bluuebunny/crossref_metadata_2025 huggingface dataset:
Moduli spaces of vortex knots for an exact fluid flow
Authors: Bogoyavlenskij Oleg
Published: January 2017

The moduli spaces S(D) of non-isotopic vortex knots are introduced for the ideal fluid flows in invariant domains D. The analogous moduli spaces of the magnetic fields B knots are defined. We derive and investigate new exact fluid flows (and analogous plasma equilibria) satisfying the Beltrami equation which have nested invariant balls Bk3 with radii Rk ≈ (k + 1) π, k⟶∞. The first flow is z-axisymmetric; the other ones do not possess any rotational symmetries. The axisymmetric flow has an invariant plane z = 0. Due to an involutive symmetry of the flow, its vortex knots in the invariant half-spaces z > 0 and z < 0 are equivalent. It is demonstrated that the moduli space 𝒮(ℝ3) for the derived fluid flow in ℝ3 is naturally isomorphic to the set of all rational numbers p/q in the interval J1:0.25<q<M̃1≈0.5847, where q is the safety factor. For the fluid flow in the first invariant ball B13, it is shown that all values of the safety factor q belong to a small interval of length ℓ ≈ 0.1261. It is established that only torus knots Kp,q with 0.25 < p/q < 0.5847 are realized as vortex knots for the constructed flow in ℝ3. Each torus knot Kp,q with 0.25 < p/q < 0.5 is realized on countably many invariant tori Tk2 located between the invariant spheres Sk2 and Sk+12, while torus knots with 0.5<p/q<M̃1 are realized only on finitely many invariant tori. The moduli spaces Sm(Ba3)(m=1,2,…) of vortex knots are constructed for some axisymmetric steady fluid flows that are solutions to the boundary eigenvalue problem for the curl  operator on a ball Ba3.
Effect of trailing edge shape on the separated flow characteristics around an airfoil at low Reynolds number: A numerical study
Authors: Thomareis Nikitas , Papadakis George
Published: January 2017

Direct numerical simulations of the flow field around a NACA 0012 airfoil at Reynolds number 50 000 and angle of attack 5° with 3 different trailing edge shapes (straight, blunt, and serrated) have been performed. Both time-averaged flow characteristics and the most dominant flow structures and their frequencies are investigated using the dynamic mode decomposition method. It is shown that for the straight trailing edge airfoil, this method can capture the fundamental as well as the subharmonic of the Kelvin-Helmholtz instability that develops naturally in the separating shear layer. The fundamental frequency matches well with relevant data in the literature. The blunt trailing edge results in periodic vortex shedding, with frequency close to the subharmonic of the natural shear layer frequency. The shedding, resulting from a global instability, has an upstream effect and forces the separating shear layer. Due to forcing, the shear layer frequency locks onto the shedding frequency while the natural frequency (and its subharmonic) is suppressed. The presence of serrations in the trailing edge creates a spanwise pressure gradient, which is responsible for the development of a secondary flow pattern in the spanwise direction. This pattern affects the mean flow in the near wake. It can explain an unexpected observation, namely, that the velocity deficit downstream of a trough is smaller than the deficit after a protrusion. Furthermore, the insertion of serrations attenuates the energy of vortex shedding by de-correlating the spanwise coherence of the vortices. This results in weaker forcing of the separating shear layer, and both the subharmonics of the natural frequency and the shedding frequency appear in the spectra.
Long-range Tamm surface plasmons supported by graphene-dielectric metamaterials
Authors: Hajian Hodjat , Caglayan Humeyra , Ozbay Ekmel
Published: January 2017

Considering the Ohmic losses of graphene in the calculations and by obtaining exact dispersion relations of the modes, we theoretically study propagation and localization characteristics of Tamm surface plasmons supported by terminated graphene metamaterials. The metamaterials are composed of alternating layers of graphene and dielectric with subwavelength periods. We also examine the Tamm modes within the framework of long-wavelength approximation. It is shown that, in case the Ohmic losses of the graphene layers are taken into account, surface plasmons are not supported in a long-wavelength region, in which the graphene-dielectric multilayer structure behaves as a hyperbolic metamaterial. We prove that, when the metamaterial is truncated with air, by choosing sufficiently thick but still subwavelength dielectric layers, i.e., d = 300 nm, these surface waves will have a moderate propagation (localization) length that is comparable with those of a single layer of graphene. On the other hand, in case a miniaturized graphene metamaterial (10 < d(nm) < 100) is truncated by a thick cap layer (dcap = 5d) with εcap > εdielectric, it is possible to considerably improve the propagation and localization characteristics of the Tamm modes supported by the system within the 5.5–50 THz range of frequency, as compared to a single layer of graphene.
Differential carrier lifetime in InGaN-based light-emitting diodes obtained by small-signal frequency-domain measurements
Authors: Reklaitis I. , Nippert F. , Kudžma R. , Malinauskas T. , Karpov S. , Pietzonka I. , Lugauer H. J. , Strassburg M. , Vitta P. , Tomašiūnas R. , Hoffmann A.
Published: January 2017

