bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of atmospheric stability on wind-turbine wakes: A large-eddy simulation study
Authors: Abkar Mahdi , Porté-Agel Fernando
Published: March 2015

In this study, large-eddy simulation is combined with a turbine model to investigate the influence of atmospheric thermal stability on wind-turbine wakes. The simulation results show that atmospheric stability has a significant effect on the spatial distribution of the mean velocity deficit and turbulence statistics in the wake region as well as the wake meandering characteristics downwind of the turbine. In particular, the enhanced turbulence level associated with positive buoyancy under the convective condition leads to a relatively larger flow entrainment and, thus, a faster wake recovery. For the particular cases considered in this study, the growth rate of the wake is about 2.4 times larger for the convective case than for the stable one. Consistent with this result, for a given distance downwind of the turbine, wake meandering is also stronger under the convective condition compared with the neutral and stable cases. It is also shown that, for all the stability cases, the growth rate of the wake and wake meandering in the vertical direction is smaller compared with the ones in the lateral direction. This is mainly related to the different turbulence levels of the incoming wind in the different directions, together with the anisotropy imposed by the presence of the ground. It is also found that the wake velocity deficit is well characterized by a modified version of a recently proposed analytical model that is based on mass and momentum conservation and the assumption of a self-similar Gaussian distribution of the velocity deficit. Specifically, using a two-dimensional elliptical (instead of axisymmetric) Gaussian distribution allows to account for the different lateral and vertical growth rates, particularly in the convective case, where the non-axisymmetry of the wake is stronger. Detailed analysis of the resolved turbulent kinetic energy budget in the wake reveals also that thermal stratification considerably affects the magnitude and spatial distribution of the turbulence production, dissipation, and transport terms.
Spectra of surface plasmon polariton enhanced electroluminescence from electroformed Al-Al2O3-Ag diodes
Authors: Hickmott T. W.
Published: March 2015

Narrow band-pass filters have been used to measure the spectral distribution of electroluminescent photons with energies between 1.8 eV and 3.0 eV from electroformed Al-Al2O3-Ag diodes with anodic Al2O3 thicknesses between 12 nm and 18 nm. Electroforming of metal-insulator-metal (MIM) diodes is a non-destructive dielectric breakdown that results in a conducting channel in the insulator and changes the initial high resistance of the MIM diode to a low resistance state. It is a critical step in the development of resistive-switching memories that utilize MIM diodes as the active element. Electroforming of Al-Al2O3-Ag diodes in vacuum results in voltage-controlled negative resistance (VCNR) in the current-voltage (I-V) characteristics. Electroluminescence (EL) and electron emission into vacuum (EM) develop simultaneously with the current increase that results in VCNR in the I-V characteristics. EL is due to recombination of electrons injected at the Al-Al2O3 interface with radiative defect centers in Al2O3. Measurements of EL photons between 1.8 eV and 3.0 eV using a wide band-pass filter showed that EL intensity is exponentially dependent on Al2O3 thickness for Al-Al2O3-Ag diodes between 12 nm and 20 nm thick. Enhanced El intensity in the thinnest diodes is attributed to an increase in the spontaneous emission rate of recombination centers due to high electromagnetic fields generated in Al2O3 when EL photons interact with electrons in Ag or Al to form surface plasmon polaritons at the Al2O3-Ag or Al2O3-Al interface. El intensity is a maximum at 2.0–2.2 eV for Al-Al2O3-Ag diodes with Al2O3 thicknesses between 12 nm and 18 nm. EL in diodes with 12 nm or 14 nm of Al2O3 is enhanced by factors of 8–10 over EL from a diode with 18 nm of Al2O3. The extent of EL enhancement in the thinnest diodes can vary significantly between samples. A narrow band of recombination centers was found in one Al-Al2O3-Ag diode with 12 nm of Al2O3; it had EL intensity 100 times greater at 2.15 eV than the diode with 18 nm of Al2O3. EL intensity for photons with energies greater than 2.6 eV is nearly the same for all diodes.
The effect of large amplitude motions on the vibrational intensities in hydrogen bonded complexes
Authors: Mackeprang Kasper , Hänninen Vesa , Halonen Lauri , Kjaergaard Henrik G.
Published: March 2015

We have developed a model to calculate accurately the intensity of the hydrogen bonded XH-stretching vibrational transition in hydrogen bonded complexes. In the Local Mode Perturbation Theory (LMPT) model, the unperturbed system is described by a local mode (LM) model, which is perturbed by the intermolecular modes of the hydrogen bonded system that couple with the intramolecular vibrations of the donor unit through the potential energy surface. We have applied the model to three complexes containing water as the donor unit and different acceptor units, providing a series of increasing complex binding energy: H2O⋯N2, H2O⋯H2O, and H2O⋯NH3. Results obtained by the LMPT model are presented and compared with calculated results obtained by other vibrational models and with previous results from gas-phase and helium-droplet experiments. We find that the LMPT model reduces the oscillator strengths of the fundamental hydrogen bonded OH-stretching transition relative to the simpler LM model.
The associating lattice gas in the presence of interacting solutes
Authors: Girardi Mauricio , Szortyka Marcia M. , Henriques Vera B. , Barbosa Marcia C.
Published: March 2015

