bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and dynamics of water molecules confined in triglyceride oils
Authors: Groot Carien C. M. , Velikov Krassimir P. , Bakker Huib J.
Published: September 2016

Water molecules confined in triglyceride oil form specific hydrogen-bonded structures involving the oil carbonyl groups.
Selective hydrogenation of levulinate esters to 1,4-pentanediol using a ternary skeletal CuAlZn catalyst
Authors: Ren Dezhang , Wan Xinyan , Jin Fangming , Song Zhiyuan , Liu Yunjie , Huo Zhibao
Published: September 2016

A non-noble ternary skeletal CuAlZn catalyst was designed for direct hydrogenation of ethyl levulinate (EL) to 1,4-pentanediol (1,4-PDO).
Transaminase biocatalysis: optimization and application
Authors: Guo Fei , Berglund Per
Published: September 2016

Transaminase biocatalysis shows immense potential in industrial applications, and optimizations of both proteins and processes are of great importance.
An unprecedentedly simple method of synthesis of aryl azides and 3-hydroxytriazenes
Authors: Gribanov Pavel S. , Topchiy Maxim A. , Golenko Yulia D. , Lichtenstein Yana I. , Eshtukov Artur V. , Terekhov Vladimir E. , Asachenko Andrey F. , Nechaev Mikhail S.
Published: September 2016

Fischer's approach towards the synthesis of aryl azides and triazinoles from diazonium salts and hydroxylammonium chloride (phenylhydraxylamine) was reinvestigated and optimized.
Neighbour-sensitized near-infrared emission of new Nd(iii) and Er(iii) complexes with 1-(anthracene-2-yl)-4,4,4-trifluoro-1,3-butanedione
Authors: Kang Jung-Soo , Leung Kam Tong , Nah Min-Kook , Shin Jung-Sik , Kang Myung-Hyun , Shong Bonggeun , Kang Jun-Gill , Lee Jisuk , Sohn Youngku
Published: September 2016

Solvatochromic effects on the luminescence of the anthracene pendant and the sensitized NIR luminescence of Nd(iii) and Er(iii).
Synthesis of Au nanoparticles dispersed on halloysite nanotubes–reduced graphene oxide nanosheets and their application for electrochemical sensing of nitrites
Authors: Zhang Sai , Sheng Qinglin , Zheng Jianbin
Published: September 2016

Electrochemical sensing of nitrite based on a novel Au–HNTs–GO nanocomposite.
Synthesis and structural characterization of titanium and zirconium complexes containing half-salen ligands as catalysts for polymerization reactions
Authors: Mandal Mrinmay , Monkowius Uwe , Chakraborty Debashis
Published: September 2016

Ti(iv) and Zr(iv) complexes of tridentate half-salen ligands were synthesized for the polymerization of lactide and ε-CL, homopolymerization, copolymerization and coupling of epoxides with CO2. All the complexes were found to be effective catalysts for different polymerization reactions.
Mono- and dinuclear palladium(ii) complexes containing both N-heterocyclic carbenes and tetrazole ligands as catalysts for Hiyama coupling
Authors: Yang Jin
Published: September 2016

Six tetrazole ligand stabilized NHC–Pd complexes have been synthesized and fully characterized. Catalytic performance of the obtained palladium catalysts has been investigated for the Hiyama coupling reaction.
Synthesis of HIV-1 capsid protein assembly inhibitor (CAP-1) and its analogues based on a biomass approach
Authors: Romashov Leonid V. , Ananikov Valentine P.
Published: September 2016

The potential of a biomass-derived platform chemical is explored in the low cost sustainable organic synthesis of an anti-HIV pharmaceutical substance with flexible and variable units.
Synthesis of substituted indolizines via radical oxidative decarboxylative annulation of 2-(pyridin-2-yl)acetate derivatives with α,β-unsaturated carboxylic acids
Authors: Gu Jian , Cai Chun
Published: September 2016

A copper mediated radical oxidative annulation of 2-(pyridin-2-yl)acetate derivatives with α,β-unsaturated carboxylic acids is developed.
C–ON bond homolysis of alkoxyamines triggered by paramagnetic copper(ii) salts
Authors: Audran Gérard , Bagryanskaya Elena , Bagryanskaya Irina , Brémond Paul , Edeleva Mariya , Marque Sylvain R. A. , Parkhomenko Dmitriy , Tretyakov Evgeny , Zhivetyeva Svetlana
Published: September 2016

Pyridine-based alkoxyamines were used as ligands for Cu(hfac)2 to prepare the first metallic complexes of alkoxyamines. Structures of complexes were determined by X-ray analysis and a 21-fold increase in the C–ON bond homolysis was observed.
pH dependent size control, formation mechanism and antimicrobial functionality of bio-inspired AgNPs
Authors: Chelli Venkatanarasimha Rao , Golder Animes Kumar
Published: September 2016

Sechium edule is rich in ascorbic acid which was extracted from aqueous media for the synthesis of AgNPs.
Pre-coating with protein fractions inhibits nano-carrier aggregation in human blood plasma
Authors: Müller L. K. , Simon J. , Schöttler S. , Landfester K. , Mailänder V. , Mohr K.
Published: September 2016

The change of a nanoparticles' physicochemical properties after incubation with defined protein fractions or whole human plasma was utilized for tailoring its properties regarding stability against aggregation and cellular response.
Two chiral alkanolamine Schiff base Cu(ii) complexes as potential anticancer agents: synthesis, structure, DNA/protein interactions, and cytotoxic activity
Authors: Niu Meiju , Li Zhen , Li Xiao , Huang Xianqiang
Published: September 2016

