bluuebunny/crossref_metadata_2025 huggingface dataset:
Reprogramming the signalling requirement for AP‐1 (activator protein‐1) activation during differentiation of precursor CD4+ T‐cells into effector Th1 and Th2 cells
Authors: Rincón Mercedes , Dérijard Benoit , Chow Chi‐Wing , Davis Roger , Flavell Richard
Published: October 2010

Upon antigenic stimulation, precursor CD4+ helper T‐cells differentiate into two subsets of effector cells, Th1 and Th2. These two subpopulations are defined by the pattern of cytokine expression that distinguishes these differentiated cells from their precursors. We have used reporter transgenic mice here to show that, during differentiation of precursor T‐cells into effector Th1 or Th2 cells, high levels of preformed activator protein (AP)‐1 complexes are accumulated. However, upon stimulation, the preformed AP‐1 complexes in effector Th2 cells, but not in Th1 cells, are able to induce high levels of AP‐1 transcriptional activity. Furthermore, in contrast to precursor T‐cells, the induction of AP‐1 transcriptional activity is independent of calcium and co‐stimulatory signals in effector Th2 cells. This AP‐1 transcriptional activity appears to correlate with the presence of JunB complexes, which accumulate differentially in effector Th2 cells, but not in precursor CD4+ T‐cells or effector Th1 cells. Unlike precursor cells, the activation of AP‐1 does not appear to be mediated by c‐Jun N‐terminal kinase (JNK) in effector Th2 cells. These results indicate that during differentiation of T‐cells, and probably other cell types, the signal requirements for the AP‐1 transcription machinery are reprogrammed to enable the differentiated cells to perform their specialized functions.
Deregulated inflammatory response in mice lacking the STK/RON receptor tyrosine kinase
Authors: Correll Pamela , Iwama Atsushi , Tondat Sandra , Mayrhofer Graham , Suda Toshio , Bernstein Alan
Published: October 2010

Immune and inflammatory responses must be tightly regulated to maintain a homoeostatic balance between an effective immune response and tissue damage to the host. NO is a principal mediator of many of the cytokine‐inducible macrophage activities during a normal cell‐mediated immune response. STK, the murine homologue of the human RON receptor tyrosine kinase, is expressed on murine resident peritoneal macrophages. The ligand for STK, macrophage‐stimulating protein (MSP), is a serum protein that is activated by members of the coagulation cascade in response to tissue damage. In addition to its potential to induce chemotaxis and phagocytosis of C3bi‐coated erythrocytes, MSP has an inhibitory effect on the production of NO by activated peritoneal macrophages in vitro. Here we demonstrate that peritoneal macrophages from mice lacking STK produce elevated levels of NO in response to interferon (IFN)‐γ in a dose‐dependent manner, without the need for a co‐stimulus. However, production of pro‐inflammatory cytokines by activated macrophages from stk−/− mice is unaltered. In vivo, stk−/− mice exhibit increased inflammation in an IFN‐γ‐mediated delayed‐type hypersensitivity reaction and increased susceptibility to lipopolysaccharide (LPS)‐induced endotoxic shock. Furthermore, the levels of NO in the serum of mice injected with LPS are significantly higher than those in control littermates. Nevertheless, the serum levels of IFN‐γ and the intermediate cytokines generated by the inflammatory response, which have previously been shown to play a role in septicaemic shock, do not differ significantly from controls. These data suggest that the STK receptor suppresses NO production, therefore ameliorating the potentially tissue‐damaging effects of a cell‐mediated immune response, through negative regulation of the IFN‐γ signalling pathway.
A mammalian homologue of the Drosophila retinal degeneration B gene: implications for the evolution of phototransduction mechanisms
Authors: Rubboli Francesca , Bulfone Alessandro , Bogni Silvia , Marchitiello Anna , Zollo Massimo , Borsani Giuseppe , Ballabio Andrea , Banfi Sandro
Published: October 2010

Comparative analysis of homologous genes in distantly related species provides important insights into the evolution of complex physiological processes. The Drosophila retinal degeneration B (rdgB) gene encodes a protein involved in phototransduction in the fly. We have isolated a human gene, DRES9, and its murine homologue (Dres9), which show a high degree of similarity to the Drosophila rdgB gene. RNA in situ hybridization studies performed on mouse‐embryo tissue sections at various developmental stages revealed that Dres9 is expressed at very high levels in the neural retina and in the central nervous system (CNS), similar to its Drosophila counterpart. The high level of sequence conservation and similarities in the expression patterns of rdgB and DRES9 during development in Drosophila and mammals indicate that Dres9 is the orthologue of RdgB, and strongly suggest a possible functional conservation of these proteins during evolution. DRES9 encodes a phosphatidylinositol‐transfer protein, suggesting that phosphatidylinositol may have a role as an intracellular messenger in vertebrate phototransduction. The identification of this gene and the study of its expression pattern in mammals will help shed new light on the evolution of vision mechanisms and suggest DRES9 as a candidate gene for human retinopathies.
Molecular heterogeneity of regulatory elements of the mouse GATA‐1 gene
Authors: Ronchi Antonella , Cirò Marco , Cairns Linda , Basilico Luca , Corbella Paola , Ricciardi‐Castagnoli Paola , Cross Michael , Ghysdael Jacques , Ottolenghi Sergio
Published: October 2010

