bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of plasma beta on the generation of lower hybrid and whistler waves by an ion velocity ring distribution
Authors: Winske D. , Daughton W.
Published: February 2015

We present results of three-dimensional electromagnetic particle-in-cell simulations of the lower hybrid ion ring instability, similar to our earlier results [D. Winske and W. Daughton, Phys. Plasma 19, 072109 (2012)], but at higher electron beta (βe = ratio of electron thermal pressure to magnetic pressure = 0.06, rather than at 0.006) with Ti = Te. At higher electron beta, the level of lower hybrid waves at saturation normalized to the ion thermal energy (βi = 0.06 also) is only slightly smaller, but the corresponding magnetic fluctuations are about an order of magnitude larger, consistent with linear theory. After saturation, the waves evolve into whistler waves, through a number of possible mechanisms, with an average growth rate considerably smaller than the linear growth rate of the lower hybrid waves, to a peak fluctuation level that is about 20% above the lower hybrid wave saturation level. The ratio of the peak magnetic fluctuations associated with the whistler waves relative to those of the saturated lower hybrid waves, the ratio of the nonlinear growth rate of whistlers relative to the linear growth rate of lower hybrid waves, the amount of energy extracted from the ring, and the amount of heating of the background ions and electrons are comparable to those in the lower electron beta 3D simulation. This suggests that even at higher electron beta, the linear and nonlinear physics of the lower hybrid ion ring instability is dominated by electrostatic, wave-particle rather than wave-wave interactions.
Optical and magneto-optical properties of Au:Conanoparticles and Co:Aunanoparticles doped magnetoplasmonic systems
Authors: Martín-Becerra D. , García-Martín J. M. , Huttel Y. , Armelles G.
Published: February 2015

We report a study of Au:CoNPs and Co:AuNPs doped magnetoplasmonic systems. In particular, we analyze the effect of adding different concentrations of Co (or Au) nanoparticles (NPs) in a Au (or Co) matrix on both the optical and magneto-optical constants. Through the use of a simple effective medium model, relevant changes in the optical properties of the Au NPs compared to those of bulk material have been identified. Such effects are not observed in the Co NPs system. However, in both systems, there is an increase of the effective diameter of the NPs as compared to the real diameter that can be due to interface effects surrounding the NPs. Moreover, the magneto-optical constants values of both systems are smaller (in absolute values) than expected, which could also be attributed to interface effects such as hybridization between Au and Co.
Thermoelectric and mechanical properties on misch metal filled p-type skutterudites Mm0.9Fe4−xCoxSb12
Authors: Dahal Tulashi , Gahlawat Sonika , Jie Qing , Dahal Keshab , Lan Yucheng , White Kenneth , Ren Zhifeng
Published: February 2015

Most of the recent work focused on improving the dimensionless figure-of-merit, ZT, of p-type skutterudites uses one or two fillers to tune the electrical and thermal properties. Considering the fact that the different fillers with varying atomic mass and ionic radii can vibrate with different amplitudes to scatter phonons of different mean free paths, we synthesized misch metal filled p-type skutterudites Mm0.9Fe4−xCoxSb12 (where Mm is La0.25Ce0.5Pr0.05Nd0.15Fe0.03, called misch metal). The samples were synthesized by hot pressing nano-powder made by ball milling the annealed ingot of Mm0.9Fe4−xCoxSb12 with varying concentration of cobalt, x. By tuning the Fe/Co ratio, we achieved a thermal conductivity of ∼2 W m−1 K−1 at room temperature and ∼2.3 W m−1 K−1 at about 530 °C and a power factor of ∼30 μW cm−1 K−2 at about 425 °C in Mm0.9Fe3.1Co0.9Sb12, leading to a peak ZT ∼1.1 at about 425 °C. The nano-indentation experiment reveals that hardness and elastic modulus of the material is about 4.2 GPa and 116 GPa, respectively.
Antireflective downconversion ZnO:Er3+,Yb3+ thin film for Si solar cell applications
Authors: Elleuch R. , Salhi R. , Deschanvres J.-L. , Maalej R.
Published: February 2015

Hexagonal wurtzite phased ZnO:Er3+/Yb3+ thin films with various Yb concentrations were deposited on Si(111) substrate by Aerosol Assisted Chemical Vapor Deposition process. Post-annealed films at 1000 °C in air atmosphere showed a crystallinity enhancement. Yb3+ (4F7/2 → 4F5/2) 1000 nm emission increased with the increase of Yb3+ concentration emanating from an Er-Yb energy transfer. The reflectance percentage of 12% was achieved in the [250–1000 nm] range, and the refractive index of 1.97 was obtained for 632 nm wavelength. These results suggest that the (3 mol. % Er, 9 mol. % Yb) codoped film is a highly efficient antireflective downconversion layer for enhancing Si solar cell efficiency.
Amorphous ZnAlSnO thin-film transistors by a combustion solution process for future displays
Authors: Jiang Qingjun , Feng Lisha , Wu Chuanjia , Sun Rujie , Li Xifeng , Lu Bin , Ye Zhizhen , Lu Jianguo
Published: February 2015