Recently, a novel method for evaluation of recombination coefficients corresponding to Shockley-Read-Hall, radiative, and Auger recombination channels has been proposed, which combines measurements of the light emitting diode (LED) external quantum efficiency under continuous wave operation with the determination of non-equilibrium carrier differential life time (DLT) by small-signal time-resolved photoluminescence [Nippert et al., Jpn. J. Appl. Phys., Part 1 55, 05FJ01 (2016)]. In this work, we suggest an alternative technique, small-signal frequency-domain lifetime measurements, which is implemented more easily and capable of operating in a wider range of LED operating currents. The DLTs measured by both techniques are shown to agree well with each other, but saturate at low currents, contrary to the trend predicted by the well-known ABC-model. We discuss possible reasons for this deviation, as well as advantages and limitations of the measurement techniques.
Design and experiment studies of a 2.6-MV diverter system
Authors: Hu Yixiang , Zeng Jiangtao , Jiang Xiaofeng , Wang Zhiguo , Liang Tianxue , Qiu Ai’ci
Published: January 2017

Malfunctions of the Marx pre-fire or in the event that the main switch does not close were analyzed. Principles of the diverter system for protection of those events were introduced in detail. A 2.6 MV diverter system, consisting of an oil trigger switch and a Marx-coupled trigger generator, was developed. Based on “JianGuang-I” facility, a diverter-system test stand was established. And experiments with 2.3-MV working voltages were carried out to study the performance of this diverter system. Experiment results show that the time delay of this diverter system (from the beginning of the Marx erection to the time that the diverter-switch closes) is about 320 ns and its jitter (standard deviation) is about 8.9 ns. This diverter system has been tested more than 180 shots, and no problem has been encountered yet.
The impact of long-range electron-hole interaction on the charge separation yield of molecular photocells
Authors: Nemati Aram Tahereh , Ernzerhof Matthias , Asgari Asghar , Mayou Didier
Published: January 2017

We discuss the effects of charge carrier interaction and recombination on the operation of molecular photocells. Molecular photocells are devices where the energy conversion process takes place in a single molecular donor-acceptor complex attached to electrodes. Our investigation is based on the quantum scattering theory, in particular on the Lippmann-Schwinger equation; this minimizes the complexity of the problem while providing useful and non-trivial insight into the mechanism governing photocell operation. In this study, both exciton pair creation and dissociation are treated in the energy domain, and therefore there is access to detailed spectral information, which can be used as a framework to interpret the charge separation yield. We demonstrate that the charge carrier separation is a complex process that is affected by different parameters, such as the strength of the electron-hole interaction and the non-radiative recombination rate. Our analysis helps to optimize the charge separation process and the energy transfer in organic solar cells and in molecular photocells.
Interelectrode bridging of carbon nanotube fibrous assembly induced by gas discharge breakdown
Authors: Sato Hideki , Mizushima Yuuki , Komatsu Yusuke
Published: January 2017

In this work, we demonstrate a fibrous assembly of carbon nanotubes (CNTs) induced by a gas discharge breakdown that bridge the distance between two planar electrodes. To achieve this, we placed the two planar electrodes, one of which was covered with a CNT film, in a chamber; a vacuum pump was used to evacuate the air from the chamber and replace it with inert gas. By then applying a voltage between the electrodes, we induced a discharge breakdown between them. This caused the CNTs coated on the electrode surface to detach and form fibrous assemblies. The assemblies elongated and reached the opposite electrode, thereby creating bridges between the electrodes. These bridges formed when the gas pressure was greater than ca. 1.0 × 103 Pa and in combination with the occurrence of a spark discharge. At lower pressures, a glow discharge occurred, and no bridge formation was observed, indicating that the discharge mode is critical for the bridge formation.
On the mechanism of highly efficient p-type conduction of Mg-doped ultra-wide-bandgap AlN nanostructures
Authors: Tran Nhung Hong , Le Binh Huy , Zhao Songrui , Mi Zetian
Published: January 2017

Free hole concentrations up to ∼6 × 1017 cm−3 were measured in Mg-doped AlN nanowires at room-temperature, which is several orders of magnitude larger than that of previously reported AlN epilayers. Detailed studies suggest that such unusually high carrier concentrations stem from the efficient hole hopping conduction in the Mg impurity band, driven by the significantly enhanced Mg-dopant incorporation in nearly defect-free AlN nanostructures. Distinct signatures of hole hopping conduction in the Mg impurity band are observed experimentally, including a relatively small activation energy for electrical conductivity and an increase in hole mobility with increasing temperature.
A study on electromigration-inducing intergranular fracture of fine silver alloy wires
Authors: Hsueh Hao-Wen , Hung Fei-Yi , Lui Truan-Sheng
Published: January 2017