The GATA‐1 gene encodes a transcription factor expressed in early multipotent haemopoietic progenitors, in more mature cells of the erythroid, megakaryocytic and other lineages, but not in late myeloid precursors; its function is essential for the normal development of the erythroid and megakaryocytic system. To define regulatory elements of the mouse GATA‐1 gene, we mapped DNaseI‐hypersensitive sites in nuclei of erythroid and haemopoietic progenitor cells. Five sites were detected. The two upstream sites, site 1 and site 2, represent a new and a previously defined erythroid enhancer respectively. The site 1 enhancer activity depends both on a GATA‐binding site (also footprinted in vivo) and on several sites capable of binding relatively ubiquitous factors. A DNA fragment encompassing site 1, placed upstream of a GATA‐1 minimal promoter, is able to drive expression of a simian virus 40 (SV40) T‐antigen in the yolk sac, but not bone‐marrow cells, obtained from mice transgenic for this construct, allowing in vitro establishment of immortalized yolk‐sac cells. A similar construct including site 2, instead of site 1, and previously shown to be able to immortalize adult marrow cells is not significantly active in yolk‐sac cells. Sites 4 and 5, located in the first large intron, have no enhancer activity; they include a long array of potential Ets‐binding sites. MnlI restriction sites, overlapping some of the Ets sites, are highly accessible, in intact nuclei, to MnlI. Although these sites are present in all GATA‐1‐expressing cells studied, they are the only strong sites detectable in FDCP‐mix multipotent progenitor cells, most of which do not yet express GATA‐1. The data indicate that appropriate GATA‐1 regulation may require the co‐operation of different regulatory elements acting at different stages of development and cell differentiation.
HIV‐1 Nef severely impairs thymocyte development and peripheral T‐cell function by a CD4‐independent mechanism
Authors: Pennington Daniel , Jenkins Sharon , Brady Hugh , Miles Colin , Dzierzak Elaine , Abraham David
Published: October 2010

Nef is a regulatory protein of the human and simian immunodeficiency viruses (HIV and SIV) whose role in infection and the viral life cycle are not fully understood. In T‐lymphocytes Nef down‐regulates cell‐surface CD4, and has been implicated in an increase in infectivity at low primary viral isolate titres. Additionally, the SIV nef gene is necessary for viraemia and AIDS‐like pathogenesis in rhesus macaques. We report here in an in vivo murine transgenic model that thymocyte and T‐cell‐specific nef gene expression results in a marked decrease in thymic cellularity from 16 days post coitus. This reduction in thymocyte cell number is independent of CD4 expression and Nef‐induced CD4 down‐regulation, but can be restored by expressing a constitutively active p56lckF505 gene. Functional analyses have revealed a severe decrease in thymocyte and T‐cell proliferation in response to both T‐cell‐receptor‐ and mitogen‐mediated stimuli. In addition, a significant proportion of Nef‐expressing peripheral T‐cells display cell‐surface characteristics associated with cellular activation. These results suggest that Nef expression in developing thymocytes can severely reduce the regeneration capacity of the immune system, whereas expression in mature T‐cells dramatically decreases their potential to respond to antigen. With the recent recognition of a persistently high viral load in HIV‐infected individuals, these findings have important implications for the mechanism of the progressive deterioration of the immune system that leads to AIDS.
Conditions for Infection of Apple by Phytophthora syringae
Authors: Harris D. C. , Xu X.‐M.
Published: October 2010

The processes leading to Phytophthora fruit rot were divided into two main stages for the purposes of investigating the effects of temperature and duration of wet periods on pathogen development: oospore germination and infection of fruit by zoospores. It was found that the first stage was markedly affected by temperature over the range 10–20°C and required a wet period of 4–7 days. At 18 and 20°C, activation was low regardless of the length of the wet period. Once oospore germination (first stage) had occurred, free water was necessary for only a few hours for fruit infection (second stage) to occur, but the incidence of infection rose rapidly over the first 48 h, regardless of temperature over the range 10–20°C. From the data obtained, mathematical models were produced relating the incidence of Phytophthora fruit rot to the two weather variables. These models can be used to develop a weather‐based risk assessment system for the disease.
Biological and Molecular Categorization of Strains of Banana bunchy top virus
Authors: Su H.‐J. , Tsao L.‐Y. , Wu M.‐L. , Hung T.‐H.
Published: October 2010

Banana bunchy top virus (BBTV), a complex circular single‐stranded DNA virus with multiple genomic components, is a destructive pathogen in banana‐cultivating areas worldwide. Based on symptoms (such as vein clearing, green streak on pseudostem, leaf atrophy, bunchy top and stunting) as well as polymerase chain reaction (PCR) amplification patterns with different primer pairs, all BBTV isolates collected from Taiwan and other countries can be divided into five distinctive strains. Three primer pairs, C1, stem‐loop common region (CR‐SL) and TS were used for PCR amplifications. Strain 1, which induces conspicuous symptoms, is a common severe strain; it reacted positively with C1 and CR‐SL but negatively with TS in the PCR assays, so its PCR pattern was indicated as ‘+/+/−’ for C1, CR‐SL and TS primer pairs, respectively. Strain 2 seemed to be a Taiwan‐specific severe strain which induced severe symptoms, and its PCR pattern was ‘+/+/+’ as it showed positive reactions with all three primer pairs. Strain 3, causing the most severe symptoms, is a Malaysia‐specific severe strain whose PCR pattern is ‘−/+/−’. Strain 4 induced moderately severe symptoms and is an intermediate strain whose PCR pattern is ‘−/+/−’. Strain 5 is a mild strain; it did not induce symptoms in banana and it reacted positively with C1, CR‐SL and TS primer pairs. Interestingly, an additional 537‐bp fragment was amplified from Strain 5 with the CR‐SL primer pair. The PCR pattern of Strain 5 is therefore indicated as ‘+/++/+’. This study demonstrates that various BBTV strains exist in nature and they differ biologically and also molecularly.
Improvement of RT‐PCR Based Detection of Two Closteroviruses Associated with Little Cherry Disease in Sweet Cherries
Authors: Rybak M. , Kountrias A. , Eppler A. , Jelkmann W. , Heinze C. , Adam G.
Published: October 2010

