bluuebunny/crossref_metadata_2025 huggingface dataset:
2.2.4 Oxidative Coupling of Nitromethane
Authors: Ballini R. , Petrini M.
Published: October 2015

Oxidation of tertiary amines under various conditions generates the corresponding iminium ions, which readily react with the methanenitronate anion, leading to β-nitro amines. Molecular oxygen, peroxides, and peracids are widely used for this purpose in transition-metal-catalyzed reactions. Conversely, organic oxidants such as (diacetoxyiodo)benzene, 2,3-dichloro-5,6-dicyanobenzo-1,4-quinone, and 2,2,6,6-tetramethylpiperidin-1-oxyl are effective without the need for any added catalyst. Visible-light photoinduced coupling reactions are emerging as a safe and environmentally friendly alternative to the above-mentioned procedures. Oxidation is mediated by organometallic complexes of iridium and ruthenium as well as organic sensitizers (rose Bengal and eosin Y) brought into their excited states by irradiation with visible light. Utilization of nitromethyl radicals, obtained by oxidation of nitromethane with ammonium cerium(IV) nitrate, in addition reactions with electron-rich alkenes is limited to the synthesis of nitrosugar derivatives.
2.4.2 Carbon Monoxide Insertion into Aziridines
Authors: Ibrahim H.
Published: October 2015

In this chapter, the most significant developments in the area of aziridine carbonylation are reviewed. The majority of procedures deal with the ring-expansion carbonylation of aziridines to β-lactams catalyzed by cobalt, rhodium, or palladium complexes. In the General Introduction, an effort is made to summarize the current mechanistic understanding of these diverse carbonylation systems. The regio- and stereoselectivity of these reactions is then discussed with regard to aziridine substitution and the type of catalytic system used. The chapter closes with short sections on the ring-expansion carbonylation of methyleneaziridines, α-lactams (aziridin-2-ones), and diaziridines.
2.6.2 Difluoro- and Fluoromethylation
Authors: Hu J. , Ni C.
Published: October 2015

This chapter summarizes the currently known synthetically useful difluoro- and fluoromethylation methods employing various fluorinated C-1 building blocks. The classical routes to difluoro- and fluoromethyl compounds are direct nucleophilic, electrophilic, and free-radical reactions, but more recent developments involving fluoroalkyl transition-metal species are also included.
2.6.3 Kharasch Reaction (Atom-Transfer Radical Addition Reactions)
Authors: Muñoz-Molina J. M. , Belderrain T. R.
Published: October 2015

Since the 1990s, highly active ruthenium and copper catalysts for atom-transfer radical addition (ATRA) reactions have been described and applications of these processes in organic synthesis have been developed. In this chapter are presented some examples of homologation reactions using carbon tetrahalide or haloform polyhalogenated compounds (halogen = Cl, Br) for atom-transfer radical addition for which isolated yields have been reported.
Background gas density and beam losses in NIO1 beam source
Authors: Sartori E. , Veltri P. , Cavenago M. , Serianni G.
Published: October 2015

NIO1 (Negative Ion Optimization 1) is a versatile ion source designed to study the physics of production and acceleration of H- beams up to 60 keV. In ion sources, the gas is steadily injected in the plasma source to sustain the discharge, while high vacuum is maintained by a dedicated pumping system located in the vessel. In this paper, the three dimensional gas flow in NIO1 is studied in the molecular flow regime by the Avocado code. The analysis of the gas density profile along the accelerator considers the influence of effective gas temperature in the source, of the gas temperature accommodation by collisions at walls, and of the gas particle mass. The calculated source and vessel pressures are compared with experimental measurements in NIO1 during steady gas injection.
Observations on variational and projector Monte Carlo methods
Authors: Umrigar C. J.
Published: October 2015

Variational Monte Carlo and various projector Monte Carlo (PMC) methods are presented in a unified manner. Similarities and differences between the methods and choices made in designing the methods are discussed. Both methods where the Monte Carlo walk is performed in a discrete space and methods where it is performed in a continuous space are considered. It is pointed out that the usual prescription for importance sampling may not be advantageous depending on the particular quantum Monte Carlo method used and the observables of interest, so alternate prescriptions are presented. The nature of the sign problem is discussed for various versions of PMC methods. A prescription for an exact PMC method in real space, i.e., a method that does not make a fixed-node or similar approximation and does not have a finite basis error, is presented. This method is likely to be practical for systems with a small number of electrons. Approximate PMC methods that are applicable to larger systems and go beyond the fixed-node approximation are also discussed.
Fractal contact spot and its application in the contact model of isotropic surfaces
Authors: Zhou An'an , Chen Tianning , Wang Xiaopeng , Xi Yanhui
Published: October 2015

