bluuebunny/crossref_metadata_2025 huggingface dataset:
IWR-1 Inhibits Collagen-Induced Platelet Activation and Protects against Thrombogenesis
Authors: Wang Wei , Lai Songqing , Xiao ZiJin , Yan Haiyue , Li Yongxi , Zhang Ye , Wu Yanqing , Wang Ling
Published: March 2019

Platelets play a crucial role in haemostasis and several pathophysiological processes. Collagen is a main initiator for platelet activation and aggregation. Given that Wnt signalling negatively regulates platelet function, and IWR-1 (a small molecule inhibitor for Wnt signalling) has the potential of inhibiting collagen synthesis, it is essential to investigate whether IWR-1 regulates collagen-induced platelet activation and protects against thrombogenesis. In the present study we found that IWR-1 pretreatment effectively suppressed collagen-induced platelet aggregation in a dose-dependent manner. In addition, IWR-1 also resulted in a decrease of P-selectin and phosphatidylserine surface exposure using fluorescence-activated cell sorting analysis. In vitro studies further revealed that IWR-1 had a negative effect on integrin a2β1 activation and platelet spreading. More importantly, the results from in vivo studies showed that IWR-1 exhibited a robust bleeding diathesis in the tail-bleeding assay and a prolonged occlusion time in the FeCl3-induced carotid injury model. Taken together, current results demonstrate that IWR-1 could effectively block collagen-induced platelet activity in vitro and in vivo, and suggest its candidacy as a new antiplatelet agent.
A Cluster of Pediatric Invasive Group A Streptococcus Disease in Melbourne, Australia, Coinciding with a High-Burden Influenza Season
Authors: Wong Nicole X. , Crawford Nigel W. , Oliver Jane , McMinn Alissa , Ching Natasha S. , Baker Ciara , Smeesters Pierre R. , Daley Andrew J. , Steer Andrew C.
Published: March 2019

Background Invasive group A streptococcal disease (IGAS) carries significant morbidity and mortality in children. Fluctuations in disease incidence are well documented. However, the modulating factors that contribute to these changes remain unclear. Prospective monitoring of IGAS cases in Victoria, Australia, showed an increased number of cases in 2017, coinciding with a peak of influenza illness.

Methods Children identified to have IGAS are prospectively monitored in Melbourne through a disease surveillance network. Data on their presentation, investigations, and clinical course are collected. An increased number of cases identified between June 1, 2017, and October 31, 2017, have been retrospectively analyzed.

Results We identified 22 cases of pediatric IGAS during the study period. Increased case detection occurred during a period of increased influenza disease. Of 11 children in our cohort who underwent respiratory viral testing, 4 were confirmed to have concurrent respiratory tract illnesses, and 2 were confirmed to have influenza.
Free-Flap Reconstruction of the Tongue
Authors: Vincent Aurora , Kohlert Scott , Lee Thomas , Inman Jared , Ducic Yadranko
Published: March 2019

The tongue is paramount to natural speech and swallowing, and good tongue function is important in the overall quality of life. Autologous free-flap reconstruction of the tongue after glossectomy allows for adequate speech, swallow, and quality-of-life outcomes in a majority of patients. Herein, the authors review autologous free-flap reconstruction of the tongue with a focus on different flap options, speech and swallow outcomes, quality-of-life outcomes, and factors that affect how patients perform after tongue reconstruction.
Free-Flap Reconstruction of Skull Base and Orbital Defects
Authors: Wang Weitao , Vincent Aurora , Sokoya Mofiyinfolu , Kohlert Scott , Kadakia Sameep , Ducic Yadranko
Published: March 2019

Orbital and anterior skull base defects present a significant challenge for reconstruction due to the complexity of the anatomy and the need for separation of intracranial and extracranial contents in this area. While endoscopic techniques have revolutionized the treatment of many anterior skull base defects, microvascular free tissue transfer is a viable option for large volume defects not suitable for traditional open approaches or for cases where endoscopic techniques have failed. The various free tissue transfer techniques for anterior skull base and orbit, as well as the advantages and disadvantages, are reviewed.
Acetaminophen Hepatotoxicity
Authors: Ramachandran Anup , Jaeschke Hartmut
Published: March 2019

