bluuebunny/crossref_metadata_2025 huggingface dataset:
Convergent synthesis of the hexasaccharide related to the repeating unit of the O-antigen from E. coli O120
Authors: Budhadev Darshita , Mukhopadhyay Balaram
Published: November 2015

The hexasaccharide repeating unit of the O-antigen from E. coli O120 has been synthesized in the form of its 4-methoxyphenyl glycoside by a convergent [2 + 4] strategy.
Online monitoring and analysis for autonomous continuous flow self-optimizing reactor systems
Authors: Fabry D. C. , Sugiono E. , Rueping M.
Published: November 2015

In this review the recent progress in the field of self-optimizing reactor systems for continuous flow chemistry is presented.
Discovery of new mutually orthogonal bioorthogonal cycloaddition pairs through computational screening
Authors: Narayanam Maruthi Kumar , Liang Yong , Houk K. N. , Murphy Jennifer M.
Published: November 2015

The sydnone-dibenzocyclooctyne and norbornene-tetrazine cycloadditions are both bioorthogonal and mutually orthogonal, used for simultaneous labeling of two targets.
Nanomechanics of layer-by-layer polyelectrolyte complexes: a manifestation of ionic cross-links and fixed charges
Authors: Han Biao , Chery Daphney R. , Yin Jie , Lu X. Lucas , Lee Daeyeon , Han Lin
Published: November 2015

This study investigates the roles of two distinct features of ionically cross-linked polyelectrolyte networks – ionic cross-links and fixed charges – in determining their nanomechanical properties.
Enzymatically triggered rupture of polymersomes
Authors: Jang Woo-Sik , Park Seung Chul , Reed Ellen H. , Dooley Kevin P. , Wheeler Samuel F. , Lee Daeyeon , Hammer Daniel A.
Published: November 2015

Polymersomes are robust vesicles made from di-block co-polymers. We have engineered a two step enzymatic cascade to trigger the release of contents from polymersomes, in which extravesicular glucose oxidase makes hydrogen peroxide, when then penetrates the membrane and is converted by entrapped catalase to oxygen, leading to vesicle failure.
Dynamics of colloid accumulation under flow over porous obstacles
Authors: Robert de Saint Vincent Matthieu , Abkarian Manouk , Tabuteau Hervé
Published: November 2015

Colloidal interactions and shear forces compete to drive the accumulation of colloidal particles over porous obstacles, resulting in a large diversity of aggregate shapes.
A rechargeable self-healing safety fuel gel
Authors: Bera Santu , Haldar Debasish
Published: November 2015

The rechargeable KOH responsive self-healing gel can be used as a safe fuel for indoor and outdoor heating without any special stove or burner.
A non-noble metal MoS2–Cd0.5Zn0.5S photocatalyst with efficient activity for high H2 evolution under visible light irradiation
Authors: Zhao Shaojian , Huang Junjian , Huo Qiuyue , Zhou Xiaozhou , Tu Weixia
Published: November 2015

ZnxCd1−xS solid solutions with uniform sizes and shapes were synthesized. Subsequent loading of MoS2 to one solution yielded a highly-active MoS2–Cd0.5Zn0.5S noble-metal-free photocatalyst; the highest H2 evolution rate was 12.30 mmol h−1 g−1 from water under visible light irradiation.
A simple method for the synthesis of porous polymeric vesicles and their application as MR contrast agents
Authors: Yan Lesan , Higbee Elizabeth , Tsourkas Andrew , Cheng Zhiliang
Published: November 2015

Highly efficient magnetic resonance contrast agents were produced from porous polymersomes by encapsulating macromolecules labeled with gadolinium.
A solution processed carbon nanotube modified conducting paper sensor for cancer detection
Authors: Kumar Saurabh , Willander Magnus , Sharma Jai G. , Malhotra Bansi D.
Published: November 2015

A solution processed poly (3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)–carbon nanotube (CNT) nano-composite has been utilized for the fabrication of a smart conducting paper (CP)viadip coating.
Surfactant effect on and luminescence tuning of lanthanide-doped ScPO4·2H2O microparticles
Authors: Chang Hongjin , Zhu Yongsheng , Xie Juan , Li Hongyu , Liu Botong , Xu Shuilin , Xie Xiaoji , Huang Ling , Huang Wei
Published: November 2015

UV-excited luminescence patterns of ‘IAM’ generated using ScPO4·2H2O:Ce,Tb(4%,12%) and ScPO4·2H2O:Ce,Eu(4%,12%) microparticles as green and red display materials, respectively.
PDLIM7 is a novel target of the ubiquitin ligase Nedd4-1 in skeletal muscle
Authors: D'Cruz Robert , Plant Pamela J. , Pablo Lesley A. , Lin Shouzhe , Chackowicz Joshua , Correa Judy , Bain James , Batt Jane
Published: November 2015

