bluuebunny/crossref_metadata_2025 huggingface dataset:
Unique quasi-vertical alignment of RGO sheets under an applied non-uniform DC electric field for enhanced field emission
Authors: Roy Rajarshi , Jha Arunava , Sen Dipayan , Banerjee Diptonil , Chattopadhyay Kalyan Kumar
Published: July 2014

Quasi-vertical alignment of as-synthesized RGO sheets under a non-uniform electric field deposited over a carbon cloth substrate and its field emission characteristics.
Theory on excitations of drift Alfvén waves by energetic particles. I. Variational formulation
Authors: Zonca Fulvio , Chen Liu
Published: July 2014

A unified theoretical framework is presented for analyzing various branches of drift Alfvén waves and describing their linear and nonlinear behaviors, covering a wide range of spatial and temporal scales. Nonlinear gyrokinetic quasineutrality condition and vorticity equation, derived for drift Alfvén waves excited by energetic particles in fusion plasmas, are cast in integral form, which is generally variational in the linear limit; and the corresponding gyrokinetic energy principle is obtained. Well known forms of the kinetic energy principle are readily recovered from this general formulation. Furthermore, it is possible to demonstrate that the general fishbone like dispersion relation, obtained within the present theoretical framework, provides a unified description of drift Alfvén waves excited by energetic particles as either Alfvén eigenmodes or energetic particle modes. The advantage of the present approach stands in its capability of extracting underlying linear and nonlinear physics as well as spatial and temporal scales of the considered fluctuation spectrum. For these reasons, this unified theoretical framework can help understanding experimental observations as well as numerical simulation and analytic results with different levels of approximation. Examples and applications are given in Paper II [F. Zonca and L. Chen, “Theory on excitations of drift Alfvén waves by energetic particles. II. The general fishbone-like dispersion relation,” Phys. Plasmas 21, 072121 (2014)].
Theory on excitations of drift Alfvén waves by energetic particles. II. The general fishbone-like dispersion relation
Authors: Zonca Fulvio , Chen Liu
Published: July 2014

The theoretical framework of the general fishbone-like dispersion relation (GFLDR), presented and discussed in the Companion Paper [Phys. Plasmas 21, 072120 (2014)], is applied to cases of practical interest of shear/drift Alfvén waves (SAWs/DAWs) excited by energetic particles (EPs) in toroidal fusion plasmas. These applications demonstrate that the GFLDR provides a unified approach that allows analytical and numerical calculations of stability properties, as well as mode structures and, in general, nonlinear evolutions, based on different models and with different levels of approximation. They also show the crucial importance of kinetic descriptions, accurate geometries and boundary conditions for predicting linear as well as nonlinear SAW/DAW and EP behaviors in burning plasmas. Thus, the GFLDR unified theoretical framework elevates the interpretative capability for both experimental and numerical simulation results.
Status of the diagnostics development for the first operation phase of the stellarator Wendelstein 7-X
Authors: König R. , Biel W. , Biedermann C. , Burhenn R. , Cseh G. , Czarnecka A. , Endler M. , Estrada T. , Grulke O. , Hathiramani D. , Hirsch M. , Jabłonski S. , Jakubowski M. , Kaczmarczyk J. , Kasparek W. , Kocsis G. , Kornejew P. , Krämer-Flecken A. , Krychowiak M. , Kubkowska M. , Langenberg A. , Laux M. , Liang Y. , Lorenz A. , Neubauer O. , Otte M. , Pablant N. , Pasch E. , Pedersen T. S. , Schmitz O. , Schneider W. , Schuhmacher H. , Schweer B. , Thomsen H. , Szepesi T. , Wiegel B. , Windisch T. , Wolf S. , Zhang D. , Zoletnik S.
Published: July 2014

An overview of the diagnostics which are essential for the first operational phase of Wendelstein 7-X and the set of diagnostics expected to be ready for operation at this time are presented. The ongoing investigations of how to cope with high levels of stray Electron Cyclotron Resonance Heating (ECRH) radiation in the ultraviolet (UV)/visible/infrared (IR) optical diagnostics are described.
Effects of non-local exchange on core level shifts for gas-phase and adsorbed molecules
Authors: Van den Bossche M. , Martin N. M. , Gustafson J. , Hakanoglu C. , Weaver J. F. , Lundgren E. , Grönbeck H.
Published: July 2014

Density functional theory calculations are often used to interpret experimental shifts in core level binding energies. Calculations based on gradient-corrected (GC) exchange-correlation functionals are known to reproduce measured core level shifts (CLS) of isolated molecules and metal surfaces with reasonable accuracy. In the present study, we discuss a series of examples where the shifts calculated within a GC-functional significantly deviate from the experimental values, namely the CLS of C 1s in ethyl trifluoroacetate, Pd 3d in PdO and the O 1s shift for CO adsorbed on PdO(101). The deviations are traced to effects of the electronic self-interaction error with GC-functionals and substantially better agreements between calculated and measured CLS are obtained when a fraction of exact exchange is used in the exchange-correlation functional.
Motor characteristics determine the rheological behavior of a suspension of microswimmers
Authors: Karmakar Richa , Gulvady Ranjit , Tirumkudulu Mahesh S. , Venkatesh K. V.
Published: July 2014

