bluuebunny/crossref_metadata_2025 huggingface dataset:
Swirl flow focusing: A novel procedure for the massive production of monodisperse microbubbles
Authors: Herrada Miguel A. , Gañán-Calvo Alfonso M.
Published: April 2009

A volume-of-fluid numerical method is used to predict the dynamics of microbubble formation in an axisymmetric flow-focusing microfluidic device for a gas-liquid system. Numerical results show that, in all the cases analyzed, the introduction of swirl into the focusing liquid stabilizes the tapering gas-liquid meniscus from which a steady gas ligament issues. Consequently, a drastic reduction in the size of bubbles generated by the device is achieved under similar gas and liquid flow rates.
A control approach to cross-coupling compensation of piezotube scanners in tapping-mode atomic force microscope imaging
Authors: Wu Ying , Shi Jian , Su Chanmin , Zou Qingze
Published: April 2009

In this article, an approach based on the recently developed inversion-based iterative control (IIC) to cancel the cross-axis coupling effect of piezoelectric tube scanners (piezoscanners) in tapping-mode atomic force microscope (AFM) imaging is proposed. Cross-axis coupling effect generally exists in piezoscanners used for three-dimensional (x-y-z axes) nanopositioning in applications such as AFM, where the vertical z-axis movement can be generated by the lateral x-y axes scanning. Such x/y-to-z cross-coupling becomes pronounced when the scanning is at large range and/or at high speed. In AFM applications, the coupling-caused position errors, when large, can generate various adverse effects, including large imaging and topography distortions, and damage of the cantilever probe and/or the sample. This paper utilizes the IIC technique to obtain the control input to precisely track the coupling-caused x/y-to-z displacement (with sign-flipped). Then the obtained input is augmented as a feedforward control to the existing feedback control in tapping-mode imaging, resulting in the cancellation of the coupling effect. The proposed approach is illustrated through two exemplary applications in industry, the pole-tip recession examination, and the nanoasperity measurement on hard-disk drive. Experimental results show that the x/y-to-z coupling effect in large-range (20 and 45 μm) tapping-mode imaging at both low to high scan rates (2, 12.2 to 24.4 Hz) can be effectively removed.
First-principles investigation of isomerization by proton transfer in β-fumaric acid crystal
Authors: Dopieralski P. , Panek J. , Latajka Z.
Published: April 2009

Crystal structure of fumaric acid was investigated by Car–Parrinello molecular dynamics and Path Integral molecular dynamics. We propose a mechanism of isomerization by proton transfer in the solid state. It is shown that the three conformers of fumaric acid observed in cryogenic Ar matrix are also present in the solid. Standard ab initio Car–Parrinello dynamics of the studied solid at 100 K indicates that barrier height for proton transfer is too high to enable thermal jump over the barrier. Path Integral method in this particular case significantly changes proton behavior in the hydrogen bridge, and the proton tunneling process is observed. Vibrational spectra of investigated system HOOC–CH=CH–COOH and its deuterated analog DOOC–CH=CH–COOD were calculated and compared with experimental data.
Analysis and classification of symmetry breaking in linear ABA-type triatomics
Authors: Li Xiangzhu , Paldus Josef
Published: April 2009

The symmetry of the nuclear framework of polyatomic molecules is qualitatively lowered by small changes in their geometry. This may lead to a dramatic change in the nature of their Hartree–Fock (HF) solutions and to a singular behavior of the corresponding potential energy surfaces (PESs), which may persist even at the correlated level if based on these HF references. We examine a general shape of the restricted HF (RHF) and open-shell RHF PESs for the linear triatomic molecules of the ABA type in the vicinity of the symmetric D2h geometries and the role played by the spin-restricted (singlet or doublet) stability of the corresponding HF solutions. This enabled us to classify the character of these surfaces into three basic types depending on the nature of the cut of the PES along the asymmetric stretching mode coordinate. We also examine the implications of the type of these nodes on the PES obtained at the post-HF correlated CCSD(T) level as well as on the determination of the vibrational frequencies for both the symmetric and asymmetric stretching modes. When using either the numerical differentiation of the PES or the solution of the Schrödinger equation for the nuclear motion for this purpose, it is shown that either method yields very good results for the symmetric mode frequencies, while the former approach may yield highly erroneous values for the asymmetric mode frequencies depending on the type of the HF PES at the equilibrium geometry in which case the latter approach still provides us with reasonably good results.
Three-dimensional fluence rate measurement and data acquisition system for minimally invasive light therapies
Authors: Lai Benjamin , Loshchenov Maxim , Douplik Alexander , Rusnov Rob , Jimenez-Davila Marcos , Netchev George , Lilge Lothar
Published: April 2009

Light based therapies such as photodynamic therapy are in need of advanced tools for light fluence rate dosimetry and monitoring within the context of therapy planning and light delivery to ensure maximum treatment efficacy. The use of a single, multisensor fiber-based fluorescent probe capable of performing spatially resolved fluence rate measurements along an axis was demonstrated. This work extends the previous technique and describes a fluence rate quantification system able to employ up to 12 multisensor probes to simultaneously measure fluence rate distribution throughout a 3D treatment volume. The system optoelectronics provides for sensor calibration, data acquisition, and weighted least-squares processing to extract localized fluence rate information in real-time. Core components include an integrating cylinder for source sensor calibration, a 2D back thin CCD detector for sensor signal detection from multiple probes, high-speed data acquisition card, and custom software for real-time extraction of fluence rate information from all sensors.
Observation of giant magnetoresistance and reversal of its sign upon boron filling in cubic TbPd3
Authors: Pandey Abhishek , Mazumdar Chandan , Ranganathan R.
Published: April 2009

