bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and computational investigations of the effect of the electrode gap on capacitively coupled radio frequency oxygen discharges
Authors: You K. H. , Schulze J. , Derzsi A. , Donkó Z. , Yeom H. J. , Kim J. H. , Seong D. J. , Lee Hyo-Chang
Published: January 2019

Geometrically symmetric capacitively coupled oxygen plasmas are studied experimentally by optical emission spectroscopy and probe measurements as well as via numerical simulations using the kinetic Particle-in-Cell/Monte Carlo collision (PIC/MCC) approach. The experiments reveal that at a fixed pressure of 20 mTorr and a driving frequency of 13.56 MHz, the central electron density increases with an increased electrode gap, while the time averaged optical emission of atomic oxygen lines decreases. These results are reproduced and understood by the PIC/MCC simulations performed under identical conditions. The simulations show that the electron density increases due to a mode transition from the Drift-Ambipolar-mode to the α-mode induced by increasing the electrode gap. This mode transition is due to a drastic change of the electronegativity and the mean electron energy, which leads to the observed reduction of the emission intensity of an atomic oxygen line. The observed mode transition is also found to cause a complex non-monotonic dependence of the O2+ ion flux to the electrodes as a function of the electrode gap. These fundamental results are correlated with measurements of the etch rate of amorphous carbon layers at different gap distances.
Electro-osmotic pumping through a bumpy microtube: Boundary perturbation and detection of roughness
Authors: Lei Jie-Chao , Chang Chien C. , Wang Chang-Yi
Published: January 2019

To machine precision, a micro-duct cannot be fabricated without producing surface roughness. It is of essential importance to examine the effects and predict the level of roughness on electro-osmotic (EO) pumping for ducts of fundamental shapes. In this study, we consider a bumpy microtube with its wall shape modeled by the product of two sinusoidal functions. Boundary perturbation is carried out with respect to the amplitude roughness ε (relative to the Debye length) up to the second-order by considering the Debye-Hückel approximation and viscous Stokes equation for the electrolyte transport. Besides the amplitude roughness ε, the key parameters include the azimuthal wave number n and the axial wave number α of the bumpiness, as well as the non-dimensional electrokinetic width K. It is shown that the EO pumping rate Q is modified by a second-order term −ε2πχ, namely, Q = Q0 − ε2πχ, where Q0 denotes the pumping rate through the smooth tube. The net effect χ = χ1 + χ2 comprises two components: χ1 = χ1(K) < 0 increases with increasing K, representing a pure gain, while χ2 has no definite sign and is a complex function of K, n, and α. In particular, χ is negative at small α whilst being positive at large α, and the dividing line of signs also depends on K. For small α (<1), χ increases with increasing n at all K, while for large α (>1), χ decreases with increasing n at large K (>20). For a given number of oscillations Ac = nα (>1), there exists an intermediate n at which the EO pumping rate is maximized at small K (<20). Moreover, we identify a long-wavelength limit singularity in the EO pumping rate as α → 0 for all n, i.e., in the longitudinal sense. In addition, the velocity component along the tube axis is modified by a second-order term of the roughness, though the same velocity component near the wavy wall exhibits periodic behaviors in phase with the wall roughness. Physical reasoning is given to all the derived mathematical results, and their implication in practical applications as a model for predicting tube roughness is explained. As the tube shape represents a conduit of practical use, a particular emphasis is placed upon potential applications of the derived result.
Effect of chain stiffness on the entropic segregation of chain ends to the surface of a polymer melt
Authors: Blaber S. , Mahmoudi P. , Spencer R. K. W. , Matsen M. W.
Published: January 2019

Entropic segregation of chain ends to the surface of a monodisperse polymer melt and its effect on surface tension are examined using self-consistent field theory (SCFT). In order to assess the dependence on chain stiffness, the SCFT is solved for worm-like chains. Our focus is still on relatively flexible polymers, where the persistence length of the polymer, ℓp, is comparable to the width of the surface profile, ξ, but still much smaller than the total contour length of the polymer, ℓc. Even this small degree of rigidity causes a substantial increase in the level of segregation, relative to that of totally flexible Gaussian chains. Nevertheless, the long-range depletion that balances the surface excess still exhibits the same universal shape derived for Gaussian chains. Furthermore, the excess continues to reduce the surface tension by one unit of kBT per chain end, which results in the usual N−1 reduction in surface tension observed by experiments. This enhanced segregation will also extend to polydisperse melts, causing the molecular-weight distribution at the surface to shift towards smaller Nn relative to the bulk. This provides a partial explanation for recent quantitative differences between experiments and SCFT calculations for flexible polymers.
Electronic and nuclear fluxes induced by quantum interference in the adiabatic and nonadiabatic dynamics in the Born-Huang representation
Authors: Matsuzaki Rei , Takatsuka Kazuo
Published: January 2019

