bluuebunny/crossref_metadata_2025 huggingface dataset:
Physics of the laser-plasma interface in the relativistic regime of interaction
Authors: Svedung Wettervik B. , Marklund M. , Gonoskov A.
Published: May 2019

The reflection of intense laser radiation from solids appears as a result of relativistic dynamics of the electrons driven by both incoming and self-generated electromagnetic fields at the periphery of the emerging dense plasma. In the case of highly relativistic motion, electrons tend to form a thin oscillating layer, which makes it possible to model the interaction and obtain the temporal structure of the reflected radiation. The modeling reveals the possibility and conditions for producing singularly intense and short extreme ultraviolet (XUV) bursts of radiation, which are interesting for many applications. However, the intensity and duration of the XUV bursts, as well as the high-energy end of the harmonic spectrum, depend on the thickness of the layer and its internal structure which are not assessed by such macroscopic modeling. Here, we analyze the microscopic physics of this layer and clarify how its parameters are bound and how this controls the outlined properties of XUV bursts.
Polarization transfer via field sweeping in parahydrogen-enhanced nuclear magnetic resonance
Authors: Eills James , Blanchard John W. , Wu Teng , Bengs Christian , Hollenbach Julia , Budker Dmitry , Levitt Malcolm H.
Published: May 2019

We show that in a spin system of two magnetically inequivalent protons coupled to a heteronucleus such as 13C, an adiabatic magnetic field sweep, passing through zero field, transfers the proton singlet order into magnetization of the coupled heteronucleus. This effect is potentially useful in parahydrogen-enhanced nuclear magnetic resonance and is demonstrated on singlet-hyperpolarized [1-13C]maleic acid, which is prepared via the reaction between [1-13C]acetylene dicarboxylic acid and para-enriched hydrogen gas. The magnetic field sweeps are of microtesla amplitudes and have durations on the order of seconds. We show a polarization enhancement by a factor of 104 in the 13C spectra of [1-13C]maleic acid in a 1.4 T magnetic field.
Direct observation of electrons in microwave vacuum components
Authors: Shaw Z. C. , Garcia A. , Powell M. , Dickens J. C. , Mankowski J. J. , Neuber A. A.
Published: May 2019

Apparatus which is used to directly observe electrons in microwave vacuum components was designed and implemented into a WR-284 like waveguide operated at 2.85 GHz with up to approx. 1 MW power. To generate desired electric field levels for driving secondary emission, the waveguide structure is manipulated by reducing the test section height to 6 mm from the standard WR-284 rectangular waveguide height of 34 mm. Both test and standard sections were operated in the dominant TE10 mode. A 1 mm aperture was cut into the broadside wall of the waveguide section enabling a portion of electrons in the waveguide to enter a properly biased electron multiplier tube mounted atop of the test section. Waveforms are presented showing the direct measurement of electrons, providing a local detection method with nanosecond temporal resolution. Future work will incorporate the test setup for multipactor studies.
On the dynamics of reaction coordinates in classical, time-dependent, many-body processes
Authors: Meyer Hugues , Voigtmann Thomas , Schilling Tanja
Published: May 2019

Complex microscopic many-body processes are often interpreted in terms of so-called “reaction coordinates,” i.e., in terms of the evolution of a small set of coarse-grained observables. A rigorous method to produce the equation of motion of such observables is to use projection operator techniques, which split the dynamics of the observables into a main contribution and a marginal one. The basis of any derivation in this framework is the classical Heisenberg equation for an observable. If the Hamiltonian of the underlying microscopic dynamics and the observable under study do not explicitly depend on time, this equation is obtained by a straightforward derivation. However, the problem is more complicated if one considers Hamiltonians which depend on time explicitly as, e.g., in systems under external driving, or if the observable of interest has an explicit dependence on time. We use an analogy to fluid dynamics to derive the classical Heisenberg picture and then apply a projection operator formalism to derive the nonstationary generalized Langevin equation for a coarse-grained variable. We show, in particular, that the results presented for time-independent Hamiltonians and observables in the study by Meyer, Voigtmann, and Schilling, J. Chem. Phys. 147, 214110 (2017) can be generalized to the time-dependent case.
Soft mode driven local ferroelectric transition in lead-based relaxors
Authors: Nuzhnyy D. , Petzelt J. , Bovtun V. , Kamba S. , Hlinka J.
Published: May 2019