A suspension of motile cells exhibits complex rheological properties due to their collective motion. We measure the shear viscosity of a suspension of Escherichia coli strains varying in motor characteristics such as duration of run and tumble. At low cell densities, all strains irrespective of their motor characteristics exhibit a linear increase in viscosity with cell density suggesting that the cells behave as a suspension of passive rods with an effective aspect ratio set by the motor characteristics of the bacteria. As the cell density is increased beyond a critical value, the viscosity drops sharply signaling the presence of strongly coordinated motion among bacteria. The critical density depends not only on the magnitude of shear but also the motor characteristics of individual cells. High shear rate disrupts the coordinated motion reducing its behavior, once again, to a suspension of inactive particles.
Intramolecular relaxation of flexible dendrimers with excluded volume
Authors: Rai Gobind Ji , Kumar Amit , Biswas Parbati
Published: July 2014

The mechanical and dielectric relaxation moduli of dendrimers with the excluded volume interactions are theoretically investigated within the framework of Rouse-Zimm theory. The excluded volume interactions in dendrimers are expressed in terms of the effective co-volume between nearest non-bonded monomers, modeled through the delta function pseudopotential. These short range interactions play a decisive role in determining the mechanical moduli of dendrimers. The characteristic feature of excluded volume effect in the mechanical moduli is typically revealed in the intermediate frequency regime, where dendrimers with varied strengths of excluded volume interactions display power-law scaling relations with frequency. The value of the power-law scaling exponents for the mechanical moduli exactly matches with the earlier results for dendrimers in good solvent conditions. The mechanical moduli are dominated by the smaller eigenvalues in the low frequency region corresponding to the collective modes with smaller relaxation rates, which increase with the corresponding increase of the excluded volume interactions. The local modes are practically independent of excluded volume. A cross-over between the loss and storage moduli is observed at the intermediate frequency regime. The position of this cross-over shifts towards the low frequency region with the decrease in the strength of the excluded volume, which resembles the behavior of dendrimers with the variation of temperature as reported in an earlier experimental work. The structure of dendrimers show a conspicuous change as a function of the effective co-volume between the nearest non-bonded monomers. The real part of dielectric relaxation moduli remains unchanged by varying excluded volume parameters, while its imaginary part varies with the change in strength of excluded volumes for the entire range of frequency except in the high frequency regime. A comparison with the model semiflexible dendrimers show that in such densely packed molecules the mechanical relaxation moduli are strongly affected by the short-ranged excluded volume interactions between the nearest non-bonded monomers.
Simulation of direct plasma injection for laser ion beam acceleration with a radio frequency quadrupole
Authors: Jin Q. Y. , Zhao H. Y. , Zhang J. J. , Sha Sh. , Zhang Zh. L. , Li Zh. M. , Liu W. , Zhang X. Zh. , Sun L. T. , Zhao H. W.
Published: July 2014

The direct plasma injection scheme (DPIS) has been being studied at Institute of Modern Physics since several years ago. A C6+ beam with peak current of 13 mA, energy of 593 keV/u has been successfully achieved after acceleration with DPIS method. To understand the process of DPIS, some simulations have been done as follows. First, with the total current intensity and the relative yields of different charge states for carbon ions measured at the different distance from the target, the absolute current intensities and time-dependences for different charge states are scaled to the exit of the laser ion source in the DPIS. Then with these derived values as the input parameters, the extraction of carbon beam from the laser ion source to the radio frequency quadrupole with DPIS is simulated, which is well agreed with the experiment results.
Modulus of convexity for operator convex functions
Authors: Kim Isaac H.
Published: July 2014

Given an operator convex function f(x), we obtain an operator-valued lower bound for cf(x) + (1 − c)f(y) − f(cx + (1 − c)y), c ∈ [0, 1]. The lower bound is expressed in terms of the matrix Bregman divergence. A similar inequality is shown to be false for functions that are convex but not operator convex.
Note: Three-dimensional linearization of optical trap position detection for precise high speed diffusion measurements
Authors: Hsu Y.-H. , Pralle A.
Published: July 2014

Studies of the details of Brownian motion, hydrodynamic of colloids, or protein diffusion measurements all require high temporal and spatial resolution of the position detector and a means to trap the colloid. Optical trap based thermal noise imaging employing a quadrant photodiode as detector provides such a method. However, optical trapping requires an objective with high numerical aperture resulting in highly nonlinear position signal and significant cross-dependence of the three spatial directions. Local diffusion measurements are especially susceptible to distance errors. Here, we present a position calibration method, which corrects nonlinearities sufficiently to allow precise local diffusion measurement throughout the entire trapping volume. This correction permits us to obtain high-resolution two- and three-dimensional diffusion maps.
Energetic-particle-induced electromagnetic geodesic acoustic mode in tokamak plasmas
Authors: Wang Lingfeng , Dong J. Q. , He Zhixiong , He Hongda , Shen Y.
Published: July 2014