Two novel chiral copper complexes have been synthesized and expressed DNA/protein binding strength and substantial cytotoxic activity.
Fast adsorption and removal of 2-methyl-4-chlorophenoxy acetic acid from aqueous solution with amine functionalized zirconium metal–organic framework
Authors: Wei Cuixiang , Feng Dan , Xia Yan
Published: September 2016

An amino functionalized zirconium-based MOF named UiO-66-NH2 was synthesized and explored as a novel adsorbent for the fast removal of 2-methyl-4-chlorophenoxy acetic acid (MCPA) in aqueous solution.
Amorphous NiB/carbon nanohybrids: synthesis and catalytic enhancement induced by electron transfer
Authors: Liu Weikai , Chen Ruifen , Liu Lijun , Li Shuangzhi , Xue Zhiyong , He Chiyang
Published: September 2016

Amorphous NiB/C shows synergistic catalysis for 4-nitrophenol reduction, induced by the electron transfer from NiB alloy to carbon support.
l-Proline as an efficient enantioinduction organo-catalyst in the solvent-free synthesis of pyrazolo[3,4-b]quinoline derivatives via one-pot multi-component reaction
Authors: Bhattacharjee Deboshikha , Kshiar Baskhemlang , Myrboh Bekington
Published: September 2016

The role of l-proline as an efficient organo-catalyst for the three-component synthesis of pyrazoloquinolinones involving dimedone, 3-methyl-1H-pyrazol-5-amine and various aryl aldehydes under mild solvent-free condition is reported.
Characterizing the denatured state ensemble of ubiquitin under native conditions using replica exchange molecular dynamics
Authors: Chang Nai-yuan , Li Yi-Ci , Jheng Cheng-Ping , Kuo Yu-Ting , Lee Cheng-I
Published: September 2016

The representative structures of the denatured state ensemble of ubiquitin under a native condition and heat-denatured ubiquitin simulated from a fully extended conformation.
Improved performance in micron-sized silicon anodes by in situ polymerization of acrylic acid-based slurry
Authors: Li Chao , Shi Tongfei , Yoshitake Hideya , Wang Hongyu
Published: September 2016

The interactions between silicon particles and polymeric binders are a key factor during the course of manufacturing high-capacity Si anodes for lithium-ion batteries.
Correction: Multi-responsive nanocomposite hydrogels with high strength and toughness
Authors: Yang Jingli , Liu Shuang , Xiao Ying , Gao Guorong , Sun Yuanna , Guo Qingzhong , Wu Jiangyu , Fu Jun
Published: September 2016

Correction for ‘Multi-responsive nanocomposite hydrogels with high strength and toughness’ by Jingli Yang et al., J. Mater. Chem. B, 2016, 4, 1733–1739.
Recommendations for Administering Early Intervention Assessments With Children Who Are Deaf/Hard of Hearing via Telehealth Technology
Authors: Blaiser Kristina M.
Published: September 2016

The use of telehealth has significantly grown in recent years as a feasible, cost-effective model. While intervention services are typically discussed, there is considerably less known about the use of assessments via telehealth, particularly in pediatric populations. A survey was completed within the National Center for Hearing Assessment and Management (NCHAM) Telehealth Learning Community to decipher telehealth assessment practices, concerns, and recommendations. The findings from this survey, combined with the Learning Community discussion that followed, were valuable in providing a framework for recommended practices for early intervention providers serving children who are deaf/hard of hearing (DHH) via telehealth.
Overcoming Barriers to Using Telehealth for Standardized Language Assessments
Authors: Sutherland Rebecca , Hodge Antoinette , Trembath David , Drevensek Suzi , Roberts Jacqueline
Published: September 2016

The clinical imperative to provide speech-language pathology services to families outside of the metropolitan area, while accounting for the barriers previously identified, was the impetus for a recent study conducted examining the use of telehealth in Australia (Sutherland et al., 2016). That study found that delivering standardized language assessments via telehealth using consumer grade equipment was feasible, reliable, and tolerated by students with language impairment. In the present article, a follow-up to Sutherland et al. (2016), the barriers to using telehealth are described, along with the steps taken to overcome these barriers in completing the original study. The current article also seeks to describe to the responses of the school-aged students and clinicians involved.
Constrained generalised minimum variance controller design using projection‐based recurrent neural network
Authors: Toshani Hamid , Farrokhi Mohammad , Alipouri Yousef
Published: September 2016

In this study, a generalised minimum variance control (GMVC) method using the projection‐based recurrent neural network (PRNN) is proposed to minimise the error variance in the output of the non‐linear plant. One the main drawbacks of the conventional GMVC approaches is the lack of a systematic procedure to deal with the input constraints. In this study, the PRNN is employed for incorporating the input constraints to the minimum variance index. This network is based on the optimality conditions of a constrained problem and is designed using projection theorem. To formulate the proposed approach, by considering an ARMAX model of the system and converting the cost function to a quadratic programming problem, the dynamics and output equations of the PRNN is obtained. The stability and global convergence of the PRNN is analytically shown. Moreover, suitable conditions for the weighting matrices of the cost function are determined to ensure the closed‐loop stability. The proposed control method is applied to the non‐linear quadruple tank and a comparative analysis between MVC, GMVC and the proposed approach is performed.
Electro-osmotic and pressure-driven flow of viscoelastic fluids in microchannels: Analytical and semi-analytical solutions
Authors: Ferrás L. L. , Afonso A. M. , Alves M. A. , Nóbrega J. M. , Pinho F. T.
Published: September 2016