All engineering surfaces are rough and composed of asperities with different scales. In conventional fractal contact models, asperities are used to build contact models between two rough surfaces. However, it is found that the deformation of asperities in the contact process is rather complex because only a small part of the asperities deform elastically or plastically. Moreover, the asperities used in conventional fractal contact models are not constructed exactly from contact mechanism and, of course, they are not fractal or self-affine. So, these fractal contact models seem like statistical models using fractal parameters rather than pure-fractal contact models. In the present paper, instead of asperities, fractal contact spots are utilized to describe the contact process of isotropic rough surfaces. The differences between fractal contact spots and asperities are analyzed to prove that fractal contact spots are more suitable to reveal the nature of contact process. Numerical method is used to simulate the contact process and study the characteristics of fractal contact spots, and the load-separation relationship of fractal contact spots is obtained using a fractal method. Then, a pure-fractal contact model is proposed and extended to calculate the contact stiffness of rough surfaces. To verify the contact model proposed, an experiment of stiffness identification of isotropic metal surfaces is carried out. The identified stiffness is in good agreement with that calculated by the contact model proposed, which indicates that the pure-fractal contact model applying the fractal contact spots is more suitable to reveal the contact mechanism of isotropic surfaces.
Photodissociation of the carbon monoxide dication in the 3Σ− manifold: Quantum control simulation towards the C2+ + O channel
Authors: Vranckx S. , Loreau J. , Vaeck N. , Meier C. , Desouter-Lecomte M.
Published: October 2015

The photodissociation and laser assisted dissociation of the carbon monoxide dication X3Π CO2+ into the 3Σ− states are investigated. Ab initio electronic structure calculations of the adiabatic potential energy curves, radial nonadiabatic couplings, and dipole moments for the X 3Π state are performed for 13 excited 3Σ− states of CO2+. The photodissociation cross section, calculated by time-dependent methods, shows that the C+ + O+ channels dominate the process in the studied energy range. The carbon monoxide dication CO2+ is an interesting candidate for control because it can be produced in a single, long lived, v = 0 vibrational state due to the instability of all the other excited vibrational states of the ground 3Π electronic state. In a spectral range of about 25 eV, perpendicular transition dipoles couple this 3Π state to a manifold of 3Σ− excited states leading to numerous C+ + O+ channels and a single C2+ + O channel. This unique channel is used as target for control calculations using local control theory. We illustrate the efficiency of this method in order to find a tailored electric field driving the photodissociation in a manifold of strongly interacting electronic states. The selected local pulses are then concatenated in a sequence inspired by the “laser distillation” strategy. Finally, the local pulse is compared with optimal control theory.
“Riemann equations” in bidifferential calculus
Authors: Chvartatskyi O. , Müller-Hoissen F. , Stoilov N.
Published: October 2015

We consider equations that formally resemble a matrix Riemann (or Hopf) equation in the framework of bidifferential calculus. With different choices of a first-order bidifferential calculus, we obtain a variety of equations, including a semi-discrete and a fully discrete version of the matrix Riemann equation. A corresponding universal solution-generating method then either yields a (continuous or discrete) Cole-Hopf transformation, or leaves us with the problem of solving Riemann equations (hence an application of the hodograph method). If the bidifferential calculus extends to second order, solutions of a system of “Riemann equations” are also solutions of an equation that arises, on the universal level of bidifferential calculus, as an integrability condition. Depending on the choice of bidifferential calculus, the latter can represent a number of prominent integrable equations, like self-dual Yang-Mills, as well as matrix versions of the two-dimensional Toda lattice, Hirota’s bilinear difference equation, (2+1)-dimensional Nonlinear Schrödinger (NLS), Kadomtsev-Petviashvili (KP) equation, and Davey-Stewartson equations. For all of them, a recent (non-isospectral) binary Darboux transformation result in bidifferential calculus applies, which can be specialized to generate solutions of the associated “Riemann equations.” For the latter, we clarify the relation between these specialized binary Darboux transformations and the aforementioned solution-generating method. From (arbitrary size) matrix versions of the “Riemann equations” associated with an integrable equation, possessing a bidifferential calculus formulation, multi-soliton-type solutions of the latter can be generated. This includes “breaking” multi-soliton-type solutions of the self-dual Yang-Mills and the (2+1)-dimensional NLS equation, which are parametrized by solutions of Riemann equations.
Trapping and desorption of complex organic molecules in water at 20 K
Authors: Burke Daren J. , Puletti Fabrizio , Woods Paul M. , Viti Serena , Slater Ben , Brown Wendy A.
Published: October 2015

The formation, chemical, and thermal processing of complex organic molecules (COMs) is currently a topic of much interest in interstellar chemistry. The isomers glycolaldehyde, methyl formate, and acetic acid are particularly important because of their role as pre-biotic species. It is becoming increasingly clear that many COMs are formed within interstellar ices which are dominated by water. Hence, the interaction of these species with water ice is crucially important in dictating their behaviour. Here, we present the first detailed comparative study of the adsorption and thermal processing of glycolaldehyde, methyl formate, and acetic acid adsorbed on and in water ices at astrophysically relevant temperatures (20 K). We show that the functional group of the isomer dictates the strength of interaction with water ice, and hence the resulting desorption and trapping behaviour. Furthermore, the strength of this interaction directly affects the crystallization of water, which in turn affects the desorption behaviour. Our detailed coverage and composition dependent data allow us to categorize the desorption behaviour of the three isomers on the basis of the strength of intermolecular and intramolecular interactions, as well as the natural sublimation temperature of the molecule. This categorization is extended to other C, H, and O containing molecules in order to predict and describe the desorption behaviour of COMs from interstellar ices.
Contactless derivation of inner fields in gate-oxide layers: SiO2 on SiC
Authors: Givon Alon , Piao Hong , McMahon James , Zorn Gilad , Cohen Hagai
Published: October 2015