Energetic-particle-induced kinetic electromagnetic geodesic acoustic modes (EKEGAMs) are numerically studied in low β (=plasma pressure/magnetic pressure) tokamak plasmas. The parallel component of the perturbed vector potential is considered along with the electrostatic potential perturbation. The effects of finite Larmor radius and finite orbit width of the bulk and energetic ions as well as electron parallel dynamics are all taken into account in the dispersion relation. Systematic harmonic and ordering analysis are performed for frequency and growth rate spectra of the EKEGAMs, assuming (kρi)∼q−3∼β≪1, where q, k, and ρi are the safety factor, radial component of the EKEGAMs wave vector, and the Larmor radius of the ions, respectively. It is found that there exist critical βh/βi values, which depend, in particular, on pitch angle of energetic ions and safety factor, for the mode to be driven unstable. The EKEGAMs may also be unstable for pitch angle λ0B<0.4 in certain parameter regions. Finite β effect of the bulk ions is shown to have damping effect on the EKEGAMs. Modes with higher radial wave vectors have higher growth rates. The damping from electron dynamics is found decreasing with decrease of the temperature ratio Te/Ti. The modes are easily to be driven unstable in low safety factor q region and high temperature ratio Th/Ti region. The harmonic features of the EKEGAMs are discussed as well.
Specific heat of twisted bilayer graphene: Engineering phonons by atomic plane rotations
Authors: Nika Denis L. , Cocemasov Alexandr I. , Balandin Alexander A.
Published: July 2014

We have studied the phonon specific heat in single-layer, bilayer, and twisted bilayer graphene. The calculations were performed using the Born-von Karman model of lattice dynamics for intralayer atomic interactions and spherically symmetric interatomic potential for interlayer interactions. We found that at temperature T < 15 K, specific heat varies with temperature as Tn, where n = 1 for graphene, n = 1.6 for bilayer graphene, and n = 1.3 for the twisted bilayer graphene. The phonon specific heat reveals an intriguing dependence on the twist angle in bilayer graphene, which is particularly pronounced at low temperature. The results suggest a possibility of phonon engineering of thermal properties of layered materials by twisting the atomic planes.
Enhancement of near-infrared absorption in graphene with metal gratings
Authors: Zhao B. , Zhao J. M. , Zhang Z. M.
Published: July 2014

Graphene has been demonstrated as a good candidate for ultrafast optoelectronic devices. However, graphene is essentially transparent in the visible and near infrared with an absorptivity of 2.3%, which has largely limited its application in photon detection. This Letter demonstrates that the absorptance in a monatomic graphene layer can be greatly enhanced to nearly 70%, thanks to the localized strong electric field resulting from magnetic resonances in deep metal gratings. Furthermore, the resonance frequency is essentially not affected by the additional graphene layer. The method presented here may benefit the design of next-generation graphene-based optical and optoelectronic devices.
Determining the refractive index of shocked [100] lithium fluoride to the limit of transmissibility
Authors: Rigg P. A. , Knudson M. D. , Scharff R. J. , Hixson R. S.
Published: July 2014

Lithium fluoride (LiF) is a common window material used in shock- and ramp-compression experiments because it displays a host of positive attributes in these applications. Most commonly, it is used to maintain stress at an interface and velocimetry techniques are used to record the particle velocity at that interface. In this application, LiF remains transparent to stresses up to 200 GPa. In this stress range, LiF has an elastic-plastic response with a very low (<0.5 GPa) elastic precursor and exhibits no known solid-solid phase transformations. However, because the density dependence of the refractive index of LiF does not follow the Gladstone-Dale relation, the measured particle velocity at this interface is not the true particle velocity and must be corrected. For that reason, the measured velocity is often referred to as the apparent velocity in these types of experiments. In this article, we describe a series of shock-compression experiments that have been performed to determine the refractive index of LiF at the two most commonly used wavelengths (532 nm and 1550 nm) between 35 and 200 GPa to high precision. A modified form of the Gladstone-Dale relation was found to work best to fit the determined values of refractive index. In addition, we provide a direct relationship between the apparent and true particle velocity to correct experimentally obtained wave profiles by others using these velocimetry techniques.
Various sizes of sliding event bursts in the plastic flow of metallic glasses based on a spatiotemporal dynamic model
Authors: Ren Jingli , Chen Cun , Wang Gang , Cheung Wing-Sum , Sun Baoan , Mattern Norbert , Siegmund Stefan , Eckert Jürgen
Published: July 2014

This paper presents a spatiotemporal dynamic model based on the interaction between multiple shear bands in the plastic flow of metallic glasses during compressive deformation. Various sizes of sliding events burst in the plastic deformation as the generation of different scales of shear branches occurred; microscopic creep events and delocalized sliding events were analyzed based on the established model. This paper discusses the spatially uniform solutions and traveling wave solution. The phase space of the spatially uniform system applied in this study reflected the chaotic state of the system at a lower strain rate. Moreover, numerical simulation showed that the microscopic creep events were manifested at a lower strain rate, whereas the delocalized sliding events were manifested at a higher strain rate.
Enhancement in light emission and electrical efficiencies of a silicon nanocrystal light-emitting diode by indium tin oxide nanowires
Authors: Huh Chul , Kim Bong Kyu , Ahn Chang-Geun , Choi Chel-Jong , Kim Sang-Hyeob
Published: July 2014