Skeletal muscle atrophy remains a complication occurring both as a natural response to muscle disuse and as a pathophysiological response to illness such as diabetes mellitus and nerve injury, such as traumatic muscle denervation. The ubiquitin–proteasome system (UPS) is the predominant proteolytic machinery responsible for atrophy of skeletal muscle, and Nedd4-1 (neural precursor cell-expressed developmentally down-regulated 4-1) is one of a series of E3 ubiquitin ligases identified to mediate inactivity-induced muscle wasting. Targets of Nedd4-1 mediated ubiquitination in skeletal muscle remain poorly understood. In the present study, we identified PDLIM7 (PDZ and LIM domain 7, Enigma), a member of the PDZ–LIM family of proteins, as a novel target of Nedd4-1 in skeletal muscle. The PDZ–LIM family of proteins is known to regulate muscle development and function. We show that Nedd4-1 expression in muscle atrophied by denervation is co-incident with a decrease in PDLIM7 and that PDLIM7 protein levels are stabilized in denervated muscle of Nedd4-1 skeletal muscle-specific knockout mice (SMS-KO). Exogenous PDLIM7 and Nedd4-1 transfected into human embryonic kidney (HEK)293 cells co-immunoprecipitate through binding between the PY motif of PDLIM7 and the second and third WW domains of Nedd4-1 and endogenous PDLIM7 and Nedd4-1 interact in the cytoplasm of differentiated C2C12 myotubes, leading to PDLIM7 ubiquitination. These results identify PDLIM7 as a bona fide skeletal muscle substrate of Nedd4-1 and suggest that this interaction may underlie the progression of skeletal muscle atrophy. This offers a novel therapeutic target that could be potentially used to attenuate muscle atrophy.
Plasma-derived and synthetic high-density lipoprotein inhibit tissue factor in endothelial cells and monocytes
Authors: Ossoli Alice , Remaley Alan T. , Vaisman Boris , Calabresi Laura , Gomaraschi Monica
Published: November 2015

HDL (high-density lipoproteins) exert anti-thrombotic activities by preventing platelet adhesion and activation and by stimulating the protein C pathway and fibrinolysis. The aim of the present study was to assess the effect of plasma-derived and synthetic HDL on endothelial and monocyte expression of TF (tissue factor), the primary initiator of coagulation. HDL inhibited TF expression and activity in stimulated endothelial cells and monocytes in a dose-dependent way. Synthetic HDL fully retain the ability to inhibit TF expression in a dose-dependent manner; lipid-free apoA-I (apolipoprotein A-I) was not effective and neither was sphingosine 1-phosphate involved. HDL-mediated TF inhibition was due to a modulation of cellular cholesterol content through the interaction with SR-BI (scavenger receptor BI); downstream, HDL inhibited the activation of p38 MAPK (mitogen-activated protein kinase) and the repression of the PI3K (phosphoinositide 3-kinase) pathway responsible for TF expression. In vivo, human apoA-I-transgenic mice displayed a reduced aortic TF expression compared with wild-type animals and TF plasma levels were increased in subjects with low HDL-C (HDL-cholesterol) levels compared with high HDL-C subjects. Thus the anti-thrombotic activity of HDL could also be mediated by the inhibition of TF expression and activity in endothelial cells and monocytes; synthetic HDL retain the inhibitory activity of plasma-derived HDL, supporting the hypothesis that synthetic HDL infusion may be beneficial in the setting of acute coronary syndrome.
High-field magneto-thermo-mechanical testing system for characterizing multiferroic bulk alloys
Authors: Bruno Nickolaus M. , Karaman Ibrahim , Ross Joseph H. , Chumlyakov Yuriy I.
Published: November 2015

Multiferroic meta-magnetic shape memory alloys are well known for exhibiting large magnetic field induced actuation strains, giant magnetocaloric effects, magneto-resistance, and structural and magnetic glassy behaviors. Thus, they are candidates for improving modern day sensing, actuation, magneto-resistance, and solid-state refrigeration processes. Until now, however, experimental apparatuses have typically been able to probe a limited ferroic parameter space in these materials, i.e., only concurrent thermal and mechanical responses, or magnetic and thermal responses. To overcome this barrier and better understand the coupling of multiple fields on materials behavior, a magneto-thermo-mechanical characterization device has been designed and implemented. This device is capable of compressing a specimen at load levels up to 5300 N collinearly with applied fields up to 9 T between temperatures of −100 °C and 120 °C. Uniaxial stress, strain, temperature, magnetic field, and the volumetric average magnetization have been simultaneously measured under mixed loading conditions on a NiCoMnIn meta-magnetic shape memory alloy and a few selected results are presented here.
Kolakoski sequence as an element to radiate giant forward and backward second harmonic signals
Authors: Parvini T. S. , Tehranchi M. M. , Hamidi S. M. , Sarkarati S.
Published: November 2015

