bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of magnetic quantization on ion acoustic waves ultra-relativistic dense plasma
Authors: Javed Asif , Rasheed A. , Jamil M. , Siddique M. , Tsintsadze N. L.
Published: November 2017

In this paper, we have studied the influence of magnetic quantization of orbital motion of the electrons on the profile of linear and nonlinear ion-acoustic waves, which are propagating in the ultra-relativistic dense magneto quantum plasmas. We have employed both Thomas Fermi and Quantum Magneto Hydrodynamic models (along with the Poisson equation) of quantum plasmas. To investigate the large amplitude nonlinear structure of the acoustic wave, Sagdeev-Pseudo-Potential approach has been adopted. The numerical analysis of the linear dispersion relation and the nonlinear acoustic waves has been presented by drawing their graphs that highlight the effects of plasma parameters on these waves in both the linear and the nonlinear regimes. It has been noticed that only supersonic ion acoustic solitary waves can be excited in the above mentioned quantum plasma even when the value of the critical Mach number is less than unity. Both width and depth of Sagdeev potential reduces on increasing the magnetic quantization parameter η. Whereas the amplitude of the ion acoustic soliton reduces on increasing η, its width appears to be directly proportional to η. The present work would be helpful to understand the excitation of nonlinear ion-acoustic waves in the dense astrophysical environments such as magnetars and in intense-laser plasma interactions.
NbRe as candidate material for fast single photon detection
Authors: Caputo M. , Cirillo C. , Attanasio C.
Published: November 2017

The suitability of NbRe as a promising material for the design of Superconducting Single Photon Detectors is investigated in order to lower both the minimum detectable photon energy and the recovery time of the devices. Both the low values determined for the quasiparticle relaxation time, τE, and its weak temperature dependence are desirable in the design of fast single photon detectors. Both properties can be further improved by coupling NbRe with a ferromagnetic layer, as demonstrated by estimating the characteristic relaxation rates in NbRe/CuNi bilayers.
Fast ion transport at a gas-metal interface
Authors: McDevitt Christopher J. , Tang Xian-Zhu , Guo Zehua
Published: November 2017

Fast ion transport and the resulting fusion yield reduction are computed at a gas-metal interface. The extent of fusion yield reduction is observed to depend sensitively on the charge state of the surrounding pusher material and the width of the atomically mixed region. These sensitivities suggest that idealized boundary conditions often implemented at the gas-pusher interface for the purpose of estimating fast ion loss will likely overestimate fusion reactivity reduction in several important limits. In addition, the impact of a spatially complex material interface is investigated by considering a collection of droplets of the pusher material immersed in a DT plasma. It is found that for small Knudsen numbers, the extent of fusion yield reduction scales with the surface area of the material interface. As the Knudsen number is increased, however, the simple surface area scaling is broken, suggesting that hydrodynamic mix has a nontrivial impact on the extent of fast ion losses.
Non-orthogonal internally contracted multi-configurational perturbation theory (NICPT): Dynamic electron correlation for large, compact active spaces
Authors: Kähler Sven , Olsen Jeppe
Published: November 2017

A computational method is presented for systems that require high-level treatments of static and dynamic electron correlation but cannot be treated using conventional complete active space self-consistent field-based methods due to the required size of the active space. Our method introduces an efficient algorithm for perturbative dynamic correlation corrections for compact non-orthogonal MCSCF calculations. In the algorithm, biorthonormal expansions of orbitals and CI-wave functions are used to reduce the scaling of the performance determining step from quadratic to linear in the number of configurations. We describe a hierarchy of configuration spaces that can be chosen for the active space. Potential curves for the nitrogen molecule and the chromium dimer are compared for different configuration spaces. Already the most compact spaces yield qualitatively correct potentials that with increasing size of configuration spaces systematically approach complete active space results.
Ballistic thermoelectric properties of nitrogenated holey graphene nanostructures
Authors: Cao Wei , Xiao Huaping , Ouyang Tao , Zhong Jianxin
Published: November 2017

In this study, we theoretically investigate the ballistic thermoelectric performance of a new two-dimensional material, nitrogenated holey graphene (NHG), using nonequilibrium Green's function method. The calculations show that compared to graphene, such novel single atomic layer structure exhibits better thermoelectric performance. At room temperature, the stable hole (electron) thermoelectric figure of merit (ZT) could approach 0.75 (0.2) and 0.6 (0.2) for zigzag-edged (Z-NHGNRs) and armchair-edged NHGNRs (A-NHGNRs), respectively. To achieve better thermoelectric performance, the effect of geometric engineering (chevron-type nanoribbons and rhomboid quantum dot) on the electronic and phononic transport properties of Z-NHGNRs is further discussed. The results indicate that structure modulation is indeed a viable approach to enhance the thermoelectric properties (the figure of merit could exceed 1.5 and 1.3 for the chevron-type and rhomboid quantum dot system, respectively). On analyzing the transport properties, such improvement on the figure of merit is mainly attributed to the increased Seebeck coefficient and reduced thermal conductance (including both electronic and phononic contributions). Our findings presented in this paper qualify NHG as a promising thermoelectric material and provide theoretical guidance for fabricating the outstanding thermoelectric devices.
Models of spin-orbit-coupled oligomers
Authors: Gligorić G. , Radosavljević A. , Petrović J. , Maluckov A. , Hadžievski Lj. , Malomed B. A.
Published: November 2017