We perform an electronic and nuclear flux analysis for nonadiabatic dynamics and its corresponding adiabatic counterpart, both of the wavefunctions of which are represented in the Born-Huang expansion. It is well known that the electronic-nuclear configurations (terms) in the expansion of the total wavefunction interfere each other through the nonadiabatic interactions and give birth to electronic and nuclear fluxes. Interestingly, even in the adiabatic dynamics without such nonadiabatic interactions, a wavefunction composed of more than one adiabatic state can undergo interference among the components and give the electronic and nuclear fluxes. That is, the individual pieces of the wavepacket components associated with the electronic wavefunctions in the adiabatic representation can propagate in time independently with no nonadiabatic interaction, and yet they can interfere among themselves to generate the specific types of electronic and nuclear fluxes. We refer to the dynamics of this class of total wavefunction as multiple-configuration adiabatic Born-Huang dynamics. A systematic way to distinguish the electronic and nuclear fluxes arising from nonadiabatic and the corresponding adiabatic dynamics is discussed, which leads to the deeper insight about the nonadiabatic dynamics and quantum interference in molecular processes. The so-called adiabatic flux will also be discussed.
Performance and application of heavy ion nuclear microbeam facility at the Nuclear Physics Institute in Řež, Czech Republic
Authors: Romanenko Oleksandr , Havranek Vladimir , Mackova Anna , Davidkova Marie , Cutroneo Mariapompea , Ponomarev Alexander G. , Nagy Gyula , Stammers James , Rajta Istvan
Published: January 2019

The Tandetron Laboratory of the Nuclear Physics Institute of the Czech Academy of Sciences is equipped with five beam lines associated with a 3 MV tandem electrostatic accelerator model 4130 MC from High Voltage Engineering Europa B.V. This accelerator is coupled with two duoplasmatron sources and a single sputter ion source and provides ions from hydrogen to gold. One of these lines is a nuclear microbeam facility, utilizing ion beams of micro- and sub-micro sizes for materials research by use of particle induced x-ray emission spectroscopy, particle induced gamma emission, Rutherford back-scattering spectroscopy, and scanning transmission ion microscopy methods as well as for ion beam writing. The major advantage of the presented microprobe is a possibility of 3D structure creation not only in polymer materials using light ions but also in other materials such as glass, ceramics, etc. by use of heavy ions. The focusing system allows focusing of charged particles with a maximum rigidity of 11 MeV amu/q2. The usual resolution in high and low current modes is 2 × 3 µm2 for a 100 pA and 0.3 × 0.5 µm2 for the 2000 ions/s of 2 MeV protons, respectively. A detailed facility description is given in the paper. The applications of focused beams of heavy ions as well as examples of light ions utilizing are also presented in the article.
A compliantly coupled dielectric elastomer actuator using magnetic repulsion
Authors: Cao C. , Gao X. , Conn A. T.
Published: January 2019

Dielectric elastomer actuators (DEAs) have attracted growing research interest over the past two decades for their large actuation strain, inherent compliance, and low cost. The conical DEA configuration is particularly attractive thanks to their simple structure and high force/stroke actuation. A double cone DEA design with two antagonistic membranes allows active bidirectional actuation. However, in existing double cone DEA designs, the two membranes are rigidly coupled, which restricts their relative actuation response under periodic electrical input to 180° out-of-phase operation. This work presents a magnetically coupled DEA with compliant coupling by a magnetic repulsion. The compliant coupling allows two separate inputs with a fully adjustable phase difference. The current prototype demonstrates a peak normalized stroke of 14% (relative to the nominal DEA height) at a phase shift of 180° and a normalized linear expansion between the two membranes of up to 8.3% (relative to the nominal DEA height) at a phase shift of 0° at 0.5 Hz. This results in several emerging actuation behaviors, which could potentially be suitable for controllable shape changing actuations, active vibration damping, and bioinspired locomotion.
X-ray spectroscopy of planar laser-plasma interaction experiments at the National Ignition Facility
Authors: Rosenberg M. J. , Epstein R. , Solodov A. A. , Seka W. , Myatt J. F. , Michel P. A. , Barrios M. A. , Thorn D. B. , Hohenberger M. , Moody J. D. , Regan S. P.
Published: January 2019

X-ray spectroscopy has been newly used to diagnose electron temperatures in planar-geometry experiments at the National Ignition Facility (NIF) designed to study laser-plasma interactions at plasma conditions relevant to direct-drive ignition. These experiments used a buried co-mixed Mn/Co microstrip in a CH ablator in experiments that generated long scale-length plasmas susceptible to stimulated Raman scattering (SRS). Time-resolved Mn and Co K-shell spectra, diagnosed using the NIF x-ray spectrometer, were analyzed by fitting to synthetic spectra based on a detailed atomic model of emission from the microstrip. The electron temperature at the time when the microstrip passes through the quarter-critical density surface, the key region for the development of SRS, was inferred to be around 2–3 keV. These measurements constrain 2-D DRACO radiation-hydrodynamic modeling of the planar experiments, important for determining plasma conditions pertinent to SRS, and demonstrate that this platform approaches direct-drive ignition-relevant conditions. The modeling is also assessed by a direct comparison of measured spectra to modeled spectra generated by DRACO in conjunction with the atomic physics postprocessor code SPECT3D.
Electrical spin injection into AlGaAs/GaAs-based two-dimensional electron gas systems with Co2MnSi spin source up to room temperature
Authors: Lin Zhichao , Pan Da , Rasly Mahmoud , Uemura Tetsuya
Published: January 2019

