bluuebunny/crossref_metadata_2025 huggingface dataset:
Polymorphism in glassy silicon: Inherited from liquid-liquid phase transition in supercooled liquid
Authors: Zhang Shiliang , Wang Li-Min , Zhang Xinyu , Qi Li , Zhang Suhong , Ma Mingzhen , Liu Riping
Published: February 2015

Combining molecular dynamics (MD) simulation and Voronoi polyhedral analyses, we discussed the microstructure evolution in liquid and glassy silicon during cooling by focusing on the fraction of various clusters. Liquid-liquid phase transition (LLPT) is detected in supercooled liquid silicon However, freezing the high-density liquid (HDL) to the glassy state is not achieved as the quenching rate goes up to 1014 K/s. The polyamorphism in glassy silicon is found to be mainly associated with low-density liquid (LDL).
Light-cleavable rapamycin dimer as an optical trigger for protein dimerization
Authors: Brown Kalyn A. , Zou Yan , Shirvanyants David , Zhang Jie , Samanta Subhas , Mantravadi Pavan K. , Dokholyan Nikolay V. , Deiters Alexander
Published: February 2015

Protein heterodimerization of FKBP12 and FRB can be optically controlled with a photocleavable rapamycin dimer.
3d single-ion magnets
Authors: Craig Gavin A. , Murrie Mark
Published: February 2015

This review describes the recent approach to obtain single-molecule magnets where the magnetic properties arise from just one first row transition metal ion in a suitable ligand field.
Palladium(ii)-1-phenylthio-2-arylchalcogenoethane complexes: palladium phosphide nano-peanut and ribbon formation controlled by chalcogen and Suzuki coupling activation
Authors: Kumar Rao Gyandshwar , Kumar Arun , Saleem Fariha , Singh Mahabir P. , Kumar Satyendra , Kumar Bharat , Mukherjee Goutam , Singh Ajai K.
Published: February 2015

Suzuki coupling (cocktail pathway) by complexes of S/Se-ligand/PdP2NPs prepared from Pd-complexes in TOP (temperature ≥ 280 °C) is efficient.
Nitrogen enriched mesoporous organic polymer anchored copper(ii) material: an efficient and reusable catalyst for the synthesis of esters and amides from aromatic systems
Authors: Molla Rostam Ali , Iqubal Md. Asif , Ghosh Kajari , Kamaluddin Kamaluddin , Islam Sk. Manirul
Published: February 2015

New mesoporous polymer anchored copper acetate (Cu-mPMF) has been synthesized and well characterized. The catalytic performance of this complex has been tested for the synthesis of esters and amides.
Solvent effects on the structures and magnetic properties of two doubly interpenetrated metal–organic frameworks
Authors: Huang Fu-Ping , Yang Cheng , Li Hai-Ye , Yao Peng-Fei , Qin Xiao-Huan , Yan Shi-Ping , Kurmoo Mohamedally
Published: February 2015

Two doubly interpenetrated Co(ii) coordination polymers were obtained, and the solvent effects on the structures and magnetic properties were investigated.
A droplet microchip with substance exchange capability for the developmental study of C. elegans
Authors: Wen Hui , Yu Yue , Zhu Guoli , Jiang Lei , Qin Jianhua
Published: February 2015

A multifunctional droplet microdevice was presented for the post-embryonic development study ofC. elegansinitiating from the L1 stage, and the effect of HIF-1 on worm development was investigated.
Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids
Authors: Aramesh M. , Shimoni O. , Fox K. , Karle T. J. , Lohrmann A. , Ostrikov K. , Prawer S. , Cervenka J.
Published: February 2015

Single-molecule-detection, selectivity, broad-range detection and biocompatibility are achieved using nanoporous diamond-like carbon coated oxide membranes.
Efficient electrochemical water oxidation catalysis by nanostructured Mn2O3
Authors: Singh A. , Roy Chowdhury D. , Amritphale S. S. , Chandra N. , Singh I. B.
Published: February 2015

Hydrothermally synthesized Mn2O3nanorods have been demonstrated as an efficient electrochemical water oxidation catalyst over MnO2despite the fact that later has a higher surface area.
Pyrrolidinyl peptide nucleic acids immobilised on cellulose paper as a DNA sensor
Authors: Jirakittiwut Nuttapon , Panyain Nattawadee , Nuanyai Thanesuan , Vilaivan Tirayut , Praneenararat Thanit
Published: February 2015

“Immobilisation of pyrrolidinyl peptide nucleic acids on paper resulted in a new DNA sensor with great specificity”.
Enhancement of photothermal toxicity and lung targeting delivery of Au nanorods via heparin-based nanogel
Authors: Shi Shuai , Wang Yuqin , Yu Jing , Zhang Binjun , Luo Zichao , Li Xingyi , Chen Hao
Published: February 2015

The scheme of preparation of heparin–PEI–LA nanogel used for the adsorption of Au nanorods.
Terminal alkyne substituted O6-benzylguanine for versatile and effective syntheses of fluorescent labels to genetically encoded SNAP-tags
Authors: Song Xinbo , Wang Chao , Han Zhuo , Xu Yongping , Xiao Yi
Published: February 2015

A versatile precursor to synthesize SNAP-tag substrates is developed for specifically labeling cells to produce high resolution fluorescent images.
Direct output of electrical signals from LSPR sensors on the basis of plasmon-induced charge separation
Authors: Tatsuma Tetsu , Katagi Yu , Watanabe Satoshi , Akiyoshi Kazutaka , Kawawaki Tokuhisa , Nishi Hiroyasu , Kazuma Emiko
Published: February 2015

