bluuebunny/crossref_metadata_2025 huggingface dataset:
Phagocyte NADPH oxidase and specific immunity
Authors: Cachat Julien , Deffert Christine , Hugues Stephanie , Krause Karl-Heinz
Published: February 2015

The phagocyte NADPH oxidase NOX2 produces reactive oxygen species (ROS) and is a well-known player in host defence. However, there is also increasing evidence for a regulatory role of NOX2 in adaptive immunity. Deficiency in phagocyte NADPH oxidase causes chronic granulomatous disease (CGD) in humans, a condition that can also be studied in CGD mice. Clinical observations in CGD patients suggest a higher susceptibility to autoimmune diseases, in particular lupus, idiopathic thrombocytopenic purpura and rheumatoid arthritis. In mice, a strong correlation exists between a polymorphism in a NOX2 subunit and the development of autoimmune arthritis. NOX2 deficiency in mice also favours lupus development. Both CGD patients and CGD mice exhibit increased levels of immunoglobulins, including autoantibodies. Despite these phenotypes suggesting a role for NOX2 in specific immunity, mechanistic explanations for the typical increase of CGD in autoimmune disease and antibody levels are still preliminary. NOX2-dependent ROS generation is well documented for dendritic cells and B-lymphocytes. It is unclear whether T-lymphocytes produce ROS themselves or whether they are exposed to ROS derived from dendritic cells during the process of antigen presentation. ROS are signalling molecules in virtually any cell type, including T- and B-lymphocytes. However, knowledge about the impact of ROS-dependent signalling on T- and B-lymphocyte phenotype and response is still limited. ROS might contribute to Th1/Th2/Th17 cell fate decisions during T-lymphocyte activation and might enhance immunoglobulin production by B-lymphocytes. In dendritic cells, NOX2-derived ROS might be important for antigen processing and cell activation.
Impact of transient hypotension on regional cerebral blood flow in humans
Authors: Lewis Nia C.S. , Smith Kurt J. , Bain Anthony R. , Wildfong Kevin W. , Numan Tianne , Ainslie Philip N.
Published: February 2015

We examined the impact of progressive hypotension with and without hypocapnia on regional extracranial cerebral blood flow (CBF) and intracranial velocities. Participants underwent progressive lower-body negative pressure (LBNP) until pre-syncope to inflict hypotension. End-tidal carbon dioxide was clamped at baseline levels (isocapnic trial) or uncontrolled (poikilocapnic trial). Middle cerebral artery (MCA) and posterior cerebral artery (PCA) blood velocities (transcranial Doppler; TCD), heart rate, blood pressure and end-tidal carbon dioxide were obtained continuously. Measurements of internal carotid artery (ICA) and vertebral artery (VA) blood flow (ICABF and VABF respectively) were also obtained. Overall, blood pressure was reduced by ∼20% from baseline in both trials (P<0.001). In the isocapnic trial, end-tidal carbon dioxide was successfully clamped at baseline with hypotension, whereas in the poikilocapnic trial it was reduced by 11.1 mmHg (P<0.001) with hypotension. The decline in the ICABF with hypotension was comparable between trials (−139±82 ml; ∼30%; P<0.0001); however, the decline in the VABF was −28±22 ml/min (∼21%) greater in the poikilocapnic trial compared with the isocapnic trial (P=0.002). Regardless of trial, the blood flow reductions in ICA (−26±14%) and VA (−27±14%) were greater than the decline in MCA (−21±15%) and PCA (−19±10%) velocities respectively (P≤0.01). Significant reductions in the diameter of both the ICA (∼5%) and the VA (∼7%) contributed to the decline in cerebral perfusion with systemic hypotension, independent of hypocapnia. In summary, our findings indicate that blood flow in the VA, unlike the ICA, is sensitive to changes hypotension and hypocapnia. We show for the first time that the decline in global CBF with hypotension is influenced by arterial constriction in the ICA and VA. Additionally, our findings suggest TCD measures of blood flow velocity may modestly underestimate changes in CBF during hypotension with and without hypocapnia, particularly in the posterior circulation.
Multi‐objective bat algorithm with time‐varying inertia weights for optimal design of passive power filters set
Authors: Yang Nien‐Che , Le Minh‐Duy
Published: February 2015

In this study, a novel method is developed to optimise the design of passive power filters (PPFs). The proposed method is based on the famous bat algorithm (BA) and is expected to make the PPF design easier and more effective than conventional trial‐and‐error approaches. Furthermore, the effects of inertia weight variations on the performance of the proposed method are examined. To optimise performance, the most suitable inertia weight, with the best effects, will be selected. For solving multi‐objective optimisation problems, a so‐called external archive is also integrated into the proposed method. A case study of PPF design is also presented to demonstrate the accuracy, efficiency and superiority of the proposed method.
Rough‐set belief rule model using multinomial subjective logic
Authors: Jia Limin , Ding Wangning , Jiao Hongqiang
Published: February 2015

