bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational study of the rovibrational spectrum of CO2–CS2
Authors: Brown James , Wang Xiao-Gang , Carrington Tucker , Grubbs G. S. , Dawes Richard
Published: March 2014

A new intermolecular potential energy surface, rovibrational transition frequencies, and line strengths are computed for CO2–CS2. The potential is made by fitting energies obtained from explicitly correlated coupled-cluster calculations using an interpolating moving least squares method. The rovibrational Schrödinger equation is solved with a symmetry-adapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. In agreement with previous experiments, the global minimum of the potential energy surface (PES) is cross shaped. The PES also has slipped-parallel minima. Rovibrational wavefunctions are localized in the cross minima and the slipped-parallel minima. Vibrational parent analysis was used to assign vibrational labels to rovibrational states. Tunneling occurs between the two cross minima. Because more than one symmetry operation interconverts the two wells, the symmetry (−oo) of the upper component of the tunneling doublet is different from the symmetry (−ee) of the tunneling coordinate. This unusual situation is due to the multidimensional nature of the double well tunneling. For the cross ground vibrational state, calculated rotational constants differ from their experimental counterparts by less than 0.0001 cm−1. Most rovibrational states were found to be incompatible with the standard effective rotational Hamiltonian often used to fit spectra. This appears to be due to coupling between internal and overall rotation of the dimer. A simple 2D model accounting for internal rotation was used for two cross-shaped fundamentals to obtain good fits.
Gas mixing system for imaging of nanomaterials under dynamic environments by environmental transmission electron microscopy
Authors: Akatay M. Cem , Zvinevich Yury , Baumann Philipp , Ribeiro Fabio H. , Stach Eric A.
Published: March 2014

A gas mixing manifold system that is capable of delivering a stable pressure stream of a desired composition of gases into an environmental transmission electron microscope has been developed. The system is designed to provide a stable imaging environment upon changes of either the composition of the gas mixture or upon switching from one gas to another. The design of the system is described and the response of the pressure inside the microscope, the sample temperature, and sample drift in response to flow and composition changes of the system are reported.
The role of large-amplitude motions in the spectroscopy and dynamics of ${\rm H}_5^+$H5+
Authors: Lin Zhou , McCoy Anne B.
Published: March 2014

Protonated hydrogen dimer, \documentclass[12pt]{minimal}\begin{document}${\rm H}_5^+$\end{document}H5+, is the intermediate in the astrochemically important proton transfer reaction between \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ and H2. To understand the mechanism for this process, we focus on how large amplitude motions in \documentclass[12pt]{minimal}\begin{document}${\rm H}_5^+$\end{document}H5+ result in scrambling of the five hydrogen atoms in the collision complex. To this end, the one-dimensional zero-point corrected potential surfaces were mapped out as functions of reaction coordinates for the \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ + H2 collision using minimized energy path diffusion Monte Carlo [C. E. Hinkle and A. B. McCoy, J. Phys. Chem. Lett. 1, 562 (2010)]. In this study, the previously developed approach was extended to allow for the investigation of selected excited states that are expected to be involved in the proton scrambling dynamics. Specifically, excited states in the shared proton motion between the two H2 groups, and in the outer H2 bending motions were investigated. Of particular interest is the minimum distance between \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ and H2 at which all five hydrogen atoms become free to exchange. In addition, this diffusion Monte Carlo-based approach was used to determine the zero-point energy E0, the dissociation energy D0, and excitation energies associated with the vibrational motions that were investigated. The evolution of the wave functions was also studied, with a focus on how the intramolecular vibrations in \documentclass[12pt]{minimal}\begin{document}${\rm H}_5^+$\end{document}H5+ evolve into motions of \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ or H2. In the case of the proton scrambling, we find that the relevant transition states become fully accessible at separations between \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ and H2 of approximately 2.15 Å, a distance that is accessed by the excited states of \documentclass[12pt]{minimal}\begin{document}${\rm H}_5^+$\end{document}H5+ with two or more quanta in the shared proton stretch. The implications of this finding on the vibrational spectroscopy of \documentclass[12pt]{minimal}\begin{document}${\rm H}_5^+$\end{document}H5+ are also discussed.
A simple scheme for injection and extraction in compact rings
Authors: Xu H. S. , Huang W. H. , Tang C. X.
Published: March 2014

There has been great interest in building compact synchrotrons for various applications, for example, inverse Compton scattering X-ray sources. However, the beam injection and extraction in compact rings require careful design for the lack of space. In this paper, we propose a simple combined injection-extraction scheme exploiting the fringe field of existing dipole magnets instead of additional septum magnets. This scheme is illustrated by using the 4.8 m ring proposed for Tsinghua Thomson scattering X-ray source as an example. Particle tracking is applied to demonstrate the validity of this scheme.
Distortion of power law blinking with binning and thresholding
Authors: Amecke Nicole , Heber André , Cichos Frank
Published: March 2014

