bluuebunny/crossref_metadata_2025 huggingface dataset:
Actin cytoskeleton in Arabidopsis thaliana under blue and red light
Authors: Krzeszowiec Weronika , Rajwa Bartek , Dobrucki Jurek , Gabryś Halina
Published: April 2007

Background information. Actin cytoskeleton is the basis of chloroplast‐orientation movements. These movements are activated by blue light in the leaves of terrestrial angiosperms. Red light has been shown to affect the spatial reorganization of F‐actin in water plants, where chloroplast movements are closely connected with cytoplasmic streaming. The aim of the present study was to determine whether blue light, which triggers characteristic responses of chloroplasts, i.e. avoidance and accumulation, also influences F‐actin organization in the mesophyll cells of Arabidopsis thaliana. Actin filaments in fixed mesophyll tissue were labelled with Alexa Fluor® 488‐conjugated phalloidin. The configuration of actin filaments, expressed as a form factor (4π·area/perimeter2), was determined for all actin formations which were measured in fluorescence confocal images.

Results. In the present study, we compare form‐factor distributions and the median form factors for strong and weak, blue‐ and red‐irradiated tissues. Spatial organization of the F‐actin network did not undergo any changes which could be attributed specifically to blue light. Actin patterns were similar in blue‐irradiated wild‐type plants and phot2 (phototropin 2) mutants which lack the avoidance response of chloroplasts. However, significant differences in the shape and distribution of F‐actin formations were observed between mesophyll cells of phot2 mutants irradiated with strong and weak red light. These differences were absent in wild‐type leaves.

Conclusions. Actin does not appear to be the main target for the blue‐light chloroplast‐orientation signal. The modes of actin involvement in chloroplast translocations are different in water and terrestrial angiosperms. The results suggest that co‐operation occurs between blue‐ and red‐light photoreceptors in the control of the actin cytoskeleton architecture in Arabidopsis.
Expression of the Longin domain of TI‐VAMP impairs lysosomal secretion and epithelial cell migration
Authors: Proux‐Gillardeaux Véronique , Raposo Graça , Irinopoulou Theano , Galli Thierry
Published: April 2007

Background information. TI‐VAMP (tetanus neurotoxin‐insensitive vesicle‐associated membrane protein; also called VAMP7) belongs to the Longin subfamily of v‐SNAREs (vesicular soluble N‐ethylmaleimide‐sensitive fusion protein‐attachment protein receptors). The regulatory N‐terminal extension, called the Longin domain, of TI‐VAMP has been shown previously to have a dual biochemical function: it inhibits the capacity of TI‐VAMP to form SNARE complexes and it binds to the δ subunit of the AP‐3 (adaptor protein 3) complex in early endosomes, thereby targeting TI‐VAMP to late endosomes.

Results. We have generated MDCK (Madin—Darby canine kidney) cell lines expressing the Longin domain of TI‐VAMP coupled to GFP (green fluorescent protein) in a doxycycline‐dependent manner. As expected, AP‐3δ (AP‐3 δ subunit) is not properly localized in Longin‐expressing cells. We have shown that the expression of the Longin domain impairs lysosomal secretion, as determined by the release of a pre‐internalized fluorescent fluid‐phase marker and by electron microscopy of the membrane‐associated released particles. Membrane repair following mechanical wounding, a process requiring lysosomal secretion, is also impaired in cells expressing the Longin domain. Furthermore, cell migration, assessed by wound healing of MDCK monolayers, is also inhibited.

Conclusions. The results of the present study suggest that the expression of the Longin domain of TI‐VAMP regulates lysosomal secretion of epithelial cells and provide molecular evidence for a role of the late endocytic system in cell migration.
Magnetic characterization of the (Zr,Sm)Co3 phase in Sm(CoFeCuZr)z magnets
Authors: de Campos M. F. , Murakami R. K. , Romero S. A. , Rechenberg H. R. , Missell F. P.
Published: April 2007

Magnets with composition Sm(CobalFe0.2Cu0.1Zrx)8 (x=0;0.02;0.04;0.06,0.08) were studied using x-ray diffraction Rietveld analysis. In addition to the majority 2:17 and 1:5 phases, the magnets present a rhombohedral (SmZr)1(CoFeCu)3 (PuNi3 structure) phase, whose volume fraction increases with Zr addition. Higher Zr contents decrease coercivity and lead to the appearance of impurity phases such as 6:23 (Th6Mn23 structure), 2:7R (Gd2Co7 structure), and 5:19R (Ce5Co19 structure) in the magnets. The 1:3R phase was reproduced in a Fe57-doped sample of Sm0.33Zr0.67Co3 and its Mössbauer spectra, at several temperatures, were adjusted using four sextets and a nonmagnetic doublet. The beneficial effect of small additions of Zr on the coercivity of the magnets is discussed.
Calculation of spin wave mode response induced by a coplanar microwave line
Authors: Kennewell K. J. , Kostylev M. , Stamps R. L.
Published: April 2007