The increasing availability of nucleotide sequence data from plant pathogenic fruit tree viruses led recently to the development of nucleic‐acid‐based detection methods as a routine tool for diagnosis. We present a simplification and modification of the previously described test procedure for the two closteroviruses Little cherry virus 1 and 2 (LChV‐1, LChV‐2). For LChV‐1, a single tube reaction reduced unspecific amplification that led to false positive results. For the detection of LChV‐2, a primer set was developed for the local isolates of the area ‘Altes Land’ in the northern part of Germany. To determine the optimal sampling conditions for a reliable detection of both viruses different types of tissue (bark, bud, leaves) were tested in monthly intervals.
Viruses Associated with Cassava Mosaic Disease in Senegal and Guinea Conakry
Authors: Okao‐Okuja G. , Legg J. P. , Traore L. , Jorge M. Alexandra
Published: October 2010

A survey in Senegal and Guinea Conakry established the presence and incidence of cassava mosaic virus disease (CMD) in both countries. CMD occurred in all the fields surveyed, although its incidence was higher in Senegal (83%) than in Guinea (64%). Populations of the whitefly vector, Bemisia tabaci, were low in both countries averaging 1.7 adults per shoot in Guinea and 3.2 in Senegal. Most infections were attributed to the use of infected cuttings, 86 and 83% in Senegal and Guinea, respectively, and there was no evidence of rapid current‐season, whitefly‐borne infection at any of the sampled locations. Disease severity was generally low in the two countries and averaged 2.5 in Guinea and 2.3 in Senegal. No plants with unusually severe CMD symptoms characteristic of the CMD pandemic in East and Central Africa were observed. Restriction fragment length polymorphism (RFLP)‐based diagnostics revealed that African cassava mosaic virus (ACMV) is exclusively associated with CMD in both the countries. Neither East African cassava mosaic virus (EACMV), nor the recombinant Uganda variant (EACMV‐UG2) was detected in any sample. These survey data indicate that CMD could be effectively controlled in both countries by phytosanitation, involving the use of CMD‐free planting material and the removal of diseased plants.
Algorithm for precision subsample timing between Gaussian-like pulses
Authors: Lerche R. A. , Golick B. P. , Holder J. P. , Kalantar D. H.
Published: October 2010

Moderately priced oscilloscopes available for the NIF power sensors and target diagnostics have 6 GHz bandwidths at 20–25 Gsamples/s (40 ps sample spacing). Some NIF experiments require cross timing between instruments be determined with accuracy better than 30 ps. A simple analysis algorithm for Gaussian-like pulses such as the 100-ps-wide NIF timing fiducial can achieve single-event cross-timing precision of 1 ps (1/50 of the sample spacing). The midpoint-timing algorithm is presented along with simulations that show why the technique produces good timing results. Optimum pulse width is found to be ∼2.5 times the sample spacing. Experimental measurements demonstrate use of the technique and highlight the conditions needed to obtain optimum timing performance.
Development of a realistic photonic modeling for the evaluation of infrared reflections in the metallic environment of ITER
Authors: Aumeunier M.-H. , Travere J.-M.
Published: October 2010

In nuclear fusion experiments, the plasma facing components are exposed to high heat fluxes and infrared (IR) imaging diagnostics are routinely used for surveying their surface temperature for preventing damages. However the future use of metallic components in the ITER tokamak adds complications in temperature estimation. Indeed, low and variable emissivity of the observed surface and the multiple reflections of the light coming from hot regions will have to be understood and then taken into account. In this paper, a realistic photonic modeling based on Monte Carlo ray-tracing codes is used to predict the global response of the complete IR survey system. This also includes the complex vessel geometry and the thermal and optical surface properties using the bidirectional reflectivity distribution function that models the photon-material interactions. The first results of this simulation applied to a reference torus are presented and are used as a benchmark to investigate the validity of the global model. Finally the most critical key model parameters in the reflected signals are identified and their contribution is discussed.
Single-shot electron bunch length measurements using a spatial electro-optical autocorrelation interferometer
Authors: Sütterlin Daniel , Erni Daniel , Schlott Volker , Sigg Hans , Jäckel Heinz , Murk Axel
Published: October 2010

