bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying catchment‐scale mixing and its effect on time‐varying travel time distributions
Authors: van der Velde Y. , Torfs P. J. J. F. , van der Zee S. E. A. T. M. , Uijlenhoet R.
Published: May 2012

Travel time distributions are often used to characterize catchment discharge behavior, catchment vulnerability to pollution and pollutant loads from catchments to downstream waters. However, these distributions vary with time because they are a function of rainfall and evapotranspiration. It is important to account for these variations when the time scale of interest is smaller than the typical time‐scale over which average travel time distributions can be derived. Recent studies have suggested that subsurface mixing controls how rainfall and evapotranspiration affect the variability in travel time distributions of discharge. To quantify this relation between subsurface mixing and dynamics of travel time distributions, we propose a new transformation of travel time that yields transformed travel time distributions, which we call Storage Outflow Probability (STOP) functions. STOP functions quantify the probability for water parcels in storage to leave a catchment via discharge or evapotranspiration. We show that this is equal to quantifying mixing within a catchment. Compared to the similar Age function introduced by Botter et al. (2011), we show that STOP functions are more constant in time, have a clearer physical meaning and are easier to parameterize. Catchment‐scale STOP functions can be approximated by a two‐parameter beta distribution. One parameter quantifies the catchment preference for discharging young water; the other parameter quantifies the preference for discharging old water from storage. Because of this simple parameterization, the STOP function is an innovative tool to explore the effects of catchment mixing behavior, seasonality and climate change on travel time distributions and the related catchment vulnerability to pollution spreading.
Oblique wave‐wave interactions of nonlinear near‐surface internal waves in the Strait of Georgia
Authors: Wang C. , Pawlowicz R.
Published: May 2012

Although nonlinear interactions that occur when two large internal waves collide at oblique angles are often observed in the natural world, quantitative and theoretical aspects of these interactions are only poorly understood. The available analyses are generally theoretical or the result of limited numerical experimentation, with few (if any) quantitative field measurements. Here we describe four cases of internal wave interactions, two of which involve the fundamentally non‐steady generation of “Mach stems” at the site of the interaction, observed in the Strait of Georgia, Canada. Details of the interactions are quantified using time sequences of photogrammetrically rectified oblique images obtained from a circling aircraft, while simultaneous observations are made of water column properties from a surface vessel. The imaging technique allows us to estimate the speed and direction of each wave, as well as details of phase shifts induced by interactions. An existing small‐amplitude theory is applied but is found to overestimate the likelihood of Mach interactions at large amplitude.
Chronostratigraphic framework for the IODP Expedition 318 cores from the Wilkes Land Margin: Constraints for paleoceanographic reconstruction
Authors: Tauxe L. , Stickley C. E. , Sugisaki S. , Bijl P. K. , Bohaty S. M. , Brinkhuis H. , Escutia C. , Flores J. A. , Houben A. J. P. , Iwai M. , Jiménez‐Espejo F. , McKay R. , Passchier S. , Pross J. , Riesselman C. R. , Röhl U. , Sangiorgi F. , Welsh K. , Klaus A. , Fehr A. , Bendle J. A. P. , Dunbar R. , Gonzàlez J. , Hayden T. , Katsuki K. , Olney M. P. , Pekar S. F. , Shrivastava P. K. , van de Flierdt T. , Williams T. , Yamane M.
Published: May 2012

The Integrated Ocean Drilling Program Expedition 318 to the Wilkes Land margin of Antarctica recovered a sedimentary succession ranging in age from lower Eocene to the Holocene. Excellent stratigraphic control is key to understanding the timing of paleoceanographic events through critical climate intervals. Drill sites recovered the lower and middle Eocene, nearly the entire Oligocene, the Miocene from about 17 Ma, the entire Pliocene and much of the Pleistocene. The paleomagnetic properties are generally suitable for magnetostratigraphic interpretation, with well‐behaved demagnetization diagrams, uniform distribution of declinations, and a clear separation into two inclination modes. Although the sequences were discontinuously recovered with many gaps due to coring, and there are hiatuses from sedimentary and tectonic processes, the magnetostratigraphic patterns are in general readily interpretable. Our interpretations are integrated with the diatom, radiolarian, calcareous nannofossils and dinoflagellate cyst (dinocyst) biostratigraphy. The magnetostratigraphy significantly improves the resolution of the chronostratigraphy, particularly in intervals with poor biostratigraphic control. However, Southern Ocean records with reliable magnetostratigraphies are notably scarce, and the data reported here provide an opportunity for improved calibration of the biostratigraphic records. In particular, we provide a rare magnetostratigraphic calibration for dinocyst biostratigraphy in the Paleogene and a substantially improved diatom calibration for the Pliocene. This paper presents the stratigraphic framework for future paleoceanographic proxy records which are being developed for the Wilkes Land margin cores. It further provides tight constraints on the duration of regional hiatuses inferred from seismic surveys of the region.
The post-transcriptional life of mammalian mitochondrial RNA
Authors: Rorbach Joanna , Minczuk Michal
Published: May 2012