The geometry and method of spin wave excitation in planar waveguide inductive resonance methods is very different from that used in resonant cavity experiments, and correct interpretation of results requires an analysis which takes into account a number of features associated with the use of broadband microwave experiments. We consider aspects of a theoretical description of the resonance modes in ferromagnetic multilayers measured by a broadband inductive technique in a coplanar waveguide geometry. The effects of finite conductivity of the magnetic sample and contributions to the measured response from finite wavelength spin waves excited in this geometry are discussed. We also include the screening action of the coplanar line on the spin wave dispersion in the theory. We show that for a proper description of intensities, the theoretical model for the spin wave excitation has to include not only the contribution to intensities from the microwave current in the central conductor as did previous theories but also contributions from reverse currents in the ground half-planes of the coplanar waveguide.
Theoretical study of the electronic structure of MCH2+(M=Fe,Co,Ni)
Authors: Villaume Sébastien , Strich Alain , Ndoye Chérif A. , Daniel Chantal , Perera S. Ajith , Bartlett Rodney J.
Published: April 2007

State of the art coupled cluster (CC) methods are applied to accurately characterize the ground state electronic structure and photoelectron spectra of transition metal carbene ions MCH2+ (M=Fe, Co, and Ni). The geometries and energies of the lowest energy quartet, triplet, and doublet electronic states as well as several low-lying vertical excitation energies of FeCH2+, CoCH2+, and NiCH2+ are reported. The excitation energies are computed using the equation-of-motion CC and for states of different symmetries, by the energy differences of single reference ground and excited states (Δ-CC). The latter employ several reference states; the unrestricted Hartree-Fock, restricted open shell Hartree-Fock, and unrestricted Kohn-Sham. We conclude that the A12 electronic ground state of NiCH2+ is separated by about 30.0kJ∕mol from the next highest state, and the lowest B14 and B24 states of FeCH2+ as well as the A23 and A13 states of CoCH2+ are nearly degenerate. The presence of metal-πMCH2* charge transfer states with significant oscillator strengths in the visible/near-UV energy domain of the theoretical spectra of FeCH2+ and CoCH2+ are at the origin of the photofragmentation of these compounds observed after irradiation between 310 and 360nm.
Magnetostatic coupling in soft/hard biphase magnetic systems based on amorphous alloys
Authors: Torrejón J. , Kraus L. , Pirota K. R. , Badini G. , Vázquez M.
Published: April 2007

We report on magnetic bias in biphase systems arising from by dipolarlike interaction. Composites consist of amorphous ribbons and wires prepared by rapid solidification techniques, surrounded by an electroplated layer. Amorphous metallic core is (Co0.94Fe0.06)72.5Si12.5B15 with ultrasoft magnetic behavior (coercivity of 10–10−1A∕m), and the electroplated coating is crystalline Co85Ni15 alloy with harder magnetic character (coercivity of 104A∕m. After premagnetizing in a dc saturating field (106A∕m), the low-field (±103A∕m) hysteresis loops are ascribed to the magnetization process of the soft core and exhibit a typical shift towards the direction of the premagnetizing field. This shift is ascribed to the magnetostatic field generated by uncompensated poles at the edges of the hard layer, which remains close to its remanence state. The influence of the geometry of both phases on magnetostatic energy term allows us to tailor the bias field and susceptibility of the core. These results open other possibilities to use these materials as sensing elements in magnetic sensor.
Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory
Authors: Coriani Sonia , Høst Stinne , Jansík Branislav , Thøgersen Lea , Olsen Jeppe , Jørgensen Poul , Reine Simen , Pawłowski Filip , Helgaker Trygve , Sałek Paweł
Published: April 2007

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.
Yield of excited CO molecules from dissociative recombination of HCO+ and HOC+ ions with electrons
Authors: Rosati Richard E. , Skrzypkowski Miroslaw P. , Johnsen Rainer , Golde Michael F.
Published: April 2007

The authors have investigated CO band emissions arising from the dissociative recombination of HCO+ and HOC+ ions with thermal electrons in a flowing afterglow plasma. The quantitative analysis of the band intensities showed that HCO+ recombination forms the long-lived CO(aΠ3) state with a yield of 0.23±0.12, while HOC+ recombination favors formation of CO(a′Σ+3) and CO(dΔ3) with a combined yield of greater than 0.4. The observed vibrational distribution for the CO(a) state reproduces theoretical predictions quite well. The vibrational distributions for CO(a′) and CO(d) are, in part, inverted, presumably as a consequence of a change in CO equilibrium bond length during recombination. The observations are compatible with current knowledge of the potential surfaces of states of HCO and HCO+.
Computer simulation of phase separation under a double temperature quench
Authors: Podariu Iulia , Chakrabarti Amitabha
Published: April 2007

The authors numerically study a two-step quench process in an asymmetric binary mixture. The mixture is first quenched to an unstable state in the two-phase region. After a large phase-separated structure is formed, the authors again quench the system deeper. The second quench induces the formation of small secondary droplets inside the large domains created by the first quench. The authors characterize this secondary droplet growth in terms of the temperature of the first quench as well as the depth of the second one.
Modeling the early stages of self-assembly in nanophase materials
Authors: Kozak John J. , Nicolis C. , Nicolis G.
Published: April 2007