We report an enhancement in light emission and electrical efficiencies of a Si nanocrystal (NC) light-emitting diode (LED) by employing indium tin oxide (ITO) nanowires (NWs). The formed ITO NWs (diameter < 50 nm) are compactly knitted and have a tendency to grow perpendicularly above the surface. The electrical characteristics of Si NC LED were significantly improved, which was attributed to an enhancement in the current spreading property due to densely interconnecting ITO NWs. In addition, light output power and wall-plug efficiency from the Si NC LED were enhanced by 45% and 38%, respectively. This was originated from an enhancement in the escape probability of the photons generated in the Si NCs due to multiple scatterings at the surface of ITO NWs acting as a light waveguide. We show here that the use of the ITO NWs can be very useful for realizing a highly efficient Si NC LED.
High efficiency membrane light emitting diode fabricated by back wafer thinning technique
Authors: Li Xin , Shi Zheng , Zhu Gangyi , Zhang Miao , Zhu Hongbo , Wang Yongjin
Published: July 2014

We demonstrate the double-side process for back wafer thinning of epitaxial film which leads to improved performance of freestanding membrane light emitting diode (LED) on GaN-on-silicon platform. The current-voltage (I-V), capacitance-voltage (C-V), and electroluminescent measurements are conducted to characterize freestanding membrane LED. After the removal of silicon substrate and back wafer thinning of epitaxial film, the I-V characteristics of membrane LED are significantly improved, and the negative capacitance accompanied by remarkable light emission becomes stronger for thinner membrane LED. The experimental results clearly exhibit the strong membrane thickness dependence. The electroluminescent intensity of membrane LED with the membrane thickness tm ∼ 3.74μm is ∼12.4 times higher than that of LED with silicon substrate. This work opens a feasible way to form high efficiency surface emitting device on GaN-on-silicon platform.
Boosting the voltage of a salinity-gradient-power electrochemical cell by means of complex-forming solutions
Authors: Marino M. , Misuri L. , Carati A. , Brogioli D.
Published: July 2014

We report experiments on a concentration cell with zinc electrodes and ZnCl2 solutions at different concentrations, separated by a porous diaphragm. The cell is aimed at the conversion of the free energy associated to the concentration difference into electrical energy, for renewable and clean energy applications. Usually, the diffusion of the solute across the diaphragm constitutes a waste of free energy, which impairs the voltage generation of the concentration cell with respect to other well-known techniques that work quasi-reversibly, such as reverse electrodialysis or the “mixing entropy battery.” Quite surprisingly, we find that the voltage produced by our concentration cell is significantly higher than the voltage obtained with the other quasi-reversible techniques. We show that the surplus voltage comes from the active transformation of the mixing free energy into electrical energy performed by the liquid junction, and we show the connection with the negative apparent transference number of the zinc ion. This fortunate consequence of using ZnCl2 solution is ultimately related to the formation of complexes. We present the results of a cell for power production, which has excellent performances with respect to known salinity-difference-power methods.
Vertical split-ring resonator based nanoplasmonic sensor
Authors: Wu Pin Chieh , Sun Greg , Chen Wei Ting , Yang Kuang-Yu , Huang Yao-Wei , Chen Yi-Hao , Huang Hsiang Lin , Hsu Wei-Lun , Chiang Hai Pang , Tsai Din Ping
Published: July 2014

Split-ring resonators (SRRs) have been the subject of investigation as plasmonic sensors that operate by sensing plasmon resonance shift δλ when exposed to a medium with a refractive index change δn. However, conventional planar SRRs have their plasmon fields spread into the substrates, reducing accessible sensing volume and its sensing performance. Such a limitation can be eradicated with vertical SRRs in which the plasmon fields localized in SRR gaps are lifted off from the substrate, allowing for greatly enhanced sensitivity. Here, we demonstrate the highest sensitivity among reported SRR-based sensors in optical frequencies.
The effect of mechanical processing of wheaten straw on intake and rumen parameters following grain feeding in sheep
Authors: White B. H. , Clayton E. H. , Friend M. A.
Published: July 2014

While the effect of roughage chop length on decreasing the risk of acidosis in cattle is well established, there is limited information on the effect of roughage processing on intake and rumen parameters in sheep. Intake and rumen parameters were assessed in 10-month-old crossbred wethers (n = 24, 48.4 kg ± 5.3) offered wheaten straw as finely chaffed (6 mm), coarsely chaffed (15–20 mm) or unprocessed (40 mm) lengths, along with barley grain. Animals were offered 300 g/head of barley grain on the first day of grain introduction, 450 g/head.day for Days 2–3, 550 g/head.day for Days 4–6, 650 g/head.day for Days 7–9 and 750 g/head on Day 10. Rumen fluid was collected 3 h post-feeding from each animal the day before grain introduction and on Days 1–3 of grain introduction. During Days 1–3 of grain introduction, roughage intake within 3 h of feed being offered was greater (P < 0.05) in sheep offered finely chaffed (0.20 kg ± 0.03) than those offered either coarsely chaffed (0.09 kg ± 0.03) or unprocessed (0.08 kg ± 0.03) straw. Rumen pH did not differ between treatments, but increased grain feeding significantly (P < 0.001) reduced pH. Sheep offered finely chaffed straw had a greater (P < 0.05) daily straw intake (0.59 kg ± 0.06) than sheep offered coarsely chaffed straw (0.37 kg ± 0.06), while sheep offered unprocessed straw had an intermediate intake (0.49 kg ± 0.06); sheep consumed all grain offered. Shorter straw particle lengths may have a role in reducing the risk of acidosis during grain introduction.
Next-generation sequencing identifies rare variants associated with Noonan syndrome
Authors: Chen Peng-Chieh , Yin Jiani , Yu Hui-Wen , Yuan Tao , Fernandez Minerva , Yung Christina K. , Trinh Quang M. , Peltekova Vanya D. , Reid Jeffrey G. , Tworog-Dube Erica , Morgan Margaret B. , Muzny Donna M. , Stein Lincoln , McPherson John D. , Roberts Amy E. , Gibbs Richard A. , Neel Benjamin G. , Kucherlapati Raju
Published: July 2014

