bluuebunny/crossref_metadata_2025 huggingface dataset:
A systematic analysis reveals an essential role for high-affinity iron uptake system, haemolysin and CFEM domain-containing protein in iron homoeostasis and virulence in Candida glabrata
Authors: Srivastava Vivek Kumar , Suneetha Korivi Jyothiraj , Kaur Rupinder
Published: July 2014

Iron is an essential nutrient for all living organisms and human pathogens employ a battery of factors to scavenge iron from the high-affinity iron-binding host proteins. In the present study, we have elucidated, via a candidate gene approach, major iron acquisition and homoeostatic mechanisms operational in an opportunistic human fungal pathogen Candida glabrata. Phenotypic, biochemical and molecular analysis of a set of 13 C. glabrata strains, deleted for proteins potentially implicated in iron metabolism, revealed that the high-affinity reductive iron uptake system is required for utilization of alternate carbon sources and for growth under both in vitro iron-limiting and in vivo conditions. Furthermore, we show for the first time that the cysteine-rich CFEM (common in fungal extracellular membranes) domain-containing cell wall structural protein, CgCcw14, and a putative haemolysin, CgMam3, are essential for maintenance of intracellular iron content, adherence to epithelial cells and virulence. Consistent with their roles in iron homoeostasis, mitochondrial aconitase activity was lower and higher in mutants disrupted for high-affinity iron transport, and haemolysin respectively. Additionally, we present evidence that the mitochondrial frataxin, CgYfh1, is pivotal to iron metabolism. Besides yielding insights into major in vitro and in vivo iron acquisition strategies, our findings establish high-affinity iron uptake mechanisms as critical virulence determinants in C. glabrata.
Experimental study on dominant sets clustering
Authors: Hou Jian , Xia Qi , Qi Nai‐Ming
Published: July 2014

Based on a graph‐theoretic concept of a cluster, dominant sets clustering has been shown to be an attractive clustering algorithm with many useful properties. In this study, the authors conduct a comprehensive study of related issues in dominant sets clustering, in an endeavour to explore the potential of this algorithm and obtain the best clustering results. Specifically, they empirically investigate how similarity parameters, similarity measures and game dynamics influence the dominant sets clustering results. From experiments on eight datasets, they conclude that distance‐based similarity measures perform evidently better than cosine and histogram intersection similarity measures potentially, and they need to find the best‐performing similarity parameter to make use of this advantage. They then study the effect of similarity parameter on dominant sets clustering results and induce the range of the best‐performing similarity parameters. Furthermore, they find that the recently proposed infection and immunisation dynamics performs better than the replicator dynamics in most cases while being much more efficient than the latter. These observations are helpful in applying dominant sets clustering to practical problems, and also indicate directions for further improvement of this algorithm.
New single‐stage, single‐switch, soft‐switching three‐phase SEPIC and Cuk‐type power factor correction converters
Authors: Foroozeshfar Reza , Adib Ehsan , Farzanehfard Hosein
Published: July 2014

A new single‐stage, single‐switch, soft‐switching three‐phase power factor correction SEPIC and Cuk converters are introduced. The proposed converters operate in discontinuous conduction mode. Therefore, near unity power factor can be achieved. Also, the efficiency is improved because of the achieved zero current and zero voltage switching at turn on and turn off instants. Moreover, the proposed converters have the capability of voltage boosting and voltage bucking. The main features of these converters are simple structure, simple control, high efficiency and low cost. The experimental results are presented in order to justify the performance of the proposed converter.
Coordinated control of multi‐functional grid‐tied inverters using conductance and susceptance limitation
Authors: Zeng Zheng , Zhao Rongxiang , Yang Huan
Published: July 2014

Owing to the numerous non‐linear and reactive local loads, the applied grid‐tied inverters etc., the quality of power supply of micro‐grids becomes a challenging issue need to be highly addressed. As the power quality can significantly affect the secure, stable, effective and economic operation of the micro‐grids, the compensation of the harmonic and reactive current in the micro‐grids by the use of power quality conditioners and/or advanced control strategies has been highlighted. In this study, the multi‐functional grid‐tied inverters (MFGTIs) are attempted to interface renewable energy resources and enhance the power quality within the micro‐grid. The MFGTIs encompassed with the coordinated control strategy based on the Fryze–Buchholz–Dpenbrock (FBD) theory. Through limiting the harmonic and reactive conductance and susceptance detected by FBD theory, the harmonic and reactive current within the micro‐grid can be shared among the MFGTIs in a coordinated and automatic fashion in accordance with their capacities without communication. A set of the experiments based on the micro‐grid test‐bed are carried out and the results confirm the effectiveness and feasibility of the suggested control strategies.
Hybrid phase shifted full bridge and LLC half bridge DC–DC converter for low‐voltage and high‐current output applications
Authors: Yu Mengyuan , Sha Deshang , Liao Xiaozhong
Published: July 2014

