bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous mapping of single bubble dynamics and heat transfer rates for SiO2/water nanofluids under nucleate pool boiling regime
Authors: Bhatt Dhairya , Kangude Prasad , Srivastava Atul
Published: January 2019

Dependence of single vapor bubble dynamics and heat transfer rates on varying concentration of SiO2 nanoparticles for a range of subcooled conditions (0–9 °C) has been experimentally studied under nucleate pool boiling configuration. Non-invasive measurements have been carried out using rainbow schlieren deflectometry. Results on bubble dynamics showed that the bubble diameter and aspect ratio decrease with increasing subcooling levels as well as concentration of nanofluids. The frequency of bubble oscillations was found to increase first and then decrease with increasing subcooling levels while it decreases monotonically with increasing nanofluid concentration. Bubble departure frequency increased significantly for nanofluids, while it decreased with increasing subcooling levels. Condensation effects at the bubble interface were reflected in the form of redistribution of colors around it. Schlieren images clearly revealed a spread in the spatial extent of the thermal boundary layer region caused by the suspended nanoparticles around the vapor bubble as well as near the heated substrate. This phenomenon has been considered as one of the factors that tends to alter the condensation effects and, in turn, affects the bubble dynamics. Quantitative analysis of schlieren images revealed that the natural convective heat flux increases with increasing subcooling levels, while it decreases with increasing nanoparticle concentration. Deterioration in the natural convection phenomenon in the presence of suspended nanoparticles has been attributed to the reduced strength of thermal gradients adjacent to the heater substrate. On the other hand, evaporative heat flux was observed to decrease with increasing subcooling levels and increase with increasing concentration of nanofluids.
A combined sinusoidal transmission grating spectrometer and x-ray diode array diagnostics for time-resolved spectral measurements in laser plasma experiments
Authors: Shpilman Ze’ev , Hurvitz Gilad , Danon Liron , Shussman Tomer , Ehrlich Yosi , Maman Shlomo , Levy Izhak , Fraenkel Moshe
Published: January 2019

A new system which combines two independent diagnostic devices on the same line of sight is used to measure the X-ray spectrum in the 50-1000 eV regime. The first device is an array of six channels of time-resolved X-ray diodes (XRD’s), arranged to cover the spectral band with low spectral resolution (λ/Δλ ∼ 3). The second device is a time-integrated sinusoidal transmission grating spectrometer (STGS) with a wide spectral range coverage and moderate spectral resolution (λ/Δλ ∼ 30). The spectral band of each XRD can be tuned by selecting a cathode, an x-ray mirror, and a filter. The novel sinusoidal shape of the STGS allows acquisition of a pure first-order spectrum without contribution of high dispersion orders, resulting in a higher accuracy spectrum measurement. The system described here has recently been used [Y. Ehrlich et al., Rev. Sci. Instrum. 88, 043507 (2017)] to demonstrate an improved unfolding algorithm of an XRD-acquired spectrum, achieved by experimental information gathered from the STGS measurement.
ODE integration schemes for plane-wave real-time time-dependent density functional theory
Authors: Rehn Daniel A. , Shen Yuan , Buchholz Marika E. , Dubey Madan , Namburu Raju , Reed Evan J.
Published: January 2019

Integration schemes are implemented with a plane-wave basis in the context of real-time time-dependent density functional theory. Crank-Nicolson methods and three classes of explicit integration schemes are explored and assessed in terms of their accuracy and stability properties. Within the framework of plane-wave density functional theory, a graphene monolayer system is used to investigate the error, stability, and serial computational cost of these methods. The results indicate that Adams-Bashforth and Adams-Bashforth-Moulton methods of orders 4 and 5 outperform commonly used methods, including Crank-Nicolson and Runge-Kutta methods, in simulations where a relatively low error is desired. Parallel runtime scaling of the most competitive serial methods is presented, further demonstrating that the Adams-Bashforth and Adams-Bashforth-Moulton methods are efficient methods for propagating the time-dependent Kohn-Sham equations. Our integration schemes are implemented as an extension to the Quantum ESPRESSO code.
Capillary wave method: An alternative approach to wave excitation and to wave profile reconstruction
Authors: Shmyrov Andrey , Mizev Aleksey , Shmyrova Anastasia , Mizeva Irina
Published: January 2019

