bluuebunny/crossref_metadata_2025 huggingface dataset:
Wavelength-encoded tomography based on optical temporal Fourier transform
Authors: Zhang Chi , Wong Kenneth K. Y.
Published: September 2014

We propose and demonstrate a technique called wavelength-encoded tomography (WET) for non-invasive optical cross-sectional imaging, particularly beneficial in biological system. The WET utilizes time-lens to perform the optical Fourier transform, and the time-to-wavelength conversion generates a wavelength-encoded image of optical scattering from internal microstructures, analogous to the interferometery-based imaging such as optical coherence tomography. Optical Fourier transform, in principle, comes with twice as good axial resolution over the electrical Fourier transform, and will greatly simplify the digital signal processing after the data acquisition. As a proof-of-principle demonstration, a 150 -μm (ideally 36 μm) resolution is achieved based on a 7.5-nm bandwidth swept-pump, using a conventional optical spectrum analyzer. This approach can potentially achieve up to 100-MHz or even higher frame rate with some proven ultrafast spectrum analyzer. We believe that this technique is innovative towards the next-generation ultrafast optical tomographic imaging application.
Quasiclassical trajectory study of the effect of antisymmetric stretch mode excitation on the O(3P) + CH4(ν3 = 1) → OH + CH3 reaction on an analytical potential energy surface. Comparison with experiment
Authors: Monge-Palacios M. , González-Lavado E. , Espinosa-Garcia J.
Published: September 2014

Motivated by a recent crossed-beam experiment on the title reaction reported by Pan and Liu [J. Chem. Phys. 140, 191101 (2014)], a detailed dynamics study was performed at three collision energies using quasiclassical trajectory (QCT) calculations based on a full-dimensional potential energy surface recently developed by our group (PES-2014). Although theory/experiment agreement is not yet quantitative, in general the theoretical results reproduce the experimental evidence: the vibrational branching ratio of OH(v = 1)/OH(v = 0) is ∼0.8/0.2, excitation of the antisymmetric CH stretching mode in methane increases reactivity by factor 2.28–1.50, although an equivalent amount as translational energy is more efficient in promoting the reaction and, finally, product angular distribution shifts from backward in the CH4(ν = 0) ground-state to sideways when the antisymmetric CH stretching mode is excited. These results give confidence to the PES-2014 surface, depend on the quantization procedure used, are comparable with recent QCT calculations or improve previous theoretical studies using a different surface, and demonstrate the utility of the theory/experiment collaboration.
Correlation consistent basis sets for explicitly correlated wavefunctions: Pseudopotential-based basis sets for the post-d main group elements Ga–Rn
Authors: Hill J. Grant , Peterson Kirk A.
Published: September 2014

New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of the spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.
Conceptual design of a divertor Thomson scattering diagnostic for NSTX-U
Authors: McLean A. G. , Soukhanovskii V. A. , Allen S. L. , Carlstrom T. N. , LeBlanc B. P. , Ono M. , Stratton B. C.
Published: September 2014

A conceptual design for a divertor Thomson scattering (DTS) diagnostic has been developed for the NSTX-U device to operate in parallel with the existing multipoint Thomson scattering system. Higher projected peak heat flux in NSTX-U will necessitate application of advanced magnetics geometries and divertor detachment. Interpretation and modeling of these divertor scenarios will depend heavily on local measurement of electron temperature, Te, and density, ne, which DTS provides in a passive manner. The DTS design for NSTX-U adopts major elements from the successful DIII-D DTS system including 7-channel polychromators measuring Te to 0.5 eV. If implemented on NSTX-U, the divertor TS system would provide an invaluable diagnostic for the boundary program to characterize the edge plasma.
Field programmable gate array-assigned complex-valued computation and its limits
Authors: Bernard-Schwarz Maria , Zwick Wolfgang , Wenzel Lothar , Klier Jochen , Gröschl Martin
Published: September 2014

We discuss how leveraging Field Programmable Gate Array (FPGA) technology as part of a high performance computing platform reduces latency to meet the demanding real time constraints of a quantum optics simulation. Implementations of complex-valued operations using fixed point numeric on a Virtex-5 FPGA compare favorably to more conventional solutions on a central processing unit. Our investigation explores the performance of multiple fixed point options along with a traditional 64 bits floating point version. With this information, the lowest execution times can be estimated. Relative error is examined to ensure simulation accuracy is maintained.
Enhanced thermoelectric power in ultrathin topological insulators with magnetic doping
Authors: Tahir M. , Manchon A. , Schwingenschlögl U.
Published: September 2014

