bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetohydrodynamic flow excited by rotating permanent magnets in an orthogonal container
Authors: Ben-David O. , Levy A. , Mikhailovich B. , Azulay A.
Published: September 2014

Liquid metal magnetohydrodynamic flow driven by a system of rotating permanent magnets in a container of orthogonal cross-section has been studied. The main objective of the work is to research the impact of magnetic forcing parameters (magnetic field value, magnets arrangement, and angular velocity of their rotation) on the generated hydrodynamic structures and flow modes. On this basis, we contemplate realizing required flow features by setting certain parameters of the driving magnetic system. A numerical study of the problem in the induction-free approximation without taking into account the effect of the variable component of electromagnetic force is presented. The parameters of spin-up modes and steady-state flow regimes have been calculated by three-dimensional direct numerical simulation based on COMSOL Multiphysics 4.3a software and experimentally verified on a specially designed setup using noninvasive Doppler ultrasound technique.
Dependence of the atomic level Green-Kubo stress correlation function on wavevector and frequency: Molecular dynamics results from a model liquid
Authors: Levashov V. A.
Published: September 2014

We report on a further investigation of a new method that can be used to address vibrational dynamics and propagation of stress waves in liquids. The method is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the atomic level stress correlation functions. This decomposition, as was demonstrated previously for a model liquid studied in molecular dynamics simulations, reveals the presence of stress waves propagating over large distances and a structure that resembles the pair density function. In this paper, by performing the Fourier transforms of the atomic level stress correlation functions, we elucidate how the lifetimes of the stress waves and the ranges of their propagation depend on their frequency, wavevector, and temperature. These results relate frequency and wavevector dependence of the generalized viscosity to the character of propagation of the shear stress waves. In particular, the results suggest that an increase in the value of the frequency dependent viscosity at low frequencies with decrease of temperature is related to the increase in the ranges of propagation of the stress waves of the corresponding low frequencies. We found that the ranges of propagation of the shear stress waves of frequencies less than half of the Einstein frequency extend well beyond the nearest neighbor shell even above the melting temperature. The results also show that the crossover from quasilocalized to propagating behavior occurs at frequencies usually associated with the Boson peak.
Optical extinction, refractive index, and multiple scattering for suspensions of interacting colloidal particles
Authors: Parola Alberto , Piazza Roberto , Degiorgio Vittorio
Published: September 2014

We provide a general microscopic theory of the scattering cross-section and of the refractive index for a system of interacting colloidal particles, exact at second order in the molecular polarizabilities. In particular: (a) we show that the structural features of the suspension are encoded into the forward scattered field by multiple scattering effects, whose contribution is essential for the so-called “optical theorem” to hold in the presence of interactions; (b) we investigate the role of radiation reaction on light extinction; (c) we discuss our results in the framework of effective medium theories, presenting a general result for the effective refractive index valid, whatever the structural properties of the suspension, in the limit of particles much larger than the wavelength; (d) by discussing strongly-interacting suspensions, we unravel subtle anomalous dispersion effects for the suspension refractive index.
Revisiting the low-temperature dielectric properties of ZnO
Authors: Wang Chunchang , Liu Lina , Li Qiuju , Huang Shouguo , Zhang Jian , Zheng Jun , Cheng Chao
Published: September 2014

Electric modulus spectroscopy and impedance analysis were used to investigate the low-temperature (∼100–333 K) dielectric properties of ZnO crystals. Two relaxations were observed. The low-temperature relaxation (R1) features a thermally activated behavior resulting from the bulk response. Our results convincingly demonstrate that this relaxation is a polaronic relaxation. The relaxing species for R1 are localized holes created by zinc vacancies instead of the commonly agreed oxygen vacancies. The high-temperature relaxation (R2) is a Maxwell-Wagner relaxation due to skin-layer effect as it can be eliminated by grinding off the sample surface. The inhomogeneous distribution of zinc interstitials leads to the formation of the skin layer. Interestingly, an abnormal dielectric behavior contrary to the thermally activated behavior was found for the R2 relaxation. This abnormal behavior was confirmed to be related to the positive temperature coefficient of resistance due to the metal-insulator transition occurring within the skin layer.
Nanoindentation response of piezoelectric nano-islands
Authors: Cheng Guang , Sriram Sharath , Bhaskaran Madhu , Venkatesh T. A.
Published: September 2014

Through three-dimensional finite element modeling, it is demonstrated that the nanoindentation response of piezoelectric nano-islands is strongly dependent on the shape of the nano-island and the depth of indentation. For indentations that are relatively deep (i.e., greater than 5% of the height of the islands), the substrate's elastic and plastic properties have a strong influence on the indentation response of piezoelectric nano-islands with substrate plasticity resulting in a significant reduction in the mechanical and electrical indentation stiffness. The predictions of the finite element models compare well with experiments on nano-islands of strontium-doped lead zirconate titanate.
Biomechanical investigation of colorectal cancer cells
Authors: Palmieri Valentina , Lucchetti Donatella , Maiorana Alessandro , Papi Massimiliano , Maulucci Giuseppe , Ciasca Gabriele , Svelto Maria , De Spirito Marco , Sgambato Alessandro
Published: September 2014