The capillary wave method is a well-known classical technique to measure surface tension and surface rheological properties. Despite the large number of theoretical works devoted to capillary waves, this technique has serious difficulties associated with its implementation, and therefore, it is not widely used by researchers. In this paper, we introduce our modifications of the existing method to overcome its drawbacks. First, a capillary wave is excited by pressure fluctuations generated locally at the interface. Being contactless, the proposed method is suitable for any liquid irrespective of its electrical properties. Second, the application of optical interferometry together with the spatial phase shifting method allows to quantify the surface profile with high accuracy. A new data processing algorithm makes it possible to subtract the parasitic deformation of the surface caused by external perturbations avoiding, thereby the thorough vibroisolation procedure. The relative error for surface measurements and surface tension calculations is 0.3%. The results of surface tension measurements of several liquids obtained by the modified method are in good agreement with the data determined by the Wilhelmy plate technique. The main advantage of our method is that is well suited for measurements of low liquid volumes, which makes it of particular interest in biological and chemistry applications. Additionally, our version of the examined method allows one to extend the frequency range to 103–104 Hz, where only the quasi-elastic light scattering technique is currently applicable.
Numerical simulations of the forced oscillation of a wire in Newtonian and shear-thinning fluids
Authors: Hopkins Cameron C. , de Bruyn John R.
Published: January 2019

Forced oscillations of a wire vibrating in Newtonian and shear-thinning fluids described by the Carreau model are studied numerically. Two-dimensional simulations were performed using a commercial finite element modeling software package. When subjected to a sinusoidal driving force, the wire exhibits resonant behavior that depends on the viscosity of the surrounding fluid. The simulations of the wire vibrating in a Newtonian fluid were extremely well described by the theory developed by Retsina et al. [“The theory of a vibrating-rod densimeter,” Appl. Sci. Res. 43, 127–158 (1986); “The theory of a vibrating-rod viscometer,” Appl. Sci. Res. 43, 325–346 (1987)]. Our simulations of a wire vibrating in a Carreau fluid also revealed resonant behavior, but the shear rate and viscosity in the fluid varied significantly in both space and time. The behavior of a wire vibrating in a Carreau fluid can be described by the Newtonian theory if the constant viscosity in that theory is set equal to the non-Newtonian fluid viscosity averaged spatially around the circumference of the wire and temporally over one period of oscillation.
Study on structural characteristics of Ka-band high power millimeter wave radial transit time oscillator
Authors: Wang Haitao , Zhang Jun , Dang Fangchao , Qian Baoliang
Published: January 2019

High power coherent electromagnetic radiation of a millimeter waveband is a tough research topic of plasma physics. In axial millimeter wave electromagnetic radiation devices, low power capacity and mode competition limited the output power. The radial structure is a promising candidate to realize high power millimeter wave radiation. Structural characteristics of a radial Ka-band high power millimeter wave transit time oscillator (TTO) are studied in this paper. Analysis without an electron beam indicates that if the average radius of radial cavities is increased, the mode of the stimulated field will not change, the power capacity will be improved, and the quality factor due to ohmic loss will remain unchanged. Particle-in-cell simulation proves that, for radial millimeter wave TTO, increasing the radius of the cathode and keeping sizes of the other parts unchanged, the output power will be increased, the efficiency will remain the same, and electric field growth will be slower than that in axial devices. Besides, taking ohmic loss into consideration, the efficiency will increase to a stable value. Therefore, by this method, high power coherent electromagnetic radiation in a millimeter wave can be realized.
Discrete unified gas kinetic scheme for flows of binary gas mixture based on the McCormack model
Authors: Zhang Yue , Zhu Lianhua , Wang Peng , Guo Zhaoli
Published: January 2019

The discrete unified gas kinetic scheme (DUGKS) was originally developed for single-species flows covering all the regimes, whereas the gas mixtures are more frequently encountered in engineering applications. Recently, the DUGKS has been extended to binary gas mixtures of Maxwell molecules on the basis of the Andries–Aoki–Perthame kinetic (AAP) model [P. Andries et al., “A consistent BGK-type model for gas mixtures,” J. Stat. Phys. 106, 993–1018 (2002)]. However, the AAP model cannot recover a correct Prandtl number. In this work, we extend the DUGKS to gas mixture flows based on the McCormack model [F. J. McCormack, “Construction of linearized kinetic models for gaseous mixtures and molecular gases,” Phys. Fluids 16, 2095–2105 (1973)], which can give all the transport coefficients correctly. The proposed method is validated by several standard tests, including the plane Couette flow, the Fourier flow, and the lid-driven cavity flow under different mass ratios and molar concentrations. Good agreement between results of the DUGKS and the other well-established numerical methods shows that the proposed DUGKS is effective and reliable for binary gas mixtures in all flow regimes. In addition, the DUGKS is about two orders of magnitude faster than the direct simulation Monte Carlo for low-speed flows in terms of the wall time and convergent iteration steps.
Identification of energy landscape of Sp1 zinc-finger in Pb(II) or Cd(II) using AFM
Authors: Gao Qi , Dai Ziwen , Fang Yuqiang , Lo Pik Kwan , Lai King Wai Chiu
Published: January 2019

