bluuebunny/crossref_metadata_2025 huggingface dataset:
In-situ extended X-ray absorption fine structure study of electrostriction in Gd doped ceria
Authors: Korobko Roman , Lerner Alyssa , Li Yuanyuan , Wachtel Ellen , Frenkel Anatoly I. , Lubomirsky Igor
Published: January 2015

Studying electric field-induced structural changes in ceramics is challenging due to the very small magnitude of the atomic displacements. We used differential X-ray absorption spectroscopy, an elementally specific and spatially sensitive method, to detect such changes in Gd-doped ceria, recently shown to exhibit giant electrostriction. We found that the large electrostrictive stress generation can be associated with a few percent of unusually short Ce-O chemical bonds that change their length and degree of order under an external electric field. The remainder of the lattice is reduced to the role of passive spectator. This mechanism is fundamentally different from that in electromechanically active materials currently in use.
Suppressed polar distortion with enhanced Curie temperature in in-plane 90°-domain structure of a-axis oriented PbTiO3 Film
Authors: Morioka Hitoshi , Yamada Tomoaki , Tagantsev Alexander K. , Ikariyama Rikyu , Nagasaki Takanori , Kurosawa Toshiyuki , Funakubo Hiroshi
Published: January 2015

PbTiO3 thin films were epitaxially grown on (001) KTaO3 single crystal substrates by metalorganic chemical vapor deposition. The coherent epitaxial growth introduced a large in-plane tensile strain to the PbTiO3 film. This tensile strain increased TC and directed the polarization to one of the in-plane ⟨100⟩ axes below TC, resulting in the formation of perfect a1/a2/a1/a2 domain structure. We found that the polar distortion is appreciably suppressed in such a1/a2/a1/a2 domain structure while TC is enhanced due to the strain.
Dynamics of pyroelectric accelerators
Authors: Ghaderi R. , Davani F. Abbasi
Published: January 2015

Pyroelectric crystals are used to produce high energy electron beams. We have derived a method to model electric potential generation on LiTaO3 crystal during heating cycle. In this method, effect of heat transfer on the potential generation is investigated by some experiments. In addition, electron emission from the crystal surface is modeled by measurements and analysis. These spectral data are used to present a dynamic equation of electric potential with respect to thickness of the crystal and variation of its temperature. The dynamic equation's results for different thicknesses are compared with measured data. As a result, to attain more energetic electrons, best thickness of the crystals could be extracted from the equation. This allows for better understanding of pyroelectric crystals and help to study about current and energy of accelerated electrons.
Optimization of relativistic backward wave oscillator with non-uniform slow wave structure and a resonant reflector
Authors: Chen Zaigao , Wang Jianguo , Wang Yue
Published: January 2015

This letter optimizes synchronously 18 parameters of a relativistic backward wave oscillator with non-uniform slow wave structure (SWS) and a resonant reflector by using the parallel genetic algorithms and particle-in-cell simulation. The optimization results show that the generation efficiency of microwave from the electron beam has increased 32% compared to that of the original device. After optimization, the electromagnetic mode propagating in the resonant changes from the original TM020 mode of reflector to higher-order TM021 mode, which has a high reflection coefficient in a broader frequency range than that of the former. The modulation of current inside the optimized device is much deeper than that in the original one. The product of the electric field and current is defined. Observing this product, it is found that the interaction of the electron beam with the electromagnetic wave in the optimized device is much stronger than that in the original device, and at the rear part of SWS of the optimized device, the electron beam dominantly gives out the energy to the electromagnetic wave, leading to the higher generation efficiency of microwave than that of the original device.
Formation of multilayered magnetic nanotracks with perpendicular anisotropy via deoxidization using ion irradiation on ultraviolet-imprinted intaglio nanostructures
Authors: Cho Eikhyun , Kim Sanghoon , Shin Sang Chul , Han Jungjin , Shim Jongmyeong , Shin Ryung , Hong Jongill , Kang Shinill
Published: January 2015

We proposed a method to fabricate perpendicular magnetic nanotracks in the cobalt oxide/palladium multilayer films using UV-nanoimprinting lithography and low-energy hydrogen-ion irradiation. This is a method to magnetize UV-imprinted intaglio nanotracks via low-energy hydrogen ion irradiation, resulting the irradiated region are magnetically separated from the non-irradiated region. Multilayered magnetic nanotracks with a line width of 140 nm, which were fabricated by this parallel process without additional dry etching process, exhibited a saturation magnetization of 290 emu cm−3 and a coercivity of 2 kOe. This study demonstrates a cost-effective mass production of multilayered perpendicular magnetic nanotracks and offers the possibility to achieve high density storage and memory devices.
Outdoor performance of organic photovoltaics: Diurnal analysis, dependence on temperature, irradiance, and degradation
Authors: Bristow N. , Kettle J.
Published: January 2015