Probing depth electrostatic potential profiles at sub-nm resolution is a major characterization challenge. An answer is frequently proposed by chemically resolved electrical measurements (CREM); yet, CREM is limited in extracting the profile details within compositionally uniform domains. Here, we show that this principal limitation can be overcome and the CREM resolution be improved significantly. Applied to nanometric SiO2 layers on SiC, hidden impurity concentration profiles are revealed and the inner fields, before and during dielectric collapse, are quantified. With this leap improvement in resolution and sensitivity, our advanced CREM analysis promises diverse applications in device contact-free electrical studies.
Acceptor-oxygen vacancy defect dipoles and fully coordinated defect centers in a ferroelectric perovskite lattice: Electron paramagnetic resonance analysis of Mn2+ in single crystal BaTiO3
Authors: Maier R. A. , Pomorski T. A. , Lenahan P. M. , Randall C. A.
Published: October 2015

Defect dipoles are significant point defects in perovskite oxides as a result of their impact on oxygen vacancy dynamics. Electron paramagnetic resonance (EPR) was used to investigate the local defect structure of single crystal BaTiO3 doped with manganese. These results, along with a re-analysis of literature data, do not support the conclusion that transition metal-oxygen vacancy nearest neighbor defect dipoles (MnTi″−VO••)× in ferroelectric BaTiO3 are majority defect centers as previously reported. Local symmetry analysis of the zero-field splitting term of the spin Hamiltonian supports the assignment of fully coordinated defect centers as opposed to defect dipoles for resonance signals at geff ∼ 2. A newly discovered defect center with g⊥ ∼ 6 is observed in the manganese doped system, and it is argued that this defect center belongs to an associated defect complex or defect dipole. This newly reported strong axial defect center, however, is present in small, minor concentrations compared to the well-known Mn2+ center with zero-field splitting of D ∼ 645 MHz. In regard to relative concentration, it is concluded that the dominant point defect related to the Mn2+ ion doped in BaTiO3 corresponds to B-site substitution with six nearest neighbor anions in octahedral coordination.
Expansion Hamiltonian model for a diatomic molecule adsorbed on a surface: Vibrational states of the CO/Cu(100) system including surface vibrations
Authors: Meng Qingyong , Meyer Hans-Dieter
Published: October 2015

Molecular-surface studies are often done by assuming a corrugated, static (i.e., rigid) surface. To be able to investigate the effects that vibrations of surface atoms may have on spectra and cross sections, an expansion Hamiltonian model is proposed on the basis of the recently reported [R. Marquardt et al., J. Chem. Phys. 132, 074108 (2010)] SAP potential energy surface (PES), which was built for the CO/Cu(100) system with a rigid surface. In contrast to other molecule-surface coupling models, such as the modified surface oscillator model, the coupling between the adsorbed molecule and the surface atoms is already included in the present expansion SAP-PES model, in which a Taylor expansion around the equilibrium positions of the surface atoms is performed. To test the quality of the Taylor expansion, a direct model, that is avoiding the expansion, is also studied. The latter, however, requests that there is only one movable surface atom included. On the basis of the present expansion and direct models, the effects of a moving top copper atom (the one to which CO is bound) on the energy levels of a bound CO/Cu(100) system are studied. For this purpose, the multiconfiguration time-dependent Hartree calculations are carried out to obtain the vibrational fundamentals and overtones of the CO/Cu(100) system including a movable top copper atom. In order to interpret the results, a simple model consisting of two coupled harmonic oscillators is introduced. From these calculations, the vibrational levels of the CO/Cu(100) system as function of the frequency of the top copper atom are discussed.
Onset of plane layer magnetoconvection at low Ekman number
Authors: Aujogue Kélig , Pothérat Alban , Sreenivasan Binod
Published: October 2015

We study the onset of magnetoconvection between two infinite horizontal planes subject to a vertical magnetic field aligned with background rotation. In order to gain insight into the convection taking place in the Earth’s tangent cylinder, we target regimes of asymptotically strong rotation. The critical Rayleigh number Rac and critical wavenumber ac are computed numerically by solving the linear stability problem in a systematic way, with either stress-free or no-slip kinematic boundary conditions. A parametric study is conducted, varying the Ekman number E (ratio of viscous to Coriolis forces) and the Elsasser number Λ (ratio of the Lorentz force to the Coriolis force). E is varied from 10−9 to 10−2 and Λ from 10−3 to 1. For a wide range of thermal and magnetic Prandtl numbers, our results verify and confirm previous experimental and theoretical results showing the existence of two distinct unstable modes at low values of E–one being controlled by the magnetic field, the other being controlled by viscosity (often called the viscous mode). It is shown that oscillatory onset does not occur in the range of parameters we are interested in. Asymptotic scalings for the onset of these modes are numerically confirmed and their domain of validity is precisely quantified. We show that with no-slip boundary conditions, the asymptotic behavior is reached for E < 10−6 and establish a map in the (E, Λ) plane. We distinguish regions where convection sets in either through the magnetic mode or through the viscous mode. Our analysis gives the regime in which the transition between magnetic and viscous modes may be observed. We also show that within the asymptotic regime, the role played by the kinematic boundary conditions is minimal.
Enhancement of phonon backscattering due to confinement of ballistic phonon pathways in silicon as studied with a microfabricated phonon spectrometer
Authors: Otelaja O. O. , Robinson R. D.
Published: October 2015