The nanomechanical properties of SW480 colon cancer cells were investigated using Atomic Force Microscopy. SW480 cells are composed of two sub-populations with different shape and invasiveness. These two cells populations showed similar adhesion properties while appeared significantly different in term of cells stiffness. Since cell stiffness is related to invasiveness and growth, we suggest elasticity as a useful parameter to distinguish invasive cells inside the colorectal tumor bulk and the high-resolution mechanical mapping as a promising diagnostic tool for the identification of malignant cells.
The effect of calcium-induced fullerene migration on the performance of thermally stable nanoparticle organic solar cells
Authors: Feron K. , Ulum S. , Sesa E. , Gong B. B. , Belcher W. J. , Zhou X. , Fell C. J. , Dastoor P. C.
Published: September 2014

The impact of a calcium interface layer in combination with a thermal annealing treatment on the performance of poly(3-hexylthiophene) (P3HT):[6,6]-phenyl-C61-buteric acid methylester (PCBM) nanoparticle photovoltaic devices is investigated. Annealing is found to disrupt the microstructure of the nanoparticle active layer leading to a reduction in fill factor. However, X-ray photoelectron spectroscopy measurements show that the calcium interface layer causes PCBM to preferentially migrate to the cathode interface upon annealing, resulting in better charge extraction from the PCBM moiety, an increase in the built-in voltage, open-circuit voltage, and power conversion efficiency. Moreover, the annealing trends could be completely explained by the observed PCBM migration. Unlike P3HT:PCBM bulk heterojunction devices, the P3HT:PCBM nanoparticle devices showed a remarkable thermal stability up to 120 °C. As such, OPVs fabricated from aqueous nanoparticle inks provide an attractive alternative to conventional organic solvent based bulk heterojunction devices.
Demonstration of magnetoelectric memory cell in (110) [Pb(Mg1/2Nb2/3)O3]0.68-[PbTiO3]0.32/Ru/FeCo heterostructures
Authors: Han Xuemeng , Xi Li , Li Yue , Guo Xiaobin , Li Dong , Wang Zhen , Zuo Yalu , Xue Desheng
Published: September 2014

An electric-field pulses driven magnetoelectric memory cell in a single layered ferromagnetic thin film was fabricated by direct-current magnetron sputtering Ru/Fe65Co35 on ferroelectric (110) [Pb(Mg1/2 Nb2/3)O3]0.68-[PbTiO3]0.32 (PMN-PT) substrates. The magnetization in the orthogonal directions can be reset by the positive/negative electric fields pulse in PMN-PT/Ru/FeCo heterostructures due to the strain mediated converse magnetoelectric effect. The high (low) resistance state was realized under the negative (positive) electric fields pulse due to the anisotropy magnetoresistance of FeCo films. Then, a non-volatile magnetic memory cell with resistance and electric field, respectively, as the media and writing field was realized.
Magnetoimpedance hysteresis in amorphous microwires induced by core–shell interaction
Authors: Ipatov M. , Zhukova V. , Gonzalez J. , Zhukov A.
Published: September 2014

We report on magneto-impedance (MI) hysteresis at MHz and GHz frequencies in amorphous microwires subject to a sufficiently high applied axial magnetic field HE. We show that this hysteresis originates from the magnetic hysteresis of the inner core which biases the outer shell causing a shift of the MI curve along the HE axis. Combined experiments (longitudinal and off-diagonal MI Z(HE), hysteresis loops M(HE) by vibrating sample magnetometer, and induction method) reveal the details of the magnetization reversal process in these microwires: Partial field dependencies Z(HE) and M(HE) are shown to be practically anhysteretic but shifted to the left or to the right about the origin by a residual magnetic field of the inner core HC. This shift can vary in the range from −35 to +35 A/m, depending on the magnetic history of the sample. We demonstrate that the hysteresis can be suppressed by application of a high enough axial magnetic field that saturates the magnetization of the inner core. A potential application of this hysteresis for memory devices is also proposed.
Full waveform investigation of a perturbation method for acoustical multipole logging in transversely isotropic medium
Authors: Zhang L. , Wang K. X. , Zhang B. X. , Wang X. T.
Published: September 2014

A new and effective analytical perturbation method is presented for the multipole acoustic logging in a transversely isotropic medium (TIM), whose symmetric principal axis is parallel to the borehole axis and the exact solutions could be found. TIM is regarded as a reference unperturbed isotropic state added to the perturbations, and three perturbation quantities about elastic modulus deviated from the isotropic medium are introduced. By searching for the zero, the first, and the second order of perturbation solutions, the multipole acoustic fields inside and outside the borehole are derived and obtained. The full waveforms in the borehole excited by a monopole, dipole, and quadrupole sources are numerical simulated by perturbation and exact solutions. It is found that the full waveforms are close to the exact solution when the first order perturbation is considered and more close to the exact solution when the second order perturbation is considered. The numerical simulation confirms that the perturbation method is a feasible method for complicated anisotropic medium in acoustic logging.
Lateral photovoltaic effect co-observed with unipolar resistive switching behavior in Cu-doped ZnO film
Authors: Lu Jing , Li Zheng , Yin Guilin , Ge Meiying , He Dannong , Wang Hui
Published: September 2014