Fluorescence intermittency is a random switching between emitting (on) and non-emitting (off) periods found for many single chromophores such as semiconductor quantum dots and organic molecules. The statistics of the duration of on- and off-periods are commonly determined by thresholding the emission time trace of a single chromophore and appear to be power law distributed. Here we test with the help of simulations if the experimentally determined power law distributions can actually reflect the underlying statistics. We find that with the experimentally limited time resolution real power law statistics with exponents αon/off ≳ 1.6, especially if αon ≠ αoff would not be observed as such in the experimental data after binning and thresholding. Instead, a power law appearance could simply be obtained from the continuous distribution of intermediate intensity levels. This challenges much of the obtained data and the models describing the so-called power law blinking.
Finite ballooning angle effects on ion temperature gradient driven mode in gyrokinetic flux tube simulations
Authors: Singh Rameswar , Brunner S. , Ganesh R. , Jenko F.
Published: March 2014

This paper presents effects of finite ballooning angles on linear ion temperature gradient (ITG) driven mode and associated heat and momentum flux in Gyrokinetic flux tube simulation GENE. It is found that zero ballooning angle is not always the one at which the linear growth rate is maximum. The ITG mode acquires a short wavelength (SW) branch (k⊥ρi > 1) when growth rates maximized over all ballooning angles are considered. However, the SW branch disappears on reducing temperature gradient showing characteristics of zero ballooning angle SWITG in case of extremely high temperature gradient. Associated heat flux is even with respect to ballooning angle and maximizes at nonzero ballooning angle while the parallel momentum flux is odd with respect to the ballooning angle.
Investigations of the electronic and magnetic structures of Co2YGa (Y=Cr, Mn) Heusler alloys and their (100) surfaces
Authors: Hamad Bothina
Published: March 2014

Density functional theory calculations are performed to investigate the structural, electronic, and magnetic properties of bulk structures of Co2YGa (Y = Cr, Mn) Heusler alloys and the surfaces along the (100) orientation. The bulk structures of both alloys show a ferromagnetic behavior with total magnetic moments of 3.03μB and 4.09μB and high spin polarizations of 99% and 67% for Co2CrGa and Co2MnGa, respectively. The surfaces are found to exhibit corrugations due to different relaxations of the surface atoms. For the case of Co2CrGa, two surfaces preserve the half metallicity, namely those with Cr-Ga and Ga– terminations with high spin polarizations above 90%, whereas it dropped to about 50% for the other surfaces. However, the spin polarizations of Co-Co and Mn-Ga terminated surfaces remain close to that of bulk Co2MnGa alloy, whereas it is suppressed down to 17% for Co– termination. The highest local magnetic moments are found to be 3.26 μB and 4.11 μB for Cr and Mn surface atoms in Cr-Ga and Mn– terminated surfaces, respectively.
Spin polarized current from multiply-coupled rings with Zeeman-split quantum dots
Authors: Hedin Eric R. , Joe Yong S.
Published: March 2014

We investigate transmission resonances and conductance properties of multiple, serially connected, direct-contact nanoscale rings using the tight-binding model. Quantum dots (QDs) are embedded in the two arms of each ring, and Zeeman-splitting of the QD energy levels is incorporated into the system Hamiltonian. Transmission bands develop as the number of rings in series increases, with a band-gap which is sensitive to the degree of Zeeman splitting and the initial settings of the QD site energy values. The current vs. voltage characteristics of the system can be modulated between Ohmic and semiconducting as a function of the Zeeman splitting. In addition, spin-polarized current results for selected ranges of the Fermi energy.
Droplet destabilization during Bi catalyzed vapor-liquuid-solid growth of GaAs
Authors: DeJarld M. , Nothern D. , Millunchick J. M.
Published: March 2014

GaAs nanodiscs are grown in a molecular beam epitaxy chamber via the vapor-liquid-solid mechanism with liquid Bi as the catalyst. Each nanostructure consists of a series of increasingly larger overlapping discs. The structure forms during deposition due to the fact that the catalyst grows until reaching a critical size whereupon it destabilizes, dropping off the disc onto the substrate, where it catalyzes the growth of a new disc of larger radius. It is shown that critical size is limited by the sidewall wetting with a contact angle significantly smaller than the Gibb's criterion.
Sensitive magnetic force detection with a carbon nanotube resonator
Authors: Willick Kyle , Haapamaki Chris , Baugh Jonathan
Published: March 2014

We propose a technique for sensitive magnetic point force detection using a suspended carbon nanotube (CNT) mechanical resonator combined with a magnetic field gradient generated by a ferromagnetic gate electrode. Numerical calculations of the mechanical resonance frequency show that single Bohr magneton changes in the magnetic state of an individual magnetic molecule grafted to the CNT can translate to detectable frequency shifts, on the order of a few kHz. The dependences of the resonator response to device parameters such as length, tension, CNT diameter, and gate voltage are explored and optimal operating conditions are identified. A signal-to-noise analysis shows that, in principle, magnetic switching at the level of a single Bohr magneton can be read out in a single shot on timescales as short as 10 μs. This force sensor should enable new studies of spin dynamics in isolated single molecule magnets, free from the crystalline or ensemble settings typically studied.
Terahertz oscillations in an In0.53Ga0.47As submicron planar Gunn diode
Authors: Khalid Ata , Dunn G. M. , Macpherson R. F. , Thoms S. , Macintyre D. , Li C. , Steer M. J. , Papageorgiou V. , Thayne I. G. , Kuball M. , Oxley C. H. , Montes Bajo M. , Stephen A. , Glover J. , Cumming D. R. S.
Published: March 2014