We have investigated the phase diagram of a statistical model for hydrogen-bonding solutions for polar solutes. The structured solvent is represented by an associating lattice gas, which presents anomalous density and liquid-liquid coexistence. Polar solute particles and solvent particles interact attractively, while the solvent-solvent interaction is made directional through bonding arms, which mimic hydrogen bonds. The model behavior is obtained via Monte Carlo simulations in the grand-canonical ensemble, for different sets of parameters. For small solute chemical potential and weak attraction between solute and solvent particles, addition of solute yields a shift in the transition lines of the pure solvent. This is the scenario explored by different authors, in the pursuit of stabilizing the water liquid-liquid coexistence line. However, as we show, in the case of larger solute chemical potentials, or of stronger solute-solvent attractions, new phases may arise.
Interfacial spin-filter assisted spin transfer torque effect in Co/BeO/Co magnetic tunnel junction
Authors: Tang Y.-H. , Chu F.-C.
Published: March 2015

The first-principles calculation is employed to demonstrate the spin-selective transport properties and the non-collinear spin-transfer torque (STT) effect in the newly proposed Co/BeO/Co magnetic tunnel junction. The subtle spin-polarized charge transfer solely at O/Co interface gives rise to the interfacial spin-filter (ISF) effect, which can be simulated within the tight binding model to verify the general expression of STT. This allows us to predict the asymmetric bias behavior of non-collinear STT directly via the interplay between the first-principles calculated spin current densities in collinear magnetic configurations. We believe that the ISF effect, introduced by the combination between wurtzite-BeO barrier and the fcc-Co electrode, may open a new and promising route in semiconductor-based spintronics applications.
Properties of solitary kinetic Alfvén wave in a plasma with non-extensive electrons
Authors: Liu Y. , Shi Z. F. , Han Y. , Dai B.
Published: March 2015

The properties of solitary kinetic Alfvén waves (SKAWs) in a finite β plasma with three dimensional non-extensive electrons are investigated. Numerical results show that there only exists sub-Alfvénic hump type SKAW. The down limit of the Alfvén Mach number Mz for the existence of SKAW increases with the increase of β. Whereas, it varies non-monotonously with respect to electron nonextensive parameter q for a given β. In the range of Mz where SKAWs exist for different values of q, a bigger q results in a denser soliton structure, making the magnitude of the static electric field along the background magnetic field enhanced. However, the dependence of the amplitudes of the perpendicular magnetic and electric field on q is non-monotonous.
High temperature oxidation and its induced coercivity loss of a 2:17 type SmCo-based magnet
Authors: Wang X. , Peng X. , Zhao H. , Guo Zh. , Li W. , Wang F.
Published: March 2015

Oxidation has been explained as one possibility for unacceptable and irreversible coercivity loss of 2:17 type SmCo-based magnets at high temperatures over 550 °C, but the question for how oxidation affects coercivity in the magnet has not been fundamentally answered. In this work, oxidation and its induced degradation of the magnetic phases of a Sm(CobalFe0.22Cu0.08Zr0.02)7.5 magnet in air at 600 °C have been investigated by using transmission electron microscopy and correlated with the demagnetization curves measured. It shows that the coercivity loss, which is significantly increased with oxidation time, is small and independent of time in the magnet unaffected by oxidation. The reason lies in that the 2:17 cell and 1:5 cell boundary, although they have been completely disintegrated in the oxidized part by external oxidation of Co, Fe, and Cu and internal oxidation of Sm, remains in the unoxidized part except that 1:5 boundary close to the oxidized part is decreased in thickness and Cu content.
Investigation of dielectric relaxation, Jahn-Teller distortion, and magnetic ordering in Y substituted Pr1−xYxMnO3 (0.1 ≤ x ≤ 0.4)
Authors: Yadav Ruchika , Nair Harikrishnan S. , Kumar Amit , Adiga Shilpa , Bhat H. L. , Yusuf S. M. , Elizabeth Suja
Published: March 2015

We report structural, magnetic, and dielectric properties of the perovskite compound Pr1−xYxMnO3 (0.1 ≤ x ≤ 0.4) studied using dc magnetization, ac susceptibility, neutron powder diffraction, and dielectric techniques. These compounds crystallize in orthorhombic space group (Pnma) in the temperature range 5–300 K. The Mn-O-Mn bond angle decreases with the Y substitution along with an increase in the Jahn-Teller distortion. The Jahn-Teller distortion for Pr0.9Y0.1MnO3 shows an anomalous change near 50 K, below which it falls sharply. Neutron powder diffraction patterns of all reported compositions at low temperature constitute additional magnetic Bragg peaks that suggest magnetic ordering. Magnetic reflections were indexed in the nuclear lattice with the propagation vector k = (0, 0, 0). Rietveld refinement of powder patterns conform to A type antiferromagnetic ordering where moments are aligned ferromagnetically in a–c plane and coupled nearly antiferromagnetically along b-axis resulting in a net ferromagnetic component along the b-direction. The antiferromagnetic transition temperature was deduced from dc magnetization and ac susceptibility data. The transition temperature decreases by nearly 22 K (from 81 K to 59 K) as yttrium content (x) increases from 0.1 to 0.4. Measurements reveal strong frequency dispersion in dielectric constant and dielectric loss. Activation energy and relaxation time are estimated from the Arrhenius plot. It is further shown that relaxation behaviour is altered with yttrium doping concentration.
Deep brain transcranial magnetic stimulation using variable “Halo coil” system
Authors: Meng Y. , Hadimani R. L. , Crowther L. J. , Xu Z. , Qu J. , Jiles D. C.
Published: March 2015