In accordance with the uncertainty of decision rules extraction process in boundary region of the rough set, this study proposes a rough‐set belief rule model using multinomial subjective logic. The model builds the belief rule expectation for classification and recognition. It not only considered the effects of single condition attributes on decision, but also the multi‐attributes. Finally, the example analysis and comparison with the R0.5(X) model indicates the validity and advantage of this model.
Divergent Synthesis of Aminocyclopentitol Analogues via Stereoselective Amination of Cyclic Polybenzyl Ether with Chlorosulfonyl Isocyanate
Authors: Jung Young , Kim Seung , Hong Yeon , Park Sook , Kang Kyung , Kim So , Park Jung , Kim In
Published: February 2015

The divergent synthesis of some novel aminocyclopentitol analogues was concisely achieved from readily available d-galactose via the highly diastereoselective amination of carbocyclic polybenzyl ether using chlorosulfonyl isocyanate, diastereoselective dihydroxylation, and epoxidation as the key steps.
Thermooptical molecule sieve on the microscale
Authors: Osterman Natan , Braun Dieter
Published: February 2015

A combination of thermophoresis and fluid flow can be used to trap molecules and particles. We show that heating by scanning motion of an elongated laser spot creates a strong thermal trap. Additionally, it induces a global fluid flow that feeds the trap. Such “thermal sieve” can accumulate molecules from a large surrounding region within seconds into a 10 μm spot. Numerical modeling gives a quantitative prediction of the effect. Traps can be dynamically created, relocated, and tuned, which can be used for particle sorting.
Binary mixtures of asymmetric continuous charge distributions: Molecular dynamics simulations and integral equations
Authors: Heyes D. M. , Rickayzen G.
Published: February 2015

An investigation is carried out of the association and clustering of mixtures of Gaussian charge distributions (CDs) of the form ∼Qexp(−r2/2α2), where Q is the total charge, r is the separation between the centers of charge and α governs the extent of charge spreading (α → 0 is the point charge limit). The general case where α and Q are different for the positive and negatives charges is considered. The Ewald method is extended to treat these systems and it is used in Molecular Dynamics (MD) simulations of electrically neutral CD mixtures in the number ratios of 1:1 and 1:4 (or charge ratio 4:1). The MD simulations reveal increased clustering with decreasing temperature, which goes through a state in which each large CD is overlapped by four of the oppositely signed CD in the 1:4 case. At very low reduced temperatures, these mini-clusters progressively coalesce into much larger tightly bound clusters. This is different from the 1:1 mixture case, where the low temperature limit is a random distribution of neutral dimers. At higher temperatures, the MD radial distribution functions g(r) agree well with those from the hypernetted chain solution of the Ornstein-Zernike integral equation, and (at not too high densities) a previously introduced mean field approximation extended to these charge distribution systems.
Scale-invariant curvature fluctuations from an extended semiclassical gravity
Authors: Pinamonti Nicola , Siemssen Daniel
Published: February 2015

We present an extension of the semiclassical Einstein equations which couple n-point correlation functions of a stochastic Einstein tensor to the n-point functions of the quantum stress-energy tensor. We apply this extension to calculate the quantum fluctuations during an inflationary period, where we take as a model a massive conformally coupled scalar field on a perturbed de Sitter space and describe how a renormalization independent, almost-scale-invariant power spectrum of the scalar metric perturbation is produced. Furthermore, we discuss how this model yields a natural basis for the calculation of non-Gaussianities of the considered metric fluctuations.
The method for measuring the groove density of variable-line-space gratings with elimination of the eccentricity effect
Authors: Wang Qingbo , Liu Zhengkun , Chen Huoyao , Wang Yu , Jiang Xiaolong , Fu Shaojun
Published: February 2015

To eliminate the eccentricity effect, a new method for measuring the groove density of a variable-line-space grating was adapted. Based on grating equation, groove density is calculated by measuring the internal angles between zeroth-order and first-order diffracted light for two different wavelengths with the same angle of incidence. The measurement system mainly includes two laser sources, a phase plate, plane mirror, and charge coupled device. The measurement results of a variable-line-space grating demonstrate that the experiment data agree well with theoretical values, and the value of measurement error (ΔN/N) is less than 2.72 × 10−4.
Crystallinity effects on scaling properties of photoinduced modes in silver nanoprisms
Authors: Ng Ming-Yaw , Ho I-Lin , Chang Yia-Chung
Published: February 2015

The crystallinity effects on scaling properties of photoinduced modes in crystalline silver nanoprisms with C3v symmetry are studied using a realistic atomistic model and group theory. Among all vibrational modes, photoinduced modes can be identified as those vibrational modes which possess larger in-phase radial atomic displacement and can be projected out by the projected density of states method. We found that the properties of vibrations in silver nanoprisms strongly depend on the particle’s aspect ratio (bisector length over thickness). By considering crystallinity of silver nanoprisms, the dominant modes with the in-plane oscillation become several closely spaced modes, and become obvious for nanoprisms with a smaller aspect ratio. The oscillation spectra show that the dominant planar modes are insensitive to thickness change. On the contrary, the atomic displacements show significantly different patterns for nanoprisms of different thicknesses. We also found that, for nanoprisms with same aspect ratio that is larger than 4, the vibrational properties of dominant modes exhibit scaling similarity. By using a simple linear transformation, the vibration frequencies for large-sized nanoprisms of aspect ratio 6 can be obtained by a corresponding scaling factor. The calculated results are in good agreement with experimental data.
A technique for error estimation of linewidth and damping parameters extracted from ferromagnetic resonance measurements
Authors: Buford Benjamin , Dhagat Pallavi , Jander Albrecht
Published: February 2015

