bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of the cationic Pt sites in the adsorption properties of water and ethanol on the Pt4/Pt(111) and Pt4/CeO2(111) substrates: A density functional theory investigation
Authors: Seminovski Yohanna , Tereshchuk Polina , Kiejna Adam , Da Silva Juarez L. F.
Published: September 2016

Finite site platinum particles, Ptn, supported on reduced or unreduced cerium oxide surfaces, i.e., CeO2−x(111) (0<x<12), have been employed and studied as catalysts for a wide range of applications, which includes hydrogen production using the ethanol steam reforming processes. Our atomic-level understanding of the interaction of Pt with CeO2−x has been improved in the last years; however, the identification of the active sites on the Ptn/CeO2−x(111) substrates is still far from complete. In this work, we applied density functional theory based calculations with the addition of the on-site Coulomb interactions (DFT+U) for the investigation of the active sites and the role of the Pt oxidation state on the adsorption properties of water and ethanol (probe molecules) on four selected substrates, namely, Pt(111), Pt4/Pt(111), CeO2(111), and Pt4/CeO2(111). Our results show that water and ethanol preferentially bind in the cationic sites of the base of the tetrahedron Pt4 cluster instead of the anionic lower-coordinated Pt atoms located on the cluster-top or in the surface Ce (cationic) and O (anionic) sites. The presence of the Pt4 cluster contributes to increase the adsorption energy of both molecules on Pt(111) and CeO2(111) surfaces; however, its magnitude increases less for the case of Pt4/CeO2(111). Thus, the cationic Pt sites play a crucial role in the adsorption properties of water and ethanol. Both water and ethanol bind to on-top sites via the O atom and adopt parallel and perpendicular configurations on the Pt(111) and CeO2(111) substrates, respectively, while their orientation is changed once the Pt4 cluster is involved, favoring H binding with the surface sites.
Photoelectron spectroscopy of the hydroxymethoxide anion, H2C(OH)O−
Authors: Oliveira Allan M. , Lehman Julia H. , McCoy Anne B. , Lineberger W. Carl
Published: September 2016

We report the negative ion photoelectron spectroscopy of the hydroxymethoxide anion, H2C(OH)O−. The photoelectron spectra show that 3.49 eV photodetachment produces two distinct electronic states of the neutral hydroxymethoxy radical (H2C(OH)O⋅). The H2C(OH)O⋅ ground state (X̃ 2A) photoelectron spectrum exhibits a vibrational progression consisting primarily of the OCO symmetric and asymmetric stretches, the OCO bend, as well as combination bands involving these modes with other, lower frequency modes. A high-resolution photoelectron spectrum aids in the assignment of several vibrational frequencies of the neutral H2C(OH)O⋅ radical, including an experimental determination of the H2C(OH)O⋅ 2ν12 overtone of the H–OCO torsional vibration as 220(10) cm−1. The electron affinity of H2C(OH)O⋅ is determined to be 2.220(2) eV. The low-lying Ã 2A excited state is also observed, with a spectrum that peaks ∼0.8 eV above the X̃ 2A state origin. The Ã 2A state photoelectron spectrum is a broad, partially resolved band. Quantum chemical calculations and photoelectron simulations aid in the interpretation of the photoelectron spectra. In addition, the gas phase acidity of methanediol is calculated to be 366(2) kcal mol−1, which results in an OH bond dissociation energy, D0(H2C(OH)O–H), of 104(2) kcal mol−1, using the experimentally determined electron affinity of the hydroxymethoxy radical.
The near-IR spectrum of NO(X̃2Π)-He detected through excitation into the Ã-state continuum: A joint experimental and theoretical study
Authors: Beutner V. , Zhang S. G. , Meyer H. , Kłos J.
Published: September 2016

We present the first measurement of a bound-state spectrum of the NO–He complex. The recorded spectrum is associated with the first overtone transition of the NO moiety. The IR absorption is detected by exciting the vibrationally excited complex to the Ã-state dissociation continuum. The resulting NO(A) fragment is subsequently ionized in the same laser pulse. We recorded two bands centered around the NO monomer rotational lines, Q11(0.5) and R11(0.5), consistent with an almost free rotation of the NO fragment within the complex. The origin of the spectrum is found at 3724.06 cm−1 blue shifted by 0.21 cm−1 from the corresponding NO monomer origin. The rotational structures of the spectrum are found to be in very good agreement with calculated spectra based on bound states derived from a set of high level ab initio potential energy surfaces [Kłos et al. J. Chem. Phys. 112, 2195 (2000)].
Q-band 4-state phase shifter in planar technology: Circuit design and performance analysis
Authors: Villa E. , Cagigas J. , Aja B. , de la Fuente L. , Artal E.
Published: September 2016

A 30% bandwidth phase shifter with four phase states is designed to be integrated in a radio astronomy receiver. The circuit has two 90° out-of-phase microwave phase-shifting branches which are combined by Wilkinson power dividers. Each branch is composed of a 180° phase shifter and a band-pass filter. The 180° phase shifter is made of cascaded hybrid rings with microwave PIN diodes as switching devices. The 90° phase shift is achieved with the two band-pass filters. Experimental characterization has shown significant results, with average phase shift values of −90.7°, −181.7°, and 88.5° within the operation band, 35–47 GHz, and mean insertion loss of 7.4 dB. The performance of its integration in a polarimetric receiver for radio astronomy is analyzed, which validates the use of the presented phase shifter in such type of receiver.
Statistics of silicate units in binary glasses
Authors: Gaddam Anuraag , Montagne Lionel , Ferreira José M. F.
Published: September 2016

