bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced SuperDARN meteor wind observations based on raw time series analysis technique
Authors: Tsutsumi M. , Yukimatu A. S. , Holdsworth D. A. , Lester M.
Published: March 2009

The meteor observation technique based on SuperDARN raw time series analysis has been upgraded. This technique extracts meteor information as biproducts and does not degrade the quality of normal SuperDARN operations. In the upgrade the radar operating system (RADOPS) has been modified so that it can oversample every 15 km during the normal operations, which have a range resolution of 45 km. As an alternative method for better range determination a frequency domain interferometry (FDI) capability was also coded in RADOPS, where the operating radio frequency can be changed every pulse sequence. Test observations were conducted using the CUTLASS Iceland East and Finland radars, where oversampling and FDI operation (two frequencies separated by 3 kHz) were simultaneously carried out. Meteor ranges obtained in both ranging techniques agreed very well. The ranges were then combined with the interferometer data to estimate meteor echo reflection heights. Although there were still some ambiguities in the arrival angles of echoes because of the rather long antenna spacing of the interferometers, the heights and arrival angles of most of meteor echoes were more accurately determined than previously. Wind velocities were successfully estimated over the height range of 84 to 110 km. The FDI technique developed here can be further applied to the common SuperDARN operation, and study of fine horizontal structures of F region plasma irregularities is expected in the future.
Microbiomic analysis of the bifidobacterial population in the human distal gut
Authors: Turroni Francesca , Marchesi Julian R , Foroni Elena , Gueimonde Miguel , Shanahan Fergus , Margolles Abelardo , van Sinderen Douwe , Ventura Marco
Published: March 2009

One of the most complex microbial ecosystems is represented by the microbiota of the human gastrointestinal tract (GIT). Although this microbial consortium has been recognized to have a crucial effect on human health, its precise composition is still not fully established. Among the GIT bacteria, bifidobacteria represent an important commensal group whose presence is often associated with health-promoting effects. In this work, we assessed the complexity of the human intestinal bifidobacterial population by analysing the diversity of several 16S rRNA gene-based libraries. These analyses showed the presence of novel bifidobacterial phylotypes, which had not been found earlier and may thus represent novel taxa within the genus Bifidobacterium.
PyrococcusCH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life
Authors: Zeng Xiang , Birrien Jean-Louis , Fouquet Yves , Cherkashov Georgy , Jebbar Mohamed , Querellou Joël , Oger Philippe , Cambon-Bonavita Marie-Anne , Xiao Xiang , Prieur Daniel
Published: March 2009

A novel hydrothermal site was discovered in March 2007, on the mid-Atlantic ridge during the cruise ‘Serpentine’. At a depth of 4100 m, the site ‘Ashadze’ is the deepest vent field known so far. Smoker samples were collected with the ROV ‘Victor 6000’ and processed in the laboratory for the enrichment of anaerobic heterotrophic microorganisms under high-temperature and high-hydrostatic pressure conditions. Strain CH1 was successfully isolated and assigned to the genus Pyrococcus, within the Euryarchaeota lineage within the Archaea domain. This organism grows within a temperature range of 80 to 108 °C and a pressure range of 20 to 120 MPa, with optima for 98 °C and 52 MPa respectively. Pyrococcus CH1 represents the first obligate piezophilic hyperthermophilic microorganism known so far. Comparisons of growth yields obtained under high-temperature/high-pressure conditions for relative organisms isolated from various depths, showed clear relationships between depth at origin and responses to hydrostatic pressure.
Two pathways for cysteine biosynthesis in Leishmania major
Authors: Williams Roderick A. M. , Westrop Gareth D. , Coombs Graham H.
Published: March 2009

Genome mining and biochemical analyses have shown that Leishmania major possesses two pathways for cysteine synthesis – the de novo biosynthesis pathway comprising SAT (serine acetyltransferase) and CS (cysteine synthase) and the RTS (reverse trans-sulfuration) pathway comprising CBS (cystathionine β-synthase) and CGL (cystathionine γ-lyase). The LmjCS (L. major CS) is similar to the type A CSs of bacteria and catalyses the synthesis of cysteine using O-acetylserine and sulfide with Kms of 17.5 and 0.13 mM respectively. LmjCS can use sulfide provided by the action of MST (mercaptopyruvate sulfurtransferase) on 3-MP (3-mercaptopyruvate). LmjCS forms a bi-enzyme complex with Leishmania SAT (and Arabidopsis SAT), with residues Lys222, His226 and Lys227 of LmjCS being involved in the complex formation. LmjCBS (L. major CBS) catalyses the synthesis of cystathionine from homocysteine, but, unlike mammalian CBS, also has high cysteine synthase activity (but with the Km for sulfide being 10.7 mM). In contrast, LmjCS does not have CBS activity. CS was up-regulated when promastigotes were grown in medium with limited availability of sulfur amino acids. Exogenous methionine stimulated growth under these conditions and also the levels of intracellular cysteine, glutathione and trypanothione, whereas cysteine had no effect on growth or the intracellular cysteine levels, correlating with the low rate of transport of cysteine into the cell. These results suggest that cysteine is generated endogenously by promastigotes of Leishmania. The absence of CS from mammals and the clear differences between CBS of mammals and Leishmania suggest that each of the parasite enzymes could be a viable drug target.
Fabrication of L11-type (Co–Ni)–Pt ordered alloy films by sputter deposition
Authors: Sato H. , Shimatsu T. , Kataoka H. , Aoi H. , Okamoto S. , Kitakami O.
Published: March 2009