In this work, we present a series of solutions for combined electro-osmotic and pressure-driven flows of viscoelastic fluids in microchannels. The solutions are semi-analytical, a feature made possible by the use of the Debye–Hückel approximation for the electrokinetic fields, thus restricted to cases with small electric double-layers, in which the distance between the microfluidic device walls is at least one order of magnitude larger than the electric double-layer thickness. To describe the complex fluid rheology, several viscoelastic differential constitutive models were used, namely, the simplified Phan-Thien–Tanner model with linear, quadratic or exponential kernel for the stress coefficient function, the Johnson-Segalman model, and the Giesekus model. The results obtained illustrate the effects of the Weissenberg number, the Johnson-Segalman slip parameter, the Giesekus mobility parameter, and the relative strengths of the electro-osmotic and pressure gradient-driven forcings on the dynamics of these viscoelastic flows.
Critical length of a one-dimensional nucleus
Authors: Joswiak Mark N. , Doherty Michael F. , Peters Baron
Published: September 2016

One-dimensional (1D) nucleation is important in crystal growth, amyloid fibril formation, and supramolecular polymerization. The nucleation rate can be readily calculated, but there is no consensus on the critical length. In this work, we employ a splitting probability to derive an analytical expression for the critical length, which corresponds to a 50% survival probability. For a 1D nucleus on a crystal step, this critical length depends on the supersaturation (driving force) and is nearly independent of the kink (surface) energy.
Discrimination of coupling structures using causality networks from multivariate time series
Authors: Koutlis Christos , Kugiumtzis Dimitris
Published: September 2016

Measures of Granger causality on multivariate time series have been used to form the so-called causality networks. A causality network represents the interdependence structure of the underlying dynamical system or coupled dynamical systems, and its properties are quantified by network indices. In this work, it is investigated whether network indices on networks generated by an appropriate Granger causality measure can discriminate different coupling structures. The information based Granger causality measure of partial mutual information from mixed embedding (PMIME) is used to form causality networks, and a large number of network indices are ranked according to their ability to discriminate the different coupling structures. The evaluation of the network indices is done with a simulation study based on two dynamical systems, the coupled Mackey-Glass delay differential equations and the neural mass model, both of 25 variables, and three prototypes of coupling structures, i.e., random, small-world, and scale-free. It is concluded that the setting of PMIME combined with a network index attains high level of discrimination of the coupling structures solely on the basis of the observed multivariate time series. This approach is demonstrated to identify epileptic seizures emerging during electroencephalogram recordings.
A single-mode external cavity diode laser using an intra-cavity atomic Faraday filter with short-term linewidth <400 kHz and long-term stability of <1 MHz
Authors: Keaveney James , Hamlyn William J. , Adams Charles S. , Hughes Ifan G.
Published: September 2016

We report on the development of a diode laser system - the “Faraday laser” - using an atomic Faraday filter as the frequency-selective element. In contrast to typical external-cavity diode laser systems which offer tunable output frequency but require additional control systems in order to achieve a stable output frequency, our system only lases at a single frequency, set by the peak transmission frequency of the internal atomic Faraday filter. Our system has both short-term and long-term stability of less than 1 MHz, which is less than the natural linewidth of alkali-atomic D-lines, making similar systems suitable for use as a “turn-key” solution for laser-cooling experiments.
Antineutrino monitoring of thorium reactors
Authors: Akindele Oluwatomi A. , Bernstein Adam , Norman Eric B.
Published: September 2016

Various groups have demonstrated that antineutrino monitoring can be successful in assessing the plutonium content in water-cooled nuclear reactors for nonproliferation applications. New reactor designs and concepts incorporate nontraditional fuel types and chemistry. Understanding how these properties affect the antineutrino emission from a reactor can extend the applicability of antineutrino monitoring. Thorium molten salt reactors breed 233U, that if diverted constitute a direct use material as defined by the International Atomic Energy Agency (IAEA). The antineutrino spectrum from the fission of 233U has been estimated for the first time, and the feasibility of detecting the diversion of 8 kg of 233U, within a 30 day timeliness goal has been evaluated. The antineutrino emission from a thorium reactor operating under normal conditions is compared to a diversion scenario by evaluating the daily antineutrino count rate and the energy spectrum of the detected antineutrinos at a 25 m standoff. It was found that the diversion of a significant quantity of 233U could not be detected within the current IAEA timeliness detection goal using either tests. A rate-time based analysis exceeded the timeliness goal by 23 days, while a spectral based analysis exceeds this goal by 31 days.
Secondary peak in the Nusselt number distribution of impinging jet flows: A phenomenological analysis
Authors: Aillaud P. , Duchaine F. , Gicquel L. Y. M. , Didorally S.
Published: September 2016