Unipolar resistive switching (RS) behavior was first observed in Cu-doped ZnO film based on ZnO/SiO2/Si structure, which was a novel phenomenon as memory films grown on Si substrate usually showed a bipolar one. The results demonstrate Cu-doped ZnO a new candidate for memory material. By introducing an external electric-field before the sweeping process, we have verified that the RS behavior was a localized effect. The non-linear I-V character, which suggested a junction of the proposed Cu-doped ZnO/SiO2/Si structure, leads to the lateral photovoltaic effect (LPE) investigation. In photovoltaic mode, which is the simplest configuration, the position sensitivity of lateral photovoltage observed on Cu-doped ZnO film achieves 24.82 mV/mm and the nonlinearity is within 9.95%, indicating that Cu-doped ZnO could serve as a LPE material directly. The dual effects accommodate functions of detector and memristor in the same structure and make Cu-doped ZnO a competitive material for advanced multi-functional device.
Solving the electrical control of magnetic coercive field paradox
Authors: Vopson M. M. , Lepadatu S.
Published: September 2014

The ability to tune magnetic properties of solids via electric voltages instead of external magnetic fields is a physics curiosity of great scientific and technological importance. Today, there is strong published experimental evidence of electrical control of magnetic coercive fields in composite multiferroic solids. Unfortunately, the literature indicates highly contradictory results. In some studies, an applied voltage increases the magnetic coercive field and in other studies the applied voltage decreases the coercive field of composite multiferroics. Here, we provide an elegant explanation to this paradox and we demonstrate why all reported results are in fact correct. It is shown that for a given polarity of the applied voltage, the magnetic coercive field depends on the sign of two tensor components of the multiferroic solid: magnetostrictive and piezoelectric coefficient. For a negative applied voltage, the magnetic coercive field decreases when the two material parameters have the same sign and increases when they have opposite signs, respectively. The effect of the material parameters is reversed when the same multiferroic solid is subjected to a positive applied voltage.
Embers of society: Firelight talk among the Ju/’hoansi Bushmen
Authors: Wiessner Polly W.
Published: September 2014

Significance

Control of fire and the capacity for cooking led to major anatomical and residential changes for early humans, starting more than a million years ago. However, little is known about what transpired when the day was extended by firelight. Data from the Ju/’hoan hunter-gatherers of southern Africa show major differences between day and night talk. Day talk centered on practicalities and sanctioning gossip; firelit activities centered on conversations that evoked the imagination, helped people remember and understand others in their external networks, healed rifts of the day, and conveyed information about cultural institutions that generate regularity of behavior and corresponding trust. Appetites for firelit settings for intimate conversations and for evening stories remain with us today.
Dendritic spinopathy in transgenic mice expressing ALS/dementia-linked mutant
UBQLN2
Authors: Gorrie George H. , Fecto Faisal , Radzicki Daniel , Weiss Craig , Shi Yong , Dong Hongxin , Zhai Hong , Fu Ronggen , Liu Erdong , Li Sisi , Arrat Hasan , Bigio Eileen H. , Disterhoft John F. , Martina Marco , Mugnaini Enrico , Siddique Teepu , Deng Han-Xiang
Published: September 2014

Significance

Mutations in the
UBQLN2
gene, which encodes the ubiquitin-like protein ubiquilin2 (UBQLN2) have been shown to cause ALS and ALS/dementia. Ubiquilin2 links familial and sporadic forms of the disease through pathology observed in the spinal cords of all ALS cases and in the brains of ALS/dementia cases with or without
UBQLN2
mutations. In this communication, we develop and characterize a mouse model of mutant
UBQLN2
-linked dementia. We demonstrate that mutant mice develop impairment in the protein degradation pathway, abnormal protein aggregation, synaptic dysfunction, and cognitive deficits. This model provides a useful tool to further study dementia and develop rational therapies.
Basis for substrate recognition and distinction by matrix metalloproteinases
Authors: Ratnikov Boris I. , Cieplak Piotr , Gramatikoff Kosi , Pierce James , Eroshkin Alexey , Igarashi Yoshinobu , Kazanov Marat , Sun Qing , Godzik Adam , Osterman Andrei , Stec Boguslaw , Strongin Alex , Smith Jeffrey W.
Published: September 2014