The length of the transit region of a Gunn diode determines the natural frequency at which it operates in fundamental mode—the shorter the device, the higher the frequency of operation. The long-held view on Gunn diode design is that for a functioning device the minimum length of the transit region is about 1.5 μm, limiting the devices to fundamental mode operation at frequencies of roughly 60 GHz. Study of these devices by more advanced Monte Carlo techniques that simulate the ballistic transport and electron-phonon interactions that govern device behaviour, offers a new lower bound of 0.5 μm, which is already being approached by the experimental evidence that has shown planar and vertical devices exhibiting Gunn operation at 600 nm and 700 nm, respectively. The paper presents results of the first ever THz submicron planar Gunn diode fabricated in In0.53Ga0.47As on an InP substrate, operating at a fundamental frequency above 300 GHz. Experimentally measured rf power of 28 μW was obtained from a 600 nm long × 120 μm wide device. At this new length, operation in fundamental mode at much higher frequencies becomes possible—the Monte Carlo model used predicts power output at frequencies over 300 GHz.
Comment on “A case study on the scaling of 1/f noise: La2∕3Sr1∕3MnO3 thin films” [J. Appl. Phys. 113, 094901 (2013)]
Authors: Barone C. , Pagano S. , Méchin L. , Guillet B. , Routoure J.-M.
Published: March 2014

The problem of non-standard scaling of the 1/f noise in thin manganite films was revisited in the above paper, suggesting the quantum theory of fundamental flicker noise for the interpretation of the unusual dependence of the normalized Hooge parameter on the sample volume. Experimental evidence has been reported, showing that in these materials such volume dependence is, instead, an artifact of extrinsic noise sources, e.g., contact noise. Moreover, the proposed theoretical model implies a linear temperature dependence of the Hooge parameter, which is against the experimental data reported here. Based on these arguments, it is possible to conclude that the quantum theory of fundamental flicker noise cannot be applied to the case of La2∕3Sr1∕3MnO3 thin films.
Ripple field losses in direct current biased superconductors: Simulations and comparison with measurements
Authors: Lahtinen Valtteri , Pardo Enric , Šouc Ján , Solovyov Mykola , Stenvall Antti
Published: March 2014

In several superconducting applications, as, for example, in some supercondcuting generators, motors, and power transmission cables, the superconductor experiences a changing magnetic field in a DC background. Simulating the losses caused by this AC ripple field is an important task from the application design point of view. In this work, we compare two formulations, the H-formulation and the minimum magnetic energy variation-formulation, based on the eddy current model (ECM) and the critical state model (CSM), respectively, for simulating ripple field losses in a DC biased coated conductor tape. Furthermore, we compare our simulation results with measurements. We investigate the frequency-dependence of the hysteresis loss predictions of the power law based ECM and verify by measurements, that in DC use, ECM clearly over-estimates the homogenization of the current density profile in the coated conductor tape: the relaxation of the local current density is not nearly as prominent in the measurement as it is in the simulation. Hence, we suggest that the power law resistivity, used as the local relation between the electric field intensity E and current density J in ECM, is not an intrinsic property of high-temperature superconductors. The difference between the models manifests itself as discrepancies in ripple field loss simulations in very low AC fields with significant DC fields or currents involved. The results also show, however, that for many practical situations, CSM and ECM are both eligible models for ripple field loss simulations.
Resonant cantilever response of static-to-sliding transitions in dynamic friction force microscopy
Authors: Mertens F. , Göddenhenrich T. , Schirmeisen A.
Published: March 2014

Dynamic friction force microscopy is a valuable tool for the investigation of friction properties on the nanometer scale. The measuring technique is based on a longitudinal tip-sample modulation, leading to bending cantilever oscillations. A lock-in detection scheme is used to determine the lever response amplitude as a measure of the longitudinal tip-sample interaction. Here, we present an approach which monitors the resonance frequencies of the cantilever during an off-resonance sample modulation. Our experiments and simulations indicate that this oscillation behavior changes characteristically with increasing modulation amplitude at the static-to-sliding transition and can be used as an imaging technique.
High-frequency switching of magnetic bistability in an asymmetric double disk nanostructure
Authors: Stebliy Maxim E. , Ognev Alexey V. , Samardak Alexander S. , Kolesnikov Alexander G. , Chebotkevich Ludmila A. , Han Xiufeng
Published: March 2014