We propose a novel type of aperiodic one-dimensional photonic crystal structures which can be used for generating giant forward and backward second harmonic signals. The studied structure is formed by stacking together the air and nonlinear layers according to the Kolakoski self-generation scheme in which each nonlinear layer contains a pair of antiparallel 180° poled LiNbO3 crystal layers. For different generation stages of the structure, conversion efficiencies of forward and backward second harmonic waves have been calculated by nonlinear transfer matrix method. Numerical simulations show that conversion efficiencies in the Kolakoski-based multilayer are larger than the perfect ones for at least one order of magnitude. Especially for 33rd and 39th generation stages, forward second harmonic wave are 42 and 19 times larger, respectively. In this paper, we validate the strong fundamental field enhancement and localization within Kolakoski-based multilayer due to periodicity breaking which consequently leads to very strong radiation of backward and forward second harmonic signals. Following the applications of analogous aperiodic structures, we expect that Kolakosi-based multilayer can play a role in optical parametric devices such as multicolor second harmonic generators with high efficiency.
A fast exact simulation method for a class of Markov jump processes
Authors: Li Yao , Hu Lili
Published: November 2015

A new method of the stochastic simulation algorithm (SSA), named the Hashing-Leaping method (HLM), for exact simulations of a class of Markov jump processes, is presented in this paper. The HLM has a conditional constant computational cost per event, which is independent of the number of exponential clocks in the Markov process. The main idea of the HLM is to repeatedly implement a hash-table-like bucket sort algorithm for all times of occurrence covered by a time step with length τ. This paper serves as an introduction to this new SSA method. We introduce the method, demonstrate its implementation, analyze its properties, and compare its performance with three other commonly used SSA methods in four examples. Our performance tests and CPU operation statistics show certain advantages of the HLM for large scale problems.
Correlated lateral phase separations in stacks of lipid membranes
Authors: Hoshino Takuma , Komura Shigeyuki , Andelman David
Published: November 2015

Motivated by the experimental study of Tayebi et al. [Nat. Mater. 11, 1074 (2012)] on phase separation of stacked multi-component lipid bilayers, we propose a model composed of stacked two-dimensional Ising spins. We study both its static and dynamical features using Monte Carlo simulations with Kawasaki spin exchange dynamics that conserves the order parameter. We show that at thermodynamical equilibrium, due to strong inter-layer correlations, the system forms a continuous columnar structure for any finite interaction across adjacent layers. Furthermore, the phase separation shows a faster dynamics as the inter-layer interaction is increased. This temporal behavior is mainly due to an effective deeper temperature quench because of the larger value of the critical temperature, Tc, for larger inter-layer interaction. When the temperature ratio, T/Tc, is kept fixed, the temporal growth exponent does not increase and even slightly decreases as a function of the increased inter-layer interaction.
On the order-disorder transition of compressible diblock copolymer melts
Authors: Zong Jing , Wang Qiang
Published: November 2015

We performed both the fast off-lattice Monte Carlo simulations of symmetric diblock copolymers (DBC) in an isothermal-isobaric ensemble and the self-consistent field calculations of asymmetric DBC to properly determine the order-disorder transition (ODT) of a model system of compressible DBC melts used in the literature when it is a first-order phase transition, and studied for the first time the co-existence of the two phases at ODT. We found that the co-existing region is quite small and decreases as the system becomes less compressible, which justifies the previous ODT results obtained by equating the Helmholtz free energy per chain of the two phases. We also found that for the most compressible system where there is no repulsion between the same type of segments, the self-consistent field theory predicts that ODT is a second-order phase transition even for asymmetric DBC melts due to its mean-field approximation.
Electrostatic microprobe for determining charge domains on surfaces
Authors: Fletcher Robert A.
Published: November 2015

An electrostatic microprobe was developed to measure charge on wipes and various test surfaces. The device is constructed on an optical microscope platform utilizing a computer controlled XY stage. Test surfaces can be optically imaged to identify microscopic features that can be correlated to the measured charge domain maps. The ultimate goal is to quantify charge on wipe cloths to determine the influence of electrostatic forces on wipe sampling efficiency. We found that certain wipe materials do not extensively charge while others accumulate charge by making contact with other surfaces (through the triboelectric effect). Charge domains are found to be nonuniform.
Electronic spectrum of the propargyl cation (H2C3H+) tagged with Ne and N2
Authors: Catani Katherine J. , Sanelli Julian A. , Dryza Viktoras , Gilka Natalie , Taylor Peter R. , Bieske Evan J.
Published: November 2015

The Ã1A1 ← X̃1A1 band system of the propargyl cation (H2C3H+) is measured over the 230-270 nm range by photodissociation of mass-selected H2C3H+-Ne and H2C3H+-N2 complexes in a tandem mass spectrometer. The band origin occurs at 37 618 cm−1 for H2C3H+-Ne and 37 703 cm−1 for H2C3H+-N2. Ground and excited state ab initio calculations for H2C3H+ using the MCSCF and coupled-cluster (CC) response methods show that the ion has C2v symmetry in the ground X̃1A1 and excited Ã1A1 states and that the strong vibronic progression with a spacing of 630 cm−1 is due to the C–C stretch vibrational mode, ν 5.
Double-bosonization and Majid’s conjecture, (I): Rank-inductions of ABCD
Authors: Hu Hongmei , Hu Naihong
Published: November 2015