Recently, we have analyzed the complex infrared (IR) and terahertz (THz) response of the relaxor ferroelectric Pb(Mg1/3Nb2/3)O3 (PMN) and suggested a new interpretation of the so-called intermediate temperature T* ≈ 400 K, where the split soft phonon mode undergoes incomplete softening. IR-THz reflectivity was fitted using effective medium approximation, which describes the uniaxially anisotropic response of polar nanodomains (PNDs). It indicated that the response perpendicular to the local polarization undergoes a classical Cochran softening toward T* with the extrapolated low-frequency permittivity obeying the Curie-Weiss (CW) law with TC ≈ T*. In this letter, we report analysis performed in a similar way on the published IR-THz response in closely related relaxor Pb(Mg1/3Ta2/3)O3 and have revealed a similar behavior: The lowest-frequency phonon polarized perpendicularly to the local polarization of PNDs softens below ∼900 K according to the Cochran law and the corresponding low-frequency permittivity obeys the CW law with TC = 340 K ≈ T* and Curie constant C = 1.16 × 105 K. This is comparable to similar parameters for PMN, TC = 380 K ≈ T* and C = 1.7 × 105 K. This explains the high-temperature CW anomaly in the low-frequency dielectric response of both materials and strongly suggests that both relaxors undergo a local ferroelectric phase transition near T* which induces a new polarization component perpendicular to the local random electric field.
Multi-species micropatterning of organic materials by liquid droplet array transfer printing
Authors: Mu Qiancheng , Wang Shuguang , Li Jianping , Zhou Luhao , Li Liqiang , Chi Lifeng , Wang Wenchong
Published: May 2019

Because techniques such as photolithography for inorganic materials are yet to have their equivalents for organic materials, multispecies patterning of functional organic materials at microscale resolution remains in development. This paper reports on a liquid droplet transfer printing method, that is, used for microscale patterning of multispecies materials. A transfer printing instrument is built with a multidimensional micropositioning stage, thereby enabling the technique to be used to pattern different materials on a single surface. The size range of the transferred liquid droplets can be tuned by manipulating the surface wettability and the gap between the surfaces of the sample and the stamp. The developed technique is used to prepare red–green–blue pixel patterns and microlenses integrated with color filters.
A molecular dynamics study of Young’s modulus of multilayer graphene
Authors: Zhong Teng , Li Jiabin , Zhang Kaiwang
Published: May 2019

In this letter, we adopt the molecular dynamics method to study Young’s modulus of 1–19 layers graphene by the nanoindentation theory and the tensile theory. The results show that the number of layers has a strong influence on Young’s modulus using the nanoindentation theory, while Young’s modulus from the tensile theory is not sensitive to the number of layers. Furthermore, we analyze the structure of multilayer graphene (MLG), the loading force-layer number curves, and the breaking force of 1–19 layers graphene based on the nanoindentation theory. The results reveal that MLG transforms into bulk graphite with an increase in the number of layers, which indicates that the nanoindentation theory has reached a limitation. Moreover, we simulate the nanoindentation for circular membranes of different radii and determine the threshold layer of the nanoindentation theory. Our study plays an important role in deepening the understanding of the mechanical properties of MLG and developing the nanoindentation and tensile theories.
Numerical investigation of planar shock wave impinging on spherical gas bubble with different densities
Authors: Zhu Yuejin , Yang Zhiwei , Luo Kai Hong , Pan Jianfeng , Pan Zhenhua
Published: May 2019

The interaction between a planar shock wave and a spherical gas bubble containing sulfur hexafluoride, Refrigerant-22, neon, or helium is studied numerically. Influences of the Atwood number (At) on the evolution of the shock wave and gas bubble are clarified by using high-resolution computational simulations. The results show that the difference in the physical properties between the ambient air and the gas bubble has a significant influence on the evolution of wave pattern and bubble deformation. For the fast/slow configuration (At > 0) in the present study (At = 0.67 and 0.51), the incident shock focuses near the interior right interface to form an outward jet. Besides, the mixedness, average vorticity, and the absolute value of circulation all increase as the Atwood number increases. By contrast, for the slow/fast configuration (At < 0) with At = −0.19 and −0.76, the rotational directions of the vorticities formed at the same position are reversed compared with those in the fast/slow configuration, which induces an inward air jet to impact on the gas bubble from the outside. In addition, the mixedness, average vorticity, and the absolute value of circulation all increase as the Atwood number decreases. Nevertheless, regardless of At > 0 or At < 0, the effective volume of the gas bubble basically decreases when the Atwood number decreases. Hence, on the whole, the Atwood number has a nonmonotonic influence on the evolution of effective volume of gas bubble, mixedness, average vorticity, and circulation simultaneously.
Synchronization of spiral wave patterns in two-layer 2D lattices of nonlocally coupled discrete oscillators
Authors: Bukh A. V. , Schöll E. , Anishchenko V. S.
Published: May 2019

The paper describes the effects of mutual and external synchronization of spiral wave structures in two coupled two-dimensional lattices of coupled discrete-time oscillators. Each lattice is given by a 2D N×N network of nonlocally coupled Nekorkin maps which model neuronal activity. We show numerically that spiral wave structures, including spiral wave chimeras, can be synchronized and establish the mechanism of the synchronization scenario. Our numerical studies indicate that when the coupling strength between the lattices is sufficiently weak, only a certain part of oscillators of the interacting networks is imperfectly synchronized, while the other part demonstrates a partially synchronous behavior. If the spatiotemporal patterns in the lattices do not include incoherent cores, imperfect synchronization is realized for most oscillators above a certain value of the coupling strength. In the regime of spiral wave chimeras, the imperfect synchronization of all oscillators cannot be achieved even for sufficiently large values of the coupling strength.
The role of chemical order in the temperature and composition dependence of the viscosity of liquid alloys
Authors: Meyer N. , Xu H. , Wax J.-F.
Published: May 2019