This paper focuses on a wall-resolved Large Eddy Simulation (LES) of an isothermal round submerged air jet impinging on a heated flat plate, at a Reynolds number of 23 000 (based on the nozzle diameter and the bulk velocity at the nozzle outlet) and for a nozzle to plate distance of two jet diameters. This specific configuration is known to lead to a non-monotonic variation of the temporal-mean Nusselt number as a function of the jet center distance, with the presence of two distinct peaks located on the jet axis and close to two nozzle diameters from the jet axis. The objectives are here twofold: first, validate the LES results against experimental data available in the literature and second to explore this validated numerical database by the use of high order statistics such as skewness and probability density functions of the temporal distribution of temperature and pressure to identify flow features at the origin of the second Nusselt peak. Skewness (Sk) of the pressure temporal distribution reveals the rebound of the primary vortices located near the location of the secondary peak and allows to identify the initiation of the unsteady separation linked to the local minimum in the mean heat transfer distribution. In the region of mean heat transfer enhancement, joint velocity-temperature analyses highlight that the most probable event is a cold fluid flux towards the plate produced by the passage of the vortical structures. In parallel, heat transfer distributions, analyzed using similar statistical tools, allow to connect the above mentioned events to the heat transfer on the plate. Thanks to such advanced analyses, the origin of the double peak is confirmed and connected to the flow dynamics.
Temperature and pressure dependence of the interfacial free energy against a hard surface in contact with water and decane
Authors: Ashbaugh Henry S. , da Silva Moura Natalia , Houser Hayden , Wang Yang , Goodson Amy , Barnett J. Wesley
Published: September 2016

Theoretical descriptions of molecular-scale solvation frequently invoke contributions proportional to the solvent exposed area, under the tacit expectation that those contributions are tied to a surface tension for macroscopic surfaces. Here we examine the application of revised scaled-particle theory (RSPT) to extrapolate molecular simulation results for the wetting of molecular-to-meso-scale repulsive solutes in liquid water and decane to determine the interfacial free energies of hard, flat surfaces. We show that the RSPT yields interfacial free energies at ambient pressures that are consistently greater than that obtained from the liquid-vapor surface tensions of water and decane by ∼4%. Nevertheless, the hard surface and liquid-vapor interfacial free energies are parallel over a broad temperature range at 1 bar indicating similar entropic contributions. With increasing pressure, the hard, flat interfacial free energies exhibit a maximum in the vicinity of ∼1000 bars. This non-monotonic behavior in both water and decane reflects solvent dewetting at low pressures, followed by wetting at higher pressures as the solvents are pushed onto the solute. By comparing the results of RSPT against classic scaled-particle theory (CSPT), we show that CSPT systematically predicts greater entropic penalties for interface formation and makes inconsistent predictions between the pressure dependence of the interfacial free energy and solvent contact density with the solute surface.
Electron spin resonance spectroscopy of small ensemble paramagnetic spins using a single nitrogen-vacancy center in diamond
Authors: Abeywardana Chathuranga , Stepanov Viktor , Cho Franklin H. , Takahashi Susumu
Published: September 2016

A nitrogen-vacancy (NV) center in diamond is a promising sensor for nanoscale magnetic sensing. Here, we report on electron spin resonance (ESR) spectroscopy using a single NV center in diamond. First, using a 230 GHz ESR spectrometer, we performed ensemble ESR of a type-Ib sample crystal and identified a substitutional single nitrogen impurity as a major paramagnetic center in the sample crystal. Then, we carried out free-induction decay and spin echo measurements of the single NV center to study static and dynamic properties of nanoscale bath spins surrounding the NV center. We also measured ESR spectrum of the bath spins using double electron-electron resonance spectroscopy with the single NV center. The spectrum analysis of the NV-based ESR measurement identified that the detected spins are the nitrogen impurity spins. The experiment was also performed with several other single NV centers in the diamond sample and demonstrated that the properties of the bath spins are unique to the NV centers indicating the probe of spins in the microscopic volume using NV-based ESR. Finally, we discussed the number of spins detected by the NV-based ESR spectroscopy. By comparing the experimental result with simulation, we estimated the number of the detected spins to be ≤50 spins.
Nonlinear effects related to circularly polarized dispersive Alfvén waves
Authors: Sharma Swati , Gaur Nidhi , Sharma R. P.
Published: September 2016

In situ measurements of solar wind have strongly implicated its turbulent behavior. The observed power spectra report a breakpoint around length scales of the order of ion scales. As one of the responsible mechanisms for the observed steepening in power spectrum, our approach includes a right circularly polarized dispersive Alfvén wave (DAW) with finite frequency correction which, when subjected to transverse collapse/filamentation instability, may possibly result in steepening of spectrum and progressive transfer of energy from larger scales to smaller scales. We have studied the nonlinear effects associated with coupling of DAW with kinetic Alfvén wave in solar wind at 1 A.U. The formation of localized structures provides a clue about the emergence of turbulence. Numerical simulation is performed to study localization and power spectral density of the field and density fluctuations. The results show steeper spectrum indicating transfer of large scale turbulent energy down to small scales.
Quantitative lateral and vertical piezoresponse force microscopy on a PbTiO3 single crystal
Authors: Lei Shiming , Koo Tae-Yeong , Cao Wenwu , Eliseev Eugene A. , Morozovska Anna N. , Cheong S.-W. , Gopalan Venkatraman
Published: September 2016

Piezoresponse force microscopy (PFM) has emerged as a powerful tool for research in ferroelectric and piezoelectric materials. While the vertical PFM (VPFM) mode is well understood and applied at a quantitative level, the lateral PFM (LPFM) mode is rarely quantified, mainly due to the lack of a practical calibration methodology. Here by PFM imaging on a LiNbO3 180° domain wall, we demonstrate a convenient way to achieve simultaneous VPFM and LPFM calibrations. Using these calibrations, we perform a full quantitative VPFM and LPFM measurement on a (001)-cut PbTiO3 single crystal. The measured effective piezoelectric coefficients d33eff and d35eff together naturally provide more information on a material's local tensorial electromechanical properties. The proposed approach can be applied to a wide variety of ferroelectric and piezoelectric systems.
Characterization of spin-orbit coupling in gated wire structures using Al2O3/In0.75Ga0.25As/In0.75Al0.25As inverted heterojunctions
Authors: Ohori Takahiro , Akabori Masashi , Hidaka Shiro , Yamada Syoji
Published: September 2016