In this paper, we derive a new model to determine the distribution of silicate units in binary glasses (or liquids). The model is based on statistical mechanics and assumes grand canonical ensemble of silicate units which exchange energy and network modifiers from the reservoir. This model complements experimental techniques, which measure short range order in glasses such as nuclear magnetic resonance (NMR) spectroscopy. The model has potential in calculating the amounts of liquid-liquid phase segregation and crystal nucleation, and it can be easily extended to more complicated compositions. The structural relaxation of the glass as probed by NMR spectroscopy is also reported, where the model could find its usefulness.
Simultaneous specific heat, thermal conductivity and imaging evaluations in thin samples of 8CB liquid crystal dispersed with microemulsion of DDAB/water micelles
Authors: Paoloni S. , Mercuri F. , Zammit U.
Published: September 2016

In this work we use a photopyroelectric calorimetric set up to analyze the transformations occurring in thin samples of liquid crystal–microemulsion system by combining the results of the simultaneously performed high temperature resolution polarization microscopy observations and the temperature dependence of the specific heat, and of the thermal conductivity. This enabled an accurate direct correlation of the observations concerning the different measured quantities for a most comprehensive interpretation of the obtained results. It is found that the I-N conversion progresses in the entire nematic range because of the micelles expelled from the nucleating nematic volumes remaining confined in the residual isotropic material. A hysteretic behavior is observed in the nematic range between cooling and heating run because of the different micelle content in the material during the cooling and heating runs. A moderate hysteresys also over the N-A transition indicated an additional material refinement from micelles during the transition. Finally in samples with different micelle concentration the same maximum micelle content is retained in the nematic and smectic phases.
Controllable growth and electrostatic properties of Bernal stacked bilayer MoS2
Authors: Hao Song , Yang Bingchu , Gao Yongli
Published: September 2016

Compared with the most studied monolayer MoS2, bilayer MoS2 possesses many distinct fascinating physical properties and potential applications owing to interlayer interactions and structural symmetry. Here, bilayer MoS2 domains with strict identical AB Bernal stacked order were controllably synthesized using chemical vapor deposition method. In addition, the electrostatic properties of bilayer MoS2 were systematically investigated by multiple means of photoemission electron microscopy, electrostatic force microscopy, and kelvin probe force microscopy. We found that the work function of monolayer MoS2 is homogeneous across single crystals and polycrystalline films except for grain boundaries. However, the work function of the Bernal stacked bilayer MoS2 decreases by 50 ± 4 meV compared with that of monolayer MoS2 due to the interlayer coupling and screening effects. The deeper understanding gained here on the electrostatic properties of the AB Bernal stacked bilayer MoS2 should help in the creation of next-generation electronic and optoelectronic devices.
Electric field induced upconversion fluorescence enhancement and its mechanism in Er3+ doped 0.75Pb(Mg1/3Nb2/3)O3-0.25PbTiO3 transparent ceramic
Authors: Liang Zhang , Sun Enwei , Liu Ziyi , Zhang Zhiguo , Zeng Jiangtao , Ruan Wei , Li Guorong , Cao Wenwu
Published: September 2016

We have conducted an in-situ upconversion (UC) mechanism study through fluorescence enhancement induced by electric field in the Er3+ doped 0.75Pb(Mg1/3Nb2/3)O3-0.25PbTiO3 transparent ceramic. Under the excitation of a 980 nm diode laser, the sample shows a strong green UC fluorescence, which increases with electric field. A maximum enhancement of 150% was achieved in fluorescence intensity by the applied electric field due the lowering of crystal symmetry by the electric field induced strains. Combined with an in-situ analysis of time-resolved spectra, we proved that the dominant UC mechanism in this system should be the energy transfer (ET) process.
Interactions between Mn dopant and oxygen vacancy for insulation performance of BaTiO3
Authors: Chikada Shunsuke , Kubota Teppei , Honda Atsushi , Higai Shin'ichi , Motoyoshi Yasuhiro , Wada Nobuyuki , Shiratsuyu Kosuke
Published: September 2016

We performed first-principles calculations and electron spin resonance (ESR) measurements on Mn-doped perovskite BaTiO3 (BT) ceramics in order to investigate the interactions between Mn dopant and O vacancy (VO). We discovered the following two. First, VOs are stabilized at the nearest neighbor O site of Mn at a Ti site and this results in the suppression of VO diffusion. Second, electrons generated by the formation of VOs are trapped in unoccupied Mn-3d orbitals in the BT bandgap. This indicates that the valence state of Mn changes according to the VO density. We synthesized Mn-doped BT by varying the partial pressure of O2 gas and examined the Mn valence states with ESR measurements. We successfully observed that the majority type of Mn ions (2+, 3+, and 4+) depends on O2 gas pressure of the firing atmosphere. According to these theoretical and experimental investigations, we concluded that Mn dopants have two effects, i.e., VO and electron carrier trapping. Moreover, the mechanisms of Mn doping in BT improved the insulation resistance, and the reliability of BT-based ceramic capacitors/condensers were thoroughly examined.
Structural order and disorder in strongly coupled Yukawa liquids
Authors: Shahzad Aamir , He Mao-Gang
Published: September 2016