We derive analytical expressions for the magnetic moment and orbital magnetization as well as for the corresponding thermal conductivity and thermoelectric power of a topological insulator film. We demonstrate enhancement of the thermoelectric transport for decreasing film thickness and for application of an exchange field due to the tunable band gap. Combining hybridization and exchange field is particularly suitable for heat to electric energy conversion and thermoelectric cooling.
InAs quantum dot growth on AlxGa1−xAs by metalorganic vapor phase epitaxy for intermediate band solar cells
Authors: Jakomin R. , Kawabata R. M. S. , Mourão R. T. , Micha D. N. , Pires M. P. , Xie H. , Fischer A. M. , Ponce F. A. , Souza P. L.
Published: September 2014

InAs quantum dot multilayers have been grown using AlxGa1−xAs spacers with dimensions and compositions near the theoretical values for optimized efficiencies in intermediate band photovoltaic cells. Using an aluminium composition of x = 0.3 and InAs dot vertical dimensions of 5 nm, transitions to an intermediate band with energy close to the ideal theoretical value have been obtained. Optimum size uniformity and density have been achieved by capping the quantum dots with GaAs following the indium-flush method. This approach has also resulted in minimization of crystalline defects in the epilayer structure.
Real-time calibration of a feedback trap
Authors: Gavrilov Momčilo , Jun Yonggun , Bechhoefer John
Published: September 2014

Feedback traps use closed-loop control to trap or manipulate small particles and molecules in solution. They have been applied to the measurement of physical and chemical properties of particles and to explore fundamental questions in the non-equilibrium statistical mechanics of small systems. These applications have been hampered by drifts in the electric forces used to manipulate the particles. Although the drifts are small for measurements on the order of seconds, they dominate on time scales of minutes or slower. Here, we show that a recursive maximum likelihood (RML) algorithm can allow real-time measurement and control of electric and stochastic forces over time scales of hours. Simulations show that the RML algorithm recovers known parameters accurately. Experimental estimates of diffusion coefficients are also consistent with expected physical properties.
Raman spectra from ab initio molecular dynamics and its application to liquid S-methyloxirane
Authors: Luber Sandra , Iannuzzi Marcella , Hutter Jürg
Published: September 2014

We describe the calculation of Raman spectra for periodic systems via ab initio molecular dynamics (AIMD) utilizing the Gaussian and plane wave method in the program package CP2K. The electric-dipole–electric-dipole polarizability tensor has been implemented for an arbitrary shape of the simulation cell. In addition, a computationally efficient approach for its decomposition into local contributions is presented. As an example for the application of computational Raman spectroscopy to liquids, the Raman spectra of S-methyloxirane in the liquid phase have been calculated together with Raman spectra obtained from static calculations employing the double-harmonic approximation. The comparison to experimental data illustrates that a very good agreement between experiment and simulated spectra can be obtained employing AIMD, which takes into account anharmonicities and dynamical effects at ambient conditions.
The electronic structure changes and the origin of the enhanced optical properties in N-doped anatase TiO2—A theoretical revisit
Authors: Kuo Chin-Lung , Chen Wei-Guang , Chen Tzu-Ying
Published: September 2014

We have investigated the electronic structure changes and the origin of the enhanced optical properties of N-doped anatase TiO2 using first-principles density-functional theory calculations. To determine the band gap variations induced by N-doping, we developed a new approach to locate the effective valence band maximum (VBM) by characterizing the degree of localization of the N-induced states in the band structures of various N-doped TiO2 systems. Our calculations show that the band gap variations are largely affected by the local bonding structures and doping concentration of the substitutional N atoms. As the N content is up to certain level, some local bonding structures can indeed cause band gap reduction due to the formation of band-like delocalized states above the VBM of TiO2, while other local bonding configurations may simply form localized impurity states in the band gap. Accordingly, the N-induced localized and delocalized electronic states can exist simultaneously to contribute to the enhanced optical properties of anatase TiO2. Our computational approach also provides a new way to investigate the band gap engineering of other wide band gap semiconductor material systems.
Asymmetric modes decomposition in an overmoded relativistic backward wave oscillator
Authors: Zhang Dian , Zhang Jun , Zhong Huihuang , Jin Zhenxing , Ju Jinchuan
Published: September 2014

Most of the investigated overmoded relativistic backward wave oscillators (RBWOs) are azimuthally symmetric; thus, they are designed through two dimensional (2-D) particle-in-cell (PIC) simulations. However, 2-D PIC simulations cannot reveal the effect of asymmetric modes on beam-wave interaction. In order to investigate whether asymmetric mode competition needs to be considered in the design of overmoded RBWOs, a numerical method of determining the composition of both symmetric and asymmetric modes in three dimensional (3-D) PIC simulations is introduced in this paper. The 2-D and 3-D PIC simulation results of an X-band overmoded RBWO are analyzed. Our analysis indicates that the 2-D and 3-D PIC simulation results of our device are quite different due to asymmetric mode competition. In fact, asymmetric surface waves, especially EH11 mode, can lead to serious mode competition when electron beam propagates near the surface of slow wave structures (SWSs). Therefore, additional method of suppressing asymmetric mode competition, such as adjusting the reflections at both ends of SWSs to decrease the Q-factor of asymmetric modes, needs to be utilized in the design of overmoded RBWOs. Besides, 3-D PIC simulation and modes decomposition are essential for designing overmoded RBWOs.
Radiative heat transfer in anisotropic many-body systems: Tuning and enhancement
Authors: Nikbakht Moladad
Published: September 2014