Significance

Noonan syndrome (NS) is one of several RASopathies, which are developmental disorders caused by mutations in genes encoding RAS-ERK pathway components. The cause of 20–30% of NS cases remains unknown, and distinguishing NS from other RASopathies and related disorders can be difficult. We used next-generation sequencing (NGS) to identify causative or candidate genes for 13 of 27 NS patients lacking known NS-associated mutations. Other patients harbor single variants in potential RAS-ERK pathway genes, suggesting rare private variants or other genetic mechanisms of NS pathogenesis. We also found mutations in causative genes for other developmental syndromes, which together with clinical reevaluation, prompted revision of the diagnosis. NGS can aid in the challenging diagnosis of young patients with developmental syndromes.
Temporal control over the initiation of cell motility by a regulator of G-protein signaling
Authors: Hartwig Johannes , Tarbashevich Katsiaryna , Seggewiß Jochen , Stehling Martin , Bandemer Jan , Grimaldi Cecilia , Paksa Azadeh , Groß-Thebing Theresa , Meyen Dana , Raz Erez
Published: July 2014

Significance

Cell motility is critical for a wide range of processes in development, homeostasis, and immune response. Conversely, abnormal regulation of cell migration leads to pathological consequences like cancer metastasis. In this study, we investigate the mechanisms controlling the timing of motility acquisition, using zebrafish primordial germ cells as an in vivo model. We defined a previously unknown role for the signaling scaffold molecule and regulator of Gα protein signaling Rgs14a in coordinating the onset of migration with the presence of migration guidance cues. Furthermore, we show that this control level involves the regulation of the cell–cell adhesion molecule E-cadherin, a molecule implicated in motility acquisition in a range of normal physiological events and in disease conditions.
RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection
Authors: Hu Wenhui , Kaminski Rafal , Yang Fan , Zhang Yonggang , Cosentino Laura , Li Fang , Luo Biao , Alvarez-Carbonell David , Garcia-Mesa Yoelvis , Karn Jonathan , Mo Xianming , Khalili Kamel
Published: July 2014

Significance

For more than three decades since the discovery of HIV-1, AIDS remains a major public health problem affecting greater than 35.3 million people worldwide. Current antiretroviral therapy has failed to eradicate HIV-1, partly due to the persistence of viral reservoirs. RNA-guided HIV-1 genome cleavage by the Cas9 technology has shown promising efficacy in disrupting the HIV-1 genome in latently infected cells, suppressing viral gene expression and replication, and immunizing uninfected cells against HIV-1 infection. These properties may provide a viable path toward a permanent cure for AIDS, and provide a means to vaccinate against other pathogenic viruses. Given the ease and rapidity of Cas9/guide RNA development, personalized therapies for individual patients with HIV-1 variants can be developed instantly.
Regulatory effects of SKAR in interferon α signaling and its role in the generation of type I IFN responses
Authors: Kroczynska Barbara , Mehrotra Swarna , Majchrzak-Kita Beata , Arslan Ahmet Dirim , Altman Jessica K. , Stein Brady L. , McMahon Brandon , Kozlowski Piotr , Kahle Philipp J. , Eklund Elizabeth A. , Fish Eleanor N. , Platanias Leonidas C.
Published: July 2014

Significance

Type I interferons (IFNs) are cytokines with important biological effects, including antileukemic and antineoplastic properties. The biological responses of type I IFNs occur via up-transcriptional activation of specific genes, called interferon-stimulated genes (ISGs), ultimately resulting in generation of protein products that mediate their biological effects. In the present study, we provide evidence that the protein S6 kinase 1 Aly/REF-like target (SKAR) plays a critical role in IFN-dependent mRNA translation of ISGs and recruits activated p90 ribosomal protein S6 kinase to the translational machinery. Our data provide evidence for critical and essential roles for SKAR in the generation of type I IFN-dependent antileukemic and antineoplastic responses, underscoring the importance of SKAR functions in IFN signaling.
A family-oriented psychosocial intervention reduces inflammation in low-SES African American youth
Authors: Miller Gregory E. , Brody Gene H. , Yu Tianyi , Chen Edith
Published: July 2014