The order-disorder structures (OD-structures) and the corresponding Yukawa thermal conductivity along with energies of three-dimensional strongly coupled Yukawa liquids (SCYLs) have been investigated by employing a modified homogenous nonequilibrium molecular dynamics (HNEMD) technique. The obtained results for Yukawa thermal conductivity with suitable normalization are measured over a wide range of various plasma states of the plasma coupling (Γ) and screening length (κ) in a canonical ensemble (NVT). The new HNEMD simulations indicate that the Yukawa system remains in disorder or weak to intermediate order states at the minimum value of thermal conductivity. In our new simulations, the system size does not affect the behavior of the lattice correlation [Ψ(τ)] while the long range order shifts toward high Γ with an increment of κ. The calculations for OD-structures show that the plasma system remains in the nonideal strongly coupled range during the complete simulation time. Investigations show that the Yukawa kinetic energy is not affected by the system size and it is also independent of time steps (Δτ) and κ but it depends on the system temperature (=1/Γ). The calculations show that the potential energy has its maximum when the Yukawa system remains in the moderate to higher degree of order (strongly coupled regime) and has a minimum value when system is in the disorder state (nonideal gas range). It is shown that an alternative method is employed to compute the long range order in dusty plasma systems, for making the HNEMD simulations very efficient and can be used to predict the OD-structures in 3D nonideal SCYLs.
Electron-acoustic solitary waves in a beam plasma with electron trapping and nonextensivity effects
Authors: Ali Shan S. , Aman-ur-Rehman  , Mushtaq A.
Published: September 2016

A theoretical investigation is carried out for understanding the properties of electron-acoustic solitary waves (EASWs) in a beam plasma whose constituents are a cold beam electron fluid, hot nonextensive electrons obeying a vortex-like distribution with nonextensive factor q, and stationary ions. An energy integral (Schamel KdV) equation is derived by employing pseudo-potential (reductive perturbation) approach. The presence of nonextensive q-distributed hot trapped electrons and cold electron beam has been shown to influence the soliton structure quite significantly. The nonlinear dispersion relation is derived to analyze the dependency of the electron acoustic solitary wave quantities. From the analysis of our results, it is shown that the present plasma model supports the compressive EASWs. As the real plasma situations are observed with plasma species having a relative flow, so our present analysis should be useful for understanding the electrostatic solitary structures observed in the dayside auroral zone and other regions of the magnetosphere.
Relation between plasma velocity and power spectrum density in atmospheric-pressure plasma plume
Authors: Yambe Kiyoyuki , Masuda Seiya
Published: September 2016

The atmospheric pressure plasma generated using a quartz tube, helium gas, and foil electrode by applying AC high voltage is investigated. A plasma plume is formed with a small bullet-like volume of plasma that travels at high speed inside of the quartz tube filled with a helium gas. The average movement velocity of the plasma bullet and the emitted light from helium plasma are observed inside the quartz tube. Both the average plasma bullet velocity and the power spectrum density (PSD) of the helium ion (He I) tend to decrease towards the tip of the plasma plume. The average plasma bullet velocity is linearly proportional to the PSD of He I. Therefore, the movement velocity of the plasma bullet is available to estimate from the PSD of He I at one measurement point.
Half-flat vs. atomically flat: Alkyl monolayers on morphologically controlled Si(100) and Si(111) have very similar structure, density, and chemical stability
Authors: DeBenedetti William J. I. , Li Thomas L. , Hines Melissa A.
Published: September 2016

Chemists have long preferred the Si(111) surface for chemical functionalization, as a simple aqueous etch can be used to produce ideal, atomically flat H/Si(111) surfaces for subsequent reactions. In contrast, industry-standard etches produce rough H/Si(100) surfaces terminated by nanohillocks. The recent discovery of an aqueous etch that produces morphologically controlled H/Si(100) surfaces with a near atomically flat or “half-flat” morphology challenges the assumption that Si(111) is an inherently preferable starting point for chemical functionalization. This study shows that alkyl functionalization of morphologically controlled, “half-flat” Si(100) surfaces by terminal alkenes produces dense, tightly packed monolayers that are essentially identical to those on atomically flat Si(111). The striking similarity between the infrared spectra on these two surfaces — in terms of absolute absorbance, line shape and position, and polarization dependence — strongly suggests that alkyl monolayers on morphologically controlled Si(111) and Si(100) have essentially identical structures. The principle difference between the two surfaces is the amount of residual H at the Si/organic interface, a difference that is dictated by the structure of the Si(100) surface. Alkyl monolayers on morphologically controlled Si(111) and Si(100) surfaces were shown to be equally resistant to harsh oxidants. As a result, there appears to be no chemical reason to prefer one surface over the other, at least for functionalization with terminal alkenes.
Fully vaporized electrical explosion of bare tungsten wire in vacuum
Authors: Shi Huantong , Zou Xiaobing , Wang Xinxin
Published: September 2016