The early stages of self-assembly of the elementary building blocks of nanophase materials are studied. The relative roles of entropic and energetic factors in determining the relative abundance of the final products present is analyzed using both a kinetic mean field model and a mesoscopic approach in which self-assembly is viewed as an encounter-controlled process on a discrete lattice. The relevance of the results in zeolite synthesis in connection with the ordered liquid phases recently discovered in these materials is discussed.
Hydrogen peroxide and ammonia on protonated ice clusters
Authors: Schmidt Martin , Masson Albert , Bréchignac Catherine , Cheng Hai-Ping
Published: April 2007

A temperature controlled source for protonated water clusters has been combined with high-resolution mass spectroscopy to study the stability pattern of ice clusters and compounds with ammonia and hydrogen peroxide depending on temperature. The stability pattern of pure protonated ice shows the two well known peaks at 21 and 28 molecules and also less pronounced structure up to n=55. Ammonia and hydrogen peroxide do not destroy this pattern but shift it by a number of water molecules. The additives are therefore integrated in the persisting crystalline structure of the pure protonated ice. Based on this structural information, density functional theory calculations reveal that hydrogen peroxide and ammonia occupy surface positions on a dodecahedral 21-molecule cluster and are not caged in the center.
Photodissociation of CO2− in water clusters via Renner-Teller and conical interactions
Authors: Habteyes Terefe , Velarde Luis , Sanov Andrei
Published: April 2007

The photochemistry of mass selected CO2−(H2O)m, m=2–40 cluster anions is investigated using 266nm photofragment spectroscopy and theoretical calculations. Similar to the previous 355nm experiment [Habteyes et al., Chem. Phys. Lett. 424, 268 (2006)], the fragmentation at 266nm yields two types of anionic products: O−(H2O)m-k (core-dissociation products) and CO2−(H2O)m-k (solvent-evaporation products). Despite the same product types, different electronic transitions and dissociation mechanisms are implicated at 355 and 266nm. The 355nm dissociation is initiated by excitation to the first excited electronic state of the CO2− cluster core, the 1B12(A″2) state, and proceeds via a glancing Renner-Teller intersection with the ground electronic state at a linear geometry. The 266nm dissociation involves the second excited electronic state of CO2−, the 2A12(A′2) state, which exhibits a conical intersection with the 3B22(A′) state at a bent geometry. The asymptotic O− based products are believed to be formed via this 3B22(A′) state. By analyzing the fragmentation results, the bond dissociation energy of CO2− to O−+CO in hydrated clusters (m⩾20) is estimated as 2.49eV, compared to 3.46eV for bare CO2−. The enthalpy of evaporation of one water molecule from asymptotically large CO2−(H2O)m clusters is determined to be 0.466±0.001eV (45.0±0.1kJ∕mol). This result compares very favorably with the heat of evaporation of bulk water, 0.456eV (43.98kJ∕mol).
Variable-free exploration of stochastic models: A gene regulatory network example
Authors: Erban Radek , Frewen Thomas A. , Wang Xiao , Elston Timothy C. , Coifman Ronald , Nadler Boaz , Kevrekidis Ioannis G.
Published: April 2007

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [R. Erban et al., J. Chem. Phys. 124, 084106 (2006)] the authors assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e., effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [R. Coifman et al., Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005)] to extract appropriate observables (“reduction coordinates”) in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free, coarse-grained computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.
Ab initio molecular dynamics simulation of ionic liquids
Authors: Ghatee Mohammad Hadi , Ansari Younes
Published: April 2007

Ab initio Car-Parinnello molecular dynamics is used to simulate the structure and the dynamics of 1-butyl-3-methylimidazolium iodide ([bmim]I) ionic liquid at 300K. Site-site pair correlation functions reveal that the anion has a strong interaction with any three C–H’s of the imidazolium ring. The ring bends over and wraps around the anion such that the two nitrogen atoms take a distance to the anion. Electron donating butyl group contributes the electronic polarization in addition to geometrical (out-of-plane) polarization of the ring due to the liquid environment. This facilitates bending of the ring along the axis passing through nitrogen atoms. The average bending angle depends largely on the alkyl chain length and slightly on the anion type. Redistribution of electron density over the ring caused by the electron donating alkyl group provides additional independent evidence to the instability of lattice structure, hence the low melting point of the ionic liquid. Simulated viscosity and diffusion coefficients of [bmim]I are in quite agreement with the experiments.
Ambipolar organic light emitting field effect transistors with modified asymmetric electrodes
Authors: Yamane Kazuhiko , Yanagi Hisao , Sawamoto Atsushi , Hotta Shu
Published: April 2007

The authors report on gate-controlled light emission from an organic field effect transistor composed of a vapor-deposited thin film of α,ω-bis(biphenyl-4-yl)-terthiophene (BP3T) with an electron injection layer of pentacene for the drain electrode. A n-triacontane thin film vapor deposited on a Si∕SiO2 wafer was used as a buffer layer for the gate dielectric. The location of emission zones within the channel where both injected carriers recombine was controlled by the gate voltage. The insertion of the pentacene and n-triacontane layers improved the threshold voltage and mobility for electrons, resulting in balanced ambipolar carrier injection and transport.
Fully automated implementation of the incremental scheme: Application to CCSD energies for hydrocarbons and transition metal compounds
Authors: Friedrich Joachim , Hanrath Michael , Dolg Michael
Published: April 2007