The influence of the chemical order on the viscosity of liquid alloys is investigated by numerical simulation of molecular dynamics. The temperature and composition dependence is discussed in the case of two contrasting alloys: K-Cs and Li-Bi. These two mixtures have different chemical orders, the first one being random and the second one having strong heterocoordination tendencies. In the case of K-Cs, the behavior of the mixture vs temperature is similar to a pure system and its viscosity varies monotonically with the composition. It is not the case for Li-Bi due to its marked chemical order and the heterocoordination tendency is accompanied by a maximum of the viscosity of the mixture when the composition is changed. For the first time, estimates of the temperature dependence of the viscosity of three representative Li-Bi alloys are given.
Bond dissociation energy of Au2+: A guided ion beam and theoretical investigation
Authors: Owen Cameron J. , Keyes Nicholas R. , Xie Changjian , Guo Hua , Armentrout P. B.
Published: May 2019

Guided ion beam tandem mass spectrometry was employed to measure the kinetic energy-dependent product ion cross sections for the collision induced dissociation of Au2+ with Xe. Gold dimer cations were formed in a glow discharge flow tube source that should create ions in their ground electronic state with thermal internal energies. Analysis of the endothermic kinetic energy dependent cross section accounts for multiple collisions, lifetime effects, and the internal energy of the reactant ion. The value obtained for the bond dissociation energy (BDE) of Au2+ is the first direct measurement and is reported here as 2.20 ± 0.21 eV. For comparison with experimental results, theoretical calculations were also completed at the B3LYP, M06-2X, and coupled cluster singles, doubles, and perturbative triples [CCSD(T,full)] levels of theory using the def2-TZVPPD basis set and at the CCSD(T)-F12/correlation-consistent polarized valence triple zeta basis with pseudopotential level. These results predict a 2Σg+ electronic ground state for Au2+ with BDEs calculated at the B3LYP and both CCSD(T) levels of theory in agreement with the experiment within the uncertainty. Several electronically excited states are also evaluated theoretically.
Electronic structure and thermoelectric properties of Sn1.2−xNbxTi0.8S3 with a quasi-one-dimensional structure
Authors: Suekuni Koichiro , Usui Hidetomo , Qiao Siying , Hashikuni Katsuaki , Hirano Tatsuya , Nishiate Hirotaka , Lee Chul-Ho , Kuroki Kazuhiko , Watanabe Kosuke , Ohtaki Michitaka
Published: May 2019

We report the electronic structure and thermoelectric properties of a tin titanium trisulfide, Sn1.2Ti0.8S3. The crystal structure is composed of infinite “ribbons” of double edge-sharing (Sn4+/Ti4+)S6 octahedra capped by Sn2+. First-principles calculations predict a nearly unidirectional transport of electrons along the ribbon axis for a single crystal and the existence of lone-pair electrons on Sn2+. Experiments on polycrystalline pressed samples demonstrate that Sn1.2Ti0.8S3 exhibits semiconducting temperature dependence of electrical resistivity and a large negative Seebeck coefficient at room temperature. Substitution of Nb5+ for Sn4+ at the octahedral sites increases the electron carrier concentration, leading to an enhancement of the thermoelectric power factor. Anisotropy in the electronic properties is weak because of a weak orientation of the ribbon axis of crystallites in the pressed sample. The lattice thermal conductivity is less than 1 W K−1 m−1 for the pristine and substituted samples, which is attributed to weak bonding between the ribbons via the lone-pair electrons of Sn2+ and to random occupation of Sn4+, Ti4+, and Nb5+ at the octahedral sites.
Theoretical investigation of real-time charge dynamics in open systems coupled to bulk materials
Authors: Wang Rulin , Lu Wencai , Xie Hang , Zheng Xiao , Yam ChiYung
Published: May 2019

Environmental effects play an important role on the electron dynamics of open systems, which provide channels for dissipation of electrons and energy in the systems. However, accurate description of the environment of quantum systems is still challenging. The environment is usually assumed to be a quasi-one-dimensional reservoir in previous theoretical studies. In this work, we focus on systems that are adsorbed on bulk surfaces. Two different approaches to describe the spectral details of the environment are adopted and compared: the Lorentzian decomposition approach and the complex absorbing potential (CAP) approach. To achieve similar accuracy for the spectral density of the environment, it is shown that the Lorentzian decomposition approach is computationally more efficient than the CAP approach, especially for bulk systems. The electron dynamics is then followed using the nonequilibrium Green’s function method for two systems: a modeling bulk surface system and a scanning tunneling microscope junction. Dissipation paths of excited charge carriers can be analyzed, which provide insights into the understanding of excitation dynamics in bulk materials.
Electron transfer in confined electromagnetic fields
Authors: Semenov Alexander , Nitzan Abraham
Published: May 2019