A flashover switch inserted between the cathode and wire end was used to enhance the deposition energy into an exploding wire in vacuum. It was found that this flashover switch can play two roles. The first one is to reduce the rise time of the current pulse, the second and more important one to greatly improve the surface radial electric field and suppress the electronic emission that is responsible for triggering the surface breakdown of the exploding wire. Only when the flashover switch is on the cathode, the second one can take effect and result in a much higher deposition energy. In this case, the deposition energy could increase by ∼three times (3.4 eV/atom–12 eV/atom) under the negative current pulse and by ∼two times (5.7 eV/atom–13 eV/atom) under the positive one, and fully vaporized wire core was observed with laser interferometry.
Tracking the amorphous to epitaxial transition in RF-sputtered cubic BFO-STO heterojunctions by means of X-ray photoelectron diffraction
Authors: Giampietri Alessio , Drera Giovanni , Píš Igor , Magnano Elena , Sangaletti Luigi
Published: September 2016

The epitaxial growth of cubic BiFeO3 ultrathin films on SrTiO3 (001) substrates by off-axis RF sputtering is demonstrated, suitable to X-ray spectroscopies interface investigation. X-ray photoelectron diffraction is used as a tool to probe the long-range crystal order and to track the transition from amorphous to epitaxial growth as a function of deposition parameters. Further spectroscopic measurements, in particular, X-ray linear dichroism on the Fe L3,2 edge, confirm the heteroepitaxial growth of BiFeO3 and clearly indicate a 3+ valence state for the iron cation. Finally, XPS is used to reconstruct the band alignment diagram, which results in a staggered configuration with a remarkable energy shift of the SrTiO3 band edges which can ultimately favor the n-type doping of SrTiO3.
Role of V-pits in the performance improvement of InGaN solar cells
Authors: Arif Muhammad , Salvestrini Jean-Paul , Streque Jérémy , Jordan Matthew B. , El Gmili Youssef , Sundaram Suresh , Li Xin , Patriarche Gilles , Voss Paul L. , Ougazzaden Abdallah
Published: September 2016

We study the influence of V-pits on the overall conversion efficiency of bulk In0.12Ga0.88N based heterojunction solar cells grown by MOVPE. We show that V-pits significantly enhances the extraction of the photogenerated carriers in the InGaN absorber, resulting in a peak external quantum efficiency of 79% and a short circuit current density (twice the state of the art) of 2.56 mA/cm−2 under AM 1.5G conditions.
Hexagonal boron-nitride nanomesh magnets
Authors: Ohata C. , Tagami R. , Nakanishi Y. , Iwaki R. , Nomura K. , Haruyama J.
Published: September 2016

The formation of magnetic and spintronic devices using two-dimensional (2D) atom-thin layers has attracted attention. Ferromagnetisms (FMs) arising from zigzag-type atomic structure of edges of 2D atom-thin materials have been experimentally observed in graphene nanoribbons, hydrogen (H)-terminated graphene nanomeshes (NMs), and few-layer oxygen (O)-terminated black phosphorus NMs. Herein, we report room-temperature edge FM in few-layer hexagonal boron-nitride (hBN) NMs. O-terminated hBNNMs annealed at 500 °C show the largest FM, while it completely disappears in H-terminated hBNNMs. When hBNNMs are annealed at other temperatures, amplitude of the FM significantly decreases. These are highly in contrast to the case of graphene NMs but similar to the cases of black phosphorus NM and suggest that the hybridization of the O atoms with B(N) dangling bonds of zigzag pore edges, formed at the 500 °C annealing, strongly contribute to this edge FM. Room-temperature FM realizable only by exposing hBNNMs into air opens the way for high-efficiency 2D flexible magnetic and spintronic devices without the use of rare magnetic elements.
Fully magnetic manganite spin filter tunnel junctions
Authors: Prasad Bhagwati , Blamire Mark G.
Published: September 2016

In this paper we demonstrate spintronic devices which combine magnetic tunnel junctions with a spin-filtering tunnel barrier. These consist of an ultrathin ferromagnetic insulating barrier, Sm0.75Sr0.25MnO3, sandwiched between two ferromagnetic half-metallic manganite electrodes, La0.7Sr0.3MnO3 and La0.7Ca0.3MnO3, in a nanopillar structure. Depending on the relative magnetic configurations of barrier and electrode layers, three resistance states are well defined, which therefore represent a potential three-state memory concept. These results open the way for the development of spintronic devices by exploiting the many degrees of freedom of perovskite manganite heterostructure systems.
AlGaN channel field effect transistors with graded heterostructure ohmic contacts
Authors: Bajaj Sanyam , Akyol Fatih , Krishnamoorthy Sriram , Zhang Yuewei , Rajan Siddharth
Published: September 2016

