bluuebunny/crossref_metadata_2025 huggingface dataset:
Mixed electric-magnetic second-order nonlinear optical response of helicenes
Authors: Botek Edith , André Jean-Marie , Champagne Benoît , Verbiest Thierry , Persoons André
Published: June 2005

The mixed electric-magnetic second-order nonlinear optical responses of oriented films of helicenes have been computed ab initio using the random phase approximation method and compared to the pure electric-dipole counterpart. It turns out that the mixed electric-magnetic responses can be of the same order of magnitude as the pure electric-dipole counterpart when there is no donor/acceptor (D/A) substituent or these D/A pairs are weak, i.e., when the pure electric-dipole response is small. When adding strong D/A substituents, the pure electric-dipole response increases substantially and much more than its mixed electric-magnetic counterpart. Consequently, the ratio between the mixed electric-magnetic and pure electric responses decreases. Although there is no general rule, the mixed responses evolve as a function of substitution quasi similarly to the pure electric contribution. This study confirms therefore the possibility of tuning the mixed electric-magnetic response by employing appropriate chiral molecules.
Theoretical fine spectroscopy with symmetry-adapted-cluster configuration-interaction method: Outer- and inner-valence ionization spectra of furan, pyrrole, and thiophene
Authors: Ehara Masahiro , Ohtsuka Yuhki , Nakatsuji Hiroshi , Takahashi Masahiko , Udagawa Yasuo
Published: June 2005

Theoretical fine spectroscopy has been performed for the valence ionization spectra of furan, pyrrole, and thiophene with the symmetry-adapted-cluster configuration-interaction general-R method. The present method described that the π1 state interacts with the π3−2π*, π2−2π*, and π2−1π3−1π* shake-up states providing the split peaks and the outer-valence satellites, both of which are in agreement with the experiments. The intensity distributions were analyzed in detail for the inner-valence region. In particular, for furan, theoretical intensities were successfully compared with the intensity measured by the electron momentum spectroscopy. The interactions of the 3b2 and 5a1 states with the shake-up states were remarkable for furan and pyrrole, while the 4b2 state of thiophene had relatively large intensity.
Electronic properties of interfaces between different sexithiophenes and gold
Authors: Schwieger T. , Liu X. , Peisert H. , Adolphi B. , Kiriy N. , Knupfer M.
Published: June 2005

We present a photoemission study of the interface between sexithiophene and polycrystalline gold. Two different sexithiophenes have been investigated—α-6T and a derivative of α-6T(ββ′-DH6T) with additionally attached alkane chains at thiophene rings, which increases its solubility and allows application in solution-based processes. We find an interface dipole of 1.2 eV and we observe chemical interactions for both sexithiophenes. Special attention has been paid to the possible influence of the chemical modification on the electronic properties of the material itself and its influence on the interface properties with gold. In addition, we discuss the differences in the electronic structure of vacuum-sublimated and spin-coated films of ββ′-DH6T. We find indications for better ordered films applying the solution-based process and the spin-coating procedure leads to oxidation of the organic film.
Dynamics of a poly(ethylene oxide) tracer in a poly(methyl methacrylate) matrix: Remarkable decoupling of local and global motions
Authors: Haley Jeffrey C. , Lodge Timothy P.
Published: June 2005

The tracer diffusion coefficient of unentangled poly(ethylene oxide) (PEO, M=1000g∕mol) in a matrix of poly(methyl methacrylate) (PMMA, M=10000g∕mol) has been measured over a temperature range from 125to220°C with forced Rayleigh scattering. The dynamic viscosities of blends of two different high molecular weight PEO tracers (M=440000 and 900000g∕mol) in the same PMMA matrix were also measured at temperatures ranging from 160to220°C; failure of time-temperature superposition was observed for these systems. The monomeric friction factors for the PEO tracers were extracted from the diffusion coefficients and the rheological relaxation times using the Rouse model. The friction factors determined by diffusion and rheology were in good agreement, even though the molecular weights of the tracers differed by about three orders of magnitude. The PEO monomeric friction factors were compared with literature data for PEO segmental relaxation times measured directly with NMR. The monomeric friction factors of the PEO tracer in the PMMA matrix were found to be from two to six orders of magnitude greater than anticipated based on direct measurements of segmental dynamics. Additionally, the PEO tracer terminal dynamics are a much stronger function of temperature than the corresponding PEO segmental dynamics. These results indicate that the fastest PEO Rouse mode, inferred from diffusion and rheology, is completely separated from the bond reorientation of PEO detected by NMR. This result is unlike other blend systems in which global and local motions have been compared.
Topography of the free-energy landscape probed via mechanical unfolding of proteins
Authors: Kirmizialtin Serdal , Huang Lei , Makarov Dmitrii E.
Published: June 2005