The outdoor dependence of temperature and diurnal irradiance on inverted organic photovoltaic (OPV) module performance has been analysed and benchmarked against monocrystalline-silicon (c-Si) photovoltaic technology. This is first such report and it is observed that OPVs exhibit poorer performance under low light conditions, such as overcast days, as a result of inflexion behaviour in the current-voltage curves, which limits the open-circuit voltage (VOC) and fill factor. These characteristics can be removed by photo-annealing at higher irradiance levels, which occur diurnally as irradiance increases after sunrise. We also report the first temperature coefficients for OPVs from outdoor data; the OPV modules showed a positive temperature coefficient, which compared to a negative coefficient from the c-Si modules. Overall, the cell degradation outdoors appears very severe for these modules and highlights the need for improved barrier.
Structural phases driven by oxygen vacancies at the La0.7Sr0.3MnO3/SrTiO3 hetero-interface
Authors: Nord M. , Vullum P. E. , Moreau M. , Boschker J. E. , Selbach S. M. , Holmestad R. , Tybell T.
Published: January 2015

An oxygen vacancy driven structural response at the epitaxial interface between La0.7Sr0.3MnO3 films and SrTiO3 substrates is reported. A combined scanning transmission electron microscopy and electron energy loss spectroscopy study reveal the presence of an elongated out-of-plane lattice parameter, coupled to oxygen vacancies and reduced manganese oxidation state at the La0.7Sr0.3MnO3 side of the interface. Density functional theory calculations support that the measured interface structure is a disordered oxygen deficient brownmillerite structure. The effect of oxygen vacancy mobility is assessed, revealing an ordering of the vacancies with time.
Highly orientated growth and characterization of La0.7Sr0.3MnO3 thin films with different orientations on SrTiO3 substrates by chemical solution deposition method
Authors: Wenhao Yin , Zhang Yuanyuan , Cao Danyan , Yang Jing , Bai Wei , Chen Ying , Wang Genshui , Dong Xianlin , Duan Chungang , Tang Xiaodong
Published: January 2015

La0.7Sr0.3MnO3 (LSMO) thin films were successfully prepared on (100), (110), and (111) oriented SrTiO3 substrates by chemical solution deposition method. The structural, magnetic, and magnetotransport properties were systematically studied. X-ray diffraction θ-2θ and ϕ-scan measurements results show that all the films have perfect crystalline orientation and in-plane alignment. Both the Curie temperature and metal-insulator transition temperature are almost the same for all the three orientations, about 339 K. The magnetoresistance value (MR value, defined as (RM − R0)/R0 × 100%, where RM and R0 are the resistivity with and without applied magnetic field) for the films reaches maximum near the Curie temperature. Both the magnetization and MR value for (100) direction LSMO are the largest, and meanwhile for (111) direction are the smallest. The saturation magnetization decreases approximately proportional to T2 at low temperature (T < Tc/2) for all the oriented film. Inversely, the resistivity increases proportional to T2 in the same temperature range, which can be attributed to the electron-electron scattering.
Magnetic nanoparticle imaging using multiple electron paramagnetic resonance activation sequences
Authors: Coene A. , Crevecoeur G. , Dupré L.
Published: January 2015

Magnetic nanoparticles play an important role in several biomedical applications such as hyperthermia, drug targeting, and disease detection. To realize an effective working of these applications, the spatial distribution of the particles needs to be accurately known, in a non-invasive way. Electron Paramagnetic Resonance (EPR) is a promising and sensitive measurement technique for recovering these distributions. In the conventional approach, EPR is applied with a homogeneous magnetic field. In this paper, we employ different heterogeneous magnetic fields that allow to stabilize the solution of the associated inverse problem and to obtain localized spatial information. A comparison is made between the two approaches and our novel adaptation shows an average increase in reconstruction quality by 5% and is 12 times more robust towards noise. Furthermore, our approach allows to speed up the EPR measurements while still obtaining reconstructions with an improved accuracy and noise robustness compared to homogeneous EPR.
How robust is dispersal-induced spatial synchrony?
Authors: Zhang Yuxiang , Lutscher Frithjof , Guichard Frédéric
Published: January 2015

Many biological populations fluctuate in synchrony over large geographic regions. This behavior may increase the chance of extinction. The combination of time-scale separation between interacting species and weak spatial linear diffusive coupling is one mechanism that can generate synchrony; however, accounting for travel time between habitat patches may destabilize this synchrony. Here, we show that ubiquitous behavioral aspects of dispersal (e.g., predator avoidance), implemented as nonlinear diffusive coupling, may also destabilize synchrony. In addition, these aspects interact with travel-time delays and amplify mechanisms that destroy synchrony. Our work suggests that dispersal-induced synchrony is more rare than typically assumed.
Ensemble averaging vs. time averaging in molecular dynamics simulations of thermal conductivity
Authors: Gordiz Kiarash , Singh David J. , Henry Asegun
Published: January 2015

In this report, we compare time averaging and ensemble averaging as two different methods for phase space sampling in molecular dynamics (MD) calculations of thermal conductivity. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium MD. We introduce two different schemes for the ensemble averaging approach and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical MD, the approaches used for generating independent trajectories may find their greatest utility in computationally expensive simulations such as first principles MD. For such simulations, where each time step is costly, time averaging can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each trajectory is independent. For this reason, particularly when using massively parallel architectures, ensemble averaging can result in much shorter simulation times (∼100–200X), but exhibits similar overall computational effort.
Ultrafast direct laser writing of cladding waveguides in the 0.8CaSiO3-0.2Ca3(PO4)2 eutectic glass doped with Nd3+ ions
Authors: Martínez de Mendívil J. , Sola D. , Vázquez de Aldana J. R. , Lifante G. , de Aza A. H. , Pena P. , Peña J. I.
Published: January 2015