We report on ultra-wide bandgap (UWBG) Al0.75Ga0.25N channel metal-insulator-semiconductor field-effect transistors (MISFETs) with heterostructure engineered low-resistance ohmic contacts. The low intrinsic electron affinity of AlN (0.6 eV) leads to large Schottky barriers at the metal-AlGaN interface, resulting in highly resistive ohmic contacts. In this work, we use a reverse compositional graded n++ AlGaN contact layer to achieve upward electron affinity grading, leading to a low specific contact resistance (ρsp) of 1.9 × 10−6 Ω cm2 to n-Al0.75Ga0.25N channels (bandgap ∼5.3 eV) with non-alloyed contacts. We also demonstrate UWBG Al0.75Ga0.25N channel MISFET device operation employing the compositional graded n++ ohmic contact layer and 20 nm atomic layer deposited Al2O3 as the gate-dielectric.
Specific heat critical behavior in Bi1-xSbx solid solutions
Authors: Rogacheva E. I. , Doroshenko A. N. , Nashchekina O. N. , Dresselhaus M. S.
Published: September 2016

Studies of the specific heat Cp room temperature concentration dependences for the Bi1-xSbx (x = 0–0.12) solid solutions have shown that in the Cp(x) curves, three peaks of Cp are observed near x = 0.015, x = 0.037, and x = 0.07. These peaks are attributed to critical phenomena accompanying second-order concentration phase transitions (PT) from dilute to concentrated solid solutions, to a gapless state, and a semimetal–semiconductor transition, respectively. The numerical values for the critical exponents of the specific heat α for the Cp peaks near x = 0.015 and x = 0.037 have been determined within the framework of fluctuation theory for second-order phase transitions and percolation theory. It was shown that the α values (α = 0.11 ± 0.005) are the same within the margin of error for both peaks and correspond to the values theoretically calculated within the framework of scale-invariant theory for three–dimensional (3D) models and determined experimentally for different physical systems undergoing second-order phase transitions.
High-photovoltage GaAs vertical epitaxial monolithic heterostructures with 20 thin p/n junctions and a conversion efficiency of 60%
Authors: Fafard S. , Proulx F. , York M. C. A. , Richard L. S. , Provost P. O. , Arès R. , Aimez V. , Masson D. P.
Published: September 2016

Photovoltaic power converting III–V semiconductor devices based on the Vertical Epitaxial HeteroStructure Architecture (VEHSA) design have been achieved with up to 20 thin p/n junctions (PT20). Open circuit photovoltages in excess of 23 V are measured for a continuous wave monochromatic optical input power of ∼1 W tuned in the 750 nm–875 nm wavelength range. Conversion efficiencies greater than 60% are demonstrated when the PT20 devices are measured near the peak of their spectral response. Noticeably, the PT20 structure is implemented with its narrowest ultrathin base having a thickness of only 24 nm. In the present study, the spectral response of the PT20 peaks at external quantum efficiency (EQE) of 89%/20 for an input wavelength of 841 nm. We also performed a detailed analysis of the EQE dependence with temperature and for VEHSA structures realised with a varied number of p/n junctions. The systematic study reveals the correlations between the measured conversion efficiencies, the EQE behavior, and the small deviations in the implementation of the optimal designs. Furthermore, we modeled the photovoltage performance of devices designed with thinner bases. For example, we derive that the narrowest subcell of a PT60 structure would have a base as thin as 8 nm, it is expected to still generate an individual subcell photovoltage of 1.14 V, and it will begin to feature 2-dimensional quantum well effects.
A thermally robust and thickness independent ferroelectric phase in laminated hafnium zirconium oxide
Authors: Riedel S. , Polakowski P. , Müller J.
Published: September 2016

Ferroelectric properties in hafnium oxide based thin films have recovered the scaling potential for ferroelectric memories due to their ultra-thin-film- and CMOS-compatibility. However, the variety of physical phenomena connected to ferroelectricity allows a wider range of applications for these materials than ferroelectric memory. Especially mixed HfxZr1-xO2 thin films exhibit a broad compositional range of ferroelectric phase stability and provide the possibility to tailor material properties for multiple applications. Here it is shown that the limited thermal stability and thick-film capability of HfxZr1-xO2 can be overcome by a laminated approach using alumina interlayers.
Electrostatic force between ellipsoids with dissimilar surface potentials
Authors: Yu Ying-Song
Published: September 2016

The electrostatic forces between ellipsoids, between an ellipsoid and a cylinder and between an ellipsoid and a plate which are immersed in a fluid have been evaluated using Derjaguin’s approximation. Both of them in the three cases have different surface potentials of less than 25 mV. We assume that the interaction range between them is distinctly smaller than the lengths of their principal axes and evaluate the electrostatic forces. Examples are given to show the effect of particle size and orientation on electrostatic force.
Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel
Authors: Cremer Jonas , Segota Igor , Yang Chih-yu , Arnoldini Markus , Sauls John T. , Zhang Zhongge , Gutierrez Edgar , Groisman Alex , Hwa Terence
Published: September 2016