Significance

Specificity-determining positions (SDPs) account for distinctions in function across a protein family. Many theories on the evolution of functional specificity have led to approaches for predicting SDPs in silico, but large experimental datasets allowing a statistical assignment are lacking. Here, the SDPs of matrix metalloproteinases are elucidated by querying the proteolytic efficiency of eight matrix metalloproteinases, representing three phylogenetic branches, in an extended and diverse substrate space. More than 10,000 measures of cleavage efficiency reveal a near-perfect correlation between similarity in proteolytic function and sequence identity at 50–57 positions on the front face of the catalytic domain. These positions are assigned as SDPs. Transmutation of proteolytic function is possible by swapping SDPs nearest to bound substrate.
Dynamical traps lead to the slowing down of intramolecular vibrational energy flow
Authors: Manikandan Paranjothy , Keshavamurthy Srihari
Published: September 2014

Significance

Facile energy flow among the vibrational modes of a molecule is the primordial step for a reaction. The energy flow pathways are determined by various anharmonic resonances coupling the modes. Assessing the importance of quantum effects like coherence and tunneling to the intramolecular energy flow process requires one to relate the classical pathways mediated by the network of nonlinear resonances, known as the Arnold web, with the quantum pathways. However, very little is known about the ways in which the features of the web can influence the quantum dynamics. In this work we take a significant first step by establishing that a ubiquitous feature of the web, the resonance junction, can slow down the quantum energy flow process.
An extended Shine–Dalgarno sequence in mRNA functionally bypasses a vital defect in initiator tRNA
Authors: Shetty Sunil , Nadimpalli HimaPriyanka , Shah Riyaz Ahmad , Arora Smriti , Das Gautam , Varshney Umesh
Published: September 2014

Significance

Initiation, a regulatory step in mRNA translation is characterized by initiator tRNA (tRNA
fMet
) binding to 30S ribosome together with initiation factors (IFs) to form 30S pre-initiation complex (PIC). This step is followed by binding of 50S ribosome and release of IFs to form elongation competent 70S complex. tRNA
fMet
is special in possessing a vital feature of three consecutive G-C (3GC) base pairs in its anticodon stem. However, the role of this feature has remained unclear. We show that the 3GC base pairs facilitate tRNA
fMet
retention in the ribosome during the transitions that mark conversion of 30S PIC into 70S complex. Furthermore, we show that translation of mRNAs having an extended Shine–Dalgarno sequence bypasses the requirement of the 3GC pairs in tRNA
fMet
.
Early modern human settlement of Europe north of the Alps occurred 43,500 years ago in a cold steppe-type environment
Authors: Nigst Philip R. , Haesaerts Paul , Damblon Freddy , Frank-Fellner Christa , Mallol Carolina , Viola Bence , Götzinger Michael , Niven Laura , Trnka Gerhard , Hublin Jean-Jacques
Published: September 2014

Significance

Modern humans dispersed into Europe and replaced Neanderthals at least 40,000 years ago. However, the precise timing and climatic context of this dispersal are heavily debated. Therefore, a new project combining paleoenvironmental and archaeological fieldwork has been undertaken at Willendorf II (Austria), a key site for this time period. This project has concluded that modern humans producing Aurignacian stone tools occupied Central Europe about 43,500 years ago in a medium-cold steppe environment with some boreal trees along valleys. This discovery represents the oldest well-documented occurrence of behaviorally modern humans in Europe and demonstrates contemporaneity with Neanderthals in other parts of Europe, showing that behaviorally modern humans and Neanderthals shared this region longer than previously thought.
Emergence of long-range order in sheets of magnetic dimers
Authors: Haravifard S. , Banerjee A. , van Wezel J. , Silevitch D. M. , dos Santos A. M. , Lang J. C. , Kermarrec E. , Srajer G. , Gaulin B. D. , Molaison J. J. , Dabkowska H. A. , Rosenbaum T. F.
Published: September 2014

Significance

Magnetic materials are composed of individual spins that interact with each other and under suitable conditions can arrange themselves in an ordered array. When spins are confined to two-dimensional sheets, small perturbations can disrupt their order and destroy the magnetic state. We show how a set of interacting, quantum-mechanical spins placed on the corners of a square array evolves from a set of locally bonded entities to a globally ordered structure. The system stabilizes itself against fluctuations through subtle local contractions, elongations, and tilts. The combination of neutron and X-ray scattering at pressures up to 60,000 atmospheres reveals the complex interplay of structural distortions and spin alignments that permit long-range order to emerge in this model quantum magnet.
Mosquito-specific microRNA-1174 targets
serine hydroxymethyltransferase
to control key functions in the gut
Authors: Liu Shiping , Lucas Keira J. , Roy Sourav , Ha Jisu , Raikhel Alexander S.
Published: September 2014

Significance

Females of several mosquito species have evolved obligatory blood-feeding to supply amino acids and other nutrients necessary for egg development, providing a mechanism for the spread of many devastating diseases in humans. The mosquito-specific microRNA (miRNA), miR-1174, is significantly upregulated post blood meal and specific to the female mosquito midgut, suggesting a role in blood meal-associated events. We have found that miR-1174 targets serine hydroxymethyltransferase and is required for key functions in
Aedes aegypti
and
Anopheles gambiae
. Its inhibition disrupts sugar absorption, fluid excretion, blood intake in the gut, and, consequently, egg maturation and survival. Mosquito-specific miRNAs, such as miR-1174, have the potential for influencing the development of a future generation of mosquito control.
Modeling putative therapeutic implications of exosome exchange between tumor and immune cells
Authors: Lu Mingyang , Huang Bin , Hanash Samir M. , Onuchic José N. , Ben-Jacob Eshel
Published: September 2014