Potentiometric and conductometric sensors based on localized surface plasmon resonance that do not require light to pass through the sample solution were developed and applied to coloured and turbid samples.
High voltage supercapacitors based on carbon-grafted NiO nanowires interfaced with an aprotic ionic liquid
Authors: Paravannoor Anjali , Nair Shantikumar V. , Pattathil Praveen , Manca Michele , Balakrishnan Avinash
Published: February 2015

The report provides a preliminary assessment of the charge storage prerogatives of an asymmetric electrochemical capacitor employing a carbon-grafted NiO electrode interfaced with 1-ethyl-3-methyl imidazoliumdicyanamide as an ionic liquid electrolyte.
IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3+–π interaction
Authors: Bouchet Aude , Schütz Markus , Chiavarino Barbara , Elisa Crestoni Maria , Fornarini Simonetta , Dopfer Otto
Published: February 2015

Calculations and IR spectra reveal the effects of anharmonicity and dispersion on the cation–π interaction in this prototypical neurotransmitter.
Solvent-free synthesis of new inorganic–organic hybrid solids with finely tuned manganese oxalate structures
Authors: Luan Lindong , Li Jing , Yin Changzhen , Lin Zhien , Huang Hui
Published: February 2015

Three new pcu-type manganese phosphate-oxalates were prepared under solvent-free conditions, which display nanobelt-like, sql-, and cds-type manganese oxalate skeletons, respectively.
Exhibition of the Brønsted acid–base character of a Schiff base in palladium(ii) complex formation: lithium complexation, fluxional properties and catalysis of Suzuki reactions in water
Authors: Kumar Rajnish , Mani Ganesan
Published: February 2015

The Brønsted acid–base character of bis(iminopyrrolylmethyl)amine was shown through the X-ray structures of palladium complexes. The bischelated palladium complex is fluxional as studied by the VT1H NMR method and effectively catalyzes Suzuki reactions in water.
Cyclic tetramers of a five-membered palladacycle based on a head-to-tail-linked isocyanate dimer and their reactivity in cyclotrimerization of isocyanates
Authors: Lee Seon Gye , Choi Keun-Young , Kim Yong-Joo , Park SuJin , Lee Soon W.
Published: February 2015

Cyclic tetramers of a five-membered palladacycle involving an isocyanate dimer were prepared, and catalytic cyclotrimerization from a palladium zero-compound or a single palladacycle with organic isocyanates was performed.
Copper-incorporated mono- and di-TeRu5metal carbonyl complexes: syntheses, structures, and an unusual skeletal arrangement
Authors: Shieh Minghuey , Miu Chia-Yeh , Hsing Kai-Jieah , Jang Li-Fing , Lin Chien-Nan
Published: February 2015

A series of semiconducting Cux-incorporated TeRu5-based clusters with differing structural features, facile skeletal arrangements, and effective electronic communication is described.
Catecholaminergic and cholinergic systems of mouse brain are modulated by LMN diet, rich in theobromine, polyphenols and polyunsaturated fatty acids
Authors: Fernández-Fernández Laura , Esteban Gerard , Giralt Mercedes , Valente Tony , Bolea Irene , Solé Montse , Sun Ping , Benítez Susana , Morelló José Ramón , Reguant Jordi , Ramírez Bartolomé , Hidalgo Juan , Unzeta Mercedes
Published: February 2015

LMN diet could benefit the cognitive reserve reducing Alzheimer's disease risk.
New insights into organic–inorganic hybrid perovskite CH3NH3PbI3nanoparticles. An experimental and theoretical study of doping in Pb2+sites with Sn2+, Sr2+, Cd2+and Ca2+
Authors: Navas Javier , Sánchez-Coronilla Antonio , Gallardo Juan Jesús , Cruz Hernández Norge , Piñero Jose Carlos , Alcántara Rodrigo , Fernández-Lorenzo Concha , De los Santos Desireé M. , Aguilar Teresa , Martín-Calleja Joaquín
Published: February 2015

Studies of the organic–inorganic hybrid perovskite, CH3NH3PbI3, doped with Sn2+, Sr2+, Cd2+and Ca2+.
Glutathione- and pH-responsive nonporous silica prodrug nanoparticles for controlled release and cancer therapy
Authors: Xu Zhigang , Liu Shiying , Kang Yuejun , Wang Mingfeng
Published: February 2015

Stimuli-responsive nonporous silica prodrug nanoparticles are developed by covalently encapsulating anticancer drugs camptothecin (CPT) and doxorubicin (DOX) into silica matrices through glutathione (GSH)-responsive disulfide and pH-responsive hydrazone bonds.
Surface plasmon coupled metal enhanced spectral and charge transport properties of poly(3,3′′′-dialkylquarterthiophene) Langmuir Schaefer films
Authors: Pandey Rajiv K. , Yadav Swatantra K. , Upadhyay Chandan , Prakash Rajiv , Mishra Hirdyesh
Published: February 2015

Coupling of nano-structure metal surface plasmons with organic molecule excitons can improve the spectral and charge transport properties of electro-luminescent devices.
3-(Benzo[d][1,3]dioxol-5-ylamino)-N-(4-fluorophenyl)thiophene-2-carboxamide overcomes cancer chemoresistance via inhibition of angiogenesis and P-glycoprotein efflux pump activity
Authors: Mudududdla Ramesh , Guru Santosh K. , Wani Abubakar , Sharma Sadhana , Joshi Prashant , Vishwakarma Ram A. , Kumar Ajay , Bhushan Shashi , Bharate Sandip B.
Published: February 2015