L 1 1 -type (Co–Ni)–Pt ordered alloy perpendicular films were successfully fabricated on MgO(111) single crystal substrates using ultrahigh vacuum sputter film deposition; the addition of Ni to Co–Pt was effective to reduce saturation magnetization, Ms, maintaining a large Ku of the order of 107 erg/cm3. L11-type ordered structures, with the ⟨111⟩ direction (easy axis of magnetization) perpendicular to the films, were successfully fabricated at a substrate temperature of 360 °C in a wide composition range with Co content less than 60 at. %. The order parameter, S, was almost a constant of about 0.5 in the stoichiometric composition of (Co1−XNiX)50Pt50, independent of Ni content, X. L11-type Co–Ni–Pt perpendicular films having a large Ku of (1–2.5)×107 erg/cm3 and a relatively low Ms of 400–700 emu/cm3 were successfully fabricated in the composition range of 10–35 at. % Co, 20–55 at. % Ni, and bal. Pt. Ku should increase further with enhanced ordering. Experimental results demonstrated the potential of these Co–Ni–Pt ordered films for use in data storage applications due to very high Ku potential comparable to L10-type Fe50Pt50 films, relatively low Ms, the relatively low fabrication temperature, and good controllability of the grain orientation.
Analysis on operational power and eddy current losses for applying coreless double-sided permanent magnet synchronous motor/generator to high-power flywheel energy storage system
Authors: Jang Seok-Myeong , Park Ji-Hoon , You Dae-Joon , Choi Sang-Ho
Published: March 2009

This paper deals with analytical approach of operational power defined as load power and rotor loss represented as eddy current loss for applying a permanent magnet (PM) synchronous motor/generator to the high-power flywheel energy storage system. The used model is composed of a double-sided Halbach magnetized PM rotor and coreless three-phase winding stator. For one such motor/generator structure, we provide the magnetic field and eddy current with space and time harmonics via magnetic vector potential in two-dimensional (2D) polar coordinate system. From these, the operational power is estimated by backelectromotive force according to the PM rotor speed, and the rotor loss is also calculated from Poynting theorem.
First principles calculation of crystal field parameter near surfaces of Nd2Fe14B
Authors: Moriya Hiroshi , Tsuchiura Hiroki , Sakuma Akimasa
Published: March 2009

We study the electronic structures of a (001) surface of crystalline Nd2Fe14B by using a slab model, and estimate the crystal field parameters A20⟨r2⟩ at Nd sites based on first principles calculations. We find that the A20⟨r2⟩ for some Nd ions are negative. The present results imply that Nd ions located around the (001) surfaces of crystalline Nd2Fe14B would be nucleation sites of reversed magnetic domains.
Pole design optimization of shielded planar writer for 2 Tbit/in2 recording
Authors: Yamakawa Kiyoshi , Ohsawa Yuichi , Greaves Simon , Muraoka Hiroaki
Published: March 2009

A shielded planar head with a multi-step-tapered main pole assuming ion-beam milling fabrication was studied to obtain a large recording field along with suppressed fringing field. The head main pole with a three-step-tapered structure was optimized in terms of the top, main, and bottom slope angles. The optimized head showed a remarkably suppressed fringing field compared with a conventional single-step-tapered pole head. The recording simulation suggests that the head has the potential for 2 Tbit/in2 recording in combination with a bit patterned medium.
Brain activity during bilateral rapid alternate finger tapping measured with magnetoencephalography
Authors: Fukuda Hiroshi , Odagaki Masato , Hiwaki Osamu , Kodabashi Atsushi , Fujimoto Toshiro
Published: March 2009

Using magnetoencephalography (MEG), brain regions involved in an alternate bimanual tapping task by index fingers triggered with spontaneous timing were investigated. The tapping mode in which both index fingers moved simultaneously was interlaced during the task. The groups of the alternate tapping (AL mode) and the simultaneous tapping (SI mode) were extracted from the successive alternating taps with a histogram of intervals between the right and left index fingers. MEG signals in each mode were averaged separately before and after the tapping initiation of the dominant index finger. The activities of the contralateral sensorimotor cortex before and after the tapping initiation in the AL mode were larger than that in the SI mode. The result indicates that the activity of the contralateral sensorimotor cortex depends on the degree of achievement in the difficult motor task such as the voluntary alternate tapping movements.
Structural, magnetic, and electronic transport properties of (Sr0.9Ca0.1)3Ru2O7 single crystal
Authors: Qian Bin , Qu Zhe , Peng Jin , Liu Tijiang , Wu Xiaoshan , Spinu L. , Mao Z. Q.
Published: March 2009