Ferromagnetic resonance (FMR) characterization, using a vector network analyzer (VNA), is widely used to determine anisotropy, g-factor, and Gilbert damping parameter of magnetic thin films, but results are typically reported without calculation of the measurement accuracy. We present a method of processing VNA-FMR measurements to determine both the value and confidence interval of these properties. The discussion is presented using FMR data obtained from stacks of MgO/CoFeB/Ta/CoFeB/MgO with varying CoFeB thickness. Measured S-parameters are de-embedded, drift corrected, fit to a Lorentzian curve, and analyzed to produce a confidence interval. A method of plotting the results of the Lorentzian fitting such that fitting errors or measurement drift can be visually analyzed is shown.
Structural and electrical characterization of CoTiN metal gates
Authors: Wongpiya Ranida , Ouyang Jiaomin , Chung Chia-Jung , Duong Duc T. , Deal Michael , Nishi Yoshio , Clemens Bruce
Published: February 2015

As the gate size continues to decrease in nanoscale transistors, having metal gates with amorphous or near amorphous structures can potentially reduce grain-induced work function variation. Furthermore, amorphous materials are known to have superior diffusion barrier properties, which can help prevent work function change due to the diffusion of metals in contact with the gate. In this work we show that with the addition of cobalt, thin films of polycrystalline TiN become more amorphous with a smaller grain size. Cox(TiN)1-x films, where x = 60–80%, appear to consist of nanocrystals embedded in an amorphous matrix, and are thermally stable with no significant crystallization up to an annealing temperature of at least 600 °C. Reducing the nitrogen gas flow ratio during sputter deposition from 9% to 2.5% further decreases the films' crystallinity, which is apparent by more sparse and even smaller nanocrystals. In addition to being partially amorphous, these CoTiN films also exhibit good thermal stability, low resistivity, low roughness, and have the potential for atomic layer deposition compatibility. Even though these materials are not completely amorphous, their small crystal size and amorphous matrix can potentially reduce work function variation and improve their diffusion barrier property. These properties make CoTiN a good candidate as a gate material for future nanoelectronic devices and technology.
Induced topological pressure for topological dynamical systems
Authors: Xing Zhitao , Chen Ercai
Published: February 2015

In this paper, inspired by the article [J. Jaerisch et al., Stochastics Dyn. 14, 1350016, pp. 1-30 (2014)], we introduce the induced topological pressure for a topological dynamical system. In particular, we prove a variational principle for the induced topological pressure.
Weak concentration and wave operator for a 3D coupled nonlinear Schrödinger system
Authors: Pastor Ademir
Published: February 2015

Reported in this paper are results concerning the Cauchy problem and the dynamics for a cubic nonlinear Schrödinger system arising in nonlinear optics. A sharp criterion is given concerned with the dichotomy global existence versus finite time blow-up. When a radial solution blows up in finite time, we prove the concentration in the critical Lebesgue space. Sufficient condition for the scattering and the construction of the wave operator in the energy space is also provided.
New set of symmetries and Lie algebraic structures of the Toda lattice hierarchy
Authors: Zhu Xiao-ying , Zhang Da-jun , Li Zong-cheng
Published: February 2015

By introducing the new time-dependence of the spectral parameter λ, we construct two sets of symmetries which are different from the centerless Kac-Moody-Virasoro algebras for the isospectral Toda lattice hierarchy.
Coexistence and interfacial properties of a triangle-well mimicking the Lennard-Jones fluid and a comparison with noble gases
Authors: Bárcenas M. , Reyes Y. , Romero-Martínez A. , Odriozola G. , Orea P.
Published: February 2015

Coexistence and interfacial properties of a triangle-well (TW) fluid are obtained with the aim of mimicking the Lennard-Jones (LJ) potential and approach the properties of noble gases. For this purpose, the scope of the TW is varied to match vapor-liquid densities and surface tension. Surface tension and coexistence curves of TW systems with different ranges were calculated with replica exchange Monte Carlo and compared to those data previously reported in the literature for truncated and shifted (STS), truncated (ST), and full Lennard-Jones (full-LJ) potentials. We observed that the scope of the TW potential must be increased to approach the STS, ST, and full-LJ properties. In spite of the simplicity of TW expression, a remarkable agreement is found. Furthermore, the variable scope of the TW allows for a good match of the experimental data of argon and xenon.
Nonlinear effects of inertial Alfvén wave in low beta plasmas
Authors: Rinawa M. L. , Gaur Nidhi , Sharma R. P.
Published: February 2015

This paper is devoted to the study of the nonlinear interaction and propagation of high frequency pump inertial Alfvén wave (IAW) with comparatively low frequency IAW with emphasis on nonlinear effects and applications within space plasma and astrophysics for low β-plasma (β≪me/mi). We have developed a set of dimensionless equations in the presence of ponderomotive nonlinearity due to high frequency pump IAW in the dynamics of comparatively low frequency IAW. Stability analysis and numerical simulation have been carried out for the coupled system comprising of pump IAW and low frequency IAW to study the localization and turbulent spectra, applicable to auroral region. The result reveals that localized structures become more complex and intense in nature at the quasi steady state. From the obtained result, we found that the present model may be useful to study the turbulent fluctuations in accordance with the observations of FAST/THEMIS spacecraft.
Introduction of DC line structures into a superconducting microwave 3D cavity
Authors: Kong Wei-Cheng , Deng Guang-Wei , Li Shu-Xiao , Li Hai-Ou , Cao Gang , Xiao Ming , Guo Guo-Ping
Published: February 2015