Significance

The human colon is occupied by trillions of microbial cells. Recent sequencing studies have shown that many diseases lead to substantial changes in the composition of this gut microbiota and suggest a strong influence of composition on host physiology. However, not much is known about the underlying physiological factors shaping the gut microbiota. Here, we focus on the role of flow and mixing by colonic wall contractions. To grow in the proximal colon, microbes have to continuously overcome flow. Our in vitro study suggests that mixing helps to overcome flow, and controlled contractions by the colon strongly influence microbiota density and composition; flow and mixing are essential components toward developing a predictive understanding of the gut microbiota.
Functional receptor molecules CD300lf and CD300ld within the CD300 family enable murine noroviruses to infect cells
Authors: Haga Kei , Fujimoto Akira , Takai-Todaka Reiko , Miki Motohiro , Doan Yen Hai , Murakami Kosuke , Yokoyama Masaru , Murata Kazuyoshi , Nakanishi Akira , Katayama Kazuhiko
Published: September 2016

Significance

Norovirus is the leading cause of acute gastroenteritis worldwide. Since the discovery of norovirus, a receptor for norovirus internalization into cells has not been identified. Murine norovirus (MNV) binding to cells that were originally not susceptible to the virus can be mediated by ectopically expressed CD300 molecule like family members f or d (CD300lf or CD300ld). The expression of CD300lf or CD300ld is sufficient to render cells permissive to infection by the virus. We conclude that CD300lf and CD300ld are essential for MNV infection and that each molecule can function independently as the viral receptor.
Early somatic mosaicism is a rare cause of long-QT syndrome
Authors: Priest James Rush , Gawad Charles , Kahlig Kristopher M. , Yu Joseph K. , O’Hara Thomas , Boyle Patrick M. , Rajamani Sridharan , Clark Michael J. , Garcia Sarah T. K. , Ceresnak Scott , Harris Jason , Boyle Sean , Dewey Frederick E. , Malloy-Walton Lindsey , Dunn Kyla , Grove Megan , Perez Marco V. , Neff Norma F. , Chen Richard , Maeda Katsuhide , Dubin Anne , Belardinelli Luiz , West John , Antolik Christian , Macaya Daniela , Quertermous Thomas , Trayanova Natalia A. , Quake Stephen R. , Ashley Euan A.
Published: September 2016

Significance

Most genetic studies and clinical genetic testing do not look for the possibility of mosaic variation. The genetic form of long-QT syndrome (LQTS) can result in life-threatening arrhythmias, but 30% of patients do not have a genetic diagnosis. We performed deep characterization of a mosaic variant in an infant with perinatal LQTS and developed a computational model showing how abnormal cellular repolarization in only 8% of heart cells may cause arrhythmia. Finally we looked at the prevalence of mosaicism among patients with LQTS; in a population of 7,500 individuals we found evidence of pathogenic early somatic mosaicism in approximately 0.17% of LQTS patients without a genetic diagnosis. Together these data establish an unreported mechanism for LQTS and other genetic arrhythmias.
MiR-155–regulated molecular network orchestrates cell fate in the innate and adaptive immune response to
Mycobacterium tuberculosis
Authors: Rothchild Alissa C. , Sissons James R. , Shafiani Shahin , Plaisier Christopher , Min Deborah , Mai Dat , Gilchrist Mark , Peschon Jacques , Larson Ryan P. , Bergthaler Andreas , Baliga Nitin S. , Urdahl Kevin B. , Aderem Alan
Published: September 2016

Significance

The mechanism by which
Mycobacterium tuberculosis
(Mtb) modulates the host immune response is not fully understood. We have used a systems biology approach to generate a microRNA regulatory network composed of 77 microRNAs that are associated with Mtb–macrophage interactions. We have determined a unique and dual role for one of these regulators, miR-155, as a rheostat regulating the survival of both innate and adaptive immune cells. On the one hand, miR-155 maintains the survival of Mtb-infected macrophages, providing a niche favoring bacterial replication. On the other hand, miR-155 maintains the survival of Mtb-specific T cells, enabling an effective adaptive response. Our work underscores the value of systems-based prediction of pathogen-specific microRNA networks as a tool to define host–pathogen interactions.
Bridging social divides: leadership and the making of an alliance for women’s land-use rights in Morocco
Authors: Berriane Yasmine
Published: September 2016

This article analyses a women’s movement that emerged in the context of increased land commodification in Morocco. It focuses on the dynamics that characterised the making of this coalition of actors across the social divide. It mainly analyses the division of tasks among the different partners, highlighting the role played by intermediate organisations and actors in connecting and merging together local, national and international norms, practices and actors. The empowerment of this intermediate layer of leaders indicates a gradual inversion of the power hierarchy and illustrates the fluidity of domination relationships within social movements.
A spectral line survey from 17.5–250 nm of plasmas created in a magnetic confinement device
Authors: McCarthy K J , Zurro B , Hollmann E M , Sánchez J Hernández
Published: September 2016