Mammalian mitochondria contain their own genome that encodes mRNAs for thirteen essential subunits of the complexes performing oxidative phosporylation as well as the RNA components (two rRNAs and 22 tRNAs) needed for their translation in mitochondria. All RNA species are produced from single polycistronic precursor RNAs, yet the relative concentrations of various RNAs differ significantly. This underscores the essential role of post-transcriptional mechanisms that control the maturation, stability and translation of mitochondrial RNAs. The present review provides a detailed summary on the role of RNA maturation in the regulation of mitochondrial gene expression, focusing mainly on messenger RNA polyadenylation and stability control. Furthermore, the role of mitochondrial ribosomal RNA stability, processing and modifications in the biogenesis of the mitochondrial ribosome is discussed.
The variable N-terminal region of DDX5 contains structural elements and auto-inhibits its interaction with NS5B of hepatitis C virus
Authors: Dutta Sujit , Gupta Garvita , Choi Yook-Wah , Kotaka Masayo , Fielding Burtram C. , Song Jianxing , Tan Yee-Joo
Published: May 2012

RNA helicases of the DEAD (Asp-Glu-Ala-Asp)-box family of proteins are involved in many aspects of RNA metabolism from transcription to RNA decay, but most of them have also been shown to be multifunctional. The DEAD-box helicase DDX5 of host cells has been shown to interact with the RNA-dependent RNA polymerase (NS5B) of HCV (hepatitis C virus). In the present study, we report the presence of two independent NS5B-binding sites in DDX5, one located at the N-terminus and another at the C-terminus. The N-terminal fragment of DDX5, which consists of the first 305 amino acids and shall be referred as DDX5-N, was expressed and crystallized. The crystal structure shows that domain 1 (residues 79–303) of DDX5 contains the typical features found in the structures of other DEAD-box helicases. DDX5-N also contains the highly variable NTR (N-terminal region) of unknown function and the crystal structure reveals structural elements in part of the NTR, namely residues 52–78. This region forms an extensive loop and an α-helix. From co-immunoprecipitation experiments, the NTR of DDX5-N was observed to auto-inhibit its interaction with NS5B. Interestingly, the α-helix in NTR is essential for this auto-inhibition and seems to mediate the interaction between the highly flexible 1–51 residues in NTR and the NS5B-binding site in DDX5-N. Furthermore, NMR investigations reveal that there is a direct interaction between DDX5 and NS5B in vitro.
Effect of calcitonin gene‐related peptide on osteoblast differentiation in an osteoblast and endothelial cell co‐culture system
Authors: Bo Yang , Yan Li , Gang Zhang , Tao Lei , Yinghui Tan
Published: May 2012

We have investigated the in vitro effects and regulatory mechanism of CGRP (calcitonin gene‐related peptide) on the differentiation of OB (osteoblasts) in co‐culture with HUVEC (human umbilical vein endothelial cells). Primary human MOB (mandibular OB) and OB‐like cells (MG‐63) were either cultured directly or indirectly co‐cultured with HUVEC at a 1:1 ratio. Expression of OC (osteocalcin) was measured by ELISA, and expression of ALP (alkaline phosphatase) and collagen mRNA was measured by quantitative fluorescent PCR. For mineralization nodus, OB were stained with Alizarin Red‐S. When co‐cultured with HUVEC, expression of OC and ALP mRNA were increased in MG‐63 (P<0.01), and the expression of OC, ALP and collagen mRNA were increased in MOB (P<0.01 or 0.05). When treated with CGRP, OC and ALP mRNA and mineralization nodus numbers were increased in the MG‐63 co‐culture system (P<0.01 or 0.05); OC, ALP and collagen mRNA, and mineralization nodus numbers were increased in the MOB co‐culture system (P<0.01 or 0.05). The effect of CGRP regulation on the differentiation of OB is not only direct but also indirect, via its effect on HUVEC and stimulation of OB.
Magnetothermal instability in laser plasmas including hydrodynamic effects
Authors: Bissell J. J. , Kingham R. J. , Ridgers C. P.
Published: May 2012

The impact of both density gradients and hydrodynamics on the evolution of the field compressing magnetothermal instability is considered [J. J. Bissell et al., Phys. Rev. Lett. 105, 175001 (2010)]. Hydrodynamic motion is found to have a limited effect on overall growth-rates; however, density gradients are shown to introduce an additional source term corresponding to a generalised description of the field generating thermal instability [D. Tidman and R. Shanny, Phys. Fluids 17, 1207 (1974)]. The field compressing and field generating source terms are contrasted, and the former is found to represent either the primary or sole instability mechanism for a range of conditions, especially those with Hall parameter χ>10-1. The generalised theory is compared to numerical simulation in the context of a recent nano-second gas-jet experiment [D. H. Froula et al., Phys. Rev. Lett. 98, 135001 (2007)] and shown to be in good agreement: exhibiting peak growth-rates and wavelengths of order 10 ns1 and 50 μm, respectively. The instability’s relevance to other experimental conditions, including those in inertial confinement fusion (I.C.F.) hohlraums, is also discussed.
Transport of particles by magnetic forces and cellular blood flow in a model microvessel
Authors: Freund J. B. , Shapiro B.
Published: May 2012

