bluuebunny/crossref_metadata_2025 huggingface dataset:
Online monitoring of oil film using electrical capacitance tomography and level set method
Authors: Xue Q. , Sun B. Y. , Cui Z. Q. , Ma M. , Wang H. X.
Published: August 2015

In the application of oil-air lubrication system, electrical capacitance tomography (ECT) provides a promising way for monitoring oil film in the pipelines by reconstructing cross sectional oil distributions in real time. While in the case of small diameter pipe and thin oil film, the thickness of the oil film is hard to be observed visually since the interface of oil and air is not obvious in the reconstructed images. And the existence of artifacts in the reconstructions has seriously influenced the effectiveness of image segmentation techniques such as level set method. Besides, level set method is also unavailable for online monitoring due to its low computation speed. To address these problems, a modified level set method is developed: a distance regularized level set evolution formulation is extended to image two-phase flow online using an ECT system, a narrowband image filter is defined to eliminate the influence of artifacts, and considering the continuity of the oil distribution variation, the detected oil-air interface of a former image can be used as the initial contour for the detection of the subsequent frame; thus, the propagation from the initial contour to the boundary can be greatly accelerated, making it possible for real time tracking. To testify the feasibility of the proposed method, an oil-air lubrication facility with 4 mm inner diameter pipe is measured in normal operation using an 8-electrode ECT system. Both simulation and experiment results indicate that the modified level set method is capable of visualizing the oil-air interface accurately online.
Hybrid (Vlasov-Fluid) simulation of ion-acoustic soliton chain formation and validity of Korteweg de-Vries model
Authors: Aminmansoor F. , Abbasi H.
Published: August 2015

The present paper is devoted to simulation of nonlinear disintegration of a localized perturbation into ion-acoustic solitons train in a plasma with hot electrons and cold ions. A Gaussian initial perturbation is used to model the localized perturbation. For this purpose, first, we reduce fluid system of equations to a Korteweg de-Vries equation by the following well-known assumptions. (i) On the ion-acoustic evolution time-scale, the electron velocity distribution function (EVDF) is assumed to be stationary. (ii) The calculation is restricted to small amplitude cases. Next, in order to generalize the model to finite amplitudes cases, the evolution of EVDF is included. To this end, a hybrid code is designed to simulate the case, in which electrons dynamics is governed by Vlasov equation, while cold ions dynamics is, like before, studied by the fluid equations. A comparison between the two models shows that although the fluid model is capable of demonstrating the general features of the process, to have a better insight into the relevant physics resulting from the evolution of EVDF, the use of kinetic treatment is of great importance.
Surface-plasmon enhanced photodetection at communication band based on hot electrons
Authors: Wu Kai , Zhan Yaohui , Wu Shaolong , Deng Jiajia , Li Xiaofeng
Published: August 2015

Surface plasmons can squeeze light into a deep-subwavelength space and generate abundant hot electrons in the nearby metallic regions, enabling a new paradigm of photoconversion by the way of hot electron collection. Unlike the visible spectral range concerned in previous literatures, we focus on the communication band and design the infrared hot-electron photodetectors with plasmonic metal-insulator-metal configuration by using full-wave finite-element method. Titanium dioxide-silver Schottky interface is employed to boost the low-energy infrared photodetection. The photodetection sensitivity is strongly improved by enhancing the plasmonic excitation from a rationally engineered metallic grating, which enables a strong unidirectional photocurrent. With a five-step electrical simulation, the optimized device exhibits an unbiased responsivity of ∼0.1 mA/W and an ultra-narrow response band (FWHM = 4.66 meV), which promises to be a candidate as the compact photodetector operating in communication band.
Two different carbon-hydrogen complexes in silicon with closely spaced energy levels
Authors: Stübner R. , Kolkovsky Vl. , Weber J.
Published: August 2015

An acceptor and a single donor state of carbon-hydrogen defects (CHA and CHB) are observed by Laplace deep level transient spectroscopy at 90 K. CHA appears directly after hydrogenation by wet chemical etching or hydrogen plasma treatment, whereas CHB can be observed only after a successive annealing under reverse bias at about 320 K. The activation enthalpies of these states are 0.16 eV for CHA and 0.14 eV for CHB. Our results reconcile previous controversial experimental results. We attribute CHA to the configuration where substitutional carbon binds a hydrogen atom on a bond centered position between carbon and the neighboring silicon and CHB to another carbon-hydrogen defect.
Enhanced tunable magnetoresistance properties over a wide temperature range in epitaxial (La0.7Sr0.3MnO3)1−x:(CeO2)x nanocomposites
Authors: Fan Meng , Zhang Wenrui , Khatkhatay Fauzia , Li Leigang , Wang Haiyan
Published: August 2015