In this work, the mechanism for enhanced phonon backscattering in silicon is investigated. An understanding of phonon propagation through substrates has implications for engineering heat flow at the nanoscale, for understanding sources of decoherence in quantum systems, and for realizing efficient phonon-mediated particle detectors. In these systems, phonons that backscatter from the bottom of substrates, within the crystal or from interfaces, often contribute to the overall detector signal. We utilize a microscale phonon spectrometer, comprising superconducting tunnel junction emitters and detectors, to specifically probe phonon backscattering in silicon substrates (∼500 μm thick). By etching phonon “enhancers” or deep trenches (∼90 μm) around the detectors, we show that the backscattered signal level increases by a factor of ∼2 for two enhancers versus one enhancer. Using a geometric analysis of the phonon pathways, we show that the mechanism of the backscattered phonon enhancement is due to confinement of the ballistic phonon pathways and increased scattering off the enhancer walls. Our result is applicable to the geometric design and patterning of substrates that are employed in phonon-mediated detection devices.
Unique effects of thermal and pressure histories on glass hardness: Structural and topological origin
Authors: Smedskjaer Morten M. , Bauchy Mathieu , Mauro John C. , Rzoska Sylwester J. , Bockowski Michal
Published: October 2015

The properties of glass are determined not only by temperature, pressure, and composition, but also by their complete thermal and pressure histories. Here, we show that glasses of identical composition produced through thermal annealing and through quenching from elevated pressure can result in samples with identical density and mean interatomic distances, yet different bond angle distributions, medium-range structures, and, thus, macroscopic properties. We demonstrate that hardness is higher when the density increase is obtained through thermal annealing rather than through pressure-quenching. Molecular dynamics simulations reveal that this arises because pressure-quenching has a larger effect on medium-range order, while annealing has a larger effect on short-range structures (sharper bond angle distribution), which ultimately determine hardness according to bond constraint theory. Our work could open a new avenue towards industrially useful glasses that are identical in terms of composition and density, but with differences in thermodynamic, mechanical, and rheological properties due to unique structural characteristics.
Tracing the plasma interactions for pulsed reactive crossed-beam laser ablation
Authors: Chen Jikun , Stender Dieter , Pichler Markus , Döbeli Max , Pergolesi Daniele , Schneider Christof W. , Wokaun Alexander , Lippert Thomas
Published: October 2015

Pulsed reactive crossed-beam laser ablation is an effective technique to govern the chemical activity of plasma species and background molecules during pulsed laser deposition. Instead of using a constant background pressure, a gas pulse with a reactive gas, synchronized with the laser beam, is injected into vacuum or a low background pressure near the ablated area of the target. It intercepts the initially generated plasma plume, thereby enhancing the physicochemical interactions between the gaseous environment and the plasma species. For this study, kinetic energy resolved mass-spectrometry and time-resolved plasma imaging were used to study the physicochemical processes occurring during the reactive crossed beam laser ablation of a partially 18O substituted La0.6Sr0.4MnO3 target using oxygen as gas pulse. The characteristics of the ablated plasma are compared with those observed during pulsed laser deposition in different oxygen background pressures.
Reduction of the resistivity of Ag/p-GaN contact by progressive breakdown of the interfacial contamination layer
Authors: Wang Li , Wu Feifei , Liu Shitao , Yang Qi , Zhao Yong , Han Daofu , Quan Zhijue , Jiang Fengyi
Published: October 2015

Ag contact was prepared on p-GaN that had been previously activated by annealing and then removing an Ag/Ni contact. The non-annealed Ag contact showed higher resistivity than the annealed Ag/Ni contact. But, we found that the resistivity of the Ag contact decreases gradually under an electrical stress. Through secondary ion mass spectroscopy analysis, we excluded the effect of enhancement of the holes concentration by the electrical stress and attributed the decrease of resistivity to the progressive breakdown of the contamination layer at the Ag/GaN interface. Our findings provide a way to obtain low-resistivity non-annealed Ag contact to p-GaN.
Oxidation of ultrathin GaSe
Authors: Beechem Thomas E. , Kowalski Brian M. , Brumbach Michael T. , McDonald Anthony E. , Spataru Catalin D. , Howell Stephen W. , Ohta Taisuke , Pask Jesse A. , Kalugin Nikolai G.
Published: October 2015