We report the observation of negative giant magnetoresistance (GMR) in the cubic intermetallic compound TbPd3, which is largest (−30%) among the RPd3 series of compounds. On introducing the nonmagnetic element boron in the lattice of TbPd3, the GMR (+18%) changes sign from negative to positive in the resultant metallic perovskite compound TbPd3B. Addition of boron also significantly modifies the magnetic and electrical transport properties of the compound. The sign of the observed magnetoresistance can be interrelated with the sign of paramagnetic Curie temperature, suggesting close correlation between the magnetotransport behavior and the nature of the magnetic exchange interaction.
Soft x-ray emission, angular distribution of hot electrons, and absorption studies of argon clusters in intense laser pulses
Authors: Liu Yunquan , Dong Quanli , Peng Xiaoyu , Jin Zan , Zhang Jie
Published: April 2009

High resolution soft x-ray spectra (3–40 nm) produced by the interaction of intense femtosecond laser pulses with argon clusters at an intensity of about 1×1016 W/cm2 are measured under different backing pressures. Soft x-ray spectra are strongly dependent on the initial size of cluster and plasma expanding process. We find that laser polarization has no evident effect on the soft x-ray emission from the lateral side. The measurement on angular distribution of hot electrons shows that the resonant absorption is the dominated mechanism. Both the x-ray yield and the laser energy absorption are more efficient when the radius of cluster is comparable with the plasma resonant length.
Single-shot coherent detection of terahertz pulse with broadband spectral coverage
Authors: Hu Guang-yue , Lei An-le , Shen Baifei , Li Ru-xin , Xu Zhi-zhan
Published: April 2009

A new scheme using centrosymmetric materials as sensor medium is presented for the single-shot coherence detection of terahertz pulse. The method relies on the electric-field-induced optical second-harmonic generation with linearly chirped optical probe pulse in centrosymmetric medium. The terahertz field is encoded onto the frequency spectrum of the second-harmonic pulse and then decoded with appropriate retrieval algorithm. This approach provides a broadband coherent spectroscopic measurement that can cover the entire terahertz gap and has transform-limited temporal resolution, which is mainly limited by the spectral bandwidth of the optical probe pulse. It can be used widely in the experiments of high field plasma physics and the diagnostics of warm dense plasmas.
Density functional study of chemical reaction equilibrium for dimerization reactions in slit and cylindrical nanopores
Authors: Malijevský Alexandr , Lísal Martin
Published: April 2009

We present a theoretical study of the effects of confinement on chemical reaction equilibrium in slit and cylindrical nanopores. We use a density functional theory (DFT) to investigate the effects of temperature, pore geometry, bulk pressure, transition layering, and capillary condensation on a dimerization reaction that mimics the nitric oxide dimerization reaction, 2NO⇌(NO)2, in carbonlike slit and cylindrical nanopores in equilibrium with a vapor reservoir. In addition to the DFT calculations, we also utilize the reaction ensemble Monte Carlo method to supplement the DFT results for reaction conversion. This work is an extension of the previous DFT study by Tripathi and Chapman [J. Chem. Phys. 118, 7993 (2003)] on the dimerization reactions confined in the planar slits.
On the effect of Al2O3 blocking layer on the performance of dye solar cells with cobalt based electrolytes
Authors: Liberatore M. , Burtone L. , Brown T. M. , Reale A. , Di Carlo A. , Decker F. , Caramori S. , Bignozzi C. A.
Published: April 2009

Dye solar cells with Co(III)/Co(II) redox mediators have been prepared. To obtain higher conversion efficiencies, the recombination between photoinjected electrons and Co(III) species was minimized by deposition of a thin Al2O3 blocking layer over the mesoporous TiO2 surface. Measurements of current-voltage characteristic curves, both under illumination and in dark conditions, together with electrochemical impedance spectroscopy demonstrate the great effectiveness of the addition of a blocking layer in cells containing cobalt based electrolyte, by substantially reducing the recombination current. The consequent power conversion efficiency increase is more than double, passing from 0.94% to 2.48% under 300 W m−2 AM 1.5 illumination.
The perfect absorber
Authors: Driessen E. F. C. , de Dood M. J. A.
Published: April 2009

We demonstrate that films of very lossy metal or dielectric, with a thickness of only a few nanometers, can absorb almost all incident radiation when illuminated from the substrate side at the critical angle for total internal reflection. The absorption for s-polarized light approaches 100%, while the absorption for p-polarized light vanishes. We demonstrate this effect by measuring the absorption as a function of the angle of incidence at a wavelength of 775 nm in a 4.5 nm thick NbN film with a dielectric constant ϵNbN=−8.2+31.4i. The measured absorption in this film reaches a maximum of 94%. We discuss the design of a near-unity efficiency single-photon detector for s-polarized light that has a broadband absorption coefficient of >90% for wavelengths from 700 to 1600 nm.
Electronic structure and vacancy formation of Li3N
Authors: Wu Shunnian , Dong Zhili , Boey Freddy , Wu Ping
Published: April 2009

