bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatially resolved detection of complex ferromagnetic dynamics using optically detected nitrogen-vacancy spins
Authors: Wolfe C. S. , Manuilov S. A. , Purser C. M. , Teeling-Smith R. , Dubs C. , Hammel P. C. , Bhallamudi V. P.
Published: June 2016

We demonstrate optical detection of a broad spectrum of ferromagnetic excitations using nitrogen-vacancy (NV) centers in an ensemble of nanodiamonds. Our recently developed approach exploits a straightforward CW detection scheme using readily available diamond detectors, making it easily implementable. The NV center is a local detector, giving the technique spatial resolution, which here is defined by our laser spot, but in principle can be extended far into the nanoscale. Among the excitations, we observe the propagating dipolar and dipolar-exchange spinwaves, as well as dynamics associated with the multi-domain state of the ferromagnet at low fields. These results offer an approach, distinct from commonly used optically detected magnetic resonance techniques, for spatially resolved spectroscopic study of magnetization dynamics at the nanoscale.
A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution
Authors: Sumi Tomonari , Maruyama Yutaka , Mitsutake Ayori , Koga Kenichiro
Published: June 2016

In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.
Measurement of the B1g and B2g components of the elastoresistivity tensor for tetragonal materials via transverse resistivity configurations
Authors: Shapiro M. C. , Hristov A. T. , Palmstrom J. C. , Chu Jiun-Haw , Fisher I. R.
Published: June 2016

The elastoresistivity tensor mij,kl relates changes in resistivity to strains experienced by a material. As a fourth-rank tensor, it contains considerably more information about the material than the simpler (second-rank) resistivity tensor; in particular, for a tetragonal material, the B1g and B2g components of the elastoresistivity tensor (mxx,xx − mxx,yy and 2mxy,xy, respectively) can be related to its nematic susceptibility. Previous experimental probes of this quantity have focused exclusively on differential longitudinal elastoresistance measurements, which determine the induced resistivity anisotropy arising from anisotropic in-plane strain based on the difference of two longitudinal resistivity measurements. Here we describe a complementary technique based on transverse elastoresistance measurements. This new approach is advantageous because it directly determines the strain-induced resistivity anisotropy from a single transverse measurement. To demonstrate the efficacy of this new experimental protocol, we present transverse elastoresistance measurements of the 2mxy,xy elastoresistivity coefficient of BaFe2As2, a representative iron-pnictide that has previously been characterized via differential longitudinal elastoresistance measurements.
Low-temperature-compatible tunneling-current-assisted scanning microwave microscope utilizing a rigid coaxial resonator
Authors: Takahashi Hideyuki , Imai Yoshinori , Maeda Atsutaka
Published: June 2016

We present a design for a tunneling-current-assisted scanning near-field microwave microscope. For stable operation at cryogenic temperatures, making a small and rigid microwave probe is important. Our coaxial resonator probe has a length of approximately 30 mm and can fit inside the 2-in. bore of a superconducting magnet. The probe design includes an insulating joint, which separates DC and microwave signals without degrading the quality factor. By applying the SMM to the imaging of an electrically inhomogeneous superconductor, we obtain the spatial distribution of the microwave response with a spatial resolution of approximately 200 nm. Furthermore, we present an analysis of our SMM probe based on a simple lumped-element circuit model along with the near-field microwave measurements of silicon wafers having different conductivities.
Corresponding-states behavior of a dipolar model fluid with variable dispersion interactions and its relevance to the anomalies of hydrogen fluoride
Authors: Weiss Volker C. , Leroy Frédéric
Published: June 2016

More than two decades ago, the elusiveness of a liquid-vapor equilibrium and a corresponding critical point in simulations of the supposedly simple model of dipolar hard spheres came as a surprise to many liquid matter theorists. van Leeuwen and Smit [Phys. Rev. Lett. 71, 3991 (1993)] showed that a minimum of attractive dispersion interactions among the dipolar particles may be needed to observe regular fluid behavior. Here, we adopt their approach and use an only slightly modified model, in which the original point dipole is replaced by a dipole moment produced by charges that are separated in space, to study the influence of dispersion interactions of variable strength on the coexistence and interfacial properties of a polar fluid. The thermophysical properties are discussed in terms of Guggenheim’s corresponding-states approach. In this way, the coexistence curve, the critical compressibility factor, the surface tension, Guggenheim’s ratio, and modifications of Guldberg’s and Trouton’s rules (related to the vapor pressure and the enthalpy of vaporization) are analyzed. As the importance of dispersion is decreased, a crossover from simple-fluid behavior to that characteristic of strongly dipolar systems takes place; for some properties, this transition is monotonic, but for others it occurs non-monotonically. For strongly dipolar systems, the reduced surface tension is very low, whereas Guggenheim’s ratio and Guldberg’s ratio are found to be high. The critical compressibility factor is smaller, and the coexistence curve is wider and more skewed than for simple fluids. For very weak dispersion, liquid-vapor equilibrium is still observable, but the interfacial tension is extremely low and may, eventually, vanish marking the end of the existence of a liquid phase. We discuss the implications of our findings for real fluids, in particular, for hydrogen fluoride.
Relativistic dynamics, Green function and pseudodifferential operators
Authors: Cirilo-Lombardo Diego Julio
Published: June 2016