A hybrid phase shifted full bridge (PSFB) and LLC half bridge (HB) DC–DC converter for low‐voltage and high‐current output applications is proposed in this study. The PSFB shares its lagging leg with the LLC‐HB and their outputs are parallel connected. When the output current is small, the energy of LLC circuit in combination with the energy stored in the leakage inductance of PSFB's transformer can help the lagging leg switches to achieve zero voltage switching (ZVS) turn on, which can reduce voltage stress and avoid annoying voltage spikes over switches. For the power distribution at rated power, the PSFB converter undergoes most of the power whereas the LLC‐HB converter working as an auxiliary part converts only a small portion of the total power. To improve the conversion efficiency, synchronous rectification technique for the PSFB DC–DC converter is implemented. The design principle is given in view of ZVS for lagging leg switches and low transconductance of LLC converter. The validity of the proposed converter has been verified by experimental results of a 2.5 kW prototype.
Current‐sharing bus and fuzzy gain scheduling of proportional–integral controller to control a parallel‐connected AC/DC converter
Authors: Kanthaphayao Yutthana , Chunkag Viboon
Published: July 2014

In this study, a current‐sharing bus and fuzzy gain scheduling of proportional–integral (PI) controller to control a parallel‐connected AC/DC converter are proposed. A simple current‐sharing circuit is applied to divide the load current to calculate the peak input current of each converter module. Fuzzy gain scheduling of PI controller is used to compensate for the error of the output voltage. The dsPIC30F6010 microcontroller is applied in the voltage loop control. In addition, a hysteresis control circuit is used to control the current loop. The experimental performance evaluation is conducted on a prototype, with three converter modules that are parallel‐connected, has 250 W/module and has a −48 V DC output voltage. The system offers the following advantages: the tight output voltage regulates both the steady‐state operation and the transient response. The current sharing is quite good, and it is simpler to operate in the redundant mode.
Comprehensive physically based modelling and simulation of power diodes with parameter extraction using MATLAB
Authors: Shaker Ahmed , Abouelatta Mohamed , Sayah Gihan Taha , Zekry Abdelhalim
Published: July 2014

In this study, we present an improved comprehensive model of power diodes. This model is based on the numerical solution of the ambipolar diffusion equation (ADE) by a modified finite difference method using MATLAB. The ADE is solved for all levels of injection instead of high‐level injection only as usually done. Local physical effects such as conductivity modulation, emitter recombination, carrier–carrier scattering and lifetime control are taken into consideration. Temperature and self‐heating effects are also included in the model. The proposed model has been validated against Silvaco mixed‐mode simulations showing very good agreement with much less simulation times for our model. To be self contained, we also present a model parameter extraction methodology for power diodes given their experimental transient waveforms.
Phosphine-stabilised Au9 clusters interacting with titania and silica surfaces: The first evidence for the density of states signature of the support-immobilised cluster
Authors: Andersson Gunther G. , Golovko Vladimir B. , Alvino Jason F. , Bennett Trystan , Wrede Oliver , Mejia Sol M. , Al Qahtani Hassan S. , Adnan Rohul , Gunby Nathaniel , Anderson David P. , Metha Gregory F.
Published: July 2014

Chemically made, atomically precise phosphine-stabilized clusters Au9(PPh3)8(NO3)3 were deposited on titania and silica from solutions at various concentrations and the samples heated under vacuum to remove the ligands. Metastable induced electron spectroscopy was used to determine the density of states at the surface, and X-ray photoelectron spectroscopy for analysing the composition of the surface. It was found for the Au9 cluster deposited on titania that the ligands react with the titania substrate. Based on analysis using the singular value decomposition algorithm, the series of MIE spectra can be described as a linear combination of 3 base spectra that are assigned to the spectra of the substrate, the phosphine ligands on the substrate, and the Au clusters anchored to titania after removal of the ligands. On silica, the Au clusters show significant agglomeration after heat treatment and no interaction of the ligands with the substrate can be identified.
Internal sensor compensation for increased Ca test sensitivity
Authors: Dameron Arrelaine A. , Kempe Michael D. , Reese Matthew O.
Published: July 2014

The development of state-of-the-art barrier films and encapsulation schema for displays and photovoltaics requires precise measurement of water vapor permeation as quickly as possible. We have demonstrated improvements to our electrical, Ca-trace-based water vapor transmission rate measurement technique without introducing any additional cost or sample handling concerns. Most importantly, the contacting scheme was changed so that the effective length of the sensor traces can be more precisely determined making the contact resistance between the Ca and Au/Ti films far less likely to affect the results. A 4-pt contacting pattern was also applied to the internal (non-data) witness trace. This expanded the potential utility of the witness trace from just an indicator for the integrity of the sample assembly, to also being used to compensate for measurement error. Lastly, we increased the relative precision of our resistance measurements by implementing a Ca sensor trace with significantly higher resistance. Principally, these changes produce significant measurement improvements for permeation rates less than 10−4 g/m2/day, by lowering the noise floor, reducing required measurement time, and increasing the reproducibility of this test method.
Theoretical investigations of the IO,q+ (q = 2, 3, 4) multi-charged ions: Metastability, characterization and spectroscopy
Authors: Hammami H. , Yazidi O. , Ben El Hadj Rhouma M. , Al Mogren M. M. , Hochlaf M.
Published: July 2014