The electronic structure and vacancy formation of Li3N were studied using first principles methods. We found Li3N exhibits strong ionic character with slight covalent bonding between N and Li. The Li vacancy formation energy decreases with an increase in nitrogen partial pressure, while the N vacancy formation energy increases with increasing nitrogen partial pressure. The Li(2) site vacancy is found to have the lowest formation energy under nitrogen-rich conditions. Formation of VLi(2)− brings about delocalization of valence electrons, and reduces the band gap by 0.2 eV. These results suggest potential ways to enhance vacancy concentration in Li3N for higher ionic conductivity.
Parametric amplification in GaAs/AlOx waveguide
Authors: Guillotel E. , Ravaro M. , Ghiglieno F. , Langlois C. , Ricolleau C. , Ducci S. , Favero I , Leo G.
Published: April 2009

We report the direct proof of parametric amplification in a semiconductor waveguide. Thanks to low propagation losses and high nonlinear efficiency, we amplified an input signal at 2 μm in a selectively oxidized GaAs/AlAs multilayer waveguide through the down conversion of a pump at 1 μm. The 4.5% single-pass gain measured for a 30 mW cw pump is compatible with parametric oscillation, provided that distributed and concentrated waveguide losses are further reduced.
Nanopatterning by solid-state dewetting on reconstructed ceramic surfaces
Authors: Basu Joysurya , Carter C. Barry , Divakar R. , Mukherjee B. , Ravishankar N.
Published: April 2009

We demonstrate ordered array formation of Au nanoparticles by controlled solid-state dewetting of a metal film on stepped alumina substrates. In situ transmission electron microscopy studies reveal that the dewetting process starts with nucleation of ordered dry regions on the substrate. The chemical potential difference between concave and convex surface regions induces anisotropic metal diffusion leading to the formation of nanowires in the valleys. The nanowires fragment due to Rayleigh instability forming arrays of metal nanoparticles on the substrate. The length scale of reconstruction relative to the starting film thickness is an important parameter in controlling the spatial order of the nanoparticles.
Ferromagnetic, ferroelectric, and fatigue behavior of (111)-oriented BiFeO3/(Bi1/2Na1/2)TiO3 lead-free bilayered thin films
Authors: Wu Jiagang , Kang Guangqing , Liu Huajun , Wang John
Published: April 2009

Lead-free bilayered thin films consisting of BiFeO3 (BFO) and (Bi1/2Na1/2)TiO3 (BNT) nanolayers were deposited on the Pt/TiO2/SiO2/Si substrate by radio frequency sputtering. The bilayered BFO/BNT film exhibits a strong (111) orientation and much enhanced ferroelectric and magnetic properties (2Pr=52.2 μC/cm2, 2Ec=554.0 kV/cm, 2Ms=96.0 emu/cm3, and 2Hc=253.2 Oe) as compared to those of the single layer BNT and BFO thin films, together with an almost fatigue-free polarization behavior. Although space charges occur at the interface between the constituent nanolayers, as confirmed by the frequency dispersion of capacitance, the bottom BNT nanolayer appears to promote the growth and crystallization of BFO layer, largely responsible for the observed ferroelectric and magnetic behavior.
Three-dimensional imaging of director field orientations in liquid crystals by polarized four-wave mixing microscopy
Authors: Chen Bi-Chang , Lim Sang-Hyun
Published: April 2009

We report that nondegenerate four-wave mixing (FWM) signals from liquid crystals (LCs) excited by near IR ultrafast pulses can probe local molecular orientations of LCs. The two laser pulses are selected out of a single broadband Ti:sapphire laser by a pulse shaper and focused on LC samples to generate strong FWM signals. We demonstrate laser-scanning FWM microscopy with topological defects in a smectic A LC material. The image contrast originates from the anisotropic nonlinear response of LC molecules and the high signal sensitivity allows fast depth-resolved imaging.
Deformation mechanisms and strength in nanoscale multilayer metallic composites with coherent and incoherent interfaces
Authors: Mastorakos Ioannis N. , Zbib Hussein M. , Bahr David F.
Published: April 2009

We investigate the deformation behavior of bimetallic and trimetallic nanoscale multilayer metallic composites under biaxial loading using molecular dynamics. Three types of structures were studied: (a) Cu–Ni fcc/fcc bilayer, (b) Cu–Nb fcc/bcc bilayer, and (c) Ni–Cu–Nb fcc/fcc/bcc trilayer. A configuration with a dislocation structure inside is generated by initially loading a perfect structure to a high strain to nucleate dislocations, then completely unloading it and loading it again. The comparison between the deformation behavior of bilayer and trilayer structures revealed that the Cu–Ni is more ductile, the Cu–Nb is stronger, and the trilayer structure exhibits both high strength and ductility.
Development of Color-Grapheme Synesthesia and its Effect on Mathematical Operations
Authors: Mills Carol Bergfeld , Metzger Shari R , Foster Catherine A , Valentine-Gresko Melaina N , Ricketts Stephanie
Published: April 2009

SE, a 19-year-old female college student and a color–grapheme synesthete, reported consistent synesthetic experiences (photisms) for digits, and most letters in the Roman and Hebrew alphabets over a 6-month period. Photisms for later-learned Hebrew letters were influenced by those of the Roman alphabet and photisms for auditorily presented words were influenced by the spelling of the words. As hypothesized, in two studies, SE's solution times for addition problems were significantly slower when the colors of the digits in the problems mismatched her synesthetic photisms than when they matched or were in black ( p < 0.001), whereas color had no effect on solution times for six female non-synesthetes (aged 19 to 22 years). Implications for learning and cognitive processing are discussed.
A review of radio and acoustic telemetry studies of freshwater fish in New Zealand
Authors: Jellyman Don
Published: April 2009

