bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic description of a plasma-loaded free-electron laser
Authors: Babaei S. , Maraghechi B.
Published: May 2007

A kinetic theory is used to find the dispersion relation of a plasma-loaded free-electron laser that takes into account the velocity spread of both beam and plasma electrons. For the weak-coupling regime, the dispersion relation for a cold electron beam and plasma is obtained and is studied numerically. The kinetic theory predicts that, for the cold beam and plasma, plasma density increases the growth rate of the higher-frequency resonance and lowers it for the lower-frequency resonance up to a certain plasma density. By increasing the plasma density further, a critical density will be reached that diminishes the instability.
Vibrational excitation energies from vibrational coupled cluster response theory
Authors: Seidler Peter , Christiansen Ove
Published: May 2007

Response theory in the context of vibrational coupled cluster (VCC) theory is introduced and used to obtain vibrational excitation energies. The relation to the vibrational configuration interaction (VCI) approach is described, and the increase in accuracy of VCC response energies relative to VCI energies is discussed theoretically in terms of a perturbational order expansion and demonstrated numerically. To illustrate the theory, a pilot implementation is used to obtain anharmonic vibrational frequencies for fundamental, first overtone and combination excitations of formaldehyde as well as for the fundamental transitions of ethylene.
Diffusion and drift of a blob of partially ionized plasma in a magnetic field
Authors: Rozhansky V. , Senichenkov I. , Veselova I.
Published: May 2007

Considered is the three-dimensional expansion and drift of a partially ionized plasma blob in a magnetic field. The pressure and density of neutrals are assumed to be strongly inhomogeneous functions of coordinates. It is shown that when the magnetic field pressure is much stronger than the net blob pressure and the mean free path of neutrals is smaller than the blob perpendicular size, the blob expands diffusively across the magnetic field. The strong radial electric field arises to provide quasineutrality, which causes the blob rotation in the azimuth direction. It is demonstrated that the blob injected with an initial velocity V0 across a magnetic field continues its motion with the same velocity due to additional polarization electric field of a dipole type. The total electric field structure of the blob is rather complicated. It is demonstrated that the partially ionized blob continues to move with the initial velocity even if the pressure of the ambient plasma is higher than the blob pressure.
Parametric up-conversion of an electron Bernstein mode by a relativistic electron beam in a plasma
Authors: Kumar Asheel , Tripathi V. K.
Published: May 2007

A relativistic electron beam, propagating with velocity v0b‖ẑ in a magnetized plasma, parametrically up-converts a pre-existing electron Bernstein wave (ω0,k0) into electromagnetic radiation when k0∙v0b<0. The Bernstein wave couples with a negative energy space-charge mode (ω,k) to produce a frequency up-converted sideband electromagnetic wave. The sideband and the Bernstein wave exert a ponderomotive force, driving space-charge mode. In the Compton regime, the growth rate of the parametric instability scales as two-third power of the pump amplitude, whereas in the Raman regime, it goes linearly.
Photophysics of Pt-porphyrin electrophosphorescent devices emitting in the near infrared
Authors: Sun Yiru , Borek Carsten , Hanson Kenneth , Djurovich Peter I. , Thompson Mark E. , Brooks Jason , Brown Julie J. , Forrest Stephen R.
Published: May 2007

The triplet annihilation dynamics of near infrared organic light-emitting devices are studied with peak electrophosphorescence at a wavelength of 772nm using a platinum-porphyrin derivative Pt(II)-tetraphenyltetrabenzoporphyrin as dopant. Both the photoluminescent decay transients of the thin films and the quantum efficiency versus current density characteristics of devices using tris(8-hydroxyquinoline) aluminum or 4,4′-bis(N-carbazolyl)biphenyl (CBP) as hosts are fitted by a model based on triplet-triplet annihilation. When the phosphor is codoped with Ir(III) bis(2-phenyl quinolyl-N,C2′) acetylacetonate in CBP, the quantum efficiency is enhanced, and the observed decrease of efficiency at high current densities is explained by field-induced charge pair dissociation. The external quantum efficiency has a maximum of (8.5±0.3)%, decreasing to (5.0±0.3)% at 1mA∕cm2.
Structural correlations of the enhancement of dielectric permittivity in the (Ta2O5)0.92(TiO2)0.08 system
Authors: Liu X. Q. , Han X. D. , Zhang Z. , Ji L. F. , Jiang Y. J.
Published: May 2007

A Ti-ion ordering which correlates to the significant enhancement of the dielectric constant was determined in the (Ta2O5)0.92(TiO2)0.08 system by high resolution electron microscopy and the corresponding simulations. The alien Ti ions were determined to selectively sit on the octahedral locations in the Ta2O5 base structure in an average of 9-time period along the ⟨110⟩ direction. The authors suggest this Ti-ion ordering induces the directional enhancement of the dielectric permittivity of the (Ta2O5)0.92(TiO2)0.08 system. The atomic mechanism of this modulated structure contributing to the enhancement of the dielectric constant was qualitatively interpreted using a one-dimensional chain model. The structural correlations of the dielectric enhancement revealed in this study suggest a way to search or design high-k materials.
Antiadhesion considerations for UV nanoimprint lithography
Authors: Houle F. A. , Rettner C. T. , Miller D. C. , Sooriyakumaran R.
Published: May 2007