The interaction between molecular (atomic) electron(s) and the vacuum field of a reflective cavity generates significant interest, thanks to the rapid developments in nanophotonics. Such interaction which lies within the realm of cavity quantum electrodynamic can substantially affect the transport properties of molecular systems. In this work, we consider a nonadiabatic electron transfer process in the presence of a cavity mode. We present a generalized framework for the interaction between a charged molecular system and a quantized electromagnetic field of a cavity and apply it to the problem of electron transfer between a donor and an acceptor placed in a confined vacuum electromagnetic field. The effective system Hamiltonian corresponds to a unified Rabi and spin-boson model which includes a self-dipole energy term. Two limiting cases are considered: one where the electron is assumed much faster than the cavity mode and another in which the electron tunneling time is significantly larger than the mode period. In both cases, a significant rate enhancement can be produced by coupling to the cavity mode in the Marcus inverted region. The results of this work offer new possibilities for controlling electron transfer processes using visible and infrared plasmonics.
Thermoreversible gelation with ion-binding cross-links of variable multiplicity
Authors: Tanaka Fumihiko , Nakagawa Yoshiyuki , Ohta Seiichi , Ito Taichi
Published: May 2019

Thermoreversible gelation and liquid-liquid phase separation are theoretically studied for the gels of polyfunctional molecules (polymers) whose network junctions are formed by complexation of functional groups on the polymer chains with added metal ions. Phase diagrams on the polymer/ion/solvent concentration plane, including both sol-gel transition lines and liquid-liquid phase separation lines (spinodals), are derived as functions of the polymer functionality, molecular weight, maximum coordination number of ions, and temperature. Binding isotherms of ions are also calculated as functions of the ion concentration. Results of the calculated sol-gel transition lines are compared with our recent experimental data on gelation of star block and telechelic, acrylic copolymers cross-linked by iron ions. It is shown that, owing to reaction stoichiometry, there is an optimal ion concentration at which the solution gels for the lowest polymer concentration and also that a re-entrant sol phase appears in the ion concentrations higher than the optimal one. The effect of stepwise complex formation constants on the re-entrant phase is studied in detail.
Monitoring cyanobacteria occurrence in freshwater reservoirs using semi-analytical algorithms and orbital remote sensing
Authors: Borges Henrique Dantas , Cicerelli Rejane Ennes , de Almeida Tati , Roig Henrique L. , Olivetti Diogo
Published: May 2019

Cyanobacterial blooms pose a serious threat to the multiple uses of inland waters because of their adverse effects on the environment and human health. Monitoring cyanobacteria concentrations using traditional methods can be expensive and impractical. Recently, alternative efforts using remote sensing techniques have been successful. In particular, semi-analytical modelling approaches have been used to successfully predict chlorophyll (Chl)-a concentrations from remote sensing reflectance. The aims of this study were to test the performance of different semi-analytical algorithms in the estimation of Chl-a concentrations and the applicability of Sentinel-2 multispectral instrument (MSI) imagery, and its atmospheric correction algorithms, in the estimation of Chl-a concentrations. For our dataset, phycocyanin concentration was strongly correlated with Chl-a concentration and the inversion model of inland waters (IIMIW) semi-analytical algorithm was the best performing model, achieving a root mean square error of 4.6mgm–3 in the prediction of Chl-a. When applying the IIMIW model to MSI data, the use of top-of-atmosphere reflectance performed better than the atmospheric correction algorithm tested. Overall, the results were satisfactory, demonstrating that even without an adequate atmospheric correction pipeline, the monitoring of cyanobacteria can be successfully achieved by applying a semi-analytical bio-optical model to MSI data.
Asian water monitors (Varanus salvator) remain common in Peninsular Malaysia, despite intense harvesting
Authors: Khadiejah Syarifah , Razak Norazlinda , Ward-Fear Georgia , Shine Richard , Natusch Daniel J. D.
Published: May 2019

Context
Each year, between 50000 and 120000 Asian water monitors (Varanus salvator, to >2 m total length) are harvested from the wild in Peninsular Malaysia for their skins. Under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), international trade is allowable only if it is sustainable.

Aims
To assess the sustainability of Malaysia’s harvest of water monitors by quantifying the abundance and demography of V. salvator in the wild, and to develop cost-effective methods for estimating the parameters needed to evaluate sustainability.

Methods
We conducted trapping surveys to determine the abundance, population demography and density of V. salvator in four habitat types in five states in Peninsular Malaysia in 2010, 2011, 2012 and 2018.

Key results
Of 1025 lizards captured, only 63% (mostly females) were within the preferred body-size range exploited for commercial trade. Densities were high (37–372 lizards km–2 based on estimated population sizes; 1–35 lizards km–2 based on number of animals captured). Anthropogenic habitats (e.g. oil palm plantations) contained denser populations of monitors than did natural habitats where no hunting occurs, but mean body sizes were smaller.

Conclusions
Despite intensive harvesting for many decades, V. salvator remains abundant and widespread. Harvesting alters the demographic structure of lizard populations, but harvests of V. salvator in Malaysia are likely to be sustainable because a significant proportion of the population is not exploited.