Radio and acoustic telemetry have been used in 24 studies of freshwater fish in New Zealand. Although most native species are too small to carry these tags, studies using telemetry have been carried out on four of the larger species, i.e. lampreys (Geotria australis), shortfin and longfin eels (Anguilla australis and A. dieffenbachii) and giant kokopu (Galaxias argenteus). Among the introduced species, telemetry has been used to study movements of brown and rainbow trout (Salmo trutta and Oncorhynchus mykiss) in both rivers and lakes, chinook salmon (Oncorhynchus tshawytscha), koi carp (Cyprinus carpio) and bullhead catfish (Ameiurus nebulosus). To date, studies have almost exclusively been of short-term movements and seasonal migrations. Study objectives range from measuring microhabitats and home ranges to determining the extent of seasonal spawning migrations. The advent of progressively smaller tags will provide increased opportunities to use this technology on a wider range of fish species. Management implications of several studies are presented. Although biotelemetry studies have not yet been used in New Zealand, there are considerable opportunities for using such technology to increase understanding of fish energetics and also stress associated with catch-and-release practices in recreational fishing.
Retention of intra-peritoneal transmitters and post-operative recovery of four Australian native fish species
Authors: Butler Gavin L. , Mackay Brad , Rowland Stuart J. , Pease Bruce C.
Published: April 2009

Regulation of the world’s rivers has permanently altered the natural flow regime in many systems. Australia’s rivers have also been subject to extensive modification; however, little is known of the effect altered flows have on many native fish species. Active transmitters offer an effective method of monitoring fish movement but there is little information on tag retention and post-tagging survival for most Australian species. Four fish species from the north-eastern rivers of New South Wales were surgically implanted with dummy transmitters to determine retention and incision healing rates. Eel-tailed catfish (Tandanus tandanus) were implanted with three types of dummy radio transmitters and the transmitter with the shortest externally exited antenna is recommended. In Australian bass (Macquaria novemaculeata), low water temperature, abdominal distention in females and the breakdown of dissolvable sutures contributed to the expulsion of dummy acoustic transmitters. Freshwater mullet (Myxus petardi) and sea mullet (Mugil cephalus) were implanted with dummy acoustic transmitters and healing rates were different between the two species. The present study demonstrated species specificity in tag suitability and recovery rates, the advantages of quarantining fish before release following the surgical implantation of transmitters and the value of controlled experiments to determine optimal transmitter design and post-operative conditions.
Electrophoretic analysis of Geoffroea (Leguminosae, Papilionoideae): taxonomic inferences in Argentinean populations
Authors: Lamarque Alicia L. , Labuckas Diana O. , Greppi Julián , Fortunato Renée H.
Published: April 2009

The genus Geoffroea Jacq. was circumscribed to two species without varietal division. Nevertheless, in the taxonomic treatment of Argentinean dry-forest flora, on the basis of habit and foliar and floral features, it was possible to distinguish G. decorticans (Hook. & Arn.) Burkart var. decorticans from var. subtropicalis (Lillo) Burkart and to recognise intraspecific variation among the populations of G. spinosa. The purposes of the present study were to provide seed-protein data of Geoffroea species, and to analyse the relationships among them. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) was carried out on mature seeds harvested at different locations. Electrophoretic profile analysis showed outstanding differences between G. decorticans var. decorticans and var. subtropicalis and supported the view that these two taxa are less closely related than previously assumed, warranting their recognition at the varietal level. Moreover, attentive to the differences in the protein patterns from the analysed population of G. spinosa (Argentina: Chaco and Salta provinces), in addition to phenotypic differences, materials from other disjunct areas where this species grows need to be studied to verify their taxonomic status.
Flg22 regulates the release of an ethylene response factor substrate from MAP kinase 6 in
Arabidopsis thaliana
via ethylene signaling
Authors: Bethke Gerit , Unthan Tino , Uhrig Joachim F. , Pöschl Yvonne , Gust Andrea A. , Scheel Dierk , Lee Justin
Published: April 2009

Mitogen-activated protein kinase (MAPK)–mediated responses are in part regulated by the repertoire of MAPK substrates, which is still poorly elucidated in plants. Here, the in vivo enzyme–substrate interaction of the
Arabidopsis thaliana
MAP kinase, MPK6, with an ethylene response factor (ERF104) is shown by fluorescence resonance energy transfer. The interaction was rapidly lost in response to flagellin-derived flg22 peptide. This complex disruption requires not only MPK6 activity, which also affects ERF104 stability via phosphorylation, but also ethylene signaling. The latter points to a novel role of ethylene in substrate release, presumably allowing the liberated ERF104 to access target genes. Microarray data show enrichment of GCC motifs in the promoters of ERF104–up-regulated genes, many of which are stress related. ERF104 is a vital regulator of basal immunity, as altered expression in both
erf104
and overexpressors led to more growth inhibition by flg22 and enhanced susceptibility to a non-adapted bacterial pathogen.
Heavy holes as a precursor to superconductivity in antiferromagnetic CeIn
3
Authors: Sebastian Suchitra E. , Harrison N. , Batista C. D. , Trugman S. A. , Fanelli V. , Jaime M. , Murphy T. P. , Palm E. C. , Harima H. , Ebihara T.
Published: April 2009