Low surface energy fluorosilane layers are widely used as release coatings for quartz templates in UV nanoimprint lithography, yet they are generally found to degrade with use. It is found that these layers are chemically attacked when used with UV cured methacrylate and vinyl ether resists, as found previously for acrylate resists, leading to the conclusion that low reactivity and not low surface energy is of importance for effective release layers. It is shown that an ion-beam deposited diamondlike carbon release coating is a useful alternative, having both stability in a reactive environment and lower adhesion despite its higher surface energy.
Enhanced current flow through meandering grain boundaries in YBa2Cu3O7−δ films
Authors: Dinner Rafael B. , Moler Kathryn A. , Beasley M. R. , Feldmann D. Matthew
Published: May 2007

In YBa2Cu3O7−δ (YBCO) coated conductors grown by metal organic deposition, in-plane meandering of grain boundaries (GBs) has been linked to higher critical current density. The authors investigate this link in individual GBs using transport measurements and scanning Hall probe microscopy with current reconstruction. They observe current-induced flux entry into a coated conductor, then model its behavior by imaging YBCO films with single, straight GBs tilted at various angles to the applied current. They find a strong dependence of critical current on angle, sufficient to explain the enhancement observed for meandering GBs.
On the relationship between densities of Shannon entropy and Fisher information for atoms and molecules
Authors: Liu Shubin
Published: May 2007

An analytical relationship between the densities of the Shannon entropy and Fisher information for atomic and molecular systems has been established in this work. Two equivalent forms of the Fisher information density are introduced as well. It is found that for electron densities of atoms and molecules the Shannon entropy density is intrinsically related to the electron density and the two forms of the Fisher information density. The formulas have been confirmed by the numerical results for the first two-row atoms.
First hyperpolarizability of polymethineimine with long-range corrected functionals
Authors: Jacquemin Denis , Perpète Eric A. , Medved’ Miroslav , Scalmani Giovanni , Frisch Michael J. , Kobayashi Rika , Adamo Carlo
Published: May 2007

Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated the longitudinal dipole moments and static electronic first hyperpolarizabilities of increasingly long polymehtineimine oligomers. For comparison purposes Hartree-Fock (HF), Møller-Plesset perturbation theory (MP2), and conventional pure and hybrid functionals have been considered as well. HF, generalized gradient approximation (GGA), and conventional hybrids provide too large dipole moments for long oligomers, while LC-DFT allows to reduce the discrepancy with respect to MP2 by a factor of 3. For the first hyperpolarizability, the incorrect evolution with the chain length predicted by HF is strongly worsened by BLYP, Perdew-Burke-Ernzerhof (PBE), and also by B3LYP and PBE0. On the reverse, LC-BLYP and LC-PBE hyperpolarizabilities are correctly predicted to be positive (but for the two smallest chains). Indeed, for medium and long oligomers LC hyperpolarizabilities are slightly smaller than MP2 hyperpolarizabilities, as it should be. CAM-B3LYP also strongly improves the B3LYP results, though a bit less impressively for small chain lengths. The present study demonstrates the efficiency of long-range DFT, even in very pathological cases.
Multiphonon Raman scattering in GaN nanowires
Authors: Dhara S. , Chandra Sharat , Mangamma G. , Kalavathi S. , Shankar P. , Nair K. G. M. , Tyagi A. K. , Hsu C. W. , Kuo C. C. , Chen L. C. , Chen K. H. , Sriram K. K.
Published: May 2007

UV Raman scattering studies show longitudinal optical (LO) mode up to fourth order in wurtzite GaN nanowire system. Fröhlich interaction of electron with the long range electrostatic field of ionic bonded GaN gives rise to enhancement in LO phonon modes. Good crystalline quality, as indicated by the crystallographic as well as luminescence studies, is thought to be responsible for this significant observation. Calculated size dependence, incorporating size corrected dielectric constants, of electron-phonon interaction energy agrees well with measured values and also predict stronger interaction energy than that of the bulk for diameter below ∼3nm.
Bias-dependent contact resistance in rubrene single-crystal field-effect transistors
Authors: Molinari Anna , Gutiérrez Ignacio , Hulea Iulian N. , Russo Saverio , Morpurgo Alberto F.
Published: May 2007

The authors report a systematic study of the bias-dependent contact resistance in rubrene single-crystal field-effect transistors with Ni, Co, Cu, Au, and Pt electrodes. They show that the reproducibility in the values of contact resistance strongly depends on the metal, ranging from a factor of 2 for Ni to more than three orders of magnitude for Au. Surprisingly, field-effect transistors with Ni, Co, and Cu contacts exhibit an unexpected reproducibility of the bias-dependent differential conductance of the contacts once this has been normalized to the value measured at zero bias. This reproducibility may enable the study of microscopic carrier injection processes into organic semiconductors.
Highly circularly polarized electroluminescence from organic light-emitting diodes with wide-band reflective polymeric cholesteric liquid crystal films
Authors: Jeong Soon Moon , Ohtsuka Youko , Ha Na Young , Takanishi Yoichi , Ishikawa Ken , Takezoe Hideo , Nishimura Suzushi , Suzaki Goroh
Published: May 2007

The authors have observed highly circularly polarized electroluminescence from organic light-emitting diodes (OLEDs) using wide-band reflector consisting of three-layered left-handed polymeric cholesteric liquid crystal (PCLC) films. By simply attaching the wide-band reflective PCLC reflector to a conventional OLED, the authors obtained a high degree of circular polarization, i.e., the ratio of brightness between right- and left-handed circularly polarized electroluminescences is over 10 over the whole emission band.
Ferroelectric and paraelectric Ba0.5Sr0.5TiO3 film structure distortions at room temperature and their effects on tunable microwave properties
Authors: Alldredge L. M. B. , Chang Wontae , Qadri Syed B. , Kirchoefer Steven W. , Pond Jeffrey M.
Published: May 2007