Oxidation of exfoliated gallium selenide (GaSe) is investigated through Raman, photoluminescence, Auger, and X-ray photoelectron spectroscopies. Photoluminescence and Raman intensity reductions associated with spectral features of GaSe are shown to coincide with the emergence of signatures emanating from the by-products of the oxidation reaction, namely, Ga2Se3 and amorphous Se. Photoinduced oxidation is initiated over a portion of a flake highlighting the potential for laser based patterning of two-dimensional heterostructures via selective oxidation.
Injection barrier induced deviations in space charge limited conduction in doped poly(3-methylthiophene) based devices
Authors: Khan Motiur Rahman , Varade Vaibhav , Koteswara Rao K. S. R. , Menon R.
Published: October 2015

The carrier density dependent current–voltage (J−V) characteristics of electrochemically prepared poly(3-methylthiophene) (P3MeT) have been investigated in Pt/P3MeT/Al devices, as a function of temperature from 280 to 84 K. In these devices, the charge transport is found to be mainly governed by different transport regimes of space charge limited conduction (SCLC). In a lightly doped device, SCLC controlled by exponentially distributed traps (Vl+1 law, l > 1) is observed in the intermediate voltage range (0.5–2 V) at all temperatures. However, at higher bias (>2 V), the current deviates from the usual Vl+1 law where the slope is found to be less than 2 of the logJ–logV plot, which is attributed to the presence of the injection barrier. These deviations gradually disappear at higher doping level due to reduction in the injection barrier. Numerical simulations of the Vl+1 law by introducing the injection barrier show good agreement with experimental data. The results show that carrier density can tune the charge transport mechanism in Pt/P3MeT/Al devices to understand the non-Ohmic behavior. The plausible reasons for the origin of injection barrier and the transitions in the transport mechanism with carrier density are discussed.
Documentation of the role of large-scale structures in the bursting process in turbulent boundary layers
Authors: Vinuesa R. , Hites M. H. , Wark C. E. , Nagib H. M.
Published: October 2015

The scaling of the bursting frequency with Reynolds number is investigated experimentally by means of hot-wire measurements in turbulent boundary layers over the range 1580 < Reθ < 23 700. Bursting events are detected by means of the u-level technique, and the effect of filtering and the choice of the threshold are also assessed. We find that the inner scaling produces excellent collapse of the high-pass filtered data in the buffer and log regions, regardless of the cutoff frequency and the threshold. This is due to the fact that the high-pass filter attenuates the low frequency component of the streamwise velocity signal, which is associated with large-scale structures in the flow. On the other hand, the bursting frequency scales with outer variables when the time-series is low-pass filtered with very low cutoff frequencies, highlighting the connection between bursting phenomena and the outer flow.
Antineutrino analysis for continuous monitoring of nuclear reactors: Sensitivity study
Authors: Stewart Christopher , Erickson Anna
Published: October 2015

This paper explores the various contributors to uncertainty on predictions of the antineutrino source term which is used for reactor antineutrino experiments and is proposed as a safeguard mechanism for future reactor installations. The errors introduced during simulation of the reactor burnup cycle from variation in nuclear reaction cross sections, operating power, and other factors are combined with those from experimental and predicted antineutrino yields, resulting from fissions, evaluated, and compared. The most significant contributor to uncertainty on the reactor antineutrino source term when the reactor was modeled in 3D fidelity with assembly-level heterogeneity was found to be the uncertainty on the antineutrino yields. Using the reactor simulation uncertainty data, the dedicated observation of a rigorously modeled small, fast reactor by a few-ton near-field detector was estimated to offer reduction of uncertainty on antineutrino yields in the 3.0–6.5 MeV range to a few percent for the primary power-producing fuel isotopes, even with zero prior knowledge of the yields.
Do micromagnets expose spin qubits to charge and Johnson noise?
Authors: Kha Allen , Joynt Robert , Culcer Dimitrie
Published: October 2015

An ideal quantum dot spin qubit architecture requires a local magnetic field for one-qubit rotations. Such an inhomogeneous magnetic field, which could be implemented via a micromagnet, couples the qubit subspace with background charge fluctuations causing dephasing of spin qubits. In addition, a micromagnet generates magnetic field evanescent-wave Johnson noise. We derive an effective Hamiltonian for the combined effect of a slanting magnetic field and charge noise on a single-spin qubit and estimate the free induction decay dephasing times T2∗ for Si and GaAs. The effect of the micromagnet on the Si qubits is comparable in size to that of spin-orbit coupling at an applied field of B = 1 T, whilst dephasing in GaAs is expected to be dominated by spin-orbit coupling. Tailoring the magnetic field gradient can efficiently reduce T2∗ in Si. In contrast, the Johnson noise generated by a micromagnet will only be important for highly coherent spin qubits.
Mid-infrared characterization of refractive indices and propagation losses in GaSb/AlXGa1−XAsSb waveguides
Authors: Roux S. , Barritault P. , Lartigue O. , Cerutti L. , Tournié E. , Gérard B. , Grisard A.
Published: October 2015