Significance

A better understanding of mechanisms of immune evasion by cancer cells and the role of the tumor microenvironment is crucial for developing new effective cancer therapeutic strategies. The challenge is posed by the enormous complexity of both the immune system and the tumor microenvironment, and the intricate cancer–immunity signaling network. Here, we develop a tractable theoretical framework to study the putative role of exosome communication in the cancer–immunity interplay. Exosomes are small (30–200 nm) vesicles that transfer proteins, mRNAs, and microRNAs to nearby and faraway cells. Guided by this model, we compare the effectiveness of administering radiation therapy alone or in combination with immunotherapy, illustrating how the model can shed light on the design and assessments of combination therapies.
PP2A-B56 opposes Mps1 phosphorylation of Knl1 and thereby promotes spindle assembly checkpoint silencing
Authors: Espert Antonio , Uluocak Pelin , Bastos Ricardo Nunes , Mangat Davinderpreet , Graab Philipp , Gruneberg Ulrike
Published: September 2014

The spindle assembly checkpoint (SAC) monitors correct attachment of chromosomes to microtubules, an important safeguard mechanism ensuring faithful chromosome segregation in eukaryotic cells. How the SAC signal is turned off once all the chromosomes have successfully attached to the spindle remains an unresolved question. Mps1 phosphorylation of Knl1 results in recruitment of the SAC proteins Bub1, Bub3, and BubR1 to the kinetochore and production of the wait-anaphase signal. SAC silencing is therefore expected to involve a phosphatase opposing Mps1. Here we demonstrate in vivo and in vitro that BubR1-associated PP2A-B56 is a key phosphatase for the removal of the Mps1-mediated Knl1 phosphorylations necessary for Bub1/BubR1 recruitment in mammalian cells. SAC silencing is thus promoted by a negative feedback loop involving the Mps1-dependent recruitment of a phosphatase opposing Mps1. Our findings extend the previously reported role for BubR1-associated PP2A-B56 in opposing Aurora B and suggest that BubR1-bound PP2A-B56 integrates kinetochore surveillance and silencing of the SAC.
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity
Authors: Duan Fei , Duitama Jorge , Al Seesi Sahar , Ayres Cory M. , Corcelli Steven A. , Pawashe Arpita P. , Blanchard Tatiana , McMahon David , Sidney John , Sette Alessandro , Baker Brian M. , Mandoiu Ion I. , Srivastava Pramod K.
Published: September 2014

The mutational repertoire of cancers creates the neoepitopes that make cancers immunogenic. Here, we introduce two novel tools that identify, with relatively high accuracy, the small proportion of neoepitopes (among the hundreds of potential neoepitopes) that protect the host through an antitumor T cell response. The two tools consist of (a) the numerical difference in NetMHC scores between the mutated sequences and their unmutated counterparts, termed the differential agretopic index, and (b) the conformational stability of the MHC I–peptide interaction. Mechanistically, these tools identify neoepitopes that are mutated to create new anchor residues for MHC binding, and render the overall peptide more rigid. Surprisingly, the protective neoepitopes identified here elicit CD8-dependent immunity, even though their affinity for Kd is orders of magnitude lower than the 500-nM threshold considered reasonable for such interactions. These results greatly expand the universe of target cancer antigens and identify new tools for human cancer immunotherapy.
Isoparametric foliations on complex projective spaces
Authors: Domínguez-Vázquez Miguel
Published: September 2014

Irreducible isoparametric foliations of arbitrary codimension

q
q

on complex projective spaces

C

P
n

\mathbb {C} P^n

are classified, for

(
q
,
n
)
≠
(
1
,
15
)

(q,n)\neq (1,15)

. Remarkably, there are noncongruent examples that pull back under the Hopf map to congruent foliations on the sphere. Moreover, there exist many inhomogeneous isoparametric foliations, even of higher codimension. In fact, every irreducible isoparametric foliation on

C

P
n

\mathbb {C} P^n

is homogeneous if and only if

n
+
1

n+1

is prime.

The main tool developed in this work is a method to study singular Riemannian foliations with closed leaves on complex projective spaces. This method is based on a certain graph that generalizes extended Vogan diagrams of inner symmetric spaces.
PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades
Authors: Guo Qingli , Qu Xiongfei , Jin Weibo
Published: September 2014

Summary: Emerging evidence has revealed phased siRNAs (phasiRNAs) as important endogenous regulators in plants. However, the integrated prediction tools for phasiRNAs are still limited. In this article, we introduce a stand-alone package PhaseTank for systematically characterizing phasiRNAs and their regulatory networks. (i) It can identify phasiRNAs/tasiRNAs functional cascades (miRNA/phasiRNA→ PHAS loci→phasiRNA→target) with high sensitivity and specificity. (ii) By one command analysis, it generates comprehensive annotation and quantification of the predicted PHAS genes from any given sequences. (iii) PhaseTank has no restriction with regards to prior information of sequence homology of unrestricted organism origins.