We report a technique that can noninvasively add multiple DC wires into a 3D superconducting microwave cavity for electronic devices that require DC electrical terminals. We studied the influence of our DC lines on the cavity performance systematically. We found that the quality factor of the cavity is reduced if any of the components of the electrical wires cross the cavity equipotential planes. Using this technique, we were able to incorporate a quantum dot (QD) device into a 3D cavity. We then controlled and measured the QD transport signal using the DC lines. We have also studied the heating effects of the QD by the microwave photons in the cavity.
Simulation of interdigitated back contact solar cell with trench structure
Authors: Kim Soo Min , Chun Seungju , Kang Min Gu , Song Hee-Eun , Lee Jong-Han , Boo Hyunpil , Bae Soohyun , Kang Yoonmook , Lee Hae-Seok , Kim Donghwan
Published: February 2015

We performed two-dimensional technology computer-aided design simulations for interdigitated back contact (IBC) solar cells with rear trench structures (TS), denoted here as TS-IBC solar cells. First, we calculated a reference simulation model for conventional IBC solar cells. We then assumed a trench structure at the rear surface of the IBC solar cell. For this structure, we analyzed solar cell performance as a function of various trench depths and type. It was found that emitter trench formation affects minority carrier collection, such that the short-circuit current density increases with increasing trench depth. However, the back-surface field (BSF) trench exhibited poor minority carrier collection, which reduced the conversion efficiency of the TS-IBC solar cells. It was also found that for the same trench depth (30 μm), the difference in conversion efficiencies of an IBC solar cell with an emitter trench and that with a BSF trench was 0.6%. We are thus convinced that the emitter trench structure is more important than the BSF trench structure.
A sequence perturbation based islanding detection for distributed generation with periodic code matching
Authors: Li Deshi , Li Lei , Yang Chenglong , Zhang Song
Published: February 2015

Islanding detection is a significant technical barrier to the distributed generation (DG) industry. When islanding occurs, the inverter current of DG has a strong correlation with load voltage of DG. With respect to the correlation, this paper proposes an islanding detection method (IDM) based on periodic matching of the sequence perturbation. In this periodic code matching detection method, a periodic sequence is introduced to perturb the inverter current amplitude. The IDM can be achieved by calculating periodic matching degree between the islanding detection coefficient and the sequence. The influence on IDM imposed by sequence characteristics and load variation is also discussed in this paper. According to IEEE Std. 1547, an islanding detection model is designed and simulated in this paper. The simulation and experiment results indicate a strong ability to anti-harmonic noise when the 1-0 non-zeroing sequence with six bits is selected as the perturbation sequence. The proposed method introduces little damage to grid. In the normal range of voltage and frequency, this method can detect the islanding of DG reliably and effectively even if load varies.
Effect of diameter and surface roughness on ultrasonic properties of GaAs nanowires
Authors: Dhawan Punit Kumar , Wan Meher , Verma S. K. , Pandey D. K. , Yadav R. R.
Published: February 2015

Second and third order elastic constants of GaAs Nanowires (NWs) are calculated using the many-body interaction potential model. The velocities of ultrasonic waves at different orientations of propagation with unique axis are evaluated using the second order elastic constants. The ultrasonic attenuation and thermal relaxation times of the single crystalline GaAs-NW are determined as a function of diameter and surface roughness by means of Mason theoretical approach using the thermal conductivity and higher order elastic constants. The diameter variation of ultrasonic attenuation and thermal relaxation exhibit second order polynomial function of diameter. It is also found that ultrasonic attenuation and thermal relaxation follow the exponential decay with the surface roughness for GaAs-NW due to reduction in thermal conductivity caused by dominance of surface asperities. Finally, the correlations among ultrasonic parameters, thermal conductivity, surface roughness, and diameter for GaAs-NWs are established leading towards potential applications.
Small signal modulation characteristics of red-emitting (λ = 610 nm) III-nitride nanowire array lasers on (001) silicon
Authors: Jahangir Shafat , Frost Thomas , Hazari Arnab , Yan Lifan , Stark Ethan , LaMountain Trevor , Millunchick Joanna M. , Ooi Boon S. , Bhattacharya Pallab
Published: February 2015

The small signal modulation characteristics of an InGaN/GaN nanowire array edge- emitting laser on (001) silicon are reported. The emission wavelength is 610 nm. Lattice matched InAlN cladding layers were incorporated in the laser heterostructure for better mode confinement. The suitability of the nanowire lasers for use in plastic fiber communication systems with direct modulation is demonstrated through their modulation bandwidth of f-3dB,max = 3.1 GHz, very low values of chirp (0.8 Å) and α-parameter, and large differential gain (3.1 × 10−17 cm2).
Surface protein gradients generated in sealed microchannels using spatially varying helium microplasma
Authors: Wettstein Pascal , Priest Craig , Al-Bataineh Sameer A. , Short Robert D. , Bryant Paul M. , Bradley James W. , Low Suet P. , Parkinson Luke , Szili Endre J.
Published: February 2015