A general fully automated implementation of the incremental scheme for molecules and embedded clusters in the framework of the coupled cluster singles and doubles theory is presented. The code can be applied to arbitrary order of the incremental expansion and is parallelized in a master/slave structure. The authors found that the error in the total correlation energy is lower than 1kcal∕mol with respect to the canonical CCSD calculation if the incremental series is truncated in a proper way.
Ferroelectric and optical properties of quasiperiodic PbZr0.5Ti0.5O3 multilayers grown on quartz wafers
Authors: Hu G. J. , Hong X. K. , Chu J. H. , Dai N.
Published: April 2007

Pb Zr 0.5 Ti 0.5 O 3 (PZT) multilayers with total thickness of a few microns have been grown on quartz substrates by using sol gel technique. The PZT multilayer displays a well-defined polarization hysteresis loop with a nominally average remanent polarization of 36.5μC∕cm2 and an average coercive field of 66.5kV∕cm under a maximum applied voltage of 100V. With 17 periods, 95% reflectivity and 62nm stop-band width have been achieved at room temperature, indicating that the quasiperiodic PZT multilayer can be used as dielectric reflectors and filters.
Charge density distribution of transparent p-type semiconductor (LaO)CuS
Authors: Takase Kouichi , Sato Ken , Shoji Osamu , Takahashi Yumiko , Takano Yoshiki , Sekizawa Kazuko , Kuroiwa Yoshihiro , Goto Manabu
Published: April 2007

The charge density distributions of layered oxysulfide (LaO)CuS, known as a p-type transparent semiconductor, have been investigated by analyzing the synchrotron radiation powder diffraction profile with the maximum entropy method/Rietveld method. The bonding character of the Cu–S bond is revealed to be covalent. Meanwhile, the O–La bonding has both ionic and covalent characters. The number of electrons estimated by integrating the charge density around each atom gave direct evidence that each CuS and LaO layer is electrically almost neutral.
Enhancing or suppressing self-focusing in nonlinear photonic crystals
Authors: Yu Xiaofang , Jiang Xunya , Fan Shanhui
Published: April 2007

The authors show that the effect of self-focusing can be controlled by exploiting spatial dispersion effects in a photonic crystal. In the positive refraction region, the critical field value for self-guiding can be significantly reduced. In the negative refraction region, the self-focusing effect can be completely suppressed in spite of a positive Kerr coefficient.
Synthesis of nanoscale composites of exchange biased MnFe2O4 and Mn-doped BiFeO3
Authors: Yang C.-H. , Yildiz F. , Lee S.-H. , Jeong Y. H. , Chon U. , Koo T. Y.
Published: April 2007

Exchange bias may be used to couple a normal ferromagnet to a ferroelectric antiferromagnet and thus create a multiferroic system with nonzero magnetization. In implementing this idea the authors developed a synthesis method for composite films of nanoscale clusters of ferromagnetic MnFe2O4 embedded in multiferroic Mn-doped BiFeO3. The method utilizes the Bi volatility to obtain the composite films via thermal annealing of multilayers composed of BiFeO3 and BiMnO3. The cluster size varies from 20to80nm depending on the film thickness. The composite films possess both ferroelectric and ferromagnetic properties; the magnetic hysteresis curves, in particular, manifest exchange bias.
Electrical stability of a 65nm technology Ni-silicided junctions under accelerated bias stressing
Authors: Mogul H. C. , McPherson J. W.
Published: April 2007

The electrical stability of nickel-silicided junctions in a 65nm technology has been investigated under accelerated bias stress (ABS) testing. The nickel-silicided junctions show some shift during the ABS testing; however, the increase in leakage for the junctions tended to saturate at safe levels. The increase in leakage is consistent with a hydrogen release mechanism, during the ABS testing, resulting in the depassivation of electrically active sites along the junction perimeter.
Domain structure sequence in ferroelectric Pb(Zr0.2Ti0.8)O3 thin film on MgO
Authors: Janolin Pierre-Eymeric , Fraisse Bernard , Dkhil Brahim , Le Marrec Françoise , Ringgaard Erling
Published: April 2007

The structural evolution of a polydomain ferroelectric Pb(Zr0.2Ti0.8)O3 film was studied by temperature-dependent x-ray diffraction. Two critical temperatures were evidenced: T*=740K, corresponding to a change in the domain structure (a∕c∕a∕c to a1∕a2∕a1∕a2), and TCfilm=825K, where the film undergoes a ferroelectric-paraelectric phase transition. The film remains tetragonal on the whole range of temperature investigated. The evolutions of the domain structure and lattice parameters were found to be in very good agreement with the calculated domain stability map and theoretical temperature-misfit strain phase diagram, respectively.
Distinct levels in the nanoscale organization of DNA-histone complex revealed by its mechanical unfolding
Authors: Soni G. V. , Brar Loveleen , Hameed Feroz M. , Raychaudhuri A. K. , Shivashankar G. V.
Published: April 2007