Availability and implementation: PhaseTank is a free and open-source tool. The package is available at http://phasetank.sourceforge.net/ .

Contact:  weibojin@gmail.com or guoql.karen@gmail.com .

Supplementary information:  Supplementary data are available at Bioinformatics online.
A kinematically distinct core and minor-axis rotation: the MUSE perspective on M87
Authors: Emsellem Eric , Krajnović Davor , Sarzi Marc
Published: September 2014

We present evidence for the presence of a low-amplitude kinematically distinct component in the giant early-type galaxy M87, via data sets obtained with the SAURON and MUSE integral-field spectroscopic units. The MUSE velocity field reveals a strong twist of ∼140° within the central 30 arcsec connecting outwards such a kinematically distinct core to a prolate-like rotation around the large-scale photometric major axis of the galaxy. The existence of these kinematic features within the apparently round central regions of M87 implies a non-axisymmetric and complex shape for this galaxy, which could be further constrained using the presented kinematics. The associated orbital structure should be interpreted together with other tracers of the gravitational potential probed at larger scales (e.g. globular clusters, ultra-compact dwarfs, planetary nebulae): it would offer an insight in the assembly history of one of the brightest galaxies in the Virgo cluster. These data also demonstrate the potential of the MUSE spectrograph to uncover low-amplitude spectral signatures.
Discovery of a new Galactic bona fide luminous blue variable with Spitzer
Authors: Gvaramadze V. V. , Kniazev A. Y. , Berdnikov L. N. , Langer N. , Grebel E. K. , Bestenlehner J. M.
Published: September 2014

We report the discovery of a circular mid-infrared shell around the emission-line star Wray 16-137 using archival data of the Spitzer Space Telescope. Follow-up optical spectroscopy of Wray 16-137 with the Southern African Large Telescope revealed a rich emission spectrum typical of the classical luminous blue variables (LBVs) like P Cygni. Subsequent spectroscopic and photometric observations showed drastic changes in the spectrum and brightness during the last three years, meaning that Wray 16-137 currently undergoes an S Dor-like outburst. Namely, we found that the star has brightened by ≈1 mag in the V and Ic bands, while its spectrum became dominated by Fe ii lines. Taken together, our observations unambiguously show that Wray 16-137 is a new member of the family of Galactic bona fide LBVs.
Self-organization in cold atomic gases: a synchronization perspective
Authors: Tesio E. , Robb G. R. M. , Oppo G.-L. , Gomes P. M. , Ackemann T. , Labeyrie G. , Kaiser R. , Firth W. J.
Published: September 2014

We study non-equilibrium spatial self-organization in cold atomic gases, where long-range spatial order spontaneously emerges from fluctuations in the plane transverse to the propagation axis of a single optical beam. The self-organization process can be interpreted as a synchronization transition in a fully connected network of fictitious oscillators, and described in terms of the Kuramoto model.
Fast and slowly evolving vector solitons in mode-locked fibre lasers
Authors: Sergeyev Sergey V.
Published: September 2014

We report on a new vector model of an erbium-doped fibre laser mode locked with carbon nanotubes. This model goes beyond the limitations of the previously used models based on either coupled nonlinear Schrödinger or Ginzburg–Landau equations. Unlike the previous models, it accounts for the vector nature of the interaction between an optical field and an erbium-doped active medium, slow relaxation dynamics of erbium ions, linear birefringence in a fibre, linear and circular birefringence of a laser cavity caused by in-cavity polarization controller and light-induced anisotropy caused by elliptically polarized pump field. Interplay of aforementioned factors changes coherent coupling of two polarization modes at a long time scale and so results in a new family of vector solitons (VSs) with fast and slowly evolving states of polarization. The observed VSs can be of interest in secure communications, trapping and manipulation of atoms and nanoparticles, control of magnetization in data storage devices and many other areas.
Strong interaction between plants induces circular barren patches: fairy circles
Authors: Fernandez-Oto C. , Tlidi M. , Escaff D. , Clerc M. G.
Published: September 2014

Fairy circles consist of isolated or randomly distributed circular areas devoid of any vegetation. They are observed in vast territories in southern Angola, Namibia and South Africa. We report on the formation of fairy circles, and we interpret them as localized structures with a varying plateau size as a function of the aridity. Their stabilization mechanism is attributed to a combined influence of the bistability between the bare state and the uniformly vegetation state, and Lorentzian-like non-local coupling that models the competition between plants. We show how a circular shape is formed, and how the aridity level influences the size of fairy circles. Finally, we show that the proposed mechanism is model-independent.
Periodic and chaotic solitons in a semiconductor laser with saturable absorber
Authors: Vahed H. , Prati F. , Turconi M. , Barland S. , Tissoni G.
Published: September 2014