A combustion solution method was developed to fabricate amorphous ZnAlSnO (a-ZATO) for thin-film transistors (TFTs). The properties of a-ZATO films and behaviors of a-ZATO TFTs were studied in detail. An appropriate Al content in the matrix could suppress the formation of oxygen vacancies efficiently and achieve densely amorphous films. The a-ZATO TFTs exhibited acceptable performances, with an on/off current ratio of ∼106, field-effect mobility of 2.33 cm2·V−1·S−1, threshold voltage of 2.39 V, and subthreshold swing of 0.52 V/decade at an optimal Al content (0.5). The relation between on- and off-resistance of the ZATO TFT was also within the range expected for fast switching devices. More importantly, the introduced Al with an appropriate content had the ability to evidently enhance the device long-term stability under working bias stress and storage durations. The obtained indium- and gallium-free a-ZATO TFTs are very promising for the next-generation displays.
Comparative study of C-III group elements codoped ZnO by first-principles
Authors: Li Honglin , Lv Yingbo , Fu Hao , Li Jinzhu , Yu Ke
Published: February 2015

First-principle calculations were performed in order to analyze the band structures, density of states, hole carriers, conductivity properties, and defect formation energies of C-mono and C-Al/Ga/In co-doped ZnO structures. The results indicated that the Fermi-level shifted into a valance band, showing p-type conductivity after doping. The analysis of the hole carriers indicated that the concentration of hole carriers in C-mono doped ZnO was larger than that of C-Al/Ga/In co-doped structures, while the latter exhibited better transfer characteristics. The defect formation energies of C-Al/Ga/In co-doped ZnO systems were lower than that of C-mono doped structure in two extreme conditions, and C-Al co-doped ZnO displayed negative defect formation energy. These results prove that C-Al acceptor-donor dual-doping scheme is a feasible approach to realize p-type ZnO.
Magnetic nondestructive testing of rotor blade tips
Authors: Cardelli E. , Faba A. , Marsili R. , Rossi G. , Tomassini R.
Published: February 2015

This paper deals with a particular magnetic nondestructive technique applied to the control of the position of the steel blades in rotating parts of turbines and engines. The working principle is based on a bridge of four identical magneto-resistive sensors. One sensor is placed near the blades, and the change in magnetic field produced by a permanent magnet and deviated by the change in position of the blade is detected by the sensor bridge. The position of the sensor is indicated, via dedicated FEM simulations, in order to have high sensitivity to the position change and high output signal. The accuracy and effectiveness of the proposed method are shown by experimental tests carried out in our laboratories. In particular, the tests indicate that the proposed magnetic nondestructive technique can be used in an almost large velocity range, and for quite different values of blade tip. The method seems also promising for the detection of blade vibrations.
Is the negative glow plasma of a direct current glow discharge negatively charged?
Authors: Bogdanov E. A. , Demidov V. I. , Kudryavtsev A. A. , Saifutdinov A. I.
Published: February 2015

A classic problem in gas discharge physics is discussed: what is the sign of charge density in the negative glow region of a glow discharge? It is shown that traditional interpretations in text-books on gas discharge physics that states a negative charge of the negative glow plasma are based on analogies with a simple one-dimensional model of discharge. Because the real glow discharges with a positive column are always two-dimensional, the transversal (radial) term in divergence with the electric field can provide a non-monotonic axial profile of charge density in the plasma, while maintaining a positive sign. The numerical calculation of glow discharge is presented, showing a positive space charge in the negative glow under conditions, where a one-dimensional model of the discharge would predict a negative space charge.
Liquid phase separation and rapid dendritic growth of highly undercooled ternary Fe62.5Cu27.5Sn10 alloy
Authors: Xia Z. C. , Wang W. L. , Luo S. B. , Wei B.
Published: February 2015

The phase separation and dendritic growth characteristics of undercooled liquid Fe62.5Cu27.5Sn10 alloy have been investigated by glass fluxing and drop tube techniques. Three critical bulk undercoolings of microstructure evolution are experimentally determined as 7, 65, and 142 K. Equilibrium peritectic solidification proceeds in the small undercooling regime below 7 K. Metastable liquid phase separation takes place if bulk undercooling increases above 65 K. Remarkable macroscopic phase separation is induced providing that bulk undercooling overtakes the third threshold of 142 K. With the continuous increase of bulk undercooling, the solidified microstructure initially appears as well-branched dendrites, then displays microscale segregation morphology, and finally evolves into macrosegregation patterns. If alloy undercooling is smaller than 142 K, the dendritic growth velocity of γFe phase varies with undercooling according to a power function relationship. Once bulk undercooling exceeds 142 K, its dendritic growth velocity increases exponentially with undercooling, which reaches 30.4 m/s at the maximum undercooling of 360 K (0.21TL). As a comparative study, the liquid phase separation of Fe62.5Cu27.5Sn10 alloy droplets is also explored under the free fall condition. Theoretical calculations reveal that the thermal and solutal Marangoni migrations are the dynamic mechanisms responsible for the development of core-shell structure.
Effect of secondary emission on the argon plasma afterglow with large dust density
Authors: Denysenko I. B. , Stefanović I. , Azarenkov N. A. , Burmaka G. P.
Published: February 2015