A general formalism for calculating the radiative heat transfer in many body systems with anisotropic component is presented. Our scheme extends the theory of radiative heat transfer in isotropic many body systems to anisotropic cases. In addition, the radiative heating of the particles by the thermal bath is taken into account in our formula. It is shown that the radiative heat exchange (HE) between anisotropic particles and their radiative cooling/heating (RCH) could be enhanced several order of magnitude than that of isotropic particles. Furthermore, we demonstrate that both the HE and RCH can be tuned dramatically by particles relative orientation in many body systems.
Optical and mechanical mode tuning in an optomechanical crystal with light-induced thermal effects
Authors: Navarro-Urrios D. , Gomis-Bresco J. , Capuj N. E. , Alzina F. , Griol A. , Puerto D. , Martínez A. , Sotomayor-Torres C. M.
Published: September 2014

We report on the modification of the optical and mechanical properties of a silicon 1D optomechanical crystal cavity due to thermo-optic effects in a high phonon/photon population regime. The cavity heats up due to light absorption in a way that shifts the optical modes towards longer wavelengths and the mechanical modes to lower frequencies. By combining the experimental optical results with finite-difference time-domain simulations, we establish a direct relation between the observed wavelength drift and the actual effective temperature increase of the cavity. By assuming that the Young's modulus decreases accordingly to the temperature increase, we find a good agreement between the mechanical mode drift predicted using a finite element method and the experimental one.
Anisotropic elastic scattering of stripe/line-shaped scatters to two-dimensional electron gas: Model and illustrations in a nonpolar AlGaN/GaN hetero-junction
Authors: Zhang Jinfeng , Li Yao , Yan Ran , Liu Guipeng , Nie Yuhu , Zhang Jincheng , Hao Yue
Published: September 2014

In a semiconductor hetero-junction, the stripe/line-shaped scatters located at the hetero-interface lead to the anisotropic transport of two-dimensional electron gas (2DEG). The elastic scattering of infinitely long and uniform stripe/line-shaped scatters to 2DEG is theoretically investigated based on a general theory of anisotropic 2DEG transport [J. Schliemann and D. Loss, Phys. Rev. B 68(16), 165311 (2003)], and the resulting 2DEG mobility along the applied electrical field is modeled to be a function of the angle between the field and the scatters. The anisotropy of the scattering and the mobility originate in essence from that the stripe/line-shaped scatters act upon the injecting two-dimensional wave vector by changing only its component perpendicular to the scatters. Three related scattering mechanisms in a nonpolar AlGaN/GaN hetero-junction are discussed as illustrations, including the striated morphology caused interface roughness scattering, and the polarization induced line charge dipole scattering and the misfit dislocation scattering at the AlGaN/GaN interface. Different anisotropic behaviors of the mobility limited by these scattering mechanisms are demonstrated, but analysis shows that all of them are determined by the combined effects of the anisotropic bare scattering potential and the anisotropic dielectric response of the 2DEG.
Effect of Ni precursor solution concentration on the magnetic properties and exchange bias of Ni-NiO nanoparticulate systems
Authors: Roy Aparna , De Toro J. A. , Amaral V. S. , Marques D. P. , Ferreira J. M. F.
Published: September 2014

We report on a comparative study of the exchange bias effect and magnetic properties of Ni-NiO nanoparticulate systems synthesized by the chemical reduction of NiCl2 solution of two different molar concentrations—1 M (high) and 0.05 M (low)—followed by annealing of the dried precipitate in the temperature range 400–600 °C in air. Interestingly, the samples derived from the low molarity solution have higher Ni content and larger crystallite size than those prepared from their high molarity counterparts. These molarity dependent features subsequently modulate the magnitude of the exchange bias field in the samples, which is found to be absent or small in the 0.05 M series, but of moderate value in the 1 M samples. The different physical attributes of the particles derived from different concentrations of Ni-precursor solution are explained by invoking different nucleation kinetics and supersaturation degrees surrounding the viable growing nucleus. Furthermore, an observed increase of exchange bias with increasing annealing temperature, in contrast to the reported agglomeration of particles on annealing and subsequent reduction in bias magnitude, has been explained in correlation to the Ni-NiO interface density.
Red blood cell as a universal optoacoustic sensor for non-invasive temperature monitoring
Authors: Petrova Elena V. , Oraevsky Alexander A. , Ermilov Sergey A.
Published: September 2014