We report experimental results on M-lines characterization of GaSb refractive index as a function of doping level and lattice mismatch in the range of 2.15–7.35 μm with an accuracy of 10−3. We apply the same procedure to quaternary AlxGa1−xAsSb alloys lattice-matched to GaSb to study the refractive index evolution with aluminum fraction and with wavelength. We compare our measurements to theory, and we establish new parameter values for the dispersion law of GaSb. These parameters are confirmed by the excellent agreement between the calculated curves and experimental measurements performed on quaternary alloys. Using these values of optical indices, we design a GaSb/AlGaAsSb ridge waveguide and characterize the losses using the Fabry-Perot method at 2 μm. Very low losses are demonstrated in the range of 1 dB/cm and below in a single mode waveguide structure.
On the differences between adnominal and external possession in Ishkashimi
Authors: Karvovskaya Elena
Published: October 2015

This paper discusses two particles that mark possession in Ishkashimi: -noand -noy. These markers are not in free variation; -noycan only mark adnominal possession, while -nocan mark external possession. This will be argued for on the basis of distributional and interpretational differences between the two markers. Unlike the marker -noy, -nocan appear in the context of nominal ellipsis and possessive predicates. A -noy-marked possessor has to be adjacent to the possessed noun and precede it; a -no-marked possessor does not have these adjacency requirements. In the context of possessor doubling, -noyis only compatible with 3rd person. In the case of negation, when the existence of the possessed is denied, only the -no marker is licensed. The differences in the distribution of the two markers correlate with their morphological differences; unlike -no, -noyis morphologically complex and encodes the person of the possessor.
Whose social values? Evaluating Canada's ‘death of evidence’ controversy
Authors: Goldenberg Maya J.
Published: October 2015

With twentieth- and twenty-first-century philosophy of science's unfolding acceptance of the nature of scientific inquiry being value-laden, the persistent worry has been that there are no means for legitimate negotiation of the social or non-epistemic values that enter into science. The rejection of the value-free ideal in science has thereby been coupled with the spectres of indiscriminate relativism and bias in scientific inquiry. I challenge this view in the context of recently expressed concerns regarding Canada's death of evidence controversy. The worry, raised by Stathis Psillos, is that as constructivist accounts of science demoted the previously secure status of evidence for drawing justified conclusions in science, we were left with no rational delineation between the right and wrong values for science. The implication for the death of evidence controversy is that we may have no rational grounds for claiming that the Canadian Government is wrong to interfere with scientific enterprise. But he does offer another avenue for reaching the conclusion that the wrong social values are directing the current stifling of some sectors of Canadian science. Psillos draws from standpoint epistemologies to devise a salient defence of ‘valuing evidence’ as a universalizable social value. That is, government bodiesoughtto enable scientific research via adequate funding as well as political non-interference. In this paper, I counter that (i) non-epistemic valuescanbe rationally evaluated and that (ii) standpoint epistemology's universalizable standpoint provides an inadequate framework for negotiating social values in science. Regarding (i), I draw from the evidence-based medicine debate in philosophy of medicine and from feminist empiricist investigations into the science–values relationship in order to make the argument for empirically driven value arbitration. If social values can berationallychosen in the context of justification, then we can have grounds for charging the Canadian leadership with being ‘at war with science’. (ii) I further argue that my recommended empiricist methodology is preferable to Psillos's search for universalizable perspectives for negotiating social values in science because the latter method permits little more than the trivial conclusion that evidence is valuable to science.
Cell wall reconstruction and DNA damage repair play a key role in the improved salt tolerance effects of He-Ne laser irradiation in tall fescue seedlings
Authors: Gao Limei , Li Yongfeng , Han Rong
Published: October 2015

The improved salt tolerance effects of He–Ne laser were further studied through the estimation of ROS levels, cell viability, DNA damage phenomena, physicochemical properties, and monosaccharide compositions of cell wall polysaccharides in tall fescue seedlings. Salt stress produced deleterious effects on seedlings growth and development. ROS levels and genomic DNA damage were markedly increased compared with controls. Physicochemical activities and monosaccharide proportions of cell wall polysaccharide were also pronouncedly altered. He–Ne laser irradiation improved plant growth retardation via increasing cell viability and reverting physicochemical parameters. According to the results of Fourier transform infrared (FTIR) scanning spectra and DNA apopladder analysis, He–Ne laser was showed to efficiently ameliorate cell wall polysaccharide damage and DNA fragmentation phenomena. The treatment with DNA synthesis inhibitor further demonstrated that DNA damage repair was correlated with the improvement effects of the laser. Therefore, our data illustrated that He–Ne laser irradiation resulted in cell wall reconstruction and genomic DNA injury repair in vivo in salt-stressed seedlings, then enhanced salt tolerance probably via interactions between plant cell wall and related resistance gene expression pattern.
Coordinated niche-associated signals promote germline homeostasis in the Drosophila ovary
Authors: Liu Zhong , Zhong Guohua , Chai Phing Chian , Luo Lichao , Liu Sen , Yang Ying , Baeg Gyeong-Hun , Cai Yu
Published: October 2015