Implications
Ongoing monitoring is required to continually reassess harvest sustainability. For this purpose, relatively simple population approaches, such as line-trapping transects to elucidate relative abundances, can provide important data on the makeup of hunted populations of water monitors more cost-effectively than can mark–recapture studies for assessments of sustainable use of these economically important lizards.
Nahua mushroom gatherers use area-restricted search strategies that conform to marginal value theorem predictions
Authors: Pacheco-Cobos Luis , Winterhalder Bruce , Cuatianquiz-Lima Cecilia , Rosetti Marcos F. , Hudson Robyn , Ross Cody T.
Published: May 2019

We develop a method of analysis for testing the marginal value theorem (MVT) in natural settings that does not require an independent definition or mapping of patches. We draw on recent theoretical work on area-restricted search (ARS) that links turning-angle and step-size changes to geographically localized encounter-rates. These models allow us to estimate “giving-up times” using encounter-annotated GPS tracking data. Applied to a case study of Nahua mushroom foragers, these models identify distinct forms of intrapatch and interpatch search behavior, with intrapatch search transitioning to interpatch search after a predictable interval of time since the last encounter with a harvested mushroom. Our empirical estimate of giving-up time coincides with the theoretically optimal giving-up time derived under the MVT in the same environment. The MVT is currently underused in studies of human foraging and settlement patterns, due in large part to the difficulty of identifying discrete resource patches and quantifying their characteristics. Our methods mitigate the need to make such discrete maps of patches and thus have the potential to broaden the scope for empirical evaluations of the MVT and related theory in humans. Beyond studies of naturalistic foraging in humans and other animals, our approach has implications for optimization of search behavior in a range of applied fields where search dynamics must be adapted to shifting patterns of environmental heterogeneity affecting prey density and patchiness.
Cis
- and
trans
-acting variants contribute to survivorship in a naïve
Drosophila melanogaster
population exposed to ryanoid insecticides
Authors: Green Llewellyn , Battlay Paul , Fournier-Level Alexandre , Good Robert T. , Robin Charles
Published: May 2019

Significance

Around the world insecticides are being deregistered and banned, as their environmental costs are deemed too great or their efficacy against pest insects is reduced through the evolution of insecticide resistance. With the introduction of replacement insecticides comes the responsibility to assess the way new insecticides perturb various levels of biological systems, from insect physiology to ecosystems. We used a systems genetics approach to identify genetic variants affecting survivorship of
Drosophila melanogaster
exposed to chlorantraniliprole. The study population was completely naïve to this insecticide chemistry and yet we find associations with variants in neuromuscular genes and coregulated detoxification genes. We predict that these variants will increase in populations of this “sentinel species” as these insecticides are applied in the environment.
Extrinsic conditions influence the self-association and structure of IF
1
, the regulatory protein of mitochondrial ATP synthase
Authors: Boreikaite Vytaute , Wicky Basile I. M. , Watt Ian N. , Clarke Jane , Walker John E.
Published: May 2019

Significance

Adenosine triphosphate (ATP), the fuel of biology, is produced by a molecular machine with a rotary action. Inside the mitochondria of eukaryotic cells, rotation is driven by a proton-motive force across the inner membranes of the organelle generated by oxidation of sugars and fats in food. Under anoxic conditions, the rotary machine hydrolyzes ATP and reverses rotation. This wastage is prevented by an intrinsically disordered region of the inhibitor protein, IF
1
, which inserts itself in the machine and stops reverse rotation. The inhibitory activity of IF
1
is regulated by self-association, which is influenced by pH and ion-types, providing a potential molecular mechanism for the modulation of ATPase activity by cellular physiology via this solution-responsive, self-associating protein.
Overview of non-destructive evaluation techniques for metal-based additive manufacturing
Authors: Mandache Catalin
Published: May 2019

Three-dimensional printing/digital or additive manufacturing is an area that is taking off with considerable rapidity and magnitude. In the same time, non-destructive evaluation (NDE) is playing an important role in the acceptance of additively manufactured parts, in order to provide the required confidence in the quality of the part and its expected safety and performance while in service. This article represents a summary addressing the subject of applicable NDE techniques to detect manufacturing anomalies and service-induced flaws. The topic is relatively new, attracting much research attention and funding, while in the meantime manufacturing processes are continuously improving. The number of publications covering additive manufacturing is increasing exponentially, and everyday new articles, conferences, and workshops are bringing out new information.
Many-body effects in quantum metrology
Authors: Czajkowski Jan , Pawłowski Krzysztof , Demkowicz-Dobrzański Rafał
Published: May 2019