We have studied the structural, magnetic, and electronic transport properties of (Sr0.9Ca0.1)3Ru2O7 using single crystals grown by a floating-zone technique. The structure analysis by Rietveld refinements reveals that the Ca substitution for Sr intensifies the structure distortion; the rotation angle of the RuO6 octahedron increases. This structure change tunes magnetic and transport properties dramatically. The magnetic ground state switches from an itinerant metamagnetic state for Sr3Ru2O7 to a nearly ferromagnetic state for (Sr0.9Ca0.1)3Ru2O7. The Fermi liquid behavior occurs in Sr3Ru2O7, but is suppressed in (Sr0.9Ca0.1)3Ru2O7. These results strongly suggest that lattice, spin, and charge degrees of freedom are strongly coupled in this system. The band width narrowing caused by the structure distortion should be responsible for the enhancement of ferromagnetic correlations and the change of transport properties.
Mechanistic benefits of millisecond annealing for diffusion and activation of boron in silicon
Authors: Kwok Charlotte T. M. , Braatz Richard D. , Paul Silke , Lerch Wilfried , Seebauer Edmund G.
Published: March 2009

Millisecond annealing techniques with flash lamps or lasers have become increasingly common for activating dopants and eliminating implantation-induced damage after ion implantation for transistor junction formation in silicon. Empirical data show that such techniques confer significant benefits, but key physical mechanisms underlying these benefits are not well understood. The present work employs numerical simulation and analytical modeling to show that for boron, millisecond annealing reduces unwanted dopant spreading by greatly reducing the time for diffusion, which more than compensates for an increased concentration of Si interstitials that promote dopant spreading. Millisecond annealing also favorably alters the relative balance of boron interstitial sequestration by the crystal lattice vs interstitial clusters, which leads to improved electrical activation at depths just short of the junction.
Excitation energies with time-dependent density matrix functional theory: Singlet two-electron systems
Authors: Giesbertz K. J. H. , Pernal K. , Gritsenko O. V. , Baerends E. J.
Published: March 2009

Time-dependent density functional theory in its current adiabatic implementations exhibits three striking failures: (a) Totally wrong behavior of the excited state surface along a bond-breaking coordinate, (b) lack of doubly excited configurations, affecting again excited state surfaces, and (c) much too low charge transfer excitation energies. We address these problems with time-dependent density matrix functional theory (TDDMFT). For two-electron systems the exact exchange-correlation functional is known in DMFT, hence exact response equations can be formulated. This affords a study of the performance of TDDMFT in the TDDFT failure cases mentioned (which are all strikingly exhibited by prototype two-electron systems such as dissociating H2 and HeH+). At the same time, adiabatic approximations, which will eventually be necessary, can be tested without being obscured by approximations in the functional. We find the following: (a) In the fully nonadiabatic (ω-dependent, exact) formulation of linear response TDDMFT, it can be shown that linear response (LR)-TDDMFT is able to provide exact excitation energies, in particular, the first order (linear response) formulation does not prohibit the correct representation of doubly excited states; (b) within previously formulated simple adiabatic approximations the bonding-to-antibonding excited state surface as well as charge transfer excitations are described without problems, but not the double excitations; (c) an adiabatic approximation is formulated in which also the double excitations are fully accounted for.
Correlation analysis of electrical and optical low frequency fluctuation in organic device degradation
Authors: Lin Ke , Cheng Lai Szu , Ramam Adelia , Jin Chua Soo
Published: March 2009

Low frequency electrical and optical noise fluctuations of organic light emitting diodes were obtained simultaneously. It had been observed that the voltage and optical noises increased gradually with time as the device was subjected to constant current stress. Correlation between the device electrical and optical noise was established. Computation of the correlation coefficients between the voltage and luminescence noises had been devised and implemented. Results suggested that the correlation increased with the noise frequency and this phenomenon was concluded to be the result of some photons going undetected at low frequencies. It was further observed that the correlation was more consistent under low device current when the current efficiency was higher.
Characterization of single diamondlike and polymerlike nanoparticles by midinfrared nanospectroscopy
Authors: Samson Jean-Sébastien , Meißner Raphaela , Bründermann Erik , Böke Marc , Winter Jörg , Havenith Martina
Published: March 2009

We report on the characterization of single nanoparticles produced in N2–C2H2 low pressure plasmas using scanning near-field infrared microscopy. We use a high power optical parametric oscillator as radiation source, which emits in the so-called fingerprint region 2500–3570 cm−1. We have probed the characteristic N–H absorption band at 3300 cm−1 to characterize single nanoparticles. The observed near-field contrast allows to distinguish between diamond- and polymerlike nanoparticles. Here, the term “diamondlike” refers to hard amorphous carbon material with abundant sp3-coordinated C atoms. Our results demonstrate the feasibility of an infrared spectral characterization of single nanoparticles with nanometer lateral resolution.
Ultrathin amorphization of single-crystal silicon by ultraviolet femtosecond laser pulse irradiation
Authors: Izawa Yusaku , Tokita Shigeki , Fujita Masayuki , Nakai Mitsuo , Norimatsu Takayoshi , Izawa Yasukazu
Published: March 2009