Optoacoustic (photoacoustic) temperature imaging could provide improved spatial resolution and temperature sensitivity as compared to other techniques of non-invasive thermometry used during thermal therapies for safe and efficient treatment of lesions. However, accuracy of the reported optoacoustic methods is compromised by biological variability and heterogeneous composition of tissues. We report our findings on the universal character of the normalized temperature dependent optoacoustic response (ThOR) in blood, which is invariant with respect to hematocrit at the isosbestic point of hemoglobin. The phenomenon is caused by the unique homeostatic compartmentalization of blood hemoglobin exclusively inside erythrocytes. On the contrary, the normalized ThOR in aqueous solutions of hemoglobin showed linear variation with respect to its concentration and was identical to that of blood when extrapolated to the hemoglobin concentration inside erythrocytes. To substantiate the conclusions, we analyzed optoacoustic images acquired from the samples of whole and diluted blood as well as hemoglobin solutions during gradual cooling from +37 to −15 °C. Our experimental methodology allowed direct observation and accurate measurement of the temperature of zero optoacoustic response, manifested as the sample's image faded into background and then reappeared in the reversed (negative) contrast. These findings provide a framework necessary for accurate correlation of measured normalized optoacoustic image intensity and local temperature in vascularized tissues independent of tissue composition.
Growth-temperature dependence of optical spin-injection dynamics in self-assembled InGaAs quantum dots
Authors: Yamamura Takafumi , Kiba Takayuki , Yang Xiaojie , Takayama Junichi , Subagyo Agus , Sueoka Kazuhisa , Murayama Akihiro
Published: September 2014

The growth-temperature dependence of the optical spin-injection dynamics in self-assembled quantum dots (QDs) of In0.5Ga0.5As was studied by increasing the sheet density of the dots from 2 × 1010 to 7 × 1010 cm−2 and reducing their size through a decrease in growth temperature from 500 to 470 °C. The circularly polarized transient photoluminescence (PL) of the resulting QD ensembles was analyzed after optical excitation of spin-polarized carriers in GaAs barriers by using rate equations that take into account spin-injection dynamics such as spin-injection time, spin relaxation during injection, spin-dependent state-filling, and subsequent spin relaxation. The excitation-power dependence of the transient circular polarization of PL in the QDs, which is sensitive to the state-filling effect, was also examined. It was found that a systematic increase occurs in the degree of circular polarization of PL with decreasing growth temperature, which reflects the transient polarization of exciton spin after spin injection. This is attributed to strong suppression of the filling effect for the majority-spin states as the dot-density of the QDs increases.
Diagonal-transition quantum cascade detector
Authors: Reininger Peter , Schwarz Benedikt , Detz Hermann , MacFarland Don , Zederbauer Tobias , Andrews Aaron Maxwell , Schrenk Werner , Baumgartner Oskar , Kosina Hans , Strasser Gottfried
Published: September 2014

We demonstrate the concept of diagonal transitions for quantum cascade detectors (QCD). Different to standard, vertical QCDs, here the active transition takes place between two energy levels in adjacent wells. Such a scheme has versatile advantages. Diagonal transitions generally yield a higher extraction efficiency and a higher resistance than vertical transitions. This leads to an improved overall performance, although the absorption strength of the active transition is smaller. Since the extraction is not based on resonant tunneling, the design is more robust, with respect to deviations from the nominal structure. In a first approach, a peak responsivity of 16.9 mA/W could be achieved, which is an improvement to the highest shown responsivity of a QCD for a wavelength of 8 μm at room-temperature by almost an order of magnitude.
Infrared spectroscopic and modeling studies of H2/CH4 microwave plasma gas phase from low to high pressure and power
Authors: Rond C. , Hamann S. , Wartel M. , Lombardi G. , Gicquel A. , Röpcke J.
Published: September 2014

InfraRed Tunable Diode Laser Absorption Spectroscopy technique has been implemented in a H2/CH4 Micro-Wave (MW frequency f = 2.45 GHz) plasma reactor dedicated to diamond deposition under high pressure and high power conditions. Parametric studies such as a function of MW power, pressure, and admixtures of methane have been carried out on a wide range of experimental conditions: the pressure up to 270 mbar and the MW power up to 4 kW. These conditions allow high purity Chemical Vapor Deposition diamond deposition at high growth rates. Line integrated absorption measurements have been performed in order to monitor hydrocarbon species, i.e., CH3, CH4, C2H2, C2H4, and C2H6. The densities of the stable detected species were found to vary in the range of 1012–1017 molecules cm−3, while the methyl radical CH3 (precursor of diamond growth under these conditions) measured into the plasma bulk was found up to 1014 molecules cm−3. The experimental densities have been compared to those provided by 1D-radial thermochemical model for low power and low pressure conditions (up to 100 mbar/2 kW). These densities have been axially integrated. Experimental measurements under high pressure and power conditions confirm a strong increase of the degree of dissociation of the precursor, CH4, associated to an increase of the C2H2 density, the most abundant reaction product in the plasma.
Communication: Phase diagram of C36 by atomistic molecular dynamics and thermodynamic integration through coexistence regions
Authors: Abramo M. C. , Caccamo C. , Costa D. , Munaò G.
Published: September 2014