Sputter-deposited Ba0.5Sr0.5TiO3 films on (001) MgO were characterized for their dielectric properties with different lattice structures. With varying Ar:O2 ratios during deposition, the films showed either in-plane (ca) tetragonal distortions, significantly affecting the dielectric constant and tunability. The dielectric constant exhibited clear hysteresis with dc bias at room temperature, indicating that the films were ferroelectric. The relationship between the dielectric properties and the distortions was the reverse of that observed in films deposited by pulsed laser deposition. The anisotropic in-plane dielectric behavior can be understood by relating polarization to film distortions and to the presence of permanent dipoles.
Rate-dependent inhomogeneous-to-homogeneous transition of plastic flows during nanoindentation of bulk metallic glasses: Fact or artifact?
Authors: Jang Jae-il , Yoo Byung-Gil , Kim Ju-Young
Published: May 2007

There has been considerable controversy over the “apparent” rate-dependent transition from inhomogeneous-to-homogeneous flow during nanoindentation of bulk metallic glasses (BMGs) at room temperature: whether it arises from the existence of homogeneous-flow regime in BMG deformation map or is an artifact due to the instrumental blurring at high rates. To provide a clue to address this dispute, the authors performed nanoindentation experiments on a Zr-based BMG with two geometrically self-similar indenters. The results are discussed in terms of the discrete plasticity ratio, which is a useful parameter in analyzing the contribution of inhomogeneous plasticity to the total plastic deformation.
On-chip surface-enhanced Raman scattering detection using integrated liquid-core waveguides
Authors: Measor Philip , Seballos Leo , Yin Dongliang , Zhang Jin Z. , Lunt Evan J. , Hawkins Aaron R. , Schmidt Holger
Published: May 2007

The authors demonstrate surface-enhanced Raman scattering (SERS) detection on an optofluidic chip. Interconnected solid- and liquid-core antiresonant reflecting optical waveguides (ARROWs) form a planar beam geometry that allows for high mode intensities along microfluidic channels containing molecules optimized for SERS. The excitation power and concentration dependence of SERS from rhodamine 6G (R6G) molecules adsorbed to silver nanoparticles were systematically studied. The data can be described by a model that takes into account the microphotonic structure. Detection sensitivity to a minimum concentration of 30nM is found, demonstrating the suitability of ARROW-based optofluidic chips for high sensitivity detection with molecular specificity.
Investigations of the light-induced scattering varied with HfO2 codoping in LiNbO3:Fe crystals
Authors: Yan Wenbo , Chen Hongjian , Shi Lihong , Liu Shiguo , Kong Yongfa
Published: May 2007

Light-induced scattering in LiNbO3:Fe crystals codoped with different concentrations of HfO2 has been investigated. Unusual behaviors with varied HfO2 codoping are observed and explained. Li vacancies are suggested to be the main contributor to the dark conductivity of the crystal and subsequently to induce the threshold effect of the pump light intensity for the light-induced scattering. High photovoltaic field produced in the crystals is thought to be the cause of the serious light-induced scattering at high pump intensity. As a result, LiNbO3:Fe, Hf crystals exhibit an enhanced ability to suppress the light-induced scattering at moderate pump intensity.
Bendable integrated circuits on plastic substrates by use of printed ribbons of single-crystalline silicon
Authors: Ahn Jong-Hyun , Kim Hoon-Sik , Menard Etienne , Lee Keon Jae , Zhu Zhengtao , Kim Dae-Hyeong , Nuzzo Ralph G. , Rogers John A. , Amlani Islamshah , Kushner Vadim , Thomas Shawn G. , Duenas Terrisa
Published: May 2007

This letter presents studies of several simple integrated circuits—n-channel metal-oxide semiconductor inverters, five-stage ring oscillators, and differential amplifiers—formed on thin, bendable plastic substrates with printed ribbons of ultrathin single-crystalline silicon as the semiconductor. The inverters exhibit gains as high as 2.5, the ring oscillators operate with oscillation frequencies between 8 and 9MHz at low supply voltages (∼4V), and the differential amplifiers show good performance and voltage gains of 1.3 for 500mV input signals. The responses of these systems to bending-induced strains show that relatively moderate changes of individual transistors can be significant for the operation of circuits that incorporate many transistors.
Improved ferroelectric and leakage properties in symmetric BiFeO3∕SrTiO3 superlattice
Authors: Bose Somenath , Krupanidhi S. B.
Published: May 2007

Symmetric BiFeO3∕SrTiO3 superlattices were fabricated by pulsed laser deposition on SrTiO3 (100) substrates. Frequency independent and near saturated P-E hysteresis was observed in the case of a superlattice (periodicity of ∼11nm) as compared to leaky hysteresis observed in epitaxial BiFeO3. Room temperature leakage current density of the superlattice was almost two orders of magnitude lower than that of BiFeO3. Observed leakage current behavior in case of both BiFeO3 and superlattice indicates the dominance of space charge limited conduction. Improvement in ferroelectric property was discussed in connection to enhanced epitaxial strain, reduced leakage current, and electrostatic interaction between BiFeO3 and SrTiO3.
Ohmic contacts to p-type GaN based on TaN, TiN, and ZrN
Authors: Voss L. F. , Stafford L. , Khanna R. , Gila B. P. , Abernathy C. R. , Pearton S. J. , Ren F. , Kravchenko I. I.
Published: May 2007