Transcranial Magnetic Stimulation has the potential to treat various neurological disorders non-invasively and safely. The “Halo coil” configuration can stimulate deeper regions of the brain with lower surface to deep-brain field ratio compared to other coil configurations. The existing “Halo coil” configuration is fixed and is limited in varying the site of stimulation in the brain. We have developed a new system based on the current “Halo coil” design along with a graphical user interface system that enables the larger coil to rotate along the transverse plane. The new system can also enable vertical movement of larger coil. Thus, this adjustable “Halo coil” configuration can stimulate different regions of the brain by adjusting the position and orientation of the larger coil on the head. We have calculated magnetic and electric fields inside a MRI-derived heterogeneous head model for various positions and orientations of the coil. We have also investigated the mechanical and thermal stability of the adjustable “Halo coil” configuration for various positions and orientations of the coil to ensure safe operation of the system.
Temperature dependent magnetic anisotropy of epitaxial Co2FeAl films grown on GaAs
Authors: Qiao Shuang , Nie Shuaihua , Zhao Jianhua , Zhang Xinhui
Published: March 2015

Co2FeAl films with different thickness were prepared at different temperature by molecular beam epitaxy. Their magnetic anisotropy was studied by rotating magneto-optical Kerr rotation measurements under different temperature. It is found that the cubic anisotropy depends only on the temperature-dependent fourth order magneto-elastic coefficients. However, the results of growth and measurement temperature-dependent uniaxial anisotropy suggest that the uniaxial anisotropy of Co2FeAl films may be attributed to contributions from both shear strain and anisotropic interfacial bonding. Our experimental findings proposed a new point of view to understand the origin of magnetic anisotropy in ferromagnet/GaAs(001) heterostructures.
Correlation between stoichiometry, strain, and metal-insulator transitions of NdNiO3 films
Authors: Hauser Adam J. , Mikheev Evgeny , Moreno Nelson E. , Hwang Jinwoo , Zhang Jack Y. , Stemmer Susanne
Published: March 2015

The interplay of film stoichiometry and strain on the metal-insulator transition (MIT) and Hall coefficient of NdNiO3 films grown under different conditions is investigated. Unstrained lattice parameters and lattice mismatch strains are evaluated for films grown under a range of growth pressures and on different substrates. It is shown that both the temperature of the MIT and the Hall coefficient in the metallic phase are highly sensitive to film strain. In films grown with lower oxygen/total growth pressures, very large compressive in-plane strains can be obtained, which can act to suppress the MIT. Both the Hall coefficient and the temperature of the MIT are relatively insensitive to growth pressure, provided that films under the same strain are compared. The results support an itinerant picture of the transition that is controlled by the Ni eg bands, and that is relatively insensitive to changes in film stoichiometry.
An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis
Authors: Wang Shuaiqin , Sun Yujia , Gan Wupeng , Liu Yan , Xiang Guangxin , Wang Dong , Wang Lei , Cheng Jing , Liu Peng
Published: March 2015

We present an integrated microfluidic device capable of performing single-stranded DNA (ssDNA) preparation and magnetic bead-based microarray analysis with a white-light detection for detecting mutations that account for hereditary hearing loss. The entire operation process, which includes loading of streptavidin-coated magnetic beads (MBs) and biotin-labeled polymerase chain reaction products, active dispersion of the MBs with DNA for binding, alkaline denaturation of DNA, dynamic hybridization of the bead-labeled ssDNA to a tag array, and white-light detection, can all be automatically accomplished in a single chamber of the microchip, which was operated on a self-contained instrument with all the necessary components for thermal control, fluidic control, and detection. Two novel mixing valves with embedded polydimethylsiloxane membranes, which can alternately generate a 3-μl pulse flow at a peak rate of around 160 mm/s, were integrated into the chip for thoroughly dispersing magnetic beads in 2 min. The binding efficiency of biotinylated oligonucleotides to beads was measured to be 80.6% of that obtained in a tube with the conventional method. To critically test the performance of this automated microsystem, we employed a commercial microarray-based detection kit for detecting nine mutation loci that account for hereditary hearing loss. The limit of detection of the microsystem was determined as 2.5 ng of input K562 standard genomic DNA using this kit. In addition, four blood samples obtained from persons with mutations were all correctly typed by our system in less than 45 min per run. The fully automated, “amplicon-in-answer-out” operation, together with the white-light detection, makes our system an excellent platform for low-cost, rapid genotyping in clinical diagnosis.
Room temperature optical anisotropy of a LaMnO3 thin-film induced by ultra-short pulse laser
Authors: Munkhbaatar Purevdorj , Marton Zsolt , Tsermaa Baatarchuluun , Choi Woo Seok , Seo Sung S. Ambrose , Kim Jin Seung , Nakagawa Naoyuki , Hwang Harold Y. , Lee Ho Nyung , Myung-Whun Kim
Published: March 2015