The transport of particles (diameter 0.56 μm) by magnetic forces in a small blood vessel (diameter D = 16.9 μm, mean velocity U = 2.89 mm/s, red cell volume fraction Hc = 0.22) is studied using a simulation model that explicitly includes hydrodynamic interactions with realistically deformable red blood cells. A biomedical application of such a system is targeted drug or hyperthermia delivery, for which transport to the vessel wall is essential for localizing therapy. In the absence of magnetic forces, it is seen that interactions with the unsteadily flowing red cells cause lateral particle velocity fluctuations with an approximately normal distribution with variance σ = 140 μm/s. The resulting dispersion is over 100 times faster than expected for Brownian diffusion, which we neglect. Magnetic forces relative to the drag force on a hypothetically fixed particle at the vessel center are selected to range from Ψ = 0.006 to 0.204. The stronger forces quickly drive the magnetic particles to the vessel wall, though in this case the red cells impede margination; for weaker forces, many of the particles are marginated more quickly than might be predicted for a homogeneous fluid by the apparently chaotic stirring induced by the motions of the red cells. A corresponding non-dimensional parameter Ψ′, which is based on the characteristic fluctuation velocity σ rather than the centerline velocity, explains the switch-over between these behaviors. Forces that are applied parallel to the vessel are seen to have a surprisingly strong effect due to the streamwise-asymmetric orientation of the flowing blood cells. In essence, the cells act as low-Reynolds number analogs of turning vanes, causing streamwise accelerated particles to be directed toward the vessel center and streamwise decelerated particles to be directed toward the vessel wall.
Formation of collimated sound beams by three-dimensional sonic crystals
Authors: Cebrecos A. , Romero-García V. , Picó R. , Pérez-Arjona I. , Espinosa V. , Sánchez-Morcillo V. J. , Staliunas K.
Published: May 2012

A theoretical and experimental study of the propagation of sound beams in- and behind three-dimensional sonic crystals at frequencies close to the band edges is presented. An efficient collimation of the beam behind the crystal is predicted and experimentally demonstrated. This effect could allow the design of sources of high spatial quality sound beams.
Experimental investigation of the micro-ramp based shock wave and turbulent boundary layer interaction control
Authors: Bo Wang , Weidong Liu , Yuxin Zhao , Xiaoqiang Fan , Chao Wang
Published: May 2012

Using a nanoparticle-based planar laser-scattering technique and supersonic particle image velocimetry, we investigated the effects of micro-ramp control on incident shockwave and boundary-layer interaction (SWBLI) in a low-noise supersonic wind-tunnel with Mach number 2.7 and Reynolds number Rθ = 5845. High spatiotemporal resolution wake structures downstream of the micro-ramps were detected, while a complex evolution process containing a streamwise counter-rotating vortex pair and large-scale hairpin-like vortices with Strouhal number Stδ of about 0.5–0.65 was revealed. The large-scale structures could survive while passing through the SWBLI region. Reflected shockwaves are clearly seen to be distorted accompanied by high-frequency fluctuations. Micro-ramp applications have a distinct influence on flow patterns of the SWBLI field that vary depending on spanwise locations. Both the shock foot and separation line exhibit undulations corresponding with modifications of the velocity distribution of the incoming boundary layer. Moreover, by energizing parts of the boundary flow, the micro-ramp is able to dampen the separation.
When complexity leads to simplicity: Ocean surface mixing simplified by vertical convection
Authors: Aharon Rotem , Rom-Kedar Vered , Gildor Hezi
Published: May 2012

The effect of weak vertical motion on the dynamics of materials that are limited to move on the ocean surface is an unresolved problem with important environmental and ecological implications (e.g., oil spills and larvae dispersion). We investigate this effect by introducing into the classical horizontal time-periodic double-gyre model vertical motion associated with diurnal convection. The classical model produces chaotic advection on the surface. In contrast, the weak vertical motion simplifies this chaotic surface mixing pattern for a wide range of parameters. Melnikov analysis is employed to demonstrate that these conclusions are general and may be applicable to realistic cases. This counter intuitive result that the very weak nocturnal convection simplifies ocean surface mixing has significant outcomes.
Structural modifications of zinc phthalocyanine thin films for organic photovoltaic applications
Authors: Zhou Ying , Taima Tetsuya , Miyadera Tetsuhiko , Yamanari Toshihiro , Yoshida Yuji
Published: May 2012