The mechanisms of amorphization for crystalline Si (c-Si) induced by ultraviolet femtosecond laser irradiation are described in this paper. The wavelength of the laser pulse was 267 nm, which is the third harmonics of a Ti:sapphire laser. We performed a laser scanning microscopy and a transmission electron microscopy for surface and structural analysis and imaging pump-probe measurements to investigate the dynamics of the process. From the analyses, we confirmed that the thickness of the amorphized layer was quite uniform and there is no lattice defect under the amorphized section. The thickness of the amorphous Si (a-Si) layer was 7 nm and the threshold fluence of the amorphization was 44 mJ/cm2. From the Imaging Pump-Probe measurement it was revealed that the melting time is less than 1 ns and ultra high speed melting and re-solidification process was occurred. The melting depth estimated by the Imaging Pump-Probe measurement was 7 nm. The melted portion completely corresponded to the amorphized section.
Transformation from angle-action variables to Cartesian coordinates for polyatomic reactions
Authors: González-Martínez M. L. , Bonnet L. , Larrégaray P. , Rayez J.-C. , Rubayo-Soneira J.
Published: March 2009

The transformation from angle-action variables to Cartesian coordinates is an important step of the semiclassical description of bimolecular collisions and photofragmentations. The basic reason is that dynamical conditions corresponding to molecular beam experiments are ideally generated in angle-action variables, whereas the classical equations of motion are ideally solved in Cartesian coordinates by standard numerical approaches. To our knowledge, this transformation is available in the literature only for atom-diatom arrangements. The goal of the present work is to derive it for diatom-polyatom ones. The analogous transformation for any type of arrangement may then be straightforwardly deduced from that presented here.
Investigation of different mechanisms of GaN growth induced on AlN and GaN nucleation layers
Authors: Tasco V. , Campa A. , Tarantini I. , Passaseo A. , González-Posada F. , Redondo-Cubero A. , Lorenz K. , Franco N. , Muñoz E.
Published: March 2009

The evolution of GaN growth on AlN and GaN nucleation layers is compared through morphological and structural analyses, including ion beam analysis. By using AlN nucleation layer grown at high temperature, improved crystalline quality is exhibited by 300 nm thin GaN epilayers. GaN (002) x-ray rocking curve as narrow as 168 arc sec and atomic-step surface morphology characterize such a thin GaN film on AlN. Defects are strongly confined into the first 50 nm of growth, whereas a fast laterally coherent growth is observed when increasing thickness, as an effect of high temperature AlN surface morphology and Ga adatom dynamics over this template.
Single photon emission from a site-controlled quantum dot-micropillar cavity system
Authors: Schneider C. , Heindel T. , Huggenberger A. , Weinmann P. , Kistner C. , Kamp M. , Reitzenstein S. , Höfling S. , Forchel A.
Published: March 2009

We demonstrate the deterministic integration of single site-controlled quantum dots (SCQDs) into micropillar cavities. Spatial resonance between single positioned QDs and GaAs/AlAs micropillar cavities was achieved using cross markers for precise SCQD-cavity alignment. Cavity effects are clearly reflected in an enhanced photoluminescence intensity when tuning SCQD emission lines through the fundamental cavity resonance. Single photon emission from a spatially and spectrally coupled SCQD-resonator system is confirmed by photon autocorrelation measurements yielding a g(2)(0) value of 0.12.
Megavoltage bremsstrahlung end point voltage diagnostic
Authors: Feroli T. , Litz M. S. , Merkel G. , Smith T. , Pereira N. R. , Carroll J. J.
Published: March 2009

In a material, a beam of x rays is accompanied by various kinds of secondary radiation, including Compton electrons from collisions between the x rays and the material’s electrons. For megavoltage bremsstrahlung in air, many of these Compton electrons are forward-directed and fast enough to be deflected outside the beam’s edge by a magnetic field perpendicular to the beam. At the beam’s edge, the dose from the deflected Compton electrons has a pattern that depends on the radiation’s end point energy. Dose patterns measured with radiochromic film on a nominally 1 and 2 MV linear accelerator agree reasonably well with the corresponding Monte Carlo computations. With further development, the dose pattern produced outside the beam by such a sweeper magnet could become a noninvasive way to monitor megavoltage bremsstrahlung, when the end point energies are difficult to determine with other methods.
Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs
Authors: Tillich Michael , Hardel Simone L. , Kupsch Christiane , Armbruster Ute , Delannoy Etienne , Gualberto José M. , Lehwark Pascal , Leister Dario , Small Ian D. , Schmitz-Linneweber Christian
Published: March 2009

Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded, highly abundant, and light-regulated RNA binding proteins. They have been shown to be involved in chloroplast RNA processing and stabilization in vitro and are phylogenetically related to the well-described heterogeneous nuclear ribonucleoproteins (hnRNPs). cpRNPs have been found associated with mRNAs present in chloroplasts and have been regarded as nonspecific stabilizers of chloroplast transcripts. Here, we demonstrate that null mutants of the cpRNP family member
CP31A
exhibit highly specific and diverse defects in chloroplast RNA metabolism. First, analysis of
cp31a
and
cp31a
/
cp31b
double mutants uncovers that these 2 paralogous genes participate nonredundantly in a combinatorial fashion in processing a subset of chloroplast editing sites in vivo. Second, a genome-wide analysis of chloroplast transcript accumulation in
cp31a
mutants detected a virtually complete loss of the chloroplast
ndhF
mRNA and lesser reductions for specific other mRNAs. Fluorescence analyses show that the activity of the NADH dehydrogenase complex, which also includes the NdhF subunit, is defective in
cp31a
mutants. This indicates that cpRNPs are important in vivo for calibrating the expression levels of specific chloroplast mRNAs and impact chloroplast physiology. Taken together, the specificity and combinatorial aspects of cpRNP functions uncovered suggest that these chloroplast proteins are functional equivalents of nucleocytosolic hnRNPs.
p110γ and p110δ isoforms of phosphoinositide 3-kinase differentially regulate natural killer cell migration in health and disease
Authors: Saudemont Aurore , Garçon Fabien , Yadi Hakim , Roche-Molina Marta , Kim Nayoung , Segonds-Pichon Anne , Martín-Fontecha Alfonso , Okkenhaug Klaus , Colucci Francesco
Published: March 2009