Spatially varied surface treatment of a fluorescently labeled Bovine Serum Albumin (BSA) protein, on the walls of a closed (sealed) microchannel is achieved via a well-defined gradient in plasma intensity. The microchips comprised a microchannel positioned in-between two microelectrodes (embedded in the chip) with a variable electrode separation along the length of the channel. The channel and electrodes were 50 μm and 100 μm wide, respectively, 50 μm deep, and adjacent to the channel for a length of 18 mm. The electrode separation distance was varied linearly from 50 μm at one end of the channel to a maximum distance of 150, 300, 500, or 1000 μm to generate a gradient in helium plasma intensity. Plasma ignition was achieved at a helium flow rate of 2.5 ml/min, 8.5 kVpk-pk, and 10 kHz. It is shown that the plasma intensity decreases with increasing electrode separation and is directly related to the residual amount of BSA left after the treatment. The plasma intensity and surface protein gradient, for the different electrode gradients studied, collapse onto master curves when plotted against electrode separation. This precise spatial control is expected to enable the surface protein gradient to be tuned for a range of applications, including high-throughput screening and cell-biomolecule-biomaterial interactions.
Dynamic response of shear thickening fluid under laser induced shock
Authors: Wu Xianqian , Zhong Fachun , Yin Qiuyun , Huang Chenguang
Published: February 2015

The dynamic response of the 57 vol./vol. % dense spherical silica particle-polyethylene glycol suspension at high pressure was investigated through short pulsed laser induced shock experiments. The measured back free surface velocities by a photonic Doppler velocimetry showed that the shock and the particle velocities decreased while the shock wave transmitted in the shear thickening fluid (STF), from which an equation of state for the STF was obtained. In addition, the peak stress decreased and the absorbed energy increased rapidly with increasing the thickness for a thin layer of the STF, which should be attributed to the impact-jammed behavior through compression of particle matrix, the deformation or crack of the hard-sphere particles, and the volume compression of the particles and the polyethylene glycol.
Inversion-mode GaAs wave-shaped field-effect transistor on GaAs (100) substrate
Authors: Zhang Jingyun , Lou Xiabing , Si Mengwei , Wu Heng , Shao Jiayi , Manfra Michael J. , Gordon Roy G. , Ye Peide D.
Published: February 2015

Inversion-mode GaAs wave-shaped metal-oxide-semiconductor field-effect transistors (WaveFETs) are demonstrated using atomic-layer epitaxy of La2O3 as gate dielectric on (111)A nano-facets formed on a GaAs (100) substrate. The wave-shaped nano-facets, which are desirable for the device on-state and off-state performance, are realized by lithographic patterning and anisotropic wet etching with optimized geometry. A well-behaved 1 μm gate length GaAs WaveFET shows a maximum drain current of 64 mA/mm, a subthreshold swing of 135 mV/dec, and an ION/IOFF ratio of greater than 107.
Multi-mode interference revealed by two photon absorption in silicon rich SiO2 waveguides
Authors: Manna S. , Ramiro-Manzano F. , Ghulinyan M. , Mancinelli M. , Turri F. , Pucker G. , Pavesi L.
Published: February 2015

Photoluminescence (PL) from Si nanocrystals (NCs) excited by two-photon absorption (TPA) has been observed in Si nanocrystal-based waveguides fabricated by plasma enhanced chemical vapor deposition. The TPA excited photoluminescence emission resembles the one-photon excited photoluminescence arising from inter-band transitions in the quantum confined Si nanocrystals. By measuring the non-linear transmission of waveguides, a large TPA coefficient of β up to 10−8 cm/W has been measured at 1550 nm. These values of β depend on the Si NCs size and are two orders of magnitude larger than the bulk silicon value. Here, we propose to use the TPA excited visible PL emission as a tool to map the spatial intensity profile of the 1550 nm propagating optical modes in multimode waveguides. In this way, multimode interference has been revealed experimentally and confirmed through a finite element simulation.
Experimental study of the proposed super-thermal-conductor: BAs
Authors: Lv Bing , Lan Yucheng , Wang Xiqu , Zhang Qian , Hu Yongjie , Jacobson Allan J. , Broido David , Chen Gang , Ren Zhifeng , Chu Ching-Wu
Published: February 2015

Recent calculations predict a super-thermal-conductivity of ∼2000 Wm−1 K−1, comparable to that of diamond, in cubic boron arsenide (BAs) crystals, which may offer inexpensive insulators with super-thermal-conductivity for microelectronic device applications. We have synthesized and characterized single crystals of BAs with a zinc blende cubic structure and lattice parameters of a = 4.7830(7) Å. A relatively high thermal conductivity of ∼200 Wm−1 K−1 is obtained, close to those of best non-carbon crystal insulators, such as SiC, although still an order of magnitude smaller than the value predicted. Based on our XPS, X-ray single crystal diffraction, and Raman scattering results, steps to achieve the predicted super-thermal conductivity in BAs are proposed.
Correlated response to selection for some egg performance traits in egg line of Japanese quail
Authors: Mahmoud B. Y. F. , Abou Khadiga G. , El-Full E. A.
Published: February 2015