We observed ultra-short laser pulse-induced transient optical anisotropy in a LaMnO3 thin film. The anisotropy was induced by laser pulse irradiation with a fluence of less than 0.1 mJ/cm2 at room temperature. The transmittance and reflectance showed strong dependence on the polarization states of the pulses. For parallel and perpendicular polarization states, there exists a difference of approximately 0.2% for transmittance and 0.05% for reflectance at 0.3 ps after the irradiation with a pump pulse, respectively. The theoretical values for optical transmittance and reflectance with an assumption of an orbital ordering of 3d eg electrons in Mn3+ ions showed good agreement with the experimental results, demonstrating that the transient optical anisotropy in LaMnO3 thin film is due to the photo-induced symmetry-breaking of orbital ordering in excited states.
Direct synthesis of large area graphene on insulating substrate by gallium vapor-assisted chemical vapor deposition
Authors: Murakami Katsuhisa , Tanaka Shunsuke , Hirukawa Ayaka , Hiyama Takaki , Kuwajima Tomoya , Kano Emi , Takeguchi Masaki , Fujita Jun-ichi
Published: March 2015

A single layer of graphene with dimensions of 20 mm × 20 mm was grown directly on an insulating substrate by chemical vapor deposition using Ga vapor catalysts. The graphene layer showed highly homogeneous crystal quality over a large area on the insulating substrate. The crystal quality of the graphene was measured by Raman spectroscopy and was found to improve with increasing Ga vapor density on the reaction area. High-resolution transmission electron microscopy observations showed that the synthesized graphene had a perfect atomic-scale crystal structure within its grains, which ranged in size from 50 nm to 200 nm.
Using digital data collection tools to improve overall cost-efficiency and provide timely analysis for decision making during invasive species eradication campaigns
Authors: Will David J. , Campbell Karl J. , Holmes Nick D.
Published: March 2015

Context Worldwide, invasive vertebrate eradication campaigns are increasing in scale and complexity, requiring improved decision making tools to achieve and validate success. For managers of these campaigns, gaining access to timely summaries of field data can increase cost-efficiency and the likelihood of success, particularly for successive control-event style eradications. Conventional data collection techniques can be time intensive and burdensome to process. Recent advances in digital tools can reduce the time required to collect and process field information. Through timely analysis, efficiently collected data can inform decision making for managers both tactically, such as where to prioritise search effort, and strategically, such as when to transition from the eradication phase to confirmation monitoring. Aims We highlighted the advantages of using digital data collection tools, particularly the potential for reduced project costs through a decrease in effort and the ability to increase eradication efficiency by enabling explicit data-informed decision making. Methods We designed and utilised digital data collection tools, relational databases and a suite of analyses during two different eradication campaigns to inform management decisions: a feral cat eradication utilising trapping, and a rodent eradication using bait stations. Key results By using digital data collection during a 2-year long cat eradication, we experienced an 89% reduction in data collection effort and an estimated USD42 845 reduction in total costs compared with conventional paper methods. During a 2-month rodent bait station eradication, we experienced an 84% reduction in data collection effort and an estimated USD4525 increase in total costs. Conclusions Despite high initial capital costs, digital data collection systems provide increasing economics as the duration and scale of the campaign increases. Initial investments can be recouped by reusing equipment and software on subsequent projects, making digital data collection more cost-effective for programs contemplating multiple eradications. Implications With proper pre-planning, digital data collection systems can be integrated with quantitative models that generate timely forecasts of the effort required to remove all target animals and estimate the probability that eradication has been achieved to a desired level of confidence, thus improving decision making power and further reducing total project costs.
Responses of two sympatric sand lizards to exotic forestations in the coastal dunes of Argentina: some implications for conservation
Authors: Cruz Félix Benjamín
Published: March 2015

Context Exotic forestations may modify habitat quality, affecting native animal populations that require specific microhabitats to remain viable. Aims We determined whether abundances and body condition of the lizard species Liolaemus wiegmannii and L. multimaculatus differed between forested and non-forested dunes. We also examined what environmental attributes are important in explaining the potential differences. Methods We sampled six sites of 300 ha each. Three of these sites had original vegetation and three were forested with exotic Acacia longifolia. We traced 120 transects per site searching for lizards. Key results Lizards were two times more abundant in non-forested sites than in sites covered by acacia trees (even as low as a fourth of the area). Sites with high densities of acacia (≥78% of coverage) had the lowest abundance of lizards. In forested sites, the snout–vent length of L. wiegmannii was 10% smaller and relative body mass 22% lower than in non-forested sites. We found no differences in the body size of L. multimaculatus. Conclusions The replacement of the native vegetation by A. longifolia has negative effects on lizard species, representing a substantial threat to L. wiegmannii and particularly to L. multimaculatus, a threatened status species. Structural and thermal characteristics of the non-forested sites seemed to be more favourable for the abundance and body condition, whereas the dense vegetation and the low temperatures on the forested sites might explain the lower presence of lizards. Implications We recommend that before the implementation of future forestation plans in the pampasic coastal dunes, the deleterious consequences that this practice generates on native lizard fauna must be considered. When necessary, we recommend that A. longifolia be planted so that the coverage does not exceed a quarter of the total area, so as to prevent the formation of continuous (or closed) forest patches and to maintain the structural heterogeneity of the habitat that these lizards need to survive. In the most affected areas, eradication and control strategies may help reduce the advancement of this exotic plant over the areas intended for conservation.
Behavioural responses of wintering black-faced spoonbills (Platalea minor) to disturbance
Authors: Choi Chang-Yong , Nam Hyun-Young , Lee Woo-Shin
Published: March 2015