Spectral emission lines continue to be a powerful tool for studying astrophysical, process, laser-produced, and magnetically confined plasmas, among others. Hence, numerous spectroscopy-based plasma diagnostics, from the x-ray to the infrared, make use of the relative intensity, width, displacement in wavelength, or temporal evolution of such emission lines emitted by the atoms and ions present in such plasmas. In this work, a spectral line survey, from 17.5–250 nm, is presented for electron cyclotron resonance heated (ECRH) and neutral beam injection (NBI) heated plasmas created and maintained in the TJ-II stellarator, a medium-sized magnetically confined plasma device. In these plasmas, for which hydrogen, deuterium or helium have been used as the working gas, central electron temperatures and densities up to 1 keV and 5 × 1019 m−3, respectively, are achieved. This work is a compilation of the identified spectral emission lines emitted by the working gas as well by the intrinsic and injected impurity ions in the above wavelength range. For this, spectra were recorded, over the past fifteen years of TJ-II operation, using a 1 m focal length normal incidence spectrometer equipped with a charge-coupled detector at its output focal plane. In total, almost 400 spectral emission lines from eighteen different elements have been identified using a number of atomic line emission databases.
Arl13b regulates Shh signaling from both inside and outside the cilium
Authors: Mariani Laura E. , Bijlsma Maarten F. , Ivanova Anna A. , Suciu Sarah K. , Kahn Richard A. , Caspary Tamara
Published: September 2016

The regulatory GTPase Arl13b localizes to primary cilia, where it regulates Sonic hedgehog (Shh) signaling. Missense mutations in ARL13B can cause the ciliopathy Joubert syndrome (JS), and the mouse null allele is embryonic lethal. We used mouse embryonic fibroblasts as a system to determine the effects of Arl13b mutations on Shh signaling. We tested seven different mutants—three JS-causing variants, two point mutants predicted to alter guanine nucleotide handling, one that disrupts cilia localization, and one that prevents palmitoylation and thus membrane binding—in assays of transcriptional and nontranscriptional Shh signaling. We found that mutations disrupting Arl13b’s palmitoylation site, cilia localization signal, or GTPase handling altered the Shh response in distinct assays of transcriptional or nontranscriptional signaling. In contrast, JS-causing mutations in Arl13b did not affect Shh signaling in these same assays, suggesting that these mutations result in more subtle defects, likely affecting only a subset of signaling outputs. Finally, we show that restricting Arl13b from cilia interferes with its ability to regulate Shh-stimulated chemotaxis, despite previous evidence that cilia themselves are not required for this nontranscriptional Shh response. This points to a more complex relationship between the ciliary and nonciliary roles of this regulatory GTPase than previously envisioned.
Babylonia: A Very Short Introduction
Authors: Bryce Trevor
Published: September 2016

Babylonia: A Very Short Introduction takes us on a journey of more than 2,000 years across the history and civilization of ancient Babylonia, from the emergence of its chief city, Babylon, as a village on the Euphrates in the 3rd millennium bc through phases of triumph, decline, and resurgence until its royal capital faded into obscurity in the Roman imperial era. Exploring key historical events as well as the day-to-day life of an ancient Babylonian—including the great Hammurabic, Kassite, and Nebuchadnezzar’s Neo-Babylonian empires as well as the periods of Persian and Macedonian rule under Alexander the Great—it provides a comprehensive guide to one of history’s most profound civilizations.
Cognitive Neuroscience: A Very Short Introduction
Authors: Passingham Richard
Published: September 2016

Cognitive neuroscience was born in the late 1970s when the study of patients who had suffered brain damage or injury to limited parts of the brain revealed different components and the processes taking place in the brain. Cognitive Neuroscience: A Very Short Introduction outlines the nature and scope of this relatively new field and the techniques available, focusing on investigation of the human brain. It explains what brain imaging shows, points out common misconceptions, and gives a brief overview of the different aspects of human cognition: perceiving, attending, remembering, reasoning, deciding, and acting. It concludes with a discussion of the exciting advances that may lie ahead.
The START App: a web-based RNAseq analysis and visualization resource
Authors: Nelson Jonathan W , Sklenar Jiri , Barnes Anthony P , Minnier Jessica
Published: September 2016

Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful methodology to quantify global gene expression patterns in various contexts from single cells to whole tissues. The tremendous amount of data generated by this profiling technology presents a daunting challenge in terms of effectively visualizing and interpreting results. Convenient and intuitive data interfaces are critical for researchers to easily upload, analyze and visualize their RNAseq data. We designed the START (Shiny Transcriptome Analysis Resource Tool) App with these requirements in mind. This application has the power and flexibility to be resident on a local computer or serve as a web-based environment, enabling easy sharing of data between researchers and collaborators.

Availability and Implementation

Source Code for the START App is written entirely in R and can be freely available to download at https://github.com/jminnier/STARTapp with the code licensed under GPLv3. It can be launched on any system that has R installed. The START App is also hosted on https://kcvi.shinyapps.io/START for researchers to temporarily upload their data.
Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis
Authors: Wang Sufang , Gribskov Michael
Published: September 2016

Motivation

With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo transcriptome assemblies and how the assembly quality influences downstream analysis.