We demonstrated electrical spin injection into an AlGaAs/GaAs-based high-mobility two-dimensional electron gas (2DEG) system using Co2MnSi as a spin source. A non-local spin-valve signal was observed from 4.2 K to room temperature. Interestingly, the spin-valve signal does not show a monotonic decrease with increasing temperature and reaches a peak at about 80 K. This contrasts with the result observed in bulk GaAs, in which a monotonic decrease in spin-valve signals with increasing temperature was observed. Moreover, the spin-valve signal decreases by a factor of about 5.6 with increasing temperature from 4.2 K to 294 K, and this factor is smaller than those values reported in bulk GaAs devices. This result suggests that the spin-valve signal in a 2DEG device is less sensitive to temperature than that in a bulk device, which is promising for realizing future spin transistors that can operate at room temperature.
Chimeras in digital phase-locked loops
Authors: Paul Bishwajit , Banerjee Tanmoy
Published: January 2019

Digital phase-locked loops (DPLLs) are nonlinear feedback-controlled systems that are widely used in electronic communication and signal processing applications. In most of the applications, they work in coupled mode; however, a vast amount of the studies on DPLLs concentrate on the dynamics of a single isolated unit. In this paper, we consider both one- and two-dimensional networks of DPLLs connected through a practically realistic nonlocal coupling and explore their collective dynamics. For the one-dimensional network, we analytically derive the parametric zone of a stable phase-locked state in which DPLLs essentially work in their normal mode of operation. We demonstrate that apart from the stable phase-locked state, a variety of spatiotemporal structures including chimeras arise in a broad parameter zone. For the two-dimensional network under nonlocal coupling, we identify several variants of chimera patterns, such as strip and spot chimeras. We identify and characterize the chimera patterns through suitable measures like local curvature and correlation function. Our study reveals the existence of chimeras in a widely used engineering system; therefore, we believe that these chimera patterns can be observed in experiments as well.
Two delays induce Hopf bifurcation and double Hopf bifurcation in a diffusive Leslie-Gower predator-prey system
Authors: Du Yanfei , Niu Ben , Wei Junjie
Published: January 2019

In this paper, the dynamics of a modified Leslie-Gower predator-prey system with two delays and diffusion is considered. By calculating stability switching curves, the stability of positive equilibrium and the existence of Hopf bifurcation and double Hopf bifurcation are investigated on the parametric plane of two delays. Taking two time delays as bifurcation parameters, the normal form on the center manifold near the double Hopf bifurcation point is derived, and the unfoldings near the critical points are given. Finally, we obtain the complex dynamics near the double Hopf bifurcation point, including the existence of quasi-periodic solutions on a 2-torus, quasi-periodic solutions on a 3-torus, and strange attractors.
A “crab-like” A6 relativistic magnetron with diffraction output driven by a transparent cathode
Authors: Liu M. , Schamiloglu E. , Fuks M. I. , Liu C. , Jiang W. , Feng J.
Published: January 2019

We present the design of an A6 relativistic magnetron with diffraction output (MDO) which looks like a crab and we named it the “crab-like” A6 MDO. This article shows that the crab-like A6 MDO driven by a transparent cathode can radiate the TE11 mode with an output power of about 1 GW when an optimized applied voltage of U=440 kV and magnetic field of B=0.43 T are used. Its electronic efficiency, as obtained using UNIPIC particle-in-cell (PIC) simulations, can be as high as 44% in S-band. The UNIPIC PIC code used in simulations also demonstrates that the crab-like A6 MDO can radiate both two electron spokes in the TE21 mode with an operating frequency of 2.1 GHz and four electron spokes in the TE21 mode with an operating frequency of 2.5 GHz when different magnetic field amplitudes are used for an applied voltage of U=400 kV. This result suggests that this configuration is favorable for mode switching. This work seeks to design a compact high power microwave source for a narrowband directed microwave wave beam that is suitable for mode switching investigations.
Control of net form of net blotch in barley from seed- and foliar-applied fungicides
Authors: McLean Mark S. , Hollaway Grant J.
Published: January 2019

Net form of net blotch (NFNB), caused by Pyrenophora teres f. teres, is a major foliar disease of barley (Hordeum vulgare L.) worldwide that can cause grain yield and quality loss in susceptible varieties. Seed- and foliar-applied fungicides were evaluated in six field experiments infected with NFNB during 5 years, for suppression of NFNB severity and protection of grain yield and quality. Suppression of NFNB severity varied between treatments and experiments. Grain yield and quality improvements were recorded in two experiments. Foliar fungicide applications at stem elongation (Zadoks growth stage Z31) and flag leaf emergence (Z39) or ear emergence (Z55) significantly reduced NFNB severity, increased grain yield by up to 23%, and improved grain-quality measurements of retention, screenings and weight. The seed-applied fungicide fluxapyroxad provided significant reductions in NFNB severity, improvements in grain yield of up to 20%, and improved grain quality. Where NFNB was severe, none of the seed or foliar fungicide application strategies provided complete control of NFNB, indicating that more than two applications were necessary when conditions were favourable for disease development in susceptible varieties.
Assessment of human–crocodile conflict in Mexico: patterns, trends and hotspots areas
Authors: García-Grajales Jesús , Buenrostro-Silva Alejandra
Published: January 2019