The interaction between the zinc finger transcription factor (ZF–TF) and a specific DNA sequence is characterized by energy landscape parameters such as the dissociation rate constant and binding free energy. Heavy metals, such as lead (Pb) and cadmium (Cd), disturb transcription processes by changing the DNA-binding affinities of ZF–TF. To investigate the interference of heavy-metal ions with DNA transcription, we determined the unbinding force between ZF–TF and DNA by atomic force microscopy (AFM). The results suggest that the binding affinity of this complex is stronger in Pb(II) solution than under normal conditions, while the binding affinity in Cd(II) solution is weaker than under normal conditions. Thus, ZF–TF is an important target for heavy metal poisoning. Gold (Au) has a high affinity with cysteine residues, and so, it effectively coordinates with ZF–TF. AFM was employed to detect the molecular interaction force between ZF–TF and DNA in an Au(I) environment. Data analysis demonstrated that Au(I) helps restore normal binding affinity. The measurement of the unbinding force enabled us to quantify the binding free energy in the dissociation process. Alterations of kinetic parameters, which describe the energy landscape, are associated with metal poisoning disease and can be used to screen drugs for heavy-metal induced disease.
Adsorption of heptane–toluene binary mixtures on a hydrophobic polymer surface
Authors: Ramsay Margo , Beutier Clémentine , McGarvey G. Bryce , Hore Dennis K.
Published: January 2019

Polymer coatings offer a means to modulate the adsorption of molecules onto solid surfaces by offering a surface functionality, charge, roughness, and hydrophobicity that is different from the underlying substrate. One application is to provide anti-fouling functions for metal surfaces. Understanding solvent-surface interactions is an essential component to gaining mechanistic insight into the adsorption process. In this work, we study the adsorption of toluene–heptane binary mixtures onto a perflurorinated polymer surface. We use a combination of IR absorption and Raman scattering spectroscopy to study the mixture in the bulk phase, and surface-specific visible-infrared sum-frequency generation to probe the surface layers. Through the use of homo- and heterospectral two-dimensional correlation spectroscopy, we conclude that the adsorption of the two solvents is reversible and that the surface structure is generally independent of the surface composition, with a small change in toluene orientation as the toluene content increases. We also find that the hydrophobic fluropolymer has very little preference for either solvent, similar to previous studies on hydrophilic surfaces.
Love waves dispersion by phononic pillars for nano-particle mass sensing
Authors: Bonhomme J. , Oudich M. , Djafari-Rouhani B. , Sarry F. , Pennec Y. , Bonello B. , Beyssen D. , Charette P. G.
Published: January 2019

We present a design of a pillared phononic crystal based structure for Love wave manipulation to achieve high mass sensitivity. The structure is made of phononic micro-pillars constructed by stacking tungsten and SiO2 layers, distributed on a substrate designed for Love wave propagation. The multilayered pillar allows the creation of bandgaps, which leads to the existence of resonant modes where the elastic energy is confined within the SiO2 free surface layer of the pillar. We study particularly a resonant mode where this layer exhibits torsional mechanical motion which can only be excited by shear horizontal surface waves. We show that Love wave interaction with the torsional mode gives rise to a sharp attenuation in the surface wave transmission spectrum with a high quality factor. We also study the variation of the mass sensitivity of the system by evaluating the resonant mode's frequency shift induced by a mass perturbation using two theoretical approaches: a perturbation theory based approximation and a numerical method. The system presents very promising mass sensitivity which provides an interesting approach to increase the detection performance of Love wave based bio-sensors.
Understanding non-covalent interactions in larger molecular complexes from first principles
Authors: Al-Hamdani Yasmine S. , Tkatchenko Alexandre
Published: January 2019

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges.
Enhanced second harmonic generation by double plasmon resonances in mesoscale flower-like silver particles
Authors: Cheng Zi-Qiang , Li Zong-Lin , Luo Xin , Shi Hai-Quan , Luo Chun-Ling , Liu Zhi-Min , Nan Fan
Published: January 2019

We investigate second harmonic generation (SHG) response of mesoscale silver (Ag) particles. The flower-like Ag mesoparticles and Ag micro-hemispheres on an indium tin oxide coated glass substrate were prepared by a simple electrochemical deposition method. We find that the mesoscale Ag particles show a strong SHG response associated with their geometries. The dependence of the SHG on the excitation wavelength reveals that the multi-resonant response occurring at the emission wavelengths plays an important role in SHG enhancement.
Demonstration of self-healing and scattering resilience of acoustic Bessel beams
Authors: Antonacci Giuseppe , Caprini Davide , Ruocco Giancarlo
Published: January 2019