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical “chemical” reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)−fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed “slow phase” in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.
A potential model for the study of ices and amorphous water: TIP4P/Ice
Authors: Abascal J. L. F. , Sanz E. , García Fernández R. , Vega C.
Published: June 2005

The ability of several water models to predict the properties of ices is discussed. The emphasis is put on the results for the densities and the coexistence curves between the different ice forms. It is concluded that none of the most commonly used rigid models is satisfactory. A new model specifically designed to cope with solid-phase properties is proposed. The parameters have been obtained by fitting the equation of state and selected points of the melting lines and of the coexistence lines involving different ice forms. The phase diagram is then calculated for the new potential. The predicted melting temperature of hexagonal ice (Ih) at 1bar is 272.2K. This excellent value does not imply a deterioration of the rest of the properties. In fact, the predictions for both the densities and the coexistence curves are better than for TIP4P, which previously yielded the best estimations of the ice properties.
Nonlinear optical property calculations by the long-range-corrected coupled-perturbed Kohn–Sham method
Authors: Kamiya Muneaki , Sekino Hideo , Tsuneda Takao , Hirao Kimihiko
Published: June 2005

The long-range correction (LC) scheme for the exchange functional of density-functional theory (DFT) was combined with the coupled-perturbed Kohn–Sham (CPKS) method to calculate nonlinear optical response properties. By using this LC-CPKS method, we calculated the hyperpolarizabilities of typical molecules and the dipole moments, polarizabilities, and hyperpolarizabilities of push–pull π-conjugated systems: p-nitroaniline, 4-amino-4′-nitrostilbene, and α,ω-nitroaminopolyenes. It was found that the LC scheme clearly improved the calculation of these optical properties for all of these systems, which have been significantly overestimated by conventional DFTs. We therefore concluded that the long-range exchange interaction played an important role in calculating the optical properties using the DFT formalism.
Numerical model of the temperature dependence of the up-conversion efficiency of fluoride crystals codoped with ytterbium and thulium
Authors: Rapaport A. , Milliez J. , Bass M. , Cassanho A. , Jenssen H.
Published: June 2005

We review the role of temperature on the up-conversion efficiency of materials that are good candidates to be used as the three primary-color emitters in optically written displays. A rate equation model is given for the blue emitting material that includes temperature-dependent coefficients for energy transfer and cross relaxation. Increased temperature leads to decreased up-conversion efficiency. The effect of pumping conditions on heating the emitting material is illustrated and explained. Steps to reduce the temperature rise when pumping up-conversion materials are described.
Interior segment regrowth configurational-bias algorithm for the efficient sampling and fast relaxation of coarse-grained polyethylene and polyoxyethylene melts on a high coordination lattice
Authors: Rane Sagar S. , Mattice Wayne L.
Published: June 2005

We demonstrate the application of a modified form of the configurational-bias algorithm for the simulation of chain molecules on the second-nearest-neighbor-diamond lattice. Using polyethylene and poly(ethylene-oxide) as model systems we show that the present configurational-bias algorithm can increase the speed of the equilibration by at least a factor of 2–3 or more as compared to the previous method of using a combination of single-bead and pivot moves along with the Metropolis sampling scheme [N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953)]. The increase in the speed of the equilibration is found to be dependent on the interactions (i.e., the polymer being simulated) and the molecular weight of the chains. In addition, other factors not considered, such as the density, would also have a significant effect. The algorithm is an extension of the conventional configurational-bias method adapted to the regrowth of interior segments of chain molecules. Appropriate biasing probabilities for the trial moves as outlined by Jain and de Pablo for the configurational-bias scheme of chain ends, suitably modified for the interior segments, are utilized [T. S. Jain and J. J. de Pablo, in Simulation Methods for Polymers, edited by M. Kotelyanskii and D. N. Theodorou (Marcel Dekker, New York, 2004), pp. 223–255]. The biasing scheme satisfies the condition of detailed balance and produces efficient sampling with the correct equilibrium probability distribution of states. The method of interior regrowth overcomes the limitations of the original configurational-bias scheme and allows for the simulation of polymers of higher molecular weight linear chains and ring polymers which lack chain ends.
Laplacian in the hyperbolic space Hn and linearization stability of the Einstein equation for Robertson-Walker models
Authors: Bruna Lluís , Girbau Joan
Published: June 2005