Ohmic contacts to p-GaN using a Ni∕Au∕X∕Ti∕Au metallization scheme, where X is TaN, TiN, or ZrN, are reported. The dependence of the contact properties on annealing temperature (25–1000°C) in N2 is examined. For annealing temperatures greater than 500°C, the contacts display Ohmic characteristics and reach a minimum of about 2×10−4Ωcm2 after annealing at 700°C for 60s in a N2 ambient. The specific contact resistance is stable on annealing up to at least 1000°C. However, at high temperatures the morphology of the contacts are very rough and there is a large degree of intermixing between the metallic layers. The thermal stability of these contacts are superior as compared to conventional Ni∕Au, which display poor characteristics at annealing temperatures greater than 500°C.
Structural and optical properties of ZnO∕Mg0.1Zn0.9O multiple quantum wells grown on ZnO substrates
Authors: Zhu Junjie , Kuznetsov A. Yu. , Han Myung-Soo , Park Young-Sik , Ahn Haeng-Keun , Ju Jin-Woo , Lee In-Hwan
Published: May 2007

Zn O ∕ Mg 0.1 Zn 0.9 O multiquantum-well (MQW) structures were grown on ZnO substrates by molecular beam epitaxy. Abrupt interfaces and well/barrier width in the MQWs were confirmed by x-ray diffraction measurement and transmission electron microscopy. The transition energy of the localized exciton in the ZnO∕Mg0.1Zn0.9O MQWs with well/barrier width of 5∕8nm was found to be about 3.375eV at low temperature, consistent with theoretical calculation. The first subband energies in the conduction and valence band were calculated to be 19.2 and 5.4meV, respectively. The transition energy showed no shift with excitation power, indicating that the polarization-induced electric field is negligible in the ZnO∕Mg0.1Zn0.9O MQW structures.
Saturated and efficient blue phosphorescent organic light emitting devices with Lambertian angular emission
Authors: Mulder C. L. , Celebi K. , Milaninia K. M. , Baldo M. A.
Published: May 2007

The authors employ a microcavity to optimize the color of a phosphorescent organic light emitting device (OLED) based on the-sky blue phosphor FIrpic. The output of the OLED is filtered by scattering media to correct the angular emission intensity profile and eliminate the angular dependence of the color. With a holographic diffuser as the scattering medium, the microcavity OLED achieves an external quantum efficiency of (5.5±0.6)%, as compared to (3.8±0.4)% for a conventional structure. The color coordinates of the microcavity OLED with holographic diffuser are (x,y)=(0.116±0.004,0.136±0.010) with minimal angular color shift and a nearly ideal Lambertian angular emission profile.
Scanning near-field electron beam induced current microscopy: Application to III-V heterostructures and quantum dots
Authors: Troyon M. , Smaali K.
Published: May 2007

High resolution electron beam induced current (EBIC) analyses were carried out on InAs quantum dots (QDs) grown on GaAs substrate, in a scanning electron microscope (SEM) and a conducting atomic force microscope (C-AFM) hybrid system. This scanning near-field EBIC microscope allows one to image a sample conventionally by SEM, to investigate by AFM the local topography and to simultaneously perform EBIC imaging. The EBIC capabilities of this combined instrument are evidenced by imaging plastic slip lines created by nanoindentation, and its performance in resolution is demonstrated to be of the order of 20nm by imaging the induced current flowing through the InAs∕GaAs QDs and the ringlike structures that surround them. The influence of the presence of QDs on the minority carrier diffusion length is also investigated. It is shown that the presence of QDs close to the surface sample increases the diffusion length.
Influence of local-scale and landscape-scale habitat characteristics on California spiny lobster (Panulirus interruptus) abundance and survival
Authors: Mai Thien T. , Hovel Kevin A.
Published: May 2007

For many marine systems, little is known about the effects of habitat structure on ecological processes that dictate population dynamics. This study focused on the effects of habitat structure on behaviour, abundance, and survival of California spiny lobster (Panulirus interruptus Randall) in the Point Loma kelp forest, San Diego, California. Habitat characteristics were quantified in 400-m2 landscapes to determine the role of shelter and understorey kelp characteristics at local (shelter) scales and landscape scales on lobster habitat use. A tethering experiment determined the effects of the presence of understorey kelp on lobster survival. At the shelter scale, lobsters preferred permanent shelters to ephemeral shelters, but did not respond to shelter size. At the landscape scale, lobster density increased with Pterygophora californica (stipitate kelp) density and decreased with Laminaria farlowii (prostrate kelp) density, but lobster density did not vary with shelter density or dispersion. Lobster size increased with P. californica density in two of three surveys, while lobster size did not vary with L. farlowii density. Lobster relative survival was higher in the presence of understorey kelp than when kelp was absent. We conclude that lobsters respond to habitat characteristics at local and landscape scales, and that understorey kelp has strong effects on lobster habitat use and survival.
Foraminiferal record of ecological impact of deforestation and oyster farms, Mahurangi Harbour, New Zealand
Authors: Grenfell Hugh R. , Hayward Bruce W. , Horrocks Mark
Published: May 2007