Context Behavioural responses can be used to understand the impacts of disturbance on animals and to develop management strategies, and there is considerable conservation interest in quantifying the effects of disturbances on wild animals. Aims We seek to formulate a management plan for the endangered black-faced spoonbills (Platalea minor) in a non-breeding ground, on the basis of their behavioural responses to different types of stimulus categorised by threat level (threatening vs non-threatening) and human involvement (anthropogenic vs natural). Methods We documented 16 stimuli from 379 disturbance events through continuous observation on 31 daily selected focal individuals, and estimated flight distances caused by human approach under different conditions at a non-breeding site in Korea. Key results The spoonbills showed the strongest behavioural response to the non-threatening anthropogenic stimuli, and human approach followed by motor vehicles caused longer responses per event than did any other type of disturbing stimulus. Flight distance caused by human approach varied depending on conditions; inactive spoonbills in mixed-species associations started to flee at the greatest distance (197.4 m, with a 50% probability), whereas the spoonbills in a single conspecific flock were the most tolerant of human approaches, regardless of their activeness (61.0–61.7 m, with a 50% probability). Conclusions Human approach had been identified as the most important disturbing stimulus that should be controlled as a priority. We also suggest that black-faced spoonbills benefit from the presence of other waterbirds and exploit them as an early warning system. Implications The tolerance of sympatric species as well as the behavioural response of target species should be considered when a buffer area for wildlife management, particularly against human disturbance, is planned. How the site has been used and what the species composition is are still important components for the design of safe refuges and roosts.
Modeling memory consolidation during posttraining periods in cerebellovestibular learning
Authors: Yamazaki Tadashi , Nagao Soichi , Lennon William , Tanaka Shigeru
Published: March 2015

Significance

An efficient way to form a new declarative memory is to repeat a short-term training many times with a rest between the training sessions, because the learned memory is consolidated after training. This suggests that the brain still keeps actively working even after training, but the synaptic dynamics during posttraining periods has been studied rarely. The posttraining memory consolidation is also observed in cerebellar motor learning. To investigate the mechanism, we formulated a simple theoretical model of the cerebellum with a minimal number of elements and learning-related changes in synaptic efficacy at multiple locations. Computer simulations with this model closely reproduced learning behavior for oculomotor reflexes in wild-type mice and explained peculiar learning behavior in genetically manipulated mice.
Quantum technologies with hybrid systems
Authors: Kurizki Gershon , Bertet Patrice , Kubo Yuimaru , Mølmer Klaus , Petrosyan David , Rabl Peter , Schmiedmayer Jörg
Published: March 2015

An extensively pursued current direction of research in physics aims at the development of practical technologies that exploit the effects of quantum mechanics. As part of this ongoing effort, devices for quantum information processing, secure communication, and high-precision sensing are being implemented with diverse systems, ranging from photons, atoms, and spins to mesoscopic superconducting and nanomechanical structures. Their physical properties make some of these systems better suited than others for specific tasks; thus, photons are well suited for transmitting quantum information, weakly interacting spins can serve as long-lived quantum memories, and superconducting elements can rapidly process information encoded in their quantum states. A central goal of the envisaged quantum technologies is to develop devices that can simultaneously perform several of these tasks, namely, reliably store, process, and transmit quantum information. Hybrid quantum systems composed of different physical components with complementary functionalities may provide precisely such multitasking capabilities. This article reviews some of the driving theoretical ideas and first experimental realizations of hybrid quantum systems and the opportunities and challenges they present and offers a glance at the near- and long-term perspectives of this fascinating and rapidly expanding field.
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity
Authors: Blair Jessica M. A. , Bavro Vassiliy N. , Ricci Vito , Modi Niraj , Cacciotto Pierpaolo , Kleinekathӧfer Ulrich , Ruggerone Paolo , Vargiu Attilio V. , Baylay Alison J. , Smith Helen E. , Brandon Yvonne , Galloway David , Piddock Laura J. V.
Published: March 2015

Significance

Genome sequencing of a multidrug-resistant clinical isolate of
Salmonella
Typhimurium from a patient that failed ciprofloxacin therapy revealed a mutation in the efflux pump gene,
acrB
. Computational modelling revealed that the G288D substitution changed the binding of drugs to the distal binding pocket of AcrB. The mutation was recreated in an unrelated
Salmonella
strain and also in
Escherichia coli
; in both species the efflux of ciprofloxacin was increased by the mutation, explaining its resistant phenotype. This is the first time a substitution within an efflux pump protein has been shown to cause drug resistance. Importantly, the finding that one amino acid change can cause resistance to some drugs, but susceptibility to others, informs those developing new antibiotics.
Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation
Authors: Suzuki Sho W. , Yamamoto Hayashi , Oikawa Yu , Kondo-Kakuta Chika , Kimura Yayoi , Hirano Hisashi , Ohsumi Yoshinori
Published: March 2015