In optics, Bessel beams have seen extensive use because they exhibit a non-diffracting propagation and a self-reconstruction capability beyond obstacles encountered along their path, with an ensuing pronounced resilience to scattering. Whether such peculiarities, characteristic of the Helmholtz equation for transverse E and B fields, are manifested by longitudinal acoustic fields is currently unknown. Here, we report the experimental demonstration of the self-healing and the scattering resilience properties of a non-diffracting zero-order acoustic Bessel beam. The beam is obtained interfering ultrasound waves with a propagating vector lying on a cone and is found to be capable of self-reconstructing beyond large spherical obstacles and multiple scattering layers.
Asymptotic soliton-like solutions to the singularly perturbed Benjamin-Bona-Mahony equation with variable coefficients
Authors: Samoilenko Valerii , Samoilenko Yuliia
Published: January 2019

The paper deals with a problem of asymptotic soliton-like solutions to the Benjamin-Bona-Mahony (BBM) equation with a small parameter at the highest derivative and variable coefficients depending on the variables x and t, as well as a small parameter. An algorithm for constructing solutions to the BBM equation has been proposed, and theorems on accuracy of such solutions have been proved.
From research to end-users, tracing the path of ocean observations in Australia
Authors: Lara-Lopez Ana , Hodgson-Johnston Indi , Cahill Madeleine , Mancini Sebastien , Blain Peter , Moltmann Tim
Published: January 2019

The mission of Australia’s Integrated Marine Observing System (IMOS), established under the Federal Government’s national collaborative research infrastructure program, is to deliver ocean observations to the marine and climate science community. However, the observations have many uses, ranging from real-time operational forecasting to understanding of processes and policy decision making. Observations need to be provided in a format that fits the purpose of the intended application. Turning observations into usable data, time series, gridded products and analyses broadens the use of such observations. Value adding by developing products that are relevant to end-user needs and easily accessible to non-scientists is also required as a strategic response to new and emerging socioeconomic, legal and policy priorities. This paper describes some of the pathways on which IMOS observations are being delivered and used in Australia, demonstrating the value that ocean observations have for society.
Direct electrochemical generation of supercooled sulfur microdroplets well below their melting temperature
Authors: Liu Nian , Zhou Guangmin , Yang Ankun , Yu Xiaoyun , Shi Feifei , Sun Jie , Zhang Jinsong , Liu Bofei , Wu Chun-Lan , Tao Xinyong , Sun Yongming , Cui Yi , Chu Steven
Published: January 2019

Significance

Since the first discovery of supercooling in 1724, the study of supercooled matter has been mainly limited to varying temperature or pressure. Here we demonstrate an electrochemical approach to generate and observe supercooled sulfur. Our methodology combines dark-field microscopy, a transparent electrochemical cell, and a fast camera to visualize the process at single microdroplet with millisecond time resolution. This platform may open up opportunities for studying supercooled liquids as the droplets approach either homogeneous nucleation to the crystalline state or enter into the glass transition. Relevant to understanding lithium-sulfur battery chemistry, liquid sulfur is observed to form in the electrochemical cell and elucidates a long-debated reaction pathway for sulfur redox reaction in this environment.
Fabrication of superhydrophobic surfaces for corrosion protection: A review
Authors: Ran Minrui , Zheng Wenyue , Wang Huimin
Published: January 2019

Steel, aluminium and magnesium are important engineering materials owing to their excellent mechanical properties. However, their applications are limited due to inadequate corrosion resistance. Various coatings and improvement technologies are used to enhance the corrosion resistance in industry and consumer products. Fabrication of hydrophobic surfaces is a very interesting approach to anticorrosion in that it is derived from the superhydrophobicity found in nature. This paper is a general review of the methods to construct a superhydrophobic surface, i.e. a thin coating layer, on various metallic materials surfaces to enhance their anticorrosion property, providing an introduction of the superhydrophobicity, including theory, properties and fabricating methods. Different methods including spray technique, laser ablation, electrochemical deposition, micro-arc oxidation and etching routes were discussed.
Characterization of Virus-specific Immune Response During Varicella Zoster Virus Encephalitis in a Young Adult
Authors: Sullivan Nicole L , Eberhardt Christiane S , Wieland Andreas , Akondy Rama S , Yi Jumi , McElroy Anita K , Ahmed Rafi
Published: January 2019

An immunocompetent adult received corticosteroids for chest pain, which later was clinically found to be herpes zoster (HZ). She developed severe disease and rapid viral dissemination that elicited an exceptionally strong varicella zoster virus–specific B-cell and CD8 T-cell response. Clinicians should consider atypical HZ presentation prior to corticosteroid administration.
Continuous Leakage-Resilient Identity-Based Encryption with Tight Security
Authors: Zhou Yanwei , Yang Bo , Hou Hongxia , Zhang Lina , Wang Tao , Hu Mingxiao
Published: January 2019