The mechanisms that regulate NK cell trafficking are unclear. Phosphoinositide-3 kinases (PI3K) control cell motility and the p110γ and p110δ isoforms are mostly expressed in leukocytes, where they transduce signals downstream of G protein coupled receptors (GPCR) or tyrosine kinase receptors, respectively. Here, we set out to determine the relative contribution of p110γ and p110δ to NK cell migration in mice. Using a combination of single-cell imaging analysis of transgenic cells reporting on PI3K activity in real time and small molecule inhibitors of p110γ and p110δ, we show here that the tyrosine-kinase coupled p110δ is linked to GPCR signaling and, depending on the GPCR, may even be preferentially activated over p110γ. Using gene-targeted mice, we showed that both isoforms were essential for NK cell chemotaxis to CXCL12 and to CCL3 and, in vivo, for normal NK cell migration during pregnancy and to the inflamed peritoneum. By contrast, only p110δ was indispensable for chemotaxis to S1P and CXCL10 and for NK cell distribution throughout lymphoid and nonlymphoid tissues and for extravasation to tumors. These results implicate p110δ downstream of GPCRs in NK cells and highlight its nonredundant role as a key regulator of NK cell trafficking in health and disease.
Malaria primes the innate immune response due to interferon-γ induced enhancement of toll-like receptor expression and function
Authors: Franklin Bernardo S. , Parroche Peggy , Ataíde Marco Antǒnio , Lauw Fanny , Ropert Catherine , de Oliveira Rosane B. , Pereira Dhelio , Tada Mauro Shugiro , Nogueira Paulo , da Silva Luiz Hildebrando Pereira , Bjorkbacka Harry , Golenbock Douglas T. , Gazzinelli Ricardo T.
Published: March 2009

Malaria-induced sepsis is associated with an intense proinflammatory cytokinemia for which the underlying mechanisms are poorly understood. It has been demonstrated that experimental infection of humans withPlasmodium falciparumprimes Toll-like receptor (TLR)-mediated proinflammatory responses. Nevertheless, the relevance of this phenomenon during natural infection and, more importantly, the mechanisms by which malaria mediates TLR hyperresponsiveness are unclear. Here we show that TLR responses are boosted in febrile patients during natural infection withP. falciparum. Microarray analyses demonstrated that an extraordinary percentage of the up-regulated genes, including genes involving TLR signaling, had sites for IFN-inducible transcription factors. To further define the mechanism involved in malaria-mediated “priming,” we infected mice withPlasmodium chabaudi. The human data were remarkably predictive of what we observed in the rodent malaria model. Malaria-induced priming of TLR responses correlated with increased expression of TLR mRNA in a TLR9-, MyD88-, and IFNγ-dependent manner. Acutely infected WT mice were highly susceptible to LPS-induced lethality while TLR9−/−, IL12−/−and to a greater extent, IFNγ−/−mice were protected. Our data provide unprecedented evidence that TLR9 and MyD88 are essential to initiate IL12 and IFNγ responses and favor host hyperresponsiveness to TLR agonists resulting in overproduction of proinflammatory cytokines and the sepsis-like symptoms of acute malaria.
Structural arrangement of the transmission interface in the antigen ABC transport complex TAP
Authors: Oancea Giani , O'Mara Megan L. , Bennett W. F. Drew , Tieleman D. Peter , Abele Rupert , Tampé Robert
Published: March 2009

The transporter associated with antigen processing (TAP) represents a focal point in the immune recognition of virally or malignantly transformed cells by translocating proteasomal degradation products into the endoplasmic reticulum–lumen for loading of MHC class I molecules. Based on a number of experimental data and the homology to the bacterial ABC exporter Sav1866, we constructed a 3D structural model of the core TAP complex and used it to examine the interface between the transmembrane and nucleotide-binding domains (NBD) by cysteine-scanning and cross-linking approaches. Herein, we demonstrate the functional importance of the newly identified X-loop in the NBD in coupling substrate binding to downstream events in the transport cycle. We further verified domain swapping in a heterodimeric ABC half-transporter complex by cysteine cross-linking. Strikingly, either substrate binding or translocation can be blocked by cross-linking the X-loop to coupling helix 2 or 1, respectively. These results resolve the structural arrangement of the transmission interface and point to different functions of the cytosolic loops and coupling helices in substrate binding, signaling, and transport.
Endometrium as an early sensor of in vitro embryo manipulation technologies
Authors: Mansouri-Attia Nadéra , Sandra Olivier , Aubert Julie , Degrelle Séverine , Everts Robin E. , Giraud-Delville Corinne , Heyman Yvan , Galio Laurent , Hue Isabelle , Yang Xiangzhong , Tian X. Cindy , Lewin Harris A. , Renard Jean-Paul
Published: March 2009