Stem cell niches provide localized signaling molecules to promote stem cell fate and to suppress differentiation. The Drosophila melanogaster ovarian niche is established by several types of stromal cells, including terminal filament cells, cap cells, and escort cells (ECs). Here, we show that, in addition to its well-known function as a niche factor expressed in cap cells, the Drosophila transforming growth factor β molecule Decapentaplegic (Dpp) is expressed at a low level in ECs to maintain a pool of partially differentiated germline cells that may dedifferentiate to replenish germline stem cells upon their depletion under normal and stress conditions. Our study further reveals that the Dpp level in ECs is modulated by Hedgehog (Hh) ligands, which originate from both cap cells and ECs. We also demonstrate that Hh signaling exerts its function by suppressing Janus kinase/signal transducer activity, which promotes Dpp expression in ECs. Collectively, our data suggest a complex interplay of niche-associated signals that controls the development of a stem cell lineage.
ARF6–JIP3/4 regulate endosomal tubules for MT1-MMP exocytosis in cancer invasion
Authors: Marchesin Valentina , Castro-Castro Antonio , Lodillinsky Catalina , Castagnino Alessia , Cyrta Joanna , Bonsang-Kitzis Hélène , Fuhrmann Laetitia , Irondelle Marie , Infante Elvira , Montagnac Guillaume , Reyal Fabien , Vincent-Salomon Anne , Chavrier Philippe
Published: October 2015

Invasion of cancer cells into collagen-rich extracellular matrix requires membrane-tethered membrane type 1–matrix metalloproteinase (MT1-MMP) as the key protease for collagen breakdown. Understanding how MT1-MMP is delivered to the surface of tumor cells is essential for cancer cell biology. In this study, we identify ARF6 together with c-Jun NH2-terminal kinase–interacting protein 3 and 4 (JIP3 and JIP4) effectors as critical regulators of this process. Silencing ARF6 or JIP3/JIP4 in breast tumor cells results in MT1-MMP endosome mispositioning and reduces MT1-MMP exocytosis and tumor cell invasion. JIPs are recruited by Wiskott-Aldrich syndrome protein and scar homologue (WASH) on MT1-MMP endosomes on which they recruit dynein–dynactin and kinesin-1. The interaction of plasma membrane ARF6 with endosomal JIPs coordinates dynactin–dynein and kinesin-1 activity in a tug-of-war mechanism, leading to MT1-MMP endosome tubulation and exocytosis. In addition, we find that ARF6, MT1-MMP, and kinesin-1 are up-regulated in high-grade triple-negative breast cancers. These data identify a critical ARF6–JIP–MT1-MMP–dynein–dynactin–kinesin-1 axis promoting an invasive phenotype of breast cancer cells.
MT1-MMP: Endosomal delivery drives breast cancer metastasis
Authors: Linder Stefan
Published: October 2015

The membrane-tethered membrane type 1–matrix metalloproteinase (MT1-MMP) mediates proteolysis-based invasive tumor growth. In this issue, Marchesin et al. (2015. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201506002) describe a tug-of-war mechanism regulating dynein and kinesin motors to drive endosome tubulation and MT1-MMP delivery to the surface of cancer cells, identifying a crucial regulatory axis for tumor metastasis.
Physiological ramifications for loggerhead turtles captured in pelagic longlines
Authors: Williard Amanda , Parga Mariluz , Sagarminaga Ricardo , Swimmer Yonat
Published: October 2015

Bycatch of endangered loggerhead turtles in longline fisheries results in high rates of post-release mortality that may negatively impact populations. The factors contributing to post-release mortality have not been well studied, but traumatic injuries and physiological disturbances experienced as a result of capture are thought to play a role. The goal of our study was to gauge the physiological status of loggerhead turtles immediately upon removal from longline gear in order to refine our understanding of the impacts of capture and the potential for post-release mortality. We analysed blood samples collected from longline- and hand-captured loggerhead turtles, and discovered that capture in longline gear results in blood loss, induction of the systemic stress response, and a moderate increase in lactate. The method by which turtles are landed and released, particularly if released with the hook or line still attached, may exacerbate stress and lead to chronic injuries, sublethal effects or delayed mortality. Our study is the first, to the best of our knowledge, to document the physiological impacts of capture in longline gear, and our findings underscore the importance of best practices gear removal to promote post-release survival in longline-captured turtles.
Limits in the evolution of biological form: a theoretical morphologic perspective
Authors: McGhee George R.
Published: October 2015

Limits in the evolution of biological form can be empirically demonstrated by using theoretical morphospace analyses, and actual analytic examples are given for univalved ammonoid shell form, bivalved brachiopod shell form and helical bryozoan colony form. Limits in the evolution of form in these animal groups can be shown to be due to functional and developmental constraints on possible evolutionary trajectories in morphospace. Future evolutionary-limit research is needed to analyse the possible existence of temporal constraint in the evolution of biological form on Earth, and in the search for the possible existence of functional alien life forms on Titan and Triton that are developmentally impossible for Earth life.
What does convergent evolution mean? The interpretation of convergence and its implications in the search for limits to evolution
Authors: Stayton C. Tristan
Published: October 2015