The microfossils in eight short sediment cores in Mahurangi Harbour, northern New Zealand, record major ecological changes since colonisation by Europeans. During the period of catchment deforestation (1850s–1900) these changes include increased sedimentation rates, decline of soft-shore molluscs, increased diatoms and seaward migration of brackish, agglutinate-dominated, foraminiferal associations, inferred to be due to increased freshwater runoff and decreased pH. The interval of most rapid change (1950s–1980s) occurred before and during the establishment of oyster farms, which therefore are not implicated. Comparison of the microfossil content of surface sediment samples taken inside and outside of four oyster farms indicates variable effects dependent on farm location. In less saline sites, the presence of oyster-shell debris in sediment beneath oyster farms appears to have buffered the foraminiferal faunas from some of the impacts of lowered salinity and pH. At more tidally flushed, saline sites, the oyster farms influence a wider surrounding area that has lower relative abundance of three species of Elphidium and other calcareous Foraminifera, attributed to slightly muddier sediment, higher nutrients and consequently lower oxygen. A newly arrived exotic foraminifer, Elphidium vellai, appears to be an indicator species for the enhanced nutrient, carbonate-rich conditions beneath oyster farms.
Very high-pressure orogenic garnet peridotites
Authors: Liou J. G. , Zhang R. Y. , Ernst W. G.
Published: May 2007

Mantle-derived garnet peridotites are a minor component in many very high-pressure metamorphic terranes that formed during continental subduction and collision. Some of these mantle rocks contain trace amounts of zircon and micrometer-sized inclusions. The constituent minerals exhibit pre- and postsubduction microstructures, including polymorphic transformation and mineral exsolution. Experimental, mineralogical, petrochemical, and geochronological characterizations using novel techniques with high spatial, temporal, and energy resolutions are resulting in unexpected discoveries of new phases, providing better constraints on deep mantle processes.
Tracking the
in vivo
evolution of multidrug resistance in
Staphylococcus aureus
by whole-genome sequencing
Authors: Mwangi Michael M. , Wu Shang Wei , Zhou Yanjiao , Sieradzki Krzysztof , de Lencastre Herminia , Richardson Paul , Bruce David , Rubin Edward , Myers Eugene , Siggia Eric D. , Tomasz Alexander
Published: May 2007

The spread of multidrug-resistant
Staphylococcus aureus
(MRSA) strains in the clinical environment has begun to pose serious limits to treatment options. Yet virtually nothing is known about how resistance traits are acquired
in vivo
. Here, we apply the power of whole-genome sequencing to identify steps in the evolution of multidrug resistance in isogenic
S. aureus
isolates recovered periodically from the bloodstream of a patient undergoing chemotherapy with vancomycin and other antibiotics. After extensive therapy, the bacterium developed resistance, and treatment failed. Sequencing the first vancomycin susceptible isolate and the last vancomycin nonsusceptible isolate identified genome wide only 35 point mutations in 31 loci. These mutations appeared in a sequential order in isolates that were recovered at intermittent times during chemotherapy in parallel with increasing levels of resistance. The vancomycin nonsusceptible isolates also showed a 100-fold decrease in susceptibility to daptomycin, although this antibiotic was not used in the therapy. One of the mutated loci associated with decreasing vancomycin susceptibility (the
vraR
operon) was found to also carry mutations in six additional vancomycin nonsusceptible
S. aureus
isolates belonging to different genetic backgrounds and recovered from different geographic sites. As costs drop, whole-genome sequencing will become a useful tool in elucidating complex pathways of
in vivo
evolution in bacterial pathogens.
Artificial selection of simulated microbial ecosystems
Authors: Williams Hywel T. P. , Lenton Timothy M.
Published: May 2007

Recent work with microbial communities has demonstrated an adaptive response to artificial selection at the level of the ecosystem. The reasons for this response and the level at which adaptation occurs are unclear: does selection act implicitly on traits of individual species, or are higher-level traits genuinely being selected? If the ecosystem response is just the additive combination of the responses of the constituent species, then the ecosystem response could be predicted
a priori
, and the ecosystem-level selection process is superfluous. However, if the ecosystem response results from ecological interactions among species, then selection at a higher level is necessary. Here we perform artificial ecosystem selection experiments on an individual-based evolutionary simulation model of microbial ecology and observe a similar response to that seen with real ecosystems. We demonstrate that a significant fraction of artificially selected ecosystem responses cannot be accounted for by implicit lower-level selection of a single type of organism within the community, and that interactions among different types of organism contribute significantly to the response in the majority of cases. However, when the ecological problem posed by the artificial ecosystem selection process can be easily solved by a single dominant species, it often is.
A connecting hinge represses the activity of endothelial nitric oxide synthase
Authors: Haque Mohammad Mahfuzul , Panda Koustubh , Tejero Jesús , Aulak Kulwant S. , Fadlalla Mohammed Adam , Mustovich Anthony T. , Stuehr Dennis J.
Published: May 2007