Implantation is crucial for placental development that will subsequently impact fetal growth and pregnancy success with consequences on postnatal health. We postulated that the pattern of genes expressed by the endometrium when the embryo becomes attached to the mother uterus could account for the final outcome of a pregnancy. As a model, we used the bovine species where the embryo becomes progressively and permanently attached to the endometrium from day 20 of gestation onwards. At that stage, we compared the endometrial genes profiles in the presence of an in vivo fertilized embryo (AI) with the endometrial patterns obtained in the presence of nuclear transfer (SCNT) or in vitro fertilized embryos (IVF), both displaying lower and different potentials for term development. Our data provide evidence that the endometrium can be considered as a biological sensor able to fine-tune its physiology in response to the presence of embryos whose development will become altered much later after the implantation process. Compared with AI, numerous biological functions and several canonical pathways with a major impact on metabolism and immune function were found to be significantly altered in the endometrium of SCNT pregnancies at implantation, whereas the differences were less pronounced with IVF embryos. Determining the limits of the endometrial plasticity at the onset of implantation should bring new insights on the contribution of the maternal environment to the development of an embryo and the success of pregnancy.
Religious Nationalism and Adaptation in Southeast Europe
Authors: Loizides Neophytos G.
Published: March 2009

Relating nationalism to other ideologies or cultural value systems is an enigmatic scholarly activity. The enigma lies in the kaleidoscopic nature of nationalism and the ease with which it adapts to philosophically opposed ideologies. Nationalism, for instance, often assumes ties to liberalism, even though it presupposes a strong commitment to a national community that transcends individualism. It accommodates conservatism fairly well despite nationalism's modernizing mission, and it has often been paired with communism, regardless of the latter's internationalist rhetoric. Finally, nationalism and religion often go hand in hand, despite their deep philosophical incompatibilities and asymmetries. For example, nationalist ideologies often encourage violence against outgroup members even where religious doctrines strictly prohibit physical force. Inherently local, philosophically poor, and limited in scope or outreach, nationalism lacks a belief in afterlife salvation or in creative intelligence as source of meaning behind the universe. Yet it frequently dominates identity construction, overshadowing the primacy of Christianity or Islam which are universal in their message of salvation.
New N-nicotinyl and N-2,4-dichlorobenzoyl phosphorictriamides: syntheses, spectroscopic study, and crystal structures
Authors: Gholivand Khodayar , Oroujzadeh Nasrin
Published: March 2009

New phosphoric triamides were synthesized and characterized by 1H, 13C, 31P NMR, IR spectroscopy and elemental analysis. It is noteworthy that as far as we know there have not been any efforts for the synthesis of phosphoric triamides with nicotinamide substituent up to now and compound 1 is the first example of this series. Compounds 1, 5, 6 indicate the coupling of diastereosterotopic CH2 protons with each other, CH proton and the corresponding P atomin 1H NMR spectra as well as two separated signals for the two CH3 moieties in 13C NMR spectra. Interestingly, the 1H NMR spectrum of compound 5 demonstrates long-range 6JP,H coupling constant. Furthermore, long-range 4JH,H coupling constant appeared for the aromatic protons of molecules 1–4. Moreover, the structures have been determined for 2–4 by X-ray crystallography.
Synthesis, characterization, and single crystal structure determination of an oxo-derivative of methylaluminum containing asymmetric carbon
Authors: Mohammadnezhad Gholamhossein , Amini Mostafa M. , Khavasi Hamidreza , Mirzaei Peiman
Published: March 2009

Dimeric dimethylaluminum compound, {Me2Al[μ-OCH(CH3)CH2OCH3]}2, was synthesized by the reaction of trimethylaluminum and 1-methoxy-2-propanol, an alkoxyalcohol containing asymmetric carbon, and characterized by 1H, 13C, and 27Al NMR spectroscopy. The 1-methoxy-2-propoxodimethylaluminum, as shown by the single crystal structure determination, exists as a dimer in the solid-state in which the ether alkoxide ligand chelates to the aluminum atom. The solution structure was probed by 1H, 13C, and 27Al NMR spectroscopy and the results showed that the five-coordinate isomer is in equilibrium with the four-coordinate isomer. However, variable-temperature 27Al NMR spectroscopy showed only the presence of five-coordinate isomer at −15°C and below.
THERE ARE COALITIONS EVERYWHERE
Authors: Nedergaard Peter
Published: March 2009

Do members of the committees under the Open Method of Coordination (OMC) find that there are coalitions of specific member states in these committees? If so, then what kind of side payments hold these coalitions together? For the first time in scholarly literature, and based on an empirical investigation, the findings in this paper document that two opposing coalitions – with the United Kingdom and France as the respective leaders – exist in OMC committees where mutual learning is the raison d’être. In the existing theory on this subject in the EU, it is claimed that consensus decision-making leads to a weakening of coalition-building. All three committees analysed in this paper build on consensus decision-making, which is achieved after intensive meetings between all the members. However, it is contended that the ‘argumentative contest’ working method of the OMC committees leads to more – not less – coalition-building. On the basis of a test, it is also shown that these committees are primarily held together by side payments in the form of ‘promises relating to policy among the like-minded’; however, ‘payments allied to subsequent decisions’ add to the cement of the coalition-building processes stemming from the OMC working method.
How to Compare Apples and Oranges: Infants' Object Identification Tested With Equally Salient Shape, Luminance, and Color Changes
Authors: Kaldy Zsuzsa , Blaser Erik
Published: March 2009