In this study, Pd-coated Cu, Ag (purity = 4 N), and Ag alloy (Ag-8Au-3Pd) wires were employed to measure the tensile properties during current stressing using the so-called dynamic current tensile (DCT) test. Both the tensile strength and elongation of the wires decreased dramatically in the DCT test, particularly of the Ag-based wires, and the fracture morphology of the Cu-based and Ag-based wires was ductile fracture and intergranular fracture, respectively. Compared to the Cu-based wires, electromigration occurred more easily in the Ag-based wires, and it always generated voids and cracks at the grain boundaries; therefore, the fracture morphology of the Ag-based wires was intergranular fracture owing to the weakened grain boundary. Further, the results indicated that the Ag-based wires could not carry a higher current density than the Cu-based wires, primarily because their extremely low strength and elongation in current stressing might cause serious reliability problems.
A model for generation of high wavenumber fluctuations by external magnetic field perturbations in edge pedestal plasmas
Authors: Singh R. , Jhang Hogun , Kim Juhyung
Published: January 2017

We study the impact of external magnetic perturbations on the stability of ballooning modes. A unique feature of our analysis is the two-step parametric process [Chaturvedi and Kaw, J. Geophys. Res. 81, 3257 (1976)], which enables us to calculate contributions from all the modes with high toroidal mode numbers. The analysis shows that the externally applied magnetic field perturbations can modify the linear dispersion characteristics of the ballooning mode. Specifically, the growth rate spectrum of the ballooning modes becomes broader in poloidal wavenumber (kθ) space, implying the generation of high-k fluctuations. The increase of high-k fluctuations (micro-turbulence) can lead to the mitigation of an edge localized mode crash by increasing turbulent transport in the pedestal. In addition to this, a new nonlinear instability is found even below the threshold of the ballooning mode instability when the amplitude of magnetic perturbation is sufficiently large (i.e., δB/B0≥1.0×10−4). A discussion is given of the implication of this new finding.
Isotopic effect of parametric instabilities during lower hybrid waves injection into hydrogen/deuterium plasmas
Authors: Zhao Aihui , Gao Zhe
Published: January 2017

Based on the local dispersion relation, the parametric instability (PI) was numerically investigated for the injection of lower hybrid waves (LHWs) into hydrogen and deuterium plasmas separately. Numerical calculations under typical scrape-off layer parameters in tokamak plasmas show that both the unstable regions of the PI and the values of growth rates are close for two cases, in spite of the decaying channel of the ion sound quasimode or ion cyclotron quasimode (ICQM). These numerical results could be understood by the analyses based on the fluid model. Parameter dependences are also similar for hydrogen and deuterium plasmas. For example, the ICQM growth rate increases with an increasing density, a decreasing temperature, and a decreasing magnetic field in deuterium plasmas as it does in hydrogen plasmas. The isotopic effect of the PI during the LHW injection is weak. As a result, the lower hybrid current drive efficiency at a high density in deuterium plasmas cannot be much improved over hydrogen plasmas if the PI process dominates the behavior of LHWs at the plasma edge.
Low threshold spaser based on deep-subwavelength spherical hyperbolic metamaterial cavities
Authors: Wan Mingjie , Gu Ping , Liu Weiyue , Chen Zhuo , Wang Zhenlin
Published: January 2017

We theoretically propose a design of a spaser based on spherical hyperbolic metamaterial cavities consisting of a dielectric core wrapped by several stacks of alternating layers of metal and dielectric, which can support the multipolar whispering-gallery modes (WGMs) with resonance wavelengths much larger than the cavity size. Depending on the mode order of the excited WGMs with the same angular momentum, we show that such cavities are capable of strongly confining the electric fields within different dielectric shell layers. By introducing gains into the different dielectric layers, we demonstrate that the hyperbolic cavities can act as multi-wavelength spasers with a lasing threshold as low as 811 cm−1, operating on the WGMs with the corresponding mode order. Furthermore, we also demonstrate that the slight variation on either the number of stacks or the core radius allows for easily tuning the lasing wavelengths over a wide spectral range.
Service induced fcc→hcp martensitic transformation in a Co-based superalloy
Authors: Vacchieri E. , Costa A. , Roncallo G. , Cacciamani G.
Published: January 2017

Co-based superalloy, ECY768, applied on gas turbine vanes, shows the presence of cracks after service. EBSD studies revealed hcp transformation in the base material near cracked regions. This phase arises from a martensitic transformation of fcc matrix and bestows high fragility. The phase transformation is related to temperature and loading distribution that characterises components in service. However, at the service temperatures, the hcp transformation is not expected for ECY768. An in-house thermodynamic database was developed using the Calphad approach and thermodynamic calculations were applied to the complicated alloy composition for phase stability range evaluation. Moreover, a testing campaign was planned to artificially create this martensitic transformation and to comprehend the influence of plastic strain on fcc-hcp transformation. The transformation mechanisms were understood and some methods were developed for hcp-phase removal through refurbishment heat treatment.

This paper is part of a thematic issue on the 9th International Charles Parsons Turbine and Generator Conference. All papers have been revised and extended before publication in Materials Science and Technology.
Improvement of pitting corrosion resistance of stainless steel by electric current pulse
Authors: Jia D. B. , Dai W. B. , Tang G. P. , Xu C. Z. , Tian X. Z. , Yu J. K.
Published: January 2017

The electric current pulse (ECP) was applied on the liquidus of 304 stainless steel during solidification and the pitting corrosion of the water-quenched specimens was explored in the present work. The results revealed that the utilisation of ECP can inhibit manganese sulphide from segregating around oxide inclusions during solidification and consequently, the pitting corrosion resistance of ECPed steel was significantly improved. Hence, the application of ECP during solidification might be an efficient way to improve the pitting corrosion resistance of the 304 stainless steel.