We report on tubular cladding optical waveguides fabricated in Neodymium doped Wollastonite-Tricalcium Phosphate glass in the eutectic composition. The glass samples were prepared by melting the eutectic powder mixture in a Pt-Rh crucible at 1600 °C and pouring it in a preheated brass mould. Afterwards, the glass was annealed to relieve the inner stresses. Cladding waveguides were fabricated by focusing beneath the sample surface using a pulsed Ti:sapphire laser with a pulsewidth of 120 fs working at 1 kHz. The optical properties of these waveguides have been assessed in terms of near-field intensity distribution and transmitted power, and these results have been compared to previously reported waveguides with double-line configuration. Optical properties have also been studied as function of the temperature. Heat treatments up to 700 °C were carried out to diminish colour centre losses where waveguide's modes and transmitted power were compared in order to establish the annealing temperature at which the optimal optical properties were reached. Laser experiments are in progress to evaluate the ability of the waveguides for 1064 nm laser light generation under 800 nm optical pumping.
Power quality assessment of a solar photovoltaic two-stage grid connected system: Using fuzzy and proportional integral controlled dynamic voltage restorer approach
Authors: Gupta Akhil , Chanana Saurabh , Thakur Tilak
Published: January 2015

Dynamic voltage restorer (DVR) is used to protect sensitive loads in voltage disturbances of distribution generation (DG) system. In this paper, a variable step size incremental resistance based incremental conductance maximum power point tracking (MPPT) technique is implemented for solar photovoltaic (PV) grid connected system. A power quality study which includes perturb & observe (P&O) MPPT comparison is carried out during fault on grid side. At the same time, proportional integral and artificial intelligence-based fuzzy-logic controlled DVR is operated which injects voltage during the faulted grid side. Simulation results during fault show fuzzy logic based DVR scheme demonstrates simultaneous exchange of active reactive power, less total harmonic distortion in voltage source converter (VSC) current and grid current, less fluctuation of DC bus voltage to VSC, less DC current injection, and fast tracking of optimum operating point at unity power factor. This paper aims at simulating and validations of MPPT technique and VSC control approach using manufacturer's solar PV data sheet; fuzzy logic controlled DVR demonstrates effectiveness of proposed control schemes. The whole framework results in a simulation PV-DG model which constitutes a computer-aided design tool that is helpful for PV professionals who require simple, fast, and accurate PV simulator to design their systems precisely.
Standard logarithmic mean velocity distribution in a band-limited restricted nonlinear model of turbulent flow in a half-channel
Authors: Bretheim J. U. , Meneveau C. , Gayme D. F.
Published: January 2015

Numerical simulations of wall-turbulence using the restricted nonlinear (RNL) model generate realistic mean velocity profiles in plane Couette and channel flow at low Reynolds numbers. The results are less accurate at higher Reynolds number, and while a logarithmic region is observed, its von Kármán constant is not consistent with the standard logarithmic law. In half-channel flow, we show that limiting the streamwise-varying wavenumber support of RNL turbulence to one or few empirically determined modes improves its predictions considerably. In particular, the mean velocity profiles obtained with the band-limited RNL model follow standard logarithmic behavior for the higher Reynolds numbers in this study.
Unipolar resistive switching behavior of amorphous gallium oxide thin films for nonvolatile memory applications
Authors: Guo D. Y. , Wu Z. P. , An Y. H. , Li P. G. , Wang P. C. , Chu X. L. , Guo X. C. , Zhi Y. S. , Lei M. , Li L. H. , Tang W. H.
Published: January 2015

Amorphous gallium oxide thin film with heavy oxygen deficiency was deposited on Pt/Ti/SiO2/Si substrate by pulsed laser deposition in order to explore the resistive switching behavior of the Pt/Ga2O3-x/Pt sandwich structure. A well unipolar resistive switching behavior was obtained in this structure, which exhibits a high resistance ratio of OFF/ON up to 104, non-overlapping switching voltages, and excellent repeatability and retention. Both I-V relation plots of ON and OFF states and temperature dependent variation resistances indicate that the observed resistive switching behavior can be explained by the formation/rupture of conductive filaments formed out of oxygen vacancies.
Land use structures fish assemblages in reservoirs of the Tennessee River
Authors: Miranda L. E. , Bies J. M. , Hann D. A.
Published: January 2015