In the actual applications, an adversary can break the security of cryptography scheme through various leakage attacks (e.g. side-channel attacks, cold-boot attacks, etc.), even the continuous leakage attacks. That is, a practical cryptography scheme must maintain its claimed security in the continuous leakage setting. However, the previous constructions on the leakage-resilient identity-based encryption (IBE) scheme could tolerate a leakage that is bounded, and cannot resist the continuous leakage attacks. In order to further achieve the better security, a novel method to build the continuous leakage-resilient IBE scheme with tight security is presented in this paper, and the scheme’s security is proved, in the standard model, based on a stronger security assumption that depends on the number of queries made by the adversary. In addition, our proposal has several advantages over previous such constructions, e.g. shorter public parameters, higher communication efficiency, tight security, etc.
Screening for poverty and intervening in a primary care setting: an acceptability and feasibility study
Authors: Pinto Andrew D , Bondy Madeleine , Rucchetto Anne , Ihnat John , Kaufman Adam
Published: January 2019

Background

A movement is emerging to encourage health providers and health organizations to take action on the social determinants of health. However, few evidence-based interventions exist. Digital tools have not been examined in depth.

Objective

To assess the acceptability and feasibility of integrating, within routine primary care, screening for poverty and an online tool that helps identify financial benefits.

Methods

The setting was a Community Health Centre serving a large number of low-income individuals in Toronto, Canada. Physicians were encouraged to use the tool at every possible encounter during a 1-month period. A link to the tool was easily accessible, and reminder emails were circulated regularly. This mixed-methods study used a combination of pre-intervention and post-intervention surveys, focus groups and interviews.

Results

Thirteen physicians participated (81.25% of all) and represented a range of genders and years in practice. Physicians reported a strong awareness of the importance of identifying poverty as a health concern, but low confidence in their ability to address poverty. The tool was used with 63 patients over a 1-month period. Although screening and intervening on poverty is logistically challenging in regular workflows, online tools could assist patients and health providers identify financial benefits quickly. Future interventions should include more robust follow-up.

Conclusions

Our study contributes to the evidence based on addressing the social determinants of health in clinical settings. Future approaches could involve routine screening, engaging other members of the team in intervening and following up, and better integration with the electronic health record.
Physics of planet trapping with applications to HL Tau
Authors: Cridland Alexander J , Pudritz Ralph E , Alessi Matthew
Published: January 2019

We explore planet formation in the HL Tau disc and possible origins of the prominent gaps and rings observed by ALMA. We investigate whether dust gaps are caused by dynamically trapped planetary embryos at the ice lines of abundant volatiles. The global properties of the HL Tau disc (total mass and size) at its current age are used to constrain an evolving analytic disc model describing its temperature and density profiles. By performing a detailed analysis of the planet–disc interaction for a planet near the water ice line including a rigorous treatment of the dust opacity, we confirm that water is sufficiently abundant (1.5 × 10−4 molecules per H) to trap planets at its ice line due to an opacity transition. When the abundance of water is reduced by 50 ${{\ \rm per\ cent}}$ planet trapping disappears. We extend our analysis to other planet traps: the heat transition, dead zone edge, and the CO2 ice line and find similar trapping. The formation of planets via planetesimal accretion is computed for dynamically trapped embryos at the water ice line, dead zone, and heat transition. The end products orbit in the inner disc (R < 3 au), unresolved by ALMA, with masses that range between sub-Earth to 5 Jupiter masses. While we find that the dust gaps correspond well with the radial positions of the CO2, CH4, and CO ice lines, the planetesimal accretion rates at these radii are too small to build large embryos within 1 Myr.
Bacillus clarussp. nov. is a newBacillus cereusgroup species isolated from soil
Authors: Acevedo Marysabel Méndez , Carroll Laura M. , Mukherjee Manjari , Mills Emma , Xiaoli Lingzi , Dudley Edward G. , Kovac Jasna
Published: January 2019

Bacillus cereusgroup orB. cereussensu lato (s.l.), is comprised of Gram-positive spore-forming, rod-like bacteria that are widespread in natural environments. Although the species in this group are known to be highly related in terms of phenotypic characteristics, they display different levels of pathogenicity. Biochemical assays are therefore considered to be insufficient for accurate taxonomic classification ofB. cereusgroup species. To facilitate accurate taxonomic classification and associated prediction of pathogenic potential, we have conducted comparative genomic analyses of publicly available genome assemblies ofB. cereusgroup isolates. Through that, we found that an isolate previously known asB. mycoidesATCC 21929 was sufficiently distant from valid and effective type strains to be considered a putative new species. We have conducted biochemical and bioinformatic characterization of strain ATCC 21929 that had been isolated from soil in Papua New Guinea. Strain ATCC 21929 most closely resemblesB. paramycoidesNH24A2T, producing ANIb and DDH values of 86.70% and 34.1%, respectively. Phenotypically, isolate ATCC 21929 does not possess cytochrome c oxidase activity, and is able to grow at a range of temperatures 15°C - 43°C and at a range of pH 6 - 9. With regards to fatty acid composition, this isolate has iso-C17:0 in highest abundance. We propose the strain ATCC 21929T(=PS00077AT= PS00077BT= PSU-0922T= BHPT) as a new species namedBacillus clarussp. nov. to facilitate accurate taxonomic classification ofB. cereusgroup isolates.
Glutamatergic and cholinergic metabotropic modulation induces plateau potentials in hippocampal OLM interneurons
Authors: Hagger-Vaughan Nicholas , Storm Johan F.
Published: January 2019

Oriens-lacunosum moleculare (OLM) cells are hippocampal inhibitory interneurons that have been implicated in regulation of information flow and synaptic plasticity in the CA1 circuit.