Estimation of correlated response to selection in female line of Japanese quail after a short-term selection experiment was conducted. The total number of 547 female (275 selected and 272 control) Japanese quail included in the selection experiment of selection depended on aggregate breeding values based on animal model Best Linear Unbiased Prediction. Correlated selection response estimates were favourable for all the studied traits and significant (–0.38, –9.89, –12.86, –16.64, –5.08 and –8.24) for first egg weight (FEW), age at the first 10 eggs (AGE10), age at first 30 eggs (AGE30), age at first 60 eggs (AGE60), days needed to produce the first 30 eggs (DN30) and the first 60 eggs (DN60), respectively. Estimates of heritability were moderate for egg mass for the first 10 eggs (EM10), the first 30 eggs (EM30), the first 60 eggs (EM60), AGE10 and AGE30 (0.17–0.30), but low for AGE60, DN30 and DN60 (0.01–0.10). Genetic correlations between the selection criteria traits (AFE, BWSM and DN10) and the studied egg production traits were positive and ranged from 0.25 to 0.97, 0.24 to 0.95 and 0.06 to 0.98 for AFE, BWSM and DN10, respectively, whereas phenotypic correlations ranged from 0.12 to 0.89, 0.01 to 0.34 and 0.06 to 0.87 for the same traits. The favourable genetic response obtained for egg traits could be an indicator for improving egg production performance in Japanese quail.
Increased proportion of female lambs by feeding Border Leicester × Merino ewes a diet high in omega-6 fatty acids around mating
Authors: Clayton E. H. , Wilkins J. F. , Friend M. A.
Published: February 2015

The proportion of female lambs was previously higher when ewes were offered a diet high in omega-6 fatty acids (n-6) based on oats and cottonseed meal (oats/CSM) around joining. The effect of the length of time of feeding the high n-6 diet on the sex ratio of lambs has not previously been reported. The aim of the present study was to determine whether the proportion of female lambs was higher when Border Leicester × Merino ewes were fed a diet high in n-6 either pre-conception only or both pre- and post-conception. Ewes were fed a low n-6 diet based on silage or a high n-6 diet based on oats/CSM for 40 days pre-mating until the end of mating (pre-mating) or 40 days pre-mating and 17 days post-mating. Liveweight, fat score, plasma fatty acid status and lamb sex was determined. Plasma n-6 concentration was higher (P < 0.001) and the time to oestrus shorter (P < 0.001) when ewes received oats/CSM compared with silage. The proportion of female lambs was higher when ewes were fed a high n-6 compared with low n-6 diet pre-mating only (54.1% vs 44.4%, P = 0.049) and both pre- and post-mating (57.2% vs 43.4%, P = 0.018). The interaction between diet and length of time of feeding was not significant (P = 0.537). The mechanism resulting in the diet high in omega-6 influencing the sex ratio of lambs appears to operate before or around conception but is yet to be determined.
The effect of mastication on surface fire behaviour, fuels consumption and tree mortality in pine flatwoods of Florida, USA
Authors: Kreye Jesse K. , Kobziar Leda N.
Published: February 2015

Mastication of understorey shrubs and small trees to reduce fire hazard has become a widespread forest management practice, but few empirical studies have quantified the effects of this mechanical treatment on actual fire behaviour and fire effects at the stand scale. We conducted experimental burns in masticated pine flatwoods with palmetto/gallberry understories, a common ecosystem of the Southern US Coastal Plain. Fire behaviour (flame height, rate of spread) and fire effects were compared between treated and untreated sites burned in the typical winter prescribed burning season. Mastication effectively reduced flame heights by 66%, but recovering shrubs (cover, height) influenced fire behaviour within six months following treatment, suggesting time-limited effectiveness. Trees had less crown scorch and bole char in masticated sites, but tree mortality was minimal on both treated and untreated sites. Consumption of masticated fuel was substantial across both treatments, but little duff was consumed under the moist soil conditions. When burning is conducted soon after treatment, mastication may effectively reduce fire behaviour in pine flatwoods sites, but the duration of treatment efficacy remains unclear.
Latour’s object-orientated politics for a post-political age
Authors: Tsouvalis Judith
Published: February 2015

What, for Latour, does politics mean? Or, to be more precise, what being for Latour is political – who or what is his political subject? To try and answer these questions, this article compares two strands of thinking concerned with the nature of politics and the political: Latour's Dingpolitik or object-orientated politics and post-foundational political writings on the post-political condition. Both Latour and critics of the post-political condition hold that the excluded and suppressed come back to haunt their suppressors, shattering illusions of Modernity and neoliberal, cosmopolitan ideals. In both accounts, the excluded hold the key to political change. However, while post-political discourse relies heavily on an abstract, universalized, absent human subject as the agent of emancipatory political change, for Latour the excluded that undermine Modernity's dichotomous constitution are the multiple beings and things that bring reality forth – concrete, variously entangled, translated and translating, mediated and mediating actants; quasi-objects, or, as he also calls them, mediators. Bringing these two different ways of thinking about politics and the political alongside each other I aim to show that Latour's ontologically grounded conception of politics has far greater transformative potential than the proposals found in post-foundational accounts of the post-political condition. These writings, in spite of their emancipatory intent, tend to remain at the level of critique while falling short of a vision for concrete, pragmatic proposals of how to compose a better common world.
Sambamba: fast processing of NGS alignment formats
Authors: Tarasov Artem , Vilella Albert J. , Cuppen Edwin , Nijman Isaac J. , Prins Pjotr
Published: February 2015

Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability.