Acetaminophen (APAP) is one of the most popular and safe pain medications worldwide. However, due to its wide availability, it is frequently implicated in intentional or unintentional overdoses where it can cause severe liver injury and even acute liver failure (ALF). In fact, APAP toxicity is responsible for 46% of all ALF cases in the United States. Early mechanistic studies in mice demonstrated the formation of a reactive metabolite, which is responsible for hepatic glutathione depletion and initiation of the toxicity. This insight led to the rapid introduction of N-acetylcysteine as a clinical antidote. However, more recently, substantial progress was made in further elucidating the detailed mechanisms of APAP-induced cell death. Mitochondrial protein adducts trigger a mitochondrial oxidant stress, which requires amplification through a MAPK cascade that ultimately results in activation of c-jun N-terminal kinase (JNK) in the cytosol and translocation of phospho-JNK to the mitochondria. The enhanced oxidant stress is responsible for the membrane permeability transition pore opening and the membrane potential breakdown. The ensuing matrix swelling causes the release of intermembrane proteins such as endonuclease G, which translocate to the nucleus and induce DNA fragmentation. These pathophysiological signaling mechanisms can be additionally modulated by removing damaged mitochondria by autophagy and replacing them by mitochondrial biogenesis. Importantly, most of the mechanisms have been confirmed in human hepatocytes and indirectly through biomarkers in plasma of APAP overdose patients. The extensive necrosis caused by APAP overdose leads to a sterile inflammatory response. Although recruitment of inflammatory cells is necessary for removal of cell debris in preparation for regeneration, these cells have the potential to aggravate the injury. This review touches on the newest insight into the intracellular mechanisms of APAP-induced cells death and the resulting inflammatory response. Furthermore, it discusses the translation of these findings to humans and the emergence of new therapeutic interventions.
Management of Pathologic Fractures Around the Hip: Part 1–Femur
Authors: Auran Richard L. , Duran Michael D. , de Comas Amalia M. , Jacofsky David J.
Published: March 2019

Evaluation and management of suspected pathologic fractures, secondary to metastatic disease, require a comprehensive understanding of the underlying disease process and a multidisciplinary treatment approach. Recognition of a pathologic fracture can be challenging, and the diagnosis today remains often missed, but is necessary for appropriate care. The incidence of cancer in the United States is on the rise, and with advances in medical and surgical care the prevalence of cancer is increasing as well. This will result in a similar trend of increased incidence and prevalence of metastatic disease requiring treatment from orthopaedic surgeons. The proximal femur is the most common location for metastatic lesions in the appendicular skeleton, and as such sees a disproportionate number of pathologic fractures. This site of injury is particularly challenging to manage due to the transmission of high forces through this region during ambulation. A combination of adjunct therapies and surgical intervention will maximize the outcomes for these patients. Obtaining a tissue diagnosis, especially in the setting of a solitary bone lesion, is a crucial and required early step in this process.
Active microswimmers in a finite two dimensional trap: The role of hydrodynamic interaction
Authors: Debnath Tanwi , Li Yunyun , Ghosh Pulak K. , Marchesoni Fabio
Published: March 2019

We investigate the dynamics of two identical artificial active particles suspended in a free-standing fluid film with a trap of finite radius in an acoustic tweezer. In the two dimensional Oseen approximation, their hydrodynamic coupling is long ranged, which naturally raises the question as under what conditions they can simultaneously reside in the trap. We determine a critical value of the hydrodynamic coupling below which that happens and study the ensuing active pair dynamics inside the trap. For larger couplings, only one particle sits in the trap, while the other diffuses freely until it eventually replaces the particle in the trap. Such a mechanism repeats itself with a characteristic noise-dependent mean residence-retrapping time.
Definition of the interlayer interaction type in magnetic multilayers analyzing the shape of the ferromagnetic resonance peaks
Authors: Udalov O. G. , Fraerman A. A. , Demidov E. S.
Published: March 2019

We present a theoretical study of the ferromagnetic resonance in a system of two coupled magnetic layers. We show that an interaction between the layers leads to the occurrence of the so-called Fano resonance. The Fano resonance changes the shape of the ferromagnetic resonance peak. It introduces a peak asymmetry. The asymmetry type is defined by the sign of the interaction between the magnetic layers. Therefore, by studying the shape of the ferromagnetic resonance peaks, one can define the type of the interlayer coupling (ferromagnetic or antiferromagnetic).
Interactions between H+ band EMIC waves and radiation belt relativistic electrons: Comparisons of test particle simulations with quasi-linear calculations
Authors: Fu Song , Ni Binbin , Tao Xin , Ge Yasong , Liu Jiang , Lou Yuequn , Gu Xudong , Cao Xing , Xiang Zheng , Zhang Wenxun , Zhang Yang
Published: March 2019

We develop a general 3-D relativistic test particle (TP) simulation code to examine the trajectories and pitch angle variations of test electrons. We investigate the conditions when the electrons transit broadband, parallel propagating H+ band electromagnetic ion cyclotron (EMIC) waves to find whether the classical quasilinear theory (QLT) can be applied to interactions between H+ band EMIC waves and radiation belt relativistic (and ultra-relativistic) electrons. We find that to reach good consistency between TP scattering coefficients and QLT calculations, the wave-particle resonant interaction time (which indicates the time of particles traveling in the wave fields and being resonant with the wave fields) must be carefully calculated to ensure the validity of the linear diffusion process. This wave-particle resonant interaction time depends largely on the wave amplitude, the bandwidth, and the initial parameters of electrons for TP simulations; once the time of electrons traveling in the wave fields becomes large enough when the pitch angles of electrons scattered by wave fields reach the maximal value limited by the resonance condition and cannot be diffused any longer, the linear diffusion process of particles defined by QLT will not be valid any longer. When the resonant electrons start to travel through the wave field, they undergo the linear diffusion process resulting from the pitch angle scattering by the H+ band EMIC wave field. As the time of traveling in the wave fields increases, the test electrons will suffer effective pitch angle scattering and the pitch angles of these electrons will reach the maximum value limited by the resonance condition, which is determined by the wave and electron parameters. These electrons are then reflected by the wave fields and the linear wave-particle interactions defined by QLT will not be valid anymore. This kind of wave-particle interaction subsequently introduces considerable deviation of TP diffusion coefficients from those predicted by QLT calculations. Our results demonstrate that the general validity of QLT in describing how broadband EMIC waves affect radiation belt relativistic electrons is highly related to the time of electron traveling in the wave fields, which tends to increase for smaller wave power and broader wave frequency spectra.
Growth and characterization of β-Ga2O3 thin films on different substrates
Authors: Hao S. J. , Hetzl M. , Schuster F. , Danielewicz K. , Bergmaier A. , Dollinger G. , Sai Q. L. , Xia C. T. , Hoffmann T. , Wiesinger M. , Matich S. , Aigner W. , Stutzmann M.
Published: March 2019