Thiophene-2-carboxamides displayed dual inhibition of angiogenesis and P-gp efflux pumps.
Vertical sidewall electrodes monolithically integrated into 3D glass microfluidic chips using water-assisted femtosecond-laser fabrication for in situ control of electrotaxis
Authors: Xu Jian , Wu Dong , Ip Joanna Y. , Midorikawa Katsumi , Sugioka Koji
Published: February 2015

Novel sidewall metal patterning with high flexibility enables facile integration of vertical electrodes in microchannels forin situcontrol of electrotaxis.
An up-converting HAP@β-TCP nanocomposite activated with Er3+/Yb3+ion pairs for bio-related applications
Authors: Wiglusz Rafal J. , Pozniak Blazej , Zawisza Katarzyna , Pazik Robert
Published: February 2015

A HAP@β-TCP nanocomposite doped with Er3+/Yb3+ions was prepared and its cytotoxicity was tested on canine osteosarcoma and murine macrophage cells. Metronidazole release from the nanocomposite was studied and its up-conversion properties measured.
Nano γ-Fe2O3-supported fluoroboric acid: a novel magnetically recyclable catalyst for the synthesis of 12-substituted-benzo[h][1,3]dioxolo[4,5-b]-acridine-10,11-diones as potent antitumor agents
Authors: Yang Xiaojuan , Zhang Chong , Wu Liqiang
Published: February 2015

Nano γ-Fe2O3-supported fluoroboric acid was synthesized as a novel magnetic catalyst, and was used for the efficient synthesis of benzoacridinediones.
Preparation of PVA hydrogel with high-transparence and investigations of its transparent mechanism
Authors: Hou Yi , Chen Chen , Liu Kemin , Tu Ying , Zhang Li , Li Yubao
Published: February 2015

The PVA hydrogel with high-transparence has been prepared, the 1DMSO/2H2O network structure and the transparent mechanism were also explored.
Photo-polymerisable electrospun fibres of N-methacrylate glycol chitosan for biomedical applications
Authors: Romano Ilaria , Mele Elisa , Heredia-Guerrero José A. , Ceseracciu Luca , Hajiali Hadi , Goldoni Luca , Marini Lara , Athanassiou Athanassia
Published: February 2015

Nanofibrous mats of MGC were produced and photo-crosslinked for controlling their degradation and the release of an antibacterial drug.
Zeolitic imidazolate frameworks as heterogeneous catalysts for a one-pot P–C bond formation reaction via Knoevenagel condensation and phospha-Michael addition
Authors: Horiuchi Yu , Toyao Takashi , Fujiwaki Mika , Dohshi Satoru , Kim Tae-Ho , Matsuoka Masaya
Published: February 2015

ZIF-8 promotes a sequential one-pot reaction efficiently to produce organophosphorus compounds via Knoevenagel condensation and phospha-Michael addition.
Design and synthesis of high performance LiFePO4/C nanomaterials for lithium ion batteries assisted by a facile H+/Li+ion exchange reaction
Authors: Wang Hongbin , Liu Lijia , Wang Runwei , Zhang Daliang , Zhu Liangkui , Qiu Shilun , Wei Yingjin , Jin Xu , Zhang Zongtao
Published: February 2015

A novel, universal method for the lithiation of amorphous hydrated FePO4, typically a nanoscale FePO4/polyaniline composite, by a facile H+/Li+ion exchange reaction for fabricating LiFePO4/C nanomaterials with high performances.
Radio‐frequency energy harvesting for wearable sensors
Authors: Borges Luís M. , Chávez‐Santiago Raul , Barroca Norberto , Velez Fernando José , Balasingham Ilangko
Published: February 2015

The use of wearable biomedical sensors for the continuous monitoring of physiological signals will facilitate the involvement of the patients in the prevention and management of chronic diseases. The fabrication of small biomedical sensors transmitting physiological data wirelessly is possible as a result of the tremendous advances in ultra‐low power electronics and radio communications. However, the widespread adoption of these devices depends very much on their ability to operate for long periods of time without the need to frequently change, recharge or even use batteries. In this context, energy harvesting (EH) is the disruptive technology that can pave the road towards the massive utilisation of wireless wearable sensors for patient self‐monitoring and daily healthcare. Radio‐frequency (RF) transmissions from commercial telecommunication networks represent reliable ambient energy that can be harvested as they are ubiquitous in urban and suburban areas. The state‐of‐the‐art in RF EH for wearable biomedical sensors specifically targeting the global system of mobile 900/1800 cellular and 700 MHz digital terrestrial television networks as ambient RF energy sources are showcased. Furthermore, guidelines for the choice of the number of stages for the RF energy harvester are presented, depending on the requirements from the embedded system to power supply, which is useful for other researchers that work in the same area. The present authors' recent advances towards the development of an efficient RF energy harvester and storing system are presented and thoroughly discussed too.
Observation of structural relaxation during exciton self-trapping via excited-state resonant impulsive stimulated Raman spectroscopy
Authors: Mance J. G. , Felver J. J. , Dexheimer S. L.
Published: February 2015