Significance

Autophagy is a highly conserved degradative process in eukaryotes. In response to starvation, a number of autophagosome-related (Atg) proteins are recruited, and these proteins govern the process of autophagosome formation. Atg9 vesicles are thought to play an essential role in the nucleation step, but it remains unclear how Atg9 vesicles are localized to the site of autophagosome formation. In this study, we found that Atg9 interacts with the HORMA (from Hop1, Rev7, and Mad2) domain of Atg13. Atg13 mutants lacking the Atg9-binding region fail to recruit Atg9 vesicles to the site of autophagosome formation and exhibit severe defects in autophagy. Thus, the HORMA domain of Atg13 facilitates recruitment of Atg9 vesicles during autophagosome formation. Our studies provide a molecular insight into how Atg9 vesicles become part of the autophagosomal membrane.
Coastal Wetland Support of Great Lakes Fisheries: Progress from Concept to Quantification
Authors: Trebitz Anett S. , Hoffman Joel C.
Published: March 2015

Fishery support is recognized as a valuable ecosystem service provided by aquatic systems, but it is harder to quantify than to describe conceptually. In this paper, we combine data on fish inhabiting Great Lakes coastal wetlands (GLCWs) with information on commercial and recreational harvest and the piscivore forage base to develop quantitative understanding of the multiple species involved in direct and indirect fishery support of this complex fishery. We then examine patterns of species co‐occurrence and life history and relationships to GLCW conditions in order to identify fishery support metrics useful in aggregating species patterns and evaluating management outcomes. Our criteria for wetland prevalence (≥10% occurrence) and fishery importance (≥1% of recreational or commercial harvest in one or more of the Great Lakes or having a major forage fish role) yielded 21 wetland‐using, fishery‐relevant species representing multiple taxonomic groups and life history attributes. Wetland‐using species are estimated to make up half the biomass and 60% of the dollar value of the fish landed commercially and ∼80% of the fish numbers harvested recreationally. All of the GLCWs studied supported species of interest to recreational and commercial fishers but with widely varying composition. A few key habitat characteristics (e.g., vegetation structure) are broadly predictive of the types of sport and panfish present, with more degraded GLCWs generally supporting abundant but lower‐value taxa (rough‐fish species) and less degraded GLCWs supporting fewer but higher‐value taxa (sport and panfish species). No single taxonomic or functional metric seems adequate to capture the diversity of fishery‐relevant species supported by GLCWs; fishery support needs to be understood and managed in a multimetric context.

Received May 16, 2014; accepted October 15, 2014
Isolation, identification, and formation conditions of a novel Maillard yellowish pigment, pyrrolothiazolate
Authors: Noda Kyoko , Yamada Shinji , Murata Masatsune
Published: March 2015

We isolated a novel yellow pigment from a model Maillard reaction system containing l-cysteine, l-lysine, and glucose and identified it as 6-hydroxy-3[R],7a[S]-dimethyl-7-oxo-2,3-dihydropyrrolo[2,1-b]thiazole-3-calboxylic acid. This compound was a novel pyrrolothiazole derivative carrying a carboxy group and was named pyrrolothiazolate. This compound showed the absorption maxima at 300 and 360 nm under acidic and neutral conditions, while 320 and 400 nm did under alkaline conditions. Pyrrolothiazolate formed from cysteine and glucose was the major low-molecular-weight Maillard pigment in the reaction mixture, and its formation was stimulated by adding lysine to the reaction cocktail. After heating at 110 °C for 2 h, 1–2 mg/mL of pyrrolothiazolate was formed in a reaction mixture containing 100 mM cysteine, 200 mM lysine, and 300 mM glucose dissolved in 0.5 m acetate buffer (pH 6.0) or 0.5 m phosphate buffer (pH 6.5).
Effects of Fish Oil Sparing on Fillet Fatty Acid Composition in Hybrid Striped Bass Are Influenced by Dietary Levels of Saturated and Unsaturated Fatty Acids
Authors: Trushenski Jesse T , Crouse Curtis C , Rombenso Artur N
Published: March 2015