In a semiconductor laser with saturable absorber, solitons may spontaneously drift and/or oscillate. We study three different regimes characterized by strong intensity oscillations, both periodic and chaotic. We show that (i) soliton dynamics may be similar to that of passively Q-switched lasers, (ii) solitons may drift and oscillate simultaneously, and (iii) chaotic solitons may coexist with stationary ones and with the laser off solution.
Localized structures in dissipative media: from optics to plant ecology
Authors: Tlidi M. , Staliunas K. , Panajotov K. , Vladimirov A. G. , Clerc M. G.
Published: September 2014

Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years.
Variation in Sulfur and Selenium Accumulation Is Controlled by Naturally Occurring Isoforms of the Key Sulfur Assimilation Enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis Species Range
Authors: Chao Dai-Yin , Baraniecka Patrycja , Danku John , Koprivova Anna , Lahner Brett , Luo Hongbing , Yakubova Elena , Dilkes Brian , Kopriva Stanislav , Salt David E.
Published: September 2014

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.
Crystal structure of 3-{1′-[3,5-bis(trifluoromethyl)phenyl]ferrocenyl}-4-bromothiophene
Authors: Poppitz Elisabeth A. , Korb Marcus , Lang Heinrich
Published: September 2014

The molecular structure of the title compound, [Fe(C9H6BrS)(C13H7F6)], consists of a ferrocene backbone with a bis(trifluoromethyl)phenyl group at one cyclopentadienyl ring and a thiophene heterocycle at the other cyclopentadienyl ring. The latter is disordered over two sets of sites in a 0.6:0.4 ratio. In the crystal structure, intramolecular π–π interactions between the thienyl and the phenyl substituent [centroid–centroid distance 3.695 (4) Å] and additional weakT-shaped π–π interactions between the thienyl and the phenyl-substituted cyclopentadienyl ring [4.688 (6) Å] consolidate the crystal packing.
“Which hat do I say I'm wearing?”: identity work of independent coaching practitioners
Authors: Evans Christina , Lines David
Published: September 2014

Purpose

– This paper aims to provide an insight into the complexities of the identity work performed by independent coaches, based on an investigation into their “lived experiences”. The emerging coaching industry has created opportunities for individuals wishing to pursue a career as independent executive/career coaches.

Design/methodology/approach

– This exploratory investigation was conducted using the principles of grounded theory, drawing on insights from “knowledgeable informants” (18 in total) gained through interviews and focus group discussion.

Findings

– Despite the attractiveness of pursuing an independent career, the findings surfaced a number of tensions in the way that independent coaches transform and perform their identity. One tension involves balancing notions of self-identity and “ideal work” with presenting a credible self to different client groups, the purchasers of their services.

Research limitations/implications

– As the research focused on a specific category of independent practitioners, more research is required to assess the generalizability of the findings to other categories of practitioners.

Practical implications

– A framework illuminating the processual nature of identity work among independent coaches is presented. This could be used to inform developmental conversations with aspiring independent coaches, or to support the content on formal coaching programmes.

Originality/value

– In drawing attention to the complexities of identity work performed by independent coaches, given the contingencies affecting their work, this research offers a different contribution to the coaching literature.
Compromise and avoidance: the response to new legislation
Authors: Haraldsson Mattias , Tagesson Torbjörn
Published: September 2014

Purpose

– The aim of this paper is to describe, analyze and explain the level of compliance of accounting practices with legislation and generally accepted accounting principles (GAAP) within the Swedish water and sewerage sector.

Design/methodology/approach

– The empirical data are based on a document study of the annual full cost accounting reports for the financial year 2010. We obtained complete data from 250 of Sweden's 290 municipalities. The data are analyzed by statistical methods. The explanations are based on an institutional theory.

Findings

– Most of the organizations surveyed in this study had taken measures in line with the new regulations, but none of them had adapted fully to the new requirements. Thus, we suggest that the industry has responded to the new regulation by compromise and avoidance. The statistical analyses show that compliance with legislation and GAAP is associated with legal form, minority governance, fee, tax base, population growth and audit firm.

Research limitations/implications

– This paper provides insight into the factors that explain compliance with accounting regulation. Future research would benefit from researching the decision process when organizations choose to comply or not to comply with specific accounting regulations in the public sector.