Numerous phenomenological parallels have been drawn between
f
- and
d
- electron systems in an attempt to understand their display of unconventional superconductivity. The microscopics of how electrons evolve from participation in large moment antiferromagnetism to superconductivity in these systems, however, remains a mystery. Knowing the origin of Cooper paired electrons in momentum space is a crucial prerequisite for understanding the pairing mechanism. Of special interest are pressure-induced superconductors CeIn
3
and CeRhIn
5
in which disparate magnetic and superconducting orders apparently coexist—arising from within the same
f
-electron degrees of freedom. Here, we present ambient pressure quantum oscillation measurements on CeIn
3
that crucially identify the electronic structure—potentially similar to high-temperature superconductors. Heavy hole pockets of
f
-character are revealed in CeIn
3
, undergoing an unexpected effective mass divergence well before the antiferromagnetic critical field. We thus uncover the softening of a branch of quasiparticle excitations located away from the traditional spin fluctuation-dominated antiferromagnetic quantum critical point. The observed Fermi surface of dispersive
f
-electrons in CeIn
3
could potentially explain the emergence of Cooper pairs from within a strong moment antiferromagnet.
Isoenzyme replacement of glucose-6-phosphate dehydrogenase in the cytosol improves stress tolerance in plants
Authors: Scharte Judith , Schön Hardy , Tjaden Zeina , Weis Engelbert , von Schaewen Antje
Published: April 2009

In source leaves of resistant tobacco, oxidative burst and subsequent formation of hypersensitive lesions after infection with
Phytophthora nicotianae
was prevented by inhibition of glucose-6-phosphate dehydrogenase (G6PDH) or NADPH oxidases. This observation indicated that plant defense could benefit from improved NADPH availability due to increased G6PDH activity in the cytosol. A plastidic isoform of the G6PDH-encoding gene,
G6PD
, displaying high NADPH tolerance was engineered for cytosolic expression (cP2), and introduced into a susceptible cultivar. After infection, transgenic (previously susceptible) lines overexpressing cP2 showed early oxidative bursts, callose deposition, and changes in metabolic parameters. These responses resulted in timely formation of hypersensitive lesions similar to resistant plants, although their extent varied considerably between different transgenic lines. Additional RNAi suppression of endogenous cytosolic
G6PD
isoforms resulted in highly uniform defense responses and also enhanced drought tolerance and flowering. Cytosolic G6PDH seems to be a crucial factor for the outcome of plant defense responses; thus, representing an important target for modulation of stress resistance. Because isoenzyme replacement of G6PDH in the cytosol was beneficial under various kinds of cues, we propose this strategy as a tool to enhance stress tolerance in general.
Dynamic hybrid materials for constitutional self-instructed membranes
Authors: Cazacu Adinela , Legrand Yves-Marie , Pasc Andreea , Nasr Gihane , Van der Lee Arie , Mahon Eugene , Barboiu Mihail
Published: April 2009

Constitutional self-instructed membranes were developed and used for mimicking the adaptive structural functionality of natural ion-channel systems. These membranes are based on dynamic hybrid materials in which the functional self-organized macrocycles are reversibly connected with the inorganic silica through hydrophobic noncovalent interactions. Supramolecular columnar ion-channel architectures can be generated by reversible confinement within scaffolding hydrophobic silica mesopores. They can be structurally determined by using X-ray diffraction and morphologically tuned by alkali-salts templating. From the conceptual point of view, these membranes express a synergistic adaptive behavior: the simultaneous binding of the fittest cation and its anion would be a case of “homotropic allosteric interactions,” because in time it increases the transport efficiency of the pore-contained superstructures by a selective evolving process toward the fittest ion channel. The hybrid membranes presented here represent dynamic constitutional systems evolving over time to form the fittest ion channels from a library of molecular and supramolecular components, or selecting the fittest ion pairs from a mixture of salts demonstrating flexible adaptation.
The effect of network topology on the stability of discrete state models of genetic control
Authors: Pomerance Andrew , Ott Edward , Girvan Michelle , Losert Wolfgang
Published: April 2009

Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed uncorrelated random network structure. Real gene networks typically have nontrivial topology significantly different from the random network paradigm. To address such situations, we present a general method for determining the stability of large Boolean networks of any specified network topology and predicting their steady-state behavior in response to small perturbations. Additionally, we generalize to the case where individual genes have a distribution of “expression biases,” and we consider a nonsynchronous update, as well as extension of our method to non-Boolean models in which there are more than two possible gene states. We find that stability is governed by the maximum eigenvalue of a modified adjacency matrix, and we test this result by comparison with numerical simulations. We also discuss the possible application of our work to experimentally inferred gene networks.
Endogenous expression of Hras
G12V
induces developmental defects and neoplasms with copy number imbalances of the oncogene
Authors: Chen Xu , Mitsutake Norisato , LaPerle Krista , Akeno Nagako , Zanzonico Pat , Longo Valerie A. , Mitsutake Shin , Kimura Edna T. , Geiger Hartmut , Santos Eugenio , Wendel Hans G. , Franco Aime , Knauf Jeffrey A. , Fagin James A.
Published: April 2009

We developed mice with germline endogenous expression of oncogenic
Hras
to study effects on development and mechanisms of tumor initiation. They had high perinatal mortality, abnormal cranial dimensions, defective dental ameloblasts, and nasal septal deviation, consistent with some of the features of human Costello syndrome. These mice developed papillomas and angiosarcomas, which were associated with