We prove that some operators related to the rough Laplacian in the hyperbolic space give isomorphisms between Sobolev spaces of 1-forms. By using these results we prove that the Einstein equation of the hyperbolic Robertson-Walker cosmological model is linearization stable. We also study the linearization stability for Robertson-Walker models, V=S×I, with S compact, complete, having either constant negative or zero curvature.
Design of a standing-wave multicell radio frequency cavity beam monitor for simultaneous position and emittance measurement
Authors: Kim Jin-Soo , Miller Roger , Nantista Christopher
Published: June 2005

High precision, nondisruptive emittance measurement through second moment monitoring requires precise beam position at the measurement location. We present the design and analysis of a multicavity standing wave structure for a pulse-to-pulse beam position-emittance measurement system in which the quadrupole and the dipole standing wave modes resonate at harmonics of a presumed beam bunch train frequency. As an application for the Next Linear Collider (NLC) beams, an optimized nine-cavity standing-wave structure is designed for simultaneous high precision beam position and emittance measurement. It operates with the π-phase advance quadrupole mode resonating at the 16th harmonic (11.424 GHz) of the NLC bunch frequency and the 3π∕4-phase advance dipole mode at the 12th harmonic (8.568 GHz). The output powers from these modes are estimated for the NLC beams. Measurement resolution is estimated to be on the micron scale for rms beam size and on the nanometer scale for beam position.
Role of a native oxide on femtosecond laser interaction with silicon (100) near the damage threshold
Authors: McDonald Joel P. , McClelland Arthur A. , Picard Yoosuf N. , Yalisove Steven M.
Published: June 2005

Si (100) with and without a 14–25Å thick native oxide was laser machined at grazing incidence using a Ti:sapphire femtosecond pulsed laser under ultrahigh vacuum conditions. The resulting damage feature size and morphology indicate that the presence or absence of the native oxide significantly affects the mechanism for femtosecond laser-induced damage. We propose that a fluence-dependent modification of the oxide by the incident laser pulse must be considered when studying femtosecond laser damage of Si (100) with a native oxide. Data are also presented that are consistent with a dose-dependent phase transformation in the amorphous oxide. The implications of the native oxide, including relative damage thresholds of the underlying Si (100) and the role of the oxide in damage morphology are addressed.
An apparatus to investigate the fragmentation of molecular dications by electron impact
Authors: Alberti G. , Fainelli E. , Maracci F. , Mastropietro M. , Platania R. , Avaldi L.
Published: June 2005

An experimental setup to study the fragmentation of molecular dications formed via inner shell ionization by electron impact is described. The main components of the setup are a cylindrical mirror analyzer, CMA, used to detect the Auger electrons, which mark the molecular site where the ionization occurred and select the state of the dication, and a time of flight mass spectrometer, TOF-MS, used to detect the parent doubly charged ion or its fragments. The fragmentation is studied via Auger electron-ion and Auger electron-ion-ion coincidence experiments. The results of the measurements used to characterize the spectrometer are presented and discussed. Then the potentialities of the setup are described via selected examples of its applications.
High-efficiency top-emissive white-light-emitting organic electrophosphorescent devices
Authors: Kanno Hiroshi , Sun Yiru , Forrest Stephen R.
Published: June 2005

We demonstrate an efficient, top-emissive, white-light-emitting organic device (WOLED) employing the phosphorescent emitters, tris-(1-(4,6-difluorophenyl)pyridinato,N,C2′)iridium(III) and iridium(III) bis(2-phenyl quinolyl-N,C2′)acetylacetonate combining a sputtered Ni anode and an ITO cathode. The electron transport layer is doped with Li for efficient electron injection from the cathode, thereby also avoiding strong microcavity effects. The operating voltage is substantially reduced compared with a top-emissive device with an undoped electron transport layer. Peak external quantum and power efficiencies of 10.5±1.0% and 9.8±1.0lm∕W are achieved at current densities of 1.6 and 1.0mA∕cm2, respectively. The emission is characterized by Commission Internationale de L’Eclairage coordinates of (x=0.42, y=0.39). The top-emissive device, useful for generating full color images when combined with color filters or for display backlights, exhibits characteristics competitive with those of a bottom-emission WOLED using the same multilayer structure.
Development of a thermal neutron focusing device using neutron supermirrors
Authors: Osakabe Toyotaka , Soyama Kazuhiko
Published: June 2005