We address the stability and dynamics of eigenmodes in linearly shaped strings (dimers, trimers, tetramers, and pentamers) built of droplets in a binary Bose-Einstein condensate (BEC). The binary BEC is composed of atoms in two pseudo-spin states with attractive interactions, dressed by properly arranged laser fields, which induce the (pseudo-) spin-orbit (SO) coupling. We demonstrate that the SO-coupling terms help to create eigenmodes of particular types in the strings. Dimer, trimer, and pentamer eigenmodes of the linear system, which correspond to the zero eigenvalue (EV, alias chemical potential) extend into the nonlinear ones, keeping an exact analytical form, while tetramers do not admit such a continuation, because the respective spectrum does not contain a zero EV. Stability areas of these modes shrink with the increasing nonlinearity. Besides these modes, other types of nonlinear states, which are produced by the continuation of their linear counterparts corresponding to some nonzero EVs, are found in a numerical form (including ones for the tetramer system). They are stable in nearly entire existence regions in trimer and pentamer systems, but only in a very small area for the tetramers. Similar results are also obtained, but not displayed in detail, for hexa- and septamers.
Simultaneous diagnosis of radial profiles and mix in NIF ignition-scale implosions via X-ray spectroscopy
Authors: Ciricosta O. , Scott H. , Durey P. , Hammel B. A. , Epstein R. , Preston T. R. , Regan S. P. , Vinko S. M. , Woolsey N. C. , Wark J. S.
Published: November 2017

In a National Ignition Facility implosion, hydrodynamic instabilities may cause the cold material from the imploding shell to be injected into the hot-spot (hot-spot mix), enhancing the radiative and conductive losses, which in turn may lead to a quenching of the ignition process. The bound-bound features of the spectrum emitted by high-Z ablator dopants that get mixed into the hot-spot have been previously used to infer the total amount of mixed mass; however, the typical errorbars are larger than the maximum tolerable mix. We present here an improved 2D model for mix spectroscopy which can be used to retrieve information on both the amount of mixed mass and the full imploded plasma profile. By performing radiation transfer and simultaneously fitting all of the features exhibited by the spectra, we are able to constrain self-consistently the effect of the opacity of the external layers of the target on the emission, thus improving the accuracy of the inferred mixed mass. The model's predictive capabilities are first validated by fitting simulated spectra arising from fully characterized hydrodynamic simulations, and then, the model is applied to previously published experimental results, providing values of mix mass in agreement with previous estimates. We show that the new self consistent procedure leads to better constrained estimates of mix and also provides insight into the sensitivity of the hot-spot spectroscopy to the spatial properties of the imploded capsule, such as the in-flight aspect ratio of the cold fuel surrounding the hotspot.
Ultrafast dynamics of coherent optical phonon correlated with the antiferromagnetic transition in a hexagonal YMnO3 epitaxial film
Authors: Hasegawa Takayuki , Fujimura Norifumi , Nakayama Masaaki
Published: November 2017

We report on the observation of the coherent optical phonon in a hexagonal YMnO3 epitaxial film using a reflection-type pump-probe technique at various temperatures, excitation powers, and energies. We detected an oscillatory structure with a frequency of ∼5.1 THz, which is assigned to the coherent optical phonon with A1 symmetry, in a time-domain signal. It was found that the coherent optical phonon can be observed at temperatures from 10 K to room temperature, while the oscillation amplitude markedly decreases with an increase in temperature around ∼70 K corresponding to the Néel temperature. The temperature dependence of the oscillation amplitude indicates that the coherent optical phonon is sensitive to the spin-lattice coupling connected with the antiferromagnetic transition.
Characterization of an active metasurface using terahertz ellipsometry
Authors: Karl Nicholas , Heimbeck Martin S. , Everitt Henry O. , Chen Hou-Tong , Taylor Antoinette J. , Brener Igal , Benz Alexander , Reno John L. , Mendis Rajind , Mittleman Daniel M.
Published: November 2017

Switchable metasurfaces fabricated on a doped epi-layer have become an important platform for developing techniques to control terahertz (THz) radiation, as a DC bias can modulate the transmission characteristics of the metasurface. To model and understand this performance in new device configurations accurately, a quantitative understanding of the bias-dependent surface characteristics is required. We perform THz variable angle spectroscopic ellipsometry on a switchable metasurface as a function of DC bias. By comparing these data with numerical simulations, we extract a model for the response of the metasurface at any bias value. Using this model, we predict a giant bias-induced phase modulation in a guided wave configuration. These predictions are in qualitative agreement with our measurements, offering a route to efficient modulation of THz signals.
Limitations of the effective field approximation for fluid modeling of high frequency discharges in atmospheric pressure air: Application in resonant structures
Authors: Kourtzanidis Konstantinos , Raja Laxminarayan
Published: November 2017