Vertically aligned nanocomposite (VAN) (La0.7Sr0.3MnO3)1−x:(CeO2)x (LSMO:CeO2) thin films have been grown on SrTiO3 (001) substrates by pulsed laser deposition. Tunable magnetoresistance properties as well as microstructures are demonstrated in these VAN films by modulating the film composition (x = 0, 0.3, 0.4, 0.45, 0.5, and 0.55). The sample of x = 0.3 shows a large low-field magnetoresistance (LFMR) in a high temperature range, i.e., over 10% at the range of 280 K to 320 K under 1 T and with a peak value of ∼13.5% at 310 K. In addition, a vast enhancement of LFMR in a low temperature range of 20–150 K with peak of ≈34.3% at 45 K for 1 T could be achieved with x = 0.5. The enhanced LFMR properties can be attributed to both the phase boundary induced spin fluctuation and the magnetic tunneling effect through vertical ferromagnetic/insulator/ferromagnetic structures. The observed enhanced LFMR performance, especially at high temperatures, as well as its simple growth method, offers a great potential for LSMO:CeO2nanocomposites to be used in spintronic devices in a large temperature range.
Focusing of surface phonon-polaritons along conical and wedge polar nanostructures
Authors: Gluchko Sergei , Ordonez-Miranda Jose , Tranchant Laurent , Antoni Thomas , Volz Sebastian
Published: August 2015

Focusing of surface phonon-polaritons propagating toward the tip of a cone and the edge of a wedge is theoretically analyzed and compared. Based on Maxwell's equations, explicit expressions for the dispersion relations in each structure are determined and solved numerically for a propagation parameter driving the surface phonon-polariton energy density. For conical and wedge structures of SiO2, it is found that: (1) the cone (wedge) supports the polariton focusing only for aperture angles in the interval 18°–68° (21°–51°), and within the range of excitation frequencies from 32.1 THz (31.5 THz) to 33.9 THz (33.9 THz). In this frequency interval, the real part of the SiO2 permittivity is negative and the presence of polaritons is significant. (2) The polariton focusing efficiency of both the cone and wedge reaches its maximum values at the critical frequency fcr=33.6 THz and at different aperture angles of about αopt=45° and αopt=30°, respectively. (3) When the polaritons travel from 100 nm to 5 nm toward the tip of the cone with this optimum angle, their Poynting vector increases by a factor of 12, which is about four times larger than the corresponding one provided by the wedge and indicates that the cone is more efficient than the wedge for the focusing of surface phonon-polaritons.
Refining finite-time Lyapunov exponent ridges and the challenges of classifying them
Authors: Allshouse Michael R. , Peacock Thomas
Published: August 2015

While more rigorous and sophisticated methods for identifying Lagrangian based coherent structures exist, the finite-time Lyapunov exponent (FTLE) field remains a straightforward and popular method for gaining some insight into transport by complex, time-dependent two-dimensional flows. In light of its enduring appeal, and in support of good practice, we begin by investigating the effects of discretization and noise on two numerical approaches for calculating the FTLE field. A practical method to extract and refine FTLE ridges in two-dimensional flows, which builds on previous methods, is then presented. Seeking to better ascertain the role of a FTLE ridge in flow transport, we adapt an existing classification scheme and provide a thorough treatment of the challenges of classifying the types of deformation represented by a FTLE ridge. As a practical demonstration, the methods are applied to an ocean surface velocity field data set generated by a numerical model.
The effect of filler aspect ratio on the electromagnetic properties of carbon-nanofibers reinforced composites
Authors: De Vivo B. , Lamberti P. , Spinelli G. , Tucci V. , Guadagno L. , Raimondo M.
Published: August 2015

The effect of filler aspect ratio on the electromagnetic properties of epoxy-amine resin reinforced with carbon nanofibers is here investigated. A heat treatment at 2500 °C of carbon nanofibers seems to increase their aspect ratio with respect to as-received ones most likely due to a lowering of structural defects and the improvement of the graphene layers within the dixie cup conformation. These morphological differences revealed by Raman's spectroscopy and scanning electron microscopy analyses may be responsible for the different electrical properties of the resulting composites. The DC characterization of the nanofilled material highlights an higher electrical conductivity and a lower electrical percolation threshold for the heat-treated carbon nanofibers based composites. In fact, the electrical conductivity is about 0.107 S/m and 1.36 × 10−3 S/m for the nanocomposites reinforced with heat-treated and as received fibers, respectively, at 1 wt. % of nanofiller loading, while the electrical percolation threshold falls in the range [0.05–0.32]wt. % for the first nanocomposites and above 0.64 wt. % for the latter. Moreover, also a different frequency response is observed since the critical frequency, which is indicative of the transition from a resistive to a capacitive-type behaviour, shifts forward of about one decade at the same filler loading. The experimental results are supported by theoretical and simulation studies focused on the role of the filler aspect ratio on the electrical properties of the nanocomposites.
Compositional dependence of the band gap in Ga(NAsP) quantum well heterostructures
Authors: Jandieri K. , Ludewig P. , Wegele T. , Beyer A. , Kunert B. , Springer P. , Baranovskii S. D. , Koch S. W. , Volz K. , Stolz W.
Published: August 2015

We present experimental and theoretical studies of the composition dependence of the direct band gap energy in Ga(NAsP)/GaP quantum well heterostructures grown on either (001) GaP- or Si-substrates. The theoretical description takes into account the band anti-crossing model for the conduction band as well as the modification of the valence subband structure due to the strain resulting from the pseudomorphic epitaxial growth on the respective substrate. The composition dependence of the direct band gap of Ga(NAsP) is obtained for a wide range of nitrogen and phosphorus contents relevant for laser applications on Si-substrate.
Spectroscopic studies of magnesium plasma produced by fundamental and second harmonics of Nd:YAG laser
Authors: Haq S. U. , Ahmat L. , Mumtaz M. , Shakeel Hira , Mahmood S. , Nadeem A.
Published: August 2015