Using ab initio methodology, we studied the IOq+ (q = 2, 3, 4) multi-charged ions. Benchmark computations on the IO(X2Π) neutral species allow validate the current procedure. For IO2+, several potential wells were found on the ground and the electronic excited states potentials with potential barriers with respect to dissociation, where this dication can exist in the gas phase as long-lived metastable molecules. We confirm hence the recent observation of the dication by mass spectrometry. Moreover, we predict the existence of the metastable IO3+ trication, where a shallow potential well along the IO internuclear distance is computed. This potential well supports more than 10 vibrational levels. The IO3+ excited states are repulsive in nature, as well as the computed potentials for the IO4+ tetracation. For the bound states, we give a set of spectroscopic parameters including excitation transition energies, equilibrium distances, harmonic and anharmonic vibrational terms, and rotational constants. At the MRCI + Q/aug-cc-pV5Z(-PP) level, the adiabatic double and triple ionization energies of IO are computed to be ∼28.1 eV and ∼55.0 eV, respectively.
Chaotic motion of charged particles in toroidal magnetic configurations
Authors: Cambon Benjamin , Leoncini Xavier , Vittot Michel , Dumont Rémi , Garbet Xavier
Published: July 2014

We study the motion of a charged particle in a tokamak magnetic field and discuss its chaotic nature. Contrary to most of recent studies, we do not make any assumption on any constant of the motion and solve numerically the cyclotron gyration using Hamiltonian formalism. We take advantage of a symplectic integrator allowing us to make long-time simulations. First considering an idealized magnetic configuration, we add a nongeneric perturbation corresponding to a magnetic ripple, breaking one of the invariant of the motion. Chaotic motion is then observed and opens questions about the link between chaos of magnetic field lines and chaos of particle trajectories. Second, we return to an axisymmetric configuration and tune the safety factor (magnetic configuration) in order to recover chaotic motion. In this last setting with two constants of the motion, the presence of chaos implies that no third global constant exists, we highlight this fact by looking at variations of the first order of the magnetic moment in this chaotic setting. We are facing a mixed phase space with both regular and chaotic regions and point out the difficulties in performing a global reduction such as gyrokinetics.
A diamond based neutron spectrometer for diagnostics of deuterium-tritium fusion plasmas
Authors: Cazzaniga C. , Nocente M. , Rebai M. , Tardocchi M. , Calvani P. , Croci G. , Giacomelli L. , Girolami M. , Griesmayer E. , Grosso G. , Pillon M. , Trucchi D. M. , Gorini G.
Published: July 2014

Single crystal Diamond Detectors (SDD) are being increasingly exploited for neutron diagnostics in high power fusion devices, given their significant radiation hardness and high energy resolution capabilities. The geometrical efficiency of SDDs is limited by the size of commercially available crystals, which is often smaller than the dimension of neutron beams along collimated lines of sight in tokamak devices. In this work, we present the design and fabrication of a 14 MeV neutron spectrometer consisting of 12 diamond pixels arranged in a matrix, so to achieve an improved geometrical efficiency. Each pixel is equipped with an independent high voltage supply and read-out electronics optimized to combine high energy resolution and fast signals (<30 ns), which are essential to enable high counting rate (>1 MHz) spectroscopy. The response function of a prototype SDD to 14 MeV neutrons has been measured at the Frascati Neutron Generator by observation of the 8.3 MeV peak from the 12C(n, α)9Be reaction occurring between neutrons and 12C nuclei in the detector. The measured energy resolution (2.5% FWHM) meets the requirements for neutron spectroscopy applications in deuterium-tritium plasmas.
Gaussian semiflexible rings under angular and dihedral restrictions
Authors: Dolgushev Maxim , Guérin Thomas , Blumen Alexander , Bénichou Olivier , Voituriez Raphaël
Published: July 2014

Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.
Direct observation of spin-resolved full and empty electron states in ferromagnetic surfaces
Authors: Berti G. , Calloni A. , Brambilla A. , Bussetti G. , Duò L. , Ciccacci F.
Published: July 2014

We present a versatile apparatus for the study of ferromagnetic surfaces, which combines spin-polarized photoemission and inverse photoemission spectroscopies. Samples can be grown by molecular beam epitaxy and analyzed in situ. Spin-resolved photoemission spectroscopy analysis is done with a hemispherical electron analyzer coupled to a 25 kV-Mott detector. Inverse photoemission spectroscopy experiments are performed with GaAs crystals as spin-polarized electron sources and a UV bandpass photon detector. As an example, measurements on the oxygen passivated Fe(100)-p(1×1)O surface are presented.
Cation non-stoichiometry in pulsed laser deposited Sr2+yFe1+xMo1-xO6 epitaxial films
Authors: Meyer T. L. , Dixit M. , Williams R. E. A. , Susner M. A. , Fraser H. L. , McComb D. W. , Sumption M. D. , Lemberger T. R. , Woodward P. M.
Published: July 2014