We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C36. We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C36, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C36 fullerite and of its liquid state, at variance with what previously experienced for C60.
Perspective: Markov models for long-timescale biomolecular dynamics
Authors: Schwantes C. R. , McGibbon R. T. , Pande V. S.
Published: September 2014

Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.
Self-formation of highly aligned metallic, semiconducting and single chiral single-walled carbon nanotubes assemblies via a crystal template method
Authors: Kawai Hideki , Hasegawa Kai , Oyane Ayako , Naitoh Yasuhisa , Yanagi Kazuhiro
Published: September 2014

The fabrication of an aligned array of single-walled carbon nanotubes (SWCNTs) with a single chiral state has been a significant challenge for SWCNT applications as well as for basic science research. Here, we developed a simple, unique technique to produce assemblies in which metallic, semiconducting, and single chiral state SWCNTs were densely and highly aligned. We utilized a crystal of surfactant as a template on which mono-dispersed SWCNTs in solution self-assembled. Micro-Raman measurements and scanning electron microscopy measurements clearly showed that the SWCNTs were highly and densely aligned parallel to the crystal axis, indicating that approximately 70% of the SWCNTs were within 7° of being parallel. Moreover, the assemblies exhibited good field effect transistor characteristics with an on/off ratio of 1.3 × 105.
Impact of barrier thickness on transistor performance in AlN/GaN high electron mobility transistors grown on free-standing GaN substrates
Authors: Deen David A. , Storm David F. , Meyer David J. , Bass Robert , Binari Steven C. , Gougousi Theodosia , Evans Keith R.
Published: September 2014

A series of six ultrathin AlN/GaN heterostructures with varied AlN thicknesses from 1.5–6 nm have been grown by molecular beam epitaxy on free-standing hydride vapor phase epitaxy GaN substrates. High electron mobility transistors (HEMTs) were fabricated from the set in order to assess the impact of barrier thickness and homo-epitaxial growth on transistor performance. Room temperature Hall characteristics revealed mobility of 1700 cm2/V s and sheet resistance of 130 Ω/□ for a 3 nm thick barrier, ranking amongst the lowest room-temperature sheet resistance values reported for a polarization-doped single heterostructure in the III-Nitride family. DC and small signal HEMT electrical characteristics from submicron gate length HEMTs further elucidated the effect of the AlN barrier thickness on device performance.
High performance unipolar inverters by utilizing organic field-effect transistors with ultraviolet/ozone treated polystyrene dielectric
Authors: Huang Wei , Yu Xinge , Fan Huidong , Yu Junsheng
Published: September 2014

High performance unipolar inverters based on a significant variation of threshold voltage (Vth) of organic field-effect transistors (OFETs), which was realized by introducing UV/ozone (UVO) treatment to polystyrene (PS) dielectric, were fabricated. A controllable Vth shift of more than 10 V was obtained in the OFETs by adjusting the UVO treating time, and the unipolar inverters exhibited inverting voltage near 1/2 driving voltage and a noise margin of more than 70% of ideal value. From the analysis of scanning electron microscopy, atom force microscopy, and X-ray photoelectron spectroscopy, the dramatic controllable Vth of OFETs, which played a key role in high performance unipolar inverters, was attributed to the newly generated oxygen functional groups in the PS dielectric induced by UVO treatment.
Incidence of
q
statistics in rank distributions
Authors: Yalcin G. Cigdem , Robledo Alberto , Gell-Mann Murray
Published: September 2014

Significance

The contents presented are of prime importance to the field of generalized statistical mechanics. We fulfill a longstanding need of exhibiting the kind of abundant real-world data that match the formal developments in this subject. These are size-rank distributions for which we provide a solid bridge between experimental data and theory. Also, this work delivers a working explanation for the existing duality between the two Tsallis-type entropy expressions that generalize the canonical expression. One relates to the distribution's power-law exponent whereas the other ensures entropy extensivity. The generalized entropies arise from a drastic reduction of configurations available to the system. We argue that this phase-space contraction is farthest for ranked data of the Zipf type.
Ubiquitin-conjugating enzyme Ubc13 controls breast cancer metastasis through a TAK1-p38 MAP kinase cascade
Authors: Wu Xuefeng , Zhang Weizhou , Font-Burgada Joan , Palmer Trenis , Hamil Alexander S. , Biswas Subhra K. , Poidinger Michael , Borcherding Nicholas , Xie Qing , Ellies Lesley G. , Lytle Nikki K. , Wu Li-Wha , Fox Raymond G. , Yang Jing , Dowdy Steven F. , Reya Tannishtha , Karin Michael
Published: September 2014