Inputs of nutrients, sediments and detritus from catchments can promote selected components of reservoir fish assemblages, while hindering others. However, investigations linking these catchment subsidies to fish assemblages have generally focussed on one or a handful of species. Considering this paucity of community-level awareness, we sought to explore the association between land use and fish assemblage composition in reservoirs. To this end, we compared fish assemblages in reservoirs of two sub-basins of the Tennessee River representing differing intensities of agricultural development, and hypothesised that fish assemblage structure indicated by species percentage composition would differ among reservoirs in the two sub-basins. Using multivariate statistical analysis, we documented inter-basin differences in land use, reservoir productivity and fish assemblages, but no differences in reservoir morphometry or water regime. Basins were separated along a gradient of forested and non-forested catchment land cover, which was directly related to total nitrogen, total phosphorous and chlorophyll-a concentrations. Considering the extensive body of knowledge linking land use to aquatic systems, it is reasonable to postulate a hierarchical model in which productivity has direct links to terrestrial inputs, and fish assemblages have direct links to both land use and productivity. We observed a shift from an invertivore-based fish assemblage in forested catchments to a detritivore-based fish assemblage in agricultural catchments that may be a widespread pattern among reservoirs and other aquatic ecosystems.
Setos' way to manage identities and well-being: shame and pride, opposition and openness
Authors: Valk Aune , Särg Taive
Published: January 2015

The paper examines how the tiny ethno-cultural group of Setos constructs its identity in the multicultural context. The study examines the validity of three acculturation models and tests earlier findings on the relationship between identity and well-being. The results suggest that Setos have clearly adopted a multicultural identity strategy while not merging different identities, and that they have managed to separate the material well-being from the pride of their identity. Despite its small size and peripheral location, the Setos' way to preserve their identity in a constantly changing context is an interesting lesson for other indigenous groups, and also for bigger neighbors.
An Introduction to Free Geographic Information Systems in Fisheries Science
Authors: Neely Ben C. , Eder Brandon L.
Published: January 2015

Geographic information systems (GIS) are powerful tools for analysis and interpretation of spatial data commonly encountered in fisheries science. We presented details of GIS use in fisheries management in a prior study and found cost to be a factor limiting GIS use. This article introduces fisheries managers to free or open-source GIS. Free or open-source GIS are readily available, powerful tools capable of performing a variety of spatial analyses. We strongly encourage managers wishing to perform spatial analyses, but who are unable to purchase software, to consider free GIS.

Los Sistemas de Información Geográfica (GIS) son una herramienta poderosa para el análisis e interpretación de datos espaciales comúnmente encontrados en la ciencia pesquera. Se presentan los detalles del uso del GIS en el manejo de pesquerías aplicado en un estudio previo, encontrando que el costo era un factor que limitaba el uso del GIS. En este artículo se introduce a los manejadores de pesquerías un GIS gratuito o de acceso abierto. Este GIS gratuito ya está disponible y contiene herramientas poderosas, capaces de realizar una variedad de análisis espaciales. Se recomienda ampliamente a los manejadores que deseen realizar análisis espaciales, pero no puedan comprar el software, a que consideren el GIS gratuito.
Guiding Principles for Development of Effective Commercial Fishery Monitoring Programs
Authors: Zollett Erika A. , Trumble Robert J. , Swasey Jill H. , Stebbins Shawn B.
Published: January 2015

Monitoring of fishing activities is an essential component of successful fisheries management that can provide verifiable fishery-dependent data on fishing activities and help assess performance and success of fisheries management plans. Fishery managers and stakeholders have often struggled in developing and implementing effective monitoring programs due to lack of information, funding, and peer-to-peer learning from existing monitoring programs. This article draws on the experience of over 25 national and international monitoring experts and reflects the most important lessons learned from commercial fisheries regarding the development and implementation of effective monitoring programs. The article discusses a set of “guiding principles,” developed in consultation with the monitoring experts, which provide fishery managers and stakeholders with cumulative knowledge and references to more easily develop comprehensive, appropriate, and effective monitoring approaches.

El monitoreo de actividades pesqueras es un componente esencial en las pesquerías manejadas adecuadamente y puede ofrecer datos verificables, dependientes de la pesquería, acerca de las actividades de pesca y ayuda a evaluar el desempeño y éxito de los planes de manejo. Manejadores e involucrados en las pesquerías suelen batallar con el desarrollo e implementación de programas efectivos de monitoreo debido a la falta de información, fondos y aprendizaje por parte de otros pares que participan en programas ya existentes de monitoreo. Este artículo muestra la experiencia de 25 expertos nacionales e internacionales y refleja las lecciones aprendidas más relevantes en lo concerniente al desarrollo e implementación de programas efectivos de monitoreo. También se discute una serie de “directrices” derivadas de la consulta con expertos en monitoreo, que brindan a manejadores e involucrados el conocimiento acumulado y las referencias que permiten más fácilmente desarrollar enfoques de monitoreo sistemáticos, adecuados y efectivos.
Sensitivity to general and specific numerical features in typical achievers and children with mathematics learning disability
Authors: Rotem Avital , Henik Avishai
Published: January 2015

We examined the development of sensitivity to general and specific numerical features in typical achievers and in 6th and 8th graders with mathematics learning disability (MLD), using two effects in mental multiplication: operand-relatedness (i.e., difficulty in avoiding errors that are related to the operands via a shared multiplication row) and decade-consistency (i.e., difficulty in avoiding errors that are operand related and also share a decade with the true result). Responses to decade-consistent products were quick but erroneous. In line with the processing sequence in adults, children first became sensitive to the general numerical feature of operand-relatedness (typical achievers—from 3rd grade; children with MLD in 8th grade) and only later to the specific feature of decade-consistency (typical achievers—from 4th grade, but only from 6th grade in a mature pattern). Implications of the numerical sensitivity in children with MLD are discussed.
A new method for constructing Anosov Lie algebras
Authors: Deré Jonas
Published: January 2015