We assessed the growth performance and fillet fatty acid composition of hybrid Striped Bass (White Bass Morone chrysops × Striped Bass M. saxatilis; initial weight = 29.1 ± 0.2 g [mean ± SE]) fed diets containing only menhaden fish oil (100 FISH); fully hydrogenated saturated fatty acid (SFA)-rich soybean oil (100 SFA SOY); 75:25, 50:50, 25:75, or 0:100 blends of fish oil and standard C18 polyunsaturated fatty acid (C18 PUFA)-rich soybean oil (25 PUFA SOY, 50 PUFA SOY, 75 PUFA SOY, 100 PUFA SOY); or nonhydrogenated monounsaturated fatty acid (MUFA)-rich soybean oil (25 MUFA SOY, 50 MUFA SOY, 75 MUFA SOY, 100 MUFA SOY) for 8 weeks. Feed conversion ratio varied, with the 100 SFA SOY feed yielding a significantly greater value (1.3) than the rest of the feeds (0.9–1.0). Although significant treatment effects were not observed for weight gain, specific growth rate, feed intake, or organosomatic indices, some variation was observed, suggesting some minor (albeit not significant) loss of growth performance among fish fed the 100 SFA SOY and, to a lesser extent, 100 MUFA SOY feeds. Fillets of fish fed diets containing soybean-derived lipids had reduced levels of fish-oil-associated, n-3 long-chain polyunsaturated fatty acids (LC-PUFAs, i.e., 20:5[n-3] and 22:6[n-3]) compared with those fed the 100 FISH feed. Conversely, fillets of fish fed diets containing C18 PUFA-rich soybean oil and nonhydrogenated MUFA-rich soybean oil had higher levels of these fatty acids (i.e., 18:2[n-6] and 18:1[n-9], respectively). Although the 100 SFA SOY diet contained substantially more SFAs (i.e., 18:0) than the other diets, these fatty acids were not proportionally elevated in the fillets. It is possible that blending SFA-rich lipids with ingredients containing some level of unsaturated fatty acids may be a means of addressing digestibility limitations while still mitigating the effects of fish oil sparing on tissue composition.
Comparison of Two Trap Net Sizes for Collecting Walleye Broodstock
Authors: Blackwell Brian G , Kaufman Todd M , Moos Tyrel S , Lucchesi David O
Published: March 2015

Trap nets are commonly used to collect Walleye Sander vitreus broodstock for spawning as part of culture and stocking programs. We compared overnight catch rates of Walleyes captured in two trap net sizes (small [0.9- × 1.5-m frame, 0.9-m-diameter hoop, single throat, 0.9- × 15.2-m lead, 19-mm knotted mesh] and large [1.5- × 1.8-m frame, 1.5-m-diameter hoop, double throated, 1.5- × 30.5-m lead, 19-mm knotless mesh]) to determine the relative efficiency of each size for broodstock collection. Sampling was completed during the spring of 2013 and 2014 soon after ice-out at three waters in South Dakota. In all but two cases, total Walleye CPUE in large trap nets was significantly higher than that in small trap nets. However, length-frequency distributions between the two net sizes generally were similar. The use of large trap nets will result in higher numbers of broodstock collected than with the smaller nets, likely offsetting the additional labor required to deploy and retrieve the larger traps.
Convexity and cylindrical estimates for mean curvature flow in the sphere
Authors: Nguyen Huy
Published: March 2015

We study mean curvature flow in the sphere with the quadratic curvature condition

|

A

|

2

≤

1

n
−
2

H

2

+
4
K

|A|^{2} \leq \frac { 1}{n-2} H^{2} + 4 K

which is related to but different from two-convexity for submanifolds of the sphere. We classify type

I
I

singularities with no further hypotheses. If

H
>
0

H> 0

, then we apply the Huisken-Sinestrari convexity estimates to this situation and show that we can classify type

I
I

II

singularities. This shows that at a singularity the surface is asymptotically convex. We then prove cylindrical estimates for the mean curvature flow and a pointwise gradient estimate which shows that near a singularity the surface is quantitatively convex.
Corners of Cuntz-Krieger algebras
Authors: Arklint Sara , Ruiz Efren
Published: March 2015

We show that if

A
A

is a unital

C

∗

C^{*}

-algebra and

B
B

is a Cuntz-Krieger algebra for which

A
⊗

K

≅
B
⊗

K

A \otimes \mathbb {K} \cong B \otimes \mathbb {K}

, then

A
A

is a Cuntz-Krieger algebra. Consequently, corners of Cuntz-Krieger algebras are Cuntz-Krieger algebras.
Some Beurling–Fourier algebras on compact groups are operator algebras
Authors: Ghandehari Mahya , Lee Hun Hee , Samei Ebrahim , Spronk Nico
Published: March 2015

LetGGbe a compact connected Lie group. The question of when a weighted Fourier algebra onGGis completely isomorphic to an operator algebra will be investigated in this paper. We will demonstrate that the dimension of the group plays an important role in the question. More precisely, we will get a positive answer to the question when we consider a polynomial type weight coming from a length function onGGwith the order of growth strictly bigger than half of the dimension of the group. The case ofSU(n)SU(n)will be examined, focusing more on the details including negative results. The proof for the positive directions depends on a non-commutative version of the Littlewood multiplier theory, which we will develop in this paper, and the negative directions will be taken care of by restricting to a maximal torus.
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals
Authors: Abascal Federico , Tress Michael L. , Valencia Alfonso
Published: March 2015

Summary: Transposable elements constitute a large fraction of vertebrate genomes and, during evolution, may be co-opted for new functions. Exonization of transposable elements inserted within or close to host genes is one possible way to generate new genes, and alternative splicing of the new exons may represent an intermediate step in this process. The genes TMPO and ZNF451 are present in all vertebrate lineages. Although they are not evolutionarily related, mammalian TMPO and ZNF451 do have something in common—they both code for splice isoforms that contain LAP2alpha domains. We found that these LAP2alpha domains have sequence similarity to repetitive sequences in non-mammalian genomes, which are in turn related to the first ORF from a DIRS1-like retrotransposon. This retrotransposon domestication happened separately and resulted in proteins that combine retrotransposon and host protein domains. The alternative splicing of the retrotransposed sequence allowed the production of both the new and the untouched original isoforms, which may have contributed to the success of the colonization process. The LAP2alpha-specific isoform of TMPO (LAP2α) has been co-opted for important roles in the cell, whereas the ZNF451 LAP2alpha isoform is evolving under strong purifying selection but remains uncharacterized.