An understanding of the factors, patterns of activities and seasonality per region that shape the response to the human–crocodile (HC) conflict in Mexico by humans is essential for prevention and mitigation of negative interactions. We compiled the publicly available data on incidents of crocodile attacks on the Gulf of Mexico and Mexican Pacific coast from January 2000 to the first days of January 2018. Of the recorded unprovoked crocodile attacks (n=149) on humans in Mexico, 102 cases correspond to the Mexican Pacific coast and 47 to the Gulf of Mexico. The age of victims involved in the majority of the attacks ranged from 19 to 40 years old. Three municipalities of high risk (hotspots areas) were Puerto Vallarta, Lázaro Cárdenas and Pinotepa Nacional in the Mexican Pacific coast, whereas, in the Gulf of Mexico, only Bénito Juárez was of high risk. To mitigate this conflict, it is necessary that local authorities in the municipalities (mainly in those of high risk) establish public-safety programs with the goal of raising awareness of the risk of crocodile attacks on the basis of information status and distribution of the crocodile population, linked to the extent of HC conflicts, as a first step for better management and risk mitigation.
The Long-Term Impacts of Low-Achieving Childhood Peers: Evidence from Project STAR
Authors: Bietenbeck Jan
Published: January 2019

This paper evaluates how sharing a kindergarten classroom with low-achieving repeaters affects the long-term educational performance of regular first-time kindergarten students. Exploiting random assignment of teachers and students to classes in Project STAR, I document three sets of causal impacts: students who are exposed to repeaters (1) score lower on a standardized math test at the end of kindergarten, an effect that fades out in later grades; (2) show persistent improvements in noncognitive skills such as effort and discipline; and (3) are more likely to graduate from high school and to take a college entrance exam around the age of 18. I argue that the positive spillovers on long-term educational attainment are driven by the differential accumulation of noncognitive skills by repeater-exposed students during childhood. Results are consistent with the hypothesis that the improvements in these skills are driven by behavioral adjustments of teachers to the presence of repeaters in the classroom.
Unconventional Monetary Policy, Fiscal Side Effects, and Euro Area (Im)balances
Authors: Hachula Michael , Piffer Michele , Rieth Malte
Published: January 2019

We study the macroeconomic effects of unconventional monetary policy in the euro area using structural vector autoregressions, identified with external instruments. The instruments are based on the common unexpected variation in euro area sovereign yields for different maturities on policy announcement days. We first show that expansionary monetary surprises are effective at lowering public and private interest rates and increasing economic activity, consumer prices, and inflation expectations. We then document that the shocks lead to a rise in primary public expenditures and a widening of internal trade balances.
Safety of Outpatient Anterior Cervical Discectomy and Fusion: A Systematic Review and Meta-Analysis
Authors: Yerneni Ketan , Burke John F , Chunduru Pranathi , Molinaro Annette M , Riew K Daniel , Traynelis Vincent C , Tan Lee A
Published: January 2019

BACKGROUND

Anterior cervical discectomy and fusion (ACDF) is being increasingly offered on an outpatient basis. However, the safety profile of outpatient ACDF remains poorly defined.

OBJECTIVE

To review the medical literature on the safety of outpatient ACDF.

METHODS

We systematically reviewed the literature for articles published before April 1, 2018, describing outpatient ACDF and associated complications, including incidence of reoperation, stroke, thrombolytic events, dysphagia, hematoma, and mortality. A random-effects analysis was performed comparing complications between the inpatient and outpatient groups.

RESULTS

We identified 21 articles that satisfied the selection criteria, of which 15 were comparative studies. Most of the existing studies were retrospective, with a lack of level I or II studies on this topic. We found no statistically significant difference between inpatient and outpatient ACDF in overall complications, incidence of stroke, thrombolytic events, dysphagia, and hematoma development. However, patients undergoing outpatient ACDF had lower reported reoperation rates (P < .001), mortality (P < .001), and hospitalization duration (P < .001).

CONCLUSION

Our meta-analysis indicates that there is a lack of high level of evidence studies regarding the safety of outpatient ACDF. However, the existing literature suggests that outpatient ACDF can be safe, with low complication rates comparable to inpatient ACDF in well-selected patients. Patients with advanced age and comorbidities such as obesity and significant myelopathy are likely not suitable for outpatient ACDF. Spine surgeons must carefully evaluate each patient to decide whether outpatient ACDF is a safe option. Higher quality, large prospective randomized control trials are needed to accurately demonstrate the safety profile of outpatient ACDF.
Understanding the Resistance Mechanism in Brassica napus to Clubroot Caused by Plasmodiophora brassicae
Authors: Mei Jiaqin , Guo Zhen , Wang Jinhua , Feng Yuxia , Ma Guanhua , Zhang Chunyu , Qian Wei , Chen Guokang
Published: January 2019

Exploring the mechanism of plant resistance has become the basis for selection of resistance varieties but reports on revealing resistant mechanism in Brassica napus against Plasmodiophora brassicae are rare. In this study, RNA-seq was conducted in the clubroot-resistant B. napus breeding line ZHE-226 and in the clubroot-susceptible rapeseed cultivar Zhongshuang 11 at 0, 3, 6, 9, and 12 days after inoculation. Strong alteration was detected specifically in ZHE-226 as soon as the root hair infection happened, and significant promotion was found in ZHE-226 on cell division or cell cycle, DNA repair and synthesis, protein synthesis, signaling, antioxidation, and secondary metabolites. Combining results from physiological, biochemical, and histochemical assays, our study highlights an effective signaling in ZHE-226 in response to P. brassicae. This response consists of a fast initiation of receptor kinases by P. brassicae; the possible activation of host intercellular G proteins which might, together with an enhanced Ca2+ signaling, promote the production of reactive oxygen species; and programmed cell death in the host. Meanwhile, a strong ability to maintain homeostasis of auxin and cytokinin in ZHE-226 might effectively limit the formation of clubs on host roots. Our study provides initial insights into resistance mechanism in rapeseed to P. brassicae.
Integrating Genomics into Psychiatric Practice: Ethical and Legal Challenges for Clinicians
Authors: Ward Eric T. , Kostick Kristin M. , Lázaro-Muñoz Gabriel
Published: January 2019