It is conjectured that every closed manifold admitting an Anosov diffeomorphism is, up to homeomorphism, finitely covered by a nilmanifold. Motivated by this conjecture, an important problem is to determine which nilmanifolds admit an Anosov diffeomorphism. The main theorem of this article gives a general method for constructing Anosov diffeomorphisms on nilmanifolds. As a consequence, we give new examples which were overlooked in a corollary of the classification of low-dimensional nilmanifolds with Anosov diffeomorphisms and a correction to this statement is proven. This method also answers some open questions about the existence of Anosov diffeomorphisms which are minimal in some sense.
Myosin‑II heavy chain and formin mediate the targeting of myosin essential light chain to the division site before and during cytokinesis
Authors: Feng Zhonghui , Okada Satoshi , Cai Guoping , Zhou Bing , Bi Erfei
Published: January 2015

MLC1 is a haploinsufficient gene encoding the essential light chain for Myo1, the sole myosin‑II heavy chain in the budding yeast Saccharomyces cerevisiae. Mlc1 defines an essential hub that coordinates actomyosin ring function, membrane trafficking, and septum formation during cytokinesis by binding to IQGAP, myosin‑II, and myosin‑V. However, the mechanism of how Mlc1 is targeted to the division site during the cell cycle remains unsolved. By constructing a GFP‑tagged MLC1 under its own promoter control and using quantitative live‑cell imaging coupled with yeast mutants, we found that septin ring and actin filaments mediate the targeting of Mlc1 to the division site before and during cytokinesis, respectively. Both mechanisms contribute to and are collectively required for the accumulation of Mlc1 at the division site during cytokinesis. We also found that Myo1 plays a major role in the septin‑dependent Mlc1 localization before cytokinesis, whereas the formin Bni1 plays a major role in the actin filament–dependent Mlc1 localization during cytokinesis. Such a two‑tiered mechanism for Mlc1 localization is presumably required for the ordered assembly and robustness of cytokinesis machinery and is likely conserved across species.
Polarity protein Par3 controls B-cell receptor dynamics and antigen extraction at the immune synapse
Authors: Reversat Anne , Yuseff Maria-Isabel , Lankar Danielle , Malbec Odile , Obino Dorian , Maurin Mathieu , Penmatcha Naga Venkata Gayathri , Amoroso Alejandro , Sengmanivong Lucie , Gundersen Gregg G. , Mellman Ira , Darchen François , Desnos Claire , Pierobon Paolo , Lennon-Duménil Ana-Maria
Published: January 2015

B-cell receptor (BCR) engagement with surface-tethered antigens leads to the formation of an immune synapse, which facilitates antigen uptake for presentation to T-lymphocytes. Antigen internalization and processing rely on the early dynein-dependent transport of BCR–antigen microclusters to the synapse center, as well as on the later polarization of the microtubule-organizing center (MTOC). MTOC repositioning allows the release of proteases and the delivery of MHC class II molecules at the synapse. Whether and how these events are coordinated have not been addressed. Here we show that the ancestral polarity protein Par3 promotes BCR–antigen microcluster gathering, as well as MTOC polarization and lysosome exocytosis, at the synapse by facilitating local dynein recruitment. Par3 is also required for antigen presentation to T-lymphocytes. Par3 therefore emerges as a key molecule in the coupling of the early and late events needed for efficient extraction and processing of immobilized antigen by B-cells.
Snapshot on carbapenemase-producing Pseudomonas aeruginosa and Acinetobacter baumannii in Bucharest hospitals reveals unusual clones and novel genetic surroundings for blaOXA-23
Authors: Gheorghe Irina , Novais Ângela , Grosso Filipa , Rodrigues Carla , Chifiriuc Mariana Carmen , Lazar Veronica , Peixe Luísa
Published: January 2015

Objectives

The present study was designed to provide a snapshot on carbapenemase-producing Pseudomonas aeruginosa (n = 11) and Acinetobacter baumannii (n = 7) isolates in hospitalized patients (November 2011, January–March 2012) from two main hospitals in Bucharest, south Romania.

Methods

Clonality among isolates was established by PFGE, MLST and Fourier transform infrared spectroscopy. Carbapenemases were screened by the Blue-Carba test, PCR and sequencing. Transferability of blaOXA-23 was tested by conjugation and plasmid typing (number, size and identity) was assessed by S1-PFGE, replicon typing, hybridization and PCR mapping.

Results

All P. aeruginosa isolates carried chromosomally located blaVIM-2, associated with a common class 1 integron (aacA7-blaVIM-2) or an atypical configuration (aacA7-blaVIM-2-dfrB5-tniC). These isolates belonged to unusual lineages; mostly ST233 disseminated in one hospital unit, with ST364 and ST1074 also being detected. A. baumannii isolates carried blaOXA-23 in Tn2008, which was found truncating a TnaphA6 transposon located in a common 60 kb GR6 (aci6) pABKp1-like conjugative plasmid in highly related CC92 clones (ST437, ST764 and ST765), where CC stands for clonal complex.