Since anatomical evidence indicate that OLM cells express metabotopic cholinergic (mAChR) and glutamatergic (mGluR) receptors, such modulation of these cells may contribute to switching between functional modes of the hippocampus.

Using a transgenic mouse line to identify the Chrna2-positive OLM cells, we investigated metabotropic neuromodulation of intrinsic properties of OLM cells.

We found that both mAChR and mGluR activation increased the spontaneous action potential rate and caused the cells to exhibit long-lasting depolarizing plateau potentials following evoked spike trains.

Both the mAChR- and mGluR-induced increased spontaneous firing rate and plateau potentials were dependent on intracellular calcium, and were eliminated by blocking Ca2+-dependent transient receptor potential (TRP) cation channels. At the receptor level, Group I mGluRs were found to be responsible for the glutamatergic modulation of the plateau potentials. There was also a pronounced synergy between the cholinergic and glutamatergic modulation of the plateau potentials.

Our findings provide insights into how OLM cells are modulated by different neurotransmitters, and are likely to have functional implications on how OLM cells regulate hippocampal information processing during different brain states.
Dynamic causal modeling for calcium imaging data reveals differential effective connectivity for sensory processing in a barrel cortical column
Authors: Jung Kyesam , Kang Jiyoung , Chung Seungsoo , Park Hae-Jeong
Published: January 2019

Multi-photon calcium imaging (CaI) is an important tool to assess activity among neural populations within a column in the sensory cortex. However, the complex asymmetrical interactions among neural populations, termed effective connectivity, cannot be directly assessed by measuring the activity of each neuron using CaI but calls for computational modeling. To estimate effective connectivity among neural populations, we proposed a dynamic causal model (DCM) for CaI by combining a convolution-based dynamic neural state model and a dynamic calcium ion concentration model for CaI signals. After conducting a simulation study to evaluate DCM for CaI, we applied it to an experimental CaI data measured at the layer 2/3 of a barrel cortical column that differentially responds to hit and error whisking trails in mice. We first identified neural populations and constructed computational models with intrinsic connectivity of neural populations within the layer 2/3 of the barrel cortex and extrinsic connectivity with latent external modes. Bayesian model inversion and comparison shows that a top-down model with latent inhibitory and excitatory external modes explains the observed CaI signals during hit and error trials better than any other model, with a single external mode or without any latent modes. The best model also showed differential intrinsic and extrinsic effective connectivity between hit and error trials (corresponding to the bottom-up and top-down processes) in the functional hierarchical architecture. Both simulation and experimental results suggest the usefulness of DCM for CaI in terms of exploration of the hierarchical interactions among neural populations observed in CaI.
Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion
Authors: Duc Céline , Yoth Marianne , Mouniée Nolwenn , Jensen Silke , Vaury Chantal , Brasset Emilie
Published: January 2019

Background

For species survival, the germline must faithfully transmit the genetic information to the progeny. Transposable elements (TEs), which are major components of eukaryotic genomes, constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs that are called PIWI-interacting RNAs (piRNAs) and are produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline is protected from transposon invasion. To address this question, we usedDrosophila melanogasterlines harboring a deletion withinflamenco,a major piRNA cluster that is specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposonZAMand to germline genome invasion.

Results

In this mutant line that expressZAMin somatic follicular cells, we identifiedde novoproduction of sense and antisenseZAM-derived piRNAs that displayed a germinal molecular signature. These piRNAs originated from a newZAMinsertion into a germline dual-strand piRNA cluster and silencedZAMexpression specifically in germ cells. Finally, we found thatZAMtrapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.