Neutron focusing is an indispensable technique used to compensate for weak signals in experiments under extreme conditions with tiny samples. We describe the development of a thermal neutron focusing device for a typical triple-axis neutron spectrometer. The device has a length of 400mm and is placed between the second collimator and the sample position. The focal length is 150mm from the downstream end of the device. The optic has 18 pieces of the circular blade consisting of 3m NiC∕Ti neutron supermirrors. The extensions of the end of each blade meet at the sample position, namely the focal point. Neutrons undergo successive reflection through the same angle from the inner surface of each blade and arrive at the sample position. The test results show that the gain of the neutron intensity at the sample position increases by a factor of 2 or more for the neutron energy below 30.5meV.
Thermal noise in a high Q ultracryogenic resonator
Authors: Vinante Andrea , Mezzena Renato , Prodi Giovanni Andrea , Vitale Stefano , Cerdonio Massimo , Bonaldi Michele , Falferi Paolo
Published: June 2005

A high Q electrical resonator based on a superconducting coil and a low loss capacitor has been realized and characterized at temperatures down to 60mK. The resonance frequency is near 10kHz, and the quality factor is higher than 105. The main purpose of the experiment is to test the feasibility of cooling to ultracryogenic temperatures the readout of the gravitational wave detector AURIGA, which is based on a high Q resonant electrical matching network. The resonator current noise, measured by a superconducting quantum interference device amplifier, scales with temperature in the full range 60mK–4.2K, showing that the system is thermal noise limited and its dissipating elements are well thermalized. Some implications of these results and possible applications are discussed.
Synthesis of blue-light-emitting Si1−xGex oxide nanowires
Authors: He J. H. , Wu W. W. , Lee S. W. , Chen L. J. , Chueh Y. L. , Chou L. J.
Published: June 2005

Blue-light-emitting Si1−xGex oxide nanowires have been grown on epitaxial Si0.8Ge0.2 alloys on silicon by thermal annealing in a quartz tube furnace in N2 ambient. The photoluminescence spectrum of Si1−xGex oxide nanostructures exhibits the blue-light emission with a peak at 415 nm, compared with the Si oxide nanowires with a peak at 470 nm. Nanowires with uncommon shapes, such as sunflowerlike and radiolarialike shape, have been observed. A field emission scanning electron microscope was used to monitor the growth of nanowires on the same patterned catalytic Au region. The growth can be understood in term of vapor-liquid-solid mechanism.
Pseudo-metal-base transistor with high gain
Authors: Meruvia Michelle S. , Benvenho Adriano R. V. , Hümmelgen Ivo A. , Pasa André A. , Schwarzacher Walther
Published: June 2005

We use evaporated C60 fullerene as emitter, a conducting polymer blend as base, and Si as collector in a vertical transistor structure similar to a metal-base transistor. The conducting polymer blend used as a base is poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate). The measured common-base current gain of our pseudo-metal-base transistor (p-MBT) is close to 1.0. The p-MBT is straightforward to fabricate and is compatible with conventional Si-based electronics.
Soliton transistor
Authors: Raissi Farshid
Published: June 2005

An all soliton transistor is introduced which uses a train of soliton-like vortices inside long Josephson junctions to turn off the movement of another train of vortices. In our practical realization, a long Josephson junction injects vortices into a reverse-biased Josephson fluxonic diode, corresponding to the ON state of the transistor. Injecting antivortices through a third long junction annihilates vortices before they could reach the Josephson fluxonic diode. This corresponds to the OFF state. Experimental results on the successful operation of this transistor as a NOT gate are provided.
Device modeling of long-channel nanotube electro-optical emitter
Authors: Tersoff J. , Freitag Marcus , Tsang James C. , Avouris Phaedon
Published: June 2005

We present a simple analytic model of long single-wall nanotube electro-optical emitters, along with experimental measurements using improved devices with reduced hysteresis. The model describes well the voltage-controlled motion of the emission spot, and provides a clear picture of the physical mechanism of device operation. It also indicates that the electric field is strongly enhanced at the emission spot, and that device performance can be greatly improved by the use of thinner gate oxides.
Microfluidic tunable dye laser with integrated mixer and ring resonator
Authors: Galas J. C. , Torres J. , Belotti M. , Kou Q. , Chen Y.
Published: June 2005

We report on results of design and fabrication of a microfluidic dye laser that consists of a ring resonator, a waveguide for laser emission output, and microfluidic elements for flow control, all integrated on a chip. The optical resonator and the waveguide were obtained by photolithography, whereas microfluidic elements such as channels, valves, and pumps were fabricated by multilayer soft lithography. As results, the prototype device worked with a few nanoliters of Rhodamine 6G dye molecules in ethanol solution and showed a laser threshold of ∼15μJ∕mm2 when optically pumped with a frequency doubled Nd:YAG laser at 532nm wavelength. The modification of the laser output intensity due to photobleaching effect was characterized by changing the dye flow velocity through the cavity. In addition, the emission wavelength of the laser could be easily tuned by changing the dye molecule concentration with the integrated microfluidic elements.
In situ observation of coalescence-related tensile stresses during metalorganic chemical vapor deposition of GaN on sapphire
Authors: Raghavan Srinivasan , Acord Jeremy , Redwing Joan M.
Published: June 2005