A zero-dimensional, space-averaged model for argon plasma afterglow with large dust density is developed. In the model, three groups of electrons in the plasma afterglow are assumed: (i) thermal electrons with Maxwellian distribution, (ii) energetic electrons generated by metastable-metastable collisions (metastable pooling), and (iii) secondary electrons generated at collisions of ions with the electrodes, which have sufficiently large negative voltages in the afterglow. The model calculates the time-dependencies for electron densities in plasma afterglow based on experimental decay times for metastable density and electrode bias. The effect of secondary emission on electron density in the afterglow is estimated by varying secondary emission yields. It is found that this effect is less important than metastable pooling. The case of dust-free plasma afterglow is considered also, and it is found that in the afterglow the effect of secondary emission may be more important than metastable pooling. The secondary emission may increase thermal electron density ne in dust-free and dusty plasma afterglows on a few ten percentages. The calculated time dependencies for ne in dust-free and dusty plasma afterglows describe well the experimental results.
Forward scattering in hard X-ray photoelectron spectroscopy: Structural investigation of buried Mn–Ga films
Authors: ViolBarbosa Carlos E. , Ouardi Siham , Kubota Takahide , Mizukami Shigemi , Fecher Gerhard H. , Miyazaki Terunobu , Ikenaga Eiji , Felser Claudia
Published: February 2015

X-ray photoelectron diffraction (XPD) in combination with hard X-ray photoelectron spectroscopy (HAXPES) has been used to study the structure of buried layers in thin multilayer films. A detailed layer-by-layer investigation was performed using the element-specific, local-probe character of XPD. In the present work, angular-resolved HAXPES at a photon energy of 7.94 keV photon energy was used to investigate a Cr/Mn62Ga38/Mg/MgO multilayer system. Differences in the angular distributions of electrons emitted from Mn and Ga atoms revealed that the structure of Mn62Ga38 changes from L10 towards D022 for increasing annealing temperatures. A c/a ratio of 1.81 ± 0.06 was determined for the buried Mn62Ga38 layer in a D022 structure from the XPD experiment. The improvement of the structural order of the Mn62Ga38 layer is accompanied by an improvement of the structure of the overlying MgO layer.
Investigation of giant Kerr nonlinearity in quantum cascade lasers using mid-infrared femtosecond pulses
Authors: Cai Hong , Liu Sheng , Lalanne Elaine , Johnson Anthony M.
Published: February 2015

We study the Kerr nonlinearity of quantum cascade lasers (QCLs) by coupling resonant and off-resonant mid-infrared (mid-IR) femtosecond (fs) pulses into an active QCL waveguide. We observe an increase in the spectral width of the transmitted fs pulses as the coupled mid-infrared (mid-IR) pulse power increases. This is explained by the self-phase modulation effect due to the large Kerr nonlinearity of QCL waveguides. We further confirm this effect by observing the intensity dependent far-field profile of the transmitted mid-IR pulses, showing the pulses undergo self-focusing as they propagate through the active QCL due to the intensity dependent refractive index. We experimentally estimate the nonlinear refractive index n2 of a QCL to be ∼8 × 10−9 cm2/W using the far-field beam profile of the transmitted pulses. The finite-difference time-domain simulations of QCL waveguides with Kerr nonlinearity incorporated show similar behavior to the experimental results.
Great reduction of loss at high electric field in the polyvinylidene fluoride/aromatic polythiourea blend films along with an irreversible phase transition
Authors: Jiang Long , Li Weiping , Zhu Jiujun , Huo Xiaoyun , Luo Laihui , Zhu Yuejin
Published: February 2015

In this paper, the polarization response of dielectric blend based on the polyvinylidene fluoride (PVDF) and aromatic polythiourea (ArPTU) was investigated. It is found that the conduction loss at high field has been reduced 2–4 times along with an interesting irreversible transition under high electric field. The loss at 700 MV/m can be kept below 20%, which is better than most other polar dielectric polymers. It is proved that the transition is a phase change from glass phase to polar β phase at a critical field. And the highly polar thiourea groups of ArPTU can act as traps for the electrons, reduce conduction loss greatly and prevent dielectric breakdown by stabilizing the electron energy.
Endurance degradation mechanisms in TiN\Ta2O5\Ta resistive random-access memory cells
Authors: Chen C. Y. , Goux L. , Fantini A. , Clima S. , Degraeve R. , Redolfi A. , Chen Y. Y. , Groeseneken G. , Jurczak M.
Published: February 2015

Impact of set/reset pulse duration and amplitude on the endurance failure modes of TiN\Ta2O5\Ta cells is investigated and is related to interaction between Oxygen and TiN bottom electrode during reset. Hourglass electrical switching simulation of conductive filament temperature during reset transient and ab-initio calculation of reaction energy further support this degradation mechanism. Based on this understanding, endurance improvement is achieved by using shorter reset pulse and/or using inert Ru bottom electrode.
Response of a shrubland mammal and reptile community to a history of landscape-scale wildfire
Authors: Doherty Tim S. , Davis Robert A. , van Etten Eddie J. B. , Collier Neil , Krawiec Josef
Published: February 2015