Availability and implementation: Sambamba is free and open source software, available under a GPLv2 license. Sambamba can be downloaded and installed from http://www.open-bio.org/wiki/Sambamba.

Sambamba v0.5.0 was released with doi:10.5281/zenodo.13200.

Contact: j.c.p.prins@umcutrecht.nl
Extending P450 site-of-metabolism models with region-resolution data
Authors: Zaretzki Jed M. , Browning Michael R. , Hughes Tyler B. , Swamidass S. Joshua
Published: February 2015

Motivation: Cytochrome P450s are a family of enzymes responsible for the metabolism of approximately 90% of FDA-approved drugs. Medicinal chemists often want to know which atoms of a molecule—its metabolized sites—are oxidized by Cytochrome P450s in order to modify their metabolism. Consequently, there are several methods that use literature-derived, atom-resolution data to train models that can predict a molecule’s sites of metabolism. There is, however, much more data available at a lower resolution, where the exact site of metabolism is not known, but the region of the molecule that is oxidized is known. Until now, no site-of-metabolism models made use of region-resolution data.

Results: Here, we describe XenoSite-Region, the first reported method for training site-of-metabolism models with region-resolution data. Our approach uses the Expectation Maximization algorithm to train a site-of-metabolism model. Region-resolution metabolism data was simulated from a large site-of-metabolism dataset, containing 2000 molecules with 3400 metabolized and 30 000 un-metabolized sites and covering nine Cytochrome P450 isozymes. When training on the same molecules (but with only region-level information), we find that this approach yields models almost as accurate as models trained with atom-resolution data. Moreover, we find that atom-resolution trained models are more accurate when also trained with region-resolution data from additional molecules. Our approach, therefore, opens up a way to extend the applicable domain of site-of-metabolism models into larger regions of chemical space. This meets a critical need in drug development by tapping into underutilized data commonly available in most large drug companies.

Availability and implementation: The algorithm, data and a web server are available at http://swami.wustl.edu/xregion.

Contact:  swamidass@wustl.edu
The GPMDB REST interface
Authors: Fenyö David , Beavis Ronald C.
Published: February 2015

Summary: The Global Proteome Machine and Database (GPMDB) representational state transfer (REST) service was designed to provide simplified access to the proteomics information in GPMDB using a stable set of methods and parameters. Version 1 of this interface gives access to 25 methods for retrieving experimental information about protein post-translational modifications, amino acid variants, alternate splicing variants and protein cleavage patterns.

Availability and implementation: GPMDB data and database tables are freely available for commercial and non-commercial use. All software is also freely available, under the Artistic License. http://rest.thegpm.org/1 (GPMDB REST Service), http://wiki.thegpm.org/wiki/GPMDB_REST (Service description and help), and http://www.thegpm.org (GPM main project description and documentation). The code for the interface and an example REST client is available at ftp://ftp.thegpm.org/repos/gpmdb_rest

Contact:  rbeavis@thegpm.org or david@fenyolab.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Acoustic biomass estimation of mesopelagic fish: backscattering from individuals, populations, and communities
Authors: Davison Peter C. , Koslow J. Anthony , Kloser Rudy J.
Published: February 2015

Acoustic survey methods are useful to estimate the distribution, abundance, and biomass of mesopelagic fish, a key component of open ocean ecosystems. However, mesopelagic fish pose several challenges for acoustic biomass estimation based on their small size, wide depth range, mixed aggregations, and length-dependent acoustic reflectance, which differentiate them from the larger epipelagic and neritic fish for which these methods were developed. Foremost, there is a strong effect of depth on swimbladder resonance, so acoustic surveys of mesopelagic fish must incorporate depth-stratification. Additionally, the 1–3 cm juveniles of many species are not only more abundant, but can also be stronger acoustic backscatterers than the larger adults that comprise most of the biomass. The dominant species in terms of biomass may thus be weak acoustic backscatters. Failure to properly incorporate depth, the full size distribution, and certain less-abundant species into mesopelagic acoustic analyses could lead to errors in estimated biomass of up to three orders of magnitude. Thus, thorough validation, or “ground-truthing ”, of the species composition, depth structure, population size distribution, capture efficiency of the sampling device, and acoustic properties of the fish present is critical for credible acoustic estimates of mesopelagic fish biomass. This is not insurmountable, but requires more ancillary data than is usually collected.
Similarity-Based Codes Sequentially Assigned to Ebolavirus Genomes Are Informative of Species Membership, Associated Outbreaks, and Transmission Chains
Authors: Weisberg Alexandra J. , Elmarakeby Haitham A. , Heath Lenwood S. , Vinatzer Boris A.
Published: February 2015

Background.  Developing a universal standardized microbial typing and nomenclature system that provides phylogenetic and epidemiological information in real time has never been as urgent in public health as it is today. We previously proposed to use genome similarity as the basis for immediate and precise typing and naming of individual organisms or viruses. In this study, we tested the validity of the proposed system and applied it to the epidemiology of infectious diseases using Ebola virus disease (EVD) outbreaks as the example.