β-Ga2O3 thin films were grown on the substrates of sapphire, GaN, and single crystals of β-Ga2O3, using plasma-assisted molecular beam epitaxy. By varying deposition conditions, pure-phase epitaxial β-Ga2O3 thin films were obtained, and the crystal quality of the as-grown films was optimized. A systematic characterization and a detailed analysis were performed on the films, including the nucleation process, surface morphology, crystal quality, thermal stability, as well as electrical and optical properties. Optical absorption was investigated using photothermal deflection spectroscopy, which provides detailed information about sub-gap optical absorption. Photocurrent measurements indicated a pronounced persistent photo-conductivity of β-Ga2O3. A blue-UV emission with an energy of 3–3.5 eV was observed by cathodoluminescence spectroscopy. The Fermi level position of the as-grown film was determined based on temperature-dependent electrical conductivity measurements. It is proposed that oxygen vacancies in the film form a defect band at around Ec-0.8 eV that pins the Fermi level and is related to the observed photocurrent and cathodoluminescence characteristics.
XFEM analysis of the fracture behavior of bulk superconductor in high magnetic field
Authors: Chen Hao , Yong Huadong , Zhou Youhe
Published: March 2019

A bulk superconductor in a high magnetic field is subjected to a large electromagnetic force, which can cause crack propagation and damage the bulk. In this paper, we study the fracture behavior of the GdBCO bulk superconductor under a large electromagnetic force based on the Extended Finite Element Method (XFEM). The critical state Kim model and H-formulations are used to obtain the electromagnetic force of a bulk superconductor in the magnetic field first. Second, the Stress Intensity Factor (SIF) of the bulk superconductor for various cracks under the electromagnetic force is presented. Numerical results show that the SIF depends not only on crack angle and length but also on the width of the bulk. For the inclined crack with a large crack angle, with the crack length increase, the SIFs increase first and decrease, while for a small crack angle, the SIFs decrease with the crack length increase. For the kinked crack, the SIFs decrease with the crack length increase. With the XFEM, the growth of the inclined and kinked cracks in the bulk superconductor during field cooling is presented. The crack propagation paths are dependent on the size of the bulk and different for two crack problems. In the process of crack propagation, the propagation path has a certain degree of deflection angle compared with the initial crack.
General coupling model for electromigration and one-dimensional numerical solutions
Authors: Cui Zhen , Fan Xuejun , Zhang Guoqi
Published: March 2019

A three-dimensional (3D) general coupling model for electromigration has been developed with the use of the mass conservation equation. The flux terms that include concentration gradient, electron wind force, stress migration, and thermal migration are considered. The constitutive equation for the electromigration strain has been derived. Then, the governing equations for one-dimensional (1D) metal lines are obtained for both totally fixed and stress-free mechanical boundary conditions. The numerical results reveal that the hydrostatic stress is significantly lower than the predicted results in the existing literature for the totally fixed configuration. Extensive discussions are presented to provide the explanations of such difference. The vacancy concentration gradient plays an important role in formulating electromigration problems. The current-driven flux can be entirely balanced by the concentration gradient that acts as an opposing force during electromigration under a stress-free condition in steady-state. The new solutions of the critical threshold jL, the product of current density, and metal line length are obtained in terms of vacancy concentration. As electromigration is eventually determined by the void growth, the critical vacancy concentration is used to reanalyze Blech's experiment data. The theoretical predictions are consistent with the experimental observations.
Improved exchange bias and blocking temperature of PtCr/PtMn bilayer antiferromagnets
Authors: Saito Masamichi , Koike Fumihito
Published: March 2019