Contact: mtress@cnio.es or valencia@cnio.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides
Authors: Madeira Fábio , Tinti Michele , Murugesan Gavuthami , Berrett Emily , Stafford Margaret , Toth Rachel , Cole Christian , MacKintosh Carol , Barton Geoffrey J.
Published: March 2015

Motivation: The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of >2000 potential interactors identified in high-throughput experiments.

Results: Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from −6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful.

Availability and implementation: A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.

Contact:  cmackintosh@dundee.ac.uk or gjbarton@dundee.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Very high energy emission as a probe of relativistic magnetic reconnection in pulsar winds
Authors: Mochol Iwona , Pétri Jérôme
Published: March 2015

The population of gamma-ray pulsars, including Crab observed in the TeV range, and Vela detected above 50 GeV, challenges existing models of pulsed high-energy emission. Such models should be universally applicable, yet they should account for spectral differences among the pulsars. We show that the gamma-ray emission of Crab and Vela can be explained by synchrotron radiation from the current sheet of a striped wind, expanding with a modest Lorentz factor Γ ≲ 100 in the Crab case, and Γ ≲ 50 in the Vela case. In the Crab spectrum, a new synchrotron self-Compton component is expected to be detected by the upcoming experiment CTA. We suggest that the gamma-ray spectrum directly probes the physics of relativistic magnetic reconnection in the striped wind. In the most energetic pulsars, like Crab, with $\dot{E}_{38}^{3/2}/P_{-2}\gtrsim 0.002$ (where $\dot{E}$ is the spin-down power, P is the pulsar period, and X = Xi × 10i in CGS units), reconnection proceeds in the radiative cooling regime and results in a soft power-law distribution of cooling particles; in less powerful pulsars, like Vela, particle energization is limited by the current sheet size, and a hard particle spectrum reflects the acceleration mechanism. A strict lower limit on the number density of radiating particles corresponds to emission close to the light cylinder, and, in units of the GJ density, it is ≳ 0.5 in the Crab wind, and κ ≳ 0.05 in the Vela wind.
Service User Involvement in Research
Authors: Wallcraft Jan
Published: March 2015

This chapter traces the development of service user involvement in research and user-controlled research, from its origins in the early 1990s to the present day where mental health researchers are expected to involve service users. It looks at why service users wanted to be involved in research and their issues of concern, including the effects of treatment, staff attitudes, and human rights. Values in research are linked to the epistemological underpinnings of research, and it is argued that service users’ ways of knowing based on experience are in conflict with mainstream research based on claims of objectivity and neutrality. Service user involvement at all levels from consultation to control is explored with examples. The benefits and problems of working in partnership are explored, and the chapter ends with an assessment of the impact of involvement in research and how it can lead to change.
Theatre
Authors: Hutson Lorna
Published: March 2015

In the 1980s, New Historicist critics suggested that Renaissance theater was marked by the Reformation; specifically, that it expressed the vanishing of ritual and sacrament from ordinary people’s lives. More recently, critics like Sarah Beckwith have shown how pre-Reformation theater worked as ritual and sacrament by revealing the extent to which it was implicated in the jurisdiction of confession, penance and absolution for sin. This article revisits the question of how the Reformation abolition of annual mandatory confession affected theater. It qualifies both the New Historicist view of Renaissance theater as evacuated ritual and Beckwith’s view of the Protestant abolition of confession as an exteriorization of penance. Reading the first English Renaissance neoclassical comedy in English, Gammer Gurton’s Needle (c.1553-60), the article shows how profoundly its neoclassical concern with proof and evidence is tied in with a rejection of priestly confession and an invitation to parishioners and neighbors to be more skeptical and less credulous in believing the worst of one another.
Utopian Pleasure
Authors: Greenblatt Stephen
Published: March 2015

Lucretius’s didactic masterpiece De rerum natura advances propositions, drawn from Epicurus, which the Renaissance book-hunter Poggio Bracciolini and his contemporaries found difficult to absorb. Epicurus’s convictions included an insistence on the superiority of reason over faith, a steadfast refusal of pious fear, a concomitant refusal to believe in afterlife, a belief in the mortality of the soul, a rejection of religion, and an advocacy of the pursuit of pleasure. To many orthodox Christians such arguments were the very definition of atheism. This article examines three responses to De rerum natura: “The Renunciation of Youthful Indiscretion” by Marsilio Ficino, “The Divorce Settlement” by Poggio Bracciolini, and “Dialogical Disavowal” by Lorenzo Valla. It also considers how the link between humanism, wealth, and the exercise of power in England conditioned the most remarkable Renaissance English response to Lucretius and to everything he brought back into circulation. Finally, it analyzes Thomas More’s Utopia, its theory of the nature of pleasure, and its treatment of Epicureanism and the afterlife.