Mechanical unfolding of nanoscale DNA-histone complex, using an atomic force microscope, shows a stepwise disassembly of histones from the nucleosome. A quantitative analysis of the rupture jump statistics and the length released per jump reveals insights into the possible histone contacts within the octamer complex. The measured ruptures correlate with the breakage of multiple contacts that stabilize the histone octamer. These results provide a mechanistic basis by which stepwise disassembly of histone proteins may result from an external force exerted by the adenosinetriphosphate (ATP) dependent chromatin remodeling machines to access regulatory sites on DNA.
Large inverse tunneling magnetoresistance in Co2Cr0.6Fe0.4Al∕MgO∕Co80Fe20 magnetic tunnel junctions
Authors: Rata A. D. , Braak H. , Bürgler D. E. , Schneider C. M.
Published: April 2007

Magnetic tunnel junctions with the layer sequence Co2Cr0.6Fe0.4Al∕MgO∕Co80Fe20 were fabricated by magnetron sputtering at room temperature (RT). The samples exhibit a large inverse tunneling magnetoresistance (TMR) effect of up to −66% at RT. The largest value of −84% at 20K reflects a rather weak influence of temperature. The dependence on the voltage drop shows an unusual behavior with two almost symmetric peaks at ±600mV with large inverse TMR ratios and small positive values around zero bias.
Stressed Fibonacci spiral patterns of definite chirality
Authors: Li Chaorong , Ji Ailing , Cao Zexian
Published: April 2007

Fibonacci spirals are ubiquitous in nature, but the spontaneous assembly of such patterns has rarely been realized in laboratory. By manipulating the stress on Ag core/SiO2 shell microstructures, the authors obtained a series of Fibonacci spirals (3×5to13×21) of definite chirality as a least elastic energy configuration. The Fibonacci spirals occur uniquely on conical supports-spherical receptacles result in triangular tessellations, and slanted receptacles introduce irregularities. These results demonstrate an effective path for the mass fabrication of patterned structures on curved surfaces; they may also provide a complementary mechanism for the formation of phyllotactic patterns.
Isolation of dehydration-responsive genes in a drought tolerant common bean cultivar and expression of a group 3 late embryogenesis abundant mRNA in tolerant and susceptible bean cultivars
Authors: Barrera-Figueroa Blanca E. , Peña-Castro Julián M. , Acosta-Gallegos Jorge A. , Ruiz-Medrano Roberto , Xoconostle-Cázares Beatriz
Published: April 2007

Drought is one of the main constraints for common bean (Phaseolus vulgaris L.) production in Latin America. The aim of this work was to identify upregulated genes in the drought-tolerant common bean cv. Pinto Villa, grown under water-deficit conditions. Twenty-eight cDNAs representing differentially-expressed mRNAs in roots and/or leaves were isolated via suppression subtractive hybridisation. Their expression profiles in plants under intermediate and severe dehydration stress were tested. Three cDNAs corresponded to genes already described as associated to drought stress in P. vulgaris, 12 were known P. vulgaris sequences without previous association with drought response, and 13 were new P. vulgaris sequences. Analysis of the deduced proteins encoded by the cDNAs revealed putative functions in cellular protection, sugar metabolism, and protein synthesis, folding and turnover. Additionally, a new member of group 3 late embryogenesis abundant (LEA) genes (PvLEA3) was cloned and its complete sequence was obtained. Given the lack of reports comparing expression of dehydration-responsive genes in bean cultivars with different response to drought, the expression of PvLEA3 transcript in five bean cultivars from different origin was analysed. The induction of PvLEA3 was directly associated with the level of drought tolerance in the cultivars studied.
Research note: Reversible birefringence suggests a role for molecular self-assembly in forisome contractility
Authors: Peters Winfried S. , Schnetter Reinhard , Knoblauch Michael
Published: April 2007

Forisomes are contractile protein bodies that control the effective diameter of the sieve elements of the faboid legumes by reversible, Ca2+-driven changes of shape. Forisomes consist of fibrils; we inferred from available electron-microscopical data (which necessarily provide images of fixed, non-functional forisomes) that a reversible assembly of ordered fibrillar arrays might be involved in the contractile mechanism. Here we examined functional forisomes isolated from Vicia faba L. by differential interference contrast microscopy and polarisation microscopy. We found them birefringent in the longitudinally expanded but not in the contracted state, showing ‘parallel extinction’ with the direction of vibration of the slow ray coinciding with their long axis (positive birefringence). These findings met predictions derived from the theory of form birefringence in rodlet composite bodies, and supported the idea of molecular self-assembly as a factor in forisome contractility.
Diversity in prion protein oligomerization pathways results from domain expansion as revealed by hydrogen/deuterium exchange and disulfide linkage
Authors: Eghiaian Frederic , Daubenfeld Thorsten , Quenet Yann , van Audenhaege Marieke , Bouin Anne-Pascale , van der Rest Guillaume , Grosclaude Jeanne , Rezaei Human
Published: April 2007