Majid developed in [S. Majid, Math. Proc. Cambridge Philos. Soc. 125, 151–192 (1999)] the double-bosonization theory to construct Uq(𝔤) and expected to generate inductively not just a line but a tree of quantum groups starting from a node. In this paper, the authors confirm Majid’s first expectation (see p. 178 [S. Majid, Math. Proc. Cambridge Philos. Soc. 125, 151–192 (1999)]) through giving and verifying the full details of the inductive constructions of Uq(𝔤) for the classical types, i.e., the ABCD series. Some examples in low ranks are given to elucidate that any quantum group of classical type can be constructed from the node corresponding to Uq(𝔰𝔩2).
Investigation of gate-diode degradation in normally-off p-GaN/AlGaN/GaN high-electron-mobility transistors
Authors: Ťapajna M. , Hilt O. , Bahat-Treidel E. , Würfl J. , Kuzmík J.
Published: November 2015

Gate diode conduction mechanisms were analyzed in normally-off p-GaN/AlGaN/GaN high-electron mobility transistors grown on Si wafers before and after forward bias stresses. Electrical characterization of the gate diodes indicates forward current to be limited by channel electrons injected through the AlGaN/p-GaN triangular barrier promoted by traps. On the other hand, reverse current was found to be consistent with carrier generation-recombination processes in the AlGaN layer. Soft breakdown observed after ∼105 s during forward bias stress at gate voltage of 7 V was attributed to formation of conductive channel in p-GaN/AlGaN gate stack via trap generation and percolation mechanism, likely due to coexistence of high electric field and high forward current density. Possible enhancement of localized conductive channels originating from spatial inhomogeneities is proposed to be responsible for the degradation.
Substrate degradation in high-Rayleigh-number reactive convection
Authors: Ward T. J. , Jensen O. E. , Power H. , Riley D. S.
Published: November 2015

We study buoyancy-induced convection of a solute in an ideal two-dimensional fluid-saturated porous medium, where the solute undergoes a second-order reaction with a chemical substrate that is fixed in the underlying matrix. Numerical simulations at high Rayleigh number show how a flow is established in which a thin dynamic boundary layer beneath the solute source feeds slender vertical plumes beneath. We examine how the substrate is reactively degraded, at a rate enhanced by convective mixing. For the case when the substrate is abundant, we derive a reduced-order model describing the slow degradation of the substrate, which is formulated as a novel one-dimensional free-boundary problem. Numerical simulations and the reduced model reveal how, when the reaction is rapid compared to the convective time scale, the plumes propagate deep into the flow domain with reaction confined to a narrow region at their base. In contrast, slow reaction allows plumes to fill the domain before degradation of the substrate proceeds homogeneously. An alternative model with a thin reaction front captures the rapid degradation of the substrate when the solute concentration is relatively high.
Exact travelling wave solutions of non-linear reaction-convection-diffusion equations—An Abel equation based approach
Authors: Harko T. , Mak M. K.
Published: November 2015

We consider quasi-stationary (travelling wave type) solutions to a general nonlinear reaction-convection-diffusion equation with arbitrary, autonomous coefficients. The second order nonlinear equation describing one dimensional travelling waves can be reduced to a first kind first order Abel equation. By using two integrability conditions for the Abel equation (the Chiellini lemma and the Lemke transformation), several classes of exact travelling wave solutions of the general reaction–convection-diffusion equation are obtained, corresponding to different functional relations imposed between the diffusion, convection and reaction functions. In particular, we obtain travelling wave solutions for two non-linear second order partial differential equations, representing generalizations of the standard diffusion equation and of the classical Fisher–Kolmogorov equation, to which they reduce for some limiting values of the model parameters. The models correspond to some specific, power law type choices of the reaction and convection functions, respectively. The travelling wave solutions of these two classes of differential equation are investigated in detail by using both numerical and semi-analytical methods.
Experimental study of plasmon in a grating coupled graphene device with a resonant cavity
Authors: Yan Bo , Fang Jingyue , Qin Shiqiao , Liu Yongtao , Zhou Yingqiu , Li Renbing , Zhang Xue-Ao
Published: November 2015

Plasmon was probed from graphene which was grown by chemical vapor deposition using terahertz time-domain spectroscopy at room temperature. Graphene was laid on a resonant cavity, and metal grating was then deposited on top of them. For the THz light polarized along the grid fingers, the optical conductivity of graphene changed from Drude response into strongly Lorentz behavior with a peak formed in the THz-region. These experimental results are highly consistent with the theoretical prediction of a single layer graphene. It confirms that the graphene plasmon frequency can be tuned by the length of grating. Moreover, the extinction in the transmission of single-layer graphene can also be increased beyond 60%.
Experimental study of shear layer instability below a free surface
Authors: André Matthieu A. , Bardet Philippe M.
Published: November 2015