Gated parallel wire structures obtained from inverted-modulation-doped heterojunctions made of high-In-content metamorphic InGaAs/InAlAs were investigated. The narrowest wire width was found to be ∼190 nm made using electron beam lithography and reactive ion etching. Magneto-transport was measured at low temperatures. Weak anti-localization and suppression with applied negative gate voltages were observed in low-mobility wide wires (1360 nm), which were considered for a two-dimensional system. The dependence on the gate voltage of spin-orbit coupling parameters was also obtained by fitting. The parameters decreased as the negative gate voltages increased. The trend might originate not from the electron system at the InGaAs/InAlAs interface but from the other electron system accumulated at the Al2O3/InGaAs interface, which can also contribute to conductivity. In high-mobility narrow wires (190 nm), which are close to a one-dimensional system, weak anti-localization peaks were still observed, indicating strong spin-orbit coupling. In addition, the critical widths of wires corresponding to zero conductance were estimated to be <100 nm. Therefore, our metamorphic modulation doped heterojunctions seem suitable for smaller spin-FETs.
Analysis of interface trap density of plasma post-nitrided Al2O3/SiGe MOS interface with high Ge content using high-temperature conductance method
Authors: Han Jae-Hoon , Takenaka Mitsuru , Takagi Shinichi
Published: September 2016

The interface trap density (Dit) of SiGe metal-oxide-semiconductor (MOS) interfaces is analyzed by the conductance method to evaluate the effect of electron cyclotron resonance plasma post-nitridation on SiGe interfaces with various Ge compositions. We find that it is important to evaluate Dit of a high-Ge-content SiGe MOS interface by the conductance method to eliminate the effect of the large series resistance and capacitance due to the SiGe/Si hetero-interface. In conjunction with the high-temperature measurement in the conductance method, an equivalent circuit corresponding to the SiGe/Si hetero-interface enables us to eliminate the effect of the series resistance and capacitance of the hetero-interface. Thus, we successfully evaluated Dit at SiGe MOS interfaces with a Ge composition of up to 0.49 and the impact of plasma post-nitridation on the high-Ge-content SiGe interfaces. Although Dit increases with the Ge composition, plasma post-nitridation is effective even for a high-Ge-content SiGe interface. Dit of the Al2O3/Si0.51Ge0.49 interface was reduced from 7.8 × 1012 cm−2 eV−1 to 2.4 × 1012 cm−2 eV−1 by plasma post-nitridation. Thus, we reveal that plasma post-nitridation is useful to achieve superior Al2O3/SiGe MOS interfaces regardless of the Ge composition.
Topological edge state with zero Hall conductivity in quasi-one dimensional system
Authors: Ye Xiao-Shan
Published: September 2016

We explore the structure of the energy spectra of quasi-one dimensional (Q1D) system subjected to spin-density-wave SDW states. The structure of the energy spectra opens energy gaps with Zeeman field. Theses gaps result in plateaus for the Quantum Hall conductivity which is associated with edge states. Different from the SSH Hofstadter model, here we show that there are a doublet of edge states contribution to zero Hall conductivity. These edge states are allowed for magnetic control of spin currents. The topological effects predicted here could be tested directly in organic conductors system.
An advanced modeling study on the impacts and atmospheric implications of multiphase dimethyl sulfide chemistry
Authors: Hoffmann Erik Hans , Tilgner Andreas , Schrödner Roland , Bräuer Peter , Wolke Ralf , Herrmann Hartmut
Published: September 2016

Significance

Climate models indicate the importance of dimethyl sulfide (DMS) oxidation in new aerosol particle formation and the activation of cloud condensation nuclei over oceans. These effects contribute to strong natural negative radiative forcing and substantially influence the Earth’s climate. However, the DMS oxidation pathway is not well-represented, because earlier model studies only parameterized gas-phase DMS oxidation and neglected multiphase chemistry. Here, we performed the most comprehensive current mechanistic studies on multiphase DMS oxidation. The studies imply that neglecting multiphase chemistry leads to significant overestimation of SO
2
production and subsequent new particle formation. These findings show that an advanced treatment of multiphase DMS chemistry is necessary to improve marine atmospheric chemistry and climate model predictions.
Oligodendrocytes contribute to motor neuron death in ALS via SOD1-dependent mechanism
Authors: Ferraiuolo Laura , Meyer Kathrin , Sherwood Thomas W. , Vick Jonathan , Likhite Shibi , Frakes Ashley , Miranda Carlos J. , Braun Lyndsey , Heath Paul R. , Pineda Ricardo , Beattie Christine E. , Shaw Pamela J. , Askwith Candice C. , McTigue Dana , Kaspar Brian K.
Published: September 2016