We study analytically and demonstrate numerically that the local effective field approximation (LEFA) for plasma fluid modeling of high-frequency (GHz-THz) discharges in atmospheric pressure air is not valid in regions where the time scale for electron energy transfer to heavy particles is less than the time-period of the electromagnetic (EM) wave. Greater than 50% modulation of the electron temperature around its mean value is found for frequencies around and under 10 GHz for atmospheric pressure air discharges. This modulation decreases significantly as the EM wave frequency increases. Fully coupled numerical simulation of a resonant metallic cut-array illuminated by high frequency EM waves demonstrates that the LEFA can lead to significant errors on both temporal and spatial evolution of the plasma, in cases where this modulation is significant. The LEFA for high pressure air discharges is found to be valid when the EM wave frequency is around or higher than 100 GHz. For lower frequencies or when the reduced electric fields are high enough, the Local Energy Approximation should be used for an accurate description of the plasma development. For low gas pressures, the modulation is very low rendering the LEFA valid over a large EM wave frequency range.
Voltage-tunable acoustic metasheet with highly asymmetric surfaces
Authors: Xiao Songwen , Tang Suet To , Yang Z.
Published: November 2017

We report the experimental demonstration of a voltage-tunable acoustic metasheet device with two highly asymmetric surfaces, made by combining two decorated membrane resonators (DMRs) separated by a sealed air column. The front surface of the metasheet is impedance matched to air and perfectly absorbing, while the back surface is hard and totally reflecting. When a suitable DC voltage is applied to the back side of the DMR via proper electrodes, the back surface of the metasheet can be tuned to impedance matched to air and perfectly absorbing, while the front surface is totally reflecting. The metasheet also exhibits high transmission contrast around two frequencies. The tunability of the reflection is over 23 dB at 388 Hz and that of the transmission is over 33 dB at 240 Hz and 590 Hz with 600 V of applied voltage.
Collective spin waves in arrays of permalloy nanowires with single-side periodically modulated width
Authors: Gubbiotti G. , Xiong L. L. , Montoncello F. , Adeyeye A. O.
Published: November 2017

We have experimentally and numerically investigated the dispersion of collective spin waves propagating through arrays of longitudinally magnetized nanowires (NWs) with a periodically modulated width. Two nanowire arrays with single-side modulation and different periodicities of modulation were studied and compared to the nanowires with a homogeneous width. The spin-wave dispersion, measured up to the third Brillouin zone of the reciprocal space, revealed the presence of two dispersive modes for the width-modulated NWs, whose amplitude of the magnonic band depends on the modulation periodicity, and a set of nondispersive modes at higher frequency. These findings are different from those observed in homogeneous width NWs where only the lowest mode exhibits sizeable dispersion. The measured spin-wave dispersion has been satisfactorily reproduced by means of the dynamical matrix method. The results presented in this work are important in view of the possible realization of tunable frequency magnonic devices.
The structure of turbulent flow around vertical plates containing holes and attached to a channel bed
Authors: Basnet K. , Constantinescu G.
Published: November 2017

High-resolution, 3-D large eddy simulations are conducted to study the physics of flow past 2-D solid and porous vertical plates of height H mounted on a horizontal surface (no bottom gap) with a fully developed, turbulent incoming flow. The porous plate consists of an array of spanwise-oriented, identical solid cylinders of rectangular cross section. The height of the solid cylinders and the spacing between the solid cylinders, corresponding to the plate’s “holes,” are kept constant for any given configuration, as the present study considers only plates of uniform porosity. The paper discusses how the mean flow and turbulence structure around the vertical plate, the unsteady forces acting on the plate, the dynamics of the large-scale turbulent eddies, the spectral content of the wake, and the distribution of the bed friction velocity on the horizontal channel bed vary as a function of the plate porosity (0% < P < 36%), the relative spacing between the solid elements of the porous plate (d/H), and the roughness of the channel bed surface. Simulation results are used to explain how the bleeding flow affects the dynamics on the larger billow eddies advected in the separated shear layer (SSL) forming at the top of the plate and the wake structure. It is found that the main recirculation eddy in the wake remains attached to the plate for P < 30%. For larger porosities, the main recirculation eddy forms away from the porous plate. The energy of the billows advected in the SSL decays monotonically with increasing plate porosity. For cases when the recirculation eddy remains attached to the plate, the larger billows advected in the downstream part of the SSL are partially reinjected inside the main recirculation eddy as a result of their interaction with the channel bed. This creates a feedback mechanism that induces large-scale disturbances of the spanwise-oriented vortex tubes advected inside the upstream part of the SSL. Results also show that the mean drag coefficient and the root-mean-square of the drag coefficient fluctuations increase mildly with increasing d/H. Meanwhile, varying d/H has a negligible effect on the position and size of the main recirculation eddy. The presence of large-scale roughness elements (2-D ribs) at the bed results in the decrease of the mean drag coefficient of the plate and, in the case of a solid plate, in a large decrease of the frequency of the large-scale eddies advected in the SSL.
Calibration of imaging plate detectors to mono-energetic protons in the range 1-200 MeV
Authors: Rabhi N. , Batani D. , Boutoux G. , Ducret J.-E. , Jakubowska K. , Lantuejoul-Thfoin I. , Nauraye C. , Patriarca A. , Saïd A. , Semsoum A. , Serani L. , Thomas B. , Vauzour B.
Published: November 2017