The central role played by pseudodifferential operators in relativistic dynamics is known very well. In this work, operators like the Schrodinger one (e.g., square root) are treated from the point of view of the non-local pseudodifferential Green functions. Starting from the explicit construction of the Green (semigroup) theoretical kernel, a theorem linking the integrability conditions and their dependence on the spacetime dimensions is given. Relativistic wave equations with arbitrary spin and the causality problem are discussed with the algebraic interpretation of the radical operator and their relation with coherent and squeezed states. Also we perform by means of pure theoretical procedures (based in physical concepts and symmetry) the relativistic position operator which satisfies the conditions of integrability: it is a non-local, Lorentz invariant and does not have the same problems as the “local”position operator proposed by Newton and Wigner. Physical examples, as zitterbewegung and rogue waves, are presented and deeply analyzed in this theoretical framework.
The continuous transition of Hamiltonian vector fields through manifolds of constant curvature
Authors: Diacu Florin , Ibrahim Slim , Śniatycki Jędrzej
Published: June 2016

We ask whether Hamiltonian vector fields defined on spaces of constant Gaussian curvature κ (spheres, for κ > 0, and hyperbolic spheres, for κ < 0) pass continuously through the value κ = 0 if the potential functions Uκ, κ ∈ ℝ, which define them satisfy the property limκ→0Uκ=U0, where U0 corresponds to the Euclidean case. We prove that the answer to this question is positive, both in the 2- and 3-dimensional cases, which are of physical interest, and then apply our conclusions to the gravitational N-body problem.
Destabilization of clouds of monodisperse and polydisperse particles falling in a quiescent and viscous fluid
Authors: Ho Thinh X. , Phan-Thien Nhan , Khoo Boo Cheong
Published: June 2016

Clouds of monodisperse and polydisperse particles settling under gravity in a quiescent fluid are analysed in the limit of zero Reynolds number using the Stokeslet model. The established numerical model is simple and generic, which can be applied to particles of multiple-size and/or density. However, only the size aspect is dealt with in the present work. Multiple-size particles slip relative to the ambient fluid at non-uniform velocities. In a swarm they may be expected to fall differently as compared to those of the same size. In this regard, the evolution of a polydisperse cloud is analyzed and compared with that of a monodisperse one. In addition, the destabilization of a cloud is characterized by the time at the onset of destabilization and the distance it travels. These quantities are found to be significantly smaller for a polydisperse cloud than for the monodisperse one, keeping the same initial number of particles, and they decrease with increasing standard deviation of particle radii. The mechanisms that govern these differences and the destabilization itself are discussed. Our model is validated against experimental data for multiple-size particles available in the literature; a good agreement is noted.
Variational formulations of guiding-center Vlasov-Maxwell theory
Authors: Brizard Alain J. , Tronci Cesare
Published: June 2016

The variational formulations of guiding-center Vlasov-Maxwell theory based on Lagrange, Euler, and Euler-Poincaré variational principles are presented. Each variational principle yields a different approach to deriving guiding-center polarization and magnetization effects into the guiding-center Maxwell equations. The conservation laws of energy, momentum, and angular momentum are also derived by Noether method, where the guiding-center stress tensor is now shown to be explicitly symmetric.
NMR longitudinal relaxation enhancement in metal halides by heteronuclear polarization exchange during magic-angle spinning
Authors: Shmyreva Anna A. , Safdari Majid , Furó István , Dvinskikh Sergey V.
Published: June 2016