This paper is part of a themed issue on Materials in External Fields.
Changes in biosynthesis of exopolysaccharide in Lactococcus lactis subspecies cremoris treated by moderate pulsed electric field treatment
Authors: Ohba Tetsuro , Uemura Kunihiko , Nabetani Hiroshi
Published: January 2017

Metabolome analysis and physicochemical analyses were executed with cell extracts of a Lactococcus lactis subspecies cremoris strain treated by moderate pulsed electric field (PEF) to elucidate the mechanism of enhanced production of exopolysaccharide (EPS) by the treatment. Metabolome analysis by capillary electrophoresis time of flight mass spectrometry annotated 224 metabolites from the cytoplasmic extract of the strain, which, however, showed no significant changes in metabolites related to the EPS production. Electron microscopic observation and chemical analysis of undecaprenoids as carrier of EPS biosynthetic intermediates suggested that PEF treatment dissociated immature EPSs from the intermediates due to the focal electro-condensation of hydrogen ions at the cell surface. Thus, liberated undecaprenyl phosphates were recycled efficiently, which resulted in mass increase of EPS with smaller molecular weight. The study suggested the feasibility of moderate PEF treatment as a food processing technique and revealed the mechanism of enhanced production of EPS by the treatment.
Arc force and shapes with high-frequency pulsed-arc welding
Authors: Yang Mingxuan , Li Ling , Qi Bojin , Zheng Hao
Published: January 2017

Arc plasma is the source of heat and force for molten pool with dynamics fluid and convections. The arc force is studied with shape surveillance and force measurement during pulsed welding process. The results indicated that the average force increased by 42–57%. And the pressures were 322 Pa (conventional welding), 409 Pa and 517 Pa (pulsed welding). Imaging process is carried out for energy distribution analysis. The core region ratio increased up to 51%, compared with 43.7% by conventional welding. The arc pressure derivation was produced and the error was discussed. The increased arc force happens with arc constriction during pulsed welding. It is supposed to create surface depression of molten pool, enhance the fluidity and improve the heat convections.
Development and application of an algorithm to compute weighted multiple glycan alignments
Authors: Hosoda Masae , Akune Yukie , Aoki-Kinoshita Kiyoko F
Published: January 2017

Motivation

A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules.

Results

We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis.

Availability and Implementation

http://www.rings.t.soka.ac.jp

Supplementary information

Supplementary data are available at Bioinformatics online.
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
Authors: Heirendt Laurent , Thiele Ines , Fleming Ronan M T
Published: January 2017

Motivation

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations.

Results

DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.

Availability and Implementation

The code is freely available on github.com/opencobra/COBRA.jl. The documentation can be found at opencobra.github.io/COBRA.jl.

Supplementary information

Supplementary data are available at Bioinformatics online.
Protein multiple sequence alignment benchmarking through secondary structure prediction
Authors: Le Quan , Sievers Fabian , Higgins Desmond G
Published: January 2017

Motivation

Multiple sequence alignment (MSA) is commonly used to analyze sets of homologous protein or DNA sequences. This has lead to the development of many methods and packages for MSA over the past 30 years. Being able to compare different methods has been problematic and has relied on gold standard benchmark datasets of ‘true’ alignments or on MSA simulations. A number of protein benchmark datasets have been produced which rely on a combination of manual alignment and/or automated superposition of protein structures. These are either restricted to very small MSAs with few sequences or require manual alignment which can be subjective. In both cases, it remains very difficult to properly test MSAs of more than a few dozen sequences. PREFAB and HomFam both rely on using a small subset of sequences of known structure and do not fairly test the quality of a full MSA.

Results

In this paper we describe QuanTest, a fully automated and highly scalable test system for protein MSAs which is based on using secondary structure prediction accuracy (SSPA) to measure alignment quality. This is based on the assumption that better MSAs will give more accurate secondary structure predictions when we include sequences of known structure. SSPA measures the quality of an entire alignment however, not just the accuracy on a handful of selected sequences. It can be scaled to alignments of any size but here we demonstrate its use on alignments of either 200 or 1000 sequences. This allows the testing of slow accurate programs as well as faster, less accurate ones. We show that the scores from QuanTest are highly correlated with existing benchmark scores. We also validate the method by comparing a wide range of MSA alignment options and by including different levels of mis-alignment into MSA, and examining the effects on the scores.

Availability and Implementation

QuanTest is available from http://www.bioinf.ucd.ie/download/QuanTest.tgz

Supplementary information

Supplementary data are available at Bioinformatics online.
FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications
Authors: Ferraro Petrillo Umberto , Roscigno Gianluca , Cattaneo Giuseppe , Giancarlo Raffaele
Published: January 2017

MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM.