In mammals, endothelial nitric oxide synthase (eNOS) has the weakest activity, being one-tenth and one-sixth as active as the inducible NOS (iNOS) and the neuronal NOS (nNOS), respectively. The basis for this weak activity is unclear. We hypothesized that a hinge element that connects the FMN module in the reductase domain but is shorter and of unique composition in eNOS may be involved. To test this hypothesis, we generated an eNOS chimera that contained the nNOS hinge and two mutants that either eliminated (P728IeNOS) or incorporated (I958PnNOS) a proline residue unique to the eNOS hinge. Incorporating the nNOS hinge into eNOS increased NO synthesis activity 4-fold, to an activity two-thirds that of nNOS. It also decreased uncoupled NADPH oxidation, increased the apparentKmO2for NO synthesis, and caused a faster heme reduction. Eliminating the hinge proline had similar, but lesser, effects. Our findings reveal that the hinge is an important regulator and show that differences in its composition restrict the activity of eNOS relative to other NOS enzymes.
β-Catenin directly regulates
Islet1
expression in cardiovascular progenitors and is required for multiple aspects of cardiogenesis
Authors: Lin Lizhu , Cui Li , Zhou Wenlai , Dufort Daniel , Zhang Xiaoxue , Cai Chen-Leng , Bu Lei , Yang Lei , Martin Jody , Kemler Rolf , Rosenfeld Michael G. , Chen Ju , Evans Sylvia M.
Published: May 2007

Recent studies have demonstrated that the LIM homeodomain transcription factor Islet1 (Isl1) marks pluripotent cardiovascular progenitor cells and is required for proliferation, survival, and migration of recently defined second heart field progenitors. Factors that are upstream of
Isl1
in cardiovascular progenitors have not yet been defined. Here we demonstrate that β-catenin is required for
Isl1
expression in cardiac progenitors, directly regulating the
Isl1
promoter. Ablation of β-
catenin
in Isl1-expressing progenitors disrupts multiple aspects of cardiogenesis, resulting in embryonic lethality at E13. β-Catenin is also required upstream of a number of genes required for pharyngeal arch, outflow tract, and/or atrial septal morphogenesis, including
Tbx2
,
Tbx3
,
Wnt11
,
Shh
, and
Pitx2
. Our findings demonstrate that β-catenin signaling regulates proliferation and survival of cardiac progenitors.
Roles of heat-shock protein 90 in maintaining and facilitating the neurodegenerative phenotype in tauopathies
Authors: Luo Wenjie , Dou Fei , Rodina Anna , Chip Sophorn , Kim Joungnam , Zhao Qi , Moulick Kamalika , Aguirre Julia , Wu Nian , Greengard Paul , Chiosis Gabriela
Published: May 2007

Neurodegeneration, a result of multiple dysregulatory events, is a lengthy multistep process manifested by accrual of mutant variants and abnormal expression, posttranslational modification, and processing of certain proteins. Accumulation of these dysregulated processes requires a mechanism that maintains their functional stability and allows the evolution of the neurodegenerative phenotype. In malignant cells, the capacity to buffer transformation has been attributed to heat-shock protein 90 (Hsp90). Although normal proteins seem to require limited assistance from the chaperone, their aberrant counterparts seem to be highly dependent on Hsp90. Whereas enhanced Hsp90 affinity for mutated or functionally deregulated client proteins has been observed for several oncoproteins, it is unknown whether Hsp90 plays a similar role for neuronal proteins and thus maintains and facilitates the transformed phenotype in neurodegenerative diseases. Tauopathies are neurodegenerative diseases characterized by aberrant phosphorylation and/or expression of Tau protein, leading to a time-dependent accumulation of Tau aggregates and subsequent neuronal death. Here, we show that the stability of p35, a neuronal protein that activates cyclin-dependent protein kinase 5 through complex formation leading to aberrant Tau phosphorylation, and that of mutant but not WT Tau protein is maintained in tauopathies by Hsp90. Inhibition of Hsp90 in cellular and mouse models of tauopathies leads to a reduction of the pathogenic activity of these proteins and results in elimination of aggregated Tau. The results identify important roles played by Hsp90 in maintaining and facilitating the degenerative phenotype in these diseases and provide a common principle governing cancer and neurodegenerative diseases.
Rapid enhancement of visual cortical response discriminability by microstimulation of the frontal eye field
Authors: Armstrong Katherine M. , Moore Tirin
Published: May 2007

Visual attention provides a means of selecting among the barrage of information reaching the retina and of enhancing the perceptual discriminability of relevant stimuli. Neurophysiological studies in monkeys and functional imaging studies in humans have demonstrated neural correlates of these perceptual improvements in visual cortex during attention. Importantly, voluntary attention improves the discriminability of visual cortical responses to relevant stimuli. Recent work aimed at identifying sources of attentional modulation has implicated the frontal eye field (FEF) in driving spatial attention. Subthreshold microstimulation of the FEF enhances the responses of area V4 neurons to spatially corresponding stimuli. However, it is not known whether these enhancements include improved visual-response discriminability, a hallmark of voluntary attention. We used receiver-operator characteristic analysis to quantify how well V4 responses discriminated visual stimuli and examined how discriminability was affected by FEF microstimulation. Discriminability of responses to stable visual stimuli decayed over time but was transiently restored after microstimulation of the FEF. As observed during voluntary attention, the enhancement resulted only from changes in the magnitude of V4 responses and not in the relationship between response magnitude and variance. Enhanced response discriminability was apparent immediately after microstimulation and was reliable within 40 ms of microstimulation onset, indicating a direct influence of FEF stimulation on visual representations. These results contribute to the mounting evidence that saccade-related signals are a source of spatial attentive selection.
Canonical Wnt signaling functions in second heart field to promote right ventricular growth
Authors: Ai Di , Fu Xueyao , Wang Jun , Lu Mei-Fang , Chen Li , Baldini Antonio , Klein William H. , Martin James F.
Published: May 2007