We study the impact of many-body effects on the fundamental precision limits in quantum metrology. On the one hand such effects may lead to nonlinear Hamiltonians, studied in the field of nonlinear quantum metrology, while on the other hand they may result in decoherence processes that cannot be described using single-body noise models. We provide a general reasoning that allows to predict the fundamental scaling of precision in such models as a function of the number of atoms present in the system. Moreover, we describe a computationally efficient approach that allows for a simple derivation of quantitative bounds. We illustrate these general considerations by a detailed analysis of fundamental precision bounds in a paradigmatic atomic interferometry experiment with standard linear Hamiltonian but with both single and two-body losses taken into account—a model which is motivated by the most recent Bose–Einstein condensate magnetometry experiments. Using this example we also highlight the impact of the atom number super-selection rule on the possibility of protecting interferometric protocols against decoherence.
Consistent Dust and Gas Models for Protoplanetary Disks. III. Models for Selected Objects from the FP7 DIANA Project*
Authors: Woitke P. , Kamp I. , Antonellini S. , Anthonioz F. , Baldovin-Saveedra C. , Carmona A. , Dionatos O. , Dominik C. , Greaves J. , Güdel M. , Ilee J. D. , Liebhardt A. , Menard F. , Min M. , Pinte C. , Rab C. , Rigon L. , Thi W. F. , Thureau N. , Waters L. B. F. M.
Published: May 2019

The European FP7 project DIANA has performed a coherent analysis of a large set of observational data of protoplanetary disks by means of thermo-chemical disk models. The collected data include extinction-corrected stellar UV and X-ray input spectra (as seen by the disk), photometric fluxes, low and high resolution spectra, interferometric data, emission line fluxes, line velocity profiles and line maps, which probe the dust, polycyclic aromatic hydrocarbons (PAHs) and the gas in these objects. We define and apply a standardized modeling procedure to fit these data by state-of-the-art modeling codes (ProDiMo, MCFOST, MCMax), solving continuum and line radiative transfer (RT), disk chemistry, and the heating and cooling balance for both the gas and the dust. 3D diagnostic RT tools (e.g., FLiTs) are eventually used to predict all available observations from the same disk model, the DIANA-standard model. Our aim is to determine the physical parameters of the disks, such as total gas and dust masses, the dust properties, the disk shape, and the chemical structure in these disks. We allow for up to two radial disk zones to obtain our best-fitting models that have about 20 free parameters. This approach is novel and unique in its completeness and level of consistency. It allows us to break some of the degeneracies arising from pure Spectral Energy Distribution (SED) modeling. In this paper, we present the results from pure SED fitting for 27 objects and from the all inclusive DIANA-standard models for 14 objects. Our analysis shows a number of Herbig Ae and T Tauri stars with very cold and massive outer disks which are situated at least partly in the shadow of a tall and gas-rich inner disk. The disk masses derived are often in excess to previously published values, since these disks are partially optically thick even at millimeter wavelength and so cold that they emit less than in the Rayleigh–Jeans limit. We fit most infrared to millimeter emission line fluxes within a factor better than 3, simultaneously with SED, PAH features and radial brightness profiles extracted from images at various wavelengths. However, some line fluxes may deviate by a larger factor, and sometimes we find puzzling data which the models cannot reproduce. Some of these issues are probably caused by foreground cloud absorption or object variability. Our data collection, the fitted physical disk parameters as well as the full model output are available to the community through an online database (http://www.univie.ac.at/diana).
Mass Gatherings and Diarrheal Disease Transmission Among Rural Communities in Coastal Ecuador
Authors: Collender Philip A , Morris Christa , Glenn-Finer Rose , Acevedo Andrés , Chang Howard H , Trostle James A , Eisenberg Joseph N S , Remais Justin V
Published: May 2019

Mass gatherings exacerbate infectious disease risks by creating crowded, high-contact conditions and straining the capacity of local infrastructure. While mass gatherings have been extensively studied in the context of epidemic disease transmission, the role of gatherings in incidence of high-burden, endemic infections has not been previously studied. Here, we examine diarrheal incidence among 17 communities in Esmeraldas, Ecuador, in relation to recurrent gatherings characterized using ethnographic data collected during and after the epidemiologic surveillance period (2004–2007). Using distributed-lag generalized estimating equations, adjusted for seasonality, trend, and heavy rainfall events, we found significant increases in diarrhea risk in host villages, peaking 2 weeks after an event’s conclusion (incidence rate ratio, 1.21; confidence interval, adjusted for false coverage rate of ≤0.05: 1.02, 1.43). Stratified analysis revealed heightened risks associated with events where crowding and travel were most likely (2-week-lag incidence rate ratio, 1.51; confidence interval, adjusted for false coverage rate of ≤0.05: 1.09, 2.10). Our findings suggest that community-scale mass gatherings might play an important role in endemic diarrheal disease transmission and could be an important focus for interventions to improve community health in low-resource settings.
Metadherin–PRMT5 complex enhances the metastasis of hepatocellular carcinoma through the WNT–β-catenin signaling pathway
Authors: Zhu Kai , Peng Yuanfei , Hu Jinwu , Zhan Hao , Yang Liuxiao , Gao Qiang , Jia Hao , Luo Rongkui , Dai Zhi , Tang Zhaoyou , Fan Jia , Zhou Jian
Published: May 2019