Originality/value

– Few prior studies focus on the actual compliance of accounting practices at the municipal level in relation to accounting regulation and the factors that explain the level of compliance. Knowledge of the factors that explain compliance to accounting regulation will benefit from future policy decisions on regulation and auditing of public sector accounting.
An Antipodean History of Interpretation
Authors: Boswell John , Corbett Jack
Published: September 2014

In this paper, we explore the connections between intepretivism's core and its peripheries in both geographical and epistemological terms, by tracing the relationship between interpretivism and Australian political scholarship. In this task, we draw on some of the most celebrated and influential work on Australian politics—by political scientists but before them historians and anthropologists—to show how the approach typically undertaken by these researchers echoes key tenets of interpretivism, especially through an interest in subjective beliefs and experiences, a desire to uncover and bring to life richly contextualised detail, and a commitment to the abductive linking of theory and practice. As such, we suggest that the spread of this counter identity to interpretive researchers in Australia risks manufacturing a sense of methodological antipathy, marginalising the work of interpretivists from mainstream political scholarship.
The Promise and Perils of Interpretivism in Australian International Relations
Authors: Hall Ian
Published: September 2014

Australian International Relations (IR) was once a hybrid of American and European styles of political science, but today it is dominated by a British‐inspired post‐positivism which has its virtues – and its vices – and which utilises various interpretive and semi‐interpretive approaches. This paper welcomes the ‘interpretive turn’ in Australian IR, but recognises its weaknesses, and argues that, to overcome them, interpretivists must be clear about what interpretivism should and should not entail. It argues that a thoroughgoing interpretivism offers two things that qualitative work in Australian IR desperately needs: a revived focus on explaining international relations, as well as understanding it, and a renewed engagement with other fields and other modes of studying the field.
Two Cheers for Interpretivism: Deconstructing the British Political Tradition
Authors: Marsh David , Hall Matthew , Fawcett Paul
Published: September 2014

This article engages with Bevir and Rhodes' version of interpretivism from a critical realist perspective. It argues that they are misguided to equate path‐dependency with path‐determinancy. Instead, we argue that there are three path‐dependencies, institutional, discursive and political‐economic, which constrain without determining the actions of agents and thus effect political outcomes. The argument is illustrated through a brief consideration of the operation of the British Political Tradition.
Interpretation in the Analysis of Policy
Authors: Colebatch H. K.
Published: September 2014

Interpretation is a critical element in both the analysis and the accomplishment of governing, and taking an interpretive approach to policy should not be seen as a methodological option for consenting adults, but as an integral element of political analysis. Understanding governing (whether by practitioners or analysts) raises questions about the shared meaning which makes action valid, and makes a reality of ‘the government’. This calls for attention to the ways in which this is done, and how this interpretive construction has been recognised in political science (and other social sciences) in Australia and elsewhere, and for a consideration of what this means for political scientists’ agenda of inquiry.
Gender Equality Architecture: The Intergovernmental Level in Federal Systems
Authors: Sawer Marian
Published: September 2014

This article provides a first overall account of the intergovernmental components of Australia's gender equality architecture in the period 1978–2014. From the 1990s this is largely a story of institutional fragility. In explaining this, factors identified by scholars of state feminism, such as lack of political will, partisan ideologies and discursive shifts, particularly the increased influence of neoliberal approaches to governance, are taken into account. The new factor introduced is that of executive federalism, characterised by decision‐making behind closed doors. When women's intergovernmental bodies attempted to open doors to community input this proved fruitless, particularly in the area of economic decision‐making. Repeated attempts to introduce gender‐disaggregated reporting on the outcomes of Commonwealth‐State agreements were also largely unsuccessful. The article concludes that the democratic deficits associated with executive federalism – lack of parliamentary oversight or accountability and lack of community consultation – are closely related to the deficits in gender mainstreaming.
Accounting for Gender: the Role of the COAG Reform Council in Tracking Outcomes for Women and Girls Across Australia
Authors: O'Loughlin Mary Ann , Newton Alex
Published: September 2014

The COAG Reform Council has played a critical role in tracking progress, nationally and on a state‐by‐state basis, against the COAG reform agenda. The council has analysed and publicly reported on governments’ performance against outcomes, performance indicators and targets agreed by COAG. However, until 2013 gender analysis was not directly incorporated in the assessment of governments’ performance. The council's first report on gender, Tracking equity: Comparing outcomes for women and girls across Australia, redressed this omission. This article explores how taking account of gender greatly enriches our understanding of governments’ performance in critical areas, and enhances public accountability as a result. An understanding of gender differences also provides a better basis for government decision‐making on ways to improve outcomes.
Income inequality, poverty and crime across nations
Authors: Pare Paul‐Philippe , Felson Richard
Published: September 2014

We examine the relationship between income inequality, poverty, and different types of crime. Our results are consistent with recent research in showing that inequality is unrelated to homicide rates when poverty is controlled. In our multi‐level analyses of theInternationalCrimeVictimizationSurvey we find that inequality is unrelated to assault, robbery, burglary, and theft when poverty is controlled. We argue that there are also theoretical reasons to doubt that the level of income inequality of a country affects the likelihood of criminal behaviour.
Provoking misunderstanding: a comment on Black's defence of value‐free sociology
Authors: Hammersley Martyn
Published: September 2014

This paper is a response to a recent article dealing with the concept of value‐free sociology by Donald Black. It argues that while a defence of Weber's position on the role of values in sociological research is necessary and important, what is offered by Black is counter‐productive in important respects. This is because it encourages some of the misunderstandings that it is aimed at remedying and, even more importantly, offers a simplistic discussion of what are complex issues.