Sr2FeMoO6 (SFMO) films were grown on SrTiO3 (100)- and (111)-oriented substrates via pulsed laser deposition (PLD). In order to study the fundamental characteristics of deposition, films were grown in two different PLD chambers. In chamber I, the best films were grown with a relatively long substrate-to-target distance (89 mm), high substrate temperature (850 °C), and low pressure (50 mTorr) in a 95% Ar/5% H2 atmosphere. Although X-ray diffraction (XRD) measurements indicate these films are single phase, Rutherford Backscattering (RBS) measurements reveal considerable non-stoichiometry, corresponding to a Sr2Fe1−xMo1+xO6 composition with x ≅ 0.2–0.3. This level of non-stoichiometry results in inferior magnetic properties. In chamber II, the best films were grown with a much shorter substrate-to-target distance (38 mm), lower temperature (680 °C), and higher pressure (225 mTorr). XRD measurements show that the films are single phase, and RBS measurements indicate that they are nearly stoichiometric. The degree of ordering between Fe and Mo was dependent on both the temperature and pressure used during deposition, reaching a maximum order parameter of 85%. The saturation magnetization increases as the Fe/Mo ordering increases, reaching a maximum of 2.4 μB/f.u. Based on prior studies of bulk samples, one would expect a higher saturation magnetization for this degree of Fe/Mo order. The presence of extra strontium oxide layers in the form of Ruddlesden-Popper intergrowths appears to be responsible for the lower than expected saturation magnetization of these films.
Unsteady asymmetric engulfment regime in a T-mixer
Authors: Fani Andrea , Camarri Simone , Salvetti Maria Vittoria
Published: July 2014

Unsteady flow regimes in a micro T-mixer are investigated. Direct numerical simulations (DNS) show that, in agreement with experimental and numerical results in the literature, when the Reynolds number is increased above a critical value larger than those typical of the steady engulfment regime, the flow remains asymmetric in the mean but becomes periodic in time. The dynamics of this regime is characterized by analyzing the evolution of the three-dimensional vortical structures forming at the confluence of the two inlet flow streams. As the Reynolds number is further increased, the flow remains time-periodic but it continuously switches between a symmetric configuration, similar to that of the vortical regime, and an asymmetric one, close to the engulfment configuration. Three-dimensional linear stability analysis is successively used to characterize the instability leading to the unsteady asymmetric regime, which is also interesting for applications due to its high mixing efficiency. The critical Reynolds number and the instability frequency are in very good agreement with those found in DNS. The sensitivity of this instability to a generic perturbation of the base flow is also investigated. It is shown that the largest sensitivity is to base-flow modifications introduced close to the three-dimensional vortical structures forming at the confluence between the inlet channels. Finally, the sensitivity analysis is specialized to investigate the effect of a generic perturbation of the inlet velocity profile.
E→H mode transition density and power in two types of inductively coupled plasma configuration
Authors: Wang Jian , Du Yin-chang , Zhang Xiao , Zheng Zhe , Liu Yu , Xu Liang , Wang Pi , Cao Jin-xiang
Published: July 2014

E → H transition power and density were investigated at various argon pressures in inductively coupled plasma (ICP) in a cylindrical interlaid chamber. The transition power versus the pressure shows a minimum transition power at 4 Pa (ν/ω=1) for argon. Then the transition density hardly changes at low pressures (ν/ω≪1), but it increases clearly when argon pressure exceeds an appropriate value. In addition, both the transition power and transition density are lower in the re-entrant configuration of ICP compared with that in the cylindrical configuration of ICP. The result may be caused from the decrease of stochastic heating in the re-entrant configuration of ICP. This work is useful to understand E → H mode transition and control the transition points in real plasma processes.
Pinning synchronization of hybrid-coupled directed delayed dynamical network via intermittent control
Authors: Cai Shuiming , Zhou Peipei , Liu Zengrong
Published: July 2014

This paper concerns the problem of exponential synchronization for a class of general delayed dynamical networks with hybrid coupling via pinning periodically intermittent control. Both the internal delay and coupling delay are taken into account in the network model. Meanwhile, the transmission delay and self-feedback delay are involved in the delayed coupling term. By establishing a new differential inequality, several simple and useful exponential synchronization criteria are derived analytically. It is shown that the controlled synchronization state can vary in comparison with the conventional synchronized solution, and the degree of the node and the inner delayed coupling matrix play important roles in the controlled synchronization state. By choosing different inner delayed coupling matrices and the degrees of the node, different controlled synchronization states can be obtained. Furthermore, the detail pinning schemes deciding what nodes should be chosen as pinned candidates and how many nodes are needed to be pinned for a fixed coupling strength are provided. The simple procedures illuminating how to design suitable intermittent controllers in real application are also given. Numerical simulations, including an undirected scale-free network and a directed small-world network, are finally presented to demonstrate the effectiveness of the theoretical results.
Strong environmental coupling in a Josephson parametric amplifier
Authors: Mutus J. Y. , White T. C. , Barends R. , Chen Yu , Chen Z. , Chiaro B. , Dunsworth A. , Jeffrey E. , Kelly J. , Megrant A. , Neill C. , O'Malley P. J. J. , Roushan P. , Sank D. , Vainsencher A. , Wenner J. , Sundqvist K. M. , Cleland A. N. , Martinis John M.
Published: July 2014