Conclusions

Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of the germline endangered by mobilization of a surrounding somatic TE.
In vitro analysis of RNA polymerase II elongation complex dynamics
Authors: Joo Yoo Jin , Ficarro Scott B. , Chun Yujin , Marto Jarrod A. , Buratowski Stephen
Published: January 2019

RNA polymerase II elongation complexes (ECs) were assembled from nuclear extract on immobilized DNA templates and analyzed by quantitative mass spectrometry. Time course experiments showed that initiation factor TFIIF can remain bound to early ECs, while levels of core elongation factors Spt4-Spt5, Paf1C, Spt6-Spn1, and Elf1 levels remain steady. Importantly, the dynamic phosphorylation patterns of the Rpb1 C-terminal domain (CTD), and the factors that recognize them, change as a function of post-initiation time, rather than distance elongated. Chemical inhibition of Kin28/Cdk7 blocks both Serine 5 and Serine 2 phosphorylation, affects initiation site choice, and inhibits elongation efficiency. EC components dependent on CTD phosphorylation include capping enzyme, Cap Binding Complex, Set2, and the PAF1 complex. By recapitulating many known features ofin vivoelongation, this system reveals new details that clarify how EC-associated core elongation factors, chromatin regulators, and RNA processing factors change at each step of transcription.
The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity
Authors: Jevtić Predrag , Schibler Andria C. , Pegoraro Gianluca , Misteli Tom , Levy Daniel L.
Published: January 2019

How intracellular organelles acquire their characteristic sizes is a fundamental cell biological question. Given the stereotypical changes in nuclear size in cancer, it is particularly important to understand the mechanisms that control nuclear size in human cells. Here we use a high-throughput imaging RNAi screen to identify and mechanistically characterize ELYS, a nucleoporin required for postmitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. We show that ELYS knockdown results in small nuclei, the accumulation of cytoplasmic lamin aggregates, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β nuclear import decreases nuclear size. Conversely, ELYS overexpression leads to increased nuclear size, enrichment of nuclear lamin B2 staining at the nuclear periphery, and elevated NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. In summary, we identify ELYS and NPC density as novel positive effectors of mammalian nuclear size and propose that nuclear size is controlled by nuclear import capacity.
Altering nuclear import in early Xenopus laevis embryos affects later development
Authors: Jevtić Predrag , Levy Daniel L.
Published: January 2019

More than just a container for DNA, the nucleus carries out a wide variety of critical and highly regulated cellular functions. One of these functions is nuclear import, and in this study we investigate how altering nuclear import impacts developmental progression and organismal size. During early Xenopus laevis embryogenesis, the timing of a key developmental event, the midblastula transition (MBT), is sensitive to nuclear import factor levels. How might altering nuclear import and MBT timing in the early embryo affect downstream development of the organism? We microinjected X.laevis two-cell embryos to increase levels of importin α or NTF2, resulting in differential amounts of nuclear import factors in the two halves of the embryo. Compared to controls, these embryos exhibited delayed gastrulation, curved neural plates, and bent tadpoles with different sized eyes. Furthermore, embryos microinjected with NTF2 developed into smaller froglets compared to control microinjected embryos. We propose that altering nuclear import and size affects MBT timing, cell size, and cell number, subsequently disrupting later development. Thus, altering nuclear import early in development can affect function and size at the organismal level.
Left anterior temporal lobe is necessary for efficient lateralised processing of spoken word identity
Authors: Cope Thomas , Shtyrov Yury , MacGregor Lucy , Holland Rachel , Pulvermüller Friedemann , Rowe James B , Patterson Karalyn
Published: January 2019

In the healthy human brain, the processing of spoken words is strongly left-lateralised, while the processing of complex non-linguistic sounds recruits brain regions bilaterally. Here we asked whether the left anterior temporal lobe, strongly implicated in semantic processing, is critical to this special treatment of linguistic stimuli. Nine patients with semantic dementia (SD) and fourteen age-matched controls underwent magnetoencephalography and structural MRI. Voxel based morphometry demonstrated the stereotypical pattern of SD: severe grey matter loss restricted to the left anterior temporal lobe. During magnetoencephalography, participants listened to word sets in which identity and meaning were ambiguous until utterance completion, for exampleplayedvsplate. Whereas left-hemispheric responses were similar across groups, patients demonstrated increased right hemisphere activity 174-294ms after stimulus disambiguation. Source reconstructions confirmed recruitment of right-sided analogues of language regions in SD: atrophy of left anterior temporal lobe was associated with increased activity in right temporal pole, middle temporal gyrus, inferior frontal gyrus and supramarginal gyrus. Moreover only healthy controls had differential responses to wordsversusnon-words in right auditory cortex and planum temporale. Overall, the results indicate that anterior temporal lobe is necessary for normal and efficient processing of word identity in the rest of the language network.
Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach
Authors: Logsdon Benjamin A. , Perumal Thanneer M. , Swarup Vivek , Wang Minghui , Funk Cory , Gaiteri Chris , Allen Mariet , Wang Xue , Dammer Eric , Srivastava Gyan , Mukherjee Sumit , Sieberts Solveig K. , Omberg Larsson , Dang Kristen D. , Eddy James A. , Snyder Phil , Chae Yooree , Amberkar Sandeep , Wei Wenbin , Hide Winston , Preuss Christoph , Ergun Ayla , Ebert Phillip J , Airey David C. , Carter Gregory W. , Mostafavi Sara , Yu Lei , Klein Hans-Ulrich ,   the AMP-AD Consortium, Collier David A. , Golde Todd , Levey Allan , Bennett David A. , Estrada Karol , Decker Michael , Liu Zhandong , Shulman Joshua M. , Zhang Bin , Schadt Eric , De Jager Phillip L. , Price Nathan D. , Ertekin-Taner Nilüfer , Mangravite Lara M.
Published: January 2019