Responses of Fuji Imaging Plates (IPs) to proton have been measured in the range 1-200 MeV. Mono-energetic protons were produced with the 15 MV ALTO-Tandem accelerator of the Institute of Nuclear Physics (Orsay, France) and, at higher energies, with the 200-MeV isochronous cyclotron of the Institut Curie—Centre de Protonthérapie d’Orsay (Orsay, France). The experimental setups are described and the measured photo-stimulated luminescence responses for MS, SR, and TR IPs are presented and compared to existing data. For the interpretation of the results, a sensitivity model based on the Monte Carlo GEANT4 code has been developed. It enables the calculation of the response functions in a large energy range, from 0.1 to 200 MeV. Finally, we show that our model reproduces accurately the response of more complex detectors, i.e., stack of high-Z filters and IPs, which could be of great interest for diagnostics of Petawatt laser accelerated particles.
Effective stochastic generator with site-dependent interactions
Authors: Khamehchi Masoumeh , Jafarpour Farhad H.
Published: November 2017

It is known that the stochastic generators of effective processes associated with the unconditioned dynamics of rare events might consist of non-local interactions; however, it can be shown that there are special cases for which these generators can include local interactions. In this paper, we investigate this possibility by considering systems of classical particles moving on a one-dimensional lattice with open boundaries. The particles might have hard-core interactions similar to the particles in an exclusion process, or there can be many arbitrary particles at a single site in a zero-range process. Assuming that the interactions in the original process are local and site-independent, we will show that under certain constraints on the microscopic reaction rules, the stochastic generator of an unconditioned process can be local but site-dependent. As two examples, the asymmetric zero-temperature Glauber model and the A-model with diffusion are presented and studied under the above-mentioned constraints.
Engineering of a membrane-triggered activity switch in coagulation factor VIIa
Authors: Nielsen Anders L. , Sorensen Anders B. , Holmberg Heidi L. , Gandhi Prafull S. , Karlsson Johan , Buchardt Jens , Lamberth Kasper , Kjelgaard-Hansen Mads , Ley Carsten Dan , Sørensen Brit B. , Ruf Wolfram , Olsen Ole H. , Østergaard Henrik
Published: November 2017

Significance

Coagulation factor VIIa (FVIIa) is an intrinsically poor serine protease that requires assistance from its cofactor tissue factor (TF) to trigger the extrinsic pathway of blood coagulation. TF stimulates FVIIa through allosteric maturation of its active site and by facilitating substrate recognition. The surface dependence of the latter property allowed us to design a potent membrane-triggered activity switch in FVIIa by engineering a disulfide cross-link between an allosterically silent FVIIa variant and soluble TF. These results show that optimization of substrate recognition remote from the active site represents a promising new route to simultaneously enhance and localize the procoagulant activity of FVIIa for therapeutic purposes.
Molecular basis of tactile specialization in the duck bill
Authors: Schneider Eve R. , Anderson Evan O. , Mastrotto Marco , Matson Jon D. , Schulz Vincent P. , Gallagher Patrick G. , LaMotte Robert H. , Gracheva Elena O. , Bagriantsev Sviatoslav N.
Published: November 2017

Significance

Tactile-specialist birds of the Anatidae family possess unique mechanosensory abilities with which they efficiently select edible matter in muddy water without visual or olfactory cues. Mechanical stimuli are transmitted by trigeminal mechanoreceptors innervating the bill, a highly specialized tactile organ. We show mechanosensory specialization in ducks involves the formation of functional rapidly adapting mechanoreceptors prior to hatching. Unlike in visually foraging chicken, most trigeminal neurons in ducks are touch receptors, which develop following a unique pattern of neurotrophic factor receptor expression and produce robust mechano-current via the Piezo2 channel with novel properties. Our results uncover possible evolutionary adaptations contributing to potentiation of mechanoreception in an organ-specific manner and reveal the molecular identity of a neuronal mechanotransducer with prolonged inactivation kinetics.
Enzyme stabilization via computationally guided protein stapling
Authors: Moore Eric J. , Zorine Dmitri , Hansen William A. , Khare Sagar D. , Fasan Rudi
Published: November 2017