Fire plays a strong role in structuring fauna communities and the habitat available to them in fire-prone regions. Human-mediated increases in fire frequency and intensity threaten many animal species and understanding how these species respond to fire history and its associated effect on vegetation is essential to effective biodiversity management. We used a shrubland mammal and reptile community in semiarid south-western Australia as a model to investigate interactions between fire history, habitat structure and fauna habitat use. Of the 15 species analysed, five were most abundant in recently burnt habitat (8–13 years since last fire), four were most abundant in long unburnt areas (25–50 years) and six showed no response to fire history. Fauna responses to fire history were divergent both within and across taxonomic groups. Fire management that homogenises large areas of habitat through either fire exclusion or frequent burning may threaten species due to these diverse requirements, so careful management of fire may be needed to maximise habitat suitability across the landscape. When establishing fire management plans, we recommend that land managers exercise caution in adopting species-specific information from different locations and broad vegetation types. Information on animal responses to fire is best gained through experimental and adaptive management approaches at the local level.
A Thematic Catalogue of the Instrumental Music of Martino Bitti (1655/6–1743)
Authors: Talbot Michael
Published: February 2015

Martino Bitti (1655/6–1743) was the leading violinist-composer working in Florence during a long period stretching from Corelli's first published works to the mature years of Vivaldi. Ironically, his nine sonatas for wind instruments are better known today than the 27 solo sonatas for his own instrument, the violin, which constitute a corpus of great technical accomplishment and musical expressiveness. Since the publication of a critical edition of Bitti's violin sonatas is currently in progress, the moment is right to present a thematic catalogue of his instrumental music, which forms the second part of the article. The first part comprises an updated biography of the composer (which for the first time proposes that Bitti briefly visited England) and a general evaluation of his highly distinctive musical style.
Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network
Authors: Artym Vira V. , Swatkoski Stephen , Matsumoto Kazue , Campbell Catherine B. , Petrie Ryan J. , Dimitriadis Emilios K. , Li Xin , Mueller Susette C. , Bugge Thomas H. , Gucek Marjan , Yamada Kenneth M.
Published: February 2015

Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM.
Left Ventricular Systolic Dysfunction in Asymptomatic Black Hypertensive Subjects
Authors: Ojji Dike , Atherton John , Sliwa Karen , Alfa Jacob , Ngabea Murtala , Opie Lionel
Published: January 2015

BACKGROUND

Hypertension has been established as one of the commonest causes of heart failure especially in sub-Saharan Africa. We have previously observed a high prevalence of left ventricular (LV) systolic dysfunction in hypertensive heart failure patients in Nigeria despite a low prevalence of ischemic heart disease. The present study was, therefore, undertaken to assess the prevalence of asymptomatic LV systolic dysfunction in hypertensive black African subjects with no history of heart failure.

METHODS

One thousand nine hundred forty-seven hypertensive subjects without heart failure presenting to the Cardiology Unit, Department of Medicine, University of Abuja Teaching Hospital, Nigeria, from April 2006 to August 2013 had clinical and echocardiographic evaluation.

RESULTS

Nine hundred fifty-three (48.9%) were males and 994 (51.1%) were females. One thousand eight hundred seventeen (93.3%) had normal LV systolic function (LV ejection fraction (LVEF) ≥ 54%), 68 (3.5%) had mild LV systolic dysfunction (LVEF 45–54%), 43 (2.3%) had moderate LV systolic dysfunction (LVEF 30–44%), and 16 (0.9%) had severe LV systolic dysfunction (LVEF < 30%). Male subjects had worse LV systolic function compared to women (mean LVEF 73.2% vs. 75.6%, P value < 0.0001) and diabetic subjects had worse LV systolic function compared to nondiabetic subjects (LVEF 72.3% vs. 75.7%, P = 0.02). In multivariate regression analysis, lower LVEF as a continuous variable was associated with older age, male sex, diabetes mellitus, LV mass indexed for body surface area, diastolic blood pressure, posterior wall thickness in diastole, left atrial diameter, and LV internal diameter in diastole.

CONCLUSIONS

In a cohort of asymptomatic Black hypertensive subjects, 6.7% had LV systolic dysfunction, which was associated with male gender, diabetes mellitus, and larger LV mass.
Variant Near FGF5 Has Stronger Effects on Blood Pressure in Chinese With a Higher Body Mass Index
Authors: Li Jin , Shi Jinxiu , Huang Wei , Sun Jielin , Wu Ying , Duan Qing , Luo Jingchun , Lange Leslie A. , Gordon-Larsen Penny , Zheng S. Lilly , Yuan Wentao , Wang Ying , Popkin Barry M. , Mo Zengnan , Xu Jianfeng , Du Shufa , Mohlke Karen L. , Lange Ethan M.
Published: January 2015

BACKGROUND

The objective of this study was to investigate the genetic association of 4 candidate variants with blood pressure and test the modifying effects of environmental factors including age, sex, and body mass index (BMI).