Conclusions

Our results show the spread of VIM-2-producing P. aeruginosa and OXA-23-producing A. baumannii clinical isolates in two hospitals from Bucharest and highlight a peculiar population structure in this Eastern European country. Also, we demonstrate the dissemination of a common and conjugative aci6 pABKp1-like plasmid scaffold in different A. baumannii clones and we report the first known identification of Tnaph6-carrying pACICU2-like plasmids in Europe.
ST-246 is a key antiviral to inhibit the viral F13L phospholipase, one of the essential proteins for orthopoxvirus wrapping
Authors: Duraffour Sophie , Lorenzo María M. , Zöller Gudrun , Topalis Dimitri , Grosenbach Doug , Hruby Dennis E. , Andrei Graciela , Blasco Rafael , Meyer Hermann , Snoeck Robert
Published: January 2015

Objectives

ST-246 is one of the key antivirals being developed to fight orthopoxvirus (OPV) infections. Its exact mode of action is not completely understood, but it has been reported to interfere with the wrapping of infectious virions, for which F13L (peripheral membrane protein) and B5R (type I glycoprotein) are required. Here we monitored the appearance of ST-246 resistance to identify its molecular target.

Methods

Vaccinia virus (VACV), cowpox virus (CPXV) and camelpox virus (CMLV) with reduced susceptibility to ST-246 were selected in cell culture and further characterized by antiviral assays and immunofluorescence. A panel of recombinant OPVs was engineered and a putative 3D model of F13L coupled with molecular docking was used to visualize drug–target interaction. The F13L gene of 65 CPXVs was sequenced to investigate F13L amino acid heterogeneity.

Results

Amino acid substitutions or insertions were found in the F13L gene of six drug-resistant OPVs and production of four F13L-recombinant viruses confirmed their role(s) in the occurrence of ST-246 resistance. F13L, but not B5R, knockout OPVs showed resistance to ST-246. ST-246 treatment of WT OPVs delocalized F13L- and B5R-encoded proteins and blocked virus wrapping. Putative modelling of F13L and ST-246 revealed a probable pocket into which ST-246 penetrates. None of the identified amino acid changes occurred naturally among newly sequenced or NCBI-derived OPV F13L sequences.

Conclusions

Besides demonstrating that F13L is a direct target of ST-246, we also identified novel F13L residues involved in the interaction with ST-246. These findings are important for ST-246 use in the clinic and crucial for future drug-resistance surveillance programmes.
Risk factors for ambulatory urinary tract infections caused by high-MIC fluoroquinolone-susceptible Escherichia coli in women: results from a large case–control study
Authors: Rattanaumpawan Pinyo , Nachamkin Irving , Bilker Warren B. , Roy Jason A. , Metlay Joshua P. , Zaoutis Theoklis E. , Lautenbach Ebbing
Published: January 2015

Objectives

The prevalence of high-MIC fluoroquinolone-susceptible Escherichia coli (FQSEC) has been increasing. These isolates are one step closer to full fluoroquinolone (FQ) resistance and may lead to delayed response to FQ therapy. Our study aimed to investigate the epidemiology of high-MIC FQSEC in ambulatory urinary tract infections (UTIs).

Patients and methods

A case–control study was conducted at outpatient services within the University of Pennsylvania Health System, Philadelphia. All female subjects with non-recurrent UTI caused by FQSEC (levofloxacin MIC < 4 mg/L) were enrolled. Cases were subjects with high-MIC FQSEC UTI (levofloxacin MIC >0.12 but < 4 mg/L) and controls were subjects with low-MIC FQSEC UTI (levofloxacin MIC ≤0.12 mg/L). Data on microbiology results and baseline characteristics were extracted from electronic medical records.

Results

During the 3 year study period (May 2008–April 2011), 11 287 episodes of E. coli bacteriuria were identified. The prevalence of FQSEC, FQ-intermediate susceptible E. coli and FQ-resistant E. coli was 75.0%, 0.4% and 24.6%, respectively. A total of 2001 female subjects with FQSEC UTI were enrolled into our study (165 cases and 1836 controls). Independent risk factors for high-MIC FQ susceptibility included Asian race (OR = 2.92; 95% CI = 1.29–6.58; P = 0.02), underlying renal disease (OR = 2.18; 95% CI = 1.15–4.14; P = 0.02) and previous nitrofurantoin exposure (OR = 8.86; 95% CI = 1.95–40.29; P = 0.005).

Conclusions

Asian race, underlying renal disease and previous exposure to nitrofurantoin were identified as independent risk factors for high-MIC FQSEC. There may be some factors that are more common in Asians, which may result in the selection of high-MIC FQSEC. Further studies are necessary to explore these findings.
Pharmacokinetic profile of raltegravir, elvitegravir and dolutegravir in plasma and mucosal secretions in rhesus macaques
Authors: Massud Ivana , Martin Amy , Dinh Chuong , Mitchell James , Jenkins Leecresia , Heneine Walid , Pau Chou-Pong , García-Lerma J. Gerardo
Published: January 2015

Objectives

Pharmacokinetic studies in animal models are important for assessing the prophylactic potential of antiretroviral drugs for HIV prevention. This study sought to identify clinically relevant doses of the marketed integrase inhibitors raltegravir, elvitegravir and dolutegravir in macaques and investigate drug penetration and antiviral activity in mucosal secretions.