Herein, we investigated exchange coupling in PtCr/CoFe, PtCr/PtMn/CoFe, and PtMn/CoFe film structures, demonstrating that Pt51Cr49(30 nm)/Co90Fe10(10 nm), Pt51Cr49(27.2 nm)/Pt50Mn50/(2.8 nm)/Co90Fe10(10 nm), and Pt50Mn50(30 nm)/Co90Fe10(10 nm) structures annealed at 350 °C for 20 h in a 10-kOe field featured unidirectional anisotropy constants (Jk) of 0.09, 0.56, and 0.32 erg/cm2, respectively. In the case of the Ni50Fe12Cr38(4 nm)/Pt51Cr49(30 − X nm)/Pt50Mn50(X nm)/Co90Fe10(10 nm)/Ta(10 nm) [X = 0–30 nm] film system, Jk linearly and steeply increased with increasing X to reach a maximum of 0.56 erg/cm2 at X = 2.8 nm and then decreased in a complicated nonlinear fashion as X further increased to 30 nm. On the other hand, the blocking temperature of Pt51Cr49(28 nm)/Pt50Mn50/(2 nm)/Co90Fe10(10 nm) was determined as 500 °C and nearly equaled that of Pt51Cr49(30 nm)/Co90Fe10(10 nm), significantly exceeding the value of 400 °C determined for Pt50Mn50(30 nm)/Co90Fe10(10 nm). These results imply that the exchange bias field of the Ni50Fe12Cr38(4 nm)/Pt51Cr49(30 − X nm)/Pt50Mn50/(X nm)/Co90Fe10(10 nm)/Ta(10 nm) system is ultimately determined by the chemical composition and the modification of the antiferromagnetic spin structure at the ferromagnet–antiferromagnet interface, while the blocking temperature is almost entirely determined by the volume fraction of the PtCr component.
Effective diffusivity of microswimmers in a crowded environment
Authors: Brun-Cosme-Bruny Marvin , Bertin Eric , Coasne Benoît , Peyla Philippe , Rafaï Salima
Published: March 2019

The microalga Chlamydomonas Reinhardtii is used here as a model system to study the effect of complex environments on the swimming of micro-organisms. Its motion can be modeled by a run and tumble mechanism so that it describes a persistent random walk from which we can extract an effective diffusion coefficient for the large-time dynamics. In our experiments, the complex medium consists of a series of pillars that are designed in a regular lattice using soft lithography microfabrication. The cells are then introduced in the lattice, and their trajectories within the pillars are tracked and analyzed. The effect of the complex medium on the swimming behavior of microswimmers is analyzed through the measure of relevant statistical observables. In particular, the mean correlation time of direction and the effective diffusion coefficient are shown to decrease when increasing the density of pillars. This provides some basis of understanding for active matter in complex environments.
A water splitting photocatalysis: Blue phosphorus/g-GeC van der Waals heterostructure
Authors: Gao Xu , Shen Yanqing , Ma Yanyan , Wu Shengyao , Zhou Zhongxiang
Published: March 2019

A boom of vertical heterostructures (HTSs) with atomically clean interfaces excited the scientists' enthusiasm in materials science and device engineering. In this letter, we perform the blue phosphorus (BlueP)/graphene-like GeC (g-GeC) HTS by DFT calculations. Direct bandgap for the g-GeC is beneficial for applications in photoelectronics. The energy levels of both water oxidation and reduction are within the bandgaps of the HTS and two separate monolayers, predicting their significant capacity for water splitting reactions. A type-II band alignment is presented for the BlueP/g-GeC HTS, ascribing to the efficient separation of the photogenerated electron–hole pairs. Modulated band edges are obtained by tailoring pH values to achieve the control of photocatalytic properties. Enhanced optical absorption in the visible region is observed for the HTS compared with others' work. These findings suggest that BlueP/g-GeC vdW HTS has promising potential in the field of photovoltaics and photocatalysis.
Track structure simulations of proximity functions in liquid water using the Geant4-DNA toolkit
Authors: Incerti S. , Kyriakou I. , Bordage M. C. , Guatelli S. , Ivanchenko V. , Emfietzoglou D.
Published: March 2019

The mechanistic Monte Carlo modeling of biological effects of ionising radiation at sub-cellular and DNA scale requires the accurate simulation of track structures in the biological medium, commonly approximated as liquid water. The formalism of microdosimetry allows one to describe quantitatively the spatial distribution of energy deposition in the irradiated medium, which is known to relate to the deleterious effects in the irradiated cellular targets. The Geant4-DNA extension of the Geant4 open-source and general-purpose Monte Carlo simulation toolkit has been recently evaluated for the simulation of microdosimetry spectra, allowing, in particular, the calculation of lineal energy distributions. In this work, we extend the microdosimetric functionalities of Geant4-DNA by the development of a new Geant4-DNA example dedicated to the simulation of differential proximity functions. Simulation results are presented for the proximity function of electrons, protons, and alpha particles over a wide energy range using the different physical models of electron interactions available in Geant4-DNA. The influence of sub-excitation processes and electron tracking cut is discussed. Results are compared to literature data when available. As an example, a simple calculation of the relative biological effectiveness (RBE) in the context of the Theory of Dual Radiation Action using the present proximity functions yields up to a factor of 2 variation of the electron RBE in the energy range from 100 eV to 100 keV.
Magnetic and electronic properties of Cr2Ge2Te6 monolayer by strain and electric-field engineering
Authors: Wang Kangying , Hu Tao , Jia Fanhao , Zhao Guodong , Liu Yuyu , Solovyev Igor V. , Pyatakov Alexander P. , Zvezdin Anatoly K. , Ren Wei
Published: March 2019