METHODS

We used a linear mixed-effects model to test for variant main effects and variant interactions with age, sex, and BMI on systolic (SBP) and diastolic (DBP) blood pressure in 7,319 Chinese adults from the China Health and Nutrition Survey (CHNS). We attempted to replicate our significant interaction findings in 1,996 Chinese men from the Fangchenggang Area Male Health and Examination Survey (FAMHES).

RESULTS

Two variants (rs11105378 near ATP2B1 and rs1458038 near FGF5) were significantly associated (P < 0.00625 = 0.05/8) with both SBP and DBP in CHNS. Variant rs1378942 near CSK was nominally associated with SBP (P = 0.01). The signal at rs1458038 exhibited a genotype-by-BMI interaction affecting blood pressure (Pinteraction = 0.0018 for SBP; Pinteraction = 0.049 for DBP), with the strongest variant effects in those with the highest BMI. In FAMHES, rs1458038 also showed stronger effects on SBP and DBP among men with the highest BMI.

CONCLUSIONS

Our findings suggest high BMI increases the effect of the blood pressure-increasing allele at rs1458038 near FGF5, further highlighting the importance of obesity prevention in reducing hypertension risk.
Prevalence of Prehypertension in Mexico and Its Association With Hypomagnesemia
Authors: Rodríguez-Ramírez Mariana , Simental-Mendía Luis E. , González-Ortiz Manuel , Martínez-Abundis Esperanza , Madero Agustín , Brito-Zurita Olga , Pérez-Fuentes Ricardo , Revilla-Monsalve Cristina , Islas-Andrade Sergio , Rodríguez-Morán Martha , Guerrero-Romero Fernando
Published: January 2015

BACKGROUND

Prehypertension (preHTN) increases the risk of developing hypertension. The objectives of this study were to estimate the prevalence of preHTN in the Mexican adult population and evaluate the association between hypomagnesemia and preHTN.

METHODS

This study was a 2-phase, population-based study. In the first phase, 4,272 Mexican adults (aged 20–65 years) were enrolled to determine the prevalence of preHTN. In the second phase, a cross-sectional analysis was performed to evaluate the association between hypomagnesemia and preHTN. The exclusion criteria were chronic diarrhea, malignancy, hepatic and renal diseases, chronic inflammatory disease, and the intake of magnesium supplements. PreHTN was defined as a systolic blood pressure (BP) of 120–139mm Hg and/or diastolic BP of 80–89mm Hg, and hypomagnesemia was defined as a serum magnesium concentration <1.8mg/dl.

RESULTS

The prevalence of preHTN was 37.5% (95% confidence interval (CI): 36.0–39.0): 46.7% were men (95% CI: 44.1–49.4) and 33.2% (95% CI: 31.5–5.0) were women. The serum magnesium data were available for 921 participants. Hypomagnesemia was identified in 276 (30.0%; 95% CI: 27.1–33.0) subjects; of them, 176 (63.8%; 95% CI: 58.3–69.6) had preHTN. Individuals with preHTN exhibited lower magnesium levels than individuals without preHTN (1.78±0.36 vs. 1.95±0.37, P < 0.0005). A multiple logistic regression analysis (adjusted for age, sex, smoking, body mass index, waist circumference, fasting glucose, total cholesterol, high-density lipoprotein cholesterol, and triglycerides levels) indicated a significant association between hypomagnesemia and preHTN (odds ratio = 1.78; 95% CI: 1.5–4.0, P < 0.0005).

CONCLUSIONS

The prevalence of preHTN in the Mexican population is 37.5%, and hypomagnesemia is strongly associated with preHTN.
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
Authors: Tobalina Luis , Bargiela Rafael , Pey Jon , Herbst Florian-Alexander , Lores Iván , Rojo David , Barbas Coral , Peláez Ana I. , Sánchez Jesús , von Bergen Martin , Seifert Jana , Ferrer Manuel , Planes Francisco J.
Published: January 2015

Motivation: With the advent of meta-‘omics’ data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited.

Results: Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data.

Contact:  fplanes@ceit.es or mferrer@icp.csic.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Prediction of potential disease-associated microRNAs based on random walk
Authors: Xuan Ping , Han Ke , Guo Yahong , Li Jin , Li Xia , Zhong Yingli , Zhang Zhaogong , Ding Jian
Published: January 2015

Motivation: Identifying microRNAs associated with diseases (disease miRNAs) is helpful for exploring the pathogenesis of diseases. Because miRNAs fulfill function via the regulation of their target genes and because the current number of experimentally validated targets is insufficient, some existing methods have inferred potential disease miRNAs based on the predicted targets. It is difficult for these methods to achieve excellent performance due to the high false-positive and false-negative rates for the target prediction results. Alternatively, several methods have constructed a network composed of miRNAs based on their associated diseases and have exploited the information within the network to predict the disease miRNAs. However, these methods have failed to take into account the prior information regarding the network nodes and the respective local topological structures of the different categories of nodes. Therefore, it is essential to develop a method that exploits the more useful information to predict reliable disease miRNA candidates.