A spatial, electro-optical autocorrelation (EOA) interferometer using the vertically polarized lobes of coherent transition radiation (CTR) has been developed as a single-shot electron bunch length monitor at an optical beam port downstream the 100 MeV preinjector LINAC of the Swiss Light Source. This EOA monitor combines the advantages of step-scan interferometers (high temporal resolution) [D. Mihalcea et al., Phys. Rev. ST Accel. Beams 9, 082801 (2006) and T. Takahashi and K. Takami, Infrared Phys. Technol. 51, 363 (2008)] and terahertz-gating technologies [U. Schmidhammer et al., Appl. Phys. B: Lasers Opt. 94, 95 (2009) and B. Steffen et al., Phys. Rev. ST Accel. Beams 12, 032802 (2009)] (fast response), providing the possibility to tune the accelerator with an online bunch length diagnostics. While a proof of principle of the spatial interferometer was achieved by step-scan measurements with far-infrared detectors, the single-shot capability of the monitor has been demonstrated by electro-optical correlation of the spatial CTR interference pattern with fairly long (500 ps) neodymium-doped yttrium aluminum garnet (Nd:YAG) laser pulses in a ZnTe crystal. In single-shot operation, variations of the bunch length between 1.5 and 4 ps due to different phase settings of the LINAC bunching cavities have been measured with subpicosecond time resolution.
Inverse scattering transform for the nonlinear Schrödinger system on a zigzag-runged ladder lattice
Authors: Vakhnenko Oleksiy O.
Published: October 2010

A detailed description of four-component nonlinear Schrödinger system on zigzag-runged ladder lattice is given. In order to support the equivalence between the two pairs of field amplitudes, we introduce the two sets of auxiliary linear problems, allowing one to develop the inverse scattering technique in the most adequate symmetrical form. The two complementary sets of discrete Marchenko equations are derived and their multisoliton solutions for the true reflectionless field amplitudes are found. The dispersion relations for the diagonal elements of reduced monodromy matrices are obtained. We explicitly present the simplest realization of soliton dynamics corresponding to the time-independent intersite coupling parameters and zero Peierls phases and show that the two-site structure of the lattice unit cell is strictly manifested as the two splitted branches of soliton excitations. In the general case of time-dependent intersite coupling parameters and nonzero Peierls phases, the theory is capable to model the dynamics of parametrically driven nonlinear ladder systems subjected to external magnetic field.
Study on the effect of measuring methods on incident photon-to-electron conversion efficiency of dye-sensitized solar cells by home-made setup
Authors: Guo Xiao-Zhi , Luo Yan-Hong , Zhang Yi-Duo , Huang Xiao-Chun , Li Dong-Mei , Meng Qing-Bo
Published: October 2010

An experimental setup is built for the measurement of monochromatic incident photon-to-electron conversion efficiency (IPCE) of solar cells. With this setup, three kinds of IPCE measuring methods as well as the convenient switching between them are achieved. The setup can also measure the response time and waveform of the short-circuit current of solar cell. Using this setup, IPCE results of dye-sensitized solar cells (DSCs) are determined and compared under different illumination conditions with each method. It is found that the IPCE values measured by AC method involving the lock-in technique are sincerely influenced by modulation frequency and bias illumination. Measurements of the response time and waveform of short-circuit current have revealed that this effect can be explained by the slow response of DSCs. To get accurate IPCE values by this method, the measurement should be carried out with a low modulation frequency and under bias illumination. The IPCE values measured by DC method under the bias light illumination will be disturbed since the short-circuit current increased with time continuously due to the temperature rise of DSC. Therefore, temperature control of DSC is considered necessary for IPCE measurement especially in DC method with bias light illumination. Additionally, high bias light intensity (>2 sun) is found to decrease the IPCE values due to the ion transport limitation of the electrolyte.
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Thomson scattering probe for high-density plasma characterization at Titan
Authors: Ross J. S. , Kline J. L. , Yang S. , Henesian M. , Weiland T. , Price D. , Pollock B. B. , Glenzer S. H.
Published: October 2010

In preparation for the upcoming experiments on the Titan laser at the Jupiter Laser Facility, a new Thomson scattering system has been designed and implemented. This system allows electron temperature and density measurements in a high-density regime (ne>1021 cm−3). A 263 nm probe has been demonstrated to produce a total energy of 15 J at 4ω(263 nm) in a 1 ns square pulse with a focal spot size of 100 μm. This probe has been used for imaging Thomson scattering of the ion feature. The goal of this study is to investigate the heating of a preformed plasma by a short-pulse heater beam.
Active spectroscopic measurements using the ITER diagnostic system
Authors: Thomas D. M. , Counsell G. , Johnson D. , Vasu P. , Zvonkov A.
Published: October 2010

Active (beam-based) spectroscopic measurements are intended to provide a number of crucial parameters for the ITER device being built in Cadarache, France. These measurements include the determination of impurity ion temperatures, absolute densities, and velocity profiles, as well as the determination of the plasma current density profile. Because ITER will be the first experiment to study long timescale (∼1 h) fusion burn plasmas, of particular interest is the ability to study the profile of the thermalized helium ash resulting from the slowing down and confinement of the fusion alphas. These measurements will utilize both the 1 MeV heating neutral beams and a dedicated 100 keV hydrogen diagnostic neutral beam. A number of separate instruments are being designed and built by several of the ITER partners to meet the different spectroscopic measurement needs and to provide the maximum physics information. In this paper, we describe the planned measurements, the intended diagnostic ensemble, and we will discuss specific physics and engineering challenges for these measurements in ITER.
Experimental investigation of thermal plasma formation from thick aluminum surfaces by pulsed multimegagauss magnetic field
Authors: Awe T. J. , Bauer B. S. , Fuelling S. , Lindemuth I. R. , Siemon R. E.
Published: October 2010