We propose a magnetoresistive memory cell on the basis of the three dimensional nanostructure “small disk on big disk” possessing the three stable configurations of magnetization. Magnetic behavior of magnetostatically interacting nanodisks under an impact of the high frequency excitation has been studied by means of micromagnetic simulation. The movement of a vortex core in the big disk can induce a change in magnetization configuration in the small one. We prove that magnetic state variation in the double disk nanostructure can be registered by the transverse magnetoresistance measurement.
A stable frequency comb directly referenced to rubidium electromagnetically induced transparency and two-photon transitions
Authors: Hou Dong , Wu Jiutao , Zhang Shuangyou , Ren Quansheng , Zhang Zhigang , Zhao Jianye
Published: March 2014

We demonstrate an approach to create a stable erbium-fiber-based frequency comb at communication band by directly locking the combs to two rubidium atomic transitions resonances (electromagnetically induced transparency absorption and two-photon absorption), respectively. This approach directly transfers the precision and stability of the atomic transitions to the comb. With its distinguishing feature of compactness by removing the conventional octave-spanning spectrum and f-to-2f beating facilities and the ability to directly control the comb's frequency at the atomic transition frequency, this stable optical comb can be widely used in optical communication, frequency standard, and optical spectroscopy and microscopy.
Device for detailed analysis of leakage current paths in photovoltaic modules under high voltage bias
Authors: Dhere Neelkanth G. , Shiradkar Narendra S. , Schneller Eric
Published: March 2014

High voltages used in photovoltaic (PV) systems are known to induce long-term power loss in PV modules due to leakage current flowing through the module packaging materials. It has been difficult to identify the specific materials and interfaces responsible for degradation based on an analysis of only the total leakage current. A detailed investigation of the leakage current paths within the PV modules, under high voltage bias, is carried out by utilizing a device that measures the independent contributions of various paths in real-time. Knowledge about dominant leakage current paths can be used to quantify the physical and chemical changes occurring within the module packaging materials.
Nano-scale characterization of GaAsP/GaAs strained superlattice structure by nano-beam electron diffraction
Authors: Jin Xiuguang , Nakahara Hirotaka , Saitoh Koh , Tanaka Nobuo , Takeda Yoshikazu
Published: March 2014

Distribution of lattice strain in a GaAsP/GaAs superlattice with a periodicity of 10 nm thickness, deposited on a 100 nm GaAs basal layer has been measured by nano-beam electron diffraction. The superlattice on the (001) plane of the basal GaAs layer shows a constant lattice strain from the bottom to the top layers, whereas the superlattice on the basal GaAs surface sloped by 16° from the (001) plane shows a variation of the lattice strain and crystal orientation. The difference of the strain distributions was discussed from the viewpoint of average strain. This tilt was explained by an atomistic model.
Magnetic anisotropy of non-interacting collinear nanocrystal-chains
Authors: Charilaou M. , Kind J. , García-Rubio I. , Schüler D. , Gehring A. U.
Published: March 2014

The magnetic anisotropy of linear chains of spherical magnetite nanocrystals was investigated by means of angle-resolved ferromagnetic resonance spectroscopy, in order to determine the different anisotropy contributions. The linear assembly of nanocrystals generates an interaction-induced uniaxial anisotropy, which is nearly an order of magnitude stronger than the intrinsic magnetocrystalline anisotropy of magnetite, and can only exist in magnetic nano-chains, where the easy axes of the nanocrystals are collinear.
Assessment of the efficacy of laser hyperthermia and nanoparticle-enhanced therapies by heat shock protein analysis
Authors: Tang Fei , Zhang Ye , Zhang Juan , Guo Junwei , Liu Ran
Published: March 2014

Tumor thermotherapy is a method of cancer treatment wherein cancer cells are killed by exposing the body tissues to high temperatures. Successful clinical implementation of this method requires a clear understanding and assessment of the changes of the tumor area after the therapy. In this study, we evaluated the effect of near-infrared laser tumor thermotherapy at the molecular, cellular, and physical levels. We used single-walled carbon nanotubes (SWNTs) in combination with this thermotherapy. We established a mouse model for breast cancer and randomly divided the mice into four groups: mice with SWNT-assisted thermotherapy; mice heat treated without SWNT; mice injected with SWNTs without thermotherapy; and a control group. Tumors were irradiated using a near-infrared laser with their surface temperature remaining at approximately 45 °C. We monitored the tumor body growth trend closely by daily physical measurements, immunohistochemical staining, and H&E (hematoxylin-eosin) staining by stage. Our results showed that infrared laser hyperthermia had a significant inhibitory effect on the transplanted breast tumor, with an inhibition rate of 53.09%, and also significantly reduced the expression of the heat shock protein Hsp70. Furthermore, we have found that protein analysis and histological analysis can be used to assess therapeutic effects effectively, presenting broad application prospects for determining the effect of different treatments on tumors. Finally, we discuss the effects of SWNT-assisted near-infrared laser tumor thermotherapy on tumor growth at the molecular, cellular, and physical levels.
Imprinting antivortex states from ferromagnetic Fe into antiferromagnetic NiO in epitaxial NiO/Fe/Ag(001) microstructures
Authors: Li J. , Tan A. , Moon K. W. , Doran A. , Marcus M. A. , Young A. T. , Arenholz E. , Ma S. , Yang R. F. , Hwang C. , Qiu Z. Q.
Published: March 2014