Zinc phthalocyanine (ZnPc) thin films are vacuum-evaporated on bare indium-tin-oxide (ITO) coated glass by varying substrate temperature and growth rate. The samples are characterized by atomic force microscopy, x-ray diffraction, and infrared spectroscopy. The temperature does not play a clear role in the crystalline growth of ZnPc possibly due to the significant structural defects on ITO surface, while it strongly influences the surface morphology and molecular alignment. The relationships between growth characteristics and performances of photovoltaics with planar heterojunction are discussed in detail. Increasing temperature or growth rate leads to a rougher surface morphology, which enables more donor/accepter interface area for photocurrent generation. Moreover, at elevated temperature, more molecules adopt standing-up geometry, resulting in a reduction in overall efficiency. The results imply that low-temperature process in order to control the molecular alignment is preferred for efficient organic photovoltaics. By simply increasing the growth rate of ZnPc up to 0.40 Å/s at room temperature, ZnPc/C60 planar heterojunction shows an efficiency of 1.66%, compared to 1.24% for the cell when ZnPc is prepared at 0.10 Å/s.
Mechanism of random telegraph noise in junction leakage current of metal-oxide-semiconductor field-effect transistor
Authors: Mori Yuki , Yoshimoto Hiroyuki , Takeda Kenichi , Yamada Ren-ichi
Published: May 2012

Evidence is given for the mechanism of hole-trap-related random telegraph noise (RTN) in reverse-biased junction leakage current occurring in the off-state of sub-micron scaled metal-oxide-semiconductor field-effect transistor (MOSFET). It was found that such RTN in junction leakage current, namely, variable junction leakage (VJL), is induced by applying hole-accumulation bias to the gate of the MOSFET. This result indicates that a hole captured in the gate oxide near the silicon surface influences the channel surface potential and causes fluctuation in generation-recombination (g-r) current generated at interface states. The fluctuation in g-r current is observed as VJL. It was also found that occurrence rate of VJL increases under hot-carrier stress. On the basis of these results, a model for VJL that can more concretely explain the mechanism of VJL quantitatively was developed.
Ferromagnetism carried by highly delocalized hybrid states in Sc-doped ZnO thin films
Authors: Benali Kanoun Mohammed , Goumri-Said Souraya , Manchon Aurélien , Schwingenschlögl Udo
Published: May 2012

We present first-principles results for Sc-doped ZnO thin films. Neighboring Sc atoms in the surface and/or subsurface layers are found to be coupled ferromagnetically, where only two of the possible configurations induce spin polarization. In the first configuration, the polarization is carried by the Sc d states as expected for transition metal doping. However, there is a second configuration which is energetically favorable. It is governed by polarized hybrid states of the Zn s, O p, and Sc d orbitals. Such highly delocalized states can be an important ingredient for understanding the magnetism of doped ZnO thin films.
Maximum spectral luminous efficacy of white light
Authors: Murphy Thomas W.
Published: May 2012

As lighting efficiency improves, it is useful to understand the theoretical limits to luminous efficacy for light that we perceive as white. Independent of the efficiency with which photons are generated, there exists a spectrally imposed limit to the luminous efficacy of any source of photons. We find that, depending on the acceptable bandpass and—to a lesser extent—the color temperature of the light, the ideal white light source achieves a spectral luminous efficacy of 250–370 lm/W. This is consistent with previous calculations, but here we explore the maximum luminous efficacy as a function of photopic sensitivity threshold, color temperature, and color rendering index; deriving peak performance as a function of all three parameters. We also present example experimental spectra from a variety of light sources, quantifying the intrinsic efficacy of their spectral distributions.
Synchronization between integer-order chaotic systems and a class of fractional-order chaotic systems via sliding mode control
Authors: Chen Diyi , Zhang Runfan , Sprott J. C. , Chen Haitao , Ma Xiaoyi
Published: May 2012

In this paper, we focus on the synchronization between integer-order chaotic systems and a class of fractional-order chaotic system using the stability theory of fractional-order systems. A new sliding mode method is proposed to accomplish this end for different initial conditions and number of dimensions. More importantly, the vector controller is one-dimensional less than the system. Furthermore, three examples are presented to illustrate the effectiveness of the proposed scheme, which are the synchronization between a fractional-order Chen chaotic system and an integer-order T chaotic system, the synchronization between a fractional-order hyperchaotic system based on Chen’s system and an integer-order hyperchaotic system, and the synchronization between a fractional-order hyperchaotic system based on Chen’s system and an integer-order Lorenz chaotic system. Finally, numerical results are presented and are in agreement with theoretical analysis.
Geometrical factor correction in grazing incident x-ray fluorescence experiment
Authors: LI Wenbin , Zhu Jingtao , Ma Xiaoying , LI Haochuan , Wang Hongchang , Sawhney Kawal J. S. , Wang Zhanshan
Published: May 2012

The geometrical factor in the grazing incident x-ray fluorescence analysis is an important angle-dependent term, which can have a great effect on the measured data. In this paper, the effects of the geometrical factor on the florescence yield have been demonstrated. A formula is presented to estimate the geometrical factor, which includes the experimental parameters of the beam and setup. The validity of this formula is proven by the good agreement between the calculated fluorescence yields with the experimental results in grazing incident x-ray fluorescence analysis.
Large magnetocaloric effect induced by intrinsic structural transition in Dy1−x HoxMnO3
Authors: Shao Mingjie , Cao Shixun , Yuan Shujuan , Shang Jin , Kang Baojuan , Lu Bo , Zhang Jincang
Published: May 2012