Hras
G12V

allelic imbalance and augmented Hras signaling. Endogenous expression of Hras
G12V
was also associated with a higher mutation rate in vivo. Tumor initiation by Hras
G12V
likely requires augmentation of signal output, which in papillomas and angiosarcomas is achieved via increased
Hras
-gene copy number, which may be favored by a higher mutation frequency in cells expressing the oncoprotein.
ISG56 is a negative-feedback regulator of virus-triggered signaling and cellular antiviral response
Authors: Li Ying , Li Chao , Xue Peng , Zhong Bo , Mao Ai-Ping , Ran Yong , Chen He , Wang Yan-Yi , Yang Fuquan , Shu Hong-Bing
Published: April 2009

IFN-stimulated gene 56 (ISG56) is one of the first identified proteins induced by viruses and type I IFNs. In this study, we identified ISG56 as a virus-induced protein associated with MITA, an adapter protein involved in virus-triggered induction of type I IFNs. Overexpression of ISG56 inhibited Sendai virus-triggered activation of IRF3, NF-κB, and the IFN-β promoter, whereas knockdown of ISG56 had opposite effects. Consistently, overexpression of ISG56 reversed cytoplasmic poly(I:C)-induced inhibition of vesicular stomatitis virus (VSV) replication, whereas knockdown of ISG56 inhibited VSV replication. Competitive coimmunoprecipitation experiments indicated that ISG56 disrupted the interactions between MITA and VISA or TBK1, two components in the virus-triggered IFN signaling pathways. These results suggest that ISG56 is a mediator of negative-feedback regulation of virus-triggered induction of type I IFNs and cellular antiviral responses.
Evolution of cooperation by phenotypic similarity
Authors: Antal Tibor , Ohtsuki Hisashi , Wakeley John , Taylor Peter D. , Nowak Martin A.
Published: April 2009

The emergence of cooperation in populations of selfish individuals is a fascinating topic that has inspired much work in theoretical biology. Here, we study the evolution of cooperation in a model where individuals are characterized by phenotypic properties that are visible to others. The population is well mixed in the sense that everyone is equally likely to interact with everyone else, but the behavioral strategies can depend on distance in phenotype space. We study the interaction of cooperators and defectors. In our model, cooperators cooperate with those who are similar and defect otherwise. Defectors always defect. Individuals mutate to nearby phenotypes, which generates a random walk of the population in phenotype space. Our analysis brings together ideas from coalescence theory and evolutionary game dynamics. We obtain a precise condition for natural selection to favor cooperators over defectors. Cooperation is favored when the phenotypic mutation rate is large and the strategy mutation rate is small. In the optimal case for cooperators, in a one-dimensional phenotype space and for large population size, the critical benefit-to-cost ratio is given by

b
/
c
=
1
+
2
/

3

. We also derive the fundamental condition for any two-strategy symmetric game and consider high-dimensional phenotype spaces.
Many different Vβ CDR3s can reveal the inherent MHC reactivity of germline-encoded TCR V regions
Authors: Rubtsova Kira , Scott-Browne James P. , Crawford Frances , Dai Shaodong , Marrack Philippa , Kappler John W.
Published: April 2009

We have hypothesized that in the prenegative selection TCR repertoire, many somatically generated complementary-determining region (CDR) 3 loops combine with evolutionarily selected germline Vα/Vβ CDR1/CDR2 loops to create highly MHC/peptide cross-reactive T cells that are subsequently deleted by negative selection. Here, we present a mutational analysis of the Vβ CDR3 of such a cross-reactive T-cell receptor (TCR), YAe62. Most YAe62 TCRs with the mutant CDR3s became less MHC promiscuous. However, others with CDR3s unrelated in sequence to the original recognized even more MHC alleles than the original TCR. Most importantly, this recognition was still dependent on the conserved CDR1/CDR2 residues. These results bolster the idea that germline TCR V elements are inherently reactive to MHC but that this reactivity is fine-tuned by the somatically generated CDR3 loops.
Characterizing the resistance generated by a molecular bond as it is forcibly separated
Authors: Freund L. B.
Published: April 2009

The goal of measurements of the resisting force generated by a molecular bond as it is being forcibly separated under controlled conditions is to determine functional characteristics of the bond. Here, we establish the dependence of force history during unbinding on both those parameters chosen to characterize the bond itself and the controllable loading parameters. This is pursued for the practical range of behavior in which unbinding occurs diffusively rather than ballistically, building on the classic work of Kramers. For a bond represented by a one-dimensional energy landscape, modified by a second time-dependent energy profile representing applied loading, we present a mathematical analysis showing the dependence of the resistance of the bond-on-bond well shape, general time dependence of the imposed loading, and stiffness of the loading apparatus. The quality of the result is established through comparison with full numerical solutions of the underlying Smoluchowski equation.
Genetic dissection of histone deacetylase requirement in tumor cells
Authors: Haberland Michael , Johnson Aaron , Mokalled Mayssa H. , Montgomery Rusty L. , Olson Eric N.
Published: April 2009