Significance

We demonstrate that ubiquitin-conjugating enzyme Ubc13, whose expression is elevated in primary and metastatic breast cancer (BCa), promotes metastatic spread of BCa cells by controlling their lung-colonizing ability while having little effect on primary tumor growth. Mechanistically, Ubc13 is required for TGFβ-induced non-SMAD signaling via TAK1 and p38, a pathway that is first activated in the primary tumor. An Ubc13- and p38-dependent metastatic gene signature was identified, explaining how p38 may control metastasis and providing a measure for monitoring the effectiveness of pharmacologic p38 inhibition, which inhibits the growth of established metastatic lesions. We suggest that p38 inhibition should be considered as a potential treatment for metastatic BCa.
Named entity recognition in Bengali using system combination
Authors: Ekbal Asif , Bandyopadhyay Sivaji
Published: September 2014

This paper reports a voted Named Entity Recognition (NER) system that exploits appropriate unlabeled data. Initially, we develop NER systems using the supervised machine learning algorithms such as Maximum Entropy (ME), Conditional Random Field (CRF) and Support Vector Machine (SVM). Each of these models makes use of the language independent features in the form of different contextual and orthographic word-level features along with the language dependent features extracted from the Part-of-Speech (POS) tagger and gazetteers. Context patterns generated from the unlabeled data using an active learning method are also used as the features in each of the classifiers. A semi-supervised method is proposed to describe the measures to automatically select effective unlabeled documents as well as sentences from the unlabeled data. Finally, the supervised models are combined together into a final system by defining appropriate weighted voting technique. Experimental results for a resource-poor language like Bengali show the effectiveness of the proposed approach with the overall recall, precision and F-measure values of 93.81%, 92.18% and 92.98%, respectively.
The importance of being earnest
Authors: Callahan Laura
Published: September 2014

Mock Spanish is a register in which Spanish words or phrases are used in otherwise English language texts or utterances to evoke humor, often indexing an unflattering image of Spanish speakers. This paper examines the occurrence of Mock Spanish in mass media, of interest in part because its use there cannot be mitigated so much as is possible in private speech by factors such as the speaker’s or writer’s intentions or relationships with addressees. Participants in previous studies have cited these factors as potential attenuators of Mock Spanish’s offensiveness. Mass media is also of interest for its role in the reproduction of elite discourses. This paper’s objective is to further engage the question of Mock Spanish as a form of racist discourse, and to examine the implications for those who are users of Spanish as a second language or are in the business of training second language users of Spanish.
Biochar: an improver of nutrient and soil water availability - what is the evidence?
Authors: Scott H. L. , Ponsonby D. , Atkinson C. J.
Published: September 2014

Biochar has consistently been proposed for improving soil fertility by increasing nutrient and soil water availability. We critically reviewed the recent literature, focussing particularly on these agronomic aspects. We clarify the differences between biochar made from plant (plant-derived biochar, PDB) and animal feedstock (animal-derived biochar, ADB) and show how the pyrolysis temperature affects biochar properties. We also tabulate crop yield data against production variables using recent field and greenhouse studies. We found evidence to suggest that ADB supplies many more nutrients than PDB and that, in general, biochar can improve nutrient availability indirectly through changes in pH, CEC, soil structure, improved fertilizer efficiency, decreased nutrient leaching and may affect nutrient availability by changing nitrogenous gas release and the soil microbial community, which, under some circumstances translates into short-term, increased crop yield. Few studies however show complete nutrient budgets particularly for N and do not elaborate on the underlying mechanisms of interaction, especially with regards to microbial-induced changes. Also the longevity of the different beneficial effects is questionable as most studies are less than a year long. A synopsis of the literature concludes that biochar application promotes soil water-holding capacity, particularly in soils that are degraded or of low quality. Despite this conclusion, it is hard to find studies that have adopted methodologies which are fully appropriate to support an increase in available water, such as available water capacity and how this changes in response to crop uptake and soil drying. We conclude that the variability in biochar, due to the variable feedstock and pyrolysis process, as well as particle size and application method necessitates and also enables production of specific purpose-driven biochars to benefit particular aspects of crop production.
Variation in adaptation mechanisms of medicinal herbs to the extreme winter conditions across the North Western Himalaya
Authors: Jan Sumira , Kamili Azra N. , Hamid Rehana , Parray Javid A.
Published: September 2014