Psychiatric genomics is a rapidly growing field that holds much promise for improving risk prediction, prevention, diagnosis, treatment selection, and understanding of the pathogenesis of patients’ symptoms. The field of psychiatry (i.e., professional organizations, mental health clinicians, educational institutions), however, needs to address numerous challenges to promote the responsible translation of genomic technologies and knowledge into psychiatric practice. The goal of this article is to review how clinicians currently encounter and use genomics in the clinic, to summarize the existing literature on how clinicians feel about the use of genomics in psychiatry, and to analyze foreseeable ethical and legal challenges for the responsible integration of genomics into psychiatric care at the structural and clinic levels. Structural challenges are defined as aspects of the larger system of psychiatric practice that constitute potential barriers to the responsible integration of genomics for the purposes of psychiatric care and prevention. These structural challenges exist at a level where professional groups can intervene to set standards and regulate the practice of psychiatry and genomics. Clinic-level challenges are day-to-day issues clinicians face when managing genomic tests in the clinic. We discuss the need for action to mitigate these challenges and maximize the clinical and social utility of psychiatric genomics, including the following: expanding genomics training among mental health clinicians; establishing practice guidelines that consider potential clinical, psychological, and social implications of psychiatric genomics; promoting an integrated care model for managing genomics in psychiatry; emphasizing patient engagement and informed consent when managing genomic testing in psychiatric care.
The contribution of second primary cancers to the mortality of patients with a gastric first primary cancer
Authors: Morais Samantha , Antunes Luís , Bento Maria J. , Lunet Nuno
Published: January 2019

Objectives

Gastric first primary cancers (FPCs) have an increased risk of developing second primary cancers (SPCs). However, their effect on mortality remains poorly understood. Thus, we aimed to estimate the contribution of SPCs to the mortality of gastric FPCs.

Patients and methods

A population-based cohort of gastric FPCs diagnosed in 2000–2006 was followed for SPCs (31 December 2012) and vital status (31 December 2017). SPCs (138 synchronous and 205 metachronous, ≤1 and >1 year after the FPC, respectively) were matched (1 : 3, by sex, 5-year age group, and year of FPC diagnosis) with those without an SPC and alive when the corresponding SPC was diagnosed.

Results

In synchronous SPCs, the hazard ratio (95% confidence interval) for death was 1.07 (0.81–1.40) in males and 0.86 (0.58–1.28) in females; the corresponding estimates for metachronous SPCs were 1.89 (1.49–2.41) and 2.08 (1.42–3.05). In synchronous SPCs, the 10-year cumulative mortality was similar to that of FPCs only; the estimates were higher in lung SPCs. The 10-year cumulative mortality was 75.5% in males and 65.5% in females with metachronous SPCs, which is more than 20% higher than for FPCs only.

Conclusion

Among patients with gastric FPCs who survive long enough for metachronous SPCs, the latter substantially increases mortality over 10 years, whereas the effect of synchronous SPCs is generally smaller.
Serum fetuin-B level is an independent marker for nonalcoholic fatty liver disease in patients with type 2 diabetes
Authors: El-Ashmawy Hazem M. , Ahmed Azza M.
Published: January 2019

Objective

Previous studies have assessed serum fetuin-B and its relation to nonalcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) and as a link between them through inducing insulin resistance (IR). Therefore, we examined the potential of serum fetuin-B to be an independent marker for NAFLD in patients with T2DM.

Patients and methods

The study group consisted of 270 patients with T2DM. Clinical and laboratory features were evaluated. The NAFLD severity was graded by ultrasound into three subgroups: grade 0 (no fatty liver), grade 1 (mild fatty liver), and grade 2–3 (medium to severe fatty liver). Fetuin-B, retinol-binding protein-4, and adiponectin were measured.

Results

Patients with grade 2–3 NAFLD had high fetuin-B levels in comparison with non-NAFLD group. Age and sex adjusted fetuin-B demonstrated positive correlations with triglycerides, γ-glutamyl transferase, fasting plasma glucose, 2-h postprandial plasma glucose, homeostasis model assessment of IR, fasting insulin, glycated hemoglobin, high-sensitivity C-reactive protein, and estimated glomerular filtration rate, but it had a negative correlation with serum creatinine. Adiponectin level was decreased with increasing NAFLD severity, but no difference was found in retinol-binding protein-4. The estimated odds ratio (OR) for the occurrence of grade 2–3 NAFLD was increased significantly with increasing levels of fetuin-B (OR: 3.92; 95% confidence interval: 2.14–8.32 vs. OR: 8.91; 95% confidence interval: 4.22–18.41). The OR of fetuin-B in the uppermost tertile group was still significant after controlling for homeostasis model assessment of IR, glycated hemoglobin, waist circumference, BMI, hepatic enzymes, high-density lipoprotein cholesterol, triglycerides, and high-sensitivity C-reactive protein.