In the present experimental work, laser induced magnesium plasma has been characterized using plasma parameters. The plasma has been generated by the fundamental (1064 nm) and second harmonics (532 nm) of Nd:YAG laser. The plasma parameters such as electron temperature and electron number density have been extracted using Boltzmann plot method and Stark broadened line profile, respectively. The laser irradiance dependence and spatial behavior of electron temperature and number density in laser induced magnesium plasma have been studied. The electron temperature as a function of laser irradiance (0.5 to 6.5 GW/cm2) ranges from (9.16–10.37) × 103 K and (8.5–10.1)× 103 K, and electron number density from (0.99–1.08) × 1016 cm−3 and (1.04–1.22) × 1016cm−3 for 1064 and 532 nm, respectively. These parameters exhibit fast increase at low laser irradiance and slow increase at high irradiance. The spatial distribution of electron temperature and electron number density shows same decreasing trend up to 2.25 mm from the target surface. The electron temperature and number density decrease from (9.5–8.6) × 103 K, (1.27–1.15) × 1016cm−3 and (10.56–8.85)× 103 K, (1.08–0.99) × 1016 cm−3 for 532 nm and 1064 nm laser ablation wavelengths, respectively.
Heat flux splitter for near-field thermal radiation
Authors: Ben-Abdallah P. , Belarouci A. , Frechette L. , Biehs S.-A.
Published: August 2015

We demonstrate the possibility to efficiently split the near-field heat flux exchanged between graphene nano-disks by tuning their doping. This result paves the way for the development of an active control of propagation directions for heat fluxes exchanged in the near field throughout integrated nanostructured networks.
Simultaneous solution-based generation and characterization of crystalline bismuth thin film by femtosecond laser spectroscopy
Authors: Zhu Liangdong , Saha Sumit , Liu Weimin , Wang Yanli , Keszler Douglas A. , Fang Chong
Published: August 2015

We demonstrate generation and characterization of crystalline bismuth thin film from triphenyl bismuth in methanol. Upon ultraviolet (267 nm) femtosecond laser irradiation of the solution, a thin film of elemental bismuth forms on the inner side of the sample cuvette, confirmed by detection of the coherent A1g optical phonon mode of crystalline bismuth at ∼90 cm−1. Probe pulses at 267 and 400 nm are used to elucidate the excited state potential energy surface and photochemical reaction coordinate of triphenyl bismuth in solution with femtosecond resolution. The observed phonon mode blueshifts with increasing irradiation time, likely due to the gradual thickening of nascent bismuth thin film to ∼80 nm in 90 min. From transient absorption with the 400 nm probe, we observe a dominant ∼4 ps decay time constant of the excited-state absorption signal, which is attributed to a characteristic metal-ligand bond-weakening/breaking intermediate enroute to crystalline metallic thin film from the solution precursor molecules. Our versatile optical setup thus opens an appealing avenue to characterize the laser-induced crystallization process in situ and prepare high-quality thin films and nanopatterns directly from solution phase.
Graphene/semiconductor silicon modified BiFeO3/indium tin oxide ferroelectric photovoltaic device for transparent self-powered windows
Authors: Gupta Surbhi , Medwal Rohit , Limbu Tej B. , Katiyar Rajesh K. , Pavunny Shojan P. , Tomar Monika , Morell G. , Gupta Vinay , Katiyar R. S.
Published: August 2015

We report photovoltaic response of highly transparent graphene/BiFe0.95Si0.05O3 (BFSiO)/ITO/glass derived from bottom-up spin coating technique. The device exhibits short-circuit-current (ISC 0.75 mA) with 1000 fold upsurge and open-circuit-voltage (VOC ∼ 0.45 V) under standard AM 1.5 illumination through graphene. In combination, ISC of 0.63 mA and VOC of 0.35 V for same illumination through ITO, reveals the prospects of harvesting indoor light. Also, crystallographic structure, red shift in band gap, leakage behavior, and ferroelectric characteristics of BFSiO thin films are reported. Reproducible transient response of ISC and VOC with quick switching (<100 ms) for 20 consecutive cycles and stability (95%) over test period of 16 weeks signifies high endurance and retentivity, promising for building integrated self-powered windows.
Preparing magnetic yttrium iron garnet nanodot arrays by ultrathin anodic alumina template on silicon substrate
Authors: Zheng Hui , Han Mangui , Zheng Liang , Zheng Peng , Wu Qiong , Deng Longjiang , Qin Huibin
Published: August 2015