We detect the change in vibrational frequency associated with the transition from a delocalized to a localized electronic state using femtosecond vibrational wavepacket techniques. The experiments are carried out in the mixed-valence linear chain material [Pt(en)2][Pt(en)2Cl2]⋅(ClO4)4 (en = ethylenediamine, C2H8N2), a quasi-one-dimensional system with strong electron-phonon coupling. Vibrational spectroscopy of the equilibrated self-trapped exciton is carried out using a multiple pulse excitation technique: an initial pump pulse creates a population of delocalized excitons that self-trap and equilibrate, and a time-delayed second pump pulse tuned to the red-shifted absorption band of the self-trapped exciton impulsively excites vibrational wavepacket oscillations at the characteristic vibrational frequencies of the equilibrated self-trapped exciton state by the resonant impulsive stimulated Raman mechanism, acting on the excited state. The measurements yield oscillations at a frequency of 160 cm−1 corresponding to a Raman-active mode of the equilibrated self-trapped exciton with Pt-Cl stretching character. The 160 cm−1 frequency is shifted from the previously observed wavepacket frequency of 185 cm−1 associated with the initially generated exciton and from the 312 cm−1 Raman-active symmetric stretching mode of the ground electronic state. We relate the frequency shifts to the changes in charge distribution and local structure that create the potential that stabilizes the self-trapped state.
Non-contact thermoacoustic detection of embedded targets using airborne-capacitive micromachined ultrasonic transducers
Authors: Nan Hao , Boyle Kevin C. , Apte Nikhil , Aliroteh Miaad S. , Bhuyan Anshuman , Nikoozadeh Amin , Khuri-Yakub Butrus T. , Arbabian Amin
Published: February 2015

A radio frequency (RF)/ultrasound hybrid imaging system using airborne capacitive micromachined ultrasonic transducers (CMUTs) is proposed for the remote detection of embedded objects in highly dispersive media (e.g., water, soil, and tissue). RF excitation provides permittivity contrast, and ultra-sensitive airborne-ultrasound detection measures thermoacoustic-generated acoustic waves that initiate at the boundaries of the embedded target, go through the medium-air interface, and finally reach the transducer. Vented wideband CMUTs interface to 0.18 μm CMOS low-noise amplifiers to provide displacement detection sensitivity of 1.3 pm at the transducer surface. The carefully designed vented CMUT structure provides a fractional bandwidth of 3.5% utilizing the squeeze-film damping of the air in the cavity.
Swimming and pumping by helical waves in viscous and viscoelastic fluids
Authors: Li Lei , Spagnolie Saverio E.
Published: February 2015

We study helical bodies of arbitrary cross-sectional profile as they swim or transport fluid by the passage of helical waves. Many cases are explored: the external flow problem of swimming in a cylindrical tube or an infinite domain, the internal fluid pumping problem, and confined/unconfined swimming and internal pumping in a viscoelastic (Oldroyd-B) fluid. A helical coordinate system allows for the analytical calculation of swimming and pumping speeds and fluid velocities in the asymptotic regime of nearly cylindrical bodies. In a Newtonian flow, a matched asymptotic analysis results in corrections to the swimming speed accurate to fourth-order in the small wave amplitude, and the results compare favorably with full numerical simulations. We find that the torque-balancing rigid body rotation generally opposes the direction of wave passage, but not always. Confinement can result in local maxima and minima of the swimming speed in the helical pitch, and the effects of confinement decrease exponentially fast with the diameter of the tube. In a viscoelastic fluid, we find that the effects of fluid elasticity on swimming and internal pumping modify the Newtonian results through the mode-dependent complex viscosity, even in a confined domain.
Generic expansion of the Jastrow correlation factor in polynomials satisfying symmetry and cusp conditions
Authors: Lüchow Arne , Sturm Alexander , Schulte Christoph , Haghighi Mood Kaveh
Published: February 2015

Jastrow correlation factors play an important role in quantum Monte Carlo calculations. Together with an orbital based antisymmetric function, they allow the construction of highly accurate correlation wave functions. In this paper, a generic expansion of the Jastrow correlation function in terms of polynomials that satisfy both the electron exchange symmetry constraint and the cusp conditions is presented. In particular, an expansion of the three-body electron-electron-nucleus contribution in terms of cuspless homogeneous symmetric polynomials is proposed. The polynomials can be expressed in fairly arbitrary scaling function allowing a generic implementation of the Jastrow factor. It is demonstrated with a few examples that the new Jastrow factor achieves 85%–90% of the total correlation energy in a variational quantum Monte Carlo calculation and more than 90% of the diffusion Monte Carlo correlation energy.
Role of neutral gas in scrape-off layer tokamak plasma
Authors: Bisai N. , Jha R. , Kaw P. K.
Published: February 2015

Neutral gas in scrape-off layer of tokamak plasma plays an important role as it can modify the plasma turbulence. In order to investigate this, we have derived a simple two-dimensional (2D) model that consists of electron continuity, quasi-neutrality, and neutral gas continuity equations using neutral gas ionization and charge exchange processes. Simple 1D profile analysis predicts neutral penetration depth into the plasma. Growth rate obtained from the linear theory has been presented. The 2D model equations have been solved numerically. It is found that the neutral gas reduces plasma fluctuations and shifts spectrum of the turbulence towards lower frequency side. The neutral gas fluctuation levels have been presented. The numerical results have been compared with Aditya tokamak experiments.
Trigonometric and hyperbolic functions method for constructing analytic solutions to nonlinear plane magnetohydrodynamics equilibrium equations
Authors: Moawad S. M.
Published: February 2015