The prion protein (PrP) propensity to adopt different structures is a clue to its biological role. PrP oligomers have been previously reported to bear prion infectivity or toxicity and were also found along the pathway of
in vitro
amyloid formation. In the present report, kinetic and structural analysis of ovine PrP (OvPrP) oligomerization showed that three distinct oligomeric species were formed in parallel, independent kinetic pathways. Only the largest oligomer gave rise to fibrillar structures at high concentration. The refolding of OvPrP into these different oligomers was investigated by analysis of hydrogen/deuterium exchange and introduction of disulfide bonds. These experiments revealed that, before oligomerization, separation of contacts in the globular part (residues 127–234) occurred between the S1–H1–S2 domain (residues 132–167) and the H2–H3 bundle (residues 174–230), implying a conformational change of the S2–H2 loop (residues 168–173). The type of oligomer to be formed depended on the site where the expansion of the OvPrP monomer was initiated. Our data bring a detailed insight into the earlier conformational changes during PrP oligomerization and account for the diversity of oligomeric entities. The kinetic and structural mechanisms proposed here might constitute a physicochemical basis of prion strain genesis.
Theoretical study of the rhenium–alkane interaction in transition metal–alkane σ-complexes
Authors: Cobar Erika A. , Khaliullin Rustam Z. , Bergman Robert G. , Head-Gordon Martin
Published: April 2007

Metal–alkane binding energies have been calculated for [CpRe(CO)2](alkane) and [(CO)2M(C5H4)CC(C5H4)M(CO)2](alkane), where M = Re or Mn. Calculated binding energies were found to increase with the number of metal–alkane interaction sites. In all cases examined, the manganese–alkane binding energies were predicted to be significantly lower than those for the analogous rhenium–alkane complexes. The metal (Mn or Re)–alkane interaction was predicted to be primarily one of charge transfer, both from the alkane to the metal complex (70–80% of total charge transfer) and from the metal complex to the alkane (20–30% of the total charge transfer).
Prospective Observational Study of Candidemia in São Paulo, Brazil: Incidence Rate, Epidemiology, and Predictors of Mortality
Authors: Colombo Arnaldo L. , Guimarães Thaís , Silva Ligia R. B. F. , Monfardini Leila Paula de Almeida , Cunha Anna Karenine B. , Rady Patrícia , Alves Thelma , Rosas Robert C.
Published: April 2007

Background.

Studies conducted in tertiary care hospitals of different European countries and the United States have shown incidence rates of candidemia ranging from 0.17 to 0.76 and 0.28 to 0.96 per 1,000 admissions, respectively. So far, only 1 study has evaluated the incidence rates of candidemia in tertiary care hospitals in Latin American countries.

Objective.

To evaluate the epidemiology of candidemia in 4 tertiary care hospitals in São Paulo, Brazil.

Design.

Multicenter, laboratory-based surveillance of candidemia.

Results.

A total of 7,038 episodes of bloodstream infection were identified, and Candida species accounted for 282 cases (4%). The incidence rate of candidemia was 1.66 candidemic episodes per 1,000 hospital admissions. Candida albicans was the most frequently isolated Candida species in all hospitals, but Candida species other than C. albicans accounted for 62% of isolates, including predominantly Candida parapsilosis and Candida tropicalis. Azole resistance was restricted to only 2% of all Candida isolates (1 isolate of Candida glabrata and 4 isolates of Candida rugosa). Candidemia was mostly documented in surgical patients with long durations of hospital stay. The crude mortality rate was 61%, and advanced age and high Acute Physiology and Chronic Health Evaluation II score were both conditions independently associated with risk of death.

Conclusions.

We observed in our series a higher incidence rate of candidemia than that reported in European countries and the United States. Advanced age and a high Acute Physiology and Chronic Health Evaluation II score were factors associated with a higher probability of death in candidemic patients. Fluconazole-resistant Candida strains are still a rare finding in our case-based study of candidemia.
Assessment of Intervention Measures for the 2003 SARS Epidemic in Taiwan by Use of a Back-Projection Method
Authors: Yip Paul S. F. , Hsieh Y. H. , Xu Ying , Lam K. F. , King C. C. , Chang H. L.
Published: April 2007

Objectives.

To reconstruct the infection curve for the 2003 severe acute respiratory syndrome (SARS) epidemic in Taiwan and to ascertain the temporal changes in the daily number of infections that occurred during the course of the outbreak.

Method.

Back-projection method.

Results.

The peaks of the epidemic correspond well with the occurrence of major infection clusters in the hospitals. The overall downward trend of the infection curve after early May corresponds well to the date (May 10) when changes in the review and classification procedure were implemented by the SARS Prevention and Extrication Committee.

Conclusion.

The major infection control measures taken by the Taiwanese government over the course of the SARS epidemic, particularly those regarding infection control in hospitals, played a crucial role in containing the outbreak.
Desert Christians
Authors: Harmless William, S.J.
Published: April 2007

In the fourth century, the deserts of Egypt became the nerve center of a radical new movement, what we now call monasticism. Groups of Christians—from illiterate peasants to learned intellectuals—moved out to the wastelands beyond the Nile Valley and, in the famous words of Saint Athanasius, made the desert a city. In so doing, they captured the imagination of the ancient world. They forged techniques of prayer and asceticism, of discipleship and spiritual direction, that have remained central to Christianity ever since. Seeking to map the soul’s long journey to God and plot out the subtle vagaries of the human heart, they created and inspired texts that became classics of Western spirituality. These Desert Fathers were also brilliant storytellers, some of Christianity’s finest. This book introduces the literature of early Christian monasticism, examining all the best-known works, including Athanasius’ Life of Antony, the Lives of Pachomius, and the Sayings of the Fathers (Apophthegmata Patrum). Later chapters focus on two pioneers of monastic theology: Evagrius Ponticus, the first great theoretician of Christian mysticism; and John Cassian, who brought Egyptian monasticism to the Latin West. Along the way, readers are introduced to path-breaking discoveries—to new texts and recent archeological finds—that have revolutionized contemporary scholarship on monastic origins. Included are snippets from papyri and from little-known Coptic, Syriac, and Ethiopic texts. Interspersed in each chapter are illustrations, maps, and diagrams that help readers sort through the key texts and the richly textured world of early monasticism.
Patriarchs, Councils, and Controversies: 300–451
Authors: Harmless William, S.J.
Published: April 2007