We report the magnetic and magnetocaloric properties of Dy1−xHoxMnO3 (0 ≤ x ≤ 1). Large entropy change of 12.5 J/kg K and refrigeration capacity of 312 J/kg at 7 T for HoMnO3 is calculated based on isothermal magnetization measurements. The peak temperature of magnetic entropy change for all samples keeps the same 10.5 K, indicating that Ho3+ doping only affects the value of magnetic entropy. An unambiguous intrinsic structural transition near 7 K is first observed by strain measurement, which is believed as the origin of magnetic symmetry transition of Dy1−xHoxMnO3 and induces the magnetocaloric effect with the cooperation interaction between Dy3+/Ho3+and Mn3+ spins.
Lutetium-doped EuO films grown by molecular-beam epitaxy
Authors: Melville A. , Mairoser T. , Schmehl A. , Shai D. E. , Monkman E. J. , Harter J. W. , Heeg T. , Holländer B. , Schubert J. , Shen K. M. , Mannhart J. , Schlom D. G.
Published: May 2012

The effect of lutetium doping on the structural, electronic, and magnetic properties of epitaxial EuO thin films grown by reactive molecular-beam epitaxy is experimentally investigated. The behavior of Lu-doped EuO is contrasted with doping by lanthanum and gadolinium. All three dopants are found to behave similarly despite differences in electronic configuration and ionic size. Andreev reflection measurements on Lu-doped EuO reveal a spin-polarization of 96% in the conduction band, despite non-magnetic carriers introduced by 5% lutetium doping.
High resolution resonant waveguide grating imager for cell cluster analysis under physiological condition
Authors: Ferrie Ann M. , Deichmann Oberon D. , Wu Qi , Fang Ye
Published: May 2012

We report on a spatially resolved resonant waveguide grating imager for cell cluster analysis under physiological condition. Compared to results obtained under ambient condition, the activation of a receptor resulted in a similar biosensor signature but with faster kinetics and greater amplitude. The imager further detected receptor signaling in and movements of single cells within small cell clusters. This opens possibility to investigate the heterogeneity and robustness of receptor signaling from single cells to cell systems.
High potential sensitivity in heterodyne amplitude-modulation Kelvin probe force microscopy
Authors: Sugawara Yasuhiro , Kou Lili , Ma Zongmin , Kamijo Takeshi , Naitoh Yoshitaka , Jun Li Yan
Published: May 2012

A surface potential measurement method using amplitude-modulation and heterodyne techniques is proposed. The effect of the stray capacitance between a cantilever and a sample in Kelvin probe force microscopy and the electrostatic force spectroscopy measurements are almost completely removed, because the distance (z) dependence of the modulated electrostatic force increases from 1/z to1/z2. This method improves the sensitivity of short range forces and reduces the surface potential measurement crosstalk that is induced by topographic feedback. This method has the advantage of high potential sensitivity due to the high cantilever Q value under vacuum. Quantitative surface potential measurements are demonstrated.
Broadband optical absorption enhancement in silicon nanofunnel arrays for photovoltaic applications
Authors: Li Li , Peng Kui-Qing , Hu Bo , Wang Xin , Hu Ya , Wu Xiao-Ling , Lee Shuit-Tong
Published: May 2012

Silicon photonic nanostructures have received considerable attention for light trapping in recent years. In this work, we demonstrate silicon nanofunnel (SiNF) array as a broadband light absorber for silicon photovoltaic devices via simulation. Due to more excellent optical couple between SiNFs and incident sunlight as well as the gradual change of the effective refractive index, the SiNF arrays exhibit significantly better optical absorption over a broad wavelength range and higher ultimate efficiencies compared to silicon nanohole array counterparts. The proposed SiNF arrays are promising for low cost ultrathin silicon solar cells and other photoactive devices.
Transistor laser optical and electrical linearity enhancement with collector current feedback
Authors: Then H. W. , Tan F. , Feng M. , Holonyak N.
Published: May 2012

The three-port quantum well (QW) transistor laser (TL) is shown to provide a unique solution for generating ultra-linear electro-optical signals. With a simple collector current feedback loop, the 3rd order intermodulation distortion in the electrical and optical output signals of the transistor laser can be suppressed by as much 18.2 dB and 8.4 dB, respectively. These results show that the TL can be used for direct electro-optical feedback linearization, because of the base QW carrier-photon interaction, without incurring signal losses at multiple stages of auxiliary external electro-optical conversion circuitry.
Nanoresolution radiology of neurons
Authors: Wu H R , Chen S T , Chu Y S , Conley R , Bouet N , Chien C C , Chen H H , Lin C H , Tung H T , Chen Y S , Margaritondo G , Je J H , Hwu Y
Published: May 2012