Orders of magnitude decrease of 207Pb and 199Hg NMR longitudinal relaxation times T1 upon magic-angle-spinning (MAS) are observed and systematically investigated in solid lead and mercury halides MeX2 (Me = Pb, Hg and X = Cl, Br, I). In lead(ii) halides, the most dramatic decrease of T1 relative to that in a static sample is in PbI2, while it is smaller but still significant in PbBr2, and not detectable in PbCl2. The effect is magnetic-field dependent but independent of the spinning speed in the range 200–15 000 Hz. The observed relaxation enhancement is explained by laboratory-frame heteronuclear polarization exchange due to crossing between energy levels of spin-1/2 metal nuclei and adjacent quadrupolar-spin halogen nuclei. The enhancement effect is also present in lead-containing organometal halide perovskites. Our results demonstrate that in affected samples, it is the relaxation data recorded under non-spinning conditions that characterize the local properties at the metal sites. A practical advantage of fast relaxation at slow MAS is that spectral shapes with orientational chemical shift anisotropy information well retained can be acquired within a shorter experimental time.
The early crystal nucleation process in hard spheres shows synchronised ordering and densification
Authors: Berryman Joshua T. , Anwar Muhammad , Dorosz Sven , Schilling Tanja
Published: June 2016

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first “solid-like” particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales.
Mesoscale studies of ionic closed membranes with polyhedral geometries
Authors: Olvera de la Cruz Monica
Published: June 2016

Large crystalline molecular shells buckle spontaneously into icosahedra while multicomponent shells buckle into various polyhedra. Continuum elastic theory explains the buckling of closed shells with one elastic component into icosahedra. A generalized elastic model, on the other hand, describes the spontaneous buckling of inhomogeneous shells into regular and irregular polyhedra. By co-assembling water-insoluble anionic (−1) amphiphiles with cationic (3+) amphiphiles, we realized ionic vesicles. Results revealed that surface crystalline domains and the unusual shell shapes observed arise from the competition of ionic correlations with charge-regulation. We explain here the mechanism by which these ionic membranes generate a mechanically heterogeneous vesicle.
The physical mechanism on the threshold voltage temperature stability improvement for GaN HEMTs with pre-fluorination argon treatment
Authors: Wang Yun-Hsiang , Liang Yung C. , Samudra Ganesh S. , Huang Chih-Fang , Kuo Wei-Hung , Lo Guo-Qiang
Published: June 2016

In this paper, a normally-off AlGaN/GaN MIS-HEMT with improved threshold voltage (VTH) thermal stability is reported with investigations on its physical mechanism. The normally-off operation of the device is achieved from novel short argon plasma treatment (APT) prior to the fluorine plasma treatment (FPT) on Al2O3 gate dielectrics. For the MIS-HEMT with FPT only, its VTH drops from 4.2 V at room temperature to 0.5 V at 200 °C. Alternatively, for the device with APT-then-FPT process, its VTH can retain at 2.5 V at 200 °C due to the increased amount of deep-level traps that do not emit electrons at 200 °C. This thermally stable VTH makes this device suitable for high power applications. The depth profile of the F atoms in Al2O3, measured by the secondary ion mass spectroscopy, reveals a significant increase in the F concentration when APT is conducted prior to FPT. The X-ray photoelectron spectroscopy (XPS) analysis on the plasma-treated Al2O3 surfaces observes higher composition of Al-F bonds if APT was applied before FPT. The enhanced breaking of Al-O bonds due to Ar bombardment assisted in the increased incorporation of F radicals at the surface during the subsequent FPT process. The Schrödinger equation of Al2OxFy cells, with the same Al-F compositions as obtained from XPS, was solved by Gaussian 09 molecular simulations to extract electron state distribution as a function of energy. The simulation results show creation of the deeper trap states in the Al2O3 bandgap when APT is used before FPT. Finally, the trap distribution extracted from the simulations is verified by the gate-stress experimental characterization to confirm the physical mechanism described.
Tip-enhanced near-field optical microscope with side-on and ATR-mode sample excitation for super-resolution Raman imaging of surfaces
Authors: Heilman A. L. , Gordon M. J.
Published: June 2016

A tip-enhanced near-field optical microscope with side-on and attenuated total reflectance (ATR) excitation and collection is described and used to demonstrate sub-diffraction-limited (super-resolution) optical and chemical characterization of surfaces. ATR illumination is combined with an Au optical antenna tip to show that (i) the tip can quantitatively transduce the optical near-field (evanescent waves) above the surface by scattering photons into the far-field, (ii) the ATR geometry enables excitation and characterization of surface plasmon polaritons (SPPs), whose associated optical fields are shown to enhance Raman scattering from a thin layer of copper phthalocyanine (CuPc), and (iii) SPPs can be used to plasmonically excite the tip for super-resolution chemical imaging of patterned CuPc via tip-enhanced Raman spectroscopy (TERS). ATR-illumination TERS is also quantitatively compared with the more conventional side-on illumination scheme. In both cases, spatial resolution was better than 40 nm and tip on/tip off Raman enhancement factors were >6500. Furthermore, ATR illumination was shown to provide similar Raman signal levels at lower “effective” pump powers due to additional optical energy delivered by SPPs to the active region in the tip-surface gap.
Fluorescence-based remote irradiation sensor in liquid-filled hollow-core photonic crystal fiber
Authors: Zeltner R. , Bykov D. S. , Xie S. , Euser T. G. , Russell P. St.J.
Published: June 2016