Histone deacetylase inhibitors (HDACi) represent a new group of drugs currently being tested in a wide variety of clinical applications. They are especially effective in preclinical models of cancer where they show antiproliferative action in many different types of cancer cells. Recently, the first HDACi was approved for the treatment of cutaneous T cell lymphomas. Most HDACi currently in clinical development act by unspecifically interfering with the enzymatic activity of all class I HDACs (HDAC1, 2, 3, and 8), and it is widely believed that the development of isoform-specific HDACi could lead to better therapeutic efficacy. The contribution of the individual class I HDACs to different disease states, however, has so far not been fully elucidated. Here, we use a genetic approach to dissect the involvement of the different class I HDACs in tumor cells. We show that deletion of a single HDAC is not sufficient to induce cell death, but that HDAC1 and 2 play redundant and essential roles in tumor cell survival. Their deletion leads to nuclear bridging, nuclear fragmentation, and mitotic catastrophe, mirroring the effects of HDACi on cancer cells. These findings suggest that pharmacological inhibition of HDAC1 and 2 may be sufficient for anticancer activity, providing an experimental framework for the development of isoform-specific HDAC inhibitors.
STATES AS MOLDERS OF INFORMAL RELATIONS?
Authors: van der Meer Thomas , Scheepers Peer , te Grotenhuis Manfred
Published: April 2009

This article studies the impact of a range of state institutions on citizens’ contacts with family and close friends in 20 countries. Recent studies have shown large country level differences in social participation. We aim to explain these differences from an actor centered institutionalist perspective. We present two lines of reasoning. According to the first, a high level of social security crowds out social participation, as intimate networks are no longer needed as an economic safety net. The second line of reasoning proposes that corruption or a lack of civil rights drive citizens to seek refuge in their secure intimate contacts. In a comparative, multi-level design we focus on participation in the nuclear family, in the extended family, and with the best friend. We test the two lines of reasoning simultaneously on ISSP 2001 data. We find that states matter. State institutions are an important determinant of social participation. Our findings mainly confirm the second line of reasoning, whereas the crowding out thesis is only supported for contact with the extended family. Moreover, we find that the contextual effects are not similar across social groups: the poor are more strongly affected by the institutional design than the rich.
THE WELFARE STATE AND SOCIAL CAPITAL INEQUALITY
Authors: van Oorschot Wim , Finsveen Ellen
Published: April 2009

In this paper we theoretically and empirically explore the question whether the unequal distribution of different aspects of social capital (networks, trust, norms) over a number of social dimensions (gender, age, income, employment status, and educational level) is smaller in countries with more developed welfare systems. Our data cover 13 Western industrialized countries and two periods in time (1981, 1999). The paper adds to the existing literature in several ways: by focusing explicitly on the empirical study of social capital inequality, by relating this subject to (quantitative and qualitative) welfare state characteristics, and by studying it from a cross-national and longitudinal perspective. We find that in the sample of countries analyzed there is no clear relationship between social capital inequality and welfare state characteristics. However, whether generally welfare states do not reduce social capital inequalities remains an issue for future research.
Performance projections for the lithium tokamak experiment (LTX)
Authors: Majeski R. , Berzak L. , Gray T. , Kaita R. , Kozub T. , Levinton F. , Lundberg D.P. , Manickam J. , Pereverzev G.V. , Snieckus K. , Soukhanovskii V. , Spaleta J. , Stotler D. , Strickler T. , Timberlake J. , Yoo J. , Zakharov L.
Published: April 2009

Use of a large-area liquid lithium limiter in the CDX-U tokamak produced the largest relative increase (an enhancement factor of 5–10) in Ohmic tokamak confinement ever observed. The confinement results from CDX-U do not agree with existing scaling laws, and cannot easily be projected to the new lithium tokamak experiment (LTX). Numerical simulations of CDX-U low recycling discharges have now been performed with the ASTRA-ESC code with a special reference transport model suitable for a diffusion-based confinement regime, incorporating boundary conditions for nonrecycling walls, with fuelling via edge gas puffing. This model has been successful at reproducing the experimental values of the energy confinement (4–6 ms), loop voltage (<0.5 V), and density for a typical CDX-U lithium discharge. The same transport model has also been used to project the performance of the LTX, in Ohmic operation, or with modest neutral beam injection (NBI). NBI in LTX, with a low recycling wall of liquid lithium, is predicted to result in core electron and ion temperatures of 1–2 keV, and energy confinement times in excess of 50 ms. Finally, the unique design features of LTX are summarized.
Burning plasma simulation and environmental assessment of tokamak, spherical tokamak and helical reactors
Authors: Yamazaki K. , Uemura S. , Oishi T. , Garcia J. , Arimoto H. , Shoji T.
Published: April 2009

Reference 1-GWe DT reactors (tokamak TR-1, spherical tokamak ST-1 and helical HR-1 reactors) are designed using physics, engineering and cost (PEC) code, and their plasma behaviours with internal transport barrier operations are analysed using toroidal transport analysis linkage (TOTAL) code, which clarifies the requirement of deep penetration of pellet fuelling to realize steady-state advanced burning operation. In addition, economical and environmental assessments were performed using extended PEC code, which shows the advantage of high beta tokamak reactors in the cost of electricity (COE) and the advantage of compact spherical tokamak in life-cycle CO2 emission reduction. Comparing with other electric power generation systems, the COE of the fusion reactor is higher than that of the fission reactor, but on the same level as the oil thermal power system. CO2 reduction can be achieved in fusion reactors the same as in the fission reactor. The energy payback ratio of the high-beta tokamak reactor TR-1 could be higher than that of other systems including the fission reactor.
Advances in singly connected closed field line plasma devices and extrapolation to POP level experiments and reactors
Authors: Hoffman A.L. , Steinhauer L.C. , Ferrari H. , Farengo R.
Published: April 2009