In this paper, we present a solution method for constructing exact analytic solutions to magnetohydrodynamics (MHD) equations. The method is constructed via all the trigonometric and hyperbolic functions. The method is applied to MHD equilibria with mass flow. Applications to a solar system concerned with the properties of coronal mass ejections that affect the heliosphere are presented. Some examples of the constructed solutions which describe magnetic structures of solar eruptions are investigated. Moreover, the constructed method can be applied to a variety classes of elliptic partial differential equations which arise in plasma physics.
Engineered phase matching for broad frequency-tunability in terahertz-wave generation from quasi-phase-matched GaP devices
Authors: Tomita Isao
Published: February 2015

A method to obtain broad frequency-tunability in terahertz (THz)-wave generation is proposed using a quasi-phase-matched GaP device that originally has narrow frequency-tunability. In this method, the phase matching curve for the GaP device is engineered via the GaP dispersion relation by shifting the signal frequency to 333.1 THz (0.90 μm) so that a flat part (i.e., a frequency-independent part) can be formed on the phase matching curve. By selecting an appropriate quasi-phase matching (QPM) period Λ such that QPM occurs at the center of the flat part of the curve, we can obtain a frequency-tunable width of 1.34 THz (37.8 μm) at around a THz-wave frequency of 3.26 THz (92.0 μm). This width is 9.9 times wider than that obtained using a similar quasi-phase-matched GaP device at a signal frequency of 193.5 THz (1.55 μm) without the reformed phase matching curve. The advantage of the proposed method is that, unlike a previous method that used a chirped χ(2) grating, broad frequency-tunability is obtained without reducing the high conversion efficiency produced by QPM. For comparison, a reduction in the conversion efficiency for the chirped χ(2) grating method is demonstrated when a 9.9 times wider frequency-tunable width is achieved.
Performance stability and functional reliability in bipolar resistive switching of bilayer ceria based resistive random access memory devices
Authors: Ismail Muhammad , Talib Ijaz , Rana Anwar Manzoor , Ahmed Ejaz , Nadeem Muhammad Younus
Published: February 2015

Memory devices based on Ti/CeO2-x:CeO2/ITO stacks with bilayer structure fabricated by rf-magnetron sputtering demonstrate promising bipolar resistive switching behavior with relatively low-voltage operation and small distribution of switching parameters. These devices show much reliable repeatability and good endurance (>104 switching cycles) without any significant degradation in their performance. The cycle-to-cycle and device-to-device distribution of resistance switching parameters, such as resistances in the low and high resistance states, set and reset voltages have been investigated and discussed. Resistive switching behavior in our devices has been proposed to originate from the electric field induced drift of defects (specifically oxygen vacancies) preferably along grain boundaries in the bilayer structure of active dielectric layer.
A linear optical trap with active medium for experiments with high power laser pulses
Authors: Mohamed Tarek , Andler Guillermo , Schuch Reinhold
Published: February 2015

A linear optical trap for circulating high power laser pulses and tuning these pulses to high repetition frequency of several tens of MHz has been developed. A ns excimer pumped dye laser pulse has been injected with help of a Wollaston prism and a synchronized Pockels cell into an optical trap formed by two highly reflecting mirrors in a linear configuration. The test was done at λ = 580 nm, but the optical trap can be used without limitations in a broad band of optical wavelengths (400–700 nm). Power considerations give an increase of the efficiency of the optical trap of about 7 times compared to single passage of the laser pulse through the experimental section. The time structure of the trapped laser pulses can be controlled by changing the distance between the two high reflecting mirrors. The efficiency of the optical trap strongly depends upon optical losses. To compensate the optical losses, an amplifying cell was introduced, and the efficiency was about 60 times higher than that by single passage of the laser pulse through the experimental section.
KOH based selective wet chemical etching of AlN, AlxGa1−xN, and GaN crystals: A way towards substrate removal in deep ultraviolet-light emitting diode
Authors: Guo W. , Kirste R. , Bryan I. , Bryan Z. , Hussey L. , Reddy P. , Tweedie J. , Collazo R. , Sitar Z.
Published: February 2015

A controllable and smooth potassium hydroxide-based wet etching technique was developed for the AlGaN system. High selectivity between AlN and AlxGa1−xN (up to 12×) was found to be critical in achieving effective substrate thinning or removal for AlGaN-based deep ultraviolet light emitting diodes, thus increasing light extraction efficiency. The mechanism of high selectivity of AlGaN as a function of Al composition can be explained as related to the formation and dissolution of oxide/hydroxide on top of N-polar surface. Cross-sectional transmission electron microscopic analysis served as ultimate proof that these hillocks were not related to underlying threading dislocations.
Effects of lithium doping on microstructure, electrical properties, and chemical bonds of sol-gel derived NKN thin films
Authors: Lin Chun-Cheng , Chen Chan-Ching , Weng Chung-Ming , Chu Sheng-Yuan , Hong Cheng-Shong , Tsai Cheng-Che
Published: February 2015

Highly (100/110) oriented lead-free Lix(Na0.5K0.5)1−xNbO3 (LNKN, x = 0, 0.02, 0.04, and 0.06) thin films are fabricated on Pt/Ti/SiO2/Si substrates via a sol-gel processing method. The lithium (Li) dopants modify the microstructure and chemical bonds of the LNKN films, and therefore improve their electrical properties. The optimal values of the remnant polarization (Pr = 14.3 μC/cm2), piezoelectric coefficient (d33 = 48.1 pm/V), and leakage current (<10−5 A/cm2) are obtained for a lithium addition of x = 0.04 (i.e., 4 at. %). The observation results suggest that the superior electrical properties are the result of an improved crystallization, a larger grain size, and a smoother surface morphology. It is shown that the ion transport mechanism is dominated by an Ohmic behavior under low electric fields and the Poole-Frenkel emission effect under high electric fields.
Heat-induced apoptosis and gene expression in bovine mammary epithelial cells
Authors: Hu Han , Wang Jiaqi , Gao Haina , Li Songli , Zhang Yangdong , Zheng Nan
Published: February 2015