Results: miRNAs with similar functions are normally associated with similar diseases and vice versa. Therefore, the functional similarity between a pair of miRNAs is calculated based on their associated diseases to construct a miRNA network. We present a new prediction method based on random walk on the network. For the diseases with some known related miRNAs, the network nodes are divided into labeled nodes and unlabeled nodes, and the transition matrices are established for the two categories of nodes. Furthermore, different categories of nodes have different transition weights. In this way, the prior information of nodes can be completely exploited. Simultaneously, the various ranges of topologies around the different categories of nodes are integrated. In addition, how far the walker can go away from the labeled nodes is controlled by restarting the walking. This is helpful for relieving the negative effect of noisy data. For the diseases without any known related miRNAs, we extend the walking on a miRNA-disease bilayer network. During the prediction process, the similarity between diseases, the similarity between miRNAs, the known miRNA-disease associations and the topology information of the bilayer network are exploited. Moreover, the importance of information from different layers of network is considered. Our method achieves superior performance for 18 human diseases with AUC values ranging from 0.786 to 0.945. Moreover, case studies on breast neoplasms, lung neoplasms, prostatic neoplasms and 32 diseases further confirm the ability of our method to discover potential disease miRNAs.

Availability and implementation: A web service for the prediction and analysis of disease miRNAs is available at http://bioinfolab.stx.hk/midp/ .

Contact:  guoyahong_hlju@163.com or lixia@hrbmu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
bbcontacts: prediction of
β
-strand pairing from direct coupling patterns
Authors: Andreani Jessica , Söding Johannes
Published: January 2015

Motivation : It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β–β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs.

Results : bbcontacts predicts β–β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modelled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with < 1000 sequences, bbcontacts achieves 50% precision for contacting β–β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure.

Availability and implementation: bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts

Contact : jessica.andreani@mines.org or soeding@mpibpc.mpg.de

Supplementary information : Supplementary data are available at Bioinformatics online.
Estimating survival of rock lobsters from long-term tagging programmes: how survey number and interval influence estimates
Authors: Kordjazi Ziya , Frusher Stewart , Buxton Colin D. , Gardner Caleb
Published: January 2015

A long-term tagging dataset on southern rock lobster (Jasus edwardsii) conducted at the Crayfish Point Scientific Reserve near Hobart, Tasmania, Australia, was used to determine how survey number and survey duration affected the precision of survival estimates of male and female lobsters to ensure sustainable exploitation of the population. Tagging surveys were undertaken twice yearly during 2000–2003 with unequal time-intervals between surveys and then once a year with equal time-intervals during 2004–2012 during the January–February period. The most parsimonious Cormack–Jolly–Seber model for estimating survival of lobsters was dependent on (i) timing of the tagging and recapture surveys, (ii) time between consecutive recapture surveys, and (iii) gender. The number of surveys required to provide a precise survival probability varied with gender and time between recapture surveys. For surveys where there was unequal time between recapture surveys, seven and five surveys were required for female and male lobsters, respectively, whereas only five surveys were required when annual surveys were undertaken. Thus, lobster tagging projects using annual surveys should ideally extend to at least 5 years, which is beyond the 3-year project duration common in marine science.
Function of the N-terminal segment of the RecA-dependent nuclease Ref
Authors: Gruber Angela J. , Olsen Tayla M. , Dvorak Rachel H. , Cox Michael M.
Published: January 2015

The bacteriophage P1 Ref (recombination enhancement function) protein is a RecA-dependent, HNH endonuclease. It can be directed to create targeted double-strand breaks within a displacement loop formed by RecA. The 76 amino acid N-terminal region of Ref is positively charged (25/76 amino acid residues) and inherently unstructured in solution. Our investigation of N-terminal truncation variants shows this region is required for DNA binding, contains a Cys involved in incidental dimerization and is necessary for efficient Ref-mediated DNA cleavage. Specifically, Ref N-terminal truncation variants lacking between 21 and 47 amino acids are more effective RecA-mediated targeting nucleases. We propose a more refined set of options for the Ref-mediated cleavage mechanism, featuring the N-terminal region as an anchor for at least one of the DNA strand cleavage events.
A basal level of DNA damage and telomere deprotection increases the sensitivity of cancer cells to G-quadruplex interactive compounds
Authors: Salvati Erica , Rizzo Angela , Iachettini Sara , Zizza Pasquale , Cingolani Chiara , D'Angelo Carmen , Porru Manuela , Mondello Chiara , Aiello Aurora , Farsetti Antonella , Gilson Eric , Leonetti Carlo , Biroccio Annamaria
Published: January 2015