The patriarchs of Alexandria would cast long shadows over the history of Egyptian monasticism. This chapter focuses on the five most influential: Alexander, Athanasius, Theophilus, Cyril, and Dioscorus. It surveys both their careers and their theological controversies, especially their doctrine-defining clashes at the ecumenical Councils of Nicaea, Ephesus, and Chalcedon. This chapter provides critical historical and theological background, since the politics and theologies of the bishops of Alexandria figure prominently in early monastic literature, and their international prominence would help draw the world’s attention to Egypt and its monks.
Evagrius Ponticus: Ascetical Theory
Authors: Harmless William, S.J.
Published: April 2007

Evagrius (c.345–399) grew up in Pontus near the Black Sea, and, after serving as a deacon in Constantinople, embarked on a monastic career, settling in Kellia in Lower Egypt. There he apprenticed under two leading desert fathers, Macarius the Egyptian and Macarius the Alexandrian. Evagrius was one of the first monastic theologians and is best known for two works, the Praktikos and the Chapters on Prayer. These and other works of his are strings of terse and somewhat cryptic proverbs, known as “chapters” (kephalaia). This introduction surveys Evagrius’s life and surviving writings and explores the ascetical side of his theology, especially his brilliant and original psychology of temptation—centered on what he called the “eight evil thoughts” (logismoi).
John Cassian
Authors: Harmless William, S.J.
Published: April 2007

John Cassian (d. after 345) was one of the key figures who brought traditions of desert monasticism to the Latin West. He grew up in what today is Romania and became a monk in Bethlehem and then moved to Egypt, settling at the monastery of Scetis, where he became a disciple of Evagrius Ponticus. In the wake of the Origenist Controversy, he left Egypt and settled in southern France, in the port city of Massilia (modern Marseilles), where he composed in Latin two profoundly influential works, the Institutes and the Conferences. This chapter surveys Cassian’s career and introduces his key works and theological themes, especially the monastic search for purity of heart and the monastic practice of unceasing prayer.
Sectoral Patterns of Technological Change
Authors: Miozzo Marcela , Walsh Vivien
Published: April 2007

This chapter explores the similarities and differences amongst sectors in terms of the sources, nature, and impact of innovation. The first section describes the taxonomy of patterns of technological change developed by Pavitt (1984). The second section presents a taxonomy of patterns of innovation in services. The third section examines innovation in construction. The fourth section is concerned with innovation in pharmaceuticals. The fifth section considers innovation in the agrofood industry. The final section examines innovation in chemicals.
Networks and Alliances
Authors: Miozzo Marcela , Walsh Vivien
Published: April 2007

This chapter explores networks and strategic alliances as a qualitative change accompanying globalization. It analyses the reasons for the growth in alliances — the databases complied by researchers to analyse them —and different approaches to studying alliances and networks (complementary assets, actornetwork theory, and transaction cost economics). A number of networks and alliances are examined (including US CRADAs, Benetton network, linkages between small and large firms in biotechnology, and the case of the Maastricht region).
Antibiotic Prophylaxis in Cochlear Implant Surgery
Authors: Hirsch Barry E. , Blikas Athanasios , Whitaker Mark
Published: April 2007

Objectives/Hypothesis: We conducted this study to determine the incidence of infection in cochlear implant surgery after using perioperative antibiotics.

Study Design: Study design was a retrospective case series.

Methods: There was a retrospective chart review of 95 patients (81 adults, 14 children) undergoing 98 cochlear implants.

Results: The incidence of infection following cochlear implant surgery was 1% with the use of perioperative antibiotics.

Conclusions: Perioperative antibiotics, usually administered as a single dose, are sufficient for the prevention of major wound infection after cochlear implant surgery.
Minimally Invasive Endoscopic Nasopharyngectomy in the Treatment of Recurrent T1‐2a Nasopharyngeal Carcinoma
Authors: Chen Mu‐Kuan , Lai Jui‐Chung , Chang Cheng‐Chaun , Liu Mu‐Tai
Published: April 2007

Objective: To study the efficacy of endoscopic nasopharyngectomy in salvaging recurrent T1 to 2a nasopharyngeal carcinoma (NPC).

Study Design: An investigation of the outcome of endoscopic nasopharyngectomy.

Methods: Six nasopharyngectomies for patients presenting with locally recurrent T1 to 2a NPC were performed exclusively by way of endoscopic resection by a single surgeon (m.‐k.c.) during the period 2001 to 2005. All patients were operated on with curative intent without postoperative radiotherapy.