Conclusions

Our study demonstrated that serum fetuin-B had an independent association with NAFLD in patients with T2DM.
Formation and dynamics of magma reservoirs
Authors: Sparks R. S. J. , Annen C. , Blundy J. D. , Cashman K. V. , Rust A. C. , Jackson M. D.
Published: January 2019

The emerging concept of a magma reservoir is one in which regions containing melt extend from the source of magma generation to the surface. The reservoir may contain regions of very low fraction intergranular melt, partially molten rock (mush) and melt lenses (or magma chambers) containing high melt fraction eruptible magma, as well as pockets of exsolved magmatic fluids. The various parts of the system may be separated by a sub-solidus rock or be connected and continuous. Magma reservoirs and their wall rocks span a vast array of rheological properties, covering as much as 25 orders of magnitude from high viscosity, sub-solidus crustal rocks to magmatic fluids. Time scales of processes within magma reservoirs range from very slow melt and fluid segregation within mush and magma chambers and deformation of surrounding host rocks to very rapid development of magma and fluid instability, transport and eruption. Developing a comprehensive model of these systems is a grand challenge that will require close collaboration between modellers, geophysicists, geochemists, geologists, volcanologists and petrologists.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Mafic tiers and transient mushes: evidence from Iceland
Authors: Maclennan J.
Published: January 2019

It is well established that magmatism is trans-crustal, with melt storage and processing occurring over a range of depths. Development of this conceptual model was based on observations of the products of magmatism at spreading ridges, including Iceland. Petrological barometry and tracking of the solidification process has been used to show that the Icelandic crust is built by crystallization over a range of depths. The available petrological evidence indicates that most of the active rift zones are not underlain by extensive and pervasive crystal mush. Instead, the microanalytical observations from Iceland are consistent with a model where magmatic processing in the lower crust occurs in sills of decimetric vertical thickness. This stacked sills mode of crustal accretion corresponds to that proposed for the oceanic crust on the basis of ophiolite studies. A key feature of these models is that the country rock for the sills is hot but subsolidus. This condition can be met if the porosity in thin crystal mushes at the margins of the sills is occluded by primitive phases, a contention that is consistent with observations from cumulate nodules in Icelandic basalts. The conditions required for the stabilization of trans-crustal mushes may not be present in magmatic systems at spreading ridges.

This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Defecation by the ctenophoreMnemiopsis leidyioccurs with an ultradian rhythm through a single transient anal pore
Authors: L. Tamm Sidney
Published: January 2019

Defecation in the ctenophoreMnemiopsis leidyiis a stereotyped sequence of effector responses that occur with a regular ultradian rhythm. Time intervals between repeated defecations of individual animals depend on body size, ranging from ~10 min in small larvae to ~1 hr in large adults. New features and corrections of previous reports of the gastrovascular system during and between defecations are described in detail by video microscopy. Contrary to the scientific literature, the defecating organ of the excretory complex is just one of the two anal canals which possesses the animal’s only anal pore. The anal pore is not visible as a permanent structure as depicted in textbooks, but appears at defecation and disappears afterward. DIC microscopy reveals that opening and closing of the anal pore resemble a reversible ring of tissue fusion between apposed endodermal and ectodermal layers at the aboral end.Mnemiopsisthus appears to have an intermittent anus and therefore an intermittent through-gut that reoccur at regular intervals. The temporality of a visible anal pore inMnemiopsisis novel, and may shed light on the evolution of a permanent anus and through-gut in animals. In addition, mirror image dimorphism of the diagonal anal complex occurs in larval ctenophores but not in adults, indicating developmental flexibility in diagonal symmetry of the anal complex.
Neural circuitry of dialects through social learning in Drosophila
Authors: Kacsoh Balint Z , Bozler Julianna , Hodge Sassan , Bosco Giovanni
Published: January 2019

Drosophila species communicate the presence of parasitoid wasps to naïve individuals. This observation suggests a rudimentary Drosophila social structure. Communication between closely related species is efficient, while more distantly related species exhibit a dampened, partial communication. Partial communication between some species is enhanced following a period of cohabitation, suggesting that species-specific variations in communication “dialects” can be learned through social interactions. However, it remains unclear as to how the behavioral acquisition and how learning dialects is facilitated by distinct brain regions. In this study, we have identified six regions of the Drosophila brain essential for dialect learning, including the odorant receptor Or69a. Furthermore, we pinpoint subgroups of neurons such as motion detecting neurons in the optic lobe, layer 5 of the fan-shaped body, and the D glomerulus in the antennal lobe, where activation of each are necessary for dialect learning. These results demonstrate that Drosophila can display complex social behaviors with inputs to multiple regions of the Drosophila brain and unique subsets of neurons that must integrate olfactory, visual and motion cues.
Genetic risk for major depressive disorder and loneliness in gender-specific associations with coronary artery disease
Authors: Dennis Jessica , Sealock Julia , Levinson Rebecca T , Farber-Eger Eric , Franco Jacob , Fong Sarah , Straub Peter , Hucks Donald , Linton MacRae F , Song Wen-Liang , Fontanillas Pierre , Elson Sarah L , Ruderfer Douglas , Abdellaoui Abdel , Sanchez-Roige Sandra , Palmer Abraham A , Boomsma Dorret I , Cox Nancy J , Chen Guanhua , Mosley Jonathan D , Wells Quinn S , Davis Lea K
Published: January 2019

Importance

Epidemiological evidence indicates that major depressive disorder (MDD) and loneliness both reduce life expectancies, but mechanisms underlying the excess morbidity are unclear. Electronic health records (EHRs) linked to genetic data offer new opportunities to address this knowledge gap.