The North Western Himalaya region is characterized by extreme seasonal variability and local changes in microclimate. Plants adapted to this region demonstrate marked variability to the extreme winter conditions. This region, designated as a biodiversity hotspot, is rich in medicinal herbs, which exhibit diverse growth and adaptation mechanisms to the harsh environment. In the present study, physiological mechanisms of adaptation to the winter season conditions were compared in five medicinal herbs. Components of the photosynthetic machinery, and osmoregulation which are of importance for secondary metabolism is not well known in these alpine herbs and was studied. The medicinal herbsRumex dentatus,Atropa accuminata,Lupinus polyphyllus,Hyoscyamus niger, andLavandula officinaliswere collected before snowfall in September–November to evaluate variability in metabolic and physiological responses to the varied seasonal regimes. Plants were followed over a period of 8 weeks (summer to early winter) in three sites which vary in altitude and thereby climatic conditions: Site I, 4175 m (Pahalgam); Site II, 3748 m (Duksum Sinthan Top); and Site III, 4100 m (Mount Apharwat). Variations in photosynthetic capacity and components of the photosynthetic machinery, a range of antioxidants, antioxidant enzymes and total non-structural carbohydrates (TNC) were studied to test their involvement in adaptation schemes and secondary metabolism under the harsh winter conditions. The results demonstrate a range of adaptations to the freezing stress conditions including high photon energy use efficiency; an increase in the proportion of Chlb, carotenoid content; specific activity of the antioxidant enzymes superoxide dismutase, catalase, glutathione reductase, ascorbate peroxidase activity, and TNCs.
Lower eccentric hamstring strength and single leg hop for distance predict hamstring injury in PETE students
Authors: Goossens L. , Witvrouw E. , Vanden Bossche L. , De Clercq D.
Published: September 2014

Hamstring injuries have not been under research in physical education teacher education (PETE) students so far. Within the frame of the development of an injury prevention program, for this study we conducted an analysis of modifiable risk factors for hamstring injuries in PETE students. Hamstring injuries of 102 freshmen bachelor PETE students were registered prospectively during one academic year. Eighty‐one students completed maximum muscle strength tests of hip extensors, hamstrings, quadriceps (isometric) and hamstrings (eccentric) at the start of the academic year. Sixty‐nine of the latter completed a single leg hop for distance (SLHD). Risk factors for hamstring injuries were statistically detected using logistic regression. Sixteen hamstring injuries (0.16 injuries/student/academic year; 0.46 injuries/1000 h) occurred to 10 participants. Eight cases were included in the risk factor analysis. Lower eccentric hamstring strength (odds ratio (ODD) = 0.977; p = 0.043), higher isometric/eccentric hamstring strength ratio (ODD = 970.500; p = 0.019) and lower score on the SLHD (ODD = 0.884; p = 0.005) were significant risk factors for hamstring injury. A combination of eccentric hamstring strength test and SLHD could give a good risk analysis of hamstring injuries in PETE students. This might offer great perspectives for easily applicable screening in a clinical setting.
Tapering strategies in elite British endurance runners
Authors: Spilsbury Kate L. , Fudge Barry W. , Ingham Stephen A. , Faulkner Steve H. , Nimmo Myra A.
Published: September 2014

The aim of the study was to explore pre‐competition training practices of elite endurance runners. Training details from elite British middle distance (MD; 800 m and 1500 m), long distance (LD; 3000 m steeplechase to 10,000 m) and marathon (MAR) runners were collected by survey for 7 days in a regular training (RT) phase and throughout a pre‐competition taper. Taper duration was [median (interquartile range)] 6 (3) days in MD, 6 (1) days in LD and 14 (8) days in MAR runners. Continuous running volume was reduced to 70 (16)%, 71 (24)% and 53 (12)% of regular levels in MD, LD and MAR runners, respectively (P < 0.05). Interval running volume was reduced compared to regular training (MD; 53 (45)%, LD; 67 (23)%, MAR; 64 (34)%, P < 0.05). During tapering, the peak interval training intensity was above race speed in LD and MAR runners (112 (27)% and 114 (3)%, respectively, P < 0.05), but not different in MD (100 (2)%). Higher weekly continuous running volume and frequency in RT were associated with greater corresponding reductions during the taper (R = −0.70 and R = −0.63, respectively, both P < 0.05). Running intensity during RT was positively associated with taper running intensity (continuous intensity; R = 0.97 and interval intensity; R = 0.81, both P < 0.05). Algorithms were generated to predict and potentially prescribe taper content based on the RT of elite runners. In conclusion, training undertaken prior to the taper in elite endurance runners is predictive of the tapering strategy implemented before competition.
Future thinking improves prospective memory performance and plan enactment in older adults
Authors: Altgassen Mareike , Rendell Peter G. , Bernhard Anka , Henry Julie D. , Bailey Phoebe E. , Phillips Louise H. , Kliegel Matthias
Published: September 2014