Magnetic vortex and antivortex are the two basic topological states in magnetic systems. While the ferromagnetic (FM) vortex state can be formed spontaneously and be imprinted into an antiferromagnetic (AFM) layer in AFM/FM disks, the antivortex state has never been realized in AFM films. By fabricating single crystalline NiO/Fe/Ag(001) microstructures, we show that the magnetic antivortex state can be created in the Fe microstructures and imprinted into the AFM NiO layer.
Single molecule tunneling spectroscopy investigation of reversibly switched dipolar vanadyl phthalocyanine on graphite
Authors: Zhang Jialin , Wang Zhunzhun , Niu Tianchao , Li Zhenyu , Chen Wei
Published: March 2014

We report a spatially resolved scanning tunneling spectroscopy (STS) investigation of reversibly switchable dipolar vanadyl phthalocyanine (VOPc) on graphite by using low temperature scanning tunneling microscopy. VOPc molecule can be switched between O-up and O-down configurations by changing the polarity of the pulse voltage applied to the tip, actuated by the inelastic tunneling electrons. The spatially resolved STS measurements allow the identification of the electronic structures of VOPc with different dipole orientation. The present approach provides geometry images and electronic characterization of a molecular switch on surface spontaneously.
Enhanced performance of wearable piezoelectric nanogenerator fabricated by two-step hydrothermal process
Authors: Qiu Yu , Lei Jixue , Yang Dechao , Yin Bing , Zhang Heqiu , Bian Jiming , Ji Jiuyu , Liu Yanhong , Zhao Yu , Luo Yingmin , Hu Lizhong
Published: March 2014

A simple two-step hydrothermal process was proposed for enhancing the performance of the nanogenerator on flexible and wearable terylene-fabric substrate. With this method, a significant enhancement in output voltage of the nanogenerator from ∼10 mV to 7 V was achieved, comparing with the one by conventional one-step process. In addition, another advantage with the devices synthesized by two-step hydrothermal process was that their output voltages are only sensitive to strain rather than strain rate. The devices with a high output voltage have the ability to power common electric devices and will have important applications in flexible electronics and wearable devices.
SiO2/SiC structures annealed in D218O: Compositional and electrical effects
Authors: Pitthan E. , Corrêa S. A. , Soares G. V. , Boudinov H. I. , Stedile F. C.
Published: March 2014

Effects of water vapor annealing on SiO2/4H-SiC structures formed following different routes were investigated using water isotopically enriched in 18O and 2H (D). Isotopic exchange between oxygen from the water vapor and oxygen from SiO2 films deposited on 4H-SiC was observed in the whole depth of the films, differently from the behavior of SiO2 films thermally grown on 4H-SiC. The highest amount of D was obtained in the sample with the highest negative fixed charge concentration, suggesting that the D incorporation occurs in defects in the structure that exist prior to the annealing. As a consequence of the water annealing, a significant reduction in the negative effective charge in metal-oxide-semiconductor capacitors and the removal of the SiO2/SiC interfacial region was observed, attributed to the reduction of the amount of SiOxCy compounds in the interfacial region.
Plasmonic planar antenna for wideband and efficient linear polarization conversion
Authors: Lévesque Quentin , Makhsiyan Mathilde , Bouchon Patrick , Pardo Fabrice , Jaeck Julien , Bardou Nathalie , Dupuis Christophe , Haïdar Riad , Pelouard Jean-Luc
Published: March 2014

In this Letter, we demonstrate both theoretically and experimentally that plasmonic planar L-shaped antenna can nearly totally convert the linear polarization of light with a high efficiency in the infrared (3–5 μm). The nanoantenna geometry is engineered so that the polarization conversion occurred on a 1 μm-wide band ([3.25–4.25] μm) with a mean polarization conversion ratio of 95%. We show that this effect is due to two localized resonances in the L-shaped antenna, which wavelengths are tunable with the in-plane geometry of the nanoantenna. Eventually, the angular independence of the polarization conversion effect is evidenced.
A loss-based, magnetic field sensor implemented in a ferrofluid infiltrated microstructured polymer optical fiber
Authors: Candiani A. , Argyros A. , Leon-Saval S. G. , Lwin R. , Selleri S. , Pissadakis S.
Published: March 2014

We report an in-fiber magnetic field sensor based on magneto-driven optical loss effects, while being implemented in a ferrofluid infiltrated microstructured polymer optical fiber. We demonstrate that magnetic field flux changes up to 2000 gauss can be detected when the magnetic field is applied perpendicular to the fiber axis. In addition, the sensor exhibits high polarization sensitivity for the interrogated wavelengths, providing the possibility of both field flux and direction measurements. The underlying physical and guidance mechanisms of this sensing transduction are further investigated using spectrophotometric, light scattering measurements, and numerical simulations, suggesting photonic Hall effect as the dominant physical, transducing mechanism.
Recognition of two new species of freshwater crabs from the Seychelles based on molecular evidence (Potamoidea : Potamonautidae)
Authors: Cumberlidge Neil , Daniels Savel R.
Published: March 2014