Significance

Children from families of low socioeconomic status (SES) are vulnerable to a variety of health problems. These risks begin in early childhood and persist across the lifecourse. Studies hint that nurturant parenting may offset these health risks, but it remains unclear whether these findings reflect a causal process and have clinical utility. Here we describe a randomized controlled trial, which sought to improve parenting and build youth competencies in low-SES African American families. The endpoint was low-grade inflammation, a process that underlies many health problems to which low-SES youth are vulnerable. Eight years after the intervention, youth who participated had significantly less inflammation than controls. If substantiated, these findings may provide a strategy for narrowing some of America’s social and racial disparities in health.
An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia
Authors: Berney Michael , Greening Chris , Conrad Ralf , Jacobs William R. , Cook Gregory M.
Published: July 2014

Significance

Obligate aerobes require survival strategies to persist in temporarily oxygen-deprived environments. In this article, we reveal a previously unidentified survival mechanism for obligately aerobic bacteria. Under oxygen-limiting conditions, the saprophytic actinomycete
Mycobacterium smegmatis
can rapidly switch between fermentative hydrogen production and hydrogen oxidation coupled to either oxygen or fumarate reduction depending on electron acceptor availability. To our knowledge, these results demonstrate for the first time (i) hydrogen production in an obligate aerobe, (ii) the unambiguous confirmation of fermentation in a mycobacterium and (iii) strong evidence that hydrogen has a role in survival and not just growth.
Molecular genetic framework for protophloem formation
Authors: Rodriguez-Villalon Antia , Gujas Bojan , Kang Yeon Hee , Breda Alice S. , Cattaneo Pietro , Depuydt Stephen , Hardtke Christian S.
Published: July 2014

Significance

The emergence of vascular tissues played a central role in the plant conquest of land. Both xylem and phloem are essential for the development of flowering plants, yet little is known about the molecular genetic control of phloem specification and differentiation. Here we show that delicate quantitative interplay between two opposing signaling pathways determines cellular commitment to protophloem sieve element fate in root meristems of the model plant
Arabidopsis thaliana
. Our data suggest that a recently described phloem-specific protein is a positive, quantitative master regulator of phloem fate.
Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes
Authors: Li Yinyin , Cross Frederick R. , Chait Brian T.
Published: July 2014

Significance

During proliferation, eukaryotic cells go through a defined series of phases. The primary regulators of this process are kinases paired with protein partners called cyclins. Exactly how these specific cyclin–kinase pairs orchestrate the myriad cellular events during each cell phase has been difficult to define largely because it has proven challenging to identify their substrates. Here, we describe a method to identify cyclin- and phase-specific substrates with high confidence and also to pinpoint their sites of modification. The method enabled us to identify the phosphatase Cdc14 as a substrate of a cyclin–kinase pair that acts during DNA synthesis in budding yeast and to uncover a new means by which this major antagonist of the cyclin–kinase pair is itself controlled.
Structure of the eukaryotic translation initiation factor eIF4E in complex with 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G
Authors: Papadopoulos Evangelos , Jenni Simon , Kabha Eihab , Takrouri Khuloud J. , Yi Tingfang , Salvi Nicola , Luna Rafael E. , Gavathiotis Evripidis , Mahalingam Poornachandran , Arthanari Haribabu , Rodriguez-Mias Ricard , Yefidoff-Freedman Revital , Aktas Bertal H. , Chorev Michael , Halperin Jose A. , Wagner Gerhard
Published: July 2014

Significance

eIF4E is critical for protein synthesis and becomes hyperactive in cancer cells. Small-molecule inhibitors of the eIF4E/eIF4G initiation factor complex have recently been found to exhibit antitumor activity in vitro and in vivo. However, their mode of action at the atomic level has remained elusive. Here, we report high-resolution crystal structures of complexes of 4EGI-1 analogue inhibitors with eIF4E. We find that inhibition of eIF4G binding must be allosteric, because the 4EGI-1 and eIF4G bind at distant epitopes on eIF4E. Compound binding induces extension of an α-helix that stretches between the two binding sites. Indeed, mutations increasing helix propensity in this region reduce eIF4G affinity in the absence of the inhibitor, which is consistent with the proposed allosteric model.
Population of sensory neurons essential for asthmatic hyperreactivity of inflamed airways
Authors: Tränkner Dimitri , Hahne Nadeau , Sugino Ken , Hoon Mark A. , Zuker Charles
Published: July 2014

Significance

Asthma is an inflammatory airway disease characterized by acute attacks in which airway constriction impedes breathing. The variable success of anti-inflammatory treatments in managing asthma attacks suggests that additional mechanisms contribute to this symptom. Here, we used a mouse model of acute asthma to show that a subset of sensory neurons mediates the hyperreactive airway responses. These findings define a cellular substrate outside the immune system that may serve as an important target in the management of asthmatic airway hyperreactivity.
Ataxia and Purkinje cell degeneration in mice lacking the CAMTA1 transcription factor
Authors: Long Chengzu , Grueter Chad E. , Song Kunhua , Qin Song , Qi Xiaoxia , Kong Y. Megan , Shelton John M. , Richardson James A. , Zhang Chun-Li , Bassel-Duby Rhonda , Olson Eric N.
Published: July 2014