A two-dimensional ferromagnetic semiconductor Cr2Ge2Te6 (CGT) was recently found to possess extraordinary characteristics and has great potential in the emerging field of spintronics. Using first-principles calculations, we examined the stabilities of this layered system by studying the cleavage energies and phonon dispersion. The ferromagnetic ground state has an in-plane spin polarization and bandgaps of about 0.26 eV by Perdew-Burke-Ernzerhof-van der Waals and 0.91 eV by the Heyd-Scuseria-Ernzerhof functional. Furthermore, we employed strain engineering and an external electric field to control the electronic and magnetic properties. In addition, we studied the magnetic anisotropy energy as well as its modulation under the electric field. We predict the CGT monolayer to be the easy plane ferromagnet, and the perpendicular electric field could affect the ferromagnetic stability along different directions. Our obtained results provide guidance for the potential applications of monolayer CGT for magnetic nanodevices, spintronic, and straintronic applications.
Simulated refraction-enhanced X-ray radiography of laser-driven shocks
Authors: Kar Arnab , Boehly T. R. , Radha P. B. , Edgell D. H. , Hu S. X. , Nilson P. M. , Shvydky A. , Theobald W. , Cao D. , Anderson K. S. , Goncharov V. N. , Regan S. P.
Published: March 2019

Refraction-enhanced x-ray radiography (REXR) is used to infer shock-wave positions of more than one shock wave, launched by a multiple-picket pulse in a planar plastic foil. This includes locating shock waves before the shocks merge, during the early time and the main drive of the laser pulse that is not possible with the velocity interferometer system for any reflector. Simulations presented in this paper of REXR show that it is necessary to incorporate the refraction and attenuation of x rays along with the appropriate opacity and refractive-index tables to interpret experimental images. Simulated REXR shows good agreement with an experiment done on the OMEGA laser facility to image a shock wave. REXR can be applied to design multiple-picket pulses with a better understanding of the shock locations. This will be beneficial to obtain the required adiabats for inertial confinement fusion implosions.
Ultrafast microscopy of the vibrational landscape of a single nanoparticle
Authors: Guillet Yannick , Abbas Allaoua , Ravaine Serge , Audoin Bertrand
Published: March 2019

The vibrational landscape of an ∼250 nm-radius single gold nanoparticle dropped on a silica substrate is imaged with an ultrafast pump-probe experiment in a transient reflectivity configuration. A movie of the picosecond dynamics of the nanoparticle is recorded over 20 ns. A spatially resolved analysis of the spectrum of the transient reflectivity is also achieved. In addition to the axial oscillation of the nanoparticle driven by the normal contact stiffness and to the breathing mode of the nanoparticle, ultrafast microscopy allows us to reveal higher order acoustic eigenmodes otherwise hidden by the noise in single point measurements. These results are confirmed by calculations of the acoustic eigenfrequencies of the nanoparticle. The shear component of the particle surface displacement associated with the higher order modes is of strong interest for probing the elasticity of the surrounding medium in the GHz to THz range.
Realization and characterization of terahertz surface plasmon light capsules
Authors: Li Heting , Wang Xinke , Wang Sen , Sun Wenfeng , Feng Shengfei , Ye Jiasheng , Han Peng , Zhang Yan
Published: March 2019

Surface plasmon waves with unique intensity profiles are important for developing integrated photonic circuits. By organically combining a Bessel-like terahertz (THz) beam in free space and a metallic semicircular slit, we generate a THz surface plasmon light capsule (TSPLC) in simulation and experiment. The TSPLC has a two-dimensional optical barrier on the surface of a metal foil. Furthermore, we propose and theoretically validate the potential use of the TSPLC in refractive index sensing. This work has major implications for manipulating and applying surface plasmon waves.
Inverted scanning microwave microscope for in vitro imaging and characterization of biological cells
Authors: Farina Marco , Jin Xin , Fabi Gianluca , Pavoni Eleonora , di Donato Andrea , Mencarelli Davide , Morini Antonio , Piacenza Francesco , Al Hadi Richard , Zhao Yan , Ning Yaqing , Pietrangelo Tiziana , Cheng Xuanhong , Hwang James C. M.
Published: March 2019

This paper presents an instrument called an inverted scanning microwave microscope (iSMM), which is capable of performing noninvasive and label-free imaging and characterization of intracellular structures of a live cell on the nanometer scale. In particular, the iSMM is sensitive to not only surface structures but also electromagnetic properties up to one micrometer below the surface. Conveniently, the iSMM can be constructed through straightforward conversion of any scanning probe microscope, such as an atomic force microscope and a scanning tunneling microscope, with a simple metal probe to outperform a traditional SMM in terms of ruggedness, bandwidth, sensitivity, and dynamic range. By contrast, the application of the traditional SMM to date has been limited to mainly surface physics and semiconductor technology because the traditional SMM requires a fragile and expensive probe and is incompatible with saline solution or live cells.
Tuning the carrier tunneling in a single quantum dot with a magnetic field in Faraday geometry
Authors: Peng Kai , Wu Shiyao , Xie Xin , Yang Jingnan , Qian Chenjiang , Song Feilong , Sun Sibai , Dang Jianchen , Yu Yang , Xiao Shan , Xu Xiulai
Published: March 2019