Methods.  One hundred twenty-eight publicly available ebolavirus genomes were compared with each other, and average nucleotide identity (ANI) was calculated. The ANI was then used to assign unique codes, hereafter referred to as Life Ide.jpegication Numbers (LINs), to every viral isolate, whereby each LIN consisted of a series of positions reflecting increasing genome similarity. Congruence of LINs with phylogenetic and epidemiological relationships was then determined.

Results.  Assigned LINs correlate with phylogeny at the species and infraspecies level and can even ide.jpegy some individual transmission chains during the 2014–2015 EVD epidemic in West Africa.

Conclusions.  Life Ide.jpegication Numbers can provide a fast, automated, standardized, and scalable approach to precisely ide.jpegy and name viral isolates upon genome sequence submission, facilitating unambiguous communication during disease epidemics among clinicians, epidemiologists, and governments.
The NLR helper protein NRC3 but not NRC1 is required for Pto-mediated cell death inNicotiana benthamiana
Authors: Wu Chih-Hang , Belhaj Khaoula , Bozkurt Tolga O. , Kamoun Sophien
Published: February 2015

Intracellular immune receptors of the nucleotide-binding leucine-rich repeat (NB-LRR or NLR) proteins often function in pairs, with “helper” proteins required for the activity of “sensors” that mediate pathogen recognition. The NLR helper NRC1 (NB-LRR proteinrequired for HR-associatedcell death1) has been described as a signalling hub required for the cell death mediated by both cell surface and intracellular immune receptors in the model plantNicotiana benthamiana. However, this work predates the availability of theN. benthamianagenome and whether NRC1 is indeed required for the reported phenotypes has not been confirmed. Here, we investigated the NRC family of solanaceous plants using a combination of genome annotation, phylogenetics, gene silencing and genetic complementation experiments. We discovered that a paralog ofNRC1, we termedNRC3, is required for the hypersensitive cell death triggered by the disease resistance protein Pto but not Rx and Mi-1.2. NRC3 may also contribute to the hypersensitive cell death triggered by the receptor-like protein Cf-4. Our results highlight the importance of applying genetic complementation to validate gene function in RNA silencing experiments.
Directional variation in evolution: consequences for the fitness landscape metaphor
Authors: Gerlee Philip
Published: February 2015

The concept of a fitness landscape, which describes the relation between genotype (or phenotype) and fitness as a surface on which the population climbs uphill towards local peaks, is a central conceptual tool in evolutionary biology. Inherent in this metaphor is the assumption that the distance between any two points can be defined in the same way as for Euclidean space. However, many of the processes which generate genetic variation, such as gene duplication and lateral gene transfer, are not symmetric by nature, but occur more readily in one direction than the other. This asymmetry is also found in phenotypes, for reasons associated with the genotype-phenotype map and developmental constraints. This article provides an overview of of these processes and suggest how existing methods can be used for incorporating these asymmetric processes when visualising fitness landscapes.
Crystal structure study of a cobaltoan dolomite from Kolwezi, Democratic Republic of Congo
Authors: Perchiazzi Natale
Published: February 2015

A structural study has been undertaken on a cobaltoan dolomite, with chemical formula CaMg0.83Co0.17(CO3)2(calcium magnesium cobalt dicarbonate), from Kolwezi, Democratic Republic of Congo. Pale-pink euhedral cobaltoan dolomite was associated with kolwezite [(Cu1.33Co0.67)(CO3)(OH)2] and cobaltoan malachite [(Cu,Co)2(CO3)(OH)2]. A crystal with a Co:Mg ratio of 1:5.6 (SEM/EDAX measurement), twinned on (11 -2 0) was used for crystal structural refinement. The refinement of the structural model of Reeder & Wenk [Am. Mineral.(1983),68, 769–776; Ca at site 3awith site symmetry -3; Mg site at site 3bwith site symmetry -3; C at site 6cwith site symmetry 3; O at site 18fwith site symmetry 1] showed that Co is totally incorporated in the Mg site, with refined occupancy Mg0.83Co0.17, which compares with Mg0.85Co0.15from chemical data. The Co substitution reflects in the expansion of the cell volume, with a pronounced increasing of theccell parameter.
Crystal structure ofcis-aquachloridobis(1,10-phenanthroline-κ2N,N′)chromium(III) tetrachloridozincate monohydrate from synchrotron data
Authors: Moon Dohyun , Choi Jong-Ha
Published: February 2015

The structure of the title compound, [CrCl(C12H8N2)2(H2O)][ZnCl4]·H2O, has been determined from synchrotron data. The CrIIIion is bonded to four N atoms from two 1,10-phenanthroline (phen) ligands, one water molecule and a Cl atom in acisarrangement, displaying an overall distorted octahedral coordination environment. The Cr—N(phen) bond lengths are in the range of 2.0495 (18) to 2.0831 (18) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2734 (7) and 1.9986 (17) Å, respectively. The tetrahedral [ZnCl4]2−anion is slightly distorted owing to its involvement in O—H...Cl hydrogen bonding with coordinating and non-coordinating water molecules. The two types of water molecules also interact through O—H...O hydrogen bonds. The observed hydrogen-bonding pattern leads to the formation of a three-dimensional network structure.