The objective of this study was to identify the apoptosis and cell-defence response of bovine mammary epithelial cells under heat stress (HS). Cells were exposed to either 38°C or 42°C for 0.5, 1, 3, 5, 8, or 12 h, and the transcription of heat shock proteins (Hsps), Bcl-2 family, caspases and apoptosis-regulated genes were quantified by quantitative real-time polymerase chain reaction. Caspase-3, -7 and -8 were markedly upregulated by HS and the peak gene abundance appeared at 5 h. However, the same family numbers, caspase-6 and -9 were sustained downregulated in HS. The expression of anti-apoptotic gene Bcl-2, Bcl-2A and Mcl-1 increased sharply in HS but returned to pre-HS levels after 8 h. The pro-apoptotic genes: Bax, Bak and Bid were downregulated during HS. The striking changes of signalling factors of apoptosis: tumour necrosis factor receptor, p53, Apaf-1 was upregulated, and Fas was downregulated in HS. Stress proteins Hsp genes (hsp27, hsp70 and hsp90) were generally increased at 42°C and this was especially apparent for hsp70 transcription as it was increased 14-fold at 1 h. Simultaneously, HS induced cell apoptosis, and the peak of apoptosis rate appeared at 3 and 5 h, which were assessed by flow cytometry. Our results suggest that HS induces cell apoptosis, disturbs the normal biological activity, and aroused intracellular thermotolerance responses of bovine mammary epithelial cells.
Establishing health-promoting workplaces in Aboriginal community organisations: healthy eating policies
Authors: MacDonald Catherine , Genat Bill , Thorpe Sharon , Browne Jennifer
Published: February 2015

Aboriginal community controlled health organisations (ACCHOs) and cooperatives function at the centre of community life for local Aboriginal people across Victoria. Local Aboriginal people govern them, work within them as managers and service providers, access health and community services from them and form the constituents who determine their directions. Victorian ACCHOs reflect the unique characteristics of the local Aboriginal community. Thus, potentially, Victorian ACCHOs are key strategic sites for health promotion activities that seek to establish and nurture healthy community, family and peer norms. The Victorian Aboriginal Community Controlled Health Organisation (VACCHO) partnered five metropolitan, regional and rural ACCHOs in a pilot project towards the establishment of healthy food policies and practices in their organisations. Project activities combined both ‘top-down’ policy-oriented and ‘bottom-up’ practice-oriented strategies. This paper, drawing upon both baseline and follow-up quantitative and qualitative data, describes initiatives leading to increases in healthy catering choices and related challenges for Aboriginal workplace health promotion practice.
Digital mapping of RUSLE slope length and steepness factor across New South Wales, Australia
Authors: Yang Xihua
Published: February 2015

The Universal Soil Loss Equation (USLE) and its main derivate, the Revised Universal Soil Loss Equation (RUSLE), are widely used in estimating hillslope erosion. The effects of topography on hillslope erosion are estimated through the product of slope length (L) and slope steepness (S) subfactors, or LS factor, which often contains the highest detail and plays the most influential role in RUSLE. However, current LS maps in New South Wales (NSW) are either incomplete (e.g. point-based) or too coarse (e.g. 250 m), limiting RUSLE-based applications. The aim of this study was to develop automated procedures in a geographic information system (GIS) to estimate and map the LS factor across NSW. The method was based on RUSLE specifications and it incorporated a variable cutoff slope angle, which improves the detection of the beginning and end of each slope length. An overland-flow length algorithm for L subfactor calculation was applied through iterative slope-length cumulation and maximum downhill slope angle. Automated GIS scripts have been developed for LS factor calculation so that the only required input data are digital elevation models (DEMs). Hydrologically corrected DEMs were used for LS factor calculation on a catchment basis, then merged to form a seamless LS-factor digital map for NSW with a spatial resolution ~30 m (or 1 s). The modelled LS values were compared with the reference LS values, and the coefficient of efficiency reached 0.97. The high-resolution digital LS map produced is now being used along with other RUSLE factors in hillslope erosion modelling and land-use planning at local and regional scales across NSW.
Manipulating Culture Conditions and Feed Quality to Increase the Survival of Larval Marble Goby Oxyeleotris marmorata
Authors: Loo Poh Leong , Chong Ving Ching , Ibrahim Shaliza , Sabaratnam Vikineswary
Published: February 2015