The thermal ionization of a thick metal surface by pulsed multimegagauss magnetic field has been examined experimentally. Thick 6061-alloy Al rods with initial radii (R0) from 1.00 to 0.25 mm, larger than the magnetic field skin depth, are pulsed to 1.0 MA peak current in 100 ns. Surface fields (Bs) rise at 30−80 MG/μs and reach 1.5 and 4 MG, respectively. For this range of parameters, plasma forms at a threshold level of Bs=2.2 MG. Novel load hardware ensures that plasma formation is thermal, by Ohmic or compression heating. Surface-plasma formation is conclusively indicated through radiometry, extreme ultraviolet spectroscopy, and gated imaging. When R0=0.50 mm rods reach peak current, Bs=3 MG, the surface temperature is 20 eV, and Al3+ and Al4+ spectra and surface instabilities are observed. In contrast, R0=1.00 mm rod surfaces [Bs(t)<2.2 MG] reach only 0.7 eV and remain extremely smooth, indicating that no plasma forms.
Symmetries, weak symmetries, and related solutions of the Grad–Shafranov equation
Authors: Cicogna G. , Pegoraro F. , Ceccherini F.
Published: October 2010

We discuss a new family of solutions of the Grad–Shafranov (GS) equation that describes D-shaped toroidal plasma equilibria with sharp gradients at the plasma edge. These solutions have been derived by exploiting the continuous Lie symmetry properties of the GS equation and in particular a special type of “weak” symmetries. In addition, we review the continuous Lie symmetry properties of the GS equation and present a short but exhaustive survey of the possible choices for the arbitrary flux functions that yield GS equations admitting some continuous Lie symmetry. Particular solutions related to these symmetries are also discussed.
A catalytic reactor for the trapping of free radicals from gas phase oxidation reactions
Authors: Conte Marco , Wilson Karen , Chechik Victor
Published: October 2010

A catalytic reactor for the trapping of free radicals originating from gas phase catalytic reactions is described and discussed. Radical trapping and identification were initially carried out using a known radical generator such as dicumyl peroxide. The trapping of radicals was further demonstrated by investigating genuine radical oxidation processes, e.g., benzaldehyde oxidation over manganese and cobalt salts. The efficiency of the reactor was finally proven by the partial oxidation of cyclohexane over MoO3, Cr2O3, and WO3, which allowed the identification of all the radical intermediates responsible for the formation of the products cyclohexanol and cyclohexanone. Assignment of the trapped radicals was carried out using spin trapping technique and X-band electron paramagnetic resonance spectroscopy.
Asymmetrically cut crystal pair as x-ray magnifier for imaging at high intensity laser facilities
Authors: Szabo C. I. , Feldman U. , Seely J. F. , Curry J. J. , Hudson L. T. , Henins A.
Published: October 2010

The potential of an x-ray magnifier prepared from a pair of asymmetrically cut crystals is studied to explore high energy x-ray imaging capabilities at high intensity laser facilities. OMEGA-EP and NIF when irradiating mid and high Z targets can be a source of high-energy x-rays whose production mechanisms and use as backlighters are a subject of active research. This paper studies the properties and potential of existing asymmetric cut crystal pairs from the National Institute of Standards and Technology (NIST) built in a new enclosure for imaging x-ray sources. The technique of the x-ray magnifier has been described previously. This new approach is aimed to find a design that could be used at laser facilities by magnifying the x-ray source into a screen far away from the target chamber center, with fixed magnification defined by the crystals’ lattice spacing and the asymmetry angles. The magnified image is monochromatic and the imaging wavelength is set by crystal asymmetry and incidence angles. First laboratory results are presented and discussed.
Characterization of a 2D soft x-ray tomography camera with discrimination in energy bands
Authors: Romano A. , Pacella D. , Mazon D. , Murtas F. , Malard P. , Gabellieri L. , Tilia B. , Piergotti V. , Corradi G.
Published: October 2010

A gas detector with a 2D pixel readout is proposed for a future soft x-ray (SXR) tomography with discrimination in energy bands separately per pixel. The detector has three gas electron multiplier foils for the electron amplification and it offers the advantage, compared with the single stage, to be less sensitive to neutrons and gammas. The energy resolution and the detection efficiency of the detector have been accurately studied in the laboratory with continuous SXR spectra produced by an electronic tube and line emissions produced by fluorescence (K, Fe, and Mo) in the range of 3–17 keV. The front-end electronics, working in photon counting mode with a selectable threshold for pulse discrimination, is optimized for high rates. The distribution of the pulse amplitude has been indirectly derived by means of scans of the threshold. Scans in detector gain have also been performed to assess the capability of selecting different energy ranges.
32 bin near-infrared time-multiplexing detector with attojoule single-shot energy resolution
Authors: Eraerds Patrick , Pomarico Enrico , Zhang Jun , Sanguinetti Bruno , Thew Rob , Zbinden Hugo
Published: October 2010