We present a lumped-element Josephson parametric amplifier designed to operate with strong coupling to the environment. In this regime, we observe broadband frequency dependent amplification with multi-peaked gain profiles. We account for this behavior using the “pumpistor” model which allows for frequency dependent variation of the external impedance. Using this understanding, we demonstrate control over the complexity of gain profiles through added variation in the environment impedance at a given frequency. With strong coupling to a suitable external impedance, we observe a significant increase in dynamic range, and large amplification bandwidth up to 700 MHz giving near quantum-limited performance.
Research Update: Retardation and acceleration of phase separation evaluated from observation of imbalance between structure and valence in LiFePO4/FePO4 electrode
Authors: Tokuda Kazuya , Kawaguchi Tomoya , Fukuda Katsutoshi , Ichitsubo Tetsu , Matsubara Eiichiro
Published: July 2014

LiFePO4 is a potential positive electrode material for lithium ion batteries. We have experimentally observed an imbalance between the valence change of Fe ions and the structure change from the LiFePO4 phase to the FePO4 phase during delithiation by simultaneous in situ XRD and XANES measurements in an LiFePO4/FePO4 electrode. The ratio of structure change to valence change clearly indicates that the phase separation from LiFePO4 to FePO4 is suppressed at the beginning of delithiation, while it is accelerated at the latter stage, which is due to the coherent strain caused by the lattice misfit between the two phases.
Effect of non-magnetic ion substitution on the magnetoelastic properties of CoFe2O4 films
Authors: Rus S. F. , Vlazan P. , Herklotz A.
Published: July 2014

We report on the structural and magnetic properties of CoFe1.9Zr0.1O4 films under epitaxial strain. The films are grown with high structural quality on MgO, SrTiO3, and piezoelectric Pb(Mg1∕3Nb2∕3)0.72Ti0.28O3 substrates by pulsed laser deposition. The substrate-induced strain is found effective to alter the magnetic anisotropy of the films. Reversible strain measurements using the piezoelectric substrates are providing evidence that nearly bulk-like magnetoelastic properties are maintained for films of down to at least 25 nm thickness. This is in contrast to unsubstituted cobalt ferrite films and suggests that a chemical control of the spinel lattice provides a promising route to optimize the tunability of the magnetic properties of thin ferrite films.
Identification of nitrogen- and host-related deep-level traps in n-type GaNAs and their evolution upon annealing
Authors: Gelczuk Ł. , Kudrawiec R. , Henini M.
Published: July 2014

Deep level traps in as-grown and annealed n-GaNAs layers (doped with Si) of various nitrogen concentrations (N = 0.2%, 0.4%, 0.8%, and 1.2%) were investigated by deep level transient spectroscopy. In addition, optical properties of GaNAs layers were studied by photoluminescence and contactless electroreflectance. The identification of N- and host-related traps has been performed on the basis of band gap diagram [Kudrawiec, Appl. Phys. Lett. 101, 082109 (2012)], which assumes that the activation energy of electron traps of the same microscopic nature decreases with the rise of nitrogen concentration in accordance with the N-related shift of the conduction band towards trap levels. The application of this diagram has allowed to investigate the evolution of donor traps in GaNAs upon annealing. In general, it was observed that the concentration of N- and host-related traps decreases after annealing and PL improves very significantly. However, it was also observed that some traps are generated due to annealing. It explains why the annealing conditions have to be carefully optimized for this material system.
Origins of Stabilization and Evidence for Charge Delocalization in the Bicyclo[3.2.1]octadienyl Anion and Related Species
Authors: Brown John M.
Published: July 2014

Bridged bicyclic allylic anions with ethene and allyl units in proximity possess enhanced stability over analogues lacking the ethene bridge. Experimental observations have encouraged much computational effort, and for many years claims for homoaromatic behaviour in anions were disputed. More recently, and especially with the advent of quantum mechanics methods that assess magnetic susceptibility, homoaromaticity has become accepted. This paper provides a review of work on this topic to date, and additional density functional theory calculations with the purpose of providing a general overview. The presence of homoaromaticity in anions of this class is supported, and their stability is augmented by inductive and counterion effects.
Tin and Mercury Compounds Supported by a Bulky Organometallic Ligand Incorporating a Pendant Guanidine Functionality
Authors: El-Hamruni Salima M. , Sözerli Sebnem E. , Smith J. David , Coles Martyn P. , Hitchcock Peter B.
Published: July 2014