Surface roughness and stress evolution were monitored in situ during the growth of GaN on sapphire substrates using low-temperature AlN buffer layers of varying thickness. A reduction in buffer layer thickness decreases the concentration of GaN nucleation sites which in turn increases the time to nuclei coalescence, thus varying the temporal evolution of surface roughness. By monitoring the accompanying changes in stress evolution, it is shown that island coalescence consisting of initial contact followed by subsequent surface roughness reduction is a source of tensile stress during growth of GaN films on sapphire. Such delayed coalescence also leads to an improvement in the structural properties of the material.
The evolution of human anti-double-stranded DNA autoantibodies
Authors: Wellmann Ute , Letz Miriam , Herrmann Martin , Angermüller Sieglinde , Kalden Joachim R. , Winkler Thomas H.
Published: June 2005

It has been proposed that the anti-double-stranded DNA (dsDNA) response in patients with systemic lupus erythematosus (SLE) is antigen driven and that DNA or nucleosomes select anti-DNA reactive, somatically mutated B cells. We have used site-directed mutagenesis to systematically revert the somatic mutations of two human anti-dsDNA antibodies from SLE patients to analyze the resulting changes in DNA binding as well as binding to other autoantigens. Our data demonstrate that high-affinity binding to dsDNA and nucleosomes is acquired by somatic replacement mutations in a stepwise manner. Reactivity to surface structures of apoptotic cells is acquired by the same somatic mutations that generate high-affinity dsDNA binding. Importantly, revertant antibodies with germ-line V regions did not show any measurable DNA reactivity. We propose that anti-DNA autoantibodies are generated from nonautoreactive B cells during a normal immune response. B cells may acquire autoreactivityde novoduring the process of somatic hypermutation. Nucleosomes, if available in lupus patients because of defects in clearing of apoptotic debris, might subsequently positively select high affinity anti-DNA B cells.
Genomic evolution of MHC class I region in primates
Authors: Fukami-Kobayashi Kaoru , Shiina Takashi , Anzai Tatsuya , Sano Kazumi , Yamazaki Masaaki , Inoko Hidetoshi , Tateno Yoshio
Published: June 2005

To elucidate the origins of the MHC-B-MHC-C pair and the MHC class I chain-related molecule (MIC)A-MICB pair, we sequenced an MHC class I genomic region of humans, chimpanzees, and rhesus monkeys and analyzed the regions from an evolutionary stand-point, focusing first on LINE sequences that are paralogous within each of the first two species and orthologous between them. Because all the long interspersed nuclear element (LINE) sequences were fragmented and nonfunctional, they were suitable for conducting phylogenetic study and, in particular, for estimating evolutionary time. Our study has revealed that MHC-B and MHC-C duplicated 22.3 million years (Myr) ago, and the ape MICA and MICB duplicated 14.1 Myr ago. We then estimated the divergence time of the rhesus monkey by using other orthologous LINE sequences in the class I regions of the three primate species. The result indicates that rhesus monkeys, and possibly the Old World monkeys in general, diverged from humans 27-30 Myr ago. Interestingly, rhesus monkeys were found to have not the pair of MHC-B and MHC-C but many repeated genes similar to MHC-B. These results support our inference that MHC-B and MHC-C duplicated after the divergence between apes and Old World monkeys.
Ovarian brain-derived neurotrophic factor (BDNF) promotes the development of oocytes into preimplantation embryos
Authors: Kawamura Kazuhiro , Kawamura Nanami , Mulders Sabine M. , Gelpke Maarten D. Sollewijn , Hsueh Aaron J. W.
Published: June 2005

Optimal development of fertilized eggs into preimplantation embryos is essential for reproduction. Although mammalian oocytes ovulated after luteinizing hormone (LH) stimulation can be fertilized and promoted into early embryosin vitro, little is known about ovarian factors important for the conditioning of eggs for early embryo development. Because LH interacts only with ovarian somatic cells, its potential regulation of oocyte functions is presumably mediated by local paracrine factors. We performed DNA microarray analyses of ovarian transcripts and identified brain-derived neurotrophic factor (BDNF) secreted by granulosa and cumulus cells as an ovarian factor stimulated by the preovulatory LH surge. Ovarian BDNF acts on TrkB receptors expressed exclusively in oocytes to enhance first polar body extrusion of oocytes and to promote thein vitrodevelopment of zygotes into preimplantation embryos. Furthermore,in vivotreatment with a Trk receptor inhibitor suppressed first polar body extrusion and the progression of zygotes into blastocysts. Thus, ovarian BDNF is important to nuclear and cytoplasmic maturation of the oocyte, which is essential for successful oocyte development into preimplantation embryos. Treatment with BDNF could condition the cultured oocytes for optimal progression into the totipotent blastocysts.
Structure of bacterial tubulin BtubA/B: Evidence for horizontal gene transfer
Authors: Schlieper Daniel , Oliva María A. , Andreu José M. , Löwe Jan
Published: June 2005