Significance

The marginal stability of most natural proteins presents a challenge for the exploitation of natural and engineered enzymes in biotechnology and industrial biocatalysis. Protein stabilization can be time- and labor-intensive and often involves extensive amino acid substitutions, which may impair the activity and/or selectivity of the enzyme. Here, we describe a computational design method for enzyme stabilization that uses structure-based modeling to introduce covalent ‟staples” in a protein scaffold via a genetically encodable noncanonical amino acid. This method was applied to obtain stapled variants of a stereoselective cyclopropanation biocatalyst featuring greatly increased thermostability and robustness to high concentrations of organic cosolvents. This minimally invasive strategy for protein stabilization should be applicable to a variety of enzymes and proteins.
Ion pair particles at the air–water interface
Authors: Kumar Manoj , Francisco Joseph S.
Published: November 2017

Significance

According to our Born–Oppenheimer molecular dynamics simulations, the ion pair particle formation from the hydrogen-bonded complex between methanesulfonic acid (HMSA) and ammonia/amines on the water droplet surface is observed within a few femtoseconds of the simulation time. This suggests a mechanism for the gas to particle conversion at the air–water interface. These results may help in understanding the aerosol particle formation in the remote marine atmosphere, particularly in polar regions, where the concentration of HMSA in the smallest particles was similar to that of nonsea salt sulfate and the mechanism of the particle formation remains unclear.
SIRPα+dendritic cells regulate homeostasis of fibroblastic reticular cells via TNF receptor ligands in the adult spleen
Authors: Saito Yasuyuki , Respatika Datu , Komori Satomi , Washio Ken , Nishimura Taichi , Kotani Takenori , Murata Yoji , Okazawa Hideki , Ohnishi Hiroshi , Kaneko Yoriaki , Yui Katsuyuki , Yasutomo Koji , Nishigori Chikako , Nojima Yoshihisa , Matozaki Takashi
Published: November 2017

Significance

Homeostasis of Pdpn+fibroblastic reticular cells (FRCs) is thought to be regulated by hematopoietic cells. However, the cellular and molecular mechanisms of such homeostasis have been poorly understood, especially under the steady-state condition in adults. We show that dendritic cells, particularly CD4+conventional dendritic cells (cDCs), are crucial for the homeostasis of FRCs in the adult spleen under the steady-state condition. The production of TNF receptor ligands by CD4+cDCs regulates such homeostasis of FRCs, with SIRPα and CD47 likely being indispensable for the production of TNFR ligands by CD4+cDCs. The CD47–SIRPα interaction on CD4+cDCs may thus control the homeostasis of FRCs, which in turn maintain homeostasis of T cells in the white pulp of the spleen.
Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily
Authors: Crow Allister , Greene Nicholas P. , Kaplan Elise , Koronakis Vassilis
Published: November 2017

Significance

Bacterial ABC transporters typically mediate transport of substrates across the cytoplasmic membrane, using either alternating access or toppling-based mechanisms. The noncanonical ABC transporter MacB does not behave in this manner, but instead couples cytoplasmic ATP hydrolysis with periplasmic conformational changes that drive substrates from the periplasm to the extracellular space via the TolC exit duct. Here we describe the mechanotransmission mechanism of MacB in molecular detail by comparing ATP-bound and nucleotide-free structures. We further show that MacB shares its structural architecture with an entire superfamily of ABC transporters responsible for fundamental bacterial processes, including cell division and outer membrane biogenesis, suggesting a common mode of operation, and raise the possibility of targeting such proteins for the development of new antibiotics.
Host-based lipid inflammation drives pathogenesis in
Francisella
infection
Authors: Scott Alison J. , Post Julia Maria , Lerner Raissa , Ellis Shane R. , Lieberman Joshua , Shirey Kari Ann , Heeren Ron M. A. , Bindila Laura , Ernst Robert K.
Published: November 2017

Significance

This work used mass spectrometry imaging to visualize a key bacterial virulence factor, lipid A within tissues infected by
Francisella novicida
, a model organism for
Francisella tularensis
ssp.
tularensis
, the causative agent of tularemia. Lipid components of the host were mapped using the same technique, leading to identification of a lethal role for host lipid metabolism in
Francisella
infection. Combined with profiling of lipid inflammatory mediators, this work defined the dramatic polarity of the cyclooxygenase-2 axis in this infection and overproduction of the proinflammatory product prostaglandin E2. The host–pathogen lipid interface was reconstructed to demonstrate the spatial organization of the host lipid response in the spleen.
Coordinated regulation of heterochromatin inheritance by Dpb3–Dpb4 complex
Authors: He Haijin , Li Yang , Dong Qianhua , Chang An-Yun , Gao Feng , Chi Zhongxuan , Su Min , Zhang Faben , Ban Hyoju , Martienssen Rob , Chen Yu-hang , Li Fei
Published: November 2017

Significance

Epigenetic modifications, such as histone methylation, are crucial for gene expression, chromatin organization, and cellular identity. These modifications can be faithfully transmitted to daughter cells during the cell cycle. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone hypoacetylation and histone H3 lysine 9 (H3K9) methylation are two conserved epigenetic marks of heterochromatin, a transcriptionally repressive form of chromatin. Here we demonstrate that the two conserved small histone-fold subunits of the DNA polymerase epsilon complex, Dpb3 and Dpb4, form a heterodimer and play an important role in coordinating the inheritance of histone hypoacetylation and H3K9 methylation during replication. This study provides mechanistic insights into how epigenetic marks in heterochromatin are transmitted through the cell cycle.
Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired
Authors: Wanrooij Paulina H. , Engqvist Martin K. M. , Forslund Josefin M. E. , Navarrete Clara , Nilsson Anna Karin , Sedman Juhan , Wanrooij Sjoerd , Clausen Anders R. , Chabes Andrei
Published: November 2017