We report on an increase in the carrier tunneling time in a single quantum dot (QD) with a magnetic field in Faraday geometry using photocurrent spectroscopy. A nearly 60% increase in hole tunneling time is observed with an applied magnetic field equal to 9 T. For a truncated pyramid QD, the hole tunnels out faster at the lateral edge of the QD due to the reduced barrier height. The magnetic field in Faraday geometry shrinks the hole wave function at the center of the QD plane, which weakens the tunneling at the lateral edge and increases the average tunneling time. This mechanism also works for the electron, but the effect is smaller. The electron wave function is more localized at the center of the QD due to the uniform confining potential; therefore, the relatively weak shrinkage caused by the magnetic field does not reduce the tunneling rate significantly.
Two-photon absorption and saturable absorption of mid-IR in graphene
Authors: Malouf Andrew , Henderson-Sapir Ori , Set Sze , Yamashita Shinji , Ottaway David J.
Published: March 2019

We report on the response of graphene to high intensity mid-IR radiation and show that graphene exhibits saturable absorption and significant two-photon absorption in the spectral region of 1.55 μm to 3.50 μm (0.35 eV to 0.80 eV). We find that the effective modulation depth of multilayer graphene is limited by two-photon absorption, which will affect its performance as a laser mode-locking element. The measured saturation intensities of femtosecond pulses were found to depend on the third power of photon energy when we combined our results with others reported in the literature, while those of longer pulses were found to have a square root dependence.
Viscoelastic planar elongational flow past an infinitely long cylinder
Authors: Gryparis Evgenios A. , Gkormpatsis Spyros D. , Housiadas Kostas D. , Tanner Roger I.
Published: March 2019

Following our previous work [K. D. Housiadas and R. I. Tanner, “Viscoelastic shear flow past an infinitely long and freely rotating cylinder,” Phys. Fluids 30, 073101 (2018)], we study analytically the effect of steady planar elongational flow past an infinitely long circular cylinder using asymptotic methods. The ambient fluid is assumed viscoelastic and modelled with the Upper Convected Maxwell, Oldroyd-B, exponential Phan-Thien and Tanner, Giesekus, and Finite Extensibility Nonlinear Elastic model with the Peterlin approximation constitutive equations under isothermal and creeping flow conditions. The solution for all the dependent variables is expanded as an asymptotic power series with the small parameter being the Weissenberg number, Wi, which is defined as the product of the single relaxation time of the fluid times the constant rate of elongation. The resulting sequence of equations is solved analytically up to fourth order in the Weissenberg number. The solution derived here is the first analytical result in the literature for the planar elongational flow of viscoelastic fluids past a cylinder. It reveals the effect of viscoelasticity and all the relevant rheological parameters on the flow variables and the extensional viscosity of the fluid.
Role of contacts in long-range protein conductance
Authors: Zhang Bintian , Song Weisi , Pang Pei , Lai Huafang , Chen Qiang , Zhang Peiming , Lindsay Stuart
Published: March 2019

Significance

The measured electronic properties of proteins are known to depend critically on contacts, although little is known at the single-molecule level. Here, we have measured the conductance of single-protein molecules in their natural aqueous environment, but in conditions where no ion current flows, finding large conductances (nanosiemens) over long paths (many nanometers) when the protein is tethered by chemical contacts formed by binding-specific ligands. This provides a method for forming reliable contacts to proteins, and for the specific detection of single molecules. Thus, single antibodies, such as anti-Ebola IgG, can be detected electrically when they bind a peptide epitope tethered to electrodes, with no background signal from molecules that do not bind specifically.
Global analysis of methionine oxidation provides a census of folding stabilities for the human proteome
Authors: Walker Ethan J. , Bettinger John Q. , Welle Kevin A. , Hryhorenko Jennifer R. , Ghaemmaghami Sina
Published: March 2019

The stability of proteins influences their tendency to aggregate, undergo degradation, or become modified in cells. Despite their significance to understanding protein folding and function, quantitative analyses of thermodynamic stabilities have been mostly limited to soluble proteins in purified systems. We have used a highly multiplexed proteomics approach, based on analyses of methionine oxidation rates, to quantify stabilities of ∼10,000 unique regions within ∼3,000 proteins in human cell extracts. The data identify lysosomal and extracellular proteins as the most stable ontological subsets of the proteome. We show that the stability of proteins impacts their tendency to become oxidized and is globally altered by the osmolyte trimethylamineN-oxide (TMAO). We also show that most proteins designated as intrinsically disordered retain their unfolded structure in the complex environment of the cell. Together, the data provide a census of the stability of the human proteome and validate a methodology for global quantitation of folding thermodynamics.
Aristoteles im Spiegel antiker Biographien
Authors: Flashar Hellmut
Published: March 2019