The Afrotropical freshwater crab genus Seychellum is endemic to the granitic Seychelles in the Indian Ocean (Mahé, Silhouette, Praslin, La Digue and Frégate). Here we describe two new cryptic species of Seychellum that represent two evolutionarily separate lineages of a previously monotypic genus. This raises to three the number of species of freshwater crabs known from Seychelles. Each species is endemic to either one island (Silhouette) or to a pair of islands (Mahé and Frégate, or Praslin and La Digue). The three species can be clearly distinguished as separate lineages by DNA analysis, haplotyping and examination of gonopod characters. The recognition of S. silhouette, sp. nov. (endemic to Silhouette) and S. mahefregate, sp. nov. (endemic to Mahé and Frégate) reduces the range of the type species, S. alluaudi (A. Milne-Edwards & Bouvier, 1893) to La Digue and Praslin. Both dispersal and vicariance may have played a role in shaping the present distribution patterns of the Seychellois freshwater crabs.
Repetition in visual word identification: Benefits and costs
Authors: Burt Jennifer S. , Kipps Tahli J. , Matthews Julian R.
Published: March 2014

University students performed lexical tasks with visually presented target words after the presentation of an identical or unrelated prime, at short (80–120 ms) or longer (410–710 ms) prime–target stimulus onset asynchronies (SOAs). Experiment 1 showed perceptual identification benefits in vocal responding at a short SOA that were reduced (accuracy) or reversed (latency) at a longer SOA. Experiment 2 showed a transition from a repetition benefit to a cost over 3 SOAs in a target-masked version of the lexical decision task (LDT; target displayed for only 141 ms). In Experiment 3 the repetition cost was replicated at a 530-ms SOA in the LDT with masked targets, but a repetition benefit was observed in the conventional LDT (target displayed until response). The dependence of repetition costs on target masking is more consistent with biases based on episodic confusions than refractoriness of lexical representations.
Intentional attention switching in dichotic listening: Exploring the efficiency of nonspatial and spatial selection
Authors: Lawo Vera , Fels Janina , Oberem Josefa , Koch Iring
Published: March 2014

Using an auditory variant of task switching, we examined the ability to intentionally switch attention in a dichotic-listening task. In our study, participants responded selectively to one of two simultaneously presented auditory number words (spoken by a female and a male, one for each ear) by categorizing its numerical magnitude. The mapping of gender (female vs. male) and ear (left vs. right) was unpredictable. The to-be-attended feature for gender or ear, respectively, was indicated by a visual selection cue prior to auditory stimulus onset. In Experiment 1, explicitly cued switches of the relevant feature dimension (e.g., from gender to ear) and switches of the relevant feature within a dimension (e.g., from male to female) occurred in an unpredictable manner. We found large performance costs when the relevant feature switched, but switches of the relevant feature dimension incurred only small additional costs. The feature-switch costs were larger in ear-relevant than in gender-relevant trials. In Experiment 2, we replicated these findings using a simplified design (i.e., only within-dimension switches with blocked dimensions). In Experiment 3, we examined preparation effects by manipulating the cueing interval and found a preparation benefit only when ear was cued. Together, our data suggest that the large part of attentional switch costs arises from reconfiguration at the level of relevant auditory features (e.g., left vs. right) rather than feature dimensions (ear vs. gender). Additionally, our findings suggest that ear-based target selection benefits more from preparation time (i.e., time to direct attention to one ear) than gender-based target selection.
Prokka: rapid prokaryotic genome annotation
Authors: Seemann Torsten
Published: March 2014

Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers.

Availability and implementation: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/ .

Contact:  torsten.seemann@monash.edu
Lysis Onset Time as Diagnostic Rotational Thromboelastometry Parameter for Fast Detection of Hyperfibrinolysis
Authors: Dekker Simone Esther , Viersen Victor Alexander , Duvekot Anne , de Jong Merijn , van den Brom Charissa Esmé , van de Ven Peter M. , Schober Patrick , Boer Christa
Published: March 2014

Background:

Rotational thromboelastometry is increasingly used to detect hyperfibrinolysis, which is a predictor of unfavorable outcome in patients with coagulation disturbances. In an in vitro study, the authors investigated which thromboelastometric hemostatic parameters could be valuable for fast diagnosis of the severity of hyperfibrinolysis and confirmed their findings in a patient population with hyperfibrinolysis.

Methods:

Thromboelastometry was performed after adding increasing concentrations of tissue plasminogen activator (0 to 400 ng/ml) to citrated blood samples of 15 healthy volunteers. Lysis parameters included the clotting time, maximum clot firmness, maximum lysis, and lysis onset time (LOT). The relation of tissue plasminogen activator with the LOT was further investigated in a patient population with out-of-hospital cardiac arrest and hyperfibrinolysis.

Results:

The LOT showed a dose-dependent association with increasing tissue plasminogen activator concentrations. Late, intermediate, or fulminant hyperfibrinolysis was associated with an average LOT (mean ± SD) of 42.7 ± 13.8, 23.2 ± 8.2, and 17.5 ± 4.6 min in the in vitro study and estimated 42.2 ± 8.3, 29.1 ± 1.2, and 14.6 ± 7.7 min in patients, respectively. The authors found a moderately negative correlation between patient plasma tissue plasminogen activator levels and the LOT (r = −0.67; P = 0.01).