αβ-Tubulin heterodimers, from which the microtubules of the cytoskeleton are built, have a complex chaperone-dependent folding pathway. They are thought to be unique to eukaryotes, whereas the homologue FtsZ can be found in bacteria. The exceptions are BtubA and BtubB from
Prosthecobacter
, which have higher sequence homology to eukaryotic tubulin than to FtsZ. Here we show that some of their properties are different from tubulin, such as weak dimerization and chaperone-independent folding. However, their structure is strikingly similar to tubulin including surface loops, and BtubA/B form tubulin-like protofilaments. Presumably, BtubA/B were transferred from a eukaryotic cell by horizontal gene transfer because their high degree of similarity to eukaryotic genes is unique within the
Prosthecobacter
genome.
Cell intrinsic alterations underlie hematopoietic stem cell aging
Authors: Rossi Derrick J. , Bryder David , Zahn Jacob M. , Ahlenius Henrik , Sonu Rebecca , Wagers Amy J. , Weissman Irving L.
Published: June 2005

Loss of immune function and an increased incidence of myeloid leukemia are two of the most clinically significant consequences of aging of the hematopoietic system. To better understand the mechanisms underlying hematopoietic aging, we evaluated the cell intrinsic functional and molecular properties of highly purified long-term hematopoietic stem cells (LT-HSCs) from young and old mice. We found that LT-HSC aging was accompanied by cell autonomous changes, including increased stem cell self-renewal, differential capacity to generate committed myeloid and lymphoid progenitors, and diminished lymphoid potential. Expression profiling revealed that LT-HSC aging was accompanied by the systemic down-regulation of genes mediating lymphoid specification and function and up-regulation of genes involved in specifying myeloid fate and function. Moreover, LT-HSCs from old mice expressed elevated levels of many genes involved in leukemic transformation. These data support a model in which age-dependent alterations in gene expression at the stem cell level presage downstream developmental potential and thereby contribute to age-dependent immune decline, and perhaps also to the increased incidence of leukemia in the elderly.
Real-time RNA profiling within a single bacterium
Authors: Le Thuc T. , Harlepp Sébastien , Guet Călin C. , Dittmar Kimberly , Emonet Thierry , Pan Tao , Cluzel Philippe
Published: June 2005

Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of
Escherichia coli
exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.
Genetic evidence for a protein-kinase-A-mediated presynaptic component in NMDA-receptor-dependent forms of long-term synaptic potentiation
Authors: Huang Yan-You , Zakharenko Stanislav S. , Schoch Susanne , Kaeser Pascal S. , Janz Roger , Südhof Thomas C. , Siegelbaum Steven A. , Kandel Eric R.
Published: June 2005

The synaptic vesicle protein Rab3A is a small GTP-binding protein that interacts with rabphilin and RIM1α, two presynaptic substrates of protein kinase A (PKA). Mice lacking RIM1α and Rab3A have a defect in PKA-dependent and NMDA receptor (NMDAR)-independent presynaptic long-term potentiation (LTP) at hippocampal mossy-fiber and cerebellar parallel-fiber synapses. In contrast, the NMDAR-dependent and PKA-independent early phase of LTP at hippocampal CA3–CA1 synapses does not require these presynaptic proteins. Here, we ask whether Rab3A and RIM1α participate in forms of LTP that require both PKA and NMDAR activation. We find that Rab3A is necessary for corticoamygdala LTP and late-phase LTP at CA3–CA1 synapses, two forms of LTP that require NMDAR and PKA activation. The latter form of LTP also requires RIM1α. These results provide genetic evidence that presynaptic proteins are required in LTP induced through the postsynaptic activation of NMDARs. Thus Rab3A and its effectors are general modules for four distinct types of PKA-dependent LTP in the brain.
In search of an auditory engram
Authors: Fritz Jonathan , Mishkin Mortimer , Saunders Richard C.
Published: June 2005