Availability and Implementation

The software and the datasets are available at http://www.di.unisa.it/FASTdoop/.

Supplementary information

Supplementary data are available at Bioinformatics online.
VCF-kit: assorted utilities for the variant call format
Authors: Cook Daniel E , Andersen Erik C
Published: January 2017

The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools.

Availability and Implementation

https://github.com/AndersenLab/VCF-kit
Genetic Diversity, Virulence, andMeloidogyne incognitaInteractions ofFusarium oxysporumIsolates Causing Cotton Wilt in Georgia
Authors: Bell Alois A. , Kemerait Robert C. , Ortiz Carlos S. , Prom Sandria , Quintana Jose , Nichols Robert L. , Liu Jinggao
Published: January 2017

Locally severe outbreaks of Fusarium wilt of cotton (Gossypium spp.) in South Georgia raised concerns about the genotypes of the causal pathogen, Fusarium oxysporum f. sp. vasinfectum. Vegetative complementation tests and DNA sequence analysis were used to determine genetic diversity among 492 F. oxysporum f. sp. vasinfectum isolates obtained from 107 wilted plants collected from seven fields in five counties. Eight vegetative complementation groups (VCG) were found, with VCG 01117B and VCG 01121 occurring in 66% of the infected plants. The newly recognized VCG 01121 was the major VCG in Berrien County, the center of the outbreaks. All eight VCG resulted in significant increases in the percentages of wilted leaves (27 to 53%) and significant reductions in leaf weight (40 to 67%) and shoot weight (33 to 60%) after being stem punctured into Gossypium hirsutum ‘Rowden’. They caused little or no significant reductions in shoot weight and height or increases in foliar symptoms and vascular browning in a soil-infestation assay. Soil infestation with Meloidogyne incognita race 3 (root-knot nematode) alone also failed to cause significant disease. When coinoculated with M. incognita race 3, all VCG caused moderate to severe wilt. Therefore, the VCG identified in this study belong to the vascular-competent pathotype, and should pose similar threats to cotton cultivars in the presence of the root-knot nematode. Use of nematode-resistant cultivars, therefore, is probably the best approach to control the disease in Georgia.
Multiple DNA Markers for Identification of Xanthomonas arboricola pv. juglandis Isolates and its Direct Detection in Plant Samples
Authors: Fernandes Camila , Albuquerque Pedro , Sousa Rui , Cruz Leonor , Tavares Fernando
Published: January 2017

Xanthomonas arboricola pv. juglandis (Xaj) is the etiological agent of walnut (Juglans regia L.) bacterial blight (WBB), and has been associated to other walnut emerging diseases, namely brown apical necrosis (BAN) and vertical oozing canker (VOC), altogether severely affecting the walnut production worldwide. Despite the research efforts carried out to disclose Xaj genetic diversity, reliable molecular methods for rapid identification of Xaj isolates and culture-independent detection of Xaj in infected plant samples are still missing. In this work, we propose nine novel specific DNA markers (XAJ1 to XAJ9) selected by dedicated in silico approaches to identify Xaj isolates and detect these bacteria in infected plant material. To confirm the efficacy and specificity of these markers, dot blot hybridization was carried out across a large set of xanthomonads. This analysis, which confirmed the pathovar specificity of these markers, allowed to identify four broad-range markers (XAJ1, XAJ4, XAJ6, and XAJ8) and five narrow-range markers (XAJ2, XAJ3, XAJ5, XAJ7, and XAJ9), originating 12 hybridization patterns (HP1 to HP12). No evident relatedness was observed between these hybridization patterns and the geographic origin from which the isolates were obtained. Interestingly, four isolates that clustered together according the gyrB phylogenetic analysis (CPBF 1507, 1508, 1514, and 1522) presented the same hybridization pattern (HP11), suggesting that these nine markers might be informative to rapidly discriminate and identify different Xaj lineages. Taking into account that a culture-independent detection of Xaj in plant material has never been described, a multiplex PCR was optimized using markers XAJ1, XAJ6, and XAJ8. This triplex PCR, besides confirming the dot blot data for each of the 52 Xaj, was able to detect Xaj in field infected walnut leaves and fruits. Altogether, these nine Xaj-specific markers allow conciliating the specificity of DNA-detection assays with typing resolution, contributing to rapid detection and identification of potential emergent and acutely virulent Xaj genotypes, infer their distribution, disclose the presence of this phytopathogen on potential alternative host species and improve phytosanitary control.
The Constitutive Endopolygalacturonase TvPG2 Regulates the Induction of Plant Systemic Resistance by Trichoderma virens
Authors: Sarrocco Sabrina , Matarese Fabiola , Baroncelli Riccardo , Vannacci Giovanni , Seidl-Seiboth Verena , Kubicek Christian Peter , Vergara Mariarosaria
Published: January 2017