We report an irradiation sensor based on a fluorescent “flying particle” that is optically trapped and propelled inside the core of a water-filled hollow-core photonic crystal fiber. When the moving particle passes through an irradiated region, its emitted fluorescence is captured by guided modes of the fiber core and so can be monitored using a filtered photodiode placed at the fiber end. The particle speed and position can be precisely monitored using in-fiber Doppler velocimetry, allowing the irradiation profile to be measured to a spatial resolution of ∼10 μm. The spectral response can be readily adjusted by appropriate choice of particle material. Using dye-doped polystyrene particles, we demonstrate detection of green (532 nm) and ultraviolet (340 nm) light.
Introduction to Focus Issue: Complex Dynamics in Networks, Multilayered Structures and Systems
Authors: Boccaletti Stefano , Criado Regino , Romance Miguel , Torres Joaquín J.
Published: June 2016

In the last years, network scientists have directed their interest to the multi-layer character of real-world systems, and explicitly considered the structural and dynamical organization of graphs made of diverse layers between its constituents. Most complex systems include multiple subsystems and layers of connectivity and, in many cases, the interdependent components of systems interact through many different channels. Such a new perspective is indeed found to be the adequate representation for a wealth of features exhibited by networked systems in the real world. The contributions presented in this Focus Issue cover, from different points of view, the many achievements and still open questions in the field of multi-layer networks, such as: new frameworks and structures to represent and analyze heterogeneous complex systems, different aspects related to synchronization and centrality of complex networks, interplay between layers, and applications to logistic, biological, social, and technological fields.
A simple approximation for the current-voltage characteristics of high-power, relativistic diodes
Authors: Ekdahl Carl
Published: June 2016

A simple approximation for the current-voltage characteristics of a relativistic electron diode is presented. The approximation is accurate from non-relativistic through relativistic electron energies. Although it is empirically developed, it has many of the fundamental properties of the exact diode solutions. The approximation is simple enough to be remembered and worked on almost any pocket calculator, so it has proven to be quite useful on the laboratory floor.
Optimal analysis of ultra broadband energy-time entanglement for high bit-rate dense wavelength division multiplexed quantum networks
Authors: Kaiser F. , Aktas D. , Fedrici B. , Lunghi T. , Labonté L. , Tanzilli S.
Published: June 2016

We demonstrate an experimental method for measuring energy-time entanglement over almost 80 nm spectral bandwidth in a single shot with a quantum bit error rate below 0.5%. Our scheme is extremely cost-effective and efficient in terms of resources as it employs only one source of entangled photons and one fixed unbalanced interferometer per phase-coded analysis basis. We show that the maximum analysis spectral bandwidth is obtained when the analysis interferometers are properly unbalanced, a strategy which can be straightforwardly applied to most of today's experiments based on energy-time and time-bin entanglement. Our scheme has therefore a great potential for boosting bit rates and reducing the resource overhead of future entanglement-based quantum key distribution systems.
Thermal energy and charge currents in multi-terminal nanorings
Authors: Kramer Tobias , Kreisbeck Christoph , Riha Christian , Chiatti Olivio , Buchholz Sven S. , Wieck Andreas D. , Reuter Dirk , Fischer Saskia F.
Published: June 2016

We study in experiment and theory thermal energy and charge transfer close to the quantum limit in a ballistic nanodevice, consisting of multiply connected one-dimensional electron waveguides. The fabricated device is based on an AlGaAs/GaAs heterostructure and is covered by a global top-gate to steer the thermal energy and charge transfer in the presence of a temperature gradient, which is established by a heating current. The estimate of the heat transfer by means of thermal noise measurements shows the device acting as a switch for charge and thermal energy transfer. The wave-packet simulations are based on the multi-terminal Landauer-Büttiker approach and confirm the experimental finding of a mode-dependent redistribution of the thermal energy current, if a scatterer breaks the device symmetry.
Biodiversity of parasite assemblages in the genus Petrogale and its relation to the phylogeny and biogeography of their hosts
Authors: Vermeulen Elke T. , Power Michelle L. , Nipperess David A. , Beveridge Ian , Eldridge Mark D. B.
Published: June 2016