Results

We used two authentic RNA-Seq datasets from Arabidopsis thaliana, and produced transcriptome assemblies using eight programs with a series of k-mer sizes (from 25 to 71), including BinPacker, Bridger, IDBA-tran, Oases-Velvet, SOAPdenovo-Trans, SSP, Trans-ABySS and Trinity. We measured the assembly quality in terms of reference genome base and gene coverage, transcriptome assembly base coverage, number of chimeras and number of recovered full-length transcripts. SOAPdenovo-Trans performed best in base coverage, while Trans-ABySS performed best in gene coverage and number of recovered full-length transcripts. In terms of chimeric sequences, BinPacker and Oases-Velvet were the worst, while IDBA-tran, SOAPdenovo-Trans, Trans-ABySS and Trinity produced fewer chimeras across all single k-mer assemblies. In differential gene expression analysis, about 70% of the significantly differentially expressed genes (DEG) were the same using reference genome and de novo assemblies. We further identify four reasons for the differences in significant DEG between reference genome and de novo transcriptome assemblies: incomplete annotation, exon level differences, transcript fragmentation and incorrect gene annotation, which we suggest that de novo assembly is beneficial even when a reference genome is available.

Availability and Implementation

Software used in this study are publicly available at the authors' websites.

Supplementary information

Supplementary data are available at Bioinformatics online.
SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data
Authors: Choudhary Krishna , Ruan Luyao , Deng Fei , Shih Nathan , Aviran Sharon
Published: September 2016

To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approaches continues to emerge, a universal framework is needed to quantitatively ensure consistent and high-quality data. We present SEQualyzer, a visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure profiling experiments. Our methods rely on features common to a wide range of protocols and can serve as standards for quality control and analyses.

Availability and Implementation

SEQualyzer is written in R, is platform-independent, and is freely available at http://bme.ucdavis.edu/aviranlab/SEQualyzer.

Supplementary information

Supplementary data are available at Bioinformatics online.
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli
Authors: Shahmuradov Ilham Ayub , Mohamad Razali Rozaimi , Bougouffa Salim , Radovanovic Aleksandar , Bajic Vladimir B
Published: September 2016

Motivation

The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli.

Results

Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters.

Availability and Implementation

bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genetic mixed-stock analysis disentangles spatial and temporal variation in composition of the West Greenland Atlantic Salmon fishery
Authors: Bradbury Ian R. , Hamilton Lorraine C. , Sheehan Timothy F. , Chaput Gerald , Robertson Martha J. , Dempson J. Brian , Reddin David , Morris Vicki , King Timothy , Bernatchez Louis
Published: September 2016

The West Greenland Atlantic Salmon (Salmo salar) fishery represents the largest remaining mixed-stock fishery for Atlantic Salmon in the Northwest Atlantic and targets multi-sea-winter (MSW) salmon from throughout North America and Europe. We evaluated stock composition of salmon harvested in the waters off West Greenland (n = 5684 individuals) using genetic mixture analysis and individual assignment to inform conservation of North American populations, many of which are failing to meet management targets. Regional contributions to this fishery were estimated using 2169 individuals sampled throughout the fishery between 2011 and 2014. Of these, 22% were identified as European in origin. Major North American contributions were detected from Labrador (∼20%), the Southern Gulf/Cape Breton (29%), and the Gaspe Peninsula (29%). Minor contributions (∼5%) were detected from Newfoundland, Ungava, and Quebec regions. Region-specific catches were extrapolated using estimates of composition and fishery catch logs and harvests ranged from 300 to 600 and 2000 to 3000 individuals for minor and major constituents, respectively. To evaluate the temporal stability of the observed fishery composition, we extended the temporal coverage through the inclusion of previously published data (1995–2006, n = 3095) and data from archived scales (1968–1998, n = 420). Examination of the complete time-series (47 years) suggests relative stability in stock proportions since the late 1980s. Genetic estimates of stock composition were significantly associated with model-based estimates of returning MSW salmon (individual years r = 0.69, and overall mean r = 0.96). This work demonstrates that the analysis of both contemporary and archived samples in a mixed-stock context can disentangle levels of regional exploitation and directly inform assessment and conservation of Atlantic Salmon in the West Greenland interceptory Atlantic Salmon fishery.
Mark-recapture estimation of mortality and migration rates for sea trout (Salmo trutta) in the northern Baltic sea
Authors: Whitlock Rebecca E. , Kopra Juho , Pakarinen Tapani , Jutila Eero , Leach Adrian W. , Levontin Polina , Kuikka Sakari , Romakkaniemi Atso
Published: September 2016

Knowledge of current fishing mortality rates is an important prerequisite for formulating management plans for the recovery of threatened stocks. We present a method for estimating migration and fishing mortality rates for anadromous fishes that combines tag return data from commercial and recreational fisheries with expert opinion in a Bayesian framework. By integrating diverse sources of information and allowing for missing data, this approach may be particularly applicable in data-limited situations.

Wild populations of anadromous sea trout (Salmo trutta) in the northern Baltic Sea have undergone severe declines, with the loss of many populations. The contribution of fisheries to this decline has not been quantified, but is thought to be significant. We apply the Bayesian mark-recapture model to two reared sea trout stocks from the Finnish Isojoki and Lestijoki Rivers. Over the study period (1987–2012), the total harvest rate was estimated to average 0.82 y–1 for the Isojoki River stock and 0.74 y−1 for the Lestijoki River stock. Recreational gillnet fishing at sea was estimated to be the most important source of fishing mortality for both stocks, particularly during the 1980s and 1990s. Our results indicate a high probability of unsustainable levels of fishing mortality for both stocks, and illustrate the importance of considering the effect of recreational fisheries on fish population dynamics.