Significance

Mitochondria are essential for energy production. However, a number of defects that affect the cellular levels of deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA, threaten the proper maintenance of mitochondrial DNA (mtDNA) and lead to human disease. We show that imbalances in the total cellular dNTP pool are transmitted into the mitochondria and that they alter the frequency of ribonucleotides, the building blocks of RNA, that are incorporated into mtDNA in yeast. We further show that yeast mitochondria lack repair pathways that remove embedded ribonucleotides. Because ribonucleotides are a known cause of genome instability, our findings may explain why altered cellular dNTP pools lead to defects in mtDNA but not in nuclear DNA in certain human diseases.
Peptidyl arginine deiminase immunization induces anticitrullinated protein antibodies in mice with particular MHC types
Authors: Arnoux Fanny , Mariot Charlotte , Peen Elisa , Lambert Nathalie C. , Balandraud Nathalie , Roudier Jean , Auger Isabelle
Published: November 2017

Significance

The presence and development of autoantibodies to citrullinated proteins (ACPAs) are highly associated with rheumatoid arthritis (RA). The mechanisms leading to the production of ACPAs are unknown. Here, we propose a model to explain the emergence of anticitrullinated protein autoantibodies in RA. Indeed, we could trigger the development of anticitrullinated fibrinogen autoantibodies in normal mice by immunization with peptidyl arginine deiminase (PAD), most likely through a hapten/carrier mechanism in which the carrier is the PAD enzyme that performs citrullination and the hapten is any protein being citrullinated (hence bound) by PAD. Our results allow us to understand the birth of anticitrullin autoimmunity.
Near-infrared remotely triggered drug-release strategies for cancer treatment
Authors: Goodman Amanda M. , Neumann Oara , Nørregaard Kamilla , Henderson Luke , Choi Mi-Ran , Clare Susan E. , Halas Naomi J.
Published: November 2017

Significance

Gold-based nanoparticles that absorb near-infrared light have shown the potential to selectively target and treat cancer through highly efficient light-to-heat conversion. This study shows that gold-based nanoparticles can be coated with drug-bearing host biomolecules for remotely triggerable release. Near-infrared light-triggered release of docetaxel from a nanoshell-based DNA host complex, and lapatinib from nanoshell-based DNA and human serum albumin host complexes, is demonstrated. There is a strong dependence upon the type of near-infrared illumination––continuous wave or pulsed––specific to the drug-laden host molecules. Localizing drug delivery both spatially and temporally by combining nanoshell-based complexes and pulsed-laser irradiation is a promising strategy for highly controlled drug delivery that can apply to a myriad of therapeutic applications.
Syntenin mediates SRC function in exosomal cell-to-cell communication
Authors: Imjeti Naga Sailaja , Menck Kerstin , Egea-Jimenez Antonio Luis , Lecointre Celine , Lembo Frederique , Bouguenina Habib , Badache Ali , Ghossoub Rania , David Guido , Roche Serge , Zimmermann Pascale
Published: November 2017

Significance

Viral-like nanovesicles of endosomal origin, or “exosomes,” are newly recognized vehicles of signals that cells use to communicate, in various systemic diseases, including cancer. Yet the molecular mechanisms that regulate the biogenesis and activity of exosomes remain obscure. Here, we establish that the oncogenic protein SRC stimulates the secretion of exosomes loaded with syntenin and syndecans, known co-receptors for a plethora of signaling and adhesion molecules. SRC phosphorylates conserved tyrosine residues in the syndecans and syntenin and stimulates their endosomal budding. Moreover, SRC-dependent exosomes have a promigratory activity that strictly depends on syntenin expression. This work sheds light on a function of SRC in cell-to-cell communication and mechanisms of exosome biogenesis and activity, with potential broad impact for physiopathology.
Poaceae-specificMS1encodes a phospholipid-binding protein for male fertility in bread wheat
Authors: Wang Zheng , Li Jian , Chen Shaoxia , Heng Yanfang , Chen Zhuo , Yang Jing , Zhou Kuanji , Pei Jiawei , He Hang , Deng Xing Wang , Ma Ligeng
Published: November 2017