Results: All six operations were successfully performed endoscopically, and no conversions to conventional open resection were necessary. Of the patients who underwent endoscopic excision, three of them had rT1 disease, and the others had rT2a disease. No surgical specimens had microscopic invasion of the resection margins. No complications associated with the operation occurred. The patients were followed up for 16 to 59 (average, 29) months. One local recurrence was noted in this series to date, and the patient was treated with intensity‐modulated radiotherapy and chemotherapy.

Conclusions: Exclusively endoscopic nasopharyngectomy is a feasible method for treatment of locally recurrent T1‐ to 2a‐staged NPC.
Candida glabrata colonizes but does not often disseminate from the mouse caecum
Authors: Wells Carol L. , Johnson Mary-Alice , Henry-Stanley Michelle J. , Bendel Catherine M.
Published: April 2007

Candida glabratais the second or third most frequent cause of candidaemia. The gastrointestinal tract is considered to be a major portal of entry for systemic candidiasis, but relatively few studies have investigated the pathogenesis ofC. glabrata. Experiments were designed to clarify the ability ofC. glabratato disseminate from the mouse intestinal tract. Following oral inoculation,C. glabratareadily colonized the caeca [approx. 107cells (g caecum)−1] of antibiotic-treated mice, but extraintestinal dissemination was not detected. Superimposing several mouse models of trauma and/or immunosuppression known to induce dissemination ofCandida albicansand other intestinal microbes did not causeC. glabratato disseminate often, although one exception was mice given high doses of dexamethasone for 4 days. These data support the hypothesis that the antibiotic-treated mouse intestine may be an epidemiological reservoir forC. glabrataand that this yeast tends to disseminate under specific clinical conditions.
Sequence-based typing of genetic targets encoded outside of the O-antigen gene cluster is indicative of Shiga toxin-producing Escherichia coli serogroup lineages
Authors: Gilmour Matthew W. , Olson Adam B. , Andrysiak Ashleigh K. , Ng Lai-King , Chui Linda
Published: April 2007

Serogroup classifications based upon the O-somatic antigen of Shiga toxin-producing Escherichia coli (STEC) provide significant epidemiological information on clinical isolates. Each O-antigen determinant is encoded by a unique cluster of genes present between the gnd and galF chromosomal genes. Alternatively, serogroup-specific polymorphisms might be encoded in loci that are encoded outside of the O-antigen gene cluster. Segments of the core bacterial loci mdh, gnd, gcl, ppk, metA, ftsZ, relA and metG for 30 O26 STEC strains have previously been sequenced, and comparative analyses to O157 distinguished these two serogroups. To screen these loci for serogroup-specific traits within a broader range of clinically significant serogroups, DNA sequences were obtained for 19 strains of 10 additional STEC serogroups. Unique alleles were observed at the gnd locus for each examined STEC serogroup, and this correlation persisted when comparative analyses were extended to 144 gnd sequences from 26 O-serogroups (comprising 42 O : H-serotypes). These included O157, O121, O103, O26, O5 : non-motile (NM), O145 : NM, O113 : H21, O111 : NM and O117 : H7 STEC; and furthermore, non-toxin encoding O157, O26, O55, O6 and O117 strains encoded distinct gnd alleles compared to STEC strains of the same serogroup. DNA sequencing of a 643 bp region of gnd was, therefore, sufficient to minimally determine the O-antigen of STEC through molecular means, and the location of gnd next to the O-antigen gene cluster offered additional support for the co-inheritance of these determinants. The gnd DNA sequence-based serogrouping method could improve the typing capabilities for STEC in clinical laboratories, and was used successfully to characterize O121 : H19, O26 : H11 and O177 : NM clinical isolates prior to serological confirmation during outbreak investigations.
Use of immunoblotting as an alternative method for serogrouping Leptospira
Authors: Doungchawee Galayanee , Sirawaraporn Worachart , Icksang-Ko Albert , Kongtim Suraphol , Naigowit Pimjai , Thongboonkerd Visith
Published: April 2007

Leptospirosis is a worldwide zoonotic disease caused by a spirochaete bacterium, Leptospira. Serological detection of this micro-organism basically relies on a conventional microscopic agglutination test (MAT), which has some limitations and disadvantages. In the present study, immunoblotting has been applied as an alternative method for differentiating serogroups and serovars of leptospires. Leptospiral whole-cell lysates from a total of 26 serovars were subjected to immunoblotting using rabbit antisera against individual serovars. The findings clearly demonstrated that the pattern of immunoreactive bands could be used to differentiate between leptospires of different serogroups, consistent with MAT results. There was a multi-band pattern that was unique for the pathogenic Leptospira antigens and was not observed in the non-pathogenic Leptospira biflexa and non-leptospiral bacteria (i.e. Escherichia coli, Burkholderia pseudomallei and Helicobacter pylori). For pathogenic Leptospira species, a prominent smear-like band at approximately 19–30 kDa was present when the antigens were probed with the homologous antisera. The molecular size of the prominent band, although it showed a cross-reaction between members within the same serogroup, differed among different serovars. The results obtained from polyclonal antibodies (antisera) were confirmed using mAb. With its simplicity and safety of experimental procedures, it is proposed that immunoblotting may potentially be useful as an alternative method for differentiating between serogroups of leptospires.