Parasites form an integral part of overall biodiversity although they are often overlooked in conservation management, where emphasis is primarily directed towards the host. Parasites are often highly specialised to particular hosts, and thus may be just as threatened as the host they inhabit. For many of Australia’s wildlife species, little is known about their associated parasite communities. To begin to address this knowledge gap, we documented the parasite fauna described in the genetically diverse marsupial genus Petrogale, which contains seven species of conservation concern. The literature evaluation showed parasites of Petrogale to be highly diverse, with 17 species of protozoa, 8 species of cestodes, 102 species of nematodes and 30 species of ectoparasites identified in 16 of 17 Petrogale host species. A comparison of the parasite communities amongst Petrogale host species indicated a highly significant correlation between the parasite community similarity, and the phylogeny (P = 0.008) and biogeography (P = 0.0001) of their Petrogale hosts, suggesting high host specificity within their associated parasite assemblages. Five Petrogale species have established species recovery programs and their parasite communities should also be considered threatened, and management of parasite diversity required as part of these conservation programs.
On the (non)-existence of verb-stranding ellipsis in Chinese
Authors: Wu Hsiao-Hung Iris
Published: June 2016

This paper develops the empirical and theoretical basis for the necessity in admitting the operation of verb-stranding ellipsis (VVPE) in Chinese. I present new arguments showing that, though two analytic possibilities — null argument analysis and VVPE analysis — are in principle available in the grammar of Chinese, they can be differentiated in specific syntactic environments. In particular, I show that the existing null argument approaches would have difficulty in accounting for the following facts: disjunction of multi-constituent elements under negation, the difference of island effects in the presence of a linguistic antecedent, the verb identity requirement and the possibility of having part of the idiomatic expression as the missing gap. Therefore, it is argued that VVPE must remain a viable syntactic operation in Chinese when a null object analysis is unavailable.
Fragment answers in Mandarin Chinese
Authors: Wei Ting-Chi
Published: June 2016

The derivational differences of the fragment answers in Mandarin Chinese lie in whether a fragment moves or not. Under the movement and ellipsis analysis (Merchant 2004), fragment answer towh-question moves to SpecFocP, followed by TP ellipsis. In contrast, fragment answer to yes-no question or for correction is a base-generated structure, [procopula fragment]. The analysis is supported not only by the existence of the copular verb and the fragment answers to questions involving the passive constructions and preposition stranding but also by cross-linguistic evidence.
Para colmo, scalar operator and additive connector
Authors: Fuentes-Rodríguez Catalina
Published: June 2016

This study addresses the development undergone bypara colmo, a form which is in the process of becoming fixed as an argumentative operator and additive connector.Para colmohas undergone a process of subjectification (Traugott 1995a), which is crucial in the development of discourse markers, where the presence of the speaker is manifested in various ways to cover important areas of meaning in the interpretation of the discourse. It has polarized its meaning in the negative and has progressed to indicate scalar saturation, or a position at the highest level of the argumentative scale, with an evaluation of excess on the part of the speaker. The study has been carried out on the basis of both diachronic and synchronic corpora compiled by the Real Academia Española, and covers the period from 1200 to 2004.
Annotating as narrative performance in subtitle groups in China
Authors: Hsiao Chi-hua
Published: June 2016

This study examines how subtitlers in underground subtitle groups in China perform skills and display competence in applying the rules around which annotations are built. I argue that by annotating, the act of creating notes, representing information not linguistically coded in the original US TV programs, subtitlers engage in a performative act in concert. Annotations reveal not only subtitlers’ stances toward the contents being translated, but also their meta­thinking on these contents. The analysis shows that two contradictory forces provide the impetus for annotations. On the one hand, the desire for objectivity refers to subtitlers’ attempts to represent a professional and organized account of how Chinese subtitles are produced in the process of explicating knowledge. On the other hand, the desire for authenticity is implicit in the subtitlers’ narrative of what they actually experience when translating US TV programs.
Developments and future opportunities for the economic and wider socio-cultural valuation of ecosystem services.
Authors: Bullock C.
Published: June 2016

This paper explores the limits to the economic valuation of ecosystem services. It observes that economics has an important role in the design of policy tools that can stimulate the delivery of beneficial ecosystem services, but acknowledges that the relationship between human beings and the environment is more complex than one that can be explained by a reliance on utility-based values alone. This paper reviews the nature and role of socio-cultural values and efforts by both social and natural scientists to recognize the range and diversity of values that people attach to the environment. It explores the contribution of alternative valuation approaches, specifically deliberative methods and indicates where we might choose to look for more integrated approaches while not losing sight of our dependence on fundamental ecosystem services.
Structural dependence, vertical integration and regional economic cooperation in Africa: a study of Southern African Development Community
Authors: Aniche Ernest Toochi , Ukaegbu Victor Emeka
Published: June 2016