Trichoderma spp. are opportunistic fungi some of which are commonly present in the rhizosphere. Several species, such as T. virens, are also efficient biocontrol agents against phytopathogenic fungi and exert beneficial effects on plants. These effects are the consequence of interactions between Trichoderma and plant roots, which trigger enhanced plant growth and induce plant resistance. We have previously shown that T. virens I10 expresses two endopolygalacturonase genes, tvpg1 and tvpg2, during the interaction with plant roots; tvpg1 is inducible while tvpg2 is constitutively transcribed. Using the same system, the tomato polygalacturonase-inhibitor gene Lepgip1 was induced at the same time as tvpg1. Here we show by gene disruption that TvPG2 performs a regulatory role on the inducible tvpg1 gene and in triggering the plant immune response. A tvpg2-knockout strain fails to transcribe the inducible tvpg1 gene in neither in vitro in inducing media containing pectin or plant cell walls, nor during the in vivo interaction with tomato roots. Likewise, the in vivo induction of Lepgip1 does not occur, and its defense against the pathogen Botrytis cinerea is significantly reduced. Our data prove the importance of a T. virens constitutively produced endopolygalacturonase in eliciting plant induced systemic resistance against pathogenic fungi.
Eye problems in a woman with Churg-Strauss syndrome
Authors: Pierce Benjamin D. , Donald Carrlene B. , Mendez Anthony P.
Published: January 2017

Churg-Strauss syndrome is a rare, systemic vasculitis of unknown cause. Ocular involvement is a rare but established complication and can lead to vision damage or blindness if not treated promptly. Treatment of ocular manifestations corresponds with systemic treatment of the disease and consists primarily of corticosteroids.
Understanding therapeutic hypothermia
Authors: Yacono Christian S. , Eider Stephanie
Published: January 2017

Therapeutic hypothermia is a relatively new protocol that can improve patients' chances of favorable neurologic outcomes after cardiac arrest. However, implementation rates remain low nationwide. This article describes recommendations for and benefits of therapeutic hypothermia in postresuscitation care.
Multidimensional Prognostic Modelling in People With Chronic Axial Low Back Pain
Authors: Rabey Martin , Smith Anne , Beales Darren , Slater Helen , O’Sullivan Peter
Published: January 2017

Objectives:

To derive prognostic models for people with chronic low back pain (CLBP) (n=294) based upon an extensive array of potentially prognostic multidimensional factors.

Materials and Methods:

This study entered multidimensional data (demographics, pain characteristics, pain responses to movement, behaviors associated with pain, pain sensitivity, psychological, social, health, lifestyle) at baseline, and interventions undertaken, into prognostic models for pain intensity, disability, global rating of change and bothersomeness at 1-year.

Results:

The prognostic model for higher pain intensity (explaining 23.2% of the variance) included higher baseline pain intensity and punishing spousal interactions, and lower years in education, while participating in exercise was prognostic of lower pain intensity. The model for higher disability (33.6% of the variance) included higher baseline disability, longer forward bending time, psychological principal component scores representing negative pain-related cognitions and punishing spousal interactions; while exercising was prognostic of lower disability. The odds of reporting global rating of change much/very much improved were increased by participating in exercise, having leg pain as well as CLBP and having greater chronic pain acceptance. The receiver operating characteristic area under the curve was 0.72 indicating acceptable discrimination. The odds of reporting very/extremely bothersome CLBP were increased by having higher baseline pain intensity, longer forward bending time and receiving injection(s); while higher age, more years in education and having leg pain decreased the odds (receiver operating characteristic area under the curve, 0.80; acceptable discrimination).

Discussion:

The variance explained by prognostic models was similar to previous reports, despite an extensive array of multidimensional baseline variables. This highlights the inherent multidimensional complexity of CLBP.
Does Transection of the C2 Nerve Roots During C1 Lateral Mass Screw Placement for Atlantoaxial Fixation Result in a Superior Outcome?
Authors: Badhiwala Jetan H. , Nassiri Farshad , Witiw Christopher D. , Mansouri Alireza , Almenawer Saleh A. , Fehlings Michael G.
Published: January 2017

Study Design.

Systematic review and meta-analysis.

Objective.

To evaluate the clinical and functional outcomes of transection of the C2 roots during C1 lateral mass screw placement for atlantoaxial fixation.

Summary of Background Data.

Transection of the C2 nerve roots has been recommended during atlantoaxial fixation to facilitate C1 lateral mass screw placement and possibly reduce postoperative occipital neuralgia, although this practice remains controversial.

Methods.

We searched MEDLINE, EMBASE, Web of Science, and the Cochrane Library for studies evaluating the outcomes of C1-2 fixation involving sacrifice of the C2 roots. We calculated transformed proportions with 95% confidence intervals (CI) for the outcomes of occipital neuralgia, numbness, bony fusion, and procedural morbidity. For studies comparing C2 transection with nerve sparing surgery, we performed meta-analyses for the outcomes of occipital neuralgia, occipital numbness, blood loss, and operative time.

Results.

Eight observational studies (N = 393) met eligibility criteria. The rate of postoperative occipital neuralgia among included studies was 0% to 25%; occipital numbness, 6.7% to100%; bony fusion, 96.7% to 100%; and procedural morbidity, 0% to 14.3%. Among comparative studies, C2 transection was associated with a higher rate of occipital numbness [odds ratio (OR) 178.6 (95% CI 26.6 to 1198.4)], lower blood loss [mean difference (MD) −195.3 mL (95% CI −317.7 to −72.8 mL)] and shorter operative times [MD −57.5 mins (95% CI −76.9 to −38.2 mins)] than when the C2 roots were spared. We found no difference in rates of occipital neuralgia [OR 1.44 (95% CI 0.45 to 4.68)].