Significance

Heterosis provides an important strategy for increasing crop yield, and breeding and adoption of hybrid crops is a feasible way to increase crop yields. Male sterility is an essential trait in hybrid seed production for monoclinous crops, including wheat. Heterosis in wheat was observed approximately 100 y ago. However, very little commercial hybrid wheat is planted in the world because of the lack of a suitable male sterility trait. Therefore, understanding the molecular nature of male fertility in wheat is critical for hybrid wheat development. Here, we report the cloning and molecular, biochemical, and cell-biological characterizations ofMale Sterility 1(Ms1) in bread wheat, and provide a foundation for large-scale commercial hybrid wheat breeding and hybrid seed production.
The objects that personalize bedrooms and their relationship with attachment and self / Los objetos que personalizan los dormitorios y su relación con el apego y el self
Authors: Poggio Lucía , Fraijo-Sing Blanca , Aragonés Juan-Ignacio , Tapia-Fonllem César
Published: November 2017

The personalization of space is constructed through the items that the resident distributes around the space they inhabit, and they can be considered part of the resident’s self. Three studies were conducted with the goal of establishing the categories into which the objects contained in bedrooms can be organized and to evaluate to what extent these categories are related to the extended self and attachment. In the first study, with 77 students, we obtained a list of the most representative objects in their bedrooms. In the next study, a group of 56 students classified these objects freely using their own criteria; a subsequent cluster analysis showed four categories: Functional, Personal Grooming, Symbolic and Free Time. In the last study, 144 students evaluated the relationship between the categories of the objects and the extended self and attachment. The results showed that the residents’ representative objects were part of their extended self more than the level of attachment attributed to these objects.
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences
Authors: Avvaru Akshay Kumar , Sowpati Divya Tej , Mishra Rakesh Kumar
Published: November 2017

Motivation

Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats of DNA motifs present in all genomes. They have long been used for a variety of purposes in the areas of population genetics, genotyping, marker-assisted selection and forensics. Numerous studies have highlighted their functional roles in genome organization and gene regulation. Though several tools are currently available to identify SSRs from genomic sequences, they have significant limitations.

Results

We present a novel algorithm called PERF for extremely fast and comprehensive identification of microsatellites from DNA sequences of any size. PERF is several fold faster than existing algorithms and uses up to 5-fold lesser memory. It provides a clean and flexible command-line interface to change the default settings, and produces output in an easily-parseable tab-separated format. In addition, PERF generates an interactive and stand-alone HTML report with charts and tables for easy downstream analysis.

Availability and implementation

PERF is implemented in the Python programming language. It is freely available on PyPI under the package name perf_ssr, and can be installed directly using pip or easy_install. The documentation of PERF is available at https://github.com/rkmlab/perf. The source code of PERF is deposited in GitHub at https://github.com/rkmlab/perf under an MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
How Am I Doing? Perceived Financial Well-Being, Its Potential Antecedents, and Its Relation to Overall Well-Being
Authors: Netemeyer Richard G , Warmath Dee , Fernandes Daniel , Lynch John G
Published: November 2017

Though perceived financial well-being is viewed as an important topic of consumer research, the literature contains no accepted definition of this construct. Further, there has been little systematic examination of how perceived financial well-being may affect overall well-being. Using consumer financial narratives, several large-scale surveys, and two experiments, we conceptualize perceived financial well-being as two related but separate constructs: 1) stress related to the management of money today (current money management stress), and 2) a sense of security in one’s financial future (expected future financial security). We develop and validate measures of these constructs (web appendix A) and then demonstrate their relationship to overall well-being, controlling for other life domains and objective measures of the financial domain. Our findings demonstrate that perceived financial well-being is a key predictor of overall well-being and comparable in magnitude to the combined effect of other life domains (job satisfaction, physical health assessment, and relationship support satisfaction). Further, the relative importance of current money management stress to overall well-being varies by income groups and due to the differing antecedents of current money management stress and expected future financial security. Implications for financial well-being and education efforts are offered.
The immediate environment of an astrophysical black hole
Authors: Contopoulos I
Published: November 2017

In view of the upcoming observations with the Event Horizon Telescope (EHT), we present our thoughts on the immediate environment of an astrophysical black hole. We are concerned that two approximations used in general relativistic magnetohydrodynamic numerical simulations, namely numerical density floors implemented near the base of the black hole jet, and a magnetic field that comes from large distances, may mislead our interpretation of the observations. We predict that three physical processes will manifest themselves in EHT observations, namely dynamic pair formation just above the horizon, electromagnetic energy dissipation along the boundary of the black hole jet, and a region of weak magnetic field separating the black hole jet from the disc wind.
Bipolar H ii regions produced by cloud–cloud collisions
Authors: Whitworth Anthony , Lomax Oliver , Balfour Scott , Mège Pierre , Zavagno Annie , Deharveng Lise
Published: November 2017