In spite of many years of regional economic integration, African regional blocs have been seriously hampered by historical, colonial, neo-colonial and vertical linkages of their economies to Western economies in terms of trade and investments. This study is essentially a qualitative research and thus relies heavily on secondary sources of data such as trade and investment indicators. The extant literature comparing the extent and depth of these horizontal and vertical integrations among member states of the Southern African Development Community (SADC) is, however, scanty. The thrust of this paper is to examine the varying degrees of vertical integration of the economies of member states to Western economies, and perhaps, within themselves. The study, therefore, argues that the dependence of other SADC member states’ economies on South African economy has resulted in the seemingly high level of integration of SADC member states.
Cancellation of drift kinetic effects between thermal and energetic particles on the resistive wall mode stabilization
Authors: Guo S.C. , Liu Y.Q. , Xu X.Y. , Wang Z.R.
Published: June 2016

Drift kinetic stabilization of the resistive wall mode (RWM) is computationally investigated using MHD-kinetic hybrid code MARS-K following the non-perturbative approach (Liu et al 2008 Phys. Plasmas
15 112503), for both reversed field pinch (RFP) and tokamak plasmas. Toroidal precessional drift resonance effects from trapped energetic ions (EIs) and various kinetic resonances between the mode and the guiding center drift motions of thermal particles are included into the self-consistent toroidal computations. The results show cancellation effects of the drift kinetic damping on the RWM between the thermal particles and EIs contributions, in both RFP and tokamak plasmas, even though each species alone can provide damping and stabilize RWM instability by respective kinetic resonances. The degree of cancellation generally depends on the EIs equilibrium distribution, the particle birth energy, as well as the toroidal flow speed of the plasma.
MIA: non-targeted mass isotopolome analysis
Authors: Weindl Daniel , Wegner Andre , Hiller Karsten
Published: June 2016

Summary: MIA detects and visualizes isotopic enrichment in gas chromatography electron ionization mass spectrometry (GC–EI-MS) datasets in a non-targeted manner. It provides an easy-to-use graphical user interface that allows for visual mass isotopomer distribution analysis across multiple datasets. MIA helps to reveal changes in metabolic fluxes, visualizes metabolic proximity of isotopically enriched compounds and shows the fate of the applied stable isotope labeled tracer.

Availability and Implementation: Linux and Windows binaries, documentation, and sample data are freely available for download at http://massisotopolomeanalyzer.lu. MIA is a stand-alone application implemented in C ++  and based on Qt5, NTFD and the MetaboliteDetector framework.

Contact:  karsten.hiller@uni.lu
TaggerOne: joint named entity recognition and normalization with semi-Markov Models
Authors: Leaman Robert , Lu Zhiyong
Published: June 2016

Motivation: Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization.

Methods: We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput.

Results: We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance.

Availability and Implementation: The TaggerOne source code and an online demonstration are available at: http://www.ncbi.nlm.nih.gov/bionlp/taggerone

Contact:  zhiyong.lu@nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online.
The organization and content of informatics doctoral dissertations
Authors: Shortliffe Edward H
Published: June 2016

This article offers suggested guidelines for graduate students who are embarking on informatics doctoral studies and anticipating the dissertation research and its documentation. Much of the guidance is pertinent for writing dissertations in other disciplines as well. The messages are largely directed at doctoral students, but some elements are also pertinent for master’s students. All are relevant for faculty research advisors. The value of the dissertation is often underestimated. Too often it is seen as a hurdle to be overcome rather than an opportunity to gain insight into one’s own research and to learn how to communicate effectively about it. Ideas that have been ill-formed often do not gel effectively until one tries to write about them. The main lesson is that the preparation of a carefully crafted, rigorous, logically evidence-based, and influential dissertation can be remarkably rewarding, both personally and professionally.
Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference?
Authors: Kaatz Anna , Lee You-Geon , Potvien Aaron , Magua Wairimu , Filut Amarette , Bhattacharya Anupama , Leatherberry Renee , Zhu Xiaojin , Carnes Molly
Published: June 2016

Purpose

Prior text analysis of R01 critiques suggested that female applicants may be disadvantaged in National Institutes of Health (NIH) peer review, particularly for renewals. NIH altered its review format in 2009. The authors examined R01 critiques and scoring in the new format for differences due to principal investigator (PI) sex.

Method

The authors analyzed 739 critiques—268 from 88 unfunded and 471 from 153 funded applications for grants awarded to 125 PIs (76 males, 49 females) at the University of Wisconsin–Madison between 2010 and 2014. The authors used seven word categories for text analysis: ability, achievement, agentic, negative evaluation, positive evaluation, research, and standout adjectives. The authors used regression models to compare priority and criteria scores, and results from text analysis for differences due to PI sex and whether the application was for a new (Type 1) or renewal (Type 2) R01.