The structure of a triclinic form of the organolithium derivative LiR, R = C(SiMe3)2(SiMe2{hpp}) (1) (hppH = 1,3,4,6,7,8,-hexahydro-2H-pyrimido[1,2-a]pyrimidine) comprises dimers [1]2 held together by Li···H3C interactions like those in the polymeric structure [1]∞ of the previously described orthorhombic form. Compound 1 reacts with the chlorides MCl2 (M = Hg or Sn) to give compounds HgRCl (2) or SnRCl (3), which have been characterised by NMR spectroscopy and X-ray crystallography. The structural parameters and conformations of the metallacycles MRLn are compared with those in related compounds containing bulky organosilicon ligands with pendant nitrogen donors. Compound 3 reacts with Li[P{H}Ar*] (Ar* = 2,4,6-tBu3C6H2) to give the crowded phosphanide SnR(P{H}Ar*) (4).
Condom use motivations and selected behaviours with new versus established sex partners
Authors: Crosby Richard A. , Milhausen Robin R. , Graham Cynthia A. , Yarber William L. , Sanders Stephanie A. , Charnigo Richard , Shrier Lydia A.
Published: July 2014

Objective To compare condom use motives and behaviours in the context of penile–vaginal intercourse (PVI) with new versus established sexual partners, using daily event-level data among a clinic-recruited sample. Methods: Participants (ages 15–65 years old) were recruited from five sexually transmissible infection (STI) clinics in three United States cities. They were provided with personal digital assistants and instructed to respond to daily questionnaire items regarding PVI events from the past 24 h. Generalised estimations equations were used to make inferences on age-adjusted estimated odds ratios, comparing events occurring with established versus new partners. Results: For males, pregnancy prevention was a more common motivation for condom use in new relationships (P < 0.001). Males with new sex partners were more likely to report condom use (P < 0.005) and also reported fewer errors or problems in condom use with new sex partners (P < 0.001). For females, pregnancy prevention (P = 0.03), STI acquisition (P < 0.001) and STI transmission (P = 0.005) were more likely to be motives for condom use with new versus established partners. Also, females with new sex partners were more likely to report condom use (P < 0.001) as well as using multiple condoms during a single event (P = 0.03). Conclusion: Event-level findings suggest that condom use motivations and behaviours vary depending on whether PVI occurs between established versus new sex partners. Condom use is more likely for PVI with new partners, but other condom-associated behaviours and motivations differ between females and males.
Rolling out new biomedical HIV prevention tools: what can be learned from Avahan, the India AIDS initiative?
Authors: Dallabetta Gina , Chandrasekaran Padma , Wheeler Tisha , Das Anjana , Ramakrishnan Lakshmi , Kumta Sameer , Moore James
Published: July 2014

More than 30 years after HIV was first identified as a disease, with disastrous consequences for many subpopulations in most countries and for entire populations in some African countries, it continues to occupy centre stage among the world’s many global health challenges. Prevention still remains the primary long-term focus. New biomedical tools such as pre-exposure propyhlaxis (PrEP) and treatment hold great promise for select groups such as key populations (KPs) who are critical to transmission dynamics, and serodiscordant couples. Programs delivering these new tools will need to layer them over existing services, with potential modifications for increased and sustained engagement between health services and beneficiaries owing to the nature of the interventions. Avahan, an HIV prevention intervention for KPs in six states in India, achieved population-level impact with conventional prevention programming, which, however, required high program–beneficiary engagement. Avahan’s implementation strategy included articulating clear service definitions and denominator-based targets; establishing routine data systems with regular, multilevel supervision that allowed for cross-learning across the program; and developing a cadre of frontline workers through KP peer outreach workers who addressed structural issues and provided viable and sustainable mechanisms for sustained interaction between health services and KPs. This basic prevention implementation infrastructure was used to expand clinical services over time. Many of the lessons from programs such as Avahan can be applied to KP programs that are expanding service scope, including PrEP and treatment.
Invasive plants have broader physiological niches
Authors: Higgins Steven I. , Richardson David M.
Published: July 2014

Significance

Invasibility (the vulnerability of a receiving environment to invasion) and invasiveness (the capacity of an organism to invade) are fundamental metrics in theoretical ecology. However, attempts to apply these concepts to the question of whether an introduced species will invade have failed. Here, we use a model that characterizes the physiological niche of plants to successfully predict invasive success of 749 species. We find that, although invasive success is dependent on different factors in different ecological contexts, the modeled global potential range of species integrates these contingencies to produce a reliable and interpretable indicator of the likelihood that a species will reproduce and spread.
Dynamic regulation of
eve
stripe 2 expression reveals transcriptional bursts in living
Drosophila
embryos
Authors: Bothma Jacques P. , Garcia Hernan G. , Esposito Emilia , Schlissel Gavin , Gregor Thomas , Levine Michael
Published: July 2014