Accumulating data suggest that metadherin (MTDH) may function as an oncogene. Our previous study showed that MTDH promotes hepatocellular carcinoma (HCC) metastasis via the epithelial-mesenchymal transition. In this study, we aim to further elucidate how MTDH promotes HCC metastasis. Using Co-immunoprecipitation (co-IP) and mass spectrometry, we found that MTDH can specifically bind to protein arginine methyltransferase 5 (PRMT5). Further functional assays revealed that PRMT5 overexpression promoted the proliferation and motility of HCC cells and that knockout of PRMT5 impeded the effect of MTDH. The immunohistochemistry assay/tissue microarray results showed that when MTDH was overexpressed in HCC cells, PRMT5 translocated from the nucleus to the cytoplasm, with the subsequent translocation of β-catenin from the cytoplasm to the nucleus and upregulation of the WNT–β-catenin signaling pathway. Further in vivo experiments suggested that PRMT5 and β-catenin played a pivotal role in MTDH-mediated HCC metastasis. We therefore concluded that the MTDH–PRMT5 complex promotes HCC metastasis by regulating the WNT–β-catenin signaling pathway.
Comparative Immunovirological and Clinical Responses to Antiretroviral Therapy Between HIV-1 Group O and HIV-1 Group M Infected Patients
Authors: Kouanfack Charles , Unal Guillemette , Schaeffer Laura , Kfutwah Anfumbom , Aghokeng Avelin , Mougnutou Rose , Tchemgui-Noumsi Nathalie , Alessandri-Gradt Elodie , Delaporte Eric , Simon François , Vray Muriel , Plantier Jean-Christophe ,   ANRS 12168 DynaMO Study, Alima Michèle , Essengué Lucie , Mounpou Georges , Ngang Peter , Ngoma Pauline , Omgba Vincent , Omam Deborah , Tonfack Léonie , Zé Flore , Akongnwi Emmanuel , Dumortier Jérôme , Ngoupo Paul-Alain , Njouom Richard , Rousset Dominique , Le Fouler Lenaig , Madec Yoann , Bodelet Marine , Dupre Jean-Michel , Pavie Juliette , Rekacewicz Claire , Garcia Paula , Colin Géraldine
Published: May 2019

Background

Little is known about impact of genetic divergence of human immunodeficiency virus type 1 group O (HIV-1/O) relative to HIV-1 group M (HIV-1/M) on therapeutic outcomes. We aimed to determine if responses to standardized combination antiretroviral therapy (cART) were similar between groups despite strain divergence.

Methods

We performed an open nonrandomized study comparing the immunological, virological, and clinical responses to cART based on 2 nucleoside reverse transcriptase inhibitors plus 1 ritonavir-boosted protease inhibitor, in naive and paired HIV-1/O vs HIV-1/M infected (+) patients (ratio 1:2), matched on several criteria. The primary endpoint was the proportion of patients with undetectable plasma viral load (pVL, threshold 60 copies/mL) at week (W) 48. Secondary endpoints were the proportion of patients with undetectable pVL at W24 and W96 and CD4 evolution between baseline and W24, W48, and W96.

Results

Forty-seven HIV-1/O+ and 94 HIV-1/M+ patients were included. Mean pVL at baseline was significantly lower by 1 log for HIV-1/O+ vs HIV-1/M+ patients. At W48, no significant difference was observed between populations with undetectable pVL and differences at W24 and W96 were not significant. A difference in CD4 gain was observed in favor of HIV-1/M at W48 and W96, but this was not significant when adjusted on both matched criteria and pVL at baseline.

Conclusions

Our data demonstrate similar immunovirological and clinical response between HIV-1/O+ and HIV-1/M+ patients. They also reveal significantly lower baseline replication for HIV-1/O variants, suggesting specific virological properties and physiopathology that now need to be addressed.

Clinical Trials Registration

NCT00658346.
Lymphogranuloma venereum proctitis mimicking inflammatory bowel diseases in 11 patients: a 4-year single-center experience
Authors: Di Altobrando Ambra , Tartari Federico , Filippini Andrea , D'Antuono Antonietta , Patrizi Annalisa , Filippi Federica , Sechi Andrea , Cuicchi Dajana , Salfi Nunzio Cosimo Mario , Gaspari Valeria
Published: May 2019

Lymphogranuloma venereum (LGV) is a sexually transmitted disease caused by Chlamydia trachomatis (CT) serovars L1–L3. Our study wants to underline the similarities between rectal LGV and idiopathic inflammatory bowel diseases (IBD), which can share clinical, endoscopic and histopathological findings.
Does pregabalin effectively and safely relieve postoperative pain in patients undergoing pulmonary resections?
Authors: Li Shuangjiang , Zhang Wenbiao , Cheng Shan , Li Yongjiang
Published: May 2019