Results

Approach scores predicted priority scores for all PIs’ applications (P < .001), but scores and critiques differed significantly for male and female PIs’ Type 2 applications. Reviewers assigned significantly worse priority, approach, and significance scores to female than male PIs’ Type 2 applications, despite using standout adjectives (e.g., “outstanding,” “excellent”) and making references to ability in more critiques (P < .05 for all comparisons).

Conclusions

The authors’ analyses suggest that subtle gender bias may continue to operate in the post-2009 NIH review format in ways that could lead reviewers to implicitly hold male and female applicants to different standards of evaluation, particularly for R01 renewals.
The microbiota in pediatric rheumatic disease: epiphenomenon or therapeutic target?
Authors: Stoll Matthew L. , Cron Randy Q.
Published: June 2016

Purpose of review

There has been increasing interest in the contents and function of the microbiota, as it relates to pediatric inflammatory diseases. Here, we discuss the factors underlying the development of the microbiota, its role in juvenile idiopathic arthritis (JIA) and prospects for therapeutic interventions in the microbiota.

Recent findings

The human microbiota undergoes a succession of changes, until it reaches a mature form. A variety of early-life exposures, including mode of delivery and form of feeding, can affect the contents of the microbiota and possibly impact upon long-term risk of developing autoimmune diseases. The microbiota is altered in children with JIA, including elevated Bacteroides genus in JIA as a whole and decreased Faecalibacterium prausnitzii in pediatric spondyloarthritis. Although there are limited data so far indicating that microbiota-based therapies can result in therapeutic improvement of arthritis, most of the data are on adults and thus may not be applicable to children.

Perturbations of the microbiota during childhood may result in the development of a microbiota associated with increased risk of pediatric rheumatic illness. Whether the microbiota can be targeted is a focus of ongoing research.
Blood Transfusion Incidence, Risk Factors, and Associated Complications in Surgical Treatment of Hip Dysplasia
Authors: Sherrod Brandon A. , Baker Dustin K. , Gilbert Shawn R.
Published: June 2016

Background:

Perioperative bleeding requiring blood transfusion is a known complication of hip dysplasia (HD) surgery. Here we examine rates of, risk factors for, and postoperative complications associated with transfusion during HD surgery.

Methods:

The National Surgical Quality Improvement Program (NSQIP) Pediatric database was queried for patients treated by an orthopaedist from 2012 to 2013. HD cases were categorized by Current Procedural Terminology codes into femoral osteotomies, acetabular osteotomies, combined femoral/acetabular osteotomies, and open reductions. Patients were grouped by comorbidities: neuromuscular (NM) disease (eg, cerebral palsy) group, non-NM with other comorbidity (Other) group, and no known comorbidity (NL) group. Patients were stratified by weight-normalized transfusion volume. Multivariate regression analysis of transfusion association with procedures, demographics, comorbidities, preoperative laboratory values, and 30-day complications was performed.

Results:

A total of 1184 HD cases were included. Transfusion rates for the NL, Other, and NM groups, respectively, were 44/451 (9.8%), 61/216 (28.2%), and 161/517 (31.1%). Transfusion volumes (mean±SD) for the NL, Other, and NM groups, respectively, were 8.4±5.4, 13.9±8.8, and 15.5±10.0 mL/kg (P<0.001). Combined osteotomies had the highest transfusion rates in the NM and Other groups (35.7% and 45.8%, respectively), whereas acetabular osteotomies had the highest rate in the NL group (15.8%). Open reductions had the lowest transfusion rate (all groups). Longer operations were independently associated with transfusion (all groups, per hour increase, OR>1.5,P<0.001). Independent patient risk factors included preoperative hematocrit <31% (NM group, OR=18.42,P=0.013), female sex (NL group, OR=3.55,P=0.008), developmental delay (NM group, OR=2.37,P=0.004), pulmonary comorbidity (NM group, OR=1.73,P=0.032), and older age (NL group, per year increase: OR=1.29,P<0.001). In all groups, transfusion was associated with longer hospitalization (P<0.001). We observed a volume-dependent increase in overall complication rate within the Other group for transfusion volumes >15 mL/kg (25.0% vs. 5.4% for <15 mL/kg,P=0.048).

Conclusions:

We identified several risk factors for transfusion in HD surgery. The incidence of transfusion in HD surgery and its association with adverse outcomes warrants development of appropriate patient management guidelines.