The second heart field (SHF), progenitor cells that are initially sequestered outside the heart, migrates into the heart and gives rise to endocardium, myocardium, and smooth muscle. Because of its distinct developmental history, the SHF is likely subjected to different signals from that of the first heart field. Previous experiments revealed that canonical Wnt signaling negatively regulated first heart field specification. We inactivated the obligate canonical Wnt effector β-catenin using a β-
catenin
conditional null allele and the
Mef2c AHF cre
driver that directs cre activity specifically in SHF. We also expressed a stabilized form of β-catenin to model continuous Wnt signaling in SHF. Our data indicate that Wnt signaling acts in a positive fashion to promote right ventricular and interventricular myocardial expansion.
Cyclin D2
and
Tgfβ2
expression was drastically reduced in β-
catenin
loss-of-function mutants, indicating that Wnt signaling is required for patterning and expansion of SHF derivatives. Our findings reveal that Wnt signaling plays a major positive role in promoting growth and diversification of SHF precursors into right ventricular and interventricular myocardium.
Early sorting of inner nuclear membrane proteins is conserved
Authors: Braunagel Sharon C. , Williamson Shawn T. , Ding Qi , Wu Xiaogiang , Summers Max D.
Published: May 2007

Spodoptera frugiperda
(Sf9) importin-α-16 is a translocon-associated protein that participates in the early sorting pathway of baculovirus integral membrane proteins destined for the inner nuclear membrane (INM). To discern whether sorting intermediate protein complexes like those observed in insect cells are also formed with mammalian INM proteins, cross-linked complexes of importin-α-16 with human lamin B receptor (LBR) and nurim were examined. Both LBR and nurim cross-link with Sf9 importin-α-16 during cotranslational membrane integration and remain proximal with importin-α-16 after integration into the endoplasmic reticulum membrane and release from the translocon. Human cells encode several isoforms of importin-α; to determine whether any of these isoforms may recognize INM-directed proteins, they were tested for their ability to cross-link with the viral-derived INM sorting motif sequence. One cross-linked adduct was detected with a 16-kDa isoform encoded from
KPNA4
(KPNA-4–16). KPNA-4–16 was easily detected in microsomal membranes prepared from
KPNA4–16
recombinant virus-infected cells and was also detected in microsomes prepared from HeLa cells. Together these observations suggest that elements of the early sorting pathway of INM-directed proteins mediated by importin-α-16 are highly conserved, and mammalian KPNA-4–16 is a candidate partner in sorting integral membrane proteins to the INM.
The emergence of a superorganism through intergroup competition
Authors: Reeve H. Kern , Hölldobler Bert
Published: May 2007

Surveys of insect societies have revealed four key, recurring organizational trends: (
i
) The most elaborated cooperation occurs in groups of relatives. (
ii
) Cooperation is typically more elaborate in species with large colony sizes than in species with small colony sizes, the latter exhibiting greater internal reproductive conflict and lesser morphological and behavioral specialization. (
iii
) Within a species, per capita brood output typically declines as colony size increases. (
iv
). The ecological factors of resource patchiness and intergroup competition are associated with the most elaborated cooperation. Predictions of all four patterns emerge elegantly from a game-theoretic model in which within-group tug-of-wars are nested within a between-group tug-of-war. In this individual selection model, individuals are faced with the problem of how to partition their energy between investment in intercolony competition versus investment in intracolony competition, i.e., internal tugs-of-war over shares of the resources gained through intergroup competition. An individual's evolutionarily stable investment in between-group competition (i.e., within-group cooperation) versus within-group competition is shown to increase as within-group relatedness increases, to decrease as group size increases (for a fixed number of competing groups), to increase as the number of competing groups in a patch increases, and to decrease as between-group relatedness increases. Moreover, if increasing patch richness increases both the number of individuals within a group and the number of competing groups, greater overall cooperation within larger groups will be observed. The model presents a simple way of determining quantitatively how intergroup conflict will propel a society forward along a “superorganism continuum.”
Development of autoimmunity in mice lacking DNA topoisomerase 3β
Authors: Kwan Kelvin Y. , Greenwald Rebecca J. , Mohanty Subhasis , Sharpe Arlene H. , Shaw Albert C. , Wang James C.
Published: May 2007

Mice lacking DNA topoisomerase 3β are predisposed to a shortened lifespan, infertility, and lesions in multiple organs resulting from inflammatory responses. Examination of the immune system of 6- and 52-week-old
top3
β
−/−
mice revealed no significant aberrations in their central and peripheral tolerance or in T lymphocyte activation. However, the older but not the younger cohort shows a high incidence of serum autoantibodies relative to their
TOP3
β
+/+
age-mates. The mutant mice also show an increase in numerical aberrations of chromosomes in splenocytes and bone marrow cells, as well as an increase in apoptotic cells in the thymus. Thus, it appears plausible that the inflammatory lesions in
top3
β
−/−
mice are caused by the development of autoimmunity as they age: Chromosomal abnormalities in
top3
β
−/−
mice might lead to a persistent increase in apoptotic cells, which might in turn lead to the progression of autoimmunity.
Acoustic mimicry in a predator–prey interaction
Authors: Barber Jesse R. , Conner William E.
Published: May 2007