Significance

Oligodendrocytes have been implicated in disease pathology in amyotrophic lateral sclerosis (ALS) using transgenic mouse models. To date there is no human coculture system available to investigate oligodendrocyte involvement in motor neuron (MN) death in ALS. Our data highlight that oligodendrocytes derived from patients with familial and sporadic ALS from induced pluripotent stem cells and induced neural progenitor cells play an active role in MN death. Oligodendrocyte toxicity is mediated through soluble factors and cell-to-cell contact, thus identifying multiple mechanisms of action and therapeutic opportunities. Their pathogenic phenotype can be reversed by achieving superoxide dismutase 1 knockdown in early oligodendrocyte progenitors in both familial and sporadic cases, but not chromosome 9 ORF 72 samples. This study provides important insights for patient subgrouping and timelines for therapeutic approaches.
Targeted imaging of urothelium carcinoma in human bladders by an ICG pHLIP peptide ex vivo
Authors: Golijanin Jovana , Amin Ali , Moshnikova Anna , Brito Joseph M. , Tran Timothy Y. , Adochite Ramona-Cosmina , Andreev Gregory O. , Crawford Troy , Engelman Donald M. , Andreev Oleg A. , Reshetnyak Yana K. , Golijanin Dragan
Published: September 2016

Significance

Bladder cancer is the fifth most common cancer. Timely diagnosis and appropriate early management protocols are of paramount significance for improving patient outcomes. This study shows efficient pH-dependent near-infrared imaging of bladder malignant tumors without targeting of normal tissue. Our results demonstrate that the indocyanine green pH low insertion peptide (pHLIP) construct is suitable for use as a predictive clinical marker, specifically staining human bladder tumors after intravesical administration ex vivo. The targeting allows delivery of various imaging probes, which may offer early diagnosis and improve the outcomes of endoscopic and radical surgical resection of urothelial carcinomas. In addition, delivery of therapeutic molecules to cancer cells by pHLIP might open an opportunity for novel targeted treatment of bladder cancers.
Transferable model for chromosome architecture
Authors: Di Pierro Michele , Zhang Bin , Aiden Erez Lieberman , Wolynes Peter G. , Onuchic José N.
Published: September 2016

Significance

Chromatin consists of DNA and hundreds of proteins that interact with the genetic material. In vivo, chromatin folds into nonrandom structures. The physical mechanism leading to these characteristic conformations, however, remains poorly understood. Here, we introduce a model that generates chromosome conformations by using the idea that chromatin can be subdivided into types based on its biochemical interactions. Chromatin types, which are distinct from DNA sequence, are partially epigenetically controlled and change during cell differentiation, thus constituting a link between epigenetics, chromosomal organization, and cell development. The degree of accuracy achieved by this model supports the viability of the proposed physical mechanism of chromatin folding and makes the computational model a powerful tool for future investigations.
Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution
Authors: Hu Jinchuan , Lieb Jason D. , Sancar Aziz , Adar Sheera
Published: September 2016

Significance

The chemotherapy drug cisplatin kills cancer cells by damaging their DNA. It has been used for treating a variety of cancer types for almost four decades. Although the drug is generally effective, it has strong adverse side effects, and some cancers exhibit or, after initial favorable response, develop drug resistance. The mechanism of drug resistance is multifactorial and involves the ability of cancer cells to repair the cisplatin-induced DNA damages. We have developed methods to map the sites of cisplatin damage and its repair for the entire human genome at single-nucleotide resolution. These methods can be used to study cancer sensitivity and resistance to the drugs, and to identify new strategies for efficient combination therapies.
Ultralight or Heavyweight? The Interactive Effects of Gear Strength and Air Exposure on Reflex Impairment in Largemouth Bass
Authors: Cooke S. J. , Cooke C. J. A. , Brownscombe J. W.
Published: September 2016

Although much is known about the factors that influence the effects of catch‐and‐release angling on fish condition and survival, relatively little is known about the effects of fishing gear strength on fight time and, hence, fish condition. Moreover, little is known about how gear strength and fight time interact with air exposure duration to ultimately influence the level of exhaustion experienced by fish at time of release. Here we systematically varied fishing gear strength (ultralight versus medium‐heavy) and air exposure duration (0 versus 120 s) when targeting Largemouth Bass Micropterus salmoides. We relied on reflex impairment (using five different reflexes) as a real‐time indicator of fish condition. Largemouth Bass fight durations were highly variable between fishing gear types and across fish sizes. Largemouth Bass captured on ultralight fishing gear experienced longer fight times, and there was a stronger positive relationship between fish length and fight time than for those captured on heavier fishing gear. However, fish captured using ultralight gear were easier to handle upon landing and thus experienced shorter hook removal times, which may result in less air exposure in actual angling scenarios. Fish captured with ultralight gear had significantly higher reflex impairment than those captured with heavy gear with no air exposure, while fish captured with both gear types had similarly high reflex impairment when exposed to the air. These results indicate that gear strength does influence the level of exhaustion experienced by Largemouth Bass. However, fish that are landed quickly are so vigorous that handling and hook removal are challenging. We submit that there is likely a compromise where neither ultralight nor ultraheavy gear (always relative to the size and species targeted) is appropriate. Moreover, our findings emphasize the importance of minimizing air exposure, particularly for fish that are exhausted already from a protracted fight.