There is much ancient material about the biographical tradition concerning Aristotle. The analysis in this article
is limited to two very different, but representive Vitae, the Vita of Diogenes Laertius and the
so called Vita Marciana. Both Vitae are also representatives of a certain sight on
Aristotle.
Topological Devil’s staircase in atomic two-leg ladders
Authors: Barbarino S , Rossini D , Rizzi M , Fazio R , Santoro G E , Dalmonte M
Published: March 2019

We show that a hierarchy of topological phases in one dimension—a topological Devil’s staircase—can emerge at fractional filling fractions in interacting systems, whose single-particle band structure describes a topological or a crystalline topological insulator. Focusing on a specific example in the BDI class, we present a field-theoretical argument based on bosonization that indicates how the system, as a function of the filling fraction, hosts a series of density waves. Subsequently, based on a numerical investigation of the low-lying energy spectrum, Wilczek–Zee phases, and entanglement spectra, we show that they are symmetry protected topological phases. In sharp contrast to the non-interacting limit, these topological density waves do not follow the bulk-edge correspondence, as their edge modes are gapped. We then discuss how these results are immediately applicable to models in the AIII class, and to crystalline topological insulators protected by inversion symmetry. Our findings are immediately relevant to cold atom experiments with alkaline-earth atoms in optical lattices, where the band structure properties we exploit have been recently realized.
Steel Traps
Authors: Nelson Dana D
Published: March 2019

Winfried Fluck’s “The Limits of Critique and the Affordances of Form” is hard to argue against. Our field largely rejects individual and collective agency, citing the enormity and ubiquity of the forces arrayed against human actors. And we largely reject the notion of historical progress. Fluck’s conclusion, however, calling on us to think beyond method by critically reevaluating the historical philosophy and aims on which our methods are based, does not offer us a path forward. Others engaging with these questions have offered suggestions. This essay surveys some and hazards that our sense of critical powerlessness in this era of declining English major enrollments may be related to our discipline’s confusion over and/or rejection of what we are actually doing as a discipline. This confusion has emerged from our commitment to theory—in its many directions and manifestations—in place of literature. Ultimately it advocates for a renewed disciplinary and pedagogical investment in literary method and value, and in simultaneously reclaiming a progressive relation to the democracy we have now, animated by the self-critical understanding that our vision of beauty, of good, of personhood, of a democratic future are neither fact nor inevitable, but instead opinions that must contend, always provisionally, with opinions of others, in public.
Interoperable and scalable data analysis with microservices: applications in metabolomics
Authors: Emami Khoonsari Payam , Moreno Pablo , Bergmann Sven , Burman Joachim , Capuccini Marco , Carone Matteo , Cascante Marta , de Atauri Pedro , Foguet Carles , Gonzalez-Beltran Alejandra N , Hankemeier Thomas , Haug Kenneth , He Sijin , Herman Stephanie , Johnson David , Kale Namrata , Larsson Anders , Neumann Steffen , Peters Kristian , Pireddu Luca , Rocca-Serra Philippe , Roger Pierrick , Rueedi Rico , Ruttkies Christoph , Sadawi Noureddin , Salek Reza M , Sansone Susanna-Assunta , Schober Daniel , Selivanov Vitaly , Thévenot Etienne A , van Vliet Michael , Zanetti Gianluigi , Steinbeck Christoph , Kultima Kim , Spjuth Ola
Published: March 2019

Motivation

Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.

Results

We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.

Availability and implementation

The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.

Supplementary information

Supplementary data are available at Bioinformatics online.
VIMCO: variational inference for multiple correlated outcomes in genome-wide association studies
Authors: Shi Xingjie , Jiao Yuling , Yang Yi , Cheng Ching-Yu , Yang Can , Lin Xinyi , Liu Jin
Published: March 2019

Motivation

In genome-wide association studies (GWASs) where multiple correlated traits have been measured on participants, a joint analysis strategy, whereby the traits are analyzed jointly, can improve statistical power over a single-trait analysis strategy. There are two questions of interest to be addressed when conducting a joint GWAS analysis with multiple traits. The first question examines whether a genetic loci is significantly associated with any of the traits being tested. The second question focuses on identifying the specific trait(s) that is associated with the genetic loci. Since existing methods primarily focus on the first question, this article seeks to provide a complementary method that addresses the second question.

Results

We propose a novel method, Variational Inference for Multiple Correlated Outcomes (VIMCO) that focuses on identifying the specific trait that is associated with the genetic loci, when performing a joint GWAS analysis of multiple traits, while accounting for correlation among the multiple traits. We performed extensive numerical studies and also applied VIMCO to analyze two datasets. The numerical studies and real data analysis demonstrate that VIMCO improves statistical power over single-trait analysis strategies when the multiple traits are correlated and has comparable performance when the traits are not correlated.

Availability and implementation

The VIMCO software can be downloaded from: https://github.com/XingjieShi/VIMCO.