Conclusion:

This study shows that the LOT may be used for fast detection of severe hyperfibrinolysis, with a better resolution than the maximum lysis, and should be further evaluated for optimization of therapeutic strategies in patients with severe clot breakdown.
Rapid Resolution of Milk Protein Intolerance in Infancy
Authors: Lazare Farrah B. , Brand Donald A. , Marciano Tuvia A. , Daum Fredric
Published: March 2014

Objectives:

Infants with milk protein intolerance are usually switched to a casein hydrolysate or amino acid–based formula, which they continue to receive until 1 year of age, when they are rechallenged with a cow's‐milk or soy protein formula. To investigate whether some of these infants actually become tolerant sooner, this study gathered preliminary data for establishing an empirical timetable for the resolution of milk protein intolerance.

Methods:

This prospective, longitudinal cohort study enrolled infants <4 months of age receiving either breast milk or a cow's‐milk or casein hydrolysate formula who presented to a pediatric subspecialty practice during an 18‐month period and had a positive stool guaiac test. After having been successfully switched to a casein hydrolysate or amino acid formula, infants who had guaiac‐negative stools for at least 2 consecutive months were rechallenged with the formula that had necessitated the most recent switch.

Results:

Of the 25 patients enrolled in the study, 16 completed the food challenge and data collection protocol. Negative stool guaiac tests following rechallenge indicated resolution of milk protein intolerance by the time subjects reached an average age of 6.7 ± 1.0 months (mean ± standard deviation). By the age of 7 months, milk protein intolerance was resolved in 12 of the 16 infants, the remainder having resolved by 10 months.

Conclusions:

It may be reasonable to treat infants with milk protein intolerance for 2 to 3 months with a hypoallergenic formula, then rechallenge them at 6 months of age, usually without causing recurrence of the hematochezia. Rechallenging before 12 months old could result in cost savings to families and insurers.
Comparison of Light and Electron Microscopy in Measurement of Esophageal Intercellular Space in Children
Authors: Altaf Muhammad A. , Ciecierega Thomas , Szabo Sara , Miranda Adrian , Gorges Christina , Simpson Pippa , Sood Manu R.
Published: March 2014

Objectives:

A good objective marker of esophageal mucosal damage from gastroesophageal reflux disease (GERD) is lacking in children. Increased esophageal epithelial intercellular (EEIC) space measured using electron microscopy (EM) has been proposed as a surrogate of esophageal mucosal damage in adults with GERD. The aim of the present study was to compare EEIC space measured using EM and light microscopy (LM) in children with nonerosive reflux disease (NERD) with asymptomatic controls.

Methods:

Distal esophageal mucosal biopsy was used to measure EEIC space using EM in 35 NERD subjects and 8 controls. In a subset of these patients we used phase contrast LM to measure EEIC space area (26 NERD subjects and 8 controls).

Results:

The median (range) EEIC space measured using EM in the NERD group was 1.15 (0.74–1.64) μm compared with 0.93 (0.67–1.11) μm in the control group (P = 0.002). The median (range) EEIC space measured using LM was 14.4% (9.6%–26.3%) in the NERD group and 9.6% (8.5%–17.2%) in controls (P = 0.003). Using a cutoff value of 1.02 μm for normal EEIC space measured by EM, we obtained 73% sensitivity and 75% specificity to distinguish the NERD group from the control group, and using a cutoff value of 11.1% for EEIC space measured by LM, we obtained 96% sensitivity and 75% specificity.

Conclusions:

EEIC space is increased in children with NERD compared with that in controls, suggesting that changes in EEIC space can be a useful marker of esophageal mucosal injury in children with NERD. Our results suggest that the accuracy of EM and LM to evaluate EEIC space changes in NERD is comparable, and LM may be a more cost‐effective option.
Homing of invasive Burmese pythons in South Florida: evidence for map and compass senses in snakes
Authors: Pittman Shannon E. , Hart Kristen M. , Cherkiss Michael S. , Snow Ray W. , Fujisaki Ikuko , Smith Brian J. , Mazzotti Frank J. , Dorcas Michael E.
Published: March 2014

Navigational ability is a critical component of an animal's spatial ecology and may influence the invasive potential of species. Burmese pythons (Python molurus bivittatus) are apex predators invasive to South Florida. We tracked the movements of 12 adult Burmese pythons in Everglades National Park, six of which were translocated 21–36 km from their capture locations. Translocated snakes oriented movement homeward relative to the capture location, and five of six snakes returned to within 5 km of the original capture location. Translocated snakes moved straighter and faster than control snakes and displayed movement path structure indicative of oriented movement. This study provides evidence that Burmese pythons have navigational map and compass senses and has implications for predictions of spatial spread and impacts as well as our understanding of reptile cognitive abilities.
Validation of a rodent model of source memory
Authors: Crystal Jonathon D. , Alford Wesley T.
Published: March 2014