Recent advances in creating stable, hot, steady-state field-reversed-configuration (FRC) plasmas using rotating magnetic fields (RMFs) have made this an appropriate time for re-examining the old field-reversed-mirror concept. The reactor advantages of such a linear, naturally high beta configuration would be enormous, but previous attempts to produce field reversal using tangential neutral beam injection (TNBI) alone were unsuccessful. Simple scalable extensions of present RMF produced FRCs can result in ideal traps for TNBI produced energetic ions, and detailed calculations show high efficiencies of TNBI production of energetic ion rings within such FRCs. If non-standard MHD effects such as strong flow and highly energetic ions are able to extend FRC stability to larger sizes, then the principal need will be to reduce present high values of anomalous cross-field resistivity. Experimental trends show how this may be achieved, and the present experimental and theoretical status of the most basic issues of FRC stability, confinement, and current drive are summarized, along with the new calculations on TNBI. The parameters for a modest sized ‘proof-of-principle’ (POP) device which can address these basic issues, as well as provide enough flux for efficient TNBI trapping, are given.
R&D of a Li2TiO3 pebble bed for a test blanket module in JAEA
Authors: Tanigawa H. , Hoshino T. , Kawamura Y. , Nakamichi M. , Ochiai K. , Akiba M. , Ando M. , Enoeda M. , Ezato K. , Hayashi K. , Hirose T. , Konno C. , Nakamura H. , Nozawa T. , Ogiwara H. , Seki Y. , Tanigawa H. , Tsuchiya K. , Tsuru D. , Yamanishi T.
Published: April 2009

At JAEA, a test blanket module (TBM) with a water-cooled solid breeder is being developed. This paper presents recent achievements of research activities for the TBM, particularly addressing the pebble bed of the tritium breeder materials and tritium behaviour. For the breeder material, the chemical stability of Li2TiO3 was improved using Li2O additives. To analyse the pebble bed behaviour, thermomechanical properties of the Li2TiO3 pebble bed were assessed experimentally. To verify the pebble bed's nuclear properties, the activation foil method was proposed and a preliminary experiment was conducted. To reduce the tritium permeation, the chemical densified coating method was developed and the coating was attached to F82H steel. For tritium behaviour, the tritium recovery system was modified in consideration of the design change of the TBM.
The Class V Myosin Myo2p Is Required for Fus2p Transport and Actin Polarization during the Yeast Mating Response
Authors: Sheltzer Jason M. , Rose Mark D.
Published: April 2009

Mating yeast cells remove their cell walls and fuse their plasma membranes in a spatially restricted cell contact region. Cell wall removal is dependent on Fus2p, an amphiphysin-associated Rho-GEF homolog. As mating cells polarize, Fus2p-GFP localizes to the tip of the mating projection, where cell fusion will occur, and to cytoplasmic puncta, which show rapid movement toward the tip. Movement requires polymerized actin, whereas tip localization is dependent on both actin and a membrane protein, Fus1p. Here, we show that Fus2p-GFP movement is specifically dependent on Myo2p, a type V myosin, and not on Myo4p, another type V myosin, or Myo3p and Myo5p, type I myosins. Fus2p-GFP tip localization and actin polarization in shmoos are also dependent on Myo2p. A temperature-sensitive tropomyosin mutation and Myo2p alleles that specifically disrupt vesicle binding caused rapid loss of actin patch organization, indicating that transport is required to maintain actin polarity. Mutant shmoos lost actin polarity more rapidly than mitotic cells, suggesting that the maintenance of cell polarity in shmoos is more sensitive to perturbation. The different velocities, differential sensitivity to mutation and lack of colocalization suggest that Fus2p and Sec4p, another Myo2p cargo associated with exocytotic vesicles, reside predominantly on different cellular organelles.
Clustering of Syndecan-4 and Integrin β1 by Laminin α3 Chain–derived Peptide Promotes Keratinocyte Migration
Authors: Araki Eri , Momota Yutaka , Togo Takeshi , Tanioka Miki , Hozumi Kentaro , Nomizu Motoyoshi , Miyachi Yoshiki , Utani Atsushi
Published: April 2009

Syndecans function as receptors for extracellular matrix (ECM) with integrins in cell spreading. However, the molecular mechanism of their specific involvement in cell migration or in wound healing has not been elucidated yet. Here, we report that a synthetic peptide, PEP75, which contains the syndecan-binding sequence of the laminin α3LG4 module, induces keratinocyte migration in in vitro and in vivo. Soluble PEP75 induced the clustering of syndecan-4 and conformation-modified integrin β1 colocalized with syndecan-4 in soluble PEP75-induced clusters. Treatment of cells in solution with PEP75 resulted in the exposure of the P4G11 antibody epitope of integrin β1 in immunostaining as well as in flow cytometry and augmented integrin β1–dependent cell adhesion to ECM. Pulldown assays demonstrated that PEP75 bound to syndecan-4, but not to integrin β1. A siRNA study revealed a role for syndecan-4 in PEP75-induced up-regulation of P4G11 antibody binding and migration of HaCaT cells. We conclude that binding of soluble PEP75 to syndecan-4 induces the coupling of integrin β1, which is associated with integrin β1-conformational changes and activation, and leads to keratinocyte migration. To activate integrin function through syndecans could be a novel therapeutic approach for chronic wound.