Fish stocking density, feed quality, and tank color were evaluated for their effects on survival of larval Marble Goby Oxyeleotris marmorata reared at 5-g/L salinity for 30 d. Feed quality was examined in terms of proximate composition and fatty acid profile. Fish larvae were given rotifers and brine shrimp Artemia spp. nauplii (R-A) that were fed condensed cells of the phototrophic bacterium Rhodovulum sulfidophilum (bPB) cultured in palm oil mill effluent (POME); under this feeding regime, fish stocked at a density of 15 larvae/L had significantly higher survival (42.0%) than those stocked at 20 larvae/L (33.5%) or 30 larvae/L (9.9%). At the best stocking density of 15 larvae/L, fish survival and growth were further improved when the larvae received either R-A that were fed the whole culture broth of unsettled bacteria (cPB; survival = 60.9%) or R-A that were fed POME (survival = 58.6%). Under similar rearing conditions, larvae reared in gray-colored tanks showed still further significant improvement in survival (79.0%) relative to larvae that were reared in black tanks (32.5%) or transparent tanks (0.7%). Thus, optimal culture conditions for larval survival (71.4–81.9%) included rearing in gray culture tanks, stocking at 15 larvae/L, and a diet of R-A that were fed cPB or bPB. Under those optimal conditions, survival during the critical larval period (first 10 d posthatch; 91.4–95.7%) was significantly improved. An approximate 2:2:1 dietary ratio of docosahexaenoic acid : eicosapentaenoic acid : arachidonic acid as compared to a fish tissue ratio of 7:2:1 is recommended to improve the survival and production of Marble Goby larvae.
The role of corpus size and syntax in deriving lexico-semantic representations for a wide range of concepts
Authors: De Deyne Simon , Verheyen Steven , Storms Gert
Published: February 2015

One of the most significant recent advances in the study of semantic processing is the advent of models based on text and other corpora. In this study, we address what impact both the quantitative and qualitative properties of corpora have on mental representations derived from them. More precisely, we evaluate models with different linguistic and mental constraints on their ability to predict semantic relatedness between items from a vast range of domains and categories. We find that a model based on syntactic dependency relations captures significantly less of the variability for all kinds of words, regardless of the semantic relation between them or their abstractness. The largest difference was found for concrete nouns, which are commonly used to assess semantic processing. For both models we find that limited amounts of data suffice in order to obtain reliable predictions. Together, these findings suggest new constraints for the construction of mental models from corpora, both in terms of the corpus size and in terms of the linguistic properties that contribute to mental representations.
PolyQ-dependent RNA–protein assemblies control symmetry breaking
Authors: Lee ChangHwan , Occhipinti Patricia , Gladfelter Amy S.
Published: February 2015

Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction of mRNAs with Whi3 and Puf2 promotes enrichment of transcripts at established sites of polarized growth and clustering of polarity transcripts throughout the cell body. Thus, aggregation-prone proteins make functional assemblies to position polarity transcripts, and nonrandom positioning of transcripts is required for symmetry-breaking events. This reveals a physiological function for polyQ-driven assemblies in regulating cell polarity.
A 𝐶*-algebra approach to complex symmetric operators
Authors: Guo Kunyu , Ji Youqing , Zhu Sen
Published: February 2015

In this paper, certain connections between complex symmetric operators and anti-automorphisms of singly generated

C
∗

C^*

-algebras are established. This provides a

C
∗

C^*

-algebra approach to the norm closure problem for complex symmetric operators. For

T
∈

B
(
H
)

T\in \mathcal {B(H)}

satisfying

C
∗

(
T
)
∩

K
(
H
)

=
{
0
}

C^*(T)\cap \mathcal {K(H)}=\{0\}

, we give several characterizations for

T
T

to be a norm limit of complex symmetric operators. As applications, we give concrete characterizations for weighted shifts with nonzero weights to be norm limits of complex symmetric operators. In particular, we prove a conjecture of Garcia and Poore. On the other hand, it is proved that an essentially normal operator is a norm limit of complex symmetric operators if and only if it is complex symmetric. We obtain a canonical decomposition for essentially normal operators which are complex symmetric.
Modulation of phosphatidylinositol 4-phosphate levels by CaBP7 controls cytokinesis in mammalian cells
Authors: Rajamanoharan Dayani , McCue Hannah V. , Burgoyne Robert D. , Haynes Lee P.
Published: February 2015

Calcium and phosphoinositide signaling regulate cell division in model systems, but their significance in mammalian cells is unclear. Calcium-binding protein-7 (CaBP7) is a phosphatidylinositol 4-kinaseIIIβ (PI4KIIIβ) inhibitor required during cytokinesis in mammalian cells, hinting at a link between these pathways. Here we characterize a novel association of CaBP7 with lysosomes that cluster at the intercellular bridge during cytokinesis in HeLa cells. We show that CaBP7 regulates lysosome clustering and that PI4KIIIβ is essential for normal cytokinesis. CaBP7 depletion induces lysosome mislocalization, extension of intercellular bridge lifetime, and cytokinesis failure. These data connect phosphoinositide and calcium pathways to lysosome localization and normal cytokinesis in mammalian cells.
Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics
Authors: Hayashi Shinichi , Okada Yasushi
Published: February 2015

Most current superresolution (SR) microscope techniques surpass the diffraction limit at the expense of temporal resolution, compromising their applications to live-cell imaging. Here we describe a new SR fluorescence microscope based on confocal microscope optics, which we name the spinning disk superresolution microscope (SDSRM). Theoretically, the SDSRM is equivalent to a structured illumination microscope (SIM) and achieves a spatial resolution of 120 nm, double that of the diffraction limit of wide-field fluorescence microscopy. However, the SDSRM is 10 times faster than a conventional SIM because SR signals are recovered by optical demodulation through the stripe pattern of the disk. Therefore a single SR image requires only a single averaged image through the rotating disk. On the basis of this theory, we modified a commercial spinning disk confocal microscope. The improved resolution around 120 nm was confirmed with biological samples. The rapid dynamics of micro­tubules, mitochondria, lysosomes, and endosomes were observed with temporal resolutions of 30–100 frames/s. Because our method requires only small optical modifications, it will enable an easy upgrade from an existing spinning disk confocal to a SR microscope for live-cell imaging.
Musashi-1 maintains blood–testis barrier structure during spermatogenesis and regulates stress granule formation upon heat stress
Authors: ErLin Sun , WenJie Wei , LiNing Wang , BingXin Lu , MingDe Lei , Yan Sun , RuiFa Han
Published: February 2015