Here, with the aim of obtaining insight into the intriguing selectivity of G-quadruplex (G4) ligands toward cancer compared to normal cells, a genetically controlled system of progressive transformation in human BJ fibroblasts was analyzed. Among the different comparative evaluations, we found a progressive increase of DNA damage response (DDR) markers throughout the genome from normal toward immortalized and transformed cells. More interestingly, sensitivity to G4 ligands strongly correlated with the presence of a basal level of DNA damage, including at the telomeres, where the chromosome ends were exposed to the DDR without concurrent induction of DNA repair activity, as revealed by the lack of 53BP1 recruitment and telomere aberrations. The link between telomere uncapping and the response to G4 stabilization was directly assessed by showing that a partial TRF2 depletion, causing a basal level of telomere localized DDR, rendered telomerized fibroblasts prone to G4-induced telomere damage and anti-proliferative defects. Taken together these data strongly indicate that the presence of a basal level of telomere-associated DDR is a determinant of susceptibility to G4 stabilization.
Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner
Authors: Ebina Isao , Takemoto-Tsutsumi Mariko , Watanabe Shun , Koyama Hiroaki , Endo Yayoi , Kimata Kaori , Igarashi Takuya , Murakami Karin , Kudo Rin , Ohsumi Arisa , Noh Abdul Latif , Takahashi Hiro , Naito Satoshi , Onouchi Hitoshi
Published: January 2015

Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.
Domain organization within the nuclear export factor Mex67:Mtr2 generates an extended mRNA binding surface
Authors: Aibara Shintaro , Valkov Eugene , Lamers Meindert , Stewart Murray
Published: January 2015

The Mex67:Mtr2 complex is the principal yeast nuclear export factor for bulk mRNA and also contributes to ribosomal subunit export. Mex67 is a modular protein constructed from four domains (RRM, LRR, NTF2-like and UBA) that have been thought to be joined by flexible linkers like beads on a string, with the RRM and LRR domains binding RNAs and the NTF2-like and UBA domains binding FG-nucleoporins to facilitate movement through nuclear pores. Here, we show that the NTF2-like domain from Saccharomyces cerevisiae Mex67:Mtr2 also contributes to RNA binding. Moreover, the 3.3 Å resolution crystal structure of the Mex67ΔUBA:Mtr2 complex, supplemented with small angle X-ray scattering data, indicated that the LRR domain has a defined spatial relationship to the Mex67NTF2L:Mtr2 region. Conversely, the RRM domain and especially the UBA domain are more mobile. The conformation assumed by the LRR and NTF2-like domains results in clusters of positively-charged residues on each becoming arranged to form a continuous interface for binding RNA on the opposite side of the complex to the region that interacts with FG-nucleoporins to facilitate passage through nuclear pores.
ANIR: Atacama near-infrared camera for the 1.0 m miniTAO telescope
Authors: Konishi Masahiro , Motohara Kentaro , Tateuchi Ken , Takahashi Hidenori , Kitagawa Yutaro , Kato Natsuko , Sako Shigeyuki , Uchimoto Yuka K. , Toshikawa Koji , Ohsawa Ryou , Yamamuro Tomoyasu , Asano Kentaro , Ita Yoshifusa , Kamizuka Takafumi , Komugi Shinya , Koshida Shintaro , Manabe Sho , Matsunaga Noriyuki , Minezaki Takeo , Morokuma Tomoki , Nakashima Asami , Takagi Toshinobu , Tanabé Toshihiko , Uchiyama Mizuho , Aoki Tsutomu , Doi Mamoru , Handa Toshihiro , Kato Daisuke , Kawara Kimiaki , Kohno Kotaro , Miyata Takashi , Nakamura Tomohiko , Okada Kazushi , Soyano Takao , Tamura Yoichi , Tanaka Masuo , Tarusawa Ken'ichi , Yoshii Yuzuru
Published: February 2015

We have developed a near-infrared camera called ANIR (Atacama Near-InfraRed camera) for the University of Tokyo Atacama Observatory 1.0 m telescope (miniTAO) installed at the summit of Cerro Chajnantor (5640 m above sea level) in the north of Chile. The camera provides a field of view of 5${^{\prime}_{.}}$1 × 5${^{\prime}_{.}}$1 with a spatial resolution of 0${^{\prime\prime}_{.}}$298 pixel−1 in the wavelength range of 0.95 to 2.4 μm, using Offner relay optics and a PACE HAWAII-2 focal plane array. Taking advantage of the dry site, the camera is capable of narrow-band imaging observations at the hydrogen Paschen-α (Paα, λ = 1.8751 μm in air) wavelength ground-based observations of which have been quite difficult due to deep atmospheric absorption, mainly from water vapor. We have been successfully obtaining Paα images of Galactic objects and nearby galaxies since the first-light observation in 2009 with ANIR. The throughputs at the narrow-band filters (N1875, N191) including the atmospheric absorption show larger dispersion (∼ 10%) than those at broad-band filters (a few percent), indicating that they are affected by temporal fluctuations in precipitable water vapor (PWV) above the site. We evaluate the PWV content via the atmospheric transmittance at the narrow-band filters, and deduce that the median and the dispersion of the distribution of the PWV are 0.40 ± 0.30 and 0.37 ± 0.21 mm, for the N1875 and N191 data respectively, which are remarkably smaller (49% ± 38% for N1875 and 59% ± 26% for N191) than radiometry measurements at the base of Cerro Chajnantor (an altitude of 5100 m). The decrease in PWV can be explained by the altitude of the site when we assume that the vertical distribution of the water vapor is approximated at an exponential profile with scale heights within 0.3–1.9 km (previously observed values at night). We thus conclude that miniTAO/ANIR at the summit of Cerro Chajnantor indeed provides us an excellent capability for a ground-based Paα observation.
Global distribution of ionizing and recombining plasmas in the supernova remnant G290.1−0.8
Authors: Kamitsukasa Fumiyoshi , Koyama Katsuji , Uchida Hiroyuki , Nakajima Hiroshi , Hayashida Kiyoshi , Mori Koji , Katsuda Satoru , Tsunemi Hiroshi
Published: February 2015