Significance

There is considerable information about the spatial regulation of gene expression during pattern formation in animal development. Significantly less is known about temporal control, in part due to our inability to analyze gene activity in real time. Using a recently developed approach for the visualization of gene expression in living
Drosophila
embryos, we examined the well-known
even-skipped
stripe 2 expression pattern. Surprisingly, we observe that this classic pattern is quite transient and generated by discontinuous surges of transcriptional activity in individual cells. These results challenge a purely static framework for dissecting developmental programs and emphasize the importance of the dynamic features of pattern formation.
Pussy Riot: a feminist band lost in history and translation
Authors: Yusupova Marina
Published: July 2014

The Pussy Riot story is clearly a story the West wanted to hear. Western journalists, politicians, and celebrities were unanimously inspired by the youthfulness and rebellion of courageous Russian feminists. Their life experience perfectly resonates with the core of these young women's messages. For Russians, however, even for those who share the most liberal values, it is not so simple. Public polls and several months of heated debates have shown that virtually everyone in this deeply conservative country has struggled to make sense of the Pussy Riot performance. So, what do Westerners not understand about Russia and what are the problems of translating feminism(s) into different cultural contexts? How does feminist protest deprived of its roots function here, and why do women in Russia not understand that Pussy Riot's story personally concerns all of them? This essay outlines the difference between Russian and Western readings of the Pussy Riot performance and, using the case of public response in Russia, contemplates the reasons for the failure of feminism in this part of the world.
Calcitonin gene-related peptide regulates mitogen-activated protein kinase pathway to decrease transforming growth factor β1-induced hepatic plasminogen activator inhibitor-1 mRNA expression in HepG2 cells
Authors: Matsui Sho , Yamane Takumi , Kobayashi-Hattori Kazuo , Oishi Yuichi
Published: July 2014

Transforming growth factor (TGF) β1-induced plasminogen activator inhibitor (PAI)-1 is one of factors associated with the development of hepatic fibrosis. Calcitonin gene-related peptide (CGRP) shows hepatoprotective effect during hepatic injuries, including fibrosis. However, the effects of CGRP on PAI-1 expression induced by TGFβ1 are unknown. In this study, we investigated the effect of CGRP on TGFβ1-induced PAI-1 expression and its regulatory mechanisms in HepG2 cells. CGRP inhibited TGFβ1-induced PAI-1 expression. H89, a protein kinase A inhibitor, abolished the inhibition of TGFβ1-induced PAI-1 expression by CGRP. TGFβ1 activated mitogen-activated protein kinase (MAPK), including extracellular signal-regulated kinase, c-jun NH2-terminal kinase, and p38, and this activation was abolished by CGRP. These results show that the CGRP-induced cAMP/PKA activation suppresses activation of MAPK induced by TGFβ1, leading to decreased PAI-1 expression in HepG2 cells.
q-Deformed U(5) Limit in s, d IBM for Nuclei
Authors: XiangZheng Fang , JianYou Guo , XianYin Li , TuNan Ruan
Published: July 2014

The q-deformed Hamiltonian with U(5) symmetry in s, d interacting boson model can be constructed by using quantum algebra SUq(2), SUq(1,1) and q-deformed boson operator. The energy spectra and E2 transition rates of 110~114Cd isotopes are calculated. The calculated results agree with the experimental data rather well. Analyses on the calculated results show that the q-deformed U(5) limit is deviated from the symmetry in the original model and the degree of deviation is dependent on the deformation parameter.
Calcium-dependent phosphorylation alters class XIVa myosin function in the protozoan parasiteToxoplasma gondii
Authors: Tang Qing , Andenmatten Nicole , Hortua Triana Miryam A. , Deng Bin , Meissner Markus , Moreno Silvia N. J. , Ballif Bryan A. , Ward Gary E.
Published: July 2014

Class XIVa myosins comprise a unique group of myosin motor proteins found in apicomplexan parasites, including those that cause malaria and toxoplasmosis. The founding member of the class XIVa family, Toxoplasma gondii myosin A (TgMyoA), is a monomeric unconventional myosin that functions at the parasite periphery to control gliding motility, host cell invasion, and host cell egress. How the motor activity of TgMyoA is regulated during these critical steps in the parasite's lytic cycle is unknown. We show here that a small-molecule enhancer of T. gondii motility and invasion (compound 130038) causes an increase in parasite intracellular calcium levels, leading to a calcium-dependent increase in TgMyoA phosphorylation. Mutation of the major sites of phosphorylation altered parasite motile behavior upon compound 130038 treatment, and parasites expressing a nonphosphorylatable mutant myosin egressed from host cells more slowly in response to treatment with calcium ionophore. These data demonstrate that TgMyoA undergoes calcium-dependent phosphorylation, which modulates myosin-driven processes in this important human pathogen.
Actin-associated protein palladin promotes tumor cell invasion by linking extracellular matrix degradation to cell cytoskeleton
Authors: von Nandelstadh Pernilla , Gucciardo Erika , Lohi Jouko , Li Rui , Sugiyama Nami , Carpen Olli , Lehti Kaisa
Published: July 2014