We present two implementations of photon counting time-multiplexing detectors for near-infrared wavelengths, based on Peltier cooled InGaAs/InP avalanche photodiodes. A first implementation is motivated by practical considerations using only commercially available components. It features 16 bins, pulse repetition rates of up to 22 kHz, and a large range of applicable pulse widths of up to 100 ns. A second implementation is based on rapid gating detectors, permitting dead times below 10 ns. This allows one to realize a high dynamic-range 32 bin detector, able to process pulse repetition rates of up to 6 MHz for pulse widths of up to 200 ps. Analysis of the detector response at 16.5% detection efficiency reveals a single-shot energy resolution on the attojoule level.
Symmetry-breaking in cumulative measures of shapes of polymer models
Authors: Millett Kenneth C. , Rawdon Eric J. , Tran Vy T. , Stasiak Andrzej
Published: October 2010

Using numerical simulations we investigate shapes of random equilateral open and closed chains, one of the simplest models of freely fluctuating polymers in a solution. We are interested in the 3D density distribution of the modeled polymers where the polymers have been aligned with respect to their three principal axes of inertia. This type of approach was pioneered by Theodorou and Suter in 1985. While individual configurations of the modeled polymers are almost always nonsymmetric, the approach of Theodorou and Suter results in cumulative shapes that are highly symmetric. By taking advantage of asymmetries within the individual configurations, we modify the procedure of aligning independent configurations in a way that shows their asymmetry. This approach reveals, for example, that the 3D density distribution for linear polymers has a bean shape predicted theoretically by Kuhn. The symmetry-breaking approach reveals complementary information to the traditional, symmetrical, 3D density distributions originally introduced by Theodorou and Suter.
Model of the response function of large mass bolometric detectors
Authors: Vignati M.
Published: October 2010

Large mass bolometers are used in particle physics experiments to search for rare processes. By operating at low temperature, they are able to detect particle energies from few keV up to several MeV, measuring the temperature rise produced by the energy released. This study was performed on the bolometers of the CUORE experiment. The response function of these detectors is not linear in the energy range of interest, and it changes with the operating temperature. The nonlinearity is found to be dominated by the thermistor and its biasing circuit, and is modeled using few measurable parameters. A method to obtain a linear response is the result of this work. It allows a great simplification of the data analysis.
Optical generation of terahertz and second-harmonic light in plasma-activated silicon nanophotonic structures
Authors: Wächter M. , Matheisen C. , Waldow M. , Wahlbrink T. , Bolten J. , Nagel M. , Kurz H.
Published: October 2010

Plasma-activated silicon structures exhibit symmetry broken surfaces through chemical surface modification leading to a considerable second-order nonlinear optical response. This nonlinear response is demonstrated in second-harmonic and difference frequency generation measurements including the generation of terahertz radiation in silicon photonic nanowires using telecom wavelength excitation pulses.
On processed splitting methods and high-order actions in path-integral Monte Carlo simulations
Authors: Casas Fernando
Published: October 2010

Processed splitting methods are particularly well adapted to carry out path-integral Monte Carlo (PIMC) simulations: since one is mainly interested in estimating traces of operators, only the kernel of the method is necessary to approximate the thermal density matrix. Unfortunately, they suffer the same drawback as standard, nonprocessed integrators: kernels of effective order greater than two necessarily involve some negative coefficients. This problem can be circumvented, however, by incorporating modified potentials into the composition, thus rendering schemes of higher effective order. In this work we analyze a family of fourth-order schemes recently proposed in the PIMC setting, paying special attention to their linear stability properties, and justify their observed behavior in practice. We also propose a new fourth-order scheme requiring the same computational cost but with an enlarged stability interval.
Cospectral polymers: Differentiation via semiflexibility
Authors: Dolgushev Maxim , Berezovska Ganna , Blumen Alexander
Published: October 2010

We consider polymer structures which are known in the mathematical literature as “cospectral.” Their graphs have (in spite of the different architectures) exactly the same Laplacian spectra. Now, these spectra determine in Gaussian (Rouse-type) approaches many static as well as dynamical polymer characteristics. Hence, in such approaches for cospectral graphs many mesoscopic quantities are predicted to be indistinguishable. Here we show that the introduction of semiflexibility into the generalized Gaussian structure scheme leads to different spectra and hence to distinct macroscopic patterns. Moreover, particular semiflexible situations allow us to distinguish well between cospectral structures. We confirm our theoretical results through Monte Carlo simulations.
Internal and free energy in a pair of like-charged colloids: Monte Carlo simulations
Authors: Cuetos Alejandro , Anta Juan A. , Puertas Antonio M.
Published: October 2010

The effective interaction between two colloidal particles in a bath of monovalent co- and counterions is studied by means of lattice Monte Carlo simulations with the primitive model. The internal electrostatic energy as a function of the colloid distance is studied fixing the position of the colloids. The free energy of the whole system is obtained introducing a bias parabolic potential, that allows us to sample efficiently small separations between the colloidal particles. For small charges, both the internal and free energy increase when the colloids approach each other, resulting in an effective repulsion driven by the electrostatic repulsion. When the colloidal charge is large enough, on the other hand, the colloid-ion coupling is strong enough to form double layers. The internal energy in this case decreases upon approaching the colloids because more ions enter the double layer. This attractive contribution to the interaction between the colloids is stronger for larger charges and larger ionic concentrations. However, the total free energy increases due to the loss of ionic entropy, and resulting finally in a repulsive interaction potential driven by the entropic contributions. The loss of ionic entropy can be almost quantitatively reproduced with the ideal contribution, the same level of approximation as the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory. The overall behavior is captured by the DLVO theory qualitatively, and a comparison is made with the functional form predicted by the theory, showing moderate agreement.
Advancing a humane alternative to sodium fluoroacetate (1080) for wildlife management - welfare and wallaby control
Authors: Eason Charles T. , Shapiro Lee , Adams Pauline , Hix Steve , Cunningham Celia , MacMorran Duncan , Statham Mick , Statham Helen
Published: October 2010