Monkeys trained preoperatively on a task designed to assess auditory recognition memory were impaired after removal of either the rostral superior temporal gyrus or the medial temporal lobe but were unaffected by lesions of the rhinal cortex. Behavioral analysis indicated that this result occurred because the monkeys did not or could not use long-term auditory recognition, and so depended instead on short-term working memory, which is unaffected by rhinal lesions. The findings suggest that monkeys may be unable to place representations of auditory stimuli into a long-term store and thus question whether the monkey's cerebral memory mechanisms in audition are intrinsically different from those in other sensory modalities. Furthermore, it raises the possibility that language is unique to humans not only because it depends on speech but also because it requires long-term auditory memory.
The optimum orientation of an absorbing barrier
Authors: Rawlins A.D
Published: June 2005

In the following work, we solve the problem of the best orientation of a rigid noise barrier, which has one face lined with absorbent material, between a noise source and a receiver point in the shadow region of the barrier. By the ‘best orientation’, we mean that positioning of the barrier which yields the least noise level at the receiving point for a given barrier and source position.
Packing regular triplets of circles on a sphere
Authors: Fowler P.W , Tarnai T , Kabai S
Published: June 2005

This article examines how 3Nnon-overlapping equal circles formingNtriplets must be packed on a sphere to ensure that the angular diameter of the circles will be as large as possible. Furthermore, this problem is solved under the constraint that, within each triplet, the circle centres lie at the vertices of an equilateral triangle inscribed into a great circle of the sphere. Computer-generated solutions to this optimization problem are presented forN=2–7 triplets. The configurations obtained are characterized as compounds (nolids) of equilateral triangles.
Reputation and the evolution of cooperation in sizable groups
Authors: Suzuki Shinsuke , Akiyama Eizo
Published: June 2005

The evolution of cooperation in social dilemmas has been of considerable concern in various fields such as sociobiology, economics and sociology. It might be that, in the real world, reputation plays an important role in the evolution of cooperation. Recently, studies that have addressed indirect reciprocity have revealed that cooperation can evolve through reputation, even though pairs of individuals interact only a few times. To our knowledge, most indirect reciprocity models have presumed dyadic interaction; no studies have attempted analysis of the evolution of cooperation in large communities where the effect of reputation is included. We investigate the evolution of cooperation in sizable groups in which the reputation of individuals affects the decision-making process. This paper presents the following: (i) cooperation can evolve in a four-person case, (ii) the evolution of cooperation becomes difficult as group size increases, even if the effect of reputation is included, and (iii) three kinds of final social states exist. In medium-sized communities, cooperative species can coexist in a stable manner with betrayal species.
Aposematism and crypsis combined as a result of distance dependence: functional versatility of the colour pattern in the swallowtail butterfly larva
Authors: Tullberg Birgitta S , Merilaita Sami , Wiklund Christer
Published: June 2005

The idea that an aposematic prey combines crypsis at a distance with conspicuousness close up was tested in an experiment using human subjects. We estimated detectability of the aposematic larva of the swallowtail butterfly,Papilio machaon, in two habitats, by presenting, on a touch screen, photographs taken at four different distances and measuring the time elapsed to discovery. The detectability of larvae in these images was compared with images that were manipulated, using existing colours either to increase or decrease conspicuousness. Detection time increased with distance for all colourations. However, at the closest distance, detection time was longer for the larvae manipulated to be more cryptic than for the natural and more conspicuous forms. This indicates that the natural colouration is not maximally cryptic at a short distance. Further, smaller increments in distance were needed to increase detection time for the natural than for the conspicuous larva. This indicates that the natural colouration is not maximally conspicuous at longer distances. Taken together, we present the first empirical support for the idea that some colour patterns may combine warning colouration at a close range with crypsis at a longer range. The implications of this result for the evolution of aposematism are discussed.
Niches, rather than neutrality, structure a grassland pioneer guild
Authors: Turnbull Lindsay A , Manley Liz , Rees Mark
Published: June 2005

Pioneer species are fast-growing, short-lived gap exploiters. They are prime candidates for neutral dynamics because they contain ecologically similar species whose low adult density is likely to cause widespread recruitment limitation, which slows competitive dynamics. However, many pioneer guilds appear to be differentiated according to seed size. In this paper, we compare predictions from a neutral model of community structure with three niche-based models in which trade-offs involving seed size form the basis of niche differentiation. We test these predictions using sowing experiments with a guild of seven pioneer species from chalk grassland. We find strong evidence for niche structure based on seed size: specifically large-seeded species produce fewer seeds but have a greater chance of establishing on a per-seed basis. Their advantage in establishment arises because there are more microsites suitable for their germination and early establishment and not directly through competition with other seedlings. In fact, seedling densities of all species were equally suppressed by the addition of competitors' seeds. By the adult stage, despite using very high sowing densities, there were no detectable effects of interspecific competition on any species. The lack of interspecific effects indicates that niche differentiation, rather than neutrality, prevails.
Higher-level mechanisms detect facial symmetry
Authors: Rhodes Gillian , Peters Marianne , Lee Kieran , Morrone M. Concetta , Burr David
Published: June 2005