We report recent advances in hard-x-ray optics—including record spatial resolution—and in staining techniques that enable synchrotron microradiology to produce neurobiology images of quality comparable to electron and visible microscopy. In addition, microradiology offers excellent penetration and effective three-dimensional detection as required for many neuron studies. Our tests include tomographic reconstruction based on projection image sets.
On the spatio-temporal development of pulsed barrier discharges: influence of duty cycle variation
Authors: Kettlitz M , Höft H , Hoder T , Reuter S , Weltmann K-D , Brandenburg R
Published: May 2012

The paper presents experiments on the spatial and temporal structure of the breakdown process of microdischarges (MD). For the first time simultaneous streak and iCCD images of individual filaments in a pulsed driven dielectric barrier discharge (DBD) with 1 mm gap in a gas mixture of 0.1 vol% O2 in N2 at atmospheric pressure are recorded. Furthermore current and voltage measurements with fast probes give access to the electrical discharge characteristics such as transferred charge and power. For asymmetric pulses there is a significant difference in the spatial structure as well as in the temporal behaviour of the MDs between the rising and the falling slopes of the high voltage pulse. If the time between rising and falling slopes is reversed all effects reverse as well. For symmetric pulses there are no significant differences between the MD at rising and falling slopes which is in accordance with a sinusoidal DBD operation.
Numerical modelling of the properties of an ion beam extracted from a low-pressure wire discharge
Authors: Gueroult R , Elias P Q , Packan D , Rax J M
Published: May 2012

The combination of a dedicated acceleration stage with direct extraction of ions from a low-pressure wire discharge enables one to generate a narrow band ion beam of tunable energy. In order to optimize this ion source concept, we conduct a numerical study emphasizing the main physical processes and the parameters controlling them. An analysis of the three-dimensional non-collisional ion trajectories inside the ion source reveals that the total beam current can be tuned by modifying the depth and radius of the diaphragm connecting the wire discharge chamber to the acceleration chamber, while the inter-electrode distance controls the beam focusing. A particle-in-cell (PIC) modelling of the beam acceleration and propagation indicates that, despite the low operating pressure (∼10−2 mbar), elastic and charge-exchange collisions are responsible for a decrease in the beam current by a factor of four. Charge-exchange collisions are also shown to be accountable for the existence of a low-energy ion population being non-uniform throughout a beam cross section.
Blockwise HMM computation for large-scale population genomic inference
Authors: Paul Joshua S. , Song Yun S.
Published: May 2012

Motivation: A promising class of methods for large-scale population genomic inference use the conditional sampling distribution (CSD), which approximates the probability of sampling an individual with a particular DNA sequence, given that a collection of sequences from the population has already been observed. The CSD has a wide range of applications, including imputing missing sequence data, estimating recombination rates, inferring human colonization history and identifying tracts of distinct ancestry in admixed populations. Most well-used CSDs are based on hidden Markov models (HMMs). Although computationally efficient in principle, methods resulting from the common implementation of the relevant HMM techniques remain intractable for large genomic datasets.

Results: To address this issue, a set of algorithmic improvements for performing the exact HMM computation is introduced here, by exploiting the particular structure of the CSD and typical characteristics of genomic data. It is empirically demonstrated that these improvements result in a speedup of several orders of magnitude for large datasets and that the speedup continues to increase with the number of sequences. The optimized algorithms can be adopted in methods for various applications, including the ones mentioned above and make previously impracticable analyses possible.

Availability: Software available upon request.

Supplementary Information:  Supplementary data are available at Bioinformatics online.

Contact:  yss@eecs.berkeley.edu
Timing in a fluctuating environment: environmental variability and asymmetric fitness curves can lead to adaptively mismatched avian reproduction
Authors: Lof Marjolein E. , Reed Thomas E. , McNamara John M. , Visser Marcel E.
Published: May 2012

Adaptation in dynamic environments depends on the grain, magnitude and predictability of ecological fluctuations experienced within and across generations. Phenotypic plasticity is a well-studied mechanism in this regard, yet the potentially complex effects of stochastic environmental variation on optimal mean trait values are often overlooked. Using an optimality model inspired by timing of reproduction in great tits, we show that temporal variation affects not only optimal reaction norm slope, but also elevation. With increased environmental variation and an asymmetric relationship between fitness and breeding date, optimal timing shifts away from the side of the fitness curve with the steepest decline. In a relatively constant environment, the timing of the birds is matched with the seasonal food peak, but they become adaptively mismatched in environments with temporal variation in temperature whenever the fitness curve is asymmetric. Various processes affecting the survival of offspring and parents influence this asymmetry, which collectively determine the ‘safest’ strategy, i.e. whether females should breed before, on, or after the food peak in a variable environment. As climate change might affect the (co)variance of environmental variables as well as their averages, risk aversion may influence how species should shift their seasonal timing in a warming world.
Extinction and ecological retreat in a community of primates
Authors: Crowley Brooke E. , Godfrey Laurie R. , Guilderson Thomas P. , Zermeño Paula , Koch Paul L. , Dominy Nathaniel J.
Published: May 2012