Convergent evolution is central to the study of life's evolutionary history. Researchers have documented the ubiquity of convergence and have used this ubiquity to make inferences about the nature of limits on evolution. However, these inferences are compromised by unrecognized inconsistencies in the definitions, measures, significance tests and inferred causes of convergent evolution. I review these inconsistencies and provide recommendations for standardizing studies of convergence. A fundamental dichotomy exists between definitions that describe convergence as a pattern and those that describe it as a pattern caused by a particular process. When this distinction is not acknowledged it becomes easy to assume that a pattern of convergence indicates that a particular process has been active, leading researchers away from alternative explanations. Convergence is not necessarily caused by limits to evolution, either adaptation or constraint; even substantial amounts of convergent evolution can be generated by a purely stochastic process. In the absence of null models, long lists of examples of convergent events do not necessarily indicate that convergence or any evolutionary process is ubiquitous throughout the history of life. Pattern-based definitions of convergence, coupled with quantitative measures and null models, must be applied before drawing inferences regarding large-scale limits to evolution.
Methods for biological data integration: perspectives and challenges
Authors: Gligorijević Vladimir , Pržulj Nataša
Published: October 2015

Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development.
Choreographed swimming of copepod nauplii
Authors: Lenz Petra H. , Takagi Daisuke , Hartline Daniel K.
Published: October 2015

Small metazoan paddlers, such as crustacean larvae (nauplii), are abundant, ecologically important and active swimmers, which depend on exploiting viscous forces for locomotion. The physics of micropaddling at low Reynolds number was investigated using a model of swimming based on slender-body theory for Stokes flow. Locomotion of nauplii of the copepod
Bestiolina similis
was quantified from high-speed video images to obtain precise measurements of appendage movements and the resulting displacement of the body. The kinematic and morphological data served as inputs to the model, which predicted the displacement in good agreement with observations. The results of interest did not depend sensitively on the parameters within the error of measurement. Model tests revealed that the commonly attributed mechanism of ‘feathering’ appendages during return strokes accounts for only part of the displacement. As important for effective paddling at low Reynolds number is the ability to generate a metachronal sequence of power strokes in combination with synchronous return strokes of appendages. The effect of feathering together with a synchronous return stroke is greater than the sum of each factor individually. The model serves as a foundation for future exploration of micropaddlers swimming at intermediate Reynolds number where both viscous and inertial forces are important.
Angled multimode interferometer for bidirectional wavelength division (de)multiplexing
Authors: Hu Y. , Thomson D. J. , Khokhar A. Z. , Stanković S. , Mitchell C. J. , Gardes F. Y. , Penades J. Soler , Mashanovich G. Z. , Reed G. T.
Published: October 2015

We have demonstrated a bidirectional wavelength division (de)multiplexer (WDM) on the silicon-on-insulator platform using two 4-channel angled multimode interferometers (AMMIs) sharing the same multimode interference waveguide. An excellent match of the peak transmission wavelength of each channel between the two AMMIs was achieved. The input and output access waveguides were arranged in a configuration such that the propagation of light of one AMMI in the multimode interference waveguide suffered minimal perturbation by the input and output waveguides of the other AMMI. This type of device is ideal for the WDM system for datacom or telecom applications, e.g. an integrated optical transceiver, where the transmission wavelengths are required to match with the receiving wavelengths. The device also benefits from simple fabrication (as only a single lithography and etching step is required), improved convenience for the transceiver layout design, a reduction in tuning power and circuitry and efficient use of layout space. A low insertion loss of 3–4 dB, and low crosstalk of −15 to −20 dB, was achieved.
Anchored analysis of variance Petrov–Galerkin projection schemes for linear stochastic structural dynamics
Authors: Gao Lin , Audouze Christophe , Nair Prasanth B.
Published: October 2015

In this paper, we propose anchored functional analysis of variance Petrov–Galerkin (AAPG) projection schemes, originally developed in the context of parabolic stochastic partial differential equations (Audouze C, Nair PB. 2014
Comput. Methods Appl. Mech. Eng.
276, 362–395. (
doi:10.1016/j.cma.2014.02.023
)) for solving a class of problems in linear stochastic structural dynamics. We consider the semi-discrete form of the governing equations in the time-domain and the proposed formulation involves approximating the dynamic response using a Hoeffding functional analysis of variance decomposition. Subsequently, we design a set of test functions for a stochastic Petrov–Galerkin projection scheme that enables the original high-dimensional problem to be decomposed into a sequence of decoupled low-dimensional subproblems that can be solved independently of each other. Numerical results are presented to demonstrate the efficiency and accuracy of AAPG projection schemes and comparisons are made to approximations obtained using Monte Carlo simulation, generalized polynomial chaos-based stochastic Galerkin projection schemes and the generalized spectral decomposition method. The results obtained suggest that the proposed approach holds significant potential for alleviating the curse of dimensionality encountered in tackling high-dimensional problems in stochastic structural dynamics with a large number of spatial and stochastic degrees of freedom.