Ultrahigh density periodically ordered magnetic yttrium iron garnet (Y3Fe5O12, YIG) nanodot arrays have been prepared by pulsed laser deposition through an ultrathin alumina mask (UTAM). UTAM having periodically ordered circularly shaped holes with 350 nm in diameter, 450 nm in inter-pore distance, and 700 nm in height has been prepared on silicon substrate. Furthermore, the microstructure and magnetic properties of YIG nanodot arrays have been characterized. Nanodot arrays with a sharp distribution in diameter centered at 340 nm with standard deviation of 10 nm have been fabricated. Moreover, typical hysteresis loops and ferromagnetic resonance spectra in in-plane and out-of-plane revealed that this unique structure greatly influences the magnetics properties of YIG. First, coercivity of YIG nanodot arrays in in-plane was increased about from 15 Oe of YIG films to 500 Oe. Then, the degree of uniformity about nanodot height decided that two or more resonance peaks in out-of-plane were detected in the spectra. The peak-to-peak linewidth values were about 94 Oe and 40 Oe in the parallel and perpendicular directions, respectively, which indicated that the values were larger by the two-magnon scattering. Consequently, this pattering method creates opportunities for studying physics in oxide nanomagnets and may be applied in spin-wave devices.
Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo
Authors: Cockram Charlotte A. , Filatenkova Milana , Danos Vincent , El Karoui Meriem , Leach David R. F.
Published: August 2015

Significance

Maintaining genomic integrity is crucial for cell survival. In
Escherichia coli
, RecA-mediated homologous recombination plays an essential role in the repair of DNA double-strand breaks (DSBs). A greater understanding of the mechanism of homologous recombination requires quantitative analysis of genomic studies in live cells. We have developed a novel method that is able to capture these interactions on a genome-wide scale by combining ChIP-seq and mathematical modeling to interpret the patterns of RecA–DNA interaction during DSB repair (DSBR). This genomic analysis has also revealed unexpected RecA binding in the terminus region of the chromosome, consistent with a second DSBR event (at a distance of 1 Mb) that is indirectly caused by the first DSBR event induced at the
lacZ.
Reciprocal regulation of two G protein-coupled receptors sensing extracellular concentrations of Ca
2+
and H
+
Authors: Wei Wei-Chun , Jacobs Benjamin , Becker Esther B. E. , Glitsch Maike D.
Published: August 2015

Significance

The composition of the extracellular fluid surrounding all cells changes in an activity-dependent manner. Cell surface receptors allow cells to respond to components of the fluid, which is vital for proper functioning of cells and tissues. Ca
2+
and H
+
are crucial for cell survival and functioning. Their extracellular concentrations are monitored by two receptors, extracellular calcium-sensing receptor (CaSR) and ovarian cancer gene receptor 1 (OGR1), respectively. We report that these two receptors can be regulated in a seesaw manner; conditions favoring activity of one receptor inhibit signaling through the other, and vice versa, allowing cells to detect subtle changes in the extracellular concentration of these ions. We provide evidence that dysregulated activity of CaSR and OGR1 may contribute to the formation and progression of pathologies.
Discovery and molecular and biocatalytic properties of hydroxynitrile lyase from an invasive millipede,Chamberlinius hualienensis
Authors: Dadashipour Mohammad , Ishida Yuko , Yamamoto Kazunori , Asano Yasuhisa
Published: August 2015

Significance

Hydroxynitrile lyase (HNL) has been isolated from plants and bacteria and is a valuable tool in the chiral-specific synthesis of cyanohydrins, which are important building blocks of fine chemicals and pharmaceuticals. To discover more efficient and stable HNLs, we focused on the invasive cyanogenic millipede as a bioresource. The HNL identified from the millipede showed not only the highest specific activity toward benzaldehyde among known HNLs, including the almond HNL in industrial use, along with wide temperature and pH stabilities, but also high enantioselectivity in the synthesis of various cyanohydrins. These properties make it suitable as an industrial biocatalyst. Arthropods are likely to be valuable sources of potential biocatalysts for the next generation of industrial biotechnology.
Concrete ensemble Kalman filters with rigorous catastrophic filter divergence
Authors: Kelly David , Majda Andrew J. , Tong Xin T.
Published: August 2015

Significance

Understanding ensemble-based data assimilation methods, including their performance when applied to high-dimensional nonlinear models with low ensemble size, is a crucial problem in science and engineering. Catastrophic filter divergence is a well-documented but mechanistically mysterious phenomenon whereby ensemble-state estimates explode to machine infinity despite the true state remaining in a bounded region. We provide breakthrough insight into the phenomenon by proposing a simple forecast model that experiences catastrophic filter divergence under all ensemble-based methods. This is the first instance to our knowledge of a forecast model that plainly and rigorously illustrates that simple mechanisms can lead to such a drastic filter malfunction and thereby sheds light on when catastrophic filter divergence should be expected and how it can be avoided.
Loss of diphthamide pre-activates NF-κB and death receptor pathways and renders MCF7 cells hypersensitive to tumor necrosis factor
Authors: Stahl Sebastian , da Silva Mateus Seidl Ana Rita , Ducret Axel , Kux van Geijtenbeek Sabine , Michel Sven , Racek Tomas , Birzele Fabian , Haas Alexander K. , Rueger Ruediger , Gerg Michael , Niederfellner Gerhard , Pastan Ira , Brinkmann Ulrich
Published: August 2015