Relaxation of a laminar boundary layer at a free surface is an inviscidly unstable process and can lead to millimeter-scale surface waves, influencing interfacial processes. Due to the small time- and length-scales involved, previous experimental studies have been limited to visual observations and point-wise measurements of the surface profile to determine instability onset and frequency. However, effects of viscosity, surface tension, and non-linearity of the wave profile have not been systematically studied. In fact, no data have been reported on the velocity fields associated with this instability. In the present study, planar laser induced fluorescence and particle image velocimetry provide surface profiles coupled with liquid phase velocity fields for this instability in a time resolved manner. Wave steepness (ak, with a the amplitude and k the wave number) and Reynolds and Weber numbers based on momentum thickness range from 0 to 1.2, 143 to 177, and 4.79 to 6.61, respectively. Large datasets are analyzed to gain statistical information on the surface behavior. Discrete vortices are resolved, showing that the shear layer becomes unstable and rolls up above a Reynolds number of 140. The detection onset and steepness of the subsequent surface deformation by the vortices depend upon the Weber number. Non-linear behavior such as vortex motion and wave profile asymmetry are observed at steepness larger than 0.5.
Communication: Three-electron coalescence points in two and three dimensions
Authors: Loos Pierre-François , Mannix Evelyn J. , Gill Peter M. W.
Published: November 2015

The form of the wave function at three-electron coalescence points is examined for several spin states using an alternative method to the usual Fock expansion. We find that, in two- and three-dimensional systems, the non-analytical nature of the wave function is characterized by the appearance of logarithmic terms, reminiscent of those that appear as both electrons approach the nucleus of the helium atom. The explicit form of these singularities is given in terms of the interelectronic distances for a doublet and two quartet states of three electrons in a harmonic well.
Effect of background density fluctuations on the localized structures of inertial Alfvén wave and turbulent spectrum
Authors: Sharma R. P. , Kumari Anju , Yadav Nitin
Published: November 2015

In the present paper, we have investigated the nonlinear evolution of three dimensionally (3D) propagating inertial Alfvén wave (IAW) in the presence of background density fluctuations for low β plasma. The ponderomotive force, due to IAW and modified background plasma density, has been taken into account in order to develop the model equation. The governing equation has been solved numerically as well as semi-analytically to study the effect of background fluctuations on the evolution of IAW. Results reveal that the IAW gets localized and breaks up into intense localized structures. These localized structures are found to be influenced by the presence of background density fluctuations. To get the physical insight of this proposed interaction, a semi-analytical model based on the paraxial approximation has been developed. Resulting turbulent spectrum has also been studied for different levels of background fluctuations. As a result, it has been found that background density fluctuations affect the nonlinear evolution of IAW which may contribute towards the heating and acceleration of the plasma particles. The significance of the present work is pointed out with the observation received by the spacecraft FAST and Hawkeye1 in the auroral region.
Are the argon metastables important in high power impulse magnetron sputtering discharges?
Authors: Gudmundsson J. T. , Lundin D. , Stancu G. D. , Brenning N. , Minea T. M.
Published: November 2015

We use an ionization region model to explore the ionization processes in the high power impulse magnetron sputtering (HiPIMS) discharge in argon with a titanium target. In conventional dc magnetron sputtering (dcMS), stepwise ionization can be an important route for ionization of the argon gas. However, in the HiPIMS discharge stepwise ionization is found to be negligible during the breakdown phase of the HiPIMS pulse and becomes significant (but never dominating) only later in the pulse. For the sputtered species, Penning ionization can be a significant ionization mechanism in the dcMS discharges, while in the HiPIMS discharge Penning ionization is always negligible as compared to electron impact ionization. The main reasons for these differences are a higher plasma density in the HiPIMS discharge, and a higher electron temperature. Furthermore, we explore the ionization fraction and the ionized flux fraction of the sputtered vapor and compare with recent experimental work.
Identification of native defects (vacancies and antisites) in CdSiP2 crystals
Authors: Golden E. M. , Giles N. C. , Maniego E. , Hopkins F. K. , Zawilski K. T. , Schunemann P. G. , Halliburton L. E.
Published: November 2015

Electron paramagnetic resonance (EPR) is used to identify four native defects in single crystals of CdSiP2. This nonlinear optical material is used in optical parametric oscillators to generate tunable output in the mid-infrared. The performance of these frequency-conversion devices is limited when infrared absorption bands associated with native defects overlap a pump wavelength. Cadmium, silicon, and phosphorus vacancies and also silicon-on-cadmium antisites are present in the as-grown undoped CdSiP2 crystals. Using near-band-edge 632.8 nm light from a He-Ne laser, a paramagnetic charge state, and thus an EPR spectrum, is formed at liquid-helium temperatures for three of the four defects. The EPR spectrum from the singly ionized silicon vacancy (VSi−) is present without light and has five hyperfine lines due to equal interactions with the four neighboring 31P nuclei. In contrast, the photoinduced EPR spectrum from the singly ionized cadmium vacancy (VCd−) has a three-line hyperfine pattern due to equal interactions with only two of its four neighboring 31P nuclei. The light-induced spectrum from the singly ionized silicon-on-cadmium antisite (Si Cd+) also has a three-line hyperfine pattern, thus indicating that the unpaired spin interacts primarily with only two 31P neighbors. For the neutral phosphorus vacancy (VP 0), the unpaired spin is primarily localized on the nearest-neighbor silicon ions and the photoinduced EPR spectrum has no resolved 31P hyperfine interactions. The silicon and cadmium vacancies are acceptors, and the silicon-on-cadmium antisite and the phosphorus vacancy are donors.
On the scaling of multicrystal data sets collected at high-intensity X-ray and electron sources
Authors: Coppens Philip , Fournier Bertrand
Published: November 2015