There is controversy regarding the continued use of sodium fluoroacetate (1080) and questions regarding its humaneness. Two studies on captive animals were undertaken to assess the effectiveness and humaneness of Feratox© cyanide pellets for culling Dama and Bennett's wallabies as an alternative to 1080. Following ingestion of the toxic pellets by the wallabies the effects of cyanide were closely observed. Feratox has few undesirable signs from the welfare perspective and on the basis of humanness offers a preferred alternative to other vertebrate toxins, including 1080, for the control of wallabies.
Gesture highlights perceptually present information for speakers
Authors: Alibali Martha W. , Kita Sotaro
Published: October 2010

Why do speakers produce gestures? This study tests the hypothesis that gesture facilitates the conceptual planning of speaking, and in particular, gesture promotes thinking about perceptually present information. This view implies that, when gesture is prohibited, people should be less likely to speak about such information. We tested this prediction among children (N = 50) who solved and explained Piagetian conservation tasks. For one set of conservation tasks, all children were allowed to gesture. For a second set of tasks, some children were prohibited from gesturing by wearing a cloth muff. When children were prohibited from gesturing, they expressed more non-present information and less perceptually present information in their explanations than when allowed to gesture. Thus, gesture production appears to highlight or lend salience to perceptually present information. We argue that gesture helps speakers decide what to attend to and therefore what to say.
Early development of gestures, object-related-actions, word comprehension and word production, and their relationships in Italian infants
Authors: Sansavini Alessandra , Bello Arianna , Guarini Annalisa , Savini Silvia , Stefanini Silvia , Caselli Maria Cristina
Published: October 2010

Our study aimed to examine longitudinally early development of gestures, object-actions (short for object-related-actions), word comprehension, and word production and their reciprocal relationships in typically developing infants. Twenty-two monolingual Italian infants were followed monthly from 0;10 up to 1;5 with the Italian short form of MacArthur-Bates CDI — Gestures and Words. Results showed that gestures, object-actions, and word comprehension increased significantly from 0;10 to 1;5, with an earlier development of gestures with respect to object-actions, while production started to increase significantly from 1;0. A developmental advantage of girls with respect to boys was found in gestures, object-actions and word comprehension. Relationships were evident between object-actions and word comprehension at all ages, between gestures and both word comprehension and word production in their phase of emergence, and between word comprehension and word production at the emergence of word production. Our findings suggest that gestures support the emergence of verbal abilities, while object-actions contribute to the construction of the representation of meanings.
Model-free unsupervised gene set screening based on information enrichment in expression profiles
Authors: Niida Atushi , Imoto Seiya , Yamaguchi Rui , Nagasaki Masao , Fujita André , Shimamura Teppei , Miyano Satoru
Published: October 2010

Motivation: A number of unsupervised gene set screening methods have recently been developed for search of putative functional gene sets based on their expression profiles. Most of the methods statistically evaluate whether the expression profiles of each gene set are fit to assumed models: e.g. co-expression across all samples or a subgroup of samples. However, it is possible that they fail to capture informative gene sets whose expression profiles are not fit to the assumed models.

Results: To overcome this limitation, we propose a model-free unsupervised gene set screening method, Matrix Information Enrichment Analysis (MIEA). Without assuming any specific models, MIEA screens gene sets based on information richness of their expression profiles. We extensively compared the performance of MIEA to those of other unsupervised gene set screening methods, using various types of simulated and real data. The benchmark tests demonstrated that MIEA can detect singular expression profiles that the other methods fail to find, and performs broadly well for various types of input data. Taken together, this study introduces MIEA as a broadly applicable gene set screening tool for mining regulatory programs from transcriptome data.

Contact:  aniida@ims.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterization of δ-Guaiene Synthases from Cultured Cells of Aquilaria, Responsible for the Formation of the Sesquiterpenes in Agarwood
Authors: Kumeta Yukie , Ito Michiho
Published: October 2010

The resinous portions of Aquilaria plants, called agarwood, have been used as medicines and incenses. Agarwood contains a great variety of sesquiterpenes, and a study using cultured cells of Aquilaria showed the production of sesquiterpenes (α-guaiene, α-humulene, and δ-guaiene) to be induced by treatment with methyl jasmonate (MJ). In this study, the accumulation and production of sesquiterpenes were quantified. The amounts accumulated and produced reached a maximum at 12 h, and the most abundant product was α-humulene at 6 h and δ-guaiene after 12 h. However, a headspace analysis of the cells revealed that α-humulene is likely to be volatilized; so overall, the most abundant sesquiterpene in the cells was δ-guaiene. A cDNA library from RNA isolated from MJ-treated cells was screened using PCR methodologies to isolate five clones with very similar amino acid sequences. These clones were expressed in Escherichia coli, and enzymatic reactions using farnesyl pyrophosphate revealed that three of the clones yielded the same compounds as extracted from MJ-treated cells, the major product being δ-guaiene. These genes and their encoded enzymes are the first sesquiterpene synthases yielding guaiane-type sesquiterpenes as their major products to be reported. Expression of a fourth terpene synthase gene in bacteria resulted in the accumulation of the protein in insoluble forms. Site-directed mutagenesis of the inactive clone and three-dimensional homology modeling suggested that the structure of the N-terminal domain was important in facilitating proper folding of the protein to form a catalytically active structure.
Protein arginine methylation modulates light‐harvesting antenna translation in Chlamydomonas reinhardtii
Authors: Blifernez Olga , Wobbe Lutz , Niehaus Karsten , Kruse Olaf
Published: October 2010