Significance

Diphthamide is a conserved modification on eukaryotic translation elongation factor 2 (eEF2). Analyses of genetically defined diphthamide-deficient cell lines indicate that this modification determines not only sensitivity of cells to the ADP-ribosylating toxinsPseudomonasexotoxin A and diphtheria toxin, but it also modulates nuclear factor of kappa light polypeptide gene enhancer in B cells (NF-κB) and TNF receptor signaling pathways.
Effects of Stocking Density on Production Traits of Channel Catfish×Blue Catfish Hybrids
Authors: Bosworth Brian , Ott Brian , Torrans Les
Published: August 2015

Channel Catfish Ictalurus punctatus × Blue Catfish I. furcatus hybrid fingerlings (mean weight, 47 g) were stocked in 0.4-ha ponds at densities of 7,425, 12,375, 17,325, 22,275, and 27,225 fish/ha in three replicate earthen ponds for each density. Fish were fed a 28% protein diet to apparent satiation once daily. Ponds were equipped with electric paddlewheel aerators (12.5 hp/ha) that were turned on when dissolved oxygen (DO) levels reached <5.0 mg/L; additional aeration was provided by power-takeoff tractor-driven paddlewheels at DO < 2.5 mg/L. Feeding was terminated at the end of October and fish were harvested and weighed. Stocking density had no significant effect on feed conversion (overall average, 1.97), survival (≥93% in all treatments), or processing yield (carcass yield = 66.2%, shank fillet yield = 34.8%, nugget yield = 10.5%). Harvest weight was not significantly different between 7,425 and 22,275 fish/ha (average, 0.85 kg) but was less at 27,225 fish/ha (0.72 kg). Net production increased significantly with increased density from 7,425 to 22,275 fish/ha but was not different between 22,275 and 27,225 fish/ha. Percentage of submarketable fish (<0.45 kg) was not significantly different from pond densities of 7,425 through 22,275 fish/ha (average, 2.3%), but was higher at 27,225 fish/ha (8.8%). Aeration hours increased and minimum DO levels decreased significantly as stocking density increased. The smaller average weight at 27,225 fish/ha may have been due to fish behavior associated with crowding, lack of equal access to feed, or degraded water quality. However, past research has demonstrated a “threshold” relationship between minimum DO levels and catfish feeding and growth. Data from this study indicate a similar DO threshold–growth relationship, suggesting the observed effect of density on growth may have been at least partially due to minimum DO levels being below that needed for optimal growth at 27,225 fish/ha.
FLT1 signaling in metastasis-associated macrophages activates an inflammatory signature that promotes breast cancer metastasis
Authors: Qian Bin-Zhi , Zhang Hui , Li Jiufeng , He Tianfang , Yeo Eun-Jin , Soong Daniel Y.H. , Carragher Neil O. , Munro Alison , Chang Alvin , Bresnick Anne R. , Lang Richard A. , Pollard Jeffrey W.
Published: August 2015

Although the link between inflammation and cancer initiation is well established, its role in metastatic diseases, the primary cause of cancer deaths, has been poorly explored. Our previous studies identified a population of metastasis-associated macrophages (MAMs) recruited to the lung that promote tumor cell seeding and growth. Here we show that FMS-like tyrosine kinase 1 (Flt1, also known as VEGFR1) labels a subset of macrophages in human breast cancers that are significantly enriched in metastatic sites. In mouse models of breast cancer pulmonary metastasis, MAMs uniquely express FLT1. Using several genetic models, we show that macrophage FLT1 signaling is critical for metastasis. FLT1 inhibition does not affect MAM recruitment to metastatic lesions but regulates a set of inflammatory response genes, including colony-stimulating factor 1 (CSF1), a central regulator of macrophage biology. Using a gain-of-function approach, we show that CSF1-mediated autocrine signaling in MAMs is downstream of FLT1 and can restore the tumor-promoting activity of FLT1-inhibited MAMs. Thus, CSF1 is epistatic to FLT1, establishing a link between FLT1 and inflammatory responses within breast tumor metastases. Importantly, FLT1 inhibition reduces tumor metastatic efficiency even after initial seeding, suggesting that these pathways represent therapeutic targets in metastatic disease.
NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
Authors: Gaudreault Francis , Morency Louis-Philippe , Najmanovich Rafael J.
Published: August 2015

Ligand protein docking simulations play a fundamental role in understanding molecular recognition. Herein we introduce the NRGsuite, a PyMOL plugin that permits the detection of surface cavities in proteins, their refinements, calculation of volume and use, individually or jointly, as target binding-sites for docking simulations with FlexAID. The NRGsuite offers the users control over a large number of important parameters in docking simulations including the assignment of flexible side-chains and definition of geometric constraints. Furthermore, the NRGsuite permits the visualization of the docking simulation in real time. The NRGsuite give access to powerful docking simulations that can be used in structure-guided drug design as well as an educational tool. The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. The NRGsuite is available for Windows, Linux and MacOS.

Availability and implementation: http://bcb.med.usherbrooke.ca/flexaid.