Source memory represents the origin (source) of information. Recently, we proposed that rats (
Rattus norvegicus
) remember the source of information. However, an alternative to source memory is the possibility that rats selectively encoded some, but not all, information rather than retrieving an episodic memory. We directly tested this ‘encoding failure’ hypothesis. Here, we show that rats remember the source of information, under conditions that cannot be attributed to encoding failure. Moreover, source memory lasted at least seven days but was no longer present 14 days after studying. Our findings suggest that long-lasting source memory may be modelled in non-humans. Our model should facilitate attempts to elucidate the biological underpinnings of source memory impairments in human memory disorders such as Alzheimer's disease.
Resolving the evolution of sterile worker castes: a window on the advantages and disadvantages of monogamy
Authors: Nonacs Peter
Published: March 2014

Many social Hymenoptera species have morphologically sterile worker castes. It is proposed that the evolutionary routes to this obligate sterility must pass through a ‘monogamy window’, because inclusive fitness favours individuals retaining their reproductive totipotency unless they can rear full siblings. Simulated evolution of sterility, however, finds that ‘point of view’ is critically important. Monogamy is facilitating if sterility is expressed altruistically (i.e. workers defer reproduction to queens), but if sterility results from manipulation by mothers or siblings, monogamy may have no effect or lessen the likelihood of sterility. Overall, the model and data from facultatively eusocial bees suggest that eusociality and sterility are more likely to originate through manipulation than by altruism, casting doubt on a mandatory role for monogamy. Simple kin selection paradigms, such as Hamilton's rule, can also fail to account for significant evolutionary dynamics created by factors, such as population structure, group-level effects or non-random mating patterns. The easy remedy is to always validate apparently insightful predictions from Hamiltonian equations with life-history appropriate genetic models.
Hydrogen peroxide thermochemical oscillator as driver for primordial RNA replication
Authors: Ball Rowena , Brindley John
Published: March 2014

This paper presents and tests a previously unrecognized mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been driven by self-sustained oscillatory thermochemical reactions. To test this hypothesis, a well-characterized hydrogen peroxide oscillator was chosen as the driver and complementary RNA strands with known association and melting kinetics were used as the substrate. An open flow system model for the self-consistent, coupled evolution of the temperature and concentrations in a simple autocatalytic scheme is solved numerically, and it is shown that thermochemical cycling drives replication of the RNA strands. For the (justifiably realistic) values of parameters chosen for the simulated example system, the mean amount of replicant produced at steady state is 6.56 times the input amount, given a constant supply of substrate species. The spontaneous onset of sustained thermochemical oscillations via slowly drifting parameters is demonstrated, and a scheme is given for prebiotic production of complementary RNA strands on rock surfaces.
Rear actomyosin contractility-driven directional cell migration in three-dimensional matrices: a mechano-chemical coupling mechanism
Authors: Chi Qingjia , Yin Tieying , Gregersen Hans , Deng Xiaoyan , Fan Yubo , Zhao Jingbo , Liao Donghua , Wang Guixue
Published: March 2014

Cell migration is of vital importance in many biological processes, including organismal development, immune response and development of vascular diseases. For instance, migration of vascular smooth muscle cells from the media to intima is an essential part of the development of atherosclerosis and restenosis after stent deployment. While it is well characterized that cells use actin polymerization at the leading edge to propel themselves to move on two-dimensional substrates, the migration modes of cells in three-dimensional matrices relevant toin vivoenvironments remain unclear. Intracellular tension, which is created by myosin II activity, fulfils a vital role in regulating cell migration. We note that there is compelling evidence from theoretical and experimental work that myosin II accumulates at the cell rear, either isoform-dependent or -independent, leading to three-dimensional migration modes driven by posterior myosin II tension. The scenario is not limited to amoeboid migration, and it is also seen in mesenchymal migration in which a two-dimensional-like migration mode based on front protrusions is often expected, suggesting that there may exist universal underlying mechanisms. In this review, we aim to shed some light on how anisotropic myosin II localization induces cell motility in three-dimensional environments from a biomechanical view. We demonstrate an interesting mechanism where an interplay between mechanical myosin II recruitment and biochemical myosin II activation triggers directional migration in three-dimensional matrices. In the case of amoeboid three-dimensional migration, myosin II first accumulates at the cell rear to induce a slight polarization displayed as a uropod-like structure under the action of a tension-dependent mechanism. Subsequent biochemical signalling pathways initiate actomyosin contractility, producing traction forces on the adhesion system or creating prominent motile forces through blebbing activity, to drive cells to move. In mesenchymal three-dimensional migration, cells can also take advantage of the elastic properties of three-dimensional matrices to move. A minor myosin isoform, myosin IIB, is retained by relatively stiff three-dimensional matrices at the posterior side, then activated by signalling cascades, facilitating prominent cell polarization by establishing front–back polarity and creating cell rear. Myosin IIB initiates cell polarization and coordinates with the major isoform myosin IIA-assembled stress fibres, to power the directional migration of cells in the three-dimensional matrix.