We report on the Suzaku results of the mixed-morphology supernova remnant (SNR) G290.1−0.8 (MSH 11-61A). The SNR has an asymmetric structure extended to the south-east and the north-west. In the X-ray spectra of the center and the north-west regions, we discover recombining plasma features with a strong Si Lyα and radiative recombination continuum at ∼ 2.7 keV. These features are the most significant in the north-west region, and the spectra are well reproduced with a recombining plasma of kTe = 0.5 keV, whereas the spectra of other regions are expressed by an ionizing plasma of kTe = 0.6 keV. The recombining plasma has over-solar abundances, while the ionizing plasma has roughly solar abundances. Hence they are likely ejecta and of interstellar medium (ISM) origin, respectively. The recombining plasma in the north-west of G290.1−0.8 would be generated by a break-out of the supernova ejecta from a high density circumstellar medium to a low density ISM.
Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions
Authors: Lopez Virginia , Barinova Natalja , Onishi Masayuki , Pobiega Sabrina , Pringle John R. , Dubrana Karine , Marcand Stéphane
Published: February 2015

Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. During mitosis, they form anaphase bridges, resulting in chromosome breakage by an unknown mechanism. In budding yeast, dicentrics generated by telomere fusion break at the fusion, a process that restores the parental karyotype and protects cells from rare accidental telomere fusion. Here, we observed that dicentrics lacking telomere fusion preferentially break within a 25- to 30-kb-long region next to the centromeres. In all cases, dicentric breakage requires anaphase exit, ruling out stretching by the elongated mitotic spindle as the cause of breakage. Instead, breakage requires cytokinesis. In the presence of dicentrics, the cytokinetic septa pinch the nucleus, suggesting that dicentrics are severed after actomyosin ring contraction. At this time, centromeres and spindle pole bodies relocate to the bud neck, explaining how cytokinesis can sever dicentrics near centromeres.
18F-FDG-PET/CT Imaging of Drug-Induced Metabolic Changes in Genetically Engineered Mouse Lung Cancer Models
Authors: Wang Yuchuan , Kung Andrew L.
Published: February 2015

The most commonly used radiotracer for cancer imaging in humans and mice is 2-deoxy-2-(18F)fluoro-d-glucose (18F-FDG). We have used FDG coupled with positron-emission tomography (PET) to assess the pharmacodynamic efficacy of a number of therapeutics in genetically engineered mouse lung cancer models. In this protocol, we present our approach for FDG–PET imaging of early tumor metabolic changes induced by drug treatment. Special consideration is given to animal preparation, anesthesia, and PET/computed tomography (CT) imaging of mice with lung tumors. Specifically, we recommend fasting the mice overnight to reduce background, using sevoflurane anesthesia and a “conscious” uptake period to minimize cardiac FDG uptake, adopting a relatively short duration of CT and PET scanning to facilitate serial imaging, and quantifying the comparison between the maximum standardized uptake values (SUVs) of lung tumors before and after treatment to determine treatment effects. Used in this manner, FDG–PET can rapidly assess tumor metabolism before and after treatment with an experimental therapeutic. In many cases, metabolic changes are apparent after just a single dose of treatment, helping to show target engagement and modulation by the drug (pharmacodynamic efficacy) within days of starting therapy.
Denaturation and Electrophoresis of RNA with Formaldehyde
Authors: Rio Donald C.
Published: February 2015

Electrophoretic size fractionation can be used to denature and separate large mRNA molecules (0.5–10 kb) on formaldehyde-containing agarose gels. Formaldehyde contains a carbonyl group that reacts to form Schiff bases with the imino or amino groups of guanine, adenine, and cytosine. These covalent adducts prevent normal base pairing and maintain the RNA in a denatured state. Because these adducts are unstable, formaldehyde must be present in the gel to maintain the RNA in the denatured state. This protocol describes the preparation of an agarose gel with formaldehyde and its setup in a horizontal electrophoresis apparatus. RNA samples are prepared and denatured in a solution of formamide and formaldehyde and, with 0.5- to 10-kb size markers, subjected to electrophoresis through the gel. Following electrophoresis, the gel is stained to visualize RNA markers or rRNA using one of several different types of stains.