Objective

To determine the medical morbidity pattern associated with genetic risk factors for MDD and loneliness, two common psychological traits with adverse health outcomes.

Design

Phenome-wide association study using EHRs spanning 1990 to 2017 from the Vanderbilt University Medical Center biobank, BioVU. Top associations with coronary artery disease (CAD) were replicated in the Atherosclerosis Risk in Communities (ARIC) cohort.

Setting

Hospital-based EHR study, with replication in a population-based cohort study.

Participants

18,385 genotyped adult patients in BioVU. Replication in ARIC included 7,197 genotyped participants. All participants were of European ancestry.

Exposures

Polygenic scores for MDD and loneliness were developed for each individual using previously published meta-GWAS summary statistics.

Main Outcomes and Measures

The phenome-wide association study included 882 clinical diagnoses ascertained via billing codes in the EHR. ARIC included 1598 incident CAD cases.

Results

BioVU patients had a median EHR length of 9.91 years. In the phenome-wide association study, polygenic scores for MDD and loneliness were significantly associated with psychiatric and cardiac phenotypes. Targeted analyses of CAD in 3,893 cases and 4,197 controls in BioVU found odds ratios of 1.11 (95% CI, 1.04-1.18; P=8.43×10−4) and 1.13 (95% CI, 1.07-1.20; P=4.51×10−6) per 1-SD increase in the polygenic scores for MDD and loneliness, respectively. Comparable hazard ratios in ARIC were 1.07 (95% CI, 0.99-1.14; P=0.07) and 1.07 (1.01-1.15; P=0.03). Across both studies, the increased risk persisted in women after adjusting for multiple conventional risk factors, a polygenic score for CAD, and psychiatric symptoms (available in BioVU). Controlling for genetic risk factors shared between MDD and loneliness, the polygenic score for loneliness conditioned on MDD remained associated with CAD risk, but the polygenic score for MDD conditioned on loneliness did not.

Conclusions and Relevance

Genetic risk factors for MDD and loneliness act pleiotropically to increase CAD risk in women. Continued research into the biological and clinical connections between the heart and mind is warranted.
ELECTOR: Evaluator for long reads correction methods
Authors: Marchet Camille , Morisse Pierre , Lecompte Lolita , Lefebvre Arnaud , Lecroq Thierry , Peterlongo Pierre , Limasset Antoine
Published: January 2019

Motivation

In the last few years, the error rates of third generation sequencing data have been capped above 5%, including many insertions and deletions. Thereby, an increasing number of long reads correction methods have been proposed to reduce the noise in these sequences. Whether hybrid or self-correction methods, there exist multiple approaches to correct long reads. As the quality of the error correction has huge impacts on downstream processes, developing methods allowing to evaluate error correction tools with precise and reliable statistics is therefore a crucial need. Since error correction is often a resource bottleneck in long reads pipelines, a key feature of assessment methods is therefore to be efficient, in order to allow the fast comparison of different tools.

Results

We propose ELECTOR, a reliable and efficient tool to evaluate long reads correction, that enables the evaluation of hybrid and self-correction methods. Our tool provides a complete and relevant set of metrics to assess the read quality improvement after correction and scales to large datasets. ELECTOR is directly compatible with a wide range of state-of-the-art error correction tools, using whether simulated or real long reads. We show that ELECTOR displays a wider range of metrics than the state-of-the-art tool, LRCstats, and additionally importantly decreases the runtime needed for assessment on all the studied datasets.

Availability

ELECTOR is available at https://github.com/kamimrcht/ELECTOR.

Contact

camille.marchet@univ-lille.fr or pierre.morisse2@univ-rouen.fr
Longitudinal single cell profiling of regulatory T cells identifies IL-33 as a driver of tumor immunosuppression
Authors: Li Amy , Herbst Rebecca H. , Canner David , Schenkel Jason M. , Smith Olivia C. , Kim Jonathan Y. , Hillman Michelle , Bhutkar Arjun , Cuoco Michael S. , Rappazzo C. Garrett , Rogers Patricia , Dang Celeste , Rozenblatt-Rosen Orit , Cong Le , Birnbaum Michael , Regev Aviv , Jacks Tyler
Published: January 2019

Regulatory T cells (Tregs) can impair anti-tumor immune responses and are associated with poor prognosis in multiple cancer types. Tregs in human tumors span diverse transcriptional states distinct from those of peripheral Tregs, but their contribution to tumor development remains unknown. Here, we used single cell RNA-Seq to longitudinally profile conventional CD4+ T cells (Tconv) and Tregs in a genetic mouse model of lung adenocarcinoma. Tissue-infiltrating and peripheral CD4+ T cells differed, highlighting divergent pathways of activation during tumorigenesis. Longitudinal shifts in Treg heterogeneity suggested increased terminal differentiation and stabilization of an effector phenotype over time. In particular, effector Tregs had enhanced expression of the interleukin 33 receptor ST2. Treg-specific deletion of ST2 reduced effector Tregs, increased infiltration of CD8+ T cells into tumors, and decreased tumor burden. Our study shows that ST2 plays a critical role in Treg-mediated immunosuppression in cancer, highlighting new potential paths for therapeutic intervention.
Evaluation of liver protective activity ofMoringa oleiferabark extract in paracetamol induced hepatotoxicity in rats
Authors: Islam Rajibul , Alam Md. Jahir
Published: January 2019

Background

Moringa oleiferahas been used in folk medicine to alleviate several diseases. In the present study, ethanolic extract ofMoringa oleiferabark has been investigated to study its potential on paracetamol induced hepatotoxicity on model rats.