Methods

Macaques received one oral dose of raltegravir, elvitegravir or dolutegravir alone or in combination with emtricitabine and tenofovir disoproxil fumarate followed by drug level measurements in blood and rectal and vaginal secretions. Antiviral activity was investigated in TZM-bl cells exposed to SHIV162p3 in the presence of rectal secretions collected from treated animals.

Results

Plasma drug concentrations with 50 mg/kg raltegravir or elvitegravir were within the range seen in humans receiving 400–800 mg of raltegravir or 800 mg of unboosted elvitegravir but lower than with 150 mg of elvitegravir boosted with cobicistat. AUC0–24 values for dolutegravir increased proportionally with the dose, with a calculated human-equivalent dose of 20 mg/kg. Elvitegravir showed the highest penetration in rectal and vaginal fluids despite the absence of pharmacological boosting, followed by raltegravir and dolutegravir. Rectal secretions collected at 24 h from treated macaques blocked infection of TZM-bl cells by 50% at dilutions of 1/1000 (raltegravir), 1/800 (dolutegravir) and >1/30 000 (elvitegravir).

Conclusions

We defined macaque doses of HIV integrase inhibitors that recapitulate human clinical doses, which will facilitate efficacy and dose escalation studies in macaques. High and sustained drug concentrations and activity in mucosal secretions suggest that integrase inhibitors are promising candidates for HIV prevention.
Emergence of azole-resistant invasive aspergillosis in HSCT recipients in Germany
Authors: Steinmann J. , Hamprecht A. , Vehreschild M. J. G. T. , Cornely O. A. , Buchheidt D. , Spiess B. , Koldehoff M. , Buer J. , Meis J. F. , Rath P.-M.
Published: January 2015

Objectives

Aspergillus fumigatus is the most common agent of invasive aspergillosis (IA). In recent years, resistance to triazoles, the mainstay of IA therapy, has emerged in different countries worldwide. IA caused by azole-resistant A. fumigatus (ARAF) shows an exceedingly high mortality. In this study, IA due to ARAF isolates in HSCT recipients in Germany was investigated.

Methods

The epidemiology of azole resistance in IA was analysed in two German haematology departments. Between 2012 and 2013, 762 patients received HSCT in Essen (n = 388) and Cologne (n = 374). Susceptibility testing of A. fumigatus isolates was performed by Etest, followed by EUCAST broth microdilution testing if elevated MICs were recorded. In all ARAF isolates the cyp51A gene was sequenced and the genotype was determined by microsatellite typing using nine short tandem repeats.

Results

In total, A. fumigatus was recovered from 27 HSCT recipients. Eight patients had azole-resistant IA after HSCT, and seven of the cases were fatal (88%). All except one patient received antifungal prophylaxis (in five cases triazoles). TR34/L98H was the most common mutation (n = 5), followed by TR46/Y121F/T289A (n = 2). In one resistant isolate no cyp51A mutation was detected. Genotyping revealed genetic diversity within the German ARAF isolates and no clustering with resistant isolates from the Netherlands, India and France.

Conclusions

This report highlights the emergence of azole-resistant IA with TR34/L98H and TR46/Y121F/T289A mutations in HSCT patients in Germany and underscores the need for systematic antifungal susceptibility testing of A. fumigatus.
Impact of imipenem and amikacin pharmacokinetic/pharmacodynamic parameters on microbiological outcome of Gram-negative bacilli ventilator-associated pneumonia
Authors: Pajot O. , Burdet C. , Couffignal C. , Massias L. , Armand-Lefevre L. , Foucrier A. , Da Silva D. , Lasocki S. , Laouénan C. , Mentec H. , Mentré F. , Wolff M.
Published: January 2015

Objectives

Despite recent advances, antibiotic therapy of ventilator-associated pneumonia (VAP) in ICU patients is still challenging. We assessed the impact of imipenem and amikacin pharmacokinetic and pharmacodynamic parameters on microbiological outcome in these patients.

Patients and methods

Patients with Gram-negative bacilli (GNB) VAP were prospectively included. Blood samples for pharmacokinetic analysis were collected after empirical administration of a combination of imipenem three times daily and one single dose of amikacin. MICs were estimated for each GNB obtained from respiratory samples. Microbiological success was defined as a ≥103 cfu/mL decrease in bacterial count in quantitative cultures between baseline and the third day of treatment.

Results

Thirty-nine patients [median (min–max) age = 60 years (28–84) and median SAPS2 at inclusion = 40 (19–73)] were included. Median MICs of imipenem and amikacin were 0.25 mg/L (0.094–16) and 2 mg/L (1–32), respectively. Median times over MIC and over 5× MIC for imipenem were 100% (8–100) and 74% (3–100), respectively. The median C1/MIC ratio for amikacin was 23 (1–76); 34 patients (87%) achieved a C1/MIC ≥10. Microbiological success occurred in 29 patients (74%). No imipenem pharmacodynamic parameter was significantly associated with the microbiological success. For amikacin, C1/MIC was significantly higher in the microbiological success group: 26 (1–76) versus 11 (3–26) (P = 0.004).