The need for data-scaling has become increasingly evident as time-resolved pump-probe photocrystallography is rapidly developing at high intensity X-ray sources. Several aspects of the scaling of data sets collected at synchrotrons, XFELs (X-ray Free Electron Lasers) and high-intensity pulsed electron sources are discussed. They include laser-ON/laser-OFF data scaling, inter- and intra-data set scaling.
Metallic interface in non-SrTiO3 based titanate superlattice
Authors: Liu Xiaoran , Choudhury D. , Cao Yanwei , Kareev M. , Middey S. , Chakhalian J.
Published: November 2015

We report on the fabrication of all perovskite Mott insulator/band insulator YTiO3/CaTiO3 superlattices by pulsed laser deposition. The combination of in situ reflection high energy electron diffraction, X-ray diffraction, and X-ray reflectivity confirms the high quality of the films grown in a layer-by-layer mode. Electrical transport measurements reveal that a non-SrTiO3 based two-dimensional electron gas system has formed at the YTiO3/CaTiO3 interface. These studies offer another route in the pursuit of complex oxide two-dimensional electron gas systems, which allows to obtain greater insights into the exotic many-body phenomena at such interfaces.
Acoustic superlens using Helmholtz-resonator-based metamaterials
Authors: Yang Xishan , Yin Jing , Yu Gaokun , Peng Linhui , Wang Ning
Published: November 2015

Acoustic superlens provides a way to overcome the diffraction limit with respect to the wavelength of the bulk wave in air. However, the operating frequency range of subwavelength imaging is quite narrow. Here, an acoustic superlens is designed using Helmholtz-resonator-based metamaterials to broaden the bandwidth of super-resolution. An experiment is carried out to verify subwavelength imaging of double slits, the imaging of which can be well resolved in the frequency range from 570 to 650 Hz. Different from previous works based on the Fabry-Pérot resonance, the corresponding mechanism of subwavelength imaging is the Fano resonance, and the strong coupling between the neighbouring Helmholtz resonators separated at the subwavelength interval leads to the enhanced sound transmission over a relatively wide frequency range.
1.9% bi-axial tensile strain in thick germanium suspended membranes fabricated in optical germanium-on-insulator substrates for laser applications
Authors: Gassenq A. , Guilloy K. , Osvaldo Dias G. , Pauc N. , Rouchon D. , Hartmann J.-M. , Widiez J. , Tardif S. , Rieutord F. , Escalante J. , Duchemin I. , Niquet Y.-M. , Geiger R. , Zabel T. , Sigg H. , Faist J. , Chelnokov A. , Reboud V. , Calvo V.
Published: November 2015

High tensile strains in Ge are currently studied for the development of integrated laser sources on Si. In this work, we developed specific Germanium-On-Insulator 200 mm wafer to improve tolerance to high strains induced via shaping of the Ge layers into micro-bridges. Building on the high crystalline quality, we demonstrate bi-axial tensile strain of 1.9%, which is currently the highest reported value measured in thick (350 nm) Ge layer. Since this strain is generally considered as the onset of the direct bandgap in Ge, our realization paves the way towards mid-infrared lasers fully compatible with CMOS fab technology.
Accelerated weathering of carbonate rocks following the 2010 wildfire on Mount Carmel, Israel
Authors: Shtober-Zisu N. , Tessler N. , Tsatskin A. , Greenbaum N.
Published: November 2015

Massive destruction of carbonate rocks occurred on the slopes of Mount Carmel during the severe wildfire in 2010. The bedrock surfaces exhibited extensive exfoliation into flakes and spalls covering up to 80–100% of the exposed rocks; detached boulders were totally fractured or disintegrated. The fire affected six carbonate units – various types of chalk, limestone and dolomite. The burned flakes show a consistent tendency towards flatness, in all lithologies. The extent of the physical disruption depends on rock composition: the most severe response was found in the chalk formations covered by calcrete (Nari crusts). These rocks reacted by extreme exfoliation, at an average depth of 7.7 to 9.6 cm and a maximum depth of 20 cm. Scorched and blackened faces under the upper layer of spalls provide strong evidence that chalk breakdown took place at an early stage of the fire. It is possible to explain the extreme response of the chalks by the laminar structure of the Nari, which served as planes of weakness for the rock destruction. Three years after the fire, the rocks continue to exfoliate and break down internally. As the harder surface of the Nari deteriorates, the more brittle underlying chalk is exposed to erosion.
Estuarine Residency and Migration of Southern Flounder Inferred from Conventional Tag Returns at Multiple Spatial Scales
Authors: Craig J. Kevin , Smith William E. , Scharf Frederick S. , Monaghan James P.
Published: November 2015