Conclusion.

Transection of the C2 nerve roots appears to be a viable, safe option when undertaking placement of C1 lateral mass screws. The procedure is associated with reduced operative duration and blood loss, increased rate of occipital numbness, and no change in the rate of occipital neuralgia. However, given the relatively low quality of evidence, prospective, controlled studies to evaluate this strategy are recommended.

Level of Evidence: N /A
Erythema Nodosum Leprosum–Like Lesions Are a Histopathologic Pattern in Whipple's Disease and a Sign of the Immune Reconstitution Inflammatory Syndrome: A Case Series and Review of the Literature
Authors: Liersch Julia , Carlotti Agnès , Theunis Anne , Leonard Alexandra , Barrett Mary , Carlson John Andrew , Schaller Jörg
Published: January 2017

Inflammatory and subcutaneous nodules can arise in treated and untreated cases of Whipple disease (WD). The inflammatory immune reconstitution syndrome describes paradoxical clinical inflammatory worsening of a preexisting condition because of a return of immune function. Clinicopathologic examination of 4 patients with WD who presented with erythema nodosum leprosum (ENL)–like lesions and the findings of a systematic review of this phenomenon revealed that ENL-like lesions occurred in predominantly middle-aged male patients who suffered from WD, mostly on the legs. Patients showed a nonvasculitic, mostly septal panniculits with neutrophils, macrophages, and lymphocytes. Numerous bacteria-laden periodic acid–Schiff + macrophages and free bacilli were detected in the dermis, as well as subcutaneous septae and adipose lobules. These lesions occurred in both untreated and treated patients as part of inflammatory immune reconstitution syndrome. In conclusion, ENL-like lesions represent a characteristic histopathologic pattern associated with WD, which can occur in different contexts whenever there is a change in the immunological status of the patient. This change can be triggered by antimicrobial treatment, immunomodulatory and immunosuppressant therapy, or occur spontaneously, rarely.
Safety and Effectiveness of Juvéderm Ultra Plus Injectable Gel in Correcting Severe Nasolabial Folds in Chinese Subjects
Authors: Li Dong , Xie Yun , Li Qin , Sun Jiaming , Jiang Ping , Jia Yi , Murphy Diane K. , Li Qingfeng
Published: January 2017

Background:

Hyaluronic acid dermal fillers are effective in correcting severe nasolabial folds (NLFs) in non-Asian populations. We assessed safety and effectiveness of Juvéderm Ultra Plus in a Chinese population.

Methods:

This double-blind study randomized Chinese subjects with severe NLFs to Juvéderm Ultra Plus (24 mg/mL) in 1 NLF and Restylane injectable gel (20 mg/mL) in the other NLF. NLFs were evaluated using the validated 5-point photonumeric Allergan NLF Severity Scale (0 is “no wrinkle” and 4 is “very deep wrinkle”). Investigator-assessed responder rates (primary outcome at 6 months), NLF mean improvements, and subject-assessed responder rates and preference were assessed.

Results:

Of 124 subjects randomized, 122 completed the 6-month visit. NLFs treated with Juvéderm Ultra Plus required less volume than those treated with Restylane (median [range]: 0.80 [0.3–2.0] vs 1.00 [0.3–1.9]; P<0.001). Investigator-assessed responder rates were 90.4% for Juvéderm Ultra Plus and 89.6% for Restylane, establishing noninferiority of Juvéderm Ultra Plus. Mean (SD) improvements in NLF Severity Scale scores from baseline at 6 months were 1.5 (0.75) for Juvéderm Ultra Plus and 1.6 (0.73) for Restylane. Subject-assessed responder rates were similar to investigator-assessed rates (87.3%, Juvéderm Ultra Plus; 83.9%, Restylane). Of subjects reporting a preference, 62.1% preferred Juvéderm Ultra Plus. The most common treatment site responses were swelling and tenderness; most were mild or moderate in severity and resolved without intervention. Juvéderm Ultra Plus had fewer severe treatment site responses than Restylane.

Conclusion:

In this study in Chinese subjects, Juvéderm Ultra Plus was safe and effective for correcting severe NLFs.
Prostaglandin E1 Increases Microcirculation in Random Pattern Flaps on Rats Measured with Laser Doppler Perfusion Imaging
Authors: Tønseth Kim Alexander , Sneistrup Christian , Berg Thomas Moe
Published: January 2017

Background:

Reconstructive procedures with pedicled and free flaps are associated with a risk of ischemia. Prostaglandin E1 (PGE1) is a hormone-like substance with known antiischemic and tissue-protective effects. The aim of this study was to evaluate the effect of PGE1 on the microcirculation in random pattern skin flaps on rats.