Received December 29, 2015; accepted June 24, 2016 Published online September 30, 2016
Brook Trout, Brown Trout, and Ectoparasitic CopepodsSalmincola edwardsii: Species Interactions as a Proximate Cause of Brook Trout Loss Under Changing Environmental Conditions
Authors: Mitro Matthew G.
Published: September 2016

Changes in environmental conditions are expected to affect stream temperature and ultimately the presence of native Brook TroutSalvelinus fontinalisin Wisconsin streams. While change in climate may be an ultimate cause of Brook Trout loss, proximate causes may involve factors other than intolerance to high temperatures. Here I present data to support the hypothesis that species interactions among Brook Trout, naturalized Brown TroutSalmo trutta, and ectoparasitic copepodsSalmincola edwardsiiin the context of changing environmental conditions can lead to declines in Brook Trout recruitment and abundance. WhileS. edwardsiiare endemic to Wisconsin streams and infect Brook Trout, they do not infect Brown Trout.Salmincola edwardsiiwere first documented in Ash Creek, Wisconsin, in 2010 and became epizootic in 2012. Conditions in 2012 conducive to an epizootic included anomalously warm stream temperatures, relative drought conditions, and an increasing sympatric population of Brown Trout. Infection prevalence increased from 42% in April 2012 to 95% in October. Average intensity of infection in 2012 was 5.5 copepods per age‐0 Brook Trout and 16.1 per Brook Trout age 1 and older. Variation in Brook Trout recruitment appeared to be related to stock size and environmental factors, including flood events, Brown Trout abundance, andS. edwardsiiepizootics. In 2012, flow conditions were conducive to salmonid recruitment, but Brook Trout recruitment fell precipitously relative to that of Brown Trout. Recruitment of age‐0 Brook Trout duringS. edwardsiiepizootics in 2012–2014 decreased about 77% and 89% compared with recruitment in 2007–2011 and 2005–2006, respectively. Following three consecutive years ofS. edwardsiiepizootics and poor recruitment, Brook Trout were nearing extirpation from Ash Creek. The data support the hypothesis that species interactions among fish and an ectoparasitic copepod under stressful environmental and ultimately climatic conditions can be a proximate cause of native Brook Trout loss.

Received February 15, 2016; accepted July 28, 2016 Published online September 30, 2016
Effects of Air Exposure on Postrelease Mortality Rates of White Marlin Caught in the U.S. Offshore Recreational Fishery
Authors: Graves John E. , Marcek Benjamin J. , Goldsmith William M.
Published: September 2016

White Marlin Kajikia albida are targeted by recreational fisheries in tropical and subtropical waters of the Atlantic Ocean. Off the U.S. East Coast, the vast majority of White Marlin are released after capture. Federal regulations prohibit anglers from removing a White Marlin from the water unless the fish is to be retained; however, numerous photographs of anglers holding White Marlin out of the water are posted on the Internet each summer, demonstrating that there is considerable noncompliance with this management measure. To better understand the effect of air exposure on postrelease survival of White Marlin, we attached pop-up satellite archival tags (PSATs; programmed to release after 30 d) to individuals that were caught on natural baits rigged with circle hooks and that were removed from the water for a period of 1 min (n = 6 fish), 3 min (n = 5 fish), or 5 min (n = 7 fish). We compared our results with those from a previous study in which PSATs were used to follow the fates of 59 White Marlin that were caught on circle hooks but not removed from the water. The proportion of postrelease mortalities increased with air exposure duration; the overall rate of postrelease mortality was significantly higher for White Marlin that were subjected to air exposure (33.3%) than for those that remained in the water (1.7%). These data provide strong support for the current U.S. regulation prohibiting the removal of a White Marlin from the water if the fish is to be released. Effective communication of the deleterious effects of air exposure on White Marlin should help to deter the practice of removing fish from the water among members of the recreational angling community, which has been supportive of other conservation measures for this species.

Received January 13, 2016; accepted June 15, 2016 Published online September 30, 2016
Control of power, torque, and instability drive using in-shot variable neutral beam energy in tokamaks
Authors: Pace D.C. , Collins C.S. , Crowley B. , Grierson B.A. , Heidbrink W.W. , Pawley C. , Rauch J. , Scoville J.T. , Van Zeeland M.A. , Zhu Y.B.
Published: September 2016

A first-ever demonstration of controlling power and torque injection through time evolution of neutral beam energy has been achieved in recent experiments at the DIII-D tokamak (Luxon 2002 Nucl. Fusion
42 614). Pre-programmed waveforms for the neutral beam energy produce power and torque inputs that can be separately and continuously controlled. Previously, these inputs were tailored using on/off modulation of neutral beams resulting in large perturbations (e.g. power swings of over 1 MW). The new method includes, importantly for experiments, the ability to maintain a fixed injected power while varying the torque. In another case, different beam energy waveforms (in the same plasma conditions) produce significant changes in the observed spectrum of beam ion-driven instabilities. Measurements of beam ion loss show that one energy waveform results in the complete avoidance of coherent losses due to Alfvénic instabilities. This new method of neutral beam operation is intended for further application in a variety of DIII-D experiments including those concerned with high-performance steady state scenarios, fast particle effects, and transport in the low torque regime. Developing this capability would provide similar benefits and improved plasma control for other magnetic confinement fusion facilities.
Global kinetic ballooning mode simulations in BOUT++
Authors: Ma C.H. , Xu X.Q.
Published: September 2016

We report on simulation results of a 3+1 gyro-Landau-fluid (GLF) model in BOUT++ framework, which contributes to increasing the physics understanding of the edge turbulence. We find that there is no second stability region of kinetic ballooning modes (KBM) in the concentric circular geometry. The first unstable β of KBM decreases below the ideal ballooning mode threshold with increasing

η

i

. In order to study the KBM in the real tokamak equilibrium, we find that the approximation of shifted circular geometry (