Contact:  rafael.najmanovich@usherbroke.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Recoverin depletion accelerates cone photoresponse recovery
Authors: Zang Jingjing , Keim Jennifer , Kastenhuber Edda , Gesemann Matthias , Neuhauss Stephan C. F.
Published: August 2015

The neuronal Ca2+-binding protein Recoverin has been shown to regulate phototransduction termination in mammalian rods. Here we identify fourrecoveringenes in the zebrafish genome,rcv1a,rcv1b,rcv2aandrcv2b, and investigate their role in modulating the cone phototransduction cascade. While Recoverin-1b is only found in the adult retina, the other Recoverins are expressed throughout development in all four cone types, except Recoverin-1a, which is expressed only in rods and UV cones. Applying a double flash electroretinogram (ERG) paradigm, downregulation of Recoverin-2a or 2b accelerates cone photoresponse recovery, albeit at different light intensities. Exclusive recording from UV cones via spectral ERG reveals that knockdown of Recoverin-1a alone has no effect, but Recoverin-1a/2a double-knockdowns showed an even shorter recovery time than Recoverin-2a-deficient larvae. We also showed that UV cone photoresponse kinetics depend on Recoverin-2a function via cone-specific kinase Grk7a. This is the firstin vivostudy demonstrating that cone opsin deactivation kinetics determine overall photoresponse shut off kinetics.
Complex relationships between species niches and environmental heterogeneity affect species co-occurrence patterns in modelled and real communities
Authors: Bar-Massada Avi
Published: August 2015

Species co-occurrence analysis is commonly used to assess how interspecific interactions dictate community assembly. Non-random co-occurrences, however, may also emerge from niche differences as well as environmental heterogeneity. The relationships between species co-occurrence patterns, environmental heterogeneity and species niches are not fully understood, due to complex interactions among them. To analyse the relationships among these patterns and processes, I developed synthetic community models and analysed a large dataset of tree species across the conterminous United States. Niche overlap and environmental heterogeneity had significant and contrasting effects on species co-occurrence patterns, in both modelled and real communities. Niche breadth, in turn, affected the effect sizes of both variables on species co-occurrence patterns. The effect of niche breadth on the relationship between co-occurrence and niche overlap was markedly consistent between modelled and real communities, while its effect on the relationship between co-occurrence and environmental heterogeneity was mostly consistent between real and modelled data. The results of this analysis highlight the complex and interactive effects of species niche overlap, niche breadth and environmental heterogeneity on species co-occurrence patterns. Therefore, inferring ecological processes from co-occurrence patterns without accounting for these fundamental characteristics of species and environments may lead to biased conclusions.
Landscape and dynamics of transcription initiation in the malaria parasitePlasmodium falciparum
Authors: Adjalley Sophie H. , Chabbert Christophe D. , Klaus Bernd , Pelechano Vicent , Steinmetz Lars M.
Published: August 2015

The lack of a comprehensive map of transcription start sites (TSS) across the highly AT-rich genome ofP. falciparumhas hindered progress towards deciphering the molecular mechanisms that underly the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single nucleotide-resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcriptional unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.
Crystal structure of bis[(phenylmethanamine-κN)(phthalocyaninato-κ4N)zinc] phenylmethanamine trisolvate
Authors: Shamsudin Norzianah , Tan Ai Ling , Wimmer Franz L. , Young David J. , Tiekink Edward R. T.
Published: August 2015

The asymmetric unit of the title compound, 2[Zn(C32H16N8)(C7H9N)]·3C7H9N, comprises two independent complex molecules and three benzylamine solvent molecules. Each complex molecule features a pentacoordinated Zn2+ion within a square-pyramidal geometry, whereby the N5donor set is defined by four atoms of the phthalocyaninate dianion (PC) and an N-bound benzylamine molecule; it is the relative orientations of the latter that differentiate between the independent complex molecules. The uncoordinated benzylamine molecules display different conformations in the structure, withsyn-Car—Car—Cm—N (ar = aromatic, m = methylene) torsion angles spanning the range −28.7 (10) to 35.1 (14)°. In the crystal, N—H...N and N—H...π interactions lead to supramolecular layers in theabplane. The layers have a zigzag topology, have the coordinating and non-coordinating benzylamine molecules directed to the inside, and present the essentially flat PC resides to the outside. This arrangement enables adjacent layers to associateviaπ–π interactions [inter-centroid distance between pyrrolyl and fused-benzene rings = 3.593 (2) Å] so that a three-dimensional architecture is formed.
Crystal structure of a mononuclear RuIIcomplex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy–tpy)]+
Authors: Rein Francisca N. , Chen Weizhong , Scott Brian L. , Rocha Reginaldo C.
Published: August 2015

We report the structural characterization of [6′,6′′-bis(pyridin-2-yl)-2,2′:4′,4′′:2′′,2′′′-quaterpyridine](2,2′-bipyridine)chloridoruthenium(II) hexafluoridophosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2′-bipyridine (bpy) and the tridendate ligand 6′,6′′-bis(pyridin-2-yl)-2,2′:4′,4′′:2′′,2′′′-quaterpyridine (tpy–tpy). The [RuCl(bpy)(tpy–tpy)]+monocation has a distorted octahedral geometry at the central RuIIion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru—N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru—Cl. For tpy–tpy, the mean Ru—N distance involving the outer N atomstransto each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru—Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy–tpy adopts atrans,transconformation about the interannular C—C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π–π stacking interactions based on tpy–tpy. The crystal structure reported here is the first for a tpy–tpy complex of ruthenium.
The relationship between international trade openness and economic growth in the developing economies
Authors: Tahir Muhammad , Azid Toseef
Published: August 2015

Purpose

– This paper aims to establish a relationship between trade openness and economic growth in the context of the developing countries. This study has proposed a new measure of trade openness to the literature, as the available measures are flawed.