Methods:

Twenty-four rats were divided into 2 groups: an intervention group given PGE1 for 6 hours and a control group given saline. The flap (2 × 10 cm) was created on the back of the rats, and the microcirculation was monitored with laser Doppler perfusion imaging in 5 different zones (1, proximal; 5, distal) before surgery and after 60, 180, and 360 minutes postoperatively.

Results:

Before surgery, there was no difference in the perfusion in any zones between the intervention group and the control group. The mean perfusion values in zone 1 in the intervention group were significantly higher than those in the control group at 60, 180, and 360 minutes postoperatively (P = 0.02, P = 0.05, and P = 0.04, respectively). At 360 minutes, we also found significantly higher levels of perfusion in the intervention group in zones 4 and 5 (P = 0.05 and P = 0.03, respectively) compared with the controls. Comparing the perfusion at 360 to 60 minutes in the intervention group, we found a significant increase in microcirculation in all zones, which were not seen in the control group.

Conclusion:

PGE1 increased perfusion in the dermal random pattern flaps on rats.
Obstetric Anesthesia Liability Concerns
Authors: DAVIES JOANNA M. , STEPHENS LINDA S.
Published: January 2017

Obstetric practice carries a high risk of medical liability and involves both obstetricians and anesthesiologists. Analysis of data from the Anesthesia Closed Claims Project database shows an increase in the proportion of anesthesia claims for maternal death and brain damage between the 1990s and 2000 and later, primarily due to hemorrhage. The proportion of claims for newborn brain damage remained unchanged while those for maternal nerve injury and minor injuries decreased. Use of massive transfusion protocols and clinical drills have been shown to improve outcomes from hemorrhage. Good communication and teamwork are critical for reducing obstetric liability.
CENTRAL MACULAR THICKNESS IN 6.5-YEAR-OLD CHILDREN BORN EXTREMELY PRETERM IS STRONGLY ASSOCIATED WITH GESTATIONAL AGE EVEN WHEN ADJUSTED FOR RISK FACTORS
Authors: Molnar Anna E. C. , Rosén Rebecka M. , Nilsson Maria , Larsson Eva K. B. , Holmström Gerd E. , Hellgren Kerstin M.
Published: January 2017

Purpose:

To assess the macular thickness in 6.5-year-old children born extremely preterm (EPT) in comparison with children born at term and to investigate risk factors associated with the macular thickness in the preterm group.

Methods:

A population-based study of 6.5-year-old children born before the gestational age of 27 weeks and age-matched control subjects. Macular assessments with optical coherence tomography were performed, and the results were compared with neonatal risk factors and sex.

Results:

Adequate optical coherence tomography measurements were obtained from 134 children born EPT (mean gestational age of 25 weeks [range 23–26]) and 145 control subjects. The mean (range) of central macula thickness was significantly increased (P < 0.001) in the EPT group (right eyes: 282 μm [238–356], left eyes: 283 μm [229–351]), compared with the control group (right eyes: 249 μm [208–293], left eyes: 248 μm [207–290]). A multiple linear mixed model analysis of the EPT group revealed gestational age, retinopathy of prematurity, and male gender as important risk factors for an increased macular thickness. The macular thickness decreased by 3.9 μm per gestational week, when adjusted for retinopathy of prematurity and sex.

Conclusion:

Extremely preterm birth constitutes a substantial risk factor for a thick central macula, even when adjusted for retinopathy of prematurity and male gender.
INCREASED INTRAOCULAR PRESSURE IS A RISK FACTOR FOR UNEXPLAINED VISUAL LOSS DURING SILICONE OIL ENDOTAMPONADE
Authors: Marti Marvin , Walton Richard , Böni Christian , Zweifel Sandrine A. , Stahel Marc , Barthelmes Daniel
Published: January 2017

Purpose:

To identify the incidence rate and risk factors for unexplained visual loss associated with silicone oil endotamponade used during primary repair of macula-sparing rhegmatogenous retinal detachments.

Methods:

This retrospective cohort study included patients undergoing pars plana vitrectomy for primary surgical repair of macula-sparing rhegmatogenous retinal detachments in whom silicone oil endotamponade was used. The primary outcome measure was the incidence rate of unexplained visual loss and identification of risk factors associated with vision loss.

Results:

Of 1,218 eyes undergoing pars plana vitrectomy for primary retinal detachment repair, 44 eyes were included for analysis. In 9 eyes (20%), an unexplained vision loss occurred. Logistic regression identified increased intraocular pressure (IOP) (prospectively defined as IOP readings during silicone oil endotamponade ≥21 mmHg on two consecutive visits or ≥25 mmHg at any time during this period) as significant predictor (odds ratio = 4.9; P = 0.04) and a classification tree ranked IOP as the most important variable for vision loss. Incidence rate of vision loss in eyes experiencing IOP increase was 4.5 vision loss events per 1,000 days at risk compared with 1 event per 1,000 days in eyes without IOP increase, yielding an incidence rate ratio of 4.5 (95% confidence interval: 1.1–17.9; P = 0.02).

Conclusion:

Sufficient control of IOP during silicone oil endotamponade for primary retinal detachment repair is warranted to reduce the probability of vision loss.