What kind of featural information do infants rely on when they are trying to recognize a previously seen object? The question of whether infants use certain features (e.g., shape or color) more than others (e.g., luminance) can only be studied legitimately if visual salience is controlled, as the magnitude of feature values—how noticeable and interesting they are—will affect results. We employed a novel methodology, interdimensional salience mapping, that allowed us to quantify and calibrate salience changes along shape, luminance, and color feature dimensions. We then compared 9‐month‐old infants' identification of objects, employing feature changes that were equally salient. These results show that infants more readily identify objects on the basis of color and shape than luminance. Additionally, we show that relative salience changes rapidly in infancy—in particular, we found significantly higher salience thresholds for color in younger (6.5‐month‐old) infants—but that individual differences within an age group are remarkably modest.
Thus I Have Seen
Authors: Rotman Andy
Published: March 2009

This book examines the ways that seeing is an integral part of Indian Buddhism, and how the practices of seeing described in Indian Buddhist narratives function as a kind of skeleton key for opening up Buddhist conceptualizations about the world and how it should be navigated. Much of what constitutes religious practice in these narratives is not reading, praying, or meditating, but visually engaging with certain kinds of objects. In trying to make sense of this connection between the religious and the visual, the book first focuses on the practices of śraddhā and prasāda—terms often, though problematically, translated as “faith.” The book analyzes how these mental states relate to practices of “seeing” (darśana) and “giving” (dāna), and what this configuration of seeing, believing, and giving can tell us about the power of images, the gift economy at the heart of Buddhist ethics, and the function of narratives in Buddhist India. The book also discusses strategies that these narratives provide for seeing the Buddha after he has passed into final nirvāṇa. By investigating the various ways of seeing and objects of sight that allow this to occur, the book considers various rationales for pilgrimage and the veneration of images, and what these may be able to tell us about early practices at Buddhist monuments and shrines.
Genetic linkage map of the guppy,Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation
Authors: Tripathi Namita , Hoffmann Margarete , Willing Eva-Maria , Lanz Christa , Weigel Detlef , Dreyer Christine
Published: March 2009

We report construction of a genetic linkage map of the guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of guppy chromosomes. The map, which spans a genetic length of 899 cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits.
The evolution of the lepidosaurian lower temporal bar: new perspectives from the Late Cretaceous of South China
Authors: Mo Jin-You , Xu Xing , Evans Susan E.
Published: March 2009

Until recently, it was considered axiomatic that the skull of lizards and snakes arose from that of a diapsid ancestor by loss of the lower temporal bar. The presence of the bar in the living New Zealand Tuatara,Sphenodon, was thus considered primitive, corroborating its status as a ‘living fossil’. A combination of new fossils and rigorous phylogeny has demonstrated unequivocally that the absence of the bar is the primitive lepidosaurian condition, prompting questions as to its function. Here we describe new material ofTianyusaurus, a remarkable lizard from the Late Cretaceous of China that is paradoxical in having a complete lower temporal bar and a fixed quadrate. New material from Jiangxi Province is more complete and less distorted than the original holotype.Tianyusaurusis shown to be a member of the Boreoteiioidea, a successful clade of large herbivorous lizards that were dispersed through eastern Asia, Europe and North America in the Late Cretaceous, but disappeared in the end-Cretaceous extinction. A unique combination of characters suggests thatTianyusaurustook food items requiring a large gape.
Does colour polymorphism enhance survival of prey populations?
Authors: Wennersten Lena , Forsman Anders
Published: March 2009

That colour polymorphism may protect prey populations from predation is an old but rarely tested hypothesis. We examine whether colour polymorphic populations of prey exposed to avian predators in an ecologically valid visual context were exposed to increased extinction risk compared with monomorphic populations. We made 2976 artificial pastry prey, resemblingLepidopteralarvae, in four different colours and presented them in 124 monomorphic and 124 tetramorphic populations on tree trunks and branches such that they would be exposed to predation by free-living birds, and monitored their ‘survival’. Among monomorphic populations, there was a significant effect of prey coloration on survival, confirming that coloration influenced susceptibility to visually oriented predators. Survival of polymorphic populations was inferior to that of monomorphic green populations, but did not differ significantly from monomorphic brown, yellow or red populations. Differences in survival within polymorphic populations paralleled those seen among monomorphic populations; the red morph most frequently went extinct first and the green morph most frequently survived the longest. Our findings do not support the traditional protective polymorphism hypothesis and are in conflict with those of earlier studies. As a possible explanation to our findings, we offer a competing ‘giveaway cue’ hypothesis: that polymorphic populations may include one morph that attracts the attention of predators and that polymorphic populations therefore may suffer increased predation compared with some monomorphic populations.
Extra-pair young in house wren broods are more likely to be male than female
Authors: Johnson L. Scott , Thompson Charles F. , Sakaluk Scott K. , Neuhäuser Markus , Johnson Bonnie G.P. , Soukup Sheryl Swartz , Forsythe Shannon Janota , Masters Brian S.
Published: March 2009