Significance

Neurodegenerative diseases are debilitating conditions that result from degeneration of the nervous system causing symptoms including ataxia and/or dementia. Calmodulin-binding transcription activator 1 (CAMTA1) is a transcription factor enriched in the brain with the highest levels of expression in the cerebellar granular layer and Purkinje cells, midbrain, pons, and hippocampus. When CAMTA1 is deleted from the nervous system of mutant mice, we observe a clear loss of Purkinje cells and reduced cerebellar size. Thus, we conclude that CAMTA1 plays a predominant role in the maturation and survival of cerebellar neurons rather than in the initial development of these cells. The neurological abnormalities associated with CAMTA1-mutant mice allow mechanistic analysis of these abnormalities and disease modeling.
MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage
Authors: Gold Marielle C. , McLaren James E. , Reistetter Joseph A. , Smyk-Pearson Sue , Ladell Kristin , Swarbrick Gwendolyn M. , Yu Yik Y.L. , Hansen Ted H. , Lund Ole , Nielsen Morten , Gerritsen Bram , Kesmir Can , Miles John J. , Lewinsohn Deborah A. , Price David A. , Lewinsohn David M.
Published: July 2014

Mucosal-associated invariant T (MAIT) cells express a semi-invariant T cell receptor (TCR) that detects microbial metabolites presented by the nonpolymorphic major histocompatibility complex (MHC)–like molecule MR1. The highly conserved nature of MR1 in conjunction with biased MAIT TCRα chain usage is widely thought to indicate limited ligand presentation and discrimination within a pattern-like recognition system. Here, we evaluated the TCR repertoire of MAIT cells responsive to three classes of microbes. Substantial diversity and heterogeneity were apparent across the functional MAIT cell repertoire as a whole, especially for TCRβ chain sequences. Moreover, different pathogen-specific responses were characterized by distinct TCR usage, both between and within individuals, suggesting that MAIT cell adaptation was a direct consequence of exposure to various exogenous MR1-restricted epitopes. In line with this interpretation, MAIT cell clones with distinct TCRs responded differentially to a riboflavin metabolite. These results suggest that MAIT cells can discriminate between pathogen-derived ligands in a clonotype-dependent manner, providing a basis for adaptive memory via recruitment of specific repertoires shaped by microbial exposure.
Peptic Ulcer Disease in Helicobacter pylori–Infected Children
Authors: Hernández Caroll , Serrano Carolina , Einisman Helly , Villagrán Andrea , Peña Alfredo , Duarte Ignacio , Torres Javiera , Riera Francisca , Harris Paul R.
Published: July 2014

Objectives:

Peptic ulcer disease (PUD) is highly prevalent among adults but less common in children. Helicobacter pylori infection, the main cause of PUD, is, however, acquired extremely early in life. The aim of the study was to analyze clinical characteristics of children with PUD in a country with a high prevalence of the disease and to evaluate which host factors could determine this clinical outcome.

Methods:

Children referred for upper gastrointestinal (GI) endoscopy with suspicion of peptic diseases were included prospectively during an 8‐year period. Antral biopsies were performed to determine H pylori presence and mucosal cytokines profile.

Results:

A total of 307 children between 3 and 18 years old were enrolled. Of the total, 237 children (46% boys) with complete data were included. H pylori infection was confirmed in 133 (56.1%) participants. Duodenal ulcer (DU) was diagnosed in 32 patients (13.5%); among them 29 were infected with H pylori (90.6%). Infected children had a nodular appearance of the gastric mucosa more often than noninfected children. Noninfected children had fewer lymphoid follicles and less inflammatory infiltrate than infected children. Only mucosal polymorphonuclear cell infiltration was more intense in DU‐infected children as compared with non–DU‐infected children. DU‐infected children had higher levels of mucosal interferon‐γ than noninfected and non–DU‐infected patients. Non–DU‐infected children had also higher levels of mucosal interleukin‐10 than noninfected patients (P < 0.05).

Conclusions:

PUD in children, especially DU, is strongly associated with H pylori infection in developing countries. There is no distinctive clinical presentation of children with PUD. T‐helper cytokine balance may influence clinical outcomes in children.
Causes and consequences of centrosome abnormalities in cancer
Authors: Godinho S. A. , Pellman D.
Published: July 2014

Centrosome amplification is a hallmark of cancer. However, despite significant progress in recent years, we are still far from understanding how centrosome amplification affects tumorigenesis. Boveri's hypothesis formulated more than 100 years ago was that aneuploidy induced by centrosome amplification promoted tumorigenesis. Although the hypothesis remains appealing 100 years later, it is also clear that the role of centrosome amplification in cancer is more complex than initially thought. Here, we review how centrosome abnormalities are generated in cancer and the mechanisms cells employ to adapt to centrosome amplification, in particular centrosome clustering. We discuss the different mechanisms by which centrosome amplification could contribute to tumour progression and the new advances in the development of therapies that target cells with extra centrosomes.
Small organelle, big responsibility: the role of centrosomes in development and disease
Authors: Chavali Pavithra L. , Pütz Monika , Gergely Fanni
Published: July 2014