An improved understanding of the spatial structure and movements of harvested populations can promote more efficient management of marine resources. Conventional tagging is a valuable approach to study the movements of marine fishes due to its relatively low expense and the typically broad spatial extent over which movements can be characterized. We present the findings of multiple tag return studies initiated in the estuaries of North Carolina during the past two decades to better understand habitat residency and migration patterns of Southern Flounder Paralichthys lethostigma, an economically important marine flatfish in the southeastern USA. Tag return data indicated large-scale (>50 km) movements of relatively large fish in the fall, which were presumably associated with offshore winter spawning migrations. Nearly all Southern Flounder that demonstrated large-scale movement were recovered to the south of the system in which they were tagged, suggesting that the spawning activity of fish using North Carolina estuaries may be concentrated mostly off the southeastern U.S. continental shelf. Tag returns from within multiple estuarine systems during the spring and summer were in close proximity to release sites (typically < 1 km), suggesting limited movement during estuarine residency. Recaptures in the spring of fish tagged the previous summer or fall were also in close proximity to release sites, in some cases within the same estuarine creek, indicating limited movement of fish overwintering in the estuary as well. Our findings reveal saltatory movement dynamics of Southern Flounder characterized by limited movement during estuarine residency and large-scale movements in the fall associated with spawning migrations. Our synthesis of several tag return studies across multiple spatial scales should contribute to a better alignment of Southern Flounder management with their spatial dynamics.

Received April 13, 2015; accepted July 20, 2015
Comparisons of the reference measuring instruments of surface parameters
Authors: Kupko Vladimir , Lysenko Valeriy
Published: November 2015

A bilateral comparison of measurements on a Type A1 roughness standard has been undertaken between metrology institutes in Ukraine and Russia. The measurand was the parameter R
max, located on two different sections of the artefact with nominal values of 0.250 μm and 49 μm. The results of the two participants are in agreement within the combined uncertainties, thus equivalence of the measurements is demonstrated.

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To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the ENEA-INMRI, Italy and the BIPM in 60Co gamma radiation
Authors: Kessler C , Pinto M , Cappadozzi G , Silvestri C , Bovi M , Toni M P
Published: November 2015

A direct comparison of the standards for air kerma of the Istituto Nazionale di Metrologia delle Radiazioni Ionizzanti (ENEA-INMRI), Italy and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in June 2015. The comparison result, evaluated as a ratio of the ENEA and the BIPM standards for air kerma, is 0.9999 with a combined standard uncertainty of 2.2 × 10−3. The results are analysed and presented in terms of degrees of equivalence for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes
Authors: Steinrücken Matthias , Jewett Ethan M. , Song Yun S.
Published: November 2015

Motivation: In the Wright–Fisher diffusion, the transition density function describes the time evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics and computing it for biologically realistic scenarios with selection and demography is an important problem.

Results: We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective population size, selection coefficients and mutation parameters vary over time in a piecewise constant manner.

Availability and implementation: The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/.

Contact:  yss@berkeley.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Flexible data integration and curation using a graph-based approach
Authors: Croset Samuel , Rupp Joachim , Romacker Martin
Published: November 2015

Motivation: The increasing diversity of data available to the biomedical scientist holds promise for better understanding of diseases and discovery of new treatments for patients. In order to provide a complete picture of a biomedical question, data from many different origins needs to be combined into a unified representation. During this data integration process, inevitable errors and ambiguities present in the initial sources compromise the quality of the resulting data warehouse, and greatly diminish the scientific value of the content. Expensive and time-consuming manual curation is then required to improve the quality of the information. However, it becomes increasingly difficult to dedicate and optimize the resources for data integration projects as available repositories are growing both in size and in number everyday.

Results: We present a new generic methodology to identify problematic records, causing what we describe as ‘data hairball’ structures. The approach is graph-based and relies on two metrics traditionally used in social sciences: the graph density and the betweenness centrality. We evaluate and discuss these measures and show their relevance for flexible, optimized and automated data curation and linkage. The methodology focuses on information coherence and correctness to improve the scientific meaningfulness of data integration endeavors, such as knowledge bases and large data warehouses.

Contact:  samuel.croset@roche.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments
Authors: Thomas Brandon R. , Chylek Lily A. , Colvin Joshua , Sirimulla Suman , Clayton Andrew H.A. , Hlavacek William S. , Posner Richard G.
Published: November 2015

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu).