Supplementary information

Supplementary data are available at Bioinformatics online.
ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline
Authors: Tahir Ul Qamar Muhammad , Zhu Xitong , Xing Feng , Chen Ling-Ling
Published: March 2019

Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity.

Availability and implementation

The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Populism of Online Communities: Constructing the Boundary Between “Blameless” People and “Culpable” Others
Authors: Hameleers Michael
Published: March 2019

Populism has become prevalent all across the globe. To date, however, we know too little about the ways in which populist discourse is constructed by citizens on social media. To advance the field, this study draws on a qualitative content analysis of Facebook posts by ordinary citizens in the Netherlands. The results indicate that Facebook offers a discursive opportunity structure for Dutch citizens to vent their populist discontent and to interact with like-minded others. Online populist discourse on Facebook is hostile and uncivil, predominately targeted at the elites and marginalized groups in society. By providing insights into how ordinary citizens construct the boundary between “us” and “them,” this article enhances our understanding of the construction of citizens’ populist discourse on social network sites (SNSs), and how these expressions contradict the principles of democratic communication.
Associations between Neighborhood SES and Functional Brain Network Development
Authors: Tooley Ursula A , Mackey Allyson P , Ciric Rastko , Ruparel Kosha , Moore Tyler M , Gur Ruben C , Gur Raquel E , Satterthwaite Theodore D , Bassett Danielle S
Published: March 2019

Higher socioeconomic status (SES) in childhood is associated with stronger cognitive abilities, higher academic achievement, and lower incidence of mental illness later in development. While prior work has mapped the associations between neighborhood SES and brain structure, little is known about the relationship between SES and intrinsic neural dynamics. Here, we capitalize upon a large cross-sectional community-based sample (Philadelphia Neurodevelopmental Cohort, ages 8–22 years, n = 1012) to examine associations between age, SES, and functional brain network topology. We characterize this topology using a local measure of network segregation known as the clustering coefficient and find that it accounts for a greater degree of SES-associated variance than mesoscale segregation captured by modularity. High-SES youth displayed stronger positive associations between age and clustering than low-SES youth, and this effect was most pronounced for regions in the limbic, somatomotor, and ventral attention systems. The moderating effect of SES on positive associations between age and clustering was strongest for connections of intermediate length and was consistent with a stronger negative relationship between age and local connectivity in these regions in low-SES youth. Our findings suggest that, in late childhood and adolescence, neighborhood SES is associated with variation in the development of functional network structure in the human brain.
The quality of employment in the early labour market experience of young Europeans
Authors: Berloffa Gabriella , Matteazzi Eleonora , Şandor Alina , Villa Paola
Published: March 2019

This paper presents a new approach to evaluating individuals’ employment quality, considering the evolution of individuals’ employment conditions over a period of time, instead of the quality of jobs held at a point in time. In particular, we present a new definition of employment quality, based on four dimensions: employment security, income security, income success and occupational success. Using EU-SILC data, we analyse the early labour market experience of young adults and the extent to which the achievement of employment quality around five years after leaving education varies according to gender, education and labour market institutions. Our findings suggest that there is still a pressing need to enhance women’s chances of remaining continuously in employment and to move up in the labour income distribution. Stricter rules on the use of temporary contracts appear to improve youth employment prospects in general, whereas a more stringent regulation of individual dismissals seems to generate some difficulties for high-school and university graduates.
Sutured and sutureless repair of postinfarction left ventricular free-wall rupture: a systematic review
Authors: Matteucci Matteo , Fina Dario , Jiritano Federica , Blankesteijn W Matthijs , Raffa Giuseppe Maria , Kowalewski Mariusz , Beghi Cesare , Lorusso Roberto
Published: March 2019

Postinfarction left ventricular free-wall rupture is a potentially catastrophic event. Emergency surgical intervention is almost invariably required, but the most appropriate surgical procedure remains controversial. A systematic review, from 1993 onwards, of all available reports in the literature about patients undergoing sutured or sutureless repair of postinfarction left ventricular free-wall rupture was performed. Twenty-five studies were selected, with a total of 209 patients analysed. Sutured repair was used in 55.5% of cases, and sutureless repair in the remaining cases. Postoperative in-hospital mortality was 13.8% in the sutured group, while it was 14% in the sutureless group. A trend towards a higher rate of in-hospital rerupture was observed in the sutureless technique. The most common cause of in-hospital mortality (44%) was low cardiac output syndrome. In conclusion, sutured and sutureless repair for postinfarction left ventricular free-wall rupture showed comparable in-hospital mortality. However, because of the limited number of patients and the variability of surgical strategies in each reported series, further studies are required to provide more consistent data and lines of evidence.
A role for the OsHKT 2;1 sodium transporter in potassium use efficiency in rice
Authors: Hartley Tom N , Thomas Alice S , Maathuis Frans J M
Published: March 2019

Genome-wide association studies were used to analyse potassium use efficiency in rice. Novel associations were found along with a role for sodium replacement via the OsHKT2;1 sodium transporter.