-trapped allele. Homozygous mice have PCD characterized by hydrocephalus, male infertility, and mucus accumulation. The infertility results from defects in spermatogenesis. Motile cilia have a structural defect in the C1d projection, indicating that the C1d assembly mechanism requires CFAP54. This structural defect results in decreased ciliary beat frequency and perturbed cilia-driven flow. This study identifies a critical role for CFAP54 in proper assembly and function of mammalian cilia and flagella and establishes the gene-trapped allele as a new model of PCD.
High-order neural networks and kernel methods for peptide-MHC binding prediction
Authors: Kuksa Pavel P. , Min Martin Renqiang , Dugar Rishabh , Gerstein Mark
Published: July 2015

Motivation: Effective computational methods for peptide-protein binding prediction can greatly help clinical peptide vaccine search and design. However, previous computational methods fail to capture key nonlinear high-order dependencies between different amino acid positions. As a result, they often produce low-quality rankings of strong binding peptides. To solve this problem, we propose nonlinear high-order machine learning methods including high-order neural networks (HONNs) with possible deep extensions and high-order kernel support vector machines to predict major histocompatibility complex-peptide binding.

Results: The proposed high-order methods improve quality of binding predictions over other prediction methods. With the proposed methods, a significant gain of up to 25–40% is observed on the benchmark and reference peptide datasets and tasks. In addition, for the first time, our experiments show that pre-training with high-order semi-restricted Boltzmann machines significantly improves the performance of feed-forward HONNs. Moreover, our experiments show that the proposed shallow HONN outperform the popular pre-trained deep neural network on most tasks, which demonstrates the effectiveness of modelling high-order feature interactions for predicting major histocompatibility complex-peptide binding.

Availability and implementation: There is no associated distributable software.

Contact:  renqiang@nec-labs.com or mark.gerstein@yale.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data
Authors: Ryall Karen A. , Shin Jimin , Yoo Minjae , Hinz Trista K. , Kim Jihye , Kang Jaewoo , Heasley Lynn E. , Tan Aik Choon
Published: July 2015

Motivation: Targeted kinase inhibitors have dramatically improved cancer treatment, but kinase dependency for an individual patient or cancer cell can be challenging to predict. Kinase dependency does not always correspond with gene expression and mutation status. High-throughput drug screens are powerful tools for determining kinase dependency, but drug polypharmacology can make results difficult to interpret.

Results: We developed Kinase Addiction Ranker (KAR), an algorithm that integrates high-throughput drug screening data, comprehensive kinase inhibition data and gene expression profiles to identify kinase dependency in cancer cells. We applied KAR to predict kinase dependency of 21 lung cancer cell lines and 151 leukemia patient samples using published datasets. We experimentally validated KAR predictions of FGFR and MTOR dependence in lung cancer cell line H1581, showing synergistic reduction in proliferation after combining ponatinib and AZD8055.

Availability and implementation: KAR can be downloaded as a Python function or a MATLAB script along with example inputs and outputs at: http://tanlab.ucdenver.edu/KAR/.

Contact:  aikchoon.tan@ucdenver.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
BackCLIP: a tool to identify common background presence in PAR-CLIP datasets
Authors: Reyes-Herrera P. H. , Speck-Hernandez C. A. , Sierra C. A. , Herrera S.
Published: July 2015

Motivation: PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify the presence of common background in PAR-CLIP datasets is not yet available.

Results: We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common background set has a score that reflects its presence in several PAR-CLIP datasets. We present a tool that uses this score to identify the amount of common backgrounds present in a PAR-CLIP dataset, and we provide the user the option to use or remove it. We used the proposed strategy in 30 PAR-CLIP datasets from nine proteins. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds.

Availability: The tool was implemented in python. The common background set and the supplementary data are available at https://github.com/phrh/BackCLIP.

Contact: phreyes@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Empedobacter stercoris sp. nov., isolated from an input sample of a biogas plant
Authors: Schauss Thorsten , Busse Hans-Jürgen , Golke Jan , Kämpfer Peter , Glaeser Stefanie P.
Published: July 2015

Two Gram-stain-negative, rod-shaped bacteria, strains 990B6_12ER2AT and 994B6_12ER2A, were isolated during microbiological analysis of a mixed manure sample which was used as input material for a German biogas plant. Phylogenetic identification based on nearly full-length 16S rRNA gene sequences placed the isolates into the family Flavobacteriaceae within the phylum Bacteroidetes. Strains 990B6_12ER2AT and 994B6_12ER2A shared identical 16S rRNA gene sequences and showed highest 16S rRNA gene sequence similarity to the type strains of Empedobacter falsenii (97.3 %) and Empedobacter brevis (96.8 %).

The major cellular fatty acids of strains 990B6_12ER2AT and 994B6_12ER2A were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH.

The polyamine pattern contained predominantly sym-homospermidine and the quinone system was menaquinone MK-6. Major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified polar lipid not containing an amino residue, a phosphate residue or a sugar moiety. In addition, moderate to minor amounts of several unidentified lipids were detected. The DNA G+C content was 31.7 and 29.0 mol%, for strains 990B6_12ER2AT and 994B6_12ER2A, respectively. On the basis of phylogenetic, chemotaxonomic and physiological analysis we propose a novel species of the genus Empedobacter, Empedobacter stercoris sp. nov. (type strain 990B6_12ER2AT = CIP 110833T = LMG 28501T).
Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes
Authors: Sorokin Dimitry Y. , Abbas Ben , Merkel Alexander Y. , Rijpstra W. Irene C. , Damsté Jaap S. Sinninghe , Sukhacheva Marina V. , van Loosdrecht Mark C. M.
Published: July 2015

Two groups of haloalkaliphilic methanogenic archaea were dominating in enrichments from hypersaline soda lake sediments at pH 10. At moderate salt concentrations with formate or H2 as electron donor, methanogens belonging to the genus Methanocalculus were enriched, while at high salt concentrations with methylated substrates, a group related to Methanosalsum zhilinae was dominating. For both groups, several pure cultures were obtained including the type strains AMF2T for the Methanocalculus group and AME2T for the Methanosalsum group. The Methanocalculus group is characterized by lithoheterotrophic growth with either formate (preferable substrate) or H2 at moderate salinity up to 1.5–2 M total Na+ and obligate alkaliphilic growth with an optimum at pH 9.5. According to phylogenetic analysis, the group also includes closely related strains isolated previously from the low-salt alkaline Lonar Lake. The novel Methanosalsum group is characterized by high salt tolerance (up to 3.5 M total Na+) and obligate alkaliphilic growth with an optimum at pH 9.5. It has a typical methylotrophic substrate profile, utilizing methanol, methylamines and dimethyl sulfide (at low concentrations) as methanogenic substrates. On the basis of physiological and phylogenetic data, it is proposed that the two groups of soda lake methanogenic isolates are assigned into two novel species, Methanocalculus alkaliphilus sp. nov. (type strain AMF2T = DSM 24457T = UNIQEM U859T) and Methanosalsum natronophilum sp. nov. (type strain AME2T = DSM 24634T = NBRC 110091T).