In mouse testes, Musashi-1 (Msi-1) was predominantly expressed in the cytoplasm and nuclei of Sertoli cells. Here we demonstrate that knockdown of Msi-1 in Sertoli cells altered the levels and distribution of blood–testis barrier (BTB)-associated proteins. Moreover, Msi-1 knockdown in vivo disrupted BTB functional structure and spermatogenesis. In addition, we report a novel role of Msi-1 in regulating Sertoli cells survival following heat-induced injury. Endogenous Msi-1 protein in heat-treated Sertoli cells was recruited to stress granules. The formation of stress granules was considerably disrupted, and apoptosis was significantly up-regulated in Msi-1–knockdown Sertoli cells after heat treatment. p-ERK1/2 acted downstream of stress granule formation, and inhibition of p-ERK1/2 signaling triggered Sertoli cell apoptosis upon heat stress. In conclusion, we demonstrate that Msi-1 is critical for constructing a functional BTB structure and maintaining spermatogenesis. We also note a role for Msi-1 in regulating Sertoli cell fate following heat-induced injury, likely through the induction of stress granule formation and subsequent activation of p-ERK1/2 signaling.
3. Ritual and society
Authors: Stephenson Barry
Published: February 2015

What does ritual do? Sociological and anthropological theory of the first half of the twentieth century proposes that ritual—secular or sacred—binds groups together, ensuring their harmonious functioning by generating and maintaining orders of meaning, purpose, and value. ‘Ritual and society’ discusses the theories of Emile Durkheim, Roy Rappaport, and Clifford Geetz and their ideas on ritual producing solidarity and effervescence and ritual's role in politics, power, and negotiation. In the 1970s, a sea change in ritual studies followed the work of Victor Turner and others who highlighted ritual's critical and creative potential. Public ritual is complex: rites can conserve, transmit, and protect tradition, but others are creatively, critically, strategically employed to enact change.
Fast, accurate, and reliable molecular docking with QuickVina 2
Authors: Alhossary Amr , Handoko Stephanus Daniel , Mu Yuguang , Kwoh Chee-Keong
Published: February 2015

Motivation: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina (‘Vina’) is a widely used docking tool with parallelization for speed. QuickVina (‘QVina 1’) then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina (‘QVina 2’) that inherits both the speed of QVina 1 and the reliability of the original Vina.

Results: We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina (i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58 kcal/mol. On the same dataset, GOLD produced RMSD smaller than 2 Å on 56.9% of the data while QVina 2 attained 63.1%.

Availability and implementation: The C++ source code of QVina 2 is available at (www.qvina.org).

Contact:  aalhossary@pmail.ntu.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry
Authors: Morimoto Kentaro , Nishikaze Takashi , Yoshizawa Akiyasu C. , Kajihara Shigeki , Aoshima Ken , Oda Yoshiya , Tanaka Koichi
Published: February 2015

Summary: Tandem mass spectrometry (MS/MS or MSn) is a potent technique for characterizing N-glycan structures. GlycanAnalysis searches a glycan database to support the identification of glycan structures from MS/MS spectra. It also calculates diagnostic ions of glycan structures registered in a glycan database (GlycomeDB or KEGG GLYCAN) and searches for MS/MS spectra of N-glycans that match diagnostic ions to determine the structures. This program functions as a plug-in for Mass++, a freeware mass spectrum visualization and analysis program.

Availability and implementation: The executable files of Mass++ are available for free at http://www.first-ms3d.jp/english/. The GlycanAnalysis plug-in is included in the standard package of Mass++ for Windows.

Contact:  k-morimt@shimadzu.co.jp or nishikaz@shimadzu.co.jp or acyshzw@shimadzu.co.jp

Supplementary information:  Supplementary material are available at Bioinformatics online.
Normalization and noise reduction for single cell RNA-seq experiments
Authors: Ding Bo , Zheng Lina , Zhu Yun , Li Nan , Jia Haiyang , Ai Rizi , Wildberg Andre , Wang Wei
Published: February 2015

A major roadblock towards accurate interpretation of single cell RNA-seq data is large technical noise resulted from small amount of input materials. The existing methods mainly aim to find differentially expressed genes rather than directly de-noise the single cell data. We present here a powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.

Availability and implementation: The software is implemented by R and the download version is available at http://wanglab.ucsd.edu/star/GRM.

Contact:  wei-wang@ucsd.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis
Authors: Glaab Enrico , Schneider Reinhard
Published: February 2015

Summary: High-throughput omics datasets often contain technical replicates included to account for technical sources of noise in the measurement process. Although summarizing these replicate measurements by using robust averages may help to reduce the influence of noise on downstream data analysis, the information on the variance across the replicate measurements is lost in the averaging process and therefore typically disregarded in subsequent statistical analyses.

We introduce RepExplore, a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets. The software builds on previously published statistical methods, which have been applied successfully to biomedical omics data but are difficult to use without prior experience in programming or scripting. RepExplore facilitates the analysis by providing a fully automated data processing and interactive ranking tables, whisker plot, heat map and principal component analysis visualizations to interpret omics data and derived statistics.

Availability and implementation: Freely available at http://www.repexplore.tk

Contact:  enrico.glaab@uni.lu

Supplementary information:  Supplementary data are available at Bioinformatics online.