Basal-like breast carcinomas, characterized by unfavorable prognosis and frequent metastases, are associated with epithelial-to-mesenchymal transition. During this process, cancer cells undergo cytoskeletal reorganization and up-regulate membrane-type 1 matrix metalloproteinase (MT1-MMP; MMP14), which functions in actin-based pseudopods to drive invasion by extracellular matrix degradation. However, the mechanisms that couple matrix proteolysis to the actin cytoskeleton in cell invasion have remained unclear. On the basis of a yeast two-hybrid screen for the MT1-MMP cytoplasmic tail-binding proteins, we identify here a novel Src-regulated protein interaction between the dynamic cytoskeletal scaffold protein palladin and MT1-MMP. These proteins were coexpressed in invasive human basal-like breast carcinomas and corresponding cell lines, where they were associated in the same matrix contacting and degrading membrane complexes. The silencing and overexpression of the 90-kDa palladin isoform revealed the functional importance of the interaction with MT1-MMP in pericellular matrix degradation and mesenchymal tumor cell invasion, whereas in MT1-MMP–negative cells, palladin overexpression was insufficient for invasion. Moreover, this invasion was inhibited in a dominant-negative manner by an immunoglobulin domain–containing palladin fragment lacking the dynamic scaffold and Src-binding domains. These results identify a novel protein interaction that links matrix degradation to cytoskeletal dynamics and migration signaling in mesenchymal cell invasion.
Ena/VASP regulates mDia2-initiated filopodial length, dynamics, and function
Authors: Barzik Melanie , McClain Leslie M. , Gupton Stephanie L. , Gertler Frank B.
Published: July 2014

Filopodia are long plasma membrane extensions involved in the formation of adhesive, contractile, and protrusive actin-based structures in spreading and migrating cells. Whether filopodia formed by different molecular mechanisms equally support these cellular functions is unresolved. We used Enabled/vasodilator-stimulated phosphoprotein (Ena/VASP)–deficient MVD7fibroblasts, which are also devoid of endogenous mDia2, as a model system to investigate how these different actin regulatory proteins affect filopodia morphology and dynamics independently of one another. Filopodia initiated by either Ena/VASP or mDia2 contained similar molecular inventory but differed significantly in parameters such as number, length, F-actin organization, lifetime, and protrusive persistence. Moreover, in the absence of Ena/VASP, filopodia generated by mDia2 did not support initiation of integrin-dependent signaling cascades required for adhesion and subsequent lamellipodial extension, thereby causing a defect in early cell spreading. Coexpression of VASP with constitutively active mDia2M/Arescued these early adhesion defects. We conclude that Ena/VASP and mDia2 support the formation of filopodia with significantly distinct properties and that Ena/VASP regulates mDia2-initiated filopodial morphology, dynamics, and function.
Screening from the Met, the NT, or the House: what changes with the live relay
Authors: Cochrane Bernadette , Bonner Frances
Published: July 2014

Theatre, opera, and dance all call for distinct performance and viewing practices, but when they are relayed into cinemas (live or faux-live) there tends to be some flattening of this distinctiveness. There are also slippages between elements of the relays in terms both of their original form and the adjustments made in the course of recording for relay. The changes made in the movement from performance space to cinema reception are adaptations that are in the first instance technically motivated rather than dramaturgically initiated. Some, such of the use of camera angles unavailable to theatre audiences, or time spent backstage during intervals, contribute to the creation of a different relationship to the play, opera, or dance, while not necessarily always making the relay more like a film. The purpose of this article is to examine the extent to which the assertions of liveness, of the sameness of the experience, and the difference from filmed or televised productions are sustainable for a range of performance types viewed close to the source of the event and remote from it. It centres on instances from NT Live, but also draw on ones from The Met in HD, NDT in cinema, and the multiple passages of the radio show ‘This American Life’ first to the stage and then on relay to cinemas.
ARBitrator: a software pipeline for on-demand retrieval of auto-curatednifHsequences from GenBank
Authors: Heller Philip , Tripp H. James , Turk-Kubo Kendra , Zehr Jonathan P.
Published: July 2014

Motivation: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N 2 ) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information’s GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank’s structure and tools are not conducive to searching solely by function. For some genes, such as the nifH gene commonly used to assess community potential for N 2 fixation, manual collection and curation are becoming intractable because of the large number of sequences in GenBank and the large number of highly similar paralogues. If analysis is to keep pace with sequence discovery, an automated retrieval and curation system is necessary.

Results: ARBitrator uses a two-step process composed of a broad collection of potential homologues followed by screening with a best hit strategy to conserved domains. 34 420 nifH sequences were identified in GenBank as of November 20, 2012. The false-positive rate is ∼0.033%. ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted for other genes.

Availability and implementation: Java source and executable code are freely available to non-commercial users at http://pmc.ucsc.edu/∼wwwzehr/research/database/ .

Contact:  zehrj@ucsc.edu

Supplementary information:  Supplementary information is available at Bioinformatics online.
RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy
Authors: Lo Kitty K. , Boustred Christopher , Chitty Lyn S. , Plagnol Vincent
Published: July 2014

Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting.

Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html .

Contact:  kitty.lo@ucl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.