Design/methodology/approach

– Empirical analyses are carried out with the help of panel econometric techniques.

Findings

– The main finding of the paper is that the relationship between trade openness and economic growth is positive and statistically significant for developing countries. Besides trade openness, other determinants of economic growth such as investment and labour force are also significantly related with economic growth and carry expected coefficients. Further, it is found that frequent fluctuations in prices are detrimental to long-run economic growth.

Practical implications

– Therefore, the developing countries are suggested to speed up the process of trade liberalization and also pay favourable attention to other determinants of economic growth to achieve high economic growth.

Originality/value

– The authors have used a new measure of trade openness apart from the conventional trade volume measure of trade openness.
SMEs, environmental management and global warming: a fusion of influencing factors?
Authors: Raar Jean
Published: August 2015

Purpose

– Stakeholder theory provided the broad theoretical lens to explore environmental issues in small and medium enterprises (SMEs). The diversity in issues examined ranged from concern for immediate stakeholders, their industry group and the influence of global warming on their business activities, to the type of environmental information included within their internal information systems. The paper aims to discuss these issues.

Design/methodology/approach

– A mailed survey was used to obtain data from SMEs operating in Australia. The focus was primarily directed to medium size firms.

Findings

– The findings indicate that SMEs were aware that their stakeholders, particularly their employees and customers were concerned with environmental issues. The respondent SMEs were also aware that global warming would influence their activities, for example, the design of their projects, occupational, health and safety, labour contracts and customer relations. Overall, the findings suggest that any tailored approach to regulate or self-regulate environmental management in SMEs, be industry and stakeholder driven.

Research limitations/implications

– The limitations of this research are primarily those applicable to the survey method, SME response rates, and the geographical location covered by the survey. The focus of this study is primarily medium size firms, rather than micro small business.

Originality/value

– This study gains insights into some of the practical aspects of environmental management in SMEs and in so doing adds to the growing body of literature in this under researched area.
The discursive construction of the recent European economic crisis in two political magazines
Authors: Mitsikopoulou Bessie , Lykou Christina
Published: August 2015

Purpose

– Acknowledging the important role of the media in shaping a European public sphere, the purpose of this paper is to explore how the recent economic crisis is discursively construed in the context of the British media discourse. It investigates discursive constructions of the economic crisis in two political magazines of different ideological positioning by placing emphasis on the economic crisis in Greece, the “weak link” of the Eurozone.

Design/methodology/approach

– The study draws on systemic functional linguistics which views language as social semiotic and conducts a transitivity analysis of a corpus consisting of 59 articles (a total of 61,820 words) from two weekly British political magazines, one of conservative and one of centre-left political position. The analysis is assisted by Wordsmith 6.0 concordance corpus tool.

Findings

– It is argued that the articles of the conservative magazine construe the crisis as primarily local and financial, discussing its effects on the British economy. On the other hand, the articles of the centre-left magazine view the crisis as a systemic one derived from and, at the same time, affecting European Union policies and stress its political and economic implications in all of Eurozone.

Originality/value

– The findings of the study contribute to the body of studies which investigate the role of language in the construction of the economic crisis and also adds to the on-going discussion regarding the development of a European public sphere as part of the wider European Project and the process of European integration.
Economic thought in the 17th and 18th centuries: a linguistic approach
Authors: Lima Iara Vigo de
Published: August 2015

Purpose

– The purpose of this paper is to analyse Michel Foucault’s new epistemological model regarding an analogy between the theory of language and economic thought in the seventeenth and eighteenth centuries.

Design/methodology/approach

– Through the scrutiny of language, Foucault intended to demonstrate that some analogies, among different branches of knowledge (interdiscursive practice), allow us to apprehend the underlying configuration of thought regarding ontological and epistemological conditions that have historically determined knowledge. He draws a parallel between four theoretical segments borrowed from general grammar (Attribution, Articulation, Designation and Derivation) and economic thought on wealth.

Findings

– One of the most remarkable propositions of this approach is that the theory of language and economic thought were epistemologically isomorphic in that context. What the theory of language stated in relation to “attribution” and “articulation” corresponded to the “theory of value” in economic thought. What grammar investigated regarding “designation” and “derivation” was analogous to the “theory of money and trade” in economic thought. The relationships that were – directly and diagonally – identified between and among them led to the conclusion that there was ‘a circular and surface causality’ in economic thought insofar as “circulation” preceded “production”. It was “superficial” because it could not find an explanation for the cause of “wealth”, which was only possible when “production” was placed in the front position of theories.

Practical implications

– Such an epistemological point of view can inspire other studies in the history of economic thought.

Originality/value

– This paper offers a perspective on how to think about the history of ontological and epistemological conditions of economic thought.
Agency culture and the banality of risk
Authors: Wehr Kevin
Published: August 2015

Purpose

– The purpose of this paper is to investigate the role that agency culture, training, and supervision play in the rates of on-the-job seatbelt use among peace officers, as well as other officer safety-related driving concerns such as cell phone use, Mobile Data Terminal use, and other sources of distraction.