Level of Evidence:

Level III—prognostic.
Robot-Assisted Abdominoperineal Resection: Clinical, Pathologic, and Oncologic Outcomes
Authors: Eftaiha Saleh M. , Pai Ajit , Sulo Suela , Park John J. , Prasad Leela M. , Marecik Slawomir J.
Published: June 2016

BACKGROUND:

The extralevator approach to abdominoperineal resection is associated with a decreased incidence of rectal perforation and circumferential resection margin positivity translating to lower recurrence rates. The abdominoperineal resection, as such, is an operation associated with poorer outcomes in comparison with low anterior resections, and any improvements in short-term outcomes are likely to be related to surgical technique. Robot assistance in extralevator abdominoperineal resection has shown improvement in these pathologic outcomes. Because these are surrogate markers for local recurrence and disease-free survival, long-term survival data are needed to assess the efficacy of this robot-assisted technique, exclusively in a dedicated abdominoperineal resection cohort.

OBJECTIVE:

We assessed the perioperative, pathologic, and oncologic outcomes of the robot-assisted extralevator abdominoperineal resection for rectal cancer.

DESIGN:

This study was a review of a prospective database of patients over a 5-year period.

SETTING:

Procedures were performed in the colorectal division of a tertiary hospital from April 2007 to July 2012.

PATIENTS:

Patients with rectal cancer were operated on robotically. Indications for abdominoperineal resection were low rectal cancers invading the sphincter complex or location in the anal canal precluding anastomosis.

INTERVENTIONS:

All patients received a robot-assisted extralevator abdominoperineal resection.

MAIN OUTCOME MEASURES:

Operative and perioperative measures, pathologic outcomes, and disease-free survival and overall survival were documented and assessed.

RESULTS:

Twenty-two patients (15 men) with a mean age of 65.5 years and mean BMI of 28.6 kg/m2 underwent robotic abdominoperineal resection. Circumferential resection margin was positive in 13.6%. There was 1 tumor/rectal perforation. At a mean follow-up of 33.9 months, overall survival was 81.8% with a disease-free survival of 72.7%. Local recurrence was 4.5%.

LIMITATIONS:

This was a single-institution study with no comparative open or laparoscopic group.

CONCLUSION:

Robot-assisted abdominoperineal resection is safe, feasible, and oncologically sound with short-term and long-term outcomes comparable to open and laparoscopic surgery.
Current trends in minilaparoscopy
Authors: Small Layne Alyssa , Pinkard Lauren , Shepherd Jessica
Published: June 2016

Purpose of review

The purpose of this review is to understand the current use of minilaparoscopy in the field and how minilaparoscopy compares with traditional laparoscopy in terms of operative times, complications, pain, and cosmesis.

Recent findings

Although there are few randomized controlled trials comparing minilaparoscopy with traditional laparoscopy in gynecologic procedures, the results suggest that minilaparoscopy can be performed safely with improved cosmetic outcomes and similar complication rates and operating times. Postoperative pain may be decreased with minimizing incisions sizes. Recently, case reports and case series have been published demonstrating the use of minilaparoscopy across many subtypes of gynecologic surgery.

Traditional laparoscopic surgery has become common practice in gynecology as it has been found to be a well tolerated procedure with improved outcomes and decreased morbidity when compared with laparotomy. Although minilaparoscopy has been used for over 2 decades, its role in gynecology is continuing to evolve. Minilaparoscopy is a growing surgical option in gynecology as we try to minimize the impact of surgery. Results of minilaparoscopy in gynecology mirror those found in urology and general surgery. Although research is limited, minilaparoscopy has proven to be a well tolerated alternative for gynecology.
Techniques in minimally invasive surgery for advanced endometriosis
Authors: King Cara R. , Lum Deirdre
Published: June 2016

Purpose of review

Surgery can be an important treatment option for women with symptomatic endometriosis. This review summarizes the recommended preoperative work up and techniques in minimally invasive surgery for treatment of deeply infiltrating endometriosis (DIE) involving the obliterated posterior cul-de-sac, bowel, urinary tract, and extrapelvic locations.

Recent findings

Surgical management of DIE can pose a challenge to the gynecologic surgeon given that an extensive dissection is usually necessary. Given the high risk of recurrence, it is vital that an adequate excision is performed. With improved imaging modalities, preoperative counseling and surgical planning can be optimized. It is essential to execute meticulous surgical technique and include a multidisciplinary surgical team when indicated for optimal results.

Advanced laparoscopic skills are often necessary to completely excise DIE. A thorough preoperative work up is essential to provide correct patient counseling and incorporation of the preferred surgical team to decrease complications and optimize surgical outcomes. Surgical management of endometriosis is aimed at ameliorating symptoms and preventing recurrence.