Methylation of protein arginines represents an important post‐translational modification mechanism, which has so far primarily been characterized in mammalian cells. In this work, we successfully identified and characterized arginine methylation as a crucial type of post‐translational modification in the activity regulation of the cytosolic translation repressor protein NAB1 in the plant model organism Chlamydomonas reinhardtii. NAB1 represses the cytosolic translation of light‐harvesting protein encoding mRNAs by sequestration into translationally silent messenger ribonucleoprotein complexes (mRNPs). Protein arginine methylation of NAB1 could be demonstrated by PRMT1 catalyzed methylation of recombinant NAB1 in vitro, and by immunodetection of methylated NAB1 arginines in vivo. Mass spectrometric analyses of NAB1 purified from C. reinhardtii revealed the asymmetric dimethylation of Arg90 and Arg92 within GAR motif I. Inhibition of arginine methylation by either adenosine‐2′‐3′‐dialdehyde (AdOx) or 7,7′‐carbonylbis(azanediyl)bis(4‐hydroxynaphthalene‐2‐sulfonic acid) sodium salt hydrate (AMI‐1) caused a dark‐green phenotype characterized by the increased accumulation of light‐harvesting complex proteins, and indicating a reduced translation repressor activity of NAB1. The extent of NAB1 arginine methylation depends on the growth conditions, with phototrophic growth causing a high methylation state and heterotrophic growth resulting in lowered methylation of the protein. In addition, we could show that NAB1 activity regulation by arginine methylation operates independently from cysteine‐based redox control, which has previously been shown to control the activity of NAB1.
CYP99A3: functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice
Authors: Wang Qiang , Hillwig Matthew L. , Peters Reuben J.
Published: October 2010

Rice (Oryza sativa) produces momilactone diterpenoids as both phytoalexins and allelochemicals. Strikingly, the rice genome contains a biosynthetic gene cluster for momilactone production, located on rice chromosome 4, which contains two cytochrome P450 (CYP) mono‐oxygenases, CYP99A2 and CYP99A3, with undefined roles; although it has been previously shown that RNA interference double knock‐down of this pair of closely related CYPs reduced momilactone accumulation. Here we attempted biochemical characterization of CYP99A2 and CYP99A3, which was ultimately achieved by complete gene recoding, enabling functional recombinant expression in bacteria. With these synthetic gene constructs it was possible to demonstrate that while CYP99A2 does not exhibit significant activity with diterpene substrates, CYP99A3 catalyzes consecutive oxidations of the C19 methyl group of the momilactone precursor syn‐pimara‐7,15‐diene to form, sequentially, syn‐pimaradien‐19‐ol, syn‐pimaradien‐19‐al, and syn‐pimaradien‐19‐oic acid. These are presumably intermediates in momilactone biosynthesis, as a C19 carboxylic acid moiety is required for formation of the core 19,6‐γ‐lactone ring structure. We further were able to detect syn‐pimaradien‐19‐oic acid in rice plants, which indicates physiological relevance for the observed activity of CYP99A3. In addition, we found that CYP99A3 also oxidized syn‐stemod‐13(17)‐ene at C19 to produce, sequentially, syn‐stemoden‐19‐ol, syn‐stemoden‐19‐al, and syn‐stemoden‐19‐oic acid, albeit with lower catalytic efficiency than with syn‐pimaradiene. Although the CYP99A3 syn‐stemodene‐derived products were not detected in planta, these results nevertheless provide a hint at the currently unknown metabolic fate of this diterpene in rice. Regardless of any wider role, our results strongly indicate that CYP99A3 acts as a multifunctional diterpene oxidase in momilactone biosynthesis.
The Burden of Motherhood: The Effect of Reproductive Load on Female Lizard Locomotor, Foraging, and Social Behavior
Authors: Johnson Michele A. , Caton Jessica L. , Cohen Rachel E. , Vandecar Joseph R. , Wade Juli
Published: October 2010

The costs of reproduction, involving demands associated with both current and future reproductive efforts, may place a substantial burden on females. However, animals may minimize these costs by modifying their behavior across the reproductive cycle. We examined the effects of reproductive load on three types of behavior (locomotion, foraging, and social displays) in green anole lizards (Anolis carolinensis) by comparing egg, follicle, and oviduct mass and volume with field observational data. We found that female locomotor and social display behaviors decreased as reproductive load increased, suggesting behavioral modification in these traits, but we detected no relationship between foraging and reproductive load. We also examined these relationships across eight Anolis species using a phylogenetically informed analysis and found no associations between the evolution of reproductive load and any of the three behaviors. These results suggest that the evolution of increased reproductive load is not associated with the interspecific variation in behavior across the anoles and may result from varying life history traits or selective ecological pressures across species.