A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was whether pregabalin could effectively and safely reduce postoperative pain in patients undergoing pulmonary resections. Altogether 23 papers were found using the reported search, of which 6 randomized controlled trials represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Five of 6 randomized controlled trials demonstrated that the application of oral pregabalin during the perioperative period could effectively reduce postoperative pain after pulmonary resections without compromising patients’ safety. One randomized controlled trial reported no difference in the postoperative pain levels between the pregabalin group and the control group. The rates of adverse effects were generally found to be decreased in patients who received pregabalin compared to the patients who received routine analgesia, although 2 studies reported significantly higher incidences of mild drowsiness and dizziness among the pregabalin-treated patients. Currently available evidence supports that the perioperative administration of pregabalin can effectively and safely relieve postoperative pain for patients undergoing pulmonary resections.
Cone reconstruction is feasible in babies under 2 kg of weight
Authors: Bautista-Rodriguez Carles , Fraisse Alain , Burmester Margarita , Ghez Oliver
Published: May 2019

Symptomatic neonates with Ebstein anomaly present with intractable heart failure. We present the first successful cone reconstruction in an ex 30 + 4-week premature below 2 kg with a favourable outcome.
Economic Crisis, Natural Resources, and Irregular Leader Removal in Autocracies
Authors: Krishnarajan Suthan
Published: May 2019

Why do autocratic leaders escape revolution, coups, and assassination during times of economic crisis? I argue that the spike in natural resource revenues since the 1960s has increased autocratic crisis resilience. The availability of this alternative revenue stream provides autocratic leaders with a constant inflow of money, increases their ability to repress dissent, and improves their access to international credit. Extending the analysis back to 1875, I show that the relationship between economic crisis and irregular leader removal in autocracies is strong and robust before the 1960s, but disappears in more recent periods. Interaction analyses confirm that the effects of economic crisis are moderated by natural resource income. These findings are robust to an array of alternative specifications, including analyses that address endogeneity concerns via instrumental variable (IV) estimation. A more particular examination of the theoretical mechanisms also supports the argument. These findings challenge widely held beliefs in the literature of a strong, direct effect of economic crisis on autocratic leader survival; they explain why economic crisis seems to destabilize some autocrats, but not others.
An ensemble of neural models for nested adverse drug events and medication extraction with subwords
Authors: Ju Meizhi , Nguyen Nhung T H , Miwa Makoto , Ananiadou Sophia
Published: May 2019

Objective

This article describes an ensembling system to automatically extract adverse drug events and drug related entities from clinical narratives, which was developed for the 2018 n2c2 Shared Task Track 2.

Materials and Methods

We designed a neural model to tackle both nested (entities embedded in other entities) and polysemous entities (entities annotated with multiple semantic types) based on MIMIC III discharge summaries. To better represent rare and unknown words in entities, we further tokenized the MIMIC III data set by splitting the words into finer-grained subwords. We finally combined all the models to boost the performance. Additionally, we implemented a featured-based conditional random field model and created an ensemble to combine its predictions with those of the neural model.

Results

Our method achieved 92.78% lenient micro F1-score, with 95.99% lenient precision, and 89.79% lenient recall, respectively. Experimental results showed that combining the predictions of either multiple models, or of a single model with different settings can improve performance.

Discussion

Analysis of the development set showed that our neural models can detect more informative text regions than feature-based conditional random field models. Furthermore, most entity types significantly benefit from subword representation, which also allows us to extract sparse entities, especially nested entities.

Conclusion

The overall results have demonstrated that the ensemble method can accurately recognize entities, including nested and polysemous entities. Additionally, our method can recognize sparse entities by reconsidering the clinical narratives at a finer-grained subword level, rather than at the word level.
Evaluation of Exclusion Netting for Spotted-Wing Drosophila (Diptera: Drosophilidae) Management in Minnesota Wine Grapes
Authors: Ebbenga Dominique N , Burkness Eric C , Hutchison William D
Published: May 2019

Spotted-wing drosophila, Drosophila suzukii (Matsumura), an economically damaging invasive species of numerous fruit crops, was first detected in Minnesota in 2012. High fecundity, and short generation times facilitated a rapid rise in the global pest status of D. suzukii, particularly in North America and Europe. To date, the majority of crop injury research has focused on fruit crops such as blueberries, raspberries, and cherries. However, little is known regarding the impact of D. suzukii on the wine grape industry in the upper Midwest region of the United States. Field trials were conducted in Minnesota during the summers of 2017–2018 to examine season-long phenology of D. suzukii in wine grape vineyards and wineries, and to assess the efficacy of exclusion netting for control of D. suzukii. Four treatments were evaluated, 1) open plot check (control), 2) open plot treated with an insecticide, 3) exclusion netting, and 4) exclusion netting, with artificial infestations of D. suzukii adults. Exclusion netting was applied at véraison and removed at harvest. On each sample date, 20 berries (10 intact and 10 injured) were collected from each plot for dissection. The number of larvae and adults were recorded for each berry to determine infestation levels. As shown by mean larval infestations and injured berries across treatments, exclusion netting provided a significant reduction in the level of D. suzukii infested berries when compared with the untreated check. These results indicate that exclusion netting could provide an effective alternative management strategy for D. suzukii in wine grapes.
Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Authors: Burrell A Millie , Goddard Jeffrey H R , Greer Paul J , Williams Ryan J , Pepper Alan E
Published: May 2019

Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.