Design/methodology/approach

– Based on semi-structured interviews with California peace officers.

Findings

– This study found an array of agency culture issues related to on-duty collisions, including distraction, failure to follow policy or procedure, fatigue, self-selection processes among officers and agencies, supervision and field training processes, morale issues, and family/lifestyle issues.

Originality/value

– To explain these agency culture findings, this paper introduces the concept of the “banality of risk” to understand why many officers choose not to use risk-attenuating equipment. The findings are suggestive of a set of best practices that agencies could consider regarding in-vehicle officer safety.
Police drowsy driving: predicting fatigue-related performance decay
Authors: James Stephen M. , Vila Bryan
Published: August 2015

Purpose

– Fatigue associated with shift work is a well-established and pervasive problem in policing that affects officer performance, safety, and health. It is critical to understand the extent to which fatigue degrades officer driving performance. Drowsy driving among post-shift workers is a well-established risk factor yet no data are available about officer injuries and deaths due to drowsy driving. The purpose of this paper is to assess the impact of fatigue associated with work shift and prior sleep on officers’ non-operational driving using laboratory experiments to assess post-shift drowsy driving risks and the ability of a well-validated vigilance and reaction-time task to assess these risks.

Design/methodology/approach

– Experienced police patrol officer volunteers (n=78) from all four shifts of a medium-sized city’s police department were tested using a within- and between-subjects design to assess the impact of fatigue on individual officers, as well as the impact of different work shifts, on post-shift driving performance. Controlled laboratory experiments were conducted during which participants drove high-fidelity driving training simulators on two occasions: immediately following five consecutive 10:40-hour patrol shifts (fatigued condition) and again 72 hours after completing the last shift in a work cycle (rested condition).

Findings

– Generalized linear mixed-model analyses of driving performance showed that officers working night shifts had significantly greater lane deviation during post-shift, non-operational driving than those working day shifts (F=4.40, df=1, 150, p=0.038). The same method also showed that easy to measure psychomotor vigilance test scores for reaction time predicted both lane deviation (F=31.48, df=1, 151, p
<
0.001) and collisions (F=14.10, df=1, 151, p
<
0.001) during the simulated drives.

Research limitations/implications

– Simulated driving tasks done by participants were generally less challenging than patrol or off-duty driving and likely underestimate the impact of fatigue on police driving post-shift or during extended shifts.

Originality/value

– This is the first experimental research to assess the impact of shiftwork, fatigue, and extended shifts on police post-shift drowsy driving, a known risk factor for shift workers in general.
Prevalence of β‐Lactamase Producing Escherichia coli from Retail Meat in Turkey
Authors: Pehlivanlar Önen Sevda , Aslantaş Özkan , Şebnem Yılmaz Ebru , Kürekci Cemil
Published: August 2015

Extended spectrum β‐lactamase (ESBL) and plasmid‐mediated AmpC β‐lactamase (pAmpC) producing Escherichia coli have been shown to be present in humans and animals representing a significant problem worldwide. This study aimed to search the presence of ESBL and/or AmpC‐producing E. coli in retail meats (chicken and beef) in Turkey. A total of 88 β‐lactamase‐producing E. coli were isolated from chicken (n = 81/100) and beef meat (n = 7/100) samples and their susceptibility to several antimicrobials were tested using disc diffusion method. E. coli isolates were further characterized for their phylogenetic groups. β‐Lactamase encoding (blaTEM, blaSHV, blaOXA, blaCTX‐M, and blaAmpC) and quinolone resistance genes (qnrA, qnrB, qnrS, qepA, and acc(6′)‐Ib‐cr) were also secreened by polymerase chain reaction (PCR). However, in regard to β‐lactamase genes, 84 of 88 isolates were positive for blaCTX‐M‐1 (n = 39), blaCTX‐M‐3 (n = 5), blaCTX‐M‐15 (n = 4), blaTEM‐1b (n = 2), blaSHV‐12 (n = 1), blaCTX‐M‐1/blaTEM‐1b (n = 10), blaCTX‐M‐1/blaTEM‐1b/blaSHV‐5 (n = 1), blaCTX‐M‐1/blaCMY‐2 (n = 1) and blaTEM‐1b/blaCMY‐2 (n = 6), blaCTX‐M‐15/blaSHV‐12 (n = 1), blaCTX‐M‐15/blaTEM‐1b (n = 1), blaTEM‐1b/blaSHV‐12 (n = 1), and blaCMY‐2 (n = 12) genes. Resistance to cefuroxime (75.6% and 85.7%), nalidixic acid (89% and 85.7%), tetracycline (91.4% and 100%), streptomycin (40.2% and 100%), and trimethoprim‐sulfamethoxazole (36.6% and 85.7%) was observed among strains isolated from chicken and beef, respectively. However, all isolates were found to be susceptible to amikacin, imipenem, and cefepime. Resistance to ampicillin and cefoxitin was significantly linked to blaCMY‐2 gene, while there was a significant correlation between CTX‐M type ESBL and antimicrobial resistance to cefuroxime and streptomycin (P < 0.05). The results of this study suggest that raw chicken retail meats are highly contaminated with ESBL‐producing E. coli implementing a great risk to human health in Turkey.