Mimicry of visual warning signals is one of the keystone concepts in evolutionary biology and has received substantial research attention. By comparison, acoustic mimicry has never been rigorously tested. Visualizing bat–moth interactions with high-speed, infrared videography, we provide empirical evidence for acoustic mimicry in the ultrasonic warning sounds that tiger moths produce in response to echolocating bats. Two species of sound-producing tiger moths were offered successively to naïve, free-flying red and big brown bats. Noctuid and pyralid moth controls were also offered each night. All bats quickly learned to avoid the noxious tiger moths first offered to them, associating the warning sounds with bad taste. They then avoided the second sound-producing species regardless of whether it was chemically protected or not, verifying both Müllerian and Batesian mimicry in the acoustic modality. A subset of the red bats subsequently discovered the palatability of the Batesian mimic, demonstrating the powerful selective force these predators exert on mimetic resemblance. Given these results and the widespread presence of tiger moth species and other sound-producing insects that respond with ultrasonic clicks to bat attack, acoustic mimicry complexes are likely common components of the acoustic landscape.
Increased susceptibility to colitis and colorectal tumors in mice lacking core 3–derived O-glycans
Authors: An Guangyu , Wei Bo , Xia Baoyun , McDaniel J. Michael , Ju Tongzhong , Cummings Richard D. , Braun Jonathan , Xia Lijun
Published: May 2007

Altered intestinal O-glycan expression has been observed in patients with ulcerative colitis and colorectal cancer, but the role of this alteration in the etiology of these diseases is unknown. O-glycans in mucin core proteins are the predominant components of the intestinal mucus, which comprises part of the intestinal mucosal barrier. Core 3–derived O-glycans, which are one of the major types of O-glycans, are primarily expressed in the colon. To investigate the biological function of core 3–derived O-glycans, we engineered mice lacking core 3 β1,3-N-acetylglucosaminyltransferase (C3GnT), an enzyme predicted to be important in the synthesis of core 3–derived O-glycans. Disruption of the C3GnT gene eliminated core 3–derived O-glycans. C3GnT-deficient mice displayed a discrete, colon-specific reduction in Muc2 protein and increased permeability of the intestinal barrier. Moreover, these mice were highly susceptible to experimental triggers of colitis and colorectal adenocarcinoma. These data reveal a requirement for core 3–derived O-glycans in resistance to colonic disease.
Emergents from Fusion
Authors: Wong Hong Yu
Published: May 2007

This is a critical discussion of Paul Humphreys's fusion view of emergence, focusing on the basal loss feature of his ontology. The discussion yields some general morals for special science ontology.
Causal Realism and the Laws of Nature
Authors: Corry Richard
Published: May 2007

This paper proposes a revision of our understanding of causation that is designed to address what Hartry Field has suggested is the central problem in the metaphysics of causation today: reconciling Bertrand Russell's arguments that the concept of causation can play no role in the advanced sciences with Nancy Cartwright's arguments that causal concepts are essential to a scientific understanding of the world. The paper shows that Russell's main argument is, ironically, very similar to an argument that Cartwright has put forward against the truth of universal laws of nature. The paper uses this insight to develop an account of causation that does justice to traditional views yet avoids the arguments of Russell.
On local irreducibility of the spectrum
Authors: Costara Constantin , Ransford Thomas
Published: May 2007

Let

M

n

\mathcal M_n

be the algebra of

n
×
n

n\times n

complex matrices, and for

x
∈

M

n

x\in \mathcal M_n

denote by

σ
(
x
)

\sigma (x)

and

ρ
(
x
)

\rho (x)

the spectrum and spectral radius of

x
x

respectively. Let

D
D

be a domain in

M

n

\mathcal M_n

containing

0
0

, and let

F
:
D
→

M

n

F:D\to \mathcal M_n

be a holomorphic map. We prove: (1) if

σ
(
F
(
x
)
)
∩
σ
(
x
)
≠
∅

\sigma (F(x))\cap \sigma (x)\ne \emptyset

for

x
∈
D

x\in D

, then

σ
(
F
(
x
)
)
=
σ
(
x
)

\sigma (F(x))=\sigma (x)

for

x
∈
D

x\in D

; (2) if

ρ
(
F
(
x
)
)
=
ρ
(
x
)

\rho (F(x))=\rho (x)

for

x
∈
D

x\in D

, then again

σ
(
F
(
x
)
)
=
σ
(
x
)

\sigma (F(x))=\sigma (x)

for

x
∈
D

x\in D

. Both results are special cases of theorems expressing the irreducibility of the spectrum

σ
(
x
)

\sigma (x)

near

x
=
0

x=0

.
From an iteration formula to Poincaré’s Isochronous Center Theorem for holomorphic vector fields
Authors: Zhang Guang
Published: May 2007

We first generalize a classical iteration formula for one variable holomorphic mappings to a formula for higher dimensional holomorphic mappings. Then, as an application, we give a short and intuitive proof of a classical theorem, due to H. Poincaré, for the condition under which a singularity of a holomorphic vector field is an isochronous center.
The characteristic function of a complex symmetric contraction
Authors: Chevrot Nicolas , Fricain Emmanuel , Timotin Dan
Published: May 2007

It is shown that a contraction on a Hilbert space is complex symmetric if and only if the values of its characteristic function are all symmetric with respect to a fixed conjugation. Applications are given to the description of complex symmetric contractions with defect indices equal to 2.
A matricial corona theorem II
Authors: Trent Tavan , Zhang Xinjun
Published: May 2007

We extend the “matricial corona theorem” of M. Andersson to general algebras of functions which satisfy a corona theorem.