The lemurs of Madagascar represent a prodigious adaptive radiation. At least 17 species ranging from 11 to 160 kg have become extinct during the past 2000 years. The effect of this loss on contemporary lemurs is unknown. The concept of competitive release favours the expansion of living species into vacant niches. Alternatively, factors that triggered the extinction of some species could have also reduced community-wide niche breadth. Here, we use radiocarbon and stable isotope data to examine temporal shifts in the niches of extant lemur species following the extinction of eight large-bodied species. We focus on southwestern Madagascar and report profound isotopic shifts, both from the time when now-extinct lemurs abounded and from the time immediately following their decline to the present. Unexpectedly, the past environments exploited by lemurs were drier than the protected (albeit often degraded) riparian habitats assumed to be ideal for lemurs today. Neither competitive release nor niche contraction can explain these observed trends. We develop an alternative hypothesis: ecological retreat, which suggests that factors surrounding extinction may force surviving species into marginal or previously unfilled niches.
Insect phylogenomics: results, problems and the impact of matrix composition
Authors: Letsch Harald O. , Meusemann Karen , Wipfler Benjamin , Schütte Kai , Beutel Rolf , Misof Bernhard
Published: May 2012

In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only fewinformativemolecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data (‘EST’: short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human lousePediculus humanusassigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genusBaetisnested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.
Patterns of Diversity of the Rissoidae (Mollusca: Gastropoda) in the Atlantic and the Mediterranean Region
Authors: Ávila Sérgio P. , Goud Jeroen , de Frias Martins António M.
Published: May 2012

The geographical distribution of the Rissoidae in the Atlantic Ocean and Mediterranean Sea was compiled and is up-to-date until July 2011. All species were classified according to their mode of larval development (planktotrophic and nonplanktotrophic), and bathymetrical zonation (shallow species—those living between the intertidal and 50 m depth, and deep species—those usually living below 50 m depth). 542 species of Rissoidae are presently reported to the Atlantic Ocean and the Mediterranean Sea, belonging to 33 genera. The Mediterranean Sea is the most diverse site, followed by Canary Islands, Caribbean, Portugal, and Cape Verde. The Mediterranean and Cape Verde Islands are the sites with higher numbers of endemic species, with predominance ofAlvaniaspp. in the first site, and ofAlvaniaandSchwartziellaat Cape Verde. In spite of the large number of rissoids at Madeira archipelago, a large number of species are shared with Canaries, Selvagens, and the Azores, thus only about 8% are endemic to the Madeira archipelago. Most of the 542-rissoid species that live in the Atlantic and in the Mediterranean are shallow species (323), 110 are considered as deep species, and 23 species are reported in both shallow and deep waters. There is a predominance of nonplanktotrophs in islands, seamounts, and at high and medium latitudes. This pattern is particularly evident in the generaCrisilla, Manzonia, Onoba, Porosalvania, Schwartziella, andSetia. Planktotrophic species are more abundant in the eastern Atlantic and in the Mediterranean Sea. The results of the analysis of the probable directions of faunal flows support the patterns found by both the Parsimony Analysis of Endemicity and the geographical distribution. Four main source areas for rissoids emerge: Mediterranean, Caribbean, Canaries/Madeira archipelagos, and the Cape Verde archipelago. We must stress the high percentage of endemics that occurs in the isolated islands of Saint Helena, Tristan da Cunha, Cape Verde archipelago and also the Azores, thus reinforcing the legislative protective actions that the local governments have implemented in these islands during the recent years.
Leishmanicidal Activity of Nine Novel Flavonoids fromDelphinium staphisagria
Authors: Ramírez-Macías Inmaculada , Marín Clotilde , Díaz Jesús G. , Rosales María José , Gutiérrez-Sánchez Ramón , Sánchez-Moreno Manuel
Published: May 2012

Objectives. To evaluate thein vitroleishmanicidal activity of nine flavonoid derivatives fromDelphinium staphisagriaagainstL. infantumandL. braziliensis.Design and Methods. Thein vitroactivity of compounds1–9was assayed on extracellular promastigote and axenic amastigote forms and on intracellular amastigote forms of the parasites. Infectivity and cytotoxicity tests were carried on J774.2 macrophage cells using Glucantime as the reference drug. The mechanisms of action were analysed performing metabolite excretion and transmission electronic microscope ultrastructural alteration studies.Results. Nine flavonoids showed leishmanicidal activity against promastigote as well as amastigote forms ofLeishmania infantumandL. braziliensis. These compounds were nontoxic to mammalian cells and were effective at similar concentrations up to or lower than that of the reference drug (Glucantime). The results showed that2″-acetylpetiolaroside (compound8) was clearly the most active.Conclusion. This study has demonstrated that flavonoid derivatives are active againstL. infantumandL. braziliensis.
Secondary Data Analyses of Subjective Outcome Evaluation Data Based on Nine Databases
Authors: Shek Daniel T. L.
Published: May 2012