The role of symmetry detection in early visual processing and the sensitivity of biological visual systems to symmetry across a wide range of organisms suggest that symmetry can be detected by low-level visual mechanisms. However, computational and functional considerations suggest that higher-level mechanisms may also play a role in facial symmetry detection. We tested this hypothesis by examining whether symmetry detection is better for faces than comparable patterns, which share low-level properties with faces. Symmetry detection was better for upright faces than for inverted faces (experiment 1) and contrast-reversed faces (experiment 2), implicating high-level mechanisms in facial symmetry detection. In addition, facial symmetry detection was sensitive to spatial scale, unlike low-level symmetry detection mechanisms (experiment 3), and showed greater sensitivity to a 45° deviation from vertical than is found for other aspects of face perception (experiment 4). These results implicate specialized, higher-level mechanisms in the detection of facial symmetry. This specialization may reflect perceptual learning resulting from extensive experience detecting symmetry in faces or evolutionary selection pressures associated with the important role of facial symmetry in mate choice and ‘mind-reading’ or both.
Flood risk management in the Thames Estuary looking ahead 100 years
Authors: Lavery Sarah , Donovan Bill
Published: June 2005

The River Thames tidal defences have provided protection against the increasing threat of tidal flooding from the North Sea for more than 2000 years. The flood of 1953 was the catalyst for the construction of the current system of River Thames tidal defences, which includes the Thames Barrier, and has provided one of the best standards of flood defence in the UK for over 20 years.

Substantial growth is planned through ‘Thames Gateway’, a regeneration initiative of the United Kingdom government. These new developments will fundamentally change the developed footprint in the Thames Estuary flood-plain, and will be in place for at least the next 100 years. This presents a challenge of planning future defence against a background of uncertainty over climate and other environmental change, while ensuring that correct decisions are made concerning the nature and location of new building in the tidal flood-plain.

Through its ‘Thames Estuary 2100’ project, the Environment Agency is developing a long-term strategy for flood risk management in the estuary. Implementation of major construction works on the River Thames could commence from around 2015. Alternatively, it may be decided that minimum works are undertaken to provide security and major investment is delayed until uncertainties over climate change have abated. Whatever long-term option is chosen, this must be preceded by a period of collaboration with the Thames Gateway developments to ensure appropriate and sustainable flood defences are incorporated in new riverside construction.
Revisiting the roots of learning organization
Authors: Yeo Roland K.
Published: June 2005

Purpose

This paper aims to provide a literature synthesis of the learning organization and discuss several pertinent theoretical concepts on the subject.

Design/methodology/approach

A range of works mainly from 1990‐2004, which aim at providing a variety of perspectives on the learning organization, have been analyzed and discussed based on its theoretical roots and ontological perspectives.

Findings

The synthesis of the literature reveals several common themes from the various learning organization definitions and discovers the greater significance of systems thinking in Senge's five disciplines.

Research limitations/implications

It is not an exhaustive coverage of the learning organization literature. However it offers great research implications where several key concepts can be further explored. For example, is systems thinking really crucial to organizational learning?

Practical implications

Practitioners may find the analysis of the various models in relation to Senge's five disciplines useful, as there are concepts that can be implemented in practice.

Originality/value

It is the amalgamation of several key concepts in the learning organization and the analysis of these concepts in relation toThe Fifth Disciplinewhich readers will be familiar and able to identify with. People who are interested in pursuing research in the learning organization will find this paper handy as it provides a useful overview of the subject.
Organizational learning vs the learning organization: a conversation with a practitioner
Authors: Gorelick Carol
Published: June 2005

Purpose

Through a conversation with a practitioner, aims to understand the definitions given to the learning organization and how they relate to a model of organizational learning.

Design/methodology/approach

Provides a brief overview of a conversation concerning organizational learning vs the learning organization.

Findings

Organizational learning and the learning organization can and should co‐exist. To be effective as a learning organization there is a need for a deep learning cycle and recognition that it will take time.

Originality/value

Offers advice on how to be an effective learning organization.
Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography
Authors: Macey J. Robert
Published: June 2005

A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004; PNAS, 101, 13820–13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the “Out of Appalachia” hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed.

© The Willi Hennig Society 2005.
Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological data
Authors: Worsaae Katrine
Published: June 2005

A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision.

© The Willi Hennig Society 2005.