The centrosome, a key microtubule organizing centre, is composed of centrioles, embedded in a protein-rich matrix. Centrosomes control the internal spatial organization of somatic cells, and as such contribute to cell division, cell polarity and migration. Upon exiting the cell cycle, most cell types in the human body convert their centrioles into basal bodies, which drive the assembly of primary cilia, involved in sensing and signal transduction at the cell surface. Centrosomal genes are targeted by mutations in numerous human developmental disorders, ranging from diseases exclusively affecting brain development, through global growth failure syndromes to diverse pathologies associated with ciliary malfunction. Despite our much-improved understanding of centrosome function in cellular processes, we know remarkably little of its role in the organismal context, especially in mammals. In this review, we examine how centrosome dysfunction impacts on complex physiological processes and speculate on the challenges we face when applying knowledge generated from
in vitro
and
in vivo
model systems to human development.
Pseudopelagicola gijangensis gen. nov., sp. nov., isolated from the sea squirt Halocynthia roretzi
Authors: Kim Young-Ok , Park Sooyeon , Nam Bo-Hye , Kim Dong-Gyun , Yoon Jung-Hoon
Published: July 2014

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated YSS-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea of South Korea. Strain YSS-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain YSS-7T clustered with the type strains of

Pelagicola litoralis

,

Planktotalea frisia

,

Pacificibacter maritimus

and

Roseovarius marinus

. Strain YSS-7T exhibited the highest 16S rRNA gene sequence similarity (97.7 %) to the type strain of

Pelagicola litoralis

and sequence similarity of more than 96.0 % to the type strains of some other species. Strain YSS-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain YSS-7T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The fatty acid and polar lipid profiles of strain YSS-7T were different from those of the type strains of phylogenetically related species. The DNA G+C content of strain YSS-7T was 55.5 mol%. Other phenotypic properties demonstrated that strain YSS-7T is distinguished from phylogenetically related species. On the basis of the data presented, strain YSS-7T is considered to represent a novel genus and species, for which the name Pseudopelagicola gijangensis gen. nov., sp. nov. is proposed. The type strain of Pseudopelagicola gijangensis is YSS-7T ( = KCTC 42049T = CECT 8540T).
Sphingobacterium paludis sp. nov., isolated from wetland soil
Authors: Feng Hao , Zeng Yanhua , Huang Yili
Published: July 2014

A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus

Sphingobacterium

and shared highest similarity with

Sphingobacterium composti

4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus

Sphingobacterium

, for which the name Sphingobacterium
paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.
Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae
Authors: Liu Qian-Qian , Li Xiao-Li , Rooney Alejandro P. , Du Zong-Jun , Chen Guan-Jun
Published: July 2014

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22T fell within the class

Bacteroidia

. Its closest phylogenetic neighbour was the recently described species
Draconibacterium orientale
, the sole member of the family

Draconibacteriaceae

, with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family

Draconibacteriaceae

. The type strain is G22T ( = CICC 10587T = DSM 27063T).
Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
Authors: Fuchs Gilad , Hollander Dror , Voichek Yoav , Ast Gil , Oren Moshe
Published: July 2014

Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs cotranscriptionally and accurately reflects the advance of RNA polymerase II (Pol II). In contrast, H3K36me3 and H3K79me2 are less dynamic and represent Pol II movement less faithfully. High-resolution ChIP-seq reveals that H2Bub1 levels are selectively reduced at exons and decrease in an exon-dependent stepwise manner toward the 3′ end of genes. Exonic depletion of H2Bub1 in gene bodies is highly correlated with Pol II pausing at exons, suggesting elongation rate changes associated with intron–exon structure. In support of this notion, H2Bub1 levels were found to be significantly correlated with transcription elongation rates measured in various cell lines. Overall, our data shed light on the organization of H2Bub1 within transcribed genes and single out H2Bub1 as a reliable marker for ongoing transcription elongation.
The Apical Actin Fringe Contributes to Localized Cell Wall Deposition and Polarized Growth in the Lily Pollen Tube
Authors: Rounds Caleb M. , Hepler Peter K. , Winship Lawrence J.
Published: July 2014

In lily (Lilium formosanum) pollen tubes, pectin, a major component of the cell wall, is delivered through regulated exocytosis. The targeted transport and secretion of the pectin-containing vesicles may be controlled by the cortical actin fringe at the pollen tube apex. Here, we address the role of the actin fringe using three different inhibitors of growth: brefeldin A, latrunculin B, and potassium cyanide. Brefeldin A blocks membrane trafficking and inhibits exocytosis in pollen tubes; it also leads to the degradation of the actin fringe and the formation of an aggregate of filamentous actin at the base of the clear zone. Latrunculin B, which depolymerizes filamentous actin, markedly slows growth but allows focused pectin deposition to continue. Of note, the locus of deposition shifts frequently and correlates with changes in the direction of growth. Finally, potassium cyanide, an electron transport chain inhibitor, briefly stops growth while causing the actin fringe to completely disappear. Pectin deposition continues but lacks focus, instead being delivered in a wide arc across the pollen tube tip. These data support a model in which the actin fringe contributes to the focused secretion of pectin to the apical cell wall and, thus, to the polarized growth of the pollen tube.