We suggest that bipolar H ii regions may be the aftermath of collisions between clouds. Such a collision will produce a shock-compressed layer, and a star cluster can then condense out of the dense gas near the center of the layer. If the clouds are sufficiently massive, the star cluster is likely to contain at least one massive star, which emits ionizing radiation, and excites an H ii region, which then expands, sweeping up the surrounding neutral gas. Once most of the matter in the clouds has accreted onto the layer, expansion of the H ii region meets little resistance in directions perpendicular to the midplane of the layer, and so it expands rapidly to produce two lobes of ionized gas, one on each side of the layer. Conversely, in directions parallel to the midplane of the layer, expansion of the H ii region stalls due to the ram pressure of the gas that continues to fall towards the star cluster from the outer parts of the layer; a ring of dense neutral gas builds up around the waist of the bipolar H ii region, and may spawn a second generation of star formation. We present a dimensionless model for the flow of ionized gas in a bipolar H ii region created according to the above scenario, and predict the characteristics of the resulting free–free continuum and recombination-line emission. This dimensionless model can be scaled to the physical parameters of any particular system. Our intention is that these predictions will be useful in testing the scenario outlined above, and thereby providing indirect support for the role of cloud–cloud collisions in triggering star formation.
Characterization of the Serralysin-Like Gene of ‘Candidatus Liberibacter solanacearum’ Associated with Potato Zebra Chip Disease
Authors: Ravindran Aravind , Saenkham Panatda , Levy Julien , Tamborindeguy Cecilia , Lin Hong , Gross Dennis C. , Pierson Elizabeth
Published: November 2017

The nonculturable bacterium ‘Candidatus Liberibacter solanacearum’ is the causative agent of zebra chip disease in potato. Computational analysis of the ‘Ca. L. solanacearum’ genome revealed a serralysin-like gene based on conserved domains characteristic of genes encoding metalloprotease enzymes similar to serralysin. Serralysin and other serralysin family metalloprotease are typically characterized as virulence factors and are secreted by the type I secretion system (T1SS). The ‘Ca. L. solanacearum’ serralysin-like gene is located next to and divergently transcribed from genes encoding a T1SS. Based on its relationship to the T1SS and the role of other serralysin family proteases in circumventing host antimicrobial defenses, it was speculated that a functional ‘Ca. L. solanacearum’ serralysin-like protease could be a potent virulence factor. Gene expression analysis showed that, from weeks 2 to 6, the expression of the ‘Ca. L. solanacearum’ serralysin-like gene was at least twofold higher than week 1, indicating that gene expression stays high as the disease progresses. A previously constructed serralysin-deficient mutant of Serratia liquefaciens FK01, an endophyte associated with insects, as well as an Escherichia coli lacking serralysin production were used as surrogates for expression analysis of the ‘Ca. L. solanacearum’ serralysin-like gene. The LsoA and LsoB proteins were expressed as both intact proteins and chimeric S. liquefaciens-‘Ca. L. solanacearum’ serralysin-like proteins to facilitate secretion in the S. liquefaciens surrogate and as intact proteins or as a truncated LsoB protein containing just the putative catalytic domains in the E. coli surrogate. None of the ‘Ca. L. solanacearum’ protein constructs expressed in either surrogate demonstrated proteolytic activity in skim milk or zymogram assays, or in colorimetric assays using purified protein, suggesting that the ‘Ca. L. solanacearum’ serralysin-like gene does not encode a functional protease, or at least not in our surrogate systems.
Technological Distractions (Part 2): A Summary of Approaches to Manage Clinical Alarms With Intent to Reduce Alarm Fatigue
Authors: Winters Bradford D. , Cvach Maria M. , Bonafide Christopher P. , Hu Xiao , Konkani Avinash , O’Connor Michael F. , Rothschild Jeffrey M. , Selby Nicholas M. , Pelter Michele M. , McLean Barbara , Kane-Gill Sandra L.
Published: November 2017

Objective:

Alarm fatigue is a widely recognized safety and quality problem where exposure to high rates of clinical alarms results in desensitization leading to dismissal of or slowed response to alarms. Nonactionable alarms are thought to be especially problematic. Despite these concerns, the number of clinical alarm signals has been increasing as an everincreasing number of medical technologies are added to the clinical care environment.

Data Sources:

PubMed, SCOPUS, Embase, and CINAHL.

Study Selection:

We performed a systematic review of the literature focused on clinical alarms. We asked a primary key question; “what interventions have been attempted and resulted in the success of reducing alarm fatigue?” and 3-secondary key questions; “what are the negative effects on patients/families; what are the balancing outcomes (unintended consequences of interventions); and what human factor approaches apply to making an effective alarm?”

Data Extraction:

Articles relevant to the Key Questions were selected through an iterative review process and relevant data was extracted using a standardized tool.

Data Synthesis:

We found 62 articles that had relevant and usable data for at least one key question. We found that no study used/developed a clear definition of “alarm fatigue.” For our primary key question 1, the relevant studies focused on three main areas: quality improvement/bundled activities; intervention comparisons; and analysis of algorithm-based false and total alarm suppression. All sought to reduce the number of total alarms and/or false alarms to improve the positive predictive value. Most studies were successful to varying degrees. None measured alarm fatigue directly.

Conclusions:

There is no agreed upon valid metric(s) for alarm fatigue, and the current methods are mostly indirect. Assuming that reducing the number of alarms and/or improving positive predictive value can reduce alarm fatigue, there are promising avenues to address patient safety and quality problem. Further investment is warranted not only in interventions that may reduce alarm fatigue but also in defining how to best measure it.