Conclusions

In ICU patients with VAP, classic imipenem pharmacodynamic targets are easily reached with usual dosing regimens. In this context, for amikacin, a higher C1/MIC ratio than previously described might be necessary.
Evaluation of three commercial assays for rapid detection of genes encoding clinically relevant carbapenemases in cultured bacteria
Authors: Findlay Jacqueline , Hopkins Katie L. , Meunier Daniele , Woodford Neil
Published: January 2015

Objectives

To assess the performance of three commercial molecular assays for detecting major families of carbapenemases in pure bacterial isolates.

Methods

A panel of 450 isolates with previously defined carbapenem resistance mechanisms was tested using the Check-Direct CPE kit, the eazyplex® SuperBug complete A kit and the Xpert® Carba-R kit. Isolates included 438 Enterobacteriaceae and 12 Pseudomonas spp. comprising 100 isolates each with KPC, NDM, VIM or OXA-48-like enzymes, two isolates producing both an NDM and an OXA-48-like enzyme, 24 IMP producers and 24 isolates without a known carbapenemase gene. Discordant results (commercial versus in-house) were investigated using in-house PCR and amplicons were sequenced to define the carbapenemase allele present.

Results

All three commercial assays detected all isolates with KPC, VIM, NDM and classic OXA-48 carbapenemases (no false-negatives). Isolates producing the OXA-181 variant (n = 18) were not detected by the Xpert® Carba-R kit or the eazyplex® SuperBug complete A kit, but were subsequently detected with modified versions of these kits. Only the Xpert® Carba-R kit could detect IMP carbapenemases, although this was limited to the IMP-1 subgroup. Invalid or false-positive results were either not observed when following the manufacturer's protocols or were eliminated by making simple interpretative adjustments to allow use with bacterial isolates rather than clinical samples.

Conclusions

Commercial assays offer a reliable means of detecting bacteria with clinically significant carbapenemases. Coverage of some assays required expansion to maximize the sensitivity for OXA-48-like carbapenemases. Choice will ultimately depend on preferred gene coverage, intended throughput, cost and ability to fit into local workflows.
Reproduction of
Pisidium casertanum
(Poli, 1791) in Arctic lake
Authors: Bespalaya Yulia , Bolotov Ivan , Aksenova Olga , Kondakov Alexander , Paltser Inga , Gofarov Mikhail
Published: January 2015

Freshwater invertebrates are able to develop specific ecological adaptations that enable them to successfully inhabit an extreme environment. We investigated the brooding bivalve of
Pisidium casertanum
in Talatinskoe Lake, Vaigach Island, Arctic Russia. Here, quantitative surveys were conducted, with the collection and dissections of 765 molluscs, on the basis of which analyses on the brood sacs length (marsupia) and the number and size of embryos, were performed. In this study, the number of brooded embryos was positively correlated with the parent's shell length. The number of extramarsupial embryos was much lower than the number of intramarsupial embryos. Our research also showed that the brood sac length and embryos within one individual can vary significantly. Thus, we detected that
P. casertanum
has a specific brooding mechanism, accompanied by asynchronous development and embryos release by the parent. We suggest that such a mode could result in the coin-flipping effect that, presumably, increases the population breeding success in the harsh environment of the Arctic lake.
Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803
Authors: Klähn Stephan , Orf Isabel , Schwarz Doreen , Matthiessen Jasper K.F. , Kopka Joachim , Hess Wolfgang R. , Hagemann Martin
Published: January 2015

The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ƊndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.
Modelling pair distribution functions (PDFs) of organic compounds: describing both intra- and intermolecular correlation functions in calculated PDFs
Authors: Prill Dragica , Juhás Pavol , Schmidt Martin U. , Billinge Simon J. L.
Published: January 2015

The methods currently used to calculate atomic pair distribution functions (PDFs) from organic structural models do not distinguish between the intramolecular and intermolecular distances. Owing to the stiff bonding between atoms within a molecule, the PDF peaks arising from intramolecular atom–atom distances are much sharper than those of the intermolecular atom–atom distances. This work introduces a simple approach to calculate PDFs of molecular systems without building a supercell model by using two different isotropic displacement parameters to describe atomic motion: one parameter is used for the intramolecular, the other one for intermolecular atom–atom distances. Naphthalene, quinacridone and paracetamol were used as examples. Calculations were done with theDiffPy-CMIcomplex modelling infrastructure. The new modelling approach produced remarkably better fits to the experimental PDFs, confirming the higher accuracy of this method for organic materials.
The NeXus data format
Authors: Könnecke Mark , Akeroyd Frederick A. , Bernstein Herbert J. , Brewster Aaron S. , Campbell Stuart I. , Clausen Björn , Cottrell Stephen , Hoffmann Jens Uwe , Jemian Pete R. , Männicke David , Osborn Raymond , Peterson Peter F. , Richter Tobias , Suzuki Jiro , Watts Benjamin , Wintersberger Eugen , Wuttke Joachim
Published: January 2015

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.