β
≪

ε

2

) is not valid for a high β global equilibrium near the second stability region of KBM. Thus we generate a series of real equilibria from a global equilibrium solver CORSICA, including both Shafranov shift and elongation effects, but not including bootstrap current. In these real equilibria, the second stability region of KBM are observed in our global linear simulations. The most unstable mode for different β are the same while the mode number spectrum near the second stability region is wider than the case near the first stability region. The nonlinear simulations show that the energy loss of an ELM keeps increasing with β, because the linear drive of the turbulence remains strong for the case near the second stability region during profile evolution.
NIMROD modeling of quiescent H-mode: reconstruction considerations and saturation mechanism
Authors: King J.R. , Burrell K.H. , Garofalo A.M. , Groebner R.J. , Kruger S.E. , Pankin A.Y. , Snyder P.B.
Published: September 2016

The extended-MHD NIMROD code (Sovinec and King 2010 J. Comput. Phys. 229 5803) models broadband-MHD activity from a reconstruction of a quiescent H-mode shot on the DIII-D tokamak (Luxon 2002 Nucl. Fusion
42 614). Computations with the reconstructed toroidal and poloidal ion flows exhibit low-

n

ϕ

perturbations (

n

ϕ

≃
1

–5) that grow and saturate into a turbulent-like MHD state. The workflow used to project the reconstructed state onto the NIMROD basis functions re-solves the Grad–Shafranov equation and extrapolates profiles to include scrape-off-layer currents. Evaluation of the transport from the turbulent-like MHD state leads to a relaxation of the density and temperature profiles.
On the width of a pedestal in the H-mode
Authors: Itoh K. , Itoh S.-I. , Kamiya K. , Kobayashi T.
Published: September 2016

The thickness of the transport barrier at the plasma edge is discussed, by analyzing the structure of the interface region between the turbulent L-mode region and the region where the transport is strongly-stabilized by the electric field. The effect of this localized radial electric field is prescribed. The spatial profile of turbulence intensity is analyzed by using a simplified model, in which the suppression and transport of turbulence intensity are introduced. The scaling property of the transport barrier is discussed.
Impact of zonal flows on edge pedestal collapse
Authors: Jhang Hogun , Kaang Helen H. , Kim S.S. , Rhee T. , Singh R. , Hahm T.S.
Published: September 2016

We perform a computational study of the role of zonal flows in edge pedestal collapse on the basis of a nonlinear three-field reduced magnetohydrodynamic (MHD) model. A dramatic change of dynamics takes place when ideal ballooning modes are completely stabilized. Analyses show that a new instability is developed due to a strong excitation of zonal vorticity, resulting in a series of secondary crashes. The presence of subsidiary bursts after a main crash increases the effective crash time and energy loss. These simulation results resemble the behavior of compound edge localized modes (ELMs). Analyses in this paper indicate that a complete understanding of ELM crash dynamics requires the self-consistent inclusion of nonlinear zonal flows-MHD interaction and transport physics.
Gyrokinetic study of turbulent convection of heavy impurities in tokamak plasmas at comparable ion and electron heat fluxes
Authors: Angioni C. , Bilato R. , Casson F.J. , Fable E. , Mantica P. , Odstrcil T. , Valisa M.
Published: September 2016

In tokamaks, the role of turbulent transport of heavy impurities, relative to that of neoclassical transport, increases with increasing size of the plasma, as clarified by means of general scalings, which use the ITER standard scenario parameters as reference, and by actual results from a selection of discharges from ASDEX Upgrade and JET. This motivates the theoretical investigation of the properties of the turbulent convection of heavy impurities by nonlinear gyrokinetic simulations in the experimentally relevant conditions of comparable ion and electron heat fluxes. These conditions also correspond to an intermediate regime between dominant ion temperature gradient turbulence and trapped electron mode turbulence. At moderate plasma toroidal rotation, the turbulent convection of heavy impurities, computed with nonlinear gyrokinetic simulations, is found to be directed outward, in contrast to that obtained by quasi-linear calculations based on the most unstable linear mode, which is directed inward. In this mixed turbulence regime, with comparable electron and ion heat fluxes, the nonlinear results of the impurity transport can be explained by the coexistence of both ion temperature gradient and trapped electron modes in the turbulent state, both contributing to the turbulent convection and diffusion of the impurity. The impact of toroidal rotation on the turbulent convection is also clarified.
Impact of ion diamagnetic drift on MHD stability at edge pedestal in JT-60U rotating plasmas
Authors: Aiba N. , Honda M. , Kamiya K.
Published: September 2016

The effect of ion diamagnetic drift on the stability of peeling–ballooning modes in rotating tokamak plasmas has been analyzed numerically. The results show that plasma toroidal rotation can not only destabilize the peeling–ballooning mode but also can reduce the ion diamagnetic drift effect on the mode stability, even though the ion diamagnetic drift effect stabilizes the mode in a static plasma. Plasma poloidal rotation can also destabilize the mode and cancel the ion diamagnetic drift effect, even when the rotation frequency is much smaller than the toroidal one. These impacts of the rotation on the stability can resolve the discrepancy between the result of the numerical stability analysis and the experimental result in type-I ELMy H-mode plasmas in JT-60U. The reduction of the ion diamagnetic drift effect on ELM stability due to plasma rotation is shown to depend on the direction of the rotation, so that the ion diamagnetic drift effect becomes negligible only when the JT-60U plasma rotates in the direction counter to the plasma current.