Efficient intention formation might improve prospective memory by reducing the need for resource-demanding strategic processes during the delayed performance interval. The present study set out to test this assumption and provides the first empirical assessment of whether imagining a future action improves prospective memory performance equivalently at different stages of the adult lifespan. Thus, younger ( n = 40) and older ( n = 40) adults were asked to complete the Dresden Breakfast Task, which required them to prepare breakfast in accordance with a set of rules and time restrictions. All participants began by generating a plan for later enactment; however, after making this plan, half of the participants were required to imagine themselves completing the task in the future (future thinking condition), while the other half received standard instructions (control condition). As expected, overall younger adults outperformed older adults. Moreover, both older and younger adults benefited equally from future thinking instructions, as reflected in a higher proportion of prospective memory responses and more accurate plan execution. Thus, for both younger and older adults, imagining the specific visual–spatial context in which an intention will later be executed may serve as an easy-to-implement strategy that enhances prospective memory function in everyday life.
Lifts of longest elements to braid groups acting on derived categories
Authors: Grant Joseph
Published: September 2014

If we have a braid group acting on a derived category by spherical twists, how does a lift of the longest element of the symmetric group act? We give an answer to this question, using periodic twists, for the derived category of modules over a symmetric algebra. The question has already been answered by Rouquier and Zimmermann in a special case. We prove a lifting theorem for periodic twists, which allows us to apply their answer to the general case.

Along the way we study tensor products in derived categories of bimodules. We also use the lifting theorem to give new proofs of two known results: the existence of braid relations and, using the theory of almost Koszul duality due to Brenner, Butler, and King, the result of Rouquier and Zimmermann mentioned above.
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers
Authors: Corpas Manuel , Jimenez Rafael C. , Bongcam-Rudloff Erik , Budd Aidan , Brazas Michelle D. , Fernandes Pedro L. , Gaeta Bruno , van Gelder Celia , Korpelainen Eija , Lewitter Fran , McGrath Annette , MacLean Daniel , Palagi Patricia M. , Rother Kristian , Taylor Jan , Via Allegra , Watson Mick , Schneider Maria Victoria , Attwood Teresa K.
Published: September 2014

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide.

Availability and implementation:  http://mygoblet.org/training-portal

Contact:  manuel.corpas@tgac.ac.uk
Low-metallicity stellar halo populations as tracers of dark matter haloes
Authors: Tissera Patricia B. , Scannapieco Cecilia
Published: September 2014

We analyse the density profiles of the stellar halo populations in eight Milky Way mass galaxies, simulated within the Λcold dark matter scenario. We find that accreted stars can be well fitted by an Einasto profile, as well as any subsample defined according to metallicity. We detect a clear correlation between the Einasto fitting parameters of the low-metallicity stellar populations and those of the dark matter (DM) haloes. The correlations for stars with [Fe/H] < −3 allow us to predict the shape of the dark matter profiles within residuals of ∼10 per cent, in case the contribution from in situ stars remains small. Using Einasto parameters estimated for the stellar halo of the Milky Way and assuming the later formed with significant contributions from accreted low-mass satellite, our simulations predict α ∼ 0.15 and r2 ∼ 15 kpc for its dark matter profile. These values, combined with observed estimations of the local DM density, yield an enclosed DM mass at ∼8 kpc in the range 3.9–6.7 × 1010 M⊙, in agreement with recent observational results. These findings suggest that low-metallicity stellar haloes could store relevant information on the DM haloes. Forthcoming observations would help us to further constrain our models and predictions.
Operational Sex Ratio and Female Competition
Authors: Dillon Haley M. , Adair Lora E. , Brase Gary L.
Published: September 2014

When there is a surplus of one sex in a population, members of that sex often compete against each other for access to the scarcer sex. This chapter reviews the theoretical foundations for this phenomenon, focusing on the concept of operational sex ratio (OSR; the ratio of viable and available males to females in a given mating market) versus overall sex ratio, as well as the phylogenetic evidence of sex ratios as an important factor influencing mating behaviors. Research on human OSR and its effects is a fairly recent development but has already led to findings that are generally coherent and consistent with the nonhuman evidence. The evidence to date indicates that people who find themselves in female-disadvantaged mating markets show systematic and adaptive changes in their behaviors, including increased female intrasexual competition. The chapter concludes with discussions of additional issues and future directions for research on OSR.
‘The London Sunday Faded Slow’
Authors: Murray Alex
Published: September 2014

This essay provides an overview of recent debates in Victorian studies over the ways in which we read urban space and literature. It places these debates in a broader theoretical and historical context, emphasizing the tension between a need to pay attention to the minutiae of city life on the one hand, and the politics of mapping space more broadly on the other. In order to crystallize these debates, the essay offers a survey of Victorian responses to the London Sunday. Beginning with Dickens’s early response to sabbatarian debates, the essay moves through the key London texts of the period, from Gissing to Stevenson and Wilde, demonstrating that despite the increasing secularity of Sundays by the end of the century the singular character of the day remained.