Sex-allocation theory predicts that females should preferentially produce offspring of the sex with greater fitness potential. In socially monogamous animal species, extra-pair mating often increases the variance in fitness of sons relative to daughters. Thus, in situations where offspring sired by a female's extra-pair mate(s) will typically have greater fitness potential than offspring sired by the within-pair mate, sex-allocation theory predicts that females will bias the sex of offspring sired by extra-pair mates towards male. We examined the relationship between offspring sex and paternity over six breeding seasons in an Illinois population of the house wren (
Troglodytes aedon
), a cavity-nesting songbird. Out of the 2345 nestlings that had both sex and paternity assigned, 350 (15%) were sired by extra-pair males. The sex ratio of extra-pair offspring, 0.534, was significantly greater than the sex ratio of within-pair offspring, 0.492, representing an increase of 8.5 per cent in the proportion of sons produced. To our knowledge, this is the first confirmed report of female birds increasing their production of sons in association with extra-pair fertilization. Our results are consistent with the oft-mentioned hypothesis that females engage in extra-pair mating to increase offspring quality.
MyoD and E-protein heterodimers switch rhabdomyosarcoma cells from an arrested myoblast phase to a differentiated state
Authors: Yang Zhihong , MacQuarrie Kyle L. , Analau Erwin , Tyler Ashlee E. , Dilworth F. Jeffery , Cao Yi , Diede Scott J. , Tapscott Stephen J.
Published: March 2009

Rhabdomyosarcomas are characterized by expression of myogenic specification genes, such as MyoD and/or Myf5, and some muscle structural genes in a population of cells that continues to replicate. Because MyoD is sufficient to induce terminal differentiation in a variety of cell types, we have sought to determine the molecular mechanisms that prevent MyoD activity in human embryonal rhabdomyosarcoma cells. In this study, we show that a combination of inhibitory Musculin:E-protein complexes and a novel splice form of E2A compete with MyoD for the generation of active full-length E-protein:MyoD heterodimers. A forced heterodimer between MyoD and the full-length E12 robustly restores differentiation in rhabdomyosarcoma cells and broadly suppresses multiple inhibitory pathways. Our studies indicate that rhabdomyosarcomas represent an arrested progress through a normal transitional state that is regulated by the relative abundance of heterodimers between MyoD and the full-length E2A proteins. The demonstration that multiple inhibitory mechanisms can be suppressed and myogenic differentiation can be induced in the RD rhabdomyosarcomas by increasing the abundance of MyoD:E-protein heterodimers suggests a central integrating function that can be targeted to force differentiation in muscle cancer cells.
Can hormones contained in mothers’ milk account for the beneficial effect of breast‐feeding on obesity in children?
Authors: Savino Francesco , Fissore Maria F. , Liguori Stefania A. , Oggero Roberto
Published: March 2009

Nutrition and growth during infancy are an emerging issue because of their potential link to metabolic health disorders in later life. Moreover, prolonged breast‐feeding appears to be associated with a lower risk of obesity than formula feeding. Human milk is a source of various hormones and growth factors, namely adipokines (leptin and adiponectin), ghrelin, resistin and obestatin, which are involved in food intake regulation and energy balance. These compounds are either not found in commercial milk formulas or their presence is still controversial. Diet‐related differences during infancy in serum levels of factors involved in energy metabolism might explain anthropometric differences and also differences in dietary habits between breast‐fed (BF) and formula‐fed (FF) infants later in life, and may thus have long‐term health consequences. In this context, the recent finding of higher leptin levels and lower ghrelin levels in BF than in FF infants suggests that differences in hormonal values together with different protein intake could account for the differences in growth between BF and FF infants both during infancy and later in life. In this review, we examine the data related to hormones contained in mothers’ milk and their potential protective effect on subsequent obesity and metabolic‐related disorders.
Molecular composition and biological activity of commercial birch pollen allergen extracts
Authors: Focke M. , Marth K. , Valenta R.
Published: March 2009

Background  Commercial extracts used for diagnosis and treatment of allergy are currently prepared from natural allergen sources. The aim of this study was to analyse birch pollen allergen extracts produced for in vivo diagnosis of birch pollen allergy regarding their contents of individual birch pollen allergens (Bet v 1, Bet v 2 and Bet v 4).

Methods  Protein contents were measured and the allergen composition was analysed by immunoblotting using antibody probes specific for Bet v 1, Bet v 2 and Bet v 4 in birch pollen extracts from five manufacturers of allergen extracts. The contents of the major birch pollen allergen, Bet v 1, were quantified with a specific two‐site binding enzyme‐linked immunosorbent assay with nanogram sensitivity for Bet v 1. The biological activities of the allergen extracts were evaluated by skin prick testing in birch pollen allergic patients and compared with their sensitization profiles.

Results  A more than 10‐fold variation regarding total protein contents (23·1–314 μg mL−1) and also regarding the amounts of the major birch pollen allergen, Bet v 1 (1·62–19·6 μg mL−1) was found. The highly cross‐reactive Bet v 4 allergen was absent in three of the five tested extracts. Furthermore, varying skin test results were obtained in birch pollen allergic patients with the allergen extracts.

Conclusions  Commercial birch pollen extracts exhibit a considerable variability regarding allergen contents and hence deliver varying in vivo test results. These problems might be overcome with recombinant allergen‐based preparations.