Methods

Rats (150–200 gm) were divided into 5 groups containing 6 animals each. Acute hepatotoxicity was induced by paracetamol (600 mg/kg body weight) administered once daily for one week whereas the extract of investigated plant was given orally throughout the whole experiment at 250 and 500mg/kg body weight. Silymarin (100mg/kg body weight) was given orally as standard hepatoprotective drug. The level of hepatic injury recovery was determined by the estimation of liver enzymes like SGPT, SGOT, ALP, Bilirubin, Total protein and Albumin.

Results

Treatment with MO extract as well as standard hepatoprotective agent silymarin ameliorated the increased plasma levels of these hepatic enzymes and indicated the hepatoprotective potential of the extract.

Conclusion

The biochemical parameters provide evidence that the ethanolic extract of ofMoringa oleiferabark has shown hepatoprotective activity.
Budding yeast centromeric DNA and A+T rich bacterial DNA can function as centromeres in the fission yeast Schizosaccharomyces pombe
Authors: Barbosa Anne C , Xu Zhengyao , Karari Kazhal , Hauf Silke , Brown William RA
Published: January 2019

Eukaryotic centromeric DNA is famously variable in evolution but currently, this cannot be reconciled with the conservation of eukaryotic centromere function. It seems likely that centromeric DNA from different organisms contains conserved functionally important features but the identity of these features is unknown. The point centromeres of the budding yeast Saccharomyces cerevisiae and the regional centromeres of the fission yeast Schizosaccharomyces pombe are separated by 350 million years of evolution and are canonical examples of the paradoxical relationship1 between centromeric DNA sequence and function. We have established a centromere-replacement strategy in Schizosaccharomyces pombe in order to resolve this paradox experimentally. Centromere-replacement shows that an A+T rich bacterial DNA sequence has weak centromere function and that elements of the Saccharomyces cerevisiae centromere embedded in short sequences from the non-centromeric S. pombe wee1 gene function almost as well as native S. pombe centromeric DNA. These observations demonstrate that determinants of centromere function are held in common by the budding and fission yeasts and that A+T rich DNA is both necessary and sufficient for function in S. pombe. Given the evolutionary distance between these yeasts, it is likely that A+T rich DNA has centromere function in a wide variety of eukaryotes. Centromere-replacement uses unidirectional serine recombinases that work well in many organisms2 3 and our experimental strategy should allow this idea to be tested in other eukaryotes.
All-optical interrogation of a direction selective retinal circuit by holographic wave front shaping
Authors: Spampinato G.L.B , Ronzitti E. , Zampini V. , Ferrari U. , Trapani F. , Khabou H. , Dalkara D. , Picaud S. , Papagiakoumou E. , Marre O. , Emiliani V.
Published: January 2019

Direction selective (DS) ganglion cells (GC) in the retina maintain their tuning across a broad range of light levels. Yet very different circuits can shape their responses from bright to dim light, and their respective contributions are difficult to tease apart. In particular, the contribution of the rod bipolar cell (RBC) primary pathway, a key player in dim light, is unclear. To understand its contribution to DSGC response, we designed an all-optical approach allowing precise manipulation of single retinal neurons. Our system activates single cells in the bipolar cell (BC) layer by two-photon (2P) temporally focused holographic illumination, while recording the activity in the ganglion cell layer by 2P Ca2 imaging. By doing so, we demonstrate that RBCs provide an asymmetric input to DSGCs, suggesting they contribute to their direction selectivity. Our results suggest that every circuit providing an input to direction selective cells can generate direction selectivity by itself. This hints at a general principle to achieve robust selectivity in sensory areas.
Disassembly of actin and keratin networks by Aurora B kinase at the midplane of cleavingXenopus laeviseggs
Authors: Field Christine M. , Pelletier James F. , Mitchison Timothy J.
Published: January 2019

We investigated how bulk cytoplasm prepares for cytokinesis inXenopus laeviseggs, which are large, rapidly dividing cells. The egg midplane is demarcated by Chromosomal Passenger Complex (CPC) localized on microtubule bundles between asters. Using an extract system and intact eggs we found that local kinase activity of the AURKB subunit of the CPC caused disassembly of F-actin and keratin between asters, and local softening of the cytoplasm as assayed by flow patterns. Beads coated with active CPC mimicked aster boundaries and caused AURKB-dependent disassembly of F-actin and keratin that propagated ~40 μm without microtubules, and much farther with microtubules present, due to CPC auto-activation. We propose that active CPC at aster boundaries locally reduces cytoplasmic stiffness by disassembling actin and keratin networks. This may help sister centrosomes move apart after mitosis, prepare a soft path for furrow ingression and/or release G-actin to build the furrow cortex.