Alzheimer’s disease (AD) is a complex and heterogenous brain disease that affects multiple inter-related biological processes. This complexity contributes, in part, to existing difficulties in the identification of successful disease-modifying therapeutic strategies. To address this, systems approaches are being used to characterize AD-related disruption in molecular state. To evaluate the consistency across these molecular models, a consensus atlas of the human brain transcriptome was developed through coexpression meta-analysis across the AMP-AD consortium. Consensus analysis was performed across five coexpression methods used to analyze RNA-seq data collected from 2114 samples across 7 brain regions and 3 research studies. From this analysis, five consensus clusters were identified that described the major sources of AD-related alterations in transcriptional state that were consistent across studies, methods, and samples. AD genetic associations, previously studied AD-related biological processes, and AD targets under active investigation were enriched in only three of these five clusters. The remaining two clusters demonstrated strong heterogeneity between males and females in AD-related expression that was consistently observed across studies. AD transcriptional modules identified by systems analysis of individual AMP-AD teams were all represented in one of these five consensus clusters except ROS/MAP-identified Module 109, which was specific for genes that showed the strongest association with changes in AD-related gene expression across consensus clusters. The other two AMP-AD transcriptional analyses reported modules that were enriched in one of the two sex-specific Consensus Clusters. The fifth cluster has not been previously identified and was enriched for genes related to proteostasis. This study provides an atlas to map across biological inquiries of AD with the goal of supporting an expansion in AD target discovery efforts.
Redox signalingvialipid peroxidation regulates retinal progenitor cell differentiation
Authors: Albadri Shahad , Naso Federica , Gauron Carole , Parolin Carola , Duroure Karine , Fiori Jessica , Boga Carla , Vriz Sophie , Calonghi Natalia , Del Bene Filippo
Published: January 2019

Reactive oxygen species (ROS) and downstream products of lipid oxidation are emerging as important secondary messengers in tissue homeostasis. However their regulation and mechanism of action remain poorly studiedin vivoduring normal development. Here we reveal that the fine regulation of hydrogen peroxide (H2O2) levels at the degradation step by its scavenger Catalase is crucial to mediate the switch from proliferation to differentiation in retinal progenitor cells (RPCs). We further show that altering the levels of downstream products of the Redox signaling can also affect this switch. Indeed, we identify9-hydroxystearic acid (9-HSA), an endogenous downstream lipid peroxidation product, as a mediator of this effect in the zebrafish retina. In fact, RPCs exposed to higher amounts of9-HSA failed to differentiate and remained proliferative. We found that9-HSA exerts its biological functionin vivoby inhibiting the activity of histone deacetylase 1. We finally show that the local and temporal manipulation of H2O2levels bycatalaseoverexpression in RPCs was sufficient to trigger their premature differentiation. Therefore the amount of H2O2in RPCs is instructive of their ability to switch from proliferation to differentiation. We propose a mechanism that acts in RPC and linking H2O2homeostasis and neuronal differentiationviathe modulation of lipid peroxidation.
Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation
Authors: Wang Shilei , Wu Qun , Nie Yao , Xu Yan
Published: January 2019

Natural microbiota plays an essential role in flavor compounds producing for traditional food fermentation. Whereas, the fluctuation of natural microbiota results in the inconstancy of food quality. Thus, it is critical to reveal the core microbiota for flavor compounds producing and construct a synthetic core microbiota for constant food fermentation. Here, we revealed the core microbiota based on their flavor-producing and co-occurrence performance, using Chinese light aroma type liquor as a model system. Five genera were identified to be the core microbiota, includingLactobacillus, Saccharomyces, Pichia, Geotrichum, andCandida. The synthetic core microbiota of these five genera presented a reproducible dynamic profile with that in the natural microbiota. Monte Carlo test showed that the interpretation of five environmental factors (lactic acid, ethanol and acetic acid contents, moisture and pH) on the synthetic microbiota distribution were highly significant (P< 0.01), which was similar with that in the natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ> 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. It is of great significance for the tractable and constant production of various fermented foods.

IMPORTANCE

The transformation from natural fermentation to synthetic fermentation is essential to construct a constant food fermentation process, which is the premise for stably making high-quality food. According to the functions of flavor-producing and co-occurring in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light aroma type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compounds production in thein vitrosystem. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota, but also be beneficial for constructing a tractable and reproducible food fermentation process.