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  bionetgen.help@gmail.com
Identifying opportunities in EHR to improve the quality of antibiotic allergy data
Authors: Moskow Jaclynn M , Cook Nicole , Champion-Lippmann Carisa , Amofah Saint Anthony , Garcia Angela S
Published: November 2015

Background Antimicrobial resistance is a growing, global public health crisis, due in large part to the overuse and misuse of antibiotics. Understanding medication allergy data and allergy reactions that are documented in electronic health records (EHRs) can help to identify opportunities to improve the quality of documentation of beta-lactam allergies, thus potentially reducing the prescribing of alternative antibiotics.

Methods Medication allergies and allergy reactions recorded in the EHR for 319 051 patients seen across 32 community health centers were reviewed. Patients with a beta-lactam allergy recorded in their EHR were identified. Free text, as well as standardized allergy and allergy reaction fields, were analyzed.

Results Among patients, 9.1% ( n  = 29 095) had evidence of a beta-lactam allergy recorded in their EHR. Women, white, and non-Hispanic patients were more likely to have a documented allergy compared to men, black, and Hispanic patients. Among all patients with a documented beta-lactam allergy, 36.2% had an empty or missing allergy reaction description in their EHR.

Conclusions Findings suggest that current EHR documentation practices among the health centers reviewed do not provide enough information on allergic reactions to allow providers to discern between true allergies and common, but anticipated, drug side effects. Improved EHR documentation guidance, training that reinforces the use of standardized data and more detailed recording of allergic reactions, combined with initiatives to address patient barriers including health literacy, may help to improve the accuracy of drug allergies in patients’ records. These initiatives, combined with antimicrobial stewardship programs, can help to reduce inappropriate prescribing of alternative antibiotics when beta-lactam antibiotics are first-line and can be tolerated.
VERTIcal Grid lOgistic regression (VERTIGO)
Authors: Li Yong , Jiang Xiaoqian , Wang Shuang , Xiong Hongkai , Ohno-Machado Lucila
Published: November 2015

Objective To develop an accurate logistic regression (LR) algorithm to support federated data analysis of vertically partitioned distributed data sets.

Material and Methods We propose a novel technique that solves the binary LR problem by dual optimization to obtain a global solution for vertically partitioned data. We evaluated this new method, VERTIcal Grid lOgistic regression (VERTIGO), in artificial and real-world medical classification problems in terms of the area under the receiver operating characteristic curve, calibration, and computational complexity. We assumed that the institutions could “align” patient records (through patient identifiers or hashed “privacy-protecting” identifiers), and also that they both had access to the values for the dependent variable in the LR model (eg, that if the model predicts death, both institutions would have the same information about death).

Results The solution derived by VERTIGO has the same estimated parameters as the solution derived by applying classical LR. The same is true for discrimination and calibration over both simulated and real data sets. In addition, the computational cost of VERTIGO is not prohibitive in practice.

Discussion There is a technical challenge in scaling up federated LR for vertically partitioned data. When the number of patients m is large, our algorithm has to invert a large Hessian matrix. This is an expensive operation of time complexity O(m3) that may require large amounts of memory for storage and exchange of information. The algorithm may also not work well when the number of observations in each class is highly imbalanced.

Conclusion The proposed VERTIGO algorithm can generate accurate global models to support federated data analysis of vertically partitioned data.
Chemical synthesis of proteins using hydrazide intermediates
Authors: Huang Yi-Chao , Fang Ge-Min , Liu Lei
Published: November 2015

Protein chemical synthesis offers useful and otherwise-difficulty-to-obtain biomacromolecules for biological and pharmaceutical studies. Recently, the hydrazide chemistry has drawn attentions in this field as peptide or protein hydrazides can be used as key intermediates for different synthesis and modification purposes. Besides being a traditional bioorthogonal chemical handle, a hydrazide group can serve as a readily accessible precursor of a thioester. This strategy significantly improves the efficiency and scope of native chemical ligation for protein chemical synthesis. Here we review the chemical transformations of peptide or protein hydrazides and total/semi/enzymatic protein synthesis methods involving peptide or protein hydrazides. Several examples of protein chemical synthesis using peptide hydrazides as key intermediates are described.
A Fungal Effector With Host Nuclear Localization and DNA-Binding Properties Is Required for Maize Anthracnose Development
Authors: Vargas Walter A. , Sanz-Martín José M. , Rech Gabriel E. , Armijos-Jaramillo Vinicio D. , Rivera Lina P. , Echeverria María Mercedes , Díaz-Mínguez José M. , Thon Michael R. , Sukno Serenella A.
Published: November 2015

Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host’s nucleus, as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein, identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems, and roots. Genetic, molecular, and biochemical studies confirmed that this effector targets the host’s nucleus and defines a novel class of double-stranded DNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process, with evidence for episodes of positive selection. We detected CgEP1 homologs in several species of a grass-infecting lineage of Colletotrichum spp., suggesting that its function may be conserved across a large number of anthracnose pathogens. Our results demonstrate that effectors targeted to the host nucleus may be key elements for disease development and aid in the understanding of the genetic basis of anthracnose development in maize plants.