The purpose of this study was to evaluate the effectiveness of the Tier 1 Program of the Project P.A.T.H.S. (Positive Adolescent Training through Holistic Social Programmes) in Hong Kong by analyzing 1,327 school-based program reports submitted by program implementers. In each report, program implementers were invited to write down five conclusions based on an integration of the subjective outcome evaluation data collected from the program participants and program implementers. Secondary data analyses were carried out by aggregating nine databases, with 14,390 meaningful units extracted from 6,618 conclusions. Results showed that most of the conclusions were positive in nature. The findings generally showed that the workers perceived the program and program implementers to be positive, and they also pointed out that the program could promote holistic development of the program participants in societal, familial, interpersonal, and personal aspects. However, difficulties encountered during program implementation (2.15%) and recommendations for improvement were also reported (16.26%). In conjunction with the evaluation findings based on other strategies, the present study suggests that the Tier 1 Program of the Project P.A.T.H.S. is beneficial to the holistic development of the program participants.
Both Freshly Prepared and Frozen-Stored Amniotic Membrane Cells Express the Complement Inhibitor CD59
Authors: Füst Ágnes , Pállinger Éva , Stündl Adrienn , Kovács Eszter , Imre László , Tóth Sára , Németh János
Published: May 2012

Amniotic membrane proved to be very effective tool in the treatment of a number of ocular surface diseases. The amniotic membrane, however, has to be stored before its transplantation onto the ocular surface followed by mandatory serologic control in order to exclude the transmission of certain viruses. Therefore it is most important to study if cryopreservation of the membrane affects cell surface expression of the molecules. We measured cell surface expression of CD59, a membrane-bound complement inhibitor on the cells of freshly prepared and cryopreserved amniotic membrane. Cells of amniotic membrane were separated mechanically. Epithelial and mesenchymal cells were identified by the intracellular expression of nanog and the cell surface ICAM1 positivity, respectively. Multicolor flow cytometric immunophenotyping was used for determination of the CD59 expression. CellQuest-Pro software program (Becton Dickinson) was used both for measurements and analysis. CD59-positive cells could be detected in all investigated samples and in all investigated cell types, although the expression level of CD59 differed. CD59 was expressed both on freshly prepared and frozen-stored samples. Higher level of CD59 was detected on ICAM1+ mesenchymal cells than on nanog+ epithelial cells. Our findings indicate that amniotic membranes maintain their complement inhibiting capacity after cryopreservation.
Turning CALM into excitement: AP180 and CALM in endocytosis and disease
Authors: Maritzen Tanja , Koo Seong Joo , Haucke Volker
Published: May 2012

Dynamic flux of membrane between intracellular compartments is a key feature of all eukaryotic cells. Soluble N‐ethylmaleimide‐sensitive factor attachment protein receptors (SNAREs) play a crucial role in membrane dynamics by facilitating membrane fusion, for example at synapses where small synaptic vesicles (SVs) undergo activity‐regulated neuroexocytosis, followed by the endocytic re‐cycling of SV proteins and lipids. Recent work shows that the assembly protein 180 (AP180) N‐terminal homology (ANTH) domain containing proteins AP180 and clathrin assembly lymphoid myeloid leukaemia (CALM) not only regulate the assembly of the endocytic machinery but also act as sorters for a subset of SNAREs, the vesicle‐associated membrane proteins (VAMPs), most notably VAMP/synaptobrevin 2 at synapses. In this review, we summarise the current state of knowledge about the roles of AP180 and CALM family members in clathrin‐dependent membrane traffic, the molecular mechanistic basis for their activities and their potential involvement in human disease.
Differences in the induction of cyp1A and related genes in cultured rainbow trout Oncorhynchus mykiss. Additional considerations for the use of EROD activity as a biomarker
Authors: Valdehita A. , Fernández‐Cruz M. L. , Torrent F. , Sericano J. L. , Navas J. M.
Published: May 2012

Two rainbow trout Oncorhynchus mykiss fish farms were repeatedly sampled in order to observe the variability of ethoxyresorufin‐O‐deethylase (EROD) activity and of related genes in the liver. Fish coming from fish farm A exhibited EROD levels that could be considered as basal according to the scientific literature, however, EROD activity in fish coming from fish farm B was significantly increased. This was accompanied by augmented aryl hydrocarbon receptor (ahr) and cytochrome P4501A (cyp1A) messenger RNA expression and reduced oestrogen receptor (er) and vitellogenin (vtg) transcription. Only sediment extracts from the entry channel of fish farm B induced EROD activity in O. mykiss cultured cells, however, this induction could not be explained by the levels of polyaromatic hydrocarbons (PAH) and polychlorinated biphenyls (PCB) measured in the sediments. The results of this study point out that O. mykiss cultured in fish farms could be used as sentinels for indication of pollution. In this particular work, however, no conclusive evidence has been found for